Darwin

@misc{kellogg1907darwinism1,
    author = "Kellogg, V. L",
    title = "Darwinism to-day",
    year = "1907",
    howpublished = "London, England, Bell \& Sons",
    note = "talkorigins\_source = {true}; raw\_reference = {Kellogg, V. L., 1907, Darwinism to-day: London, England, Bell \& Sons.}"
}

@book{lack1947darwins4,
    author = "Lack, D",
    title = "Darwin's Finches",
    year = "1947",
    publisher = "An essay on the General Biological Theory of Evolution: Cambridge, Cambridge University Press",
    note = "talkorigins\_source = {true}; raw\_reference = {Lack, D., 1947, Darwin's Finches: An essay on the General Biological Theory of Evolution: Cambridge, Cambridge University Press.}"
}

@misc{moorehead1969darwin5,
    author = "Moorehead, A",
    title = "Darwin and the Beagle",
    year = "1969",
    howpublished = "London, Hamish Hamilton",
    note = "talkorigins\_source = {true}; raw\_reference = {Moorehead, A., 1969, Darwin and the Beagle: London, Hamish Hamilton.}"
}

@book{keynes1979the2,
    author = "Keynes, R. D",
    title = "The Beagle Record",
    year = "1979",
    publisher = "Cambridge, Cambridge University Press",
    note = "talkorigins\_source = {true}; raw\_reference = {Keynes, R. D., 1979, The Beagle Record: Cambridge, Cambridge University Press.}"
}

Survival of Darwin's finches through a drought on Daphne Major Island was nonrandom. Large birds, especially males with large beaks, survived best because they were able to crack the large and hard seeds that predominated in the drought. Selection intensities, calculated by O'Donald's method, are the highest yet recorded for a vertebrate population.

@article{doi101126science214451682,
    author = "Boag, Peter T. and Grant, Peter R.",
    title = "Intense Natural Selection in a Population of Darwin's Finches (Geospizinae) in the Galápagos",
    year = "1981",
    journal = "Science",
    abstract = "Survival of Darwin's finches through a drought on Daphne Major Island was nonrandom. Large birds, especially males with large beaks, survived best because they were able to crack the large and hard seeds that predominated in the drought. Selection intensities, calculated by O'Donald's method, are the highest yet recorded for a vertebrate population.",
    url = "https://doi.org/10.1126/science.214.4516.82",
    doi = "10.1126/science.214.4516.82",
    openalex = "W2070036851"
}

@book{ospovat1981the6,
    author = "Ospovat, D",
    title = "The Development of Darwin's Theory",
    year = "1981",
    publisher = "Natural History, Natural Theology, and Natural Selection, 1838-1859: Cambridge, Cambridge University Press",
    note = "talkorigins\_source = {true}; raw\_reference = {Ospovat, D., 1981, The Development of Darwin's Theory: Natural History, Natural Theology, and Natural Selection, 1838-1859: Cambridge, Cambridge University Press.}"
}

@article{doi101007bf00132004,
    author = "Sulloway, Frank J.",
    title = "Darwin and his finches: The evolution of a legend",
    year = "1982",
    journal = "Journal of the History of Biology",
    url = "https://doi.org/10.1007/bf00132004",
    doi = "10.1007/bf00132004",
    openalex = "W2020068972",
    references = "doi101007bf00133143, doi10106313050879, doi1023071421785, doi1023071868881, doi1023072217783, doi1023072412932, doi105962bhltitle4489, doi105962bhltitle50683, doi105962bhltitle59991, doi105962bhltitle82303, openalexw1973833797, openalexw645218623"
}

@article{doi101007bf00133143,
    author = "Sulloway, Frank J.",
    title = "Darwin's conversion: The Beagle voyage and its aftermath",
    year = "1982",
    journal = "Journal of the History of Biology",
    url = "https://doi.org/10.1007/bf00133143",
    doi = "10.1007/bf00133143",
    openalex = "W1987884313",
    references = "doi101007bf00132004, doi101126science18341301164, doi1023071421785, doi1023071868881, doi1023072412191, doi105962bhltitle46249, doi105962bhltitle50683, doi105962bhltitle50860, doi105962bhltitle59991, doi105962bhltitle82303, doi105962bhltitle84435, hindle1964charles, openalexw1600651929"
}

@article{sulloway1982darwin7,
    author = "Sulloway, F",
    title = "Darwin and his finches",
    year = "1982",
    journal = "the evolution of a legend: Journal of Historical Biology, v. 15, p. 1-53",
    note = "talkorigins\_source = {true}; raw\_reference = {Sulloway, F., 1982, Darwin and his finches: the evolution of a legend: Journal of Historical Biology, v. 15, p. 1-53.}"
}

Part I. Description: 1. Galapagos scene 2. Classification 3. Ecology 4. Female plumage 5. Male plumage and sexual selection 6. Beak differences and food 7. Size differences between island forms 8. Size differences between species 9. Individual variation 10. Hybridisation 11. An evolutionary tree Part II. Interpretation: 12. The origin of the Galapagos fauna 13. The origin of subspecies 14. The origin of species 15. The persistence of species 16. Adaptive radiation Summary Acknowledgements Tables of measurements References Indexes.

@book{openalexw1973833797,
    author = "Lack, David",
    title = "Darwin's Finches",
    year = "1983",
    journal = "Medical Entomology and Zoology",
    abstract = "Part I. Description: 1. Galapagos scene 2. Classification 3. Ecology 4. Female plumage 5. Male plumage and sexual selection 6. Beak differences and food 7. Size differences between island forms 8. Size differences between species 9. Individual variation 10. Hybridisation 11. An evolutionary tree Part II. Interpretation: 12. The origin of the Galapagos fauna 13. The origin of subspecies 14. The origin of species 15. The persistence of species 16. Adaptive radiation Summary Acknowledgements Tables of measurements References Indexes.",
    openalex = "W1973833797"
}

A procedure is developed and applied to evaluate alternative explanations for morphological patterns in communities of Darwin's ground finches. The first step in the procedure is the computation of expected population density for a hypothetical solitary finch species on an island, as a function of beak depth. This was done for 15 Galapagos islands where food characteristics have been measured. The second step involves construction of hypothetical finch communities for these islands using five different models. Models differ in the extent to which processes of assembly and/or evolution favor species of high expected density, and in the extent to which interspecific competition influences these processes. By comparing predictions of models to actual communities, the roles of food supply and competition could be assessed. Results reveal that expected density is usually a polymodal function of beak depth. Islands differ substantially in the shapes of their density functions. Mean beak sizes of species actually present on each island correspond to local maxima in expected density. However, two species never occupy the same or closely adjacent local maxima. Simple models incorporating the effects of both food supply and interspecific competition on assembly/evolution are shown to accurately predict observed morphological patterns. The results support the hypothesis that both food supply and interspecific competition have determined morphological properties in communities of these finches.

@article{doi101086284196,
    author = "Schluter, Dolph and Grant, Peter R.",
    title = "Determinants of Morphological Patterns in Communities of Darwin's Finches",
    year = "1984",
    journal = "The American Naturalist",
    abstract = "A procedure is developed and applied to evaluate alternative explanations for morphological patterns in communities of Darwin's ground finches. The first step in the procedure is the computation of expected population density for a hypothetical solitary finch species on an island, as a function of beak depth. This was done for 15 Galapagos islands where food characteristics have been measured. The second step involves construction of hypothetical finch communities for these islands using five different models. Models differ in the extent to which processes of assembly and/or evolution favor species of high expected density, and in the extent to which interspecific competition influences these processes. By comparing predictions of models to actual communities, the roles of food supply and competition could be assessed. Results reveal that expected density is usually a polymodal function of beak depth. Islands differ substantially in the shapes of their density functions. Mean beak sizes of species actually present on each island correspond to local maxima in expected density. However, two species never occupy the same or closely adjacent local maxima. Simple models incorporating the effects of both food supply and interspecific competition on assembly/evolution are shown to accurately predict observed morphological patterns. The results support the hypothesis that both food supply and interspecific competition have determined morphological properties in communities of these finches.",
    url = "https://doi.org/10.1086/284196",
    doi = "10.1086/284196",
    openalex = "W2015341730",
    references = "doi10100797814899732526, doi101007bf00132004, doi101016004058097690054x, doi101093auk972321, doi101111j155856461976tb00911x, doi1023071937166, doi1023072288753, doi1023072405671, doi1023072984653, openalexw1973833797"
}

Charles Darwin's historic visit to the Galápagos Islands in 1835 represents a landmark in the annals of science. But contrary to the legend long surrounding Darwin's famous Galápagos visit, he continued to believe that species were immutable for nearly a year and a half after leaving these islands. This delay in Darwin's evolutionary appreciation of the Galápagos evidence is largely owing to numerous misconceptions that he entertained about the islands, and their unique organic inhabitants, during the Beagle voyage. For example, Darwin mistakenly thought that the Galápagos tortoise–adult specimens of which he did not collect for scientific purposes–was not native to these islands. Hence he apparently interpreted reports of island-to-island differences among the tortoises as analogous to changes that are commonly undergone by species removed from their natural habitats. As for Darwin's finches, Darwin initially failed to recognize the closely related nature of the group, mistaking certain species for the forms that they appear, through adaptive radiation, to mimic. Moreover, what locality information he later published for his Galápagos finch specimens was derived almost entirely from the collections of three other Beagle shipmates, following his return to England. Even after he became an evolutionist, in March of 1837 (when he discussed his Galápagos birds with the eminent ornithologist John Gould), Darwin's theoretical understanding of evolution in the Galápagos continued to undergo significant developments for almost as many years as it took him to publish the Origin of Species (1859). The Darwin-Galápagos legend, with its romantic portrait of Darwin's ‘eureka-like’ insight into the Galápagos as a microcosmic ‘laboratory of evolution’, masks the complex nature of scientific discovery, and, thereby, the real nature of Darwin's genius.

@article{doi101111j109583121984tb02052x,
    author = "Sulloway, Frank J.",
    title = "Darwin and the Galapagos",
    year = "1984",
    journal = "Biological Journal of the Linnean Society",
    abstract = "Charles Darwin's historic visit to the Galápagos Islands in 1835 represents a landmark in the annals of science. But contrary to the legend long surrounding Darwin's famous Galápagos visit, he continued to believe that species were immutable for nearly a year and a half after leaving these islands. This delay in Darwin's evolutionary appreciation of the Galápagos evidence is largely owing to numerous misconceptions that he entertained about the islands, and their unique organic inhabitants, during the Beagle voyage. For example, Darwin mistakenly thought that the Galápagos tortoise–adult specimens of which he did not collect for scientific purposes–was not native to these islands. Hence he apparently interpreted reports of island-to-island differences among the tortoises as analogous to changes that are commonly undergone by species removed from their natural habitats. As for Darwin's finches, Darwin initially failed to recognize the closely related nature of the group, mistaking certain species for the forms that they appear, through adaptive radiation, to mimic. Moreover, what locality information he later published for his Galápagos finch specimens was derived almost entirely from the collections of three other Beagle shipmates, following his return to England. Even after he became an evolutionist, in March of 1837 (when he discussed his Galápagos birds with the eminent ornithologist John Gould), Darwin's theoretical understanding of evolution in the Galápagos continued to undergo significant developments for almost as many years as it took him to publish the Origin of Species (1859). The Darwin-Galápagos legend, with its romantic portrait of Darwin's ‘eureka-like’ insight into the Galápagos as a microcosmic ‘laboratory of evolution’, masks the complex nature of scientific discovery, and, thereby, the real nature of Darwin's genius.",
    url = "https://doi.org/10.1111/j.1095-8312.1984.tb02052.x",
    doi = "10.1111/j.1095-8312.1984.tb02052.x",
    openalex = "W2081541193",
    references = "doi10106313050879, doi101126science214451682, doi1023071421785, doi1023072412191, doi105962bhltitle59991, doi105962bhltitle82303, doi105962bhltitle84435, openalexw2997954996"
}

@book{kohn1985the3,
    author = "Kohn, D",
    title = "The Darwinian Heritage",
    year = "1985",
    publisher = "Princeton, Princeton University Press",
    note = "talkorigins\_source = {true}; raw\_reference = {Kohn, D., 1985, The Darwinian Heritage: Princeton, Princeton University Press.}"
}

@article{doi1010160169534787900280,
    author = "Pimm, Stuart L.",
    title = "Ecology and evolution of Darwin's finches",
    year = "1987",
    journal = "Trends in Ecology \& Evolution",
    url = "https://doi.org/10.1016/0169-5347(87)90028-0",
    doi = "10.1016/0169-5347(87)90028-0",
    openalex = "W2154327289",
    references = "doi101017cbo9780511693281002"
}

@article{doi105962p314520,
    author = "Porter, Duncan M.",
    title = "Darwin's notes on Beagle plants",
    year = "1987",
    journal = "Bulletin of the British Museum (Natural History) Historical Series",
    url = "https://doi.org/10.5962/p.314520",
    doi = "10.5962/p.314520",
    openalex = "W3166623575"
}

After his famous visit to the Galapagos Islands, Darwin speculated that might fancy that, from an original paucity of birds in this archipelago, one species had been taken and modified for different ends. This book is the classic account of how much we have since learned about the evolution of these remarkable birds. Based upon over a decade's research, Grant shows how interspecific competition and natural selection act strongly enough on contemporary populations to produce observable and measurable evolutionary change. In this new edition, Grant outlines new discoveries made in the thirteen years since the book's publication. Ecology and Evolution of Darwin's Finches is an extraordinary account of evolution in action.

@article{doi1023074785,
    author = "Snow, D. W. and Grant, Peter R.",
    title = "Ecology and Evolution of Darwin's Finches",
    year = "1988",
    journal = "Journal of Animal Ecology",
    abstract = "After his famous visit to the Galapagos Islands, Darwin speculated that might fancy that, from an original paucity of birds in this archipelago, one species had been taken and modified for different ends. This book is the classic account of how much we have since learned about the evolution of these remarkable birds. Based upon over a decade's research, Grant shows how interspecific competition and natural selection act strongly enough on contemporary populations to produce observable and measurable evolutionary change. In this new edition, Grant outlines new discoveries made in the thirteen years since the book's publication. Ecology and Evolution of Darwin's Finches is an extraordinary account of evolution in action.",
    url = "https://doi.org/10.2307/4785",
    doi = "10.2307/4785",
    openalex = "W2005862991"
}

Allele length variation at 16 microsatellite loci was used to estimate the phylogeny of 13 out of the 14 species of Darwin's finches. The resulting topology was similar to previous phylogenies based on morphological and allozyme variation. An unexpected result was that genetic divergence among Galápagos Island populations of the warbler finch (Certhidea olivacea) predates the radiation of all other Darwin's finches. This deep split is surprising in view of the relatively weak morphological differentiation among Certhidea populations and supports the hypothesis that the ancestor of all Darwin's finches was phenotypically similar to Certhidea. The results also resolve a biogeographical problem: the Cocos Island finch evolved after the Galápagos finch radiation was under way, supporting the hypothesis that this distant island was colonized from the Galápagos Islands. Monophyletic relationships are supported for both major groups, the ground finches (Geospiza) and the tree finches (Camarhynchus and Cactospiza), although the vegetarian finch (Platyspiza crassirostris) appears to have diverged prior to the separation of ground and tree finches. These results demonstrate the use of microsatellites for reconstructing phylogenies of closely related species and interpreting their evolutionary and biogeographic histories.

@article{doi101098rspb19990641,
    author = "Petren, Kenneth and Grant, B. Rosemary and Grant, Peter R.",
    title = "A phylogeny of Darwin's finches based on microsatellite DNA length variation",
    year = "1999",
    journal = "Proceedings of the Royal Society B Biological Sciences",
    abstract = "Allele length variation at 16 microsatellite loci was used to estimate the phylogeny of 13 out of the 14 species of Darwin's finches. The resulting topology was similar to previous phylogenies based on morphological and allozyme variation. An unexpected result was that genetic divergence among Galápagos Island populations of the warbler finch (Certhidea olivacea) predates the radiation of all other Darwin's finches. This deep split is surprising in view of the relatively weak morphological differentiation among Certhidea populations and supports the hypothesis that the ancestor of all Darwin's finches was phenotypically similar to Certhidea. The results also resolve a biogeographical problem: the Cocos Island finch evolved after the Galápagos finch radiation was under way, supporting the hypothesis that this distant island was colonized from the Galápagos Islands. Monophyletic relationships are supported for both major groups, the ground finches (Geospiza) and the tree finches (Camarhynchus and Cactospiza), although the vegetarian finch (Platyspiza crassirostris) appears to have diverged prior to the separation of ground and tree finches. These results demonstrate the use of microsatellites for reconstructing phylogenies of closely related species and interpreting their evolutionary and biogeographic histories.",
    url = "https://doi.org/10.1098/rspb.1999.0641",
    doi = "10.1098/rspb.1999.0641",
    openalex = "W2001166438",
    references = "doi1010079781461523819, doi101086282771, doi101093genetics1391463, doi101093genetics1441389, doi101093hmg281123, doi101093oso97801951218340030001, doi101111jbi14281, doi101126science1553760279, doi1023074785, doi104324978020376680411, openalexw3199943451"
}

@article{doi10103835051570,
    author = "Podos, Jeffrey",
    title = "Correlated evolution of morphology and vocal signal structure in Darwin's finches",
    year = "2001",
    journal = "Nature",
    url = "https://doi.org/10.1038/35051570",
    doi = "10.1038/35051570",
    openalex = "W1680083609",
    references = "doi1010160169534787900280, doi101086284325, doi101086284398, doi101086413215, doi101093aibsbulletin2214b, doi101098rspb19990641, doi101111j155856461993tb01257x, doi101126science2875451306, doi1023071439305, doi1023074785, doi104159harvard9780674865327, openalexw2128666103"
}

Evolution can be predicted in the short term from a knowledge of selection and inheritance. However, in the long term evolution is unpredictable because environments, which determine the directions and magnitudes of selection coefficients, fluctuate unpredictably. These two features of evolution, the predictable and unpredictable, are demonstrated in a study of two populations of Darwin's finches on the Galápagos island of Daphne Major. From 1972 to 2001, Geospiza fortis (medium ground finch) and Geospiza scandens (cactus finch) changed several times in body size and two beak traits. Natural selection occurred frequently in both species and varied from unidirectional to oscillating, episodic to gradual. Hybridization occurred repeatedly though rarely, resulting in elevated phenotypic variances in G. scandens and a change in beak shape. The phenotypic states of both species at the end of the 30-year study could not have been predicted at the beginning. Continuous, long-term studies are needed to detect and interpret rare but important events and nonuniform evolutionary change.

@article{doi101126science1070315,
    author = "Grant, Peter R. and Grant, B. Rosemary",
    title = "Unpredictable Evolution in a 30-Year Study of Darwin's Finches",
    year = "2002",
    journal = "Science",
    abstract = "Evolution can be predicted in the short term from a knowledge of selection and inheritance. However, in the long term evolution is unpredictable because environments, which determine the directions and magnitudes of selection coefficients, fluctuate unpredictably. These two features of evolution, the predictable and unpredictable, are demonstrated in a study of two populations of Darwin's finches on the Galápagos island of Daphne Major. From 1972 to 2001, Geospiza fortis (medium ground finch) and Geospiza scandens (cactus finch) changed several times in body size and two beak traits. Natural selection occurred frequently in both species and varied from unidirectional to oscillating, episodic to gradual. Hybridization occurred repeatedly though rarely, resulting in elevated phenotypic variances in G. scandens and a change in beak shape. The phenotypic states of both species at the end of the 30-year study could not have been predicted at the beginning. Continuous, long-term studies are needed to detect and interpret rare but important events and nonuniform evolutionary change.",
    url = "https://doi.org/10.1126/science.1070315",
    doi = "10.1126/science.1070315",
    openalex = "W2104511903",
    references = "doi10103827900, doi101073pnas91156808, doi101086319193, doi101093oso97801950997440010001, doi101093oso97801985498330010001, doi101098rspb19980514, doi1023074785, doi105860choice350883, openalexw1546962148, openalexw1840956397, openalexw2080618944"
}

Darwin's finches are a classic example of species diversification by natural selection. Their impressive variation in beak morphology is associated with the exploitation of a variety of ecological niches, but its developmental basis is unknown. We performed a comparative analysis of expression patterns of various growth factors in species comprising the genus Geospiza. We found that expression of Bmp4 in the mesenchyme of the upper beaks strongly correlated with deep and broad beak morphology. When misexpressed in chicken embryos, Bmp4 caused morphological transformations paralleling the beak morphology of the large ground finch G. magnirostris.

@article{doi101126science1098095,
    author = "Abzhanov, Arhat and Protas, Meredith and Grant, B. Rosemary and Grant, Peter R. and Tabin, Clifford J.",
    title = "Bmp4 and Morphological Variation of Beaks in Darwin's Finches",
    year = "2004",
    journal = "Science",
    abstract = "Darwin's finches are a classic example of species diversification by natural selection. Their impressive variation in beak morphology is associated with the exploitation of a variety of ecological niches, but its developmental basis is unknown. We performed a comparative analysis of expression patterns of various growth factors in species comprising the genus Geospiza. We found that expression of Bmp4 in the mesenchyme of the upper beaks strongly correlated with deep and broad beak morphology. When misexpressed in chicken embryos, Bmp4 caused morphological transformations paralleling the beak morphology of the large ground finch G. magnirostris.",
    url = "https://doi.org/10.1126/science.1098095",
    doi = "10.1126/science.1098095",
    openalex = "W2046108663",
    references = "doi101093oso97801985052350010001, doi101098rspb19990641, doi101126science1077827, doi101126science1098109, doi101242dev00397, doi101242dev1242391, doi101242dev12751095, doi101242dev128142755, doi1023074785"
}

When Charles Darwin, then age 22, first saw the HMS Beagle, he thought it looked like a wreck than a vessel commissioned to go round the world. But travel around the world it did, taking Darwin to South America, Australia, New Zealand, Tahiti, and of course the Galapagos Islands, in a journey of discovery that lasted almost five years. Now, in Fossils, Finches and Fuegians, Richard Keynes, Darwin's great grandson, offers the first modern full-length account of Darwin's epoch-making expedition. This was the great adventure of Charles Darwin's life. Indeed, it would have been a great adventure for anyone-tracking condor in Chile, surviving the great earthquake of 1835, riding across country on horseback in the company of gauchos, watching whales leaping skyward off Tierra del Fuego, hunting ostriches with a bolo, discovering prehistoric fossils and previously unknown species, and meeting primitive peoples such as the Fuegians. Keynes captures many of the natural wonders that Darwin witnessed, including an incredible swarm of butterflies a mile wide and ten miles long. Keynes also illuminates Darwin's scientific work-his important findings in geology and biology-and traces the slow revolution in Darwin's thought about species and how they might evolve. Numerous illustrations-mostly by artists who traveled with Darwin on the Beagle-grace the pages, including finely rendered drawings of many points of interest discussed in the book. There has probably been no greater or more important scientific expedition than Darwin's voyage on the Beagle. Packed with colorful details of life aboard ship and in the wild, here is a fascinating portrait of Charles Darwin and of 19th century science.

@article{doi105860choice413408,
    title = "Fossils, finches and Fuegians: Darwin's adventures and discoveries on the Beagle",
    year = "2004",
    journal = "Choice Reviews Online",
    abstract = "When Charles Darwin, then age 22, first saw the HMS Beagle, he thought it looked like a wreck than a vessel commissioned to go round the world. But travel around the world it did, taking Darwin to South America, Australia, New Zealand, Tahiti, and of course the Galapagos Islands, in a journey of discovery that lasted almost five years. Now, in Fossils, Finches and Fuegians, Richard Keynes, Darwin's great grandson, offers the first modern full-length account of Darwin's epoch-making expedition. This was the great adventure of Charles Darwin's life. Indeed, it would have been a great adventure for anyone-tracking condor in Chile, surviving the great earthquake of 1835, riding across country on horseback in the company of gauchos, watching whales leaping skyward off Tierra del Fuego, hunting ostriches with a bolo, discovering prehistoric fossils and previously unknown species, and meeting primitive peoples such as the Fuegians. Keynes captures many of the natural wonders that Darwin witnessed, including an incredible swarm of butterflies a mile wide and ten miles long. Keynes also illuminates Darwin's scientific work-his important findings in geology and biology-and traces the slow revolution in Darwin's thought about species and how they might evolve. Numerous illustrations-mostly by artists who traveled with Darwin on the Beagle-grace the pages, including finely rendered drawings of many points of interest discussed in the book. There has probably been no greater or more important scientific expedition than Darwin's voyage on the Beagle. Packed with colorful details of life aboard ship and in the wild, here is a fascinating portrait of Charles Darwin and of 19th century science.",
    url = "https://doi.org/10.5860/choice.41-3408",
    doi = "10.5860/choice.41-3408",
    openalex = "W650425722"
}

@article{doi101038nature04843,
    author = "Abzhanov, Arhat and Kuo, Winston Patrick and Hartmann, Christine and Grant, B. Rosemary and Grant, Peter R. and Tabin, Clifford J.",
    title = "The calmodulin pathway and evolution of elongated beak morphology in Darwin's finches",
    year = "2006",
    journal = "Nature",
    url = "https://doi.org/10.1038/nature04843",
    doi = "10.1038/nature04843",
    openalex = "W2074067714",
    references = "doi101002jmor1050880104, doi10103841786, doi101038nature02415, doi101098rspb19990641, doi101126science1070315, doi101126science1098095, doi101242dev1212333, doi10129879780300128673, doi1023074785, doi105860choice434010, openalexw2128666103"
}

@article{doi105860choice455580,
    title = "How and why species multiply: the radiation of Darwin's finches",
    year = "2008",
    journal = "Choice Reviews Online",
    url = "https://doi.org/10.5860/choice.45-5580",
    doi = "10.5860/choice.45-5580",
    openalex = "W1488644339"
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@article{doi101007s1073900991899,
    author = "Brinkman, Paul D.",
    title = "Charles Darwin’s Beagle Voyage, Fossil Vertebrate Succession, and “The Gradual Birth \& Death of Species”",
    year = "2009",
    journal = "Journal of the History of Biology",
    url = "https://doi.org/10.1007/s10739-009-9189-9",
    doi = "10.1007/s10739-009-9189-9",
    openalex = "W2016832898",
    references = "doi101007s1205200801032, doi101177007327538402200401, doi105860choice413408"
}

INTRODUCTION Finches of the Galápagos Islands were first described by Charles Darwin during his voyage on the HMS Beagle in 1835. Since then, through the subsequent work of many biologists, Darwin’s finches have become a classic textbook example of many important processes in evolution. Today, this group of birds continues to be a significant source of information on such processes as speciation, niche partitioning, morphological adaptation, and species ecology. The approximately 14 species of Darwin’s finches are closely related to one another and display a remarkable degree of diversity in bill shapes and sizes that are adapted for different food sources (e.g., seeds, insects, and even young leaves or blood from sea birds) in an otherwise scarce environment. For example, the deep and wide bills of the Ground Finches, one of the subgroups of Darwin’s finches, are used to feed on seeds, whereas the Cactus Finches use their elongated and narrow bills to probe cactus fruit and flowers. These differences in bill shapes are not due to their differential usage or other external factors; rather, the differences are genetically and developmentally regulated and can be observed and studied during embryogenesis. Therefore, Darwin’s finches are becoming a very useful non-model animal and avian system in which to investigate the molecular basis of morphological changes during evolution.

@article{doi101101pdbemo119,
    author = "Abzhanov, Arhat",
    title = "Darwin’s Finches: Analysis of Beak Morphological Changes During Evolution: Figure 1.",
    year = "2009",
    journal = "Cold Spring Harbor Protocols",
    abstract = "INTRODUCTION Finches of the Galápagos Islands were first described by Charles Darwin during his voyage on the HMS Beagle in 1835. Since then, through the subsequent work of many biologists, Darwin’s finches have become a classic textbook example of many important processes in evolution. Today, this group of birds continues to be a significant source of information on such processes as speciation, niche partitioning, morphological adaptation, and species ecology. The approximately 14 species of Darwin’s finches are closely related to one another and display a remarkable degree of diversity in bill shapes and sizes that are adapted for different food sources (e.g., seeds, insects, and even young leaves or blood from sea birds) in an otherwise scarce environment. For example, the deep and wide bills of the Ground Finches, one of the subgroups of Darwin’s finches, are used to feed on seeds, whereas the Cactus Finches use their elongated and narrow bills to probe cactus fruit and flowers. These differences in bill shapes are not due to their differential usage or other external factors; rather, the differences are genetically and developmentally regulated and can be observed and studied during embryogenesis. Therefore, Darwin’s finches are becoming a very useful non-model animal and avian system in which to investigate the molecular basis of morphological changes during evolution.",
    url = "https://doi.org/10.1101/pdb.emo119",
    doi = "10.1101/pdb.emo119",
    openalex = "W1990210979",
    references = "doi101002jmor1050880104, doi10103835051570, doi101038nature04843, doi101098rspb19990641, doi101126science1098095, doi10129879780300237856, doi1023074785, doi102307jctt1xp3v3r, doi105860choice321538, doi105860choice455580"
}

INTRODUCTION There are no breeding colonies of Darwin’s finches anywhere in the world. Thus, all of the embryonic material is collected in the wild. This protocol describes how, in a field setting, fertilized eggs are collected and incubated at a precise temperature and how the resulting embryos are harvested and processed for in situ hybridization, antibody staining, and microarray analyses. In addition, the protocol includes steps for preparing the heads of older embryos for histological staining of bone and cartilage with alcian blue and alizarin red. It is likely that the same or similar methods can be used to obtain embryonic tissue from other species of songbirds. The main limitation of this protocol is that, when used in the field without external constant electricity sources, it requires power generators that need to run on a more or less constant basis, as well as stockpiles of supplies (fuel, oil, and fresh water).

@article{doi101101pdbprot5174,
    author = "Abzhanov, Arhat",
    title = "Collection of Embryos from Darwin’s Finches (Thraupidae, Passeriformes)",
    year = "2009",
    journal = "Cold Spring Harbor Protocols",
    abstract = "INTRODUCTION There are no breeding colonies of Darwin’s finches anywhere in the world. Thus, all of the embryonic material is collected in the wild. This protocol describes how, in a field setting, fertilized eggs are collected and incubated at a precise temperature and how the resulting embryos are harvested and processed for in situ hybridization, antibody staining, and microarray analyses. In addition, the protocol includes steps for preparing the heads of older embryos for histological staining of bone and cartilage with alcian blue and alizarin red. It is likely that the same or similar methods can be used to obtain embryonic tissue from other species of songbirds. The main limitation of this protocol is that, when used in the field without external constant electricity sources, it requires power generators that need to run on a more or less constant basis, as well as stockpiles of supplies (fuel, oil, and fresh water).",
    url = "https://doi.org/10.1101/pdb.prot5174",
    doi = "10.1101/pdb.prot5174",
    openalex = "W2050204136",
    references = "doi101101pdbemo119"
}

INTRODUCTION The beaks of Darwin’s finches develop their distinct shapes during embryogenesis. To visualize where and when mRNA transcripts of genes involved in beak development are present during embryogenesis, this protocol describes how to analyze embryonic tissue samples using in situ hybridization. The principle of this technique is to use probes specific to mRNAs coding for proteins of interest to reveal how the corresponding genes are expressed in the beaks of different species of Darwin’s finches.

@article{doi101101pdbprot5175,
    author = "Abzhanov, Arhat",
    title = "In Situ Hybridization Analysis of Embryonic Beak Tissue from Darwin’s Finches",
    year = "2009",
    journal = "Cold Spring Harbor Protocols",
    abstract = "INTRODUCTION The beaks of Darwin’s finches develop their distinct shapes during embryogenesis. To visualize where and when mRNA transcripts of genes involved in beak development are present during embryogenesis, this protocol describes how to analyze embryonic tissue samples using in situ hybridization. The principle of this technique is to use probes specific to mRNAs coding for proteins of interest to reveal how the corresponding genes are expressed in the beaks of different species of Darwin’s finches.",
    url = "https://doi.org/10.1101/pdb.prot5175",
    doi = "10.1101/pdb.prot5175",
    openalex = "W2033342982",
    references = "doi101101pdbemo119"
}

INTRODUCTION In this protocol, microarray technology is used as a very sensitive and rapid method to identify genes that are potentially involved in beak development and morphology in Darwin’s finches. The method allows for the direct comparison between cDNA targets from two different species (each labeled with a different dye). The prevalence of one of the dyes for any of the genes on the resulting scan indicates a higher level of accumulation of transcripts from that gene in a particular beak morphology/species. The obtained expression profiles can be clustered to identify transcripts that are expressed in a species- and/or size-specific manner.

@article{doi101101pdbprot5176,
    author = "Abzhanov, Arhat",
    title = "Microarray Analysis of Embryonic Beak mRNA from Darwin’s Finches",
    year = "2009",
    journal = "Cold Spring Harbor Protocols",
    abstract = "INTRODUCTION In this protocol, microarray technology is used as a very sensitive and rapid method to identify genes that are potentially involved in beak development and morphology in Darwin’s finches. The method allows for the direct comparison between cDNA targets from two different species (each labeled with a different dye). The prevalence of one of the dyes for any of the genes on the resulting scan indicates a higher level of accumulation of transcripts from that gene in a particular beak morphology/species. The obtained expression profiles can be clustered to identify transcripts that are expressed in a species- and/or size-specific manner.",
    url = "https://doi.org/10.1101/pdb.prot5176",
    doi = "10.1101/pdb.prot5176",
    openalex = "W1988423179",
    references = "doi101101pdbemo119"
}

This paper reports 24 newly discovered specimens of 21 species made by Charles Darwin in Argentina, Australia, Brazil, Chile, Ecuador and Uruguay while on the 1831–1836 voyage of HMS Beagle. They have been found in Cambridge University Herbarium and the herbaria of the Missouri Botanical Garden, Natural History Museum, London, New York Botanical Garden and the Royal Botanic Gardens, Kew, since the earlier publications of Porter. Included are type specimens of Calceolaria darwinii (isotype; = C. uniflora), Cuscuta gymnocarpa (holotype and isotypes), C. sandwichiana var. mimosae (isolectotypes = C. gymnocarpa), Ephedra frustillata (lectotype and isolectotypes), Ourisia breviflora (isolectotype), Polypodium paleaceum (syntype?; = Ctenitis sloanei) and Urera gaudichaudiana (holotype; = Laportea aestuans).

@article{doi101111j10958339200800943x,
    author = "Porter, Duncan M. and Murrell, Gina and Parker, John",
    title = "Some new Darwin vascular plant specimens from the Beagle voyage",
    year = "2009",
    journal = "Botanical Journal of the Linnean Society",
    abstract = "This paper reports 24 newly discovered specimens of 21 species made by Charles Darwin in Argentina, Australia, Brazil, Chile, Ecuador and Uruguay while on the 1831–1836 voyage of HMS Beagle. They have been found in Cambridge University Herbarium and the herbaria of the Missouri Botanical Garden, Natural History Museum, London, New York Botanical Garden and the Royal Botanic Gardens, Kew, since the earlier publications of Porter. Included are type specimens of Calceolaria darwinii (isotype; = C. uniflora), Cuscuta gymnocarpa (holotype and isotypes), C. sandwichiana var. mimosae (isolectotypes = C. gymnocarpa), Ephedra frustillata (lectotype and isolectotypes), Ourisia breviflora (isolectotype), Polypodium paleaceum (syntype?; = Ctenitis sloanei) and Urera gaudichaudiana (holotype; = Laportea aestuans).",
    url = "https://doi.org/10.1111/j.1095-8339.2008.00943.x",
    doi = "10.1111/j.1095-8339.2008.00943.x",
    openalex = "W2085838149"
}

During his five year sea voyage with the “Beagle”, Darwin, at the suggestion of the botanist J.S. Henslow, collected more than 1400 vascular plants, and more than 200 of them alone during his short stay on the Galápagos Islands. The unique collection of plants from the Galápagos archipelago was examined in 1845 by J.D. Hooker. Unlike the birds, Darwin had collected the plants separately for each island. Hooker described 78 of them as new species and analyzed the close biogeographical relations of the Galápagos flora with the South-American continent. The finding that more than 50% of the species are not found anywhere else on the globe – are hence endemics, many of them restricted to individual islands – was a sensation for Hooker and Darwin. Hooker correctly characterized the Asteraceae as the most remarkable family of the Galápagos Islands, due to the great number of their endemic genera and species. He also discussed the adaptations which might have allowed the plants of the different families to reach the isolated islands. Hooker’s results played an important role for Darwin in his developing the theory of evolution, and – besides the examples of birds, tortoises, and lizards – provided him with weighty arguments to defend it. There are seven endemic plant genera on the Galápagos Islands, and 19 genera that are adaptively diversified. With 19 endemic taxa, the genus Scalesia (Asteraceae) is the most spectacular example of an adaptive radiation, followed by the prickly pear cactuses (Opuntia) with 14 endemic taxa. While Darwin’s finches meanwhile represent one of the best-studied examples of evolution and adaptive radiation, only little research has been done so far into evolutionary processes in plants of the Galápagos archipelago. The prominent role that Darwin’s plants played for his scientific insights is even less known.

@article{doi1012685bauhinia1687,
    author = "Stöcklin, Jürg",
    title = "Darwin and the Plants of the Galápagos-Islands",
    year = "2009",
    journal = "BAUHINIA – Zeitschrift der Basler Botanischen Gesellschaft",
    abstract = "During his five year sea voyage with the “Beagle”, Darwin, at the suggestion of the botanist J.S. Henslow, collected more than 1400 vascular plants, and more than 200 of them alone during his short stay on the Galápagos Islands. The unique collection of plants from the Galápagos archipelago was examined in 1845 by J.D. Hooker. Unlike the birds, Darwin had collected the plants separately for each island. Hooker described 78 of them as new species and analyzed the close biogeographical relations of the Galápagos flora with the South-American continent. The finding that more than 50\% of the species are not found anywhere else on the globe – are hence endemics, many of them restricted to individual islands – was a sensation for Hooker and Darwin. Hooker correctly characterized the Asteraceae as the most remarkable family of the Galápagos Islands, due to the great number of their endemic genera and species. He also discussed the adaptations which might have allowed the plants of the different families to reach the isolated islands. Hooker’s results played an important role for Darwin in his developing the theory of evolution, and – besides the examples of birds, tortoises, and lizards – provided him with weighty arguments to defend it. There are seven endemic plant genera on the Galápagos Islands, and 19 genera that are adaptively diversified. With 19 endemic taxa, the genus Scalesia (Asteraceae) is the most spectacular example of an adaptive radiation, followed by the prickly pear cactuses (Opuntia) with 14 endemic taxa. While Darwin’s finches meanwhile represent one of the best-studied examples of evolution and adaptive radiation, only little research has been done so far into evolutionary processes in plants of the Galápagos archipelago. The prominent role that Darwin’s plants played for his scientific insights is even less known.",
    url = "https://doi.org/10.12685/bauhinia.1687",
    doi = "10.12685/bauhinia.1687",
    openalex = "W2616920889",
    references = "doi101111j109583121984tb02052x, doi101111j109583121984tb02065x, doi101111j10958339200800943x, doi1023071219253, doi1023072989650, doi105860choice321538, doi105860choice375660, doi105962p314520"
}

Genetic analysis of museum specimens offers a direct window into a past that can predate the loss of extinct forms. We genotyped 18 Galápagos finches collected by Charles Darwin and companions during the voyage of the Beagle in 1835, and 22 specimens collected in 1901. Our goals were to determine if significant genetic diversity has been lost since the Beagle voyage and to determine the genetic source of specimens for which the collection locale was not recorded. Using 'ancient' DNA techniques, we quantified variation at 14 autosomal microsatellite loci. Assignment tests showed several museum specimens genetically matched recently field-sampled birds from their island of origin. Some were misclassified or were difficult to classify. Darwin's exceptionally large ground finches (Geospiza magnirostris) from Floreana and San Cristóbal were genetically distinct from several other currently existing populations. Sharp-beaked ground finches (Geospiza difficilis) from Floreana and Isabela were also genetically distinct. These four populations are currently extinct, yet they were more genetically distinct from congeners than many other species of Darwin's finches are from each other. We conclude that a significant amount of the finch biodiversity observed and collected by Darwin has been lost since the voyage of the Beagle.

@article{doi101098rstb20090316,
    author = "Petren, Kenneth and Grant, Peter R. and Grant, B. Rosemary and Clack, Andrew A. and Lescano, Ninnia V.",
    title = "Multilocus genotypes from Charles Darwin's finches: biodiversity lost since the voyage of the Beagle",
    year = "2010",
    journal = "Philosophical Transactions of the Royal Society B Biological Sciences",
    abstract = "Genetic analysis of museum specimens offers a direct window into a past that can predate the loss of extinct forms. We genotyped 18 Galápagos finches collected by Charles Darwin and companions during the voyage of the Beagle in 1835, and 22 specimens collected in 1901. Our goals were to determine if significant genetic diversity has been lost since the Beagle voyage and to determine the genetic source of specimens for which the collection locale was not recorded. Using 'ancient' DNA techniques, we quantified variation at 14 autosomal microsatellite loci. Assignment tests showed several museum specimens genetically matched recently field-sampled birds from their island of origin. Some were misclassified or were difficult to classify. Darwin's exceptionally large ground finches (Geospiza magnirostris) from Floreana and San Cristóbal were genetically distinct from several other currently existing populations. Sharp-beaked ground finches (Geospiza difficilis) from Floreana and Isabela were also genetically distinct. These four populations are currently extinct, yet they were more genetically distinct from congeners than many other species of Darwin's finches are from each other. We conclude that a significant amount of the finch biodiversity observed and collected by Darwin has been lost since the voyage of the Beagle.",
    url = "https://doi.org/10.1098/rstb.2009.0316",
    doi = "10.1098/rstb.2009.0316",
    openalex = "W2135303321",
    references = "doi101017cbo9780511693281002, doi101038nrg1348, doi101046j1365294x200402008x, doi101086282771, doi101093bioinformaticsbts460, doi101093genetics1552945, doi101093jheredesh074, doi101093nar24163189, doi101111j14718286200501155x, doi1023072485224"
}

One of the classic examples of adaptive radiation under natural selection is the evolution of 15 closely related species of Darwin's finches (Passeriformes), whose primary diversity lies in the size and shape of their beaks. Since Charles Darwin and other members of the Beagle expedition collected these birds on the Galápagos Islands in 1835 and introduced them to science, they have been the subjects of intense research. Many biology textbooks use Darwin's finches to illustrate a variety of topics of evolutionary theory, such as speciation, natural selection and niche partitioning. Today, as this Theme Issue illustrates, Darwin's finches continue to be a very valuable source of biological discovery. Certain advantages of studying this group allow further breakthroughs in our understanding of changes in recent island biodiversity, mechanisms of speciation and hybridization, evolution of cognitive behaviours, principles of beak/jaw biomechanics as well as the underlying developmental genetic mechanisms in generating morphological diversity. Our objective was to bring together some of the key workers in the field of ecology and evolutionary biology who study Darwin's finches or whose studies were inspired by research on Darwin's finches. Insights provided by papers collected in this Theme Issue will be of interest to a wide audience.

@article{doi101098rstb20090321,
    author = "Abzhanov, Arhat",
    title = "Darwin's Galápagos finches in modern biology",
    year = "2010",
    journal = "Philosophical Transactions of the Royal Society B Biological Sciences",
    abstract = "One of the classic examples of adaptive radiation under natural selection is the evolution of 15 closely related species of Darwin's finches (Passeriformes), whose primary diversity lies in the size and shape of their beaks. Since Charles Darwin and other members of the Beagle expedition collected these birds on the Galápagos Islands in 1835 and introduced them to science, they have been the subjects of intense research. Many biology textbooks use Darwin's finches to illustrate a variety of topics of evolutionary theory, such as speciation, natural selection and niche partitioning. Today, as this Theme Issue illustrates, Darwin's finches continue to be a very valuable source of biological discovery. Certain advantages of studying this group allow further breakthroughs in our understanding of changes in recent island biodiversity, mechanisms of speciation and hybridization, evolution of cognitive behaviours, principles of beak/jaw biomechanics as well as the underlying developmental genetic mechanisms in generating morphological diversity. Our objective was to bring together some of the key workers in the field of ecology and evolutionary biology who study Darwin's finches or whose studies were inspired by research on Darwin's finches. Insights provided by papers collected in this Theme Issue will be of interest to a wide audience.",
    url = "https://doi.org/10.1098/rstb.2009.0321",
    doi = "10.1098/rstb.2009.0321",
    openalex = "W2120787716",
    references = "doi1010160169534787900280, doi1010160169534789900372, doi101038nature04843, doi101098rspb19990641, doi101098rstb20090316, doi101111j155856461981tb04864x, doi101126science1098095, doi101126science28554311265, doi1023074785, openalexw1973833797"
}

Click here for all previous articles in the History of the Ecological Sciences series by F. N. Egerton …I was very much interested and surprised at seeing a large black and scarlet Hemipterous insect, many moths (Zygaena) and a Cicindela, which are not found in Shropshire. I almost made up my mind to begin collecting all the insects which I could find dead, for on consulting my sister, I concluded that it was not right to kill insects for the sake of making a collection. Six years later, in October 1825, he went to the University of Edinburgh to study medicine. He stayed only two years and learned as much or more outside the classroom as he did in it. He associated with zoologist Robert Grant, who encouraged his studies on marine life and told him about Lamarck's theory of transformism, and probably discussed Erasmus Darwin's also (Desmond and Moore 1991:40). Darwin made some original discoveries about several marine invertebrates from the Firth of Forth, which he reported to the Plinian Society (Allan 1977:35, Darwin 1977, II:285–291, Desmond and Moore 1991:37–39, Browne 1995:82–87, Stott 2003:35–36). Although Darwin later remembered Professor Robert Jameson's geology lectures as boring (Darwin 1959:52), he probably heard or read Jameson's comprehensive "On the Growth of Coral Islands" (1827 [Sponsel 2009:83]). After two years, Darwin decided against a medical career and left Edinburgh. His four years at Cambridge University (1828–1831) were meant to prepare him to become a Church of England clergyman, but his most important education there came outside clerical preparatory classes (van Wyhe 2009), from friendship with Professor of Botany John Stevens Henslow (1796–1861) (Barlow 1967, Mathew 1972, Walters and Stow 2001:78–104, Walters 2004a, b, Kohn et al. 2005) and his geological field trip with Prof. Adam Sedgwick (1785–1873) in the summer of 1831 (Barrett 1974, Dolan 2004, Herbert 2005:36–46, Secord 2005). "But no pursuit at Cambridge was followed with nearly so much eagerness or gave me so much pleasure as collecting beetles" (1959:62). Darwin had been inspired by reading Humboldt's Personal Narrative of travels in Spanish America to plan his own expedition to Teneriffe, Canary Islands (Darwin 1959:67–68), but it never materialized. Then, in August 1831, Henslow received an appeal to serve as a naturalist on a naval survey ship, Beagle, under Captain Robert FitzRoy (1805–1865); Henslow declined and recommended Darwin instead (Darwin 1985–1988, I:127–129). The purpose of the voyage was to map the coastlines of South America and some oceanic islands. During most of the 1800s the best British education in physical sciences was offered to army engineers and naval officers (Ratcliff 2008:26). FitzRoy was an officer who benefited from this training, and he made important contributions to hydrography and meteorology (Mellersh 1968, Basalla 1972, Nichols 2003, Gribbin and Gribbin 2004, McConnell 2004a, b). His habits of precision and thoroughness set a good example for Darwin. Contrary to the assumption of two historians (Gruber 1969, Burstyn 1975), Darwin went on the voyage as the official naturalist, though his expenses were paid by his father, Dr. Robert Darwin. There was a substantial library aboard the Beagle, including multi-volume reference works on zoology (Stoddart 1962:118–120, Burkhardt and Smith 1985a). As a parting gift, Henslow gave Darwin a copy of Humboldt's Personal Narrative. Like all great scientists, Darwin was a hard worker, and during the almost five years voyage (27 December 1831–1832 to October 1836), he diligently observed, collected specimens, took notes, and preserved superb evidence of his work. Virtually all his evidence still exists, mostly published. All his works that he himself published are now accessible at 〈Darwin-online.org.uk〉. His surviving correspondence from the period of the voyage consists of 152 letters, about half of which he wrote (Darwin 1985–1988, I:192–504). He drew upon his records, collections, and his memories to write one of the most valuable science travel books ever published, Journal of Researches into the Geology and Natural History of the Various Countries Visited by H. M. S. Beagle 1839. Three modern books discuss his voyage (Barlow 1945, Moorehead 1969, Keynes 2003), and numerous briefer accounts add to our understanding and appreciation of what he experienced and achieved (including von Hagen 1945:169–229, Life Editors and Barnett 1960, Hopkins 1969, Armstrong 1991, Armstrong 1992, 2004, Rice 1999:230–259, McCalman 2009:15–81). Darwin made a good collection of fishes, though he said little about them in his Journal of Researches (Pauly 2004:213–240). Although he would have four entomologists describe his new species of insects, he did have interesting discussions of insects in his Journal of Researches (Riley 1882:71–73, Remington and Remington 1961). Duncan Porter points out (1980:515) that Darwin's geological notes from the voyage (1383 pages) are almost four times longer than his biological notes (368 pages), and Darwin's geological observations have now received the attention they deserve (Herbert 2005). Since Darwin had learned little geology before participating in geological field work in the summer of 1831, a few months before the voyage began, why did he so quickly become a geologist? He became deeply influenced by Charles Lyell's Principles of Geology (three volumes, 1830–1833), volume I of which was given to him by FitzRoy, while Henslow sent him volume II (1832) during the voyage (Darwin 1959:77, 101, Barlow 1967:10–11, Gruber 1985:15–18, Herbert 2005:63–70). A major attraction was that Lyell defended the uniformitarian theory that Darwin found more creditable than Georges Cuvier's catastrophist theory. Natural histories of plants and animals contained very limited theories—in contrast to Lyell's theory of geology, which seemed to encompass all geological phenomena (1959:77). Geology and natural history merged in Darwin's studies of fossils and of coral islands. The first of three volumes he published on the geology of the voyage (Freeman 1965:41) was on the structure of coral reefs. The Beagle's first landing was at St. Jago in the Cape Verde Islands on 18 January 1832 (Armstrong 2004:38–45, Chancellor and van Wyhe 2009:3–6). Darwin wanted to see the kind of tropical vegetation that Humboldt had described at Teneriffe in the Canary Islands and was at first disappointed because the Cape Verde Islands were rather arid. However, he eventually found a deep valley that retained moisture and provided the emotional experience he sought (Darwin 1988:23). The commonest bird was a kingfisher (Dacelo jagoensis) that sat on castor-oil plants and darted out to catch grasshoppers and lizards (Darwin 1839:2). He took extensive notes on marine invertebrates (Darwin 2000:9–21), but only the notes on an octopus appeared in his Journal of Researches (1839:6–7). He watched it change color, squirt ink, and when he bent down to look more closely, it squirted water at him. They departed on 8 February, and their second stop, 16–19 February 1832, was at the uninhabited (by people) St. Paul's Rocks, near the equator (Edwards 1985, Campbell 1997:42–48, Armstrong 2004:46–50, Chancellor and van Wyhe 2009:6). Darwin (1839:8) gave the location as 0°58′ North latitude and 29°5″ West longitude, and 540 miles from South America. From a distance, the rocks appeared white, due partly to a glossy white substance in some rocks and partly to accumulated bird guano. In 1813 H.M.S. Rhin visited the rocks and Lt. George Chrichton drew a map and profile chart, but in 1832 FitzRoy did both again (Edwards 1985: Figs. 1a and 2). St. Paul's highest point is only about 60 feet (18.3 m) above sea level, and the islets are only 3/4 of a mile (2 km) in diameter. The route of H. M. S. Beagle in its voyage around the world. De Beer 1967:39. St. Paul's Rocks, from the east. Illustrated London News. By the side of many of these nests a small flying-fish was placed, which I suppose, had been brought by the male bird for its partner…quickly a large and active crab (Graspus), which inhabits the crevices of the rock, stole the fish from the side of the nest, as soon as we had disturbed the birds. The following list completes, I believe, the terrestrial fauna: a species of Feronia and an acarus, which must have come here as parasites on the birds; a small brown moth, belonging to a genus that feeds on feathers; a staphylinus (Quedius) and a wood louse from beneath the dung; and lastly, numerous spiders, which I suppose prey on these small attendants on, and scavengers of the waterfowl. After reading this account, Rear-Admiral William Symonds told Darwin that he had seen at St. Paul's crabs drag young birds from nests and eat them. Darwin added this information to this account in the second edition of his Journal (1845:10). Because this is the earliest known food web (Egerton 2007:51), Darwin's brief observations now carry a historical significance that they lacked when published, and so more details about the species he observed are desirable. He collected two unknown tick species, now named Amblyomma hirtum (Neumann 1906:201–203) and A. darwini (Hirst and Hirst 1910:239–240), which are only known from two locations: St. Paul's Rocks and the Galapagos Islands. He was first to collect them in both places. His specimens are now in the Natural History Museum, London (Robinson 1926:156–158, 221–222). He also collected the argasid tick, Ornithodoros capensis, and a bird louse, Actornithophilus sp. from the brown booby nests and hippoboscid flies from dead brown boobies. No spiders were in his collections, but Scytodes sp. now lives there and may be what he saw (Edwards and Lubbock 1983:54–55). Darwin's brown moth, Erechthias darwini, was only named in 1983, because no specimen survived in his collections. It resembles the genus Darwin had in mind but is in a different family that cannot digest the keratin of feathers. It eats instead the dried seaweed of the nests (Robinson 1983). As previously mentioned, (Egerton 2009), Darwin was the second known user of what we now call a plankton net (with Lesueur earlier using a dip net). He drew a crude sketch of his, four feet deep, and first discussed its use on 10 January 1832 in his Beagle diary, which he never published (Darwin 1988:21). On 11 January he wrote in his diary (1988:22): "I am quite tired having worked all day at the produce of my net—The number of animals that the net collects is very great & fully explains the manner so many animals of a large size live so far from land." His Zoology Notes (2000:3–7) contain notes and drawings on the animals collected in his net on these two days. In Journal of Researches (1839:14–18), he first discussed phytoplankton observations after his account of St. Paul's Rocks, on 18 March; the account consists mostly of superficial anatomical descriptions. Next, he discussed numerous small crustaceans which sealers called whale-food, but he failed to make explicit here a food chain that was implicit–from minute organisms to crustaceans to whales—and only much later in his Journal of Researches (1839:189) did he even mention using his net. The day has passed delightfully: delight is however a weak term for such transports of pleasure: I have been wandering by myself in a Brazilian forest: amongst the multitude it is hard to say what set of objects is most striking: the general luxuriance of the vegetation bears the victory, the elegance of the grasses, the novelty of the parasitical plants, the beauty of the flowers.—the glossy green of the foliage, all tend to this end.—A most paradoxical mixture of sound & silence pervades the shady parts of the wood.—the noise from the insects is so loud that in the evening it can be heard even in a vessel anchored several hundred yards from the shore. Darwin's South American travels. Von Hagen 1945:228. The next day, he gushed: "I can only add raptures to the former raptures." However, rapture does not necessarily lead to discernment. A commentator on his bird watching in South America points out (Haupt 2006:54–56) that he was on the continent having the greatest diversity of bird species and in the forest that contains most of that diversity, yet he was unable to see much more than the vegetation and insects. This was early into the voyage, and he lacked the binoculars which every birder now takes to any rain forest. Near the Guardia we find the southern limit of two European plants, now become excessively common. The fennel in great profusion covers the ditch banks in the neighbourhood of Buenos Ayres, Monte Video, and other towns. But the cardoon (Cynara cardunculus) has a far wider range: it occurs in these latitudes on both sides of the Cordillera, across the continent. I saw it in unfrequented spots in Chile, Entre Bios, and Banda Oriental. In the latter country alone, very many (probably several hundred) square miles are covered by one mass of these prickly plants, and are impenetrable by man or beast. This was "the earliest documented transformation of a landscape by alien plants" (Mack 1989:160). …if what was told me in London is true, viz. that there are no small insects in the collections from the Tropics, I tell entomologists to look out and have their pens ready for describing. I have taken as minute (if not more so) as in England, Hydropori, Hygroti, Hydrobii, Pselaphi, Staphglini, Cuscaliones, Bimbidia, &c. &c. It is exceedingly interesting to observe the difference of genera and species from those which I know…as a specimen how little the insects are known, Noterus, according to Dic[tionnaire] Class[ique d'histoire naturelle, 17 volumes] consists solely of three European species. I, in one haul of my net, took five distinct species… Many of Darwin's biological observations recorded at Rio were not entirely new to science, though new to him and seen in newly discovered species, and so not previously published (Chancellor and van Wyhe 2009:7–49). He had been preceded in biological exploration of South America by Azara (see below), Humboldt (Egerton 2009), and Alcide Charles Victor Dessalines d'Orbigny (1802–1857); d'Orbigny collected zoological specimens for the Muséum d'Histoire Naturelle in Paris in 1826–1834 and published Voyage dans l'Amerique meridionale (10 volumes, 1834–1847; for English translated extracts, see von Hagen 1948:182–200), a notable achievement, which did not attract as wide an audience as did Darwin's Journal of Researches (Goodman 1972:301–303, Tobien 1974, Boulinier 1995, Brygoo 1995, Legre-Zaidline 2002, Moreau and Dory 2005:11–17, 81–89), though his contributions are now well appreciated (Taquet 2002). Near Rio de Janeiro Darwin observed army ants which caused other insects to either flee or be eaten, he watched a wasp paralyze a spider to provide food for its young when they hatched from eggs, and he watched spiders kill and feed on insects (1839:39–42). The insects he collected and his notes about them are now published and his specimens surveyed (Smith 1987). Some of his specimens were described in print by specialists, and Smith (1987:115–123) includes citations to that literature in his bibliography. The Zoology of the Voyage of H.M.S. Beagle (Darwin 1839–1843) was limited to vertebrates. Darwin's remarks about the people he encountered were what one expects in a travel book, but he also followed Humboldt's example of providing figures or estimates of human populations (Egerton 1970). Both travelers frequently commented on environmental conditions in places visited that either favored or inhibited population increase. Henslow had given Darwin the first two volumes of the English translation of Humboldt's Personal Narrative to take on the voyage, and the Beagle diary that he never published has frequent references to Humboldt (Darwin 1988); some of these references later appeared in his Journal of Researches 1839. He reported that Buenos Ayres had 60,000 people, Monte Video 15,000 (1839:140), Coquimbo 6000–8000 (1839:421), Charles Island in the Galapagos Cape and the and St. Island people and species, of which only were In Darwin that the country would a population when the became more Darwin at the of near the what can be they Darwin on and birds not in the rain forest they were though but they were more on "the around of at the of Rio de His (Darwin Chancellor and van Wyhe he was there from to The Beagle had visited from to August 1832, and in his Journal of Researches Darwin his there on I those parts of my which to the to the in which we visited his observations on and birds not from During that in he the Beagle's to be his to collect biological specimens and also to be his The number of specimens Darwin this of his Journal of Researches by a that was in to up and them. The only large on this was a which was as far as Rio It could be to kill by but it from on it was not by was very numerous in species. was common. was feet two with a of feet 8 They on at the of Rio de and more of and and they They were because had been and did not them. On Rio they were the prey of was a small with habits of a in with a They were and The from its it was earlier Spanish and naturalist, de Azara had discovered that were in their Egerton as were in Darwin later that he had discovered work only after he had published his Journal of Researches (Darwin probably because Azara is not in the In he three times dans l'Amerique meridionale on Darwin was quite interested in this in two species on different They had very different and and and with Azara had observed this in and probably Darwin observed the species in the near Monte Video, though there were two other species in the one of which while the other does not Darwin an extensive of and notes (Darwin to and which the parts of South America. He found them though at times also They were Many of his notes on them were into his Journal of Researches He discussed four species of the and and from the of and Azara reported that they also and They also and them to up was than and than the A species to but was seen in only one and a species, on the and other but not on the The in country from Cape to North America and was or in near were in and and never of latitude Since were in he discussed them Darwin found on the of naturalist William who had up near Buenos this in these only the from on one side to on the Darwin Azara in of his (Darwin Darwin a in the of species and in species that are were and He had a number of to observe on the in (Chancellor and van Wyhe and he a account of its natural history in Journal of Researches Like in and in in a and and tend the Although when of water are they there and catch small Rio in he heard of a species, and one day when a was for he that this bird was of the species, and he its and and sent them to after his John named it though d'Orbigny had named it in 1972, England 2004, observed that Darwin his observations of at in when there were in and so he had the when he have that have a on their and the have a A species, lives in the The Beagle visited Island and in Darwin found the of more geological than biological (Darwin Armstrong 1992, Chancellor and van Wyhe A modern found more interesting there than Darwin did Darwin observed the which had no of He with the that black in the were and were the species as the of the as they when However, he was that the which he was a distinct species because the and said there was no such on the he saw the and it was a different species. have the may have been a a and an or Spanish He of no other so far from a that had so large a The stole food when it and Darwin that it would soon be (Armstrong On from Chile, he encountered and collected Darwin's also of (Darwin It was not found again and now is Although the seemed the did Darwin discovered that the a of and he this important account of them in his Zoology Notes Darwin now Darwin The Zoology of the sea is I the here as in is the & of of which are with the This of is to From those which are at water & those in it even frequently is to in From the in which these are by & the in which the may well be but not to a than it I can only these great to terrestrial in the most of the yet the latter in any country were to be I not that nearly the number of animals would in them as would in the of All the & birds the by the number of small fish which live amongst the are not so very my specimens I nearly the invertebrates I mention them in of their of my collection no of the minute & are excessively those on the is white with such or & & these with a of minute be The number of & is a very as in a are the On the great it is to see the of which This latter I have much the is but & on all the is an & most interesting this was to with it would the the & the small fish & or later the man must The number of the invertebrates would but how many it is hard to There are a number of and in the Darwin is the of the on the of the to that of the tropical rain population size of and species diversity of He to using the of food and species, of these were not nearly a He that there are and and very that are to their The a and A modern on the forest Darwin on it with et al. Darwin's Darwin a zoologist who three books on the Beagle voyage and wrote one on Darwin as a of and as evidence the above from the Zoology The Darwin's as it had Humboldt's (Egerton Humboldt saw it in the of its who around South from to could its rather It the and the as far as the Rio latitude but only around Like Darwin reported about young and John had reported in which he that and had a of he covered with near birds and they it the was Darwin the with and the His and seemed but we now that can but cannot The of Darwin with its Some but the Spanish to the had He collected a which Henslow described and named Darwin also collected a few be

@article{doi10189000129623914398,
    author = "Egerton, Frank N.",
    title = "History of Ecological Sciences, Part 37: Charles Darwin's Voyage on the Beagle",
    year = "2010",
    journal = "Bulletin of the Ecological Society of America",
    abstract = {Click here for all previous articles in the History of the Ecological Sciences series by F. N. Egerton …I was very much interested and surprised at seeing a large black and scarlet Hemipterous insect, many moths (Zygaena) and a Cicindela, which are not found in Shropshire. I almost made up my mind to begin collecting all the insects which I could find dead, for on consulting my sister, I concluded that it was not right to kill insects for the sake of making a collection. Six years later, in October 1825, he went to the University of Edinburgh to study medicine. He stayed only two years and learned as much or more outside the classroom as he did in it. He associated with zoologist Robert Grant, who encouraged his studies on marine life and told him about Lamarck's theory of transformism, and probably discussed Erasmus Darwin's also (Desmond and Moore 1991:40). Darwin made some original discoveries about several marine invertebrates from the Firth of Forth, which he reported to the Plinian Society (Allan 1977:35, Darwin 1977, II:285–291, Desmond and Moore 1991:37–39, Browne 1995:82–87, Stott 2003:35–36). Although Darwin later remembered Professor Robert Jameson's geology lectures as boring (Darwin 1959:52), he probably heard or read Jameson's comprehensive "On the Growth of Coral Islands" (1827 [Sponsel 2009:83]). After two years, Darwin decided against a medical career and left Edinburgh. His four years at Cambridge University (1828–1831) were meant to prepare him to become a Church of England clergyman, but his most important education there came outside clerical preparatory classes (van Wyhe 2009), from friendship with Professor of Botany John Stevens Henslow (1796–1861) (Barlow 1967, Mathew 1972, Walters and Stow 2001:78–104, Walters 2004a, b, Kohn et al. 2005) and his geological field trip with Prof. Adam Sedgwick (1785–1873) in the summer of 1831 (Barrett 1974, Dolan 2004, Herbert 2005:36–46, Secord 2005). "But no pursuit at Cambridge was followed with nearly so much eagerness or gave me so much pleasure as collecting beetles" (1959:62). Darwin had been inspired by reading Humboldt's Personal Narrative of travels in Spanish America to plan his own expedition to Teneriffe, Canary Islands (Darwin 1959:67–68), but it never materialized. Then, in August 1831, Henslow received an appeal to serve as a naturalist on a naval survey ship, Beagle, under Captain Robert FitzRoy (1805–1865); Henslow declined and recommended Darwin instead (Darwin 1985–1988, I:127–129). The purpose of the voyage was to map the coastlines of South America and some oceanic islands. During most of the 1800s the best British education in physical sciences was offered to army engineers and naval officers (Ratcliff 2008:26). FitzRoy was an officer who benefited from this training, and he made important contributions to hydrography and meteorology (Mellersh 1968, Basalla 1972, Nichols 2003, Gribbin and Gribbin 2004, McConnell 2004a, b). His habits of precision and thoroughness set a good example for Darwin. Contrary to the assumption of two historians (Gruber 1969, Burstyn 1975), Darwin went on the voyage as the official naturalist, though his expenses were paid by his father, Dr. Robert Darwin. There was a substantial library aboard the Beagle, including multi-volume reference works on zoology (Stoddart 1962:118–120, Burkhardt and Smith 1985a). As a parting gift, Henslow gave Darwin a copy of Humboldt's Personal Narrative. Like all great scientists, Darwin was a hard worker, and during the almost five years voyage (27 December 1831–1832 to October 1836), he diligently observed, collected specimens, took notes, and preserved superb evidence of his work. Virtually all his evidence still exists, mostly published. All his works that he himself published are now accessible at 〈Darwin-online.org.uk〉. His surviving correspondence from the period of the voyage consists of 152 letters, about half of which he wrote (Darwin 1985–1988, I:192–504). He drew upon his records, collections, and his memories to write one of the most valuable science travel books ever published, Journal of Researches into the Geology and Natural History of the Various Countries Visited by H. M. S. Beagle 1839. Three modern books discuss his voyage (Barlow 1945, Moorehead 1969, Keynes 2003), and numerous briefer accounts add to our understanding and appreciation of what he experienced and achieved (including von Hagen 1945:169–229, Life Editors and Barnett 1960, Hopkins 1969, Armstrong 1991, Armstrong 1992, 2004, Rice 1999:230–259, McCalman 2009:15–81). Darwin made a good collection of fishes, though he said little about them in his Journal of Researches (Pauly 2004:213–240). Although he would have four entomologists describe his new species of insects, he did have interesting discussions of insects in his Journal of Researches (Riley 1882:71–73, Remington and Remington 1961). Duncan Porter points out (1980:515) that Darwin's geological notes from the voyage (1383 pages) are almost four times longer than his biological notes (368 pages), and Darwin's geological observations have now received the attention they deserve (Herbert 2005). Since Darwin had learned little geology before participating in geological field work in the summer of 1831, a few months before the voyage began, why did he so quickly become a geologist? He became deeply influenced by Charles Lyell's Principles of Geology (three volumes, 1830–1833), volume I of which was given to him by FitzRoy, while Henslow sent him volume II (1832) during the voyage (Darwin 1959:77, 101, Barlow 1967:10–11, Gruber 1985:15–18, Herbert 2005:63–70). A major attraction was that Lyell defended the uniformitarian theory that Darwin found more creditable than Georges Cuvier's catastrophist theory. Natural histories of plants and animals contained very limited theories—in contrast to Lyell's theory of geology, which seemed to encompass all geological phenomena (1959:77). Geology and natural history merged in Darwin's studies of fossils and of coral islands. The first of three volumes he published on the geology of the voyage (Freeman 1965:41) was on the structure of coral reefs. The Beagle's first landing was at St. Jago in the Cape Verde Islands on 18 January 1832 (Armstrong 2004:38–45, Chancellor and van Wyhe 2009:3–6). Darwin wanted to see the kind of tropical vegetation that Humboldt had described at Teneriffe in the Canary Islands and was at first disappointed because the Cape Verde Islands were rather arid. However, he eventually found a deep valley that retained moisture and provided the emotional experience he sought (Darwin 1988:23). The commonest bird was a kingfisher (Dacelo jagoensis) that sat on castor-oil plants and darted out to catch grasshoppers and lizards (Darwin 1839:2). He took extensive notes on marine invertebrates (Darwin 2000:9–21), but only the notes on an octopus appeared in his Journal of Researches (1839:6–7). He watched it change color, squirt ink, and when he bent down to look more closely, it squirted water at him. They departed on 8 February, and their second stop, 16–19 February 1832, was at the uninhabited (by people) St. Paul's Rocks, near the equator (Edwards 1985, Campbell 1997:42–48, Armstrong 2004:46–50, Chancellor and van Wyhe 2009:6). Darwin (1839:8) gave the location as 0°58′ North latitude and 29°5″ West longitude, and 540 miles from South America. From a distance, the rocks appeared white, due partly to a glossy white substance in some rocks and partly to accumulated bird guano. In 1813 H.M.S. Rhin visited the rocks and Lt. George Chrichton drew a map and profile chart, but in 1832 FitzRoy did both again (Edwards 1985: Figs. 1a and 2). St. Paul's highest point is only about 60 feet (18.3 m) above sea level, and the islets are only 3/4 of a mile (2 km) in diameter. The route of H. M. S. Beagle in its voyage around the world. De Beer 1967:39. St. Paul's Rocks, from the east. Illustrated London News. By the side of many of these nests a small flying-fish was placed, which I suppose, had been brought by the male bird for its partner…quickly a large and active crab (Graspus), which inhabits the crevices of the rock, stole the fish from the side of the nest, as soon as we had disturbed the birds. The following list completes, I believe, the terrestrial fauna: a species of Feronia and an acarus, which must have come here as parasites on the birds; a small brown moth, belonging to a genus that feeds on feathers; a staphylinus (Quedius) and a wood louse from beneath the dung; and lastly, numerous spiders, which I suppose prey on these small attendants on, and scavengers of the waterfowl. After reading this account, Rear-Admiral William Symonds told Darwin that he had seen at St. Paul's crabs drag young birds from nests and eat them. Darwin added this information to this account in the second edition of his Journal (1845:10). Because this is the earliest known food web (Egerton 2007:51), Darwin's brief observations now carry a historical significance that they lacked when published, and so more details about the species he observed are desirable. He collected two unknown tick species, now named Amblyomma hirtum (Neumann 1906:201–203) and A. darwini (Hirst and Hirst 1910:239–240), which are only known from two locations: St. Paul's Rocks and the Galapagos Islands. He was first to collect them in both places. His specimens are now in the Natural History Museum, London (Robinson 1926:156–158, 221–222). He also collected the argasid tick, Ornithodoros capensis, and a bird louse, Actornithophilus sp. from the brown booby nests and hippoboscid flies from dead brown boobies. No spiders were in his collections, but Scytodes sp. now lives there and may be what he saw (Edwards and Lubbock 1983:54–55). Darwin's brown moth, Erechthias darwini, was only named in 1983, because no specimen survived in his collections. It resembles the genus Darwin had in mind but is in a different family that cannot digest the keratin of feathers. It eats instead the dried seaweed of the nests (Robinson 1983). As previously mentioned, (Egerton 2009), Darwin was the second known user of what we now call a plankton net (with Lesueur earlier using a dip net). He drew a crude sketch of his, four feet deep, and first discussed its use on 10 January 1832 in his Beagle diary, which he never published (Darwin 1988:21). On 11 January he wrote in his diary (1988:22): "I am quite tired having worked all day at the produce of my net—The number of animals that the net collects is very great \& fully explains the manner so many animals of a large size live so far from land." His Zoology Notes (2000:3–7) contain notes and drawings on the animals collected in his net on these two days. In Journal of Researches (1839:14–18), he first discussed phytoplankton observations after his account of St. Paul's Rocks, on 18 March; the account consists mostly of superficial anatomical descriptions. Next, he discussed numerous small crustaceans which sealers called whale-food, but he failed to make explicit here a food chain that was implicit–from minute organisms to crustaceans to whales—and only much later in his Journal of Researches (1839:189) did he even mention using his net. The day has passed delightfully: delight is however a weak term for such transports of pleasure: I have been wandering by myself in a Brazilian forest: amongst the multitude it is hard to say what set of objects is most striking: the general luxuriance of the vegetation bears the victory, the elegance of the grasses, the novelty of the parasitical plants, the beauty of the flowers.—the glossy green of the foliage, all tend to this end.—A most paradoxical mixture of sound \& silence pervades the shady parts of the wood.—the noise from the insects is so loud that in the evening it can be heard even in a vessel anchored several hundred yards from the shore. Darwin's South American travels. Von Hagen 1945:228. The next day, he gushed: "I can only add raptures to the former raptures." However, rapture does not necessarily lead to discernment. A commentator on his bird watching in South America points out (Haupt 2006:54–56) that he was on the continent having the greatest diversity of bird species and in the forest that contains most of that diversity, yet he was unable to see much more than the vegetation and insects. This was early into the voyage, and he lacked the binoculars which every birder now takes to any rain forest. Near the Guardia we find the southern limit of two European plants, now become excessively common. The fennel in great profusion covers the ditch banks in the neighbourhood of Buenos Ayres, Monte Video, and other towns. But the cardoon (Cynara cardunculus) has a far wider range: it occurs in these latitudes on both sides of the Cordillera, across the continent. I saw it in unfrequented spots in Chile, Entre Bios, and Banda Oriental. In the latter country alone, very many (probably several hundred) square miles are covered by one mass of these prickly plants, and are impenetrable by man or beast. This was "the earliest documented transformation of a landscape by alien plants" (Mack 1989:160). …if what was told me in London is true, viz. that there are no small insects in the collections from the Tropics, I tell entomologists to look out and have their pens ready for describing. I have taken as minute (if not more so) as in England, Hydropori, Hygroti, Hydrobii, Pselaphi, Staphglini, Cuscaliones, Bimbidia, \&c. \&c. It is exceedingly interesting to observe the difference of genera and species from those which I know…as a specimen how little the insects are known, Noterus, according to Dic[tionnaire] Class[ique d'histoire naturelle, 17 volumes] consists solely of three European species. I, in one haul of my net, took five distinct species… Many of Darwin's biological observations recorded at Rio were not entirely new to science, though new to him and seen in newly discovered species, and so not previously published (Chancellor and van Wyhe 2009:7–49). He had been preceded in biological exploration of South America by Azara (see below), Humboldt (Egerton 2009), and Alcide Charles Victor Dessalines d'Orbigny (1802–1857); d'Orbigny collected zoological specimens for the Muséum d'Histoire Naturelle in Paris in 1826–1834 and published Voyage dans l'Amerique meridionale (10 volumes, 1834–1847; for English translated extracts, see von Hagen 1948:182–200), a notable achievement, which did not attract as wide an audience as did Darwin's Journal of Researches (Goodman 1972:301–303, Tobien 1974, Boulinier 1995, Brygoo 1995, Legre-Zaidline 2002, Moreau and Dory 2005:11–17, 81–89), though his contributions are now well appreciated (Taquet 2002). Near Rio de Janeiro Darwin observed army ants which caused other insects to either flee or be eaten, he watched a wasp paralyze a spider to provide food for its young when they hatched from eggs, and he watched spiders kill and feed on insects (1839:39–42). The insects he collected and his notes about them are now published and his specimens surveyed (Smith 1987). Some of his specimens were described in print by specialists, and Smith (1987:115–123) includes citations to that literature in his bibliography. The Zoology of the Voyage of H.M.S. Beagle (Darwin 1839–1843) was limited to vertebrates. Darwin's remarks about the people he encountered were what one expects in a travel book, but he also followed Humboldt's example of providing figures or estimates of human populations (Egerton 1970). Both travelers frequently commented on environmental conditions in places visited that either favored or inhibited population increase. Henslow had given Darwin the first two volumes of the English translation of Humboldt's Personal Narrative to take on the voyage, and the Beagle diary that he never published has frequent references to Humboldt (Darwin 1988); some of these references later appeared in his Journal of Researches 1839. He reported that Buenos Ayres had 60,000 people, Monte Video 15,000 (1839:140), Coquimbo 6000–8000 (1839:421), Charles Island in the Galapagos Cape and the and St. Island people and species, of which only were In Darwin that the country would a population when the became more Darwin at the of near the what can be they Darwin on and birds not in the rain forest they were though but they were more on "the around of at the of Rio de His (Darwin Chancellor and van Wyhe he was there from to The Beagle had visited from to August 1832, and in his Journal of Researches Darwin his there on I those parts of my which to the to the in which we visited his observations on and birds not from During that in he the Beagle's to be his to collect biological specimens and also to be his The number of specimens Darwin this of his Journal of Researches by a that was in to up and them. The only large on this was a which was as far as Rio It could be to kill by but it from on it was not by was very numerous in species. was common. was feet two with a of feet 8 They on at the of Rio de and more of and and they They were because had been and did not them. On Rio they were the prey of was a small with habits of a in with a They were and The from its it was earlier Spanish and naturalist, de Azara had discovered that were in their Egerton as were in Darwin later that he had discovered work only after he had published his Journal of Researches (Darwin probably because Azara is not in the In he three times dans l'Amerique meridionale on Darwin was quite interested in this in two species on different They had very different and and and with Azara had observed this in and probably Darwin observed the species in the near Monte Video, though there were two other species in the one of which while the other does not Darwin an extensive of and notes (Darwin to and which the parts of South America. He found them though at times also They were Many of his notes on them were into his Journal of Researches He discussed four species of the and and from the of and Azara reported that they also and They also and them to up was than and than the A species to but was seen in only one and a species, on the and other but not on the The in country from Cape to North America and was or in near were in and and never of latitude Since were in he discussed them Darwin found on the of naturalist William who had up near Buenos this in these only the from on one side to on the Darwin Azara in of his (Darwin Darwin a in the of species and in species that are were and He had a number of to observe on the in (Chancellor and van Wyhe and he a account of its natural history in Journal of Researches Like in and in in a and and tend the Although when of water are they there and catch small Rio in he heard of a species, and one day when a was for he that this bird was of the species, and he its and and sent them to after his John named it though d'Orbigny had named it in 1972, England 2004, observed that Darwin his observations of at in when there were in and so he had the when he have that have a on their and the have a A species, lives in the The Beagle visited Island and in Darwin found the of more geological than biological (Darwin Armstrong 1992, Chancellor and van Wyhe A modern found more interesting there than Darwin did Darwin observed the which had no of He with the that black in the were and were the species as the of the as they when However, he was that the which he was a distinct species because the and said there was no such on the he saw the and it was a different species. have the may have been a a and an or Spanish He of no other so far from a that had so large a The stole food when it and Darwin that it would soon be (Armstrong On from Chile, he encountered and collected Darwin's also of (Darwin It was not found again and now is Although the seemed the did Darwin discovered that the a of and he this important account of them in his Zoology Notes Darwin now Darwin The Zoology of the sea is I the here as in is the \& of of which are with the This of is to From those which are at water \& those in it even frequently is to in From the in which these are by \& the in which the may well be but not to a than it I can only these great to terrestrial in the most of the yet the latter in any country were to be I not that nearly the number of animals would in them as would in the of All the \& birds the by the number of small fish which live amongst the are not so very my specimens I nearly the invertebrates I mention them in of their of my collection no of the minute \& are excessively those on the is white with such or \& \& these with a of minute be The number of \& is a very as in a are the On the great it is to see the of which This latter I have much the is but \& on all the is an \& most interesting this was to with it would the the \& the small fish \& or later the man must The number of the invertebrates would but how many it is hard to There are a number of and in the Darwin is the of the on the of the to that of the tropical rain population size of and species diversity of He to using the of food and species, of these were not nearly a He that there are and and very that are to their The a and A modern on the forest Darwin on it with et al. Darwin's Darwin a zoologist who three books on the Beagle voyage and wrote one on Darwin as a of and as evidence the above from the Zoology The Darwin's as it had Humboldt's (Egerton Humboldt saw it in the of its who around South from to could its rather It the and the as far as the Rio latitude but only around Like Darwin reported about young and John had reported in which he that and had a of he covered with near birds and they it the was Darwin the with and the His and seemed but we now that can but cannot The of Darwin with its Some but the Spanish to the had He collected a which Henslow described and named Darwin also collected a few be},
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Charles Darwin (1809–82) was the English naturalist famous for the theory of evolution by natural selection. He began studying medicine at the University of Edinburgh, but developed a fascination for natural history and left Edinburgh to attend Christ's College, Cambridge, where he pursued his new interest while taking a Bachelor of Arts degree. After graduating, he had the opportunity to secure a position as ship's naturalist aboard H.M.S. Beagle for a five-year, round-the-world voyage which would make him famous. Published in 1845, this book is the second edition of Darwin's expedition journal, more popularly known as The Voyage of the Beagle. Throughout the journey he made observations and discoveries that would lead him to develop his revolutionary theory of evolution, which later appeared in On the Origin of Species and created a storm in the scientific and religious communities

@book{doi101017cbo9781139103831,
    author = "Darwin, Charles",
    title = "Journal of Researches into the Natural History and Geology of the Countries Visited during the Voyage of HMS Beagle round the World, under the Command of Capt. Fitz Roy, R.N.",
    year = "2011",
    booktitle = "Cambridge University Press eBooks",
    abstract = "Charles Darwin (1809–82) was the English naturalist famous for the theory of evolution by natural selection. He began studying medicine at the University of Edinburgh, but developed a fascination for natural history and left Edinburgh to attend Christ's College, Cambridge, where he pursued his new interest while taking a Bachelor of Arts degree. After graduating, he had the opportunity to secure a position as ship's naturalist aboard H.M.S. Beagle for a five-year, round-the-world voyage which would make him famous. Published in 1845, this book is the second edition of Darwin's expedition journal, more popularly known as The Voyage of the Beagle. Throughout the journey he made observations and discoveries that would lead him to develop his revolutionary theory of evolution, which later appeared in On the Origin of Species and created a storm in the scientific and religious communities",
    url = "https://doi.org/10.1017/cbo9781139103831",
    doi = "10.1017/cbo9781139103831",
    openalex = "W1969638819"
}

Abstract Population monitoring is a vital tool for conservation management and for testing hypotheses about population trends in changing environments. Darwin’s finches on Santa Cruz Island in the Galápagos archipelago have experienced habitat alteration because of human activity, introduced predators, parasites and disease. We used point counts to conduct systematic quantitative surveys of Darwin’s finches and other land birds between 1997 and 2010. The temporal analysis revealed that six of the nine species investigated declined significantly and that this decline was most pronounced at higher elevations in humid native forest and agricultural areas; the highland areas have been most affected by introduced species or direct human impact. Five of the six declining species are insectivorous, which suggests that changes in insect abundance or insect availability are a critical factor in the declines. Further study is required to test this idea. Other factors including habitat alteration and introduced parasites or pathogens may be contributing to the observed declines.

@article{doi101017s0030605311000597,
    author = "Dvorak, Michael and Feßl, Birgit and Nemeth, Erwin and Kleindorfer, Sonia and Tebbich, Sabine",
    title = "Distribution and abundance of Darwin’s finches and other land birds on Santa Cruz Island, Galápagos: evidence for declining populations",
    year = "2011",
    journal = "Oryx",
    abstract = "Abstract Population monitoring is a vital tool for conservation management and for testing hypotheses about population trends in changing environments. Darwin’s finches on Santa Cruz Island in the Galápagos archipelago have experienced habitat alteration because of human activity, introduced predators, parasites and disease. We used point counts to conduct systematic quantitative surveys of Darwin’s finches and other land birds between 1997 and 2010. The temporal analysis revealed that six of the nine species investigated declined significantly and that this decline was most pronounced at higher elevations in humid native forest and agricultural areas; the highland areas have been most affected by introduced species or direct human impact. Five of the six declining species are insectivorous, which suggests that changes in insect abundance or insect availability are a critical factor in the declines. Further study is required to test this idea. Other factors including habitat alteration and introduced parasites or pathogens may be contributing to the observed declines.",
    url = "https://doi.org/10.1017/s0030605311000597",
    doi = "10.1017/s0030605311000597",
    openalex = "W2103953427"
}

Bird beaks display tremendous variation in shape and size, which is closely associated with the exploitation of multiple ecological niches and likely played a key role in the diversification of thousands of avian species. Previous studies have demonstrated some of the molecular mechanisms that regulate morphogenesis of the prenasal cartilage, which forms the initial beak skeleton. However, much of the beak diversity in birds depends on variation in the premaxillary bone. It forms later in development and becomes the most prominent functional and structural component of the adult upper beak/jaw, yet its regulation is unknown. Here, we studied a group of Darwin's finch species with different beak shapes. We found that TGFβIIr, β-catenin, and Dickkopf-3, the top candidate genes from a cDNA microarray screen, are differentially expressed in the developing premaxillary bone of embryos of species with different beak shapes. Furthermore, our functional experiments demonstrate that these molecules form a regulatory network governing the morphology of the premaxillary bone, which differs from the network controlling the prenasal cartilage, but has the same species-specific domains of expression. These results offer potential mechanisms that may explain how the tightly coupled depth and width dimensions can evolve independently. The two-module program of development involving independent regulating molecules offers unique insights into how different developmental pathways may be modified and combined to induce multidimensional shifts in beak morphology. Similar modularity in development may characterize complex traits in other organisms to a greater extent than is currently appreciated.

@article{doi101073pnas1011480108,
    author = "Mallarino, Ricardo and Grant, Peter R. and Grant, B. Rosemary and Herrel, Anthony and Kuo, Winston Patrick and Abzhanov, Arhat",
    title = "Two developmental modules establish 3D beak-shape variation in Darwin's finches",
    year = "2011",
    journal = "Proceedings of the National Academy of Sciences",
    abstract = "Bird beaks display tremendous variation in shape and size, which is closely associated with the exploitation of multiple ecological niches and likely played a key role in the diversification of thousands of avian species. Previous studies have demonstrated some of the molecular mechanisms that regulate morphogenesis of the prenasal cartilage, which forms the initial beak skeleton. However, much of the beak diversity in birds depends on variation in the premaxillary bone. It forms later in development and becomes the most prominent functional and structural component of the adult upper beak/jaw, yet its regulation is unknown. Here, we studied a group of Darwin's finch species with different beak shapes. We found that TGFβIIr, β-catenin, and Dickkopf-3, the top candidate genes from a cDNA microarray screen, are differentially expressed in the developing premaxillary bone of embryos of species with different beak shapes. Furthermore, our functional experiments demonstrate that these molecules form a regulatory network governing the morphology of the premaxillary bone, which differs from the network controlling the prenasal cartilage, but has the same species-specific domains of expression. These results offer potential mechanisms that may explain how the tightly coupled depth and width dimensions can evolve independently. The two-module program of development involving independent regulating molecules offers unique insights into how different developmental pathways may be modified and combined to induce multidimensional shifts in beak morphology. Similar modularity in development may characterize complex traits in other organisms to a greater extent than is currently appreciated.",
    url = "https://doi.org/10.1073/pnas.1011480108",
    doi = "10.1073/pnas.1011480108",
    openalex = "W2070502859",
    references = "doi101016009286749290395s, doi101016jcell200806030, doi101016s0092867401006225, doi101016s009286740300432x, doi101038nature02415, doi101038nrg2267, doi101038sjonc1210054, doi101056nejmoa055695, doi101101pdbemo119, doi101242dev02480, doi1023074785"
}

Click here for all previous articles in the History of the Ecological Sciences series by F. N. Egerton Charles Darwin (1809–1882) was the greatest biological scientist and a major contributor to ecological sciences (Vorzimmer 1965, Acot 1983 Dajoz 1984:46–50, 58–83). Natural history before Darwin had many ingredients of ecology, but was weak in theory. The balance of nature, including Linnaeus' version, economy of nature (Egerton 2007b:81–84), was the main example, and it was never developed as a precise theory (Egerton 1973, Kricher 2009). The evolutionary ideas of Erasmus Darwin and Lamarck had ecological relevance (Egerton 2008, 2010a) but were not developed into an elaborate theory like Charles Darwin's theory of evolution by natural selection. What do I mean by evolutionary ecology? A coyote might eat different prey in different parts of its geographic range, so that is not much of an evolved relationship. However, other relationships have evolved. Augustin-Pyramus de Candolle, one of the leading botanists during the first three decades of the 1800s, was uninterested in studies on floral mechanisms that seemed to guide specific species of insects into pollinating a specific species of plants, because he did not believe that one biological species was modified to meet the needs of another species. He was aware of Lamarck's evolutionary speculations about species striving to change, but he was among the majority of botanists and zoologists who did not find Lamarck's teachings convincing. Darwin's first book after publishing the Origin of Species was on the mechanisms among orchid species that guide particular insect species to pollinate that orchid species—caused by natural selection, not by Lamarckian striving—one example of evolutionary ecology. Another example is a harmless animal species evolving by natural selection to mimic a dangerous species as a protection from predators. Darwin's Origin unleashed this line of thought before ecology became an organized science, and later ecologists readily adopted this intellectual tool (Kolasa 2011:28, 39). Darwin's Journal of Researches 1839 made substantial contributions to ecology (Egerton 2010b), and he was as well equipped after his voyage to advance understanding of the economy of nature as to advance evolutionary biology. After the Beagle publications, Darwin continued being an observational naturalist, but he also became an experimentalist. Darwin followed in the footsteps of three role models: Gilbert White, an observer, Humboldt, an observer–correlationist–experimenter, and Lyell, an observer–theoretician. Darwin commonly investigated several different subjects in a year, and even when our scope is limited to ecological subjects, a strictly chronological presentation is impractical. His post-Beagle books (Freeman 1965) usually were preceded by articles in periodicals on the subject. Fortunately, these articles are mostly republished in The Collected Papers of Charles Darwin (two volumes, 1977), and more completely in Darwin's Shorter Publications, 1829–1883 (Darwin 2009). All of Darwin's books are available on the Internet 〈Darwin–online.org.uk〉, and are also republished (Darwin 1986–1990). His Correspondence has been published by Cambridge University Press since 1985 (18 volumes extend to 1870) and is also online 〈darwinproject.ac.uk〉. The present discussion is organized in the chronological order in which he published relevant books, since the Beagle volumes covered in part 37 (Egerton 2010b). Darwin was one of the world's greatest correspondents, and many of his correspondents were happy to send useful information to him. His publications are also available in a collected set (1986–1990) and at Darwin online. After leaving the Galapagos Islands, Darwin had wondered in 1836 whether mockingbirds from different islands were varieties or species (Egerton 2010b:412–414). In March 1837, ornithologist John Gould convinced Darwin that his finch and mockingbird specimens from the Galapagos Islands were different species, and that realization made Darwin an evolutionist (Egerton 2010b:416). Darwin then began keeping notebooks in which he recorded his readings and thoughts on transmutation. His eureka moment came on 28 September 1838 (Darwin 1987:375), when he read Thomas Robert Malthus' Essay on the Principle of Population (Edition 6, 1826). Why did he read a book that would seem to be peripheral to his quest? He had recently finished his Journal of Researches 1839, which he had modeled on Humboldt's Personal Narrative of Travels, and Humboldt had praised Malthus' Essay (Egerton 1970:331–332). Using information in his notebooks, Darwin wrote two early drafts of his theory, 1842 and 1844 (1909). Those notebooks and drafts provide insights into the literature he read and the progress in his thinking, 1837–1844 (Limoges 1970, Manier 1978, Kohn 1980, 1985, Ospovat 1981, Hodge 2003). Anonymous publication of Robert Chambers' Vestiges of the Natural History of Creation 1844, followed by unfavorable reviews from naturalists, inhibited Darwin from publishing his theory at that time. Instead, he wrote two monographs on living barnacles and two on fossils (1851–1854) that “brought about a new way of thinking about morphological comparisons” (Ghiselin 1969:109), and one cirripedologist (Crisp 1983:73–74) even suggested that these monographs could be considered Darwin's greatest works, even though Darwin had misunderstood aspects of female anatomy! The interest he developed in invertebrates at Edinburgh continued throughout the voyage of the Beagle, and he had wanted to include a volume on invertebrates to Zoology of the Voyage of H. M. S. Beagle, but had not managed to do so (Love 2002:266–269). His specific interest in barnacles had been piqued in January 1835 when he discovered in the Chonos Archipelago, off the mainland of Chile, the smallest known barnacle (seen with his microscope), which he named Cryptophialus minutus (Darwin 1854:23, 566–586, 2000:274–276, Richmond 1988, Keynes 2003:264–265, Stott 2003:xx–xxi, 62–63). C. minutus was a parasite that bored through the shell of a conch Concholepas peruviana and lived in its body. While overseeing the volumes describing his vast collections from his voyage and also writing his Journal of Researches, he did not pause to explore this oddity, but after those Beagle volumes appeared, he returned to this species and was soon studying all of the barnacles. His monographs mostly contain systematic descriptions and classifications of species (Winsor 1969a, b, Ghiselin and Jaffe 1973, Southward 1983, Richmond 1988); however their introductions are relevant. Barnacles ate “infusoria” (plankton), minute spiral univalves (snails), and crustacea, including larvae of other barnacles (Darwin 1851:45–46). Pedunculated barnacles (Fig. 2) extend over the whole world, and most species have large ranges, especially those that attach to floating objects. Of those species that attach to fixed objects or to littoral animals, one rarely finds more than three or four species in any locality (Darwin 1851:65–66). Cirripedes are usually bisexual, differing from all other crustacean; when sexes are separate, males are minute and permanently epizoic on females (Darwin 1854:15). Sessil barnacles (Fig. 3) live from latitude 74° 18′ North, south to Cape Horn. Charles Darwin, about 1854. Seward 1909:Frontispiece.. Pedunculated Pollicipes. By George Sowerby. Darwin 1851: from Plate 7, 1964. Sessile barnacle: larvae of Lepus australis. By George Sowerby. Darwin 1854: from Plate 30, 1964. The area between the north Philippine Archipelago and south Australia, extending to New Zealand on the right and Sumatra on the left, has a greater number of species than the rest of the world. Probably this is mainly due to the broken nature of the land, providing diversified habitats and due to much of the coast being rocky. There are more species on the rocky coast of western South America than on its sandy or muddy eastern coast. Coral reefs are unfavorable for all barnacles except Pyrgoma, and few barnacles are known from Pacific islands. Where they can live, species are few and individuals are infinite. No genus with more than one species is confined to the torrid zone. Pyrgoma species are confined to the torrid zone except for one species that is found from the Cape Verde Islands to England and Ireland (1854:159–160). James Dana's great work, Crustacea (1852–1855), has an excellent chart with isocrymal lines, showing mean temperature of waters along their course for the coldest 30 consecutive days in any season. He showed that these lines are most influential for the distribution of marine animals. These measurements were a further elaboration on the isothermal lines that Humboldt introduced into environmental studies (Egerton 2011:158). Dana divided the torrid and sub-torrid zones from the temperate zones at isocryme 68°, and the temperate zones from the sub-frigid and frigid zones at 44°. Darwin found no barnacles confined to frigid zones. Darwin knew 147 species, seven of doubtful habitat. Of the remaining 140, 37 inhabited both torrid and temperate zones, 46 were exclusively in torrid, and 57 were exclusively in temperate zones. The temperate zones, though smaller in area with considerably less lengthy coastlines, had the most species. There are two temperate zones, separated by torrid zones, and the number of species in any zone seems to depend on the isolation of sub-zones. Balanus was the largest known genus, with 36 species of known habitats: 9 in the torrid zone, 15 in temperate zones, and 12 in both zones (Darwin 1854:160–162). Darwin divided the oceans with barnacles into five provinces and listed the species in each province (Darwin 1854:164–171). His two volumes on living and two on fossil barnacles won the Royal Society Medal in 1854. D. T. Anderson, Barnacles: Structure, Function, Development and Evolution 1994, provides a modern perspective on Darwin's work. After publishing on barnacles, at Lyell's urging, Darwin returned to his natural selection project and was in the midst of writing a huge monograph, when he was interrupted by arrival in his mail of Alfred Russel Wallace's manuscript, “On the Tendency of Varieties to Depart Indefinitely from the Original Type,” in 1858. Wallace became a co-discoverer of evolution by natural selection, and Lyell and Joseph Hooker arranged for extracts of Darwin's work, along with Wallace's article, to be read on 1 July and published in 1859 by the Linnean Society of London (Darwin and Wallace 1859). Darwin then abandoned his large manuscript and wrote a more readable abridgment, On the Origin of Species 1859. His longer manuscript was partly used in later books, but those parts not so used are now published (Darwin 1975) and provide many citations to his sources not included in Origin. Darwin presented his theory in the first four chapters, followed by nine chapters on diverse supporting evidence. Origin chapters 1–2 presented noncontroversial evidence that variation occurs in both domestic and wild populations of species. …it breeds when thirty years old, and goes on breeding till ninety years old, bringing forth three pair of young in this interval; if this be so, at the end of the fifth century there would be alive fifteen million elephants, descended from the first pair. …it breeds when thirty years old, and goes on breeding till ninety years old, bringing forth six young in the interval, and surviving till one hundred years old; if this be so, after a period of from 740 to 750 years there would be nearly nineteen million elephants alive, descended from the first pair. But since there would never be nineteen million elephants, descended from one pair, alive at the same time, there must be checks on the growth of populations of all species. To illustrate the complexity of such checks, Darwin explained the interrelationships of red clover, humble bees, mice, and cats: only humble bees pollinate red clover, but field mice eat humble bees, and cats eat mice. Therefore, the success of red clover fields might depend on the local population of cats (1859:73–74). Although we now know that this food chain is more complex than Darwin realized (Egerton 2007a:52–53), his conclusion is still valid: if we speculate on those checks and their magnitudes, “It will convince us of our ignorance on the mutual relations of all organic beings…” (1859:78). Revolutionary paradigms, such as Origin, reorient sciences and uncover new problems to study (Kuhn 1970). When we see leaf-eating insects green, and bark-feeders mottled-grey; the alpine ptarmigan white in winter, the red-grouse the colour of heather, and the black-grouse that of peaty earth, we must believe that these tints are of service to these birds and insects in preserving them from danger. Grouse, if not destroyed at some period of their lives, would increase in countless numbers; they are known to suffer largely from birds of prey; and hawks are guided by eyesight to their prey—so much so, that on parts of the Continent persons are not to white as being the most to I can see no to that natural selection might be most in the colour to each of and in keeping that when and He is here of though is to an with many of many with birds on the with insects and with through the earth, and to that these so different from each and on each other in so complex a have all been by Sessile barnacles By George Sowerby. Darwin 1854: from Plate 1964. study and John of early by Sowerby. Darwin of all these this Darwin a for a and it into an and found that the to it then at a right to be in to pollinate the orchid the by Sowerby. Darwin Darwin's theory might have the of the economy of nature and the balance of nature, but this it did not (Egerton theory of evolution by natural selection is an ecological on the ecological by the greatest of all is no that one of Darwin's most realized the not only for a new of evolutionary but also for a new of ecology, which he named and in his (two volumes, to and Darwin, and a to Although Darwin had some he found to and and might not have read of In the years after publishing Origin, Darwin published more books and His subjects were but they all had the same of and for his theory. we in part 37 (Egerton 2010b), made a of on the Galapagos Islands and Darwin thought of as a and during and after his voyage on the Beagle, and his new publications after his Beagle volumes were on barnacles. his and publications were as much or more on as on He was usually by his a and by his George who also had However, Darwin's and with Joseph Hooker after was a most of information and 1978, and of with seven pair of of to its Darwin Those which had the largest or and which most would be by and would be and so in the would the Those which had their and in to the and of the particular insects which so as to in any the of their from to would be or A with a By George Darwin was Darwin's to that the of many orchid were not a of or but of natural selection His orchid book first specific species were and then to the evolved between and insect to between than of his and in the number of its in his there was no for the or and of some Darwin explained both and were the insect chapters and illustrate different of and their He began with a early and to its parts and their the of to which he this was a and this book was a history of Darwin's theory. was by his but convinced few of his Darwin that had not collected information on the between and but he could his as he did with Using a as a (Darwin he showed that the to the then 30 at a right which it to the of the orchid the studies to (Darwin that with were by bees or and those with by or F. Darwin species of that he had to their After Darwin published his orchid suggested that was insects the through the large on the and by one of the two to the and (Darwin Darwin this by into the of C. but when he a into the it as The has a to 12 and Darwin that there must be a with a to its (Darwin In found a with a a was discovered and has been The book a major in and in as a completely our of and to literature on ecology. that has been on the of and has been or by this John it of the most books of all Darwin listed in the of (Darwin of publications that had since he published the first to this Darwin's On the and of (Darwin first as parts of the Journal of the Linnean Society of London (Freeman and only as a book in the (Darwin He was in the evolution of this and its for these include in which the another and The in most species which he were from or but he also from by and (Darwin included and including and and F. to or with their He did not study the of on their and he did not the that its Darwin later his book in a of studies on this (Darwin in 1 and and to and Darwin a Darwin (Darwin in the same as the of but it was a more substantial book by and Darwin was his and during the in part (Egerton that had in that the and all but he did not their or Darwin had read in 1839 2009). Darwin first the in the of when he on the of the them on but he had to the to and had on to other subjects by He returned to the on (Darwin and a and for this Darwin he had off in with his of the two of showing the to Darwin of the book He and to and to the to and also the to did not the that live in do not for further The remaining chapters the mechanisms of the and a few M. of had his of the of that and and had and that a of than not (Darwin to both botanists and and modern literature and these species as and Darwin's books, The of and in the and The of on of the Species are relevant to ecology since insects were the had been a in his and in this new book he those more Darwin the of for and and he the that had evolved in to some had and so that the were separated from the and did not Darwin to some and was by other botanists of field on which and had been about 15 years after it had been and and Darwin considered The of in Darwin's greatest work. Darwin the of his on its was on and there were and of had in the of though it some of in that he had been by and Darwin's at Darwin later the of this but not the with He the with in his (Darwin Charles Darwin in By John for the Linnean Society of A is also in the Darwin's book was The of through the of with on He had with this on 12 he had his for four and his Darwin later showed fields that had been covered with or with and some years but at the they were those were even though the fields had not been since the His thought that the of had those Darwin had in that could so he could believe that the of might also have an on He the and wrote a for the Society of which he read on 1 1837, and which was published in In the book he that are at and so do not see them at work, but if one one can find their of their He even that were on the had due to both the them and the that were He that which as with a the of the land, has all many through their (Darwin The or into their to a of or (Darwin but their can to or or more (Darwin The book in measurements and such as at was by to the on a in the course of a (Darwin their on the land, the in an excellent for the growth of and for of all (Darwin “It be whether there are many other which have so a part in the history of the world, as have these organized this book as in the field of the in such subjects as at the of the and ecology, and ecologists also have a for Darwin's book In Darwin's a of his (two which named and a new of Darwin's has or though not the ecology discussion and Darwin's are of ecological and His Journal of Researches 1839 and other Beagle were (Egerton the of his ecological was in the Origin, with contributions in other had first an ecological in the economy of nature (Egerton but since he species were so was his economy of In the first of the 1800s, developed a economy of nature (Egerton it the of an more was before that and Darwin's evolutionary ecology became a on which ecological sciences would be two decades after his his I Darwin and University of

@article{doi10189000129623924351,
    author = "Egerton, Frank N.",
    title = "History of Ecological Sciences, Part 40: Darwin's Evolutionary Ecology",
    year = "2011",
    journal = "Bulletin of the Ecological Society of America",
    abstract = "Click here for all previous articles in the History of the Ecological Sciences series by F. N. Egerton Charles Darwin (1809–1882) was the greatest biological scientist and a major contributor to ecological sciences (Vorzimmer 1965, Acot 1983 Dajoz 1984:46–50, 58–83). Natural history before Darwin had many ingredients of ecology, but was weak in theory. The balance of nature, including Linnaeus' version, economy of nature (Egerton 2007b:81–84), was the main example, and it was never developed as a precise theory (Egerton 1973, Kricher 2009). The evolutionary ideas of Erasmus Darwin and Lamarck had ecological relevance (Egerton 2008, 2010a) but were not developed into an elaborate theory like Charles Darwin's theory of evolution by natural selection. What do I mean by evolutionary ecology? A coyote might eat different prey in different parts of its geographic range, so that is not much of an evolved relationship. However, other relationships have evolved. Augustin-Pyramus de Candolle, one of the leading botanists during the first three decades of the 1800s, was uninterested in studies on floral mechanisms that seemed to guide specific species of insects into pollinating a specific species of plants, because he did not believe that one biological species was modified to meet the needs of another species. He was aware of Lamarck's evolutionary speculations about species striving to change, but he was among the majority of botanists and zoologists who did not find Lamarck's teachings convincing. Darwin's first book after publishing the Origin of Species was on the mechanisms among orchid species that guide particular insect species to pollinate that orchid species—caused by natural selection, not by Lamarckian striving—one example of evolutionary ecology. Another example is a harmless animal species evolving by natural selection to mimic a dangerous species as a protection from predators. Darwin's Origin unleashed this line of thought before ecology became an organized science, and later ecologists readily adopted this intellectual tool (Kolasa 2011:28, 39). Darwin's Journal of Researches 1839 made substantial contributions to ecology (Egerton 2010b), and he was as well equipped after his voyage to advance understanding of the economy of nature as to advance evolutionary biology. After the Beagle publications, Darwin continued being an observational naturalist, but he also became an experimentalist. Darwin followed in the footsteps of three role models: Gilbert White, an observer, Humboldt, an observer–correlationist–experimenter, and Lyell, an observer–theoretician. Darwin commonly investigated several different subjects in a year, and even when our scope is limited to ecological subjects, a strictly chronological presentation is impractical. His post-Beagle books (Freeman 1965) usually were preceded by articles in periodicals on the subject. Fortunately, these articles are mostly republished in The Collected Papers of Charles Darwin (two volumes, 1977), and more completely in Darwin's Shorter Publications, 1829–1883 (Darwin 2009). All of Darwin's books are available on the Internet 〈Darwin–online.org.uk〉, and are also republished (Darwin 1986–1990). His Correspondence has been published by Cambridge University Press since 1985 (18 volumes extend to 1870) and is also online 〈darwinproject.ac.uk〉. The present discussion is organized in the chronological order in which he published relevant books, since the Beagle volumes covered in part 37 (Egerton 2010b). Darwin was one of the world's greatest correspondents, and many of his correspondents were happy to send useful information to him. His publications are also available in a collected set (1986–1990) and at Darwin online. After leaving the Galapagos Islands, Darwin had wondered in 1836 whether mockingbirds from different islands were varieties or species (Egerton 2010b:412–414). In March 1837, ornithologist John Gould convinced Darwin that his finch and mockingbird specimens from the Galapagos Islands were different species, and that realization made Darwin an evolutionist (Egerton 2010b:416). Darwin then began keeping notebooks in which he recorded his readings and thoughts on transmutation. His eureka moment came on 28 September 1838 (Darwin 1987:375), when he read Thomas Robert Malthus' Essay on the Principle of Population (Edition 6, 1826). Why did he read a book that would seem to be peripheral to his quest? He had recently finished his Journal of Researches 1839, which he had modeled on Humboldt's Personal Narrative of Travels, and Humboldt had praised Malthus' Essay (Egerton 1970:331–332). Using information in his notebooks, Darwin wrote two early drafts of his theory, 1842 and 1844 (1909). Those notebooks and drafts provide insights into the literature he read and the progress in his thinking, 1837–1844 (Limoges 1970, Manier 1978, Kohn 1980, 1985, Ospovat 1981, Hodge 2003). Anonymous publication of Robert Chambers' Vestiges of the Natural History of Creation 1844, followed by unfavorable reviews from naturalists, inhibited Darwin from publishing his theory at that time. Instead, he wrote two monographs on living barnacles and two on fossils (1851–1854) that “brought about a new way of thinking about morphological comparisons” (Ghiselin 1969:109), and one cirripedologist (Crisp 1983:73–74) even suggested that these monographs could be considered Darwin's greatest works, even though Darwin had misunderstood aspects of female anatomy! The interest he developed in invertebrates at Edinburgh continued throughout the voyage of the Beagle, and he had wanted to include a volume on invertebrates to Zoology of the Voyage of H. M. S. Beagle, but had not managed to do so (Love 2002:266–269). His specific interest in barnacles had been piqued in January 1835 when he discovered in the Chonos Archipelago, off the mainland of Chile, the smallest known barnacle (seen with his microscope), which he named Cryptophialus minutus (Darwin 1854:23, 566–586, 2000:274–276, Richmond 1988, Keynes 2003:264–265, Stott 2003:xx–xxi, 62–63). C. minutus was a parasite that bored through the shell of a conch Concholepas peruviana and lived in its body. While overseeing the volumes describing his vast collections from his voyage and also writing his Journal of Researches, he did not pause to explore this oddity, but after those Beagle volumes appeared, he returned to this species and was soon studying all of the barnacles. His monographs mostly contain systematic descriptions and classifications of species (Winsor 1969a, b, Ghiselin and Jaffe 1973, Southward 1983, Richmond 1988); however their introductions are relevant. Barnacles ate “infusoria” (plankton), minute spiral univalves (snails), and crustacea, including larvae of other barnacles (Darwin 1851:45–46). Pedunculated barnacles (Fig. 2) extend over the whole world, and most species have large ranges, especially those that attach to floating objects. Of those species that attach to fixed objects or to littoral animals, one rarely finds more than three or four species in any locality (Darwin 1851:65–66). Cirripedes are usually bisexual, differing from all other crustacean; when sexes are separate, males are minute and permanently epizoic on females (Darwin 1854:15). Sessil barnacles (Fig. 3) live from latitude 74° 18′ North, south to Cape Horn. Charles Darwin, about 1854. Seward 1909:Frontispiece.. Pedunculated Pollicipes. By George Sowerby. Darwin 1851: from Plate 7, 1964. Sessile barnacle: larvae of Lepus australis. By George Sowerby. Darwin 1854: from Plate 30, 1964. The area between the north Philippine Archipelago and south Australia, extending to New Zealand on the right and Sumatra on the left, has a greater number of species than the rest of the world. Probably this is mainly due to the broken nature of the land, providing diversified habitats and due to much of the coast being rocky. There are more species on the rocky coast of western South America than on its sandy or muddy eastern coast. Coral reefs are unfavorable for all barnacles except Pyrgoma, and few barnacles are known from Pacific islands. Where they can live, species are few and individuals are infinite. No genus with more than one species is confined to the torrid zone. Pyrgoma species are confined to the torrid zone except for one species that is found from the Cape Verde Islands to England and Ireland (1854:159–160). James Dana's great work, Crustacea (1852–1855), has an excellent chart with isocrymal lines, showing mean temperature of waters along their course for the coldest 30 consecutive days in any season. He showed that these lines are most influential for the distribution of marine animals. These measurements were a further elaboration on the isothermal lines that Humboldt introduced into environmental studies (Egerton 2011:158). Dana divided the torrid and sub-torrid zones from the temperate zones at isocryme 68°, and the temperate zones from the sub-frigid and frigid zones at 44°. Darwin found no barnacles confined to frigid zones. Darwin knew 147 species, seven of doubtful habitat. Of the remaining 140, 37 inhabited both torrid and temperate zones, 46 were exclusively in torrid, and 57 were exclusively in temperate zones. The temperate zones, though smaller in area with considerably less lengthy coastlines, had the most species. There are two temperate zones, separated by torrid zones, and the number of species in any zone seems to depend on the isolation of sub-zones. Balanus was the largest known genus, with 36 species of known habitats: 9 in the torrid zone, 15 in temperate zones, and 12 in both zones (Darwin 1854:160–162). Darwin divided the oceans with barnacles into five provinces and listed the species in each province (Darwin 1854:164–171). His two volumes on living and two on fossil barnacles won the Royal Society Medal in 1854. D. T. Anderson, Barnacles: Structure, Function, Development and Evolution 1994, provides a modern perspective on Darwin's work. After publishing on barnacles, at Lyell's urging, Darwin returned to his natural selection project and was in the midst of writing a huge monograph, when he was interrupted by arrival in his mail of Alfred Russel Wallace's manuscript, “On the Tendency of Varieties to Depart Indefinitely from the Original Type,” in 1858. Wallace became a co-discoverer of evolution by natural selection, and Lyell and Joseph Hooker arranged for extracts of Darwin's work, along with Wallace's article, to be read on 1 July and published in 1859 by the Linnean Society of London (Darwin and Wallace 1859). Darwin then abandoned his large manuscript and wrote a more readable abridgment, On the Origin of Species 1859. His longer manuscript was partly used in later books, but those parts not so used are now published (Darwin 1975) and provide many citations to his sources not included in Origin. Darwin presented his theory in the first four chapters, followed by nine chapters on diverse supporting evidence. Origin chapters 1–2 presented noncontroversial evidence that variation occurs in both domestic and wild populations of species. …it breeds when thirty years old, and goes on breeding till ninety years old, bringing forth three pair of young in this interval; if this be so, at the end of the fifth century there would be alive fifteen million elephants, descended from the first pair. …it breeds when thirty years old, and goes on breeding till ninety years old, bringing forth six young in the interval, and surviving till one hundred years old; if this be so, after a period of from 740 to 750 years there would be nearly nineteen million elephants alive, descended from the first pair. But since there would never be nineteen million elephants, descended from one pair, alive at the same time, there must be checks on the growth of populations of all species. To illustrate the complexity of such checks, Darwin explained the interrelationships of red clover, humble bees, mice, and cats: only humble bees pollinate red clover, but field mice eat humble bees, and cats eat mice. Therefore, the success of red clover fields might depend on the local population of cats (1859:73–74). Although we now know that this food chain is more complex than Darwin realized (Egerton 2007a:52–53), his conclusion is still valid: if we speculate on those checks and their magnitudes, “It will convince us of our ignorance on the mutual relations of all organic beings…” (1859:78). Revolutionary paradigms, such as Origin, reorient sciences and uncover new problems to study (Kuhn 1970). When we see leaf-eating insects green, and bark-feeders mottled-grey; the alpine ptarmigan white in winter, the red-grouse the colour of heather, and the black-grouse that of peaty earth, we must believe that these tints are of service to these birds and insects in preserving them from danger. Grouse, if not destroyed at some period of their lives, would increase in countless numbers; they are known to suffer largely from birds of prey; and hawks are guided by eyesight to their prey—so much so, that on parts of the Continent persons are not to white as being the most to I can see no to that natural selection might be most in the colour to each of and in keeping that when and He is here of though is to an with many of many with birds on the with insects and with through the earth, and to that these so different from each and on each other in so complex a have all been by Sessile barnacles By George Sowerby. Darwin 1854: from Plate 1964. study and John of early by Sowerby. Darwin of all these this Darwin a for a and it into an and found that the to it then at a right to be in to pollinate the orchid the by Sowerby. Darwin Darwin's theory might have the of the economy of nature and the balance of nature, but this it did not (Egerton theory of evolution by natural selection is an ecological on the ecological by the greatest of all is no that one of Darwin's most realized the not only for a new of evolutionary but also for a new of ecology, which he named and in his (two volumes, to and Darwin, and a to Although Darwin had some he found to and and might not have read of In the years after publishing Origin, Darwin published more books and His subjects were but they all had the same of and for his theory. we in part 37 (Egerton 2010b), made a of on the Galapagos Islands and Darwin thought of as a and during and after his voyage on the Beagle, and his new publications after his Beagle volumes were on barnacles. his and publications were as much or more on as on He was usually by his a and by his George who also had However, Darwin's and with Joseph Hooker after was a most of information and 1978, and of with seven pair of of to its Darwin Those which had the largest or and which most would be by and would be and so in the would the Those which had their and in to the and of the particular insects which so as to in any the of their from to would be or A with a By George Darwin was Darwin's to that the of many orchid were not a of or but of natural selection His orchid book first specific species were and then to the evolved between and insect to between than of his and in the number of its in his there was no for the or and of some Darwin explained both and were the insect chapters and illustrate different of and their He began with a early and to its parts and their the of to which he this was a and this book was a history of Darwin's theory. was by his but convinced few of his Darwin that had not collected information on the between and but he could his as he did with Using a as a (Darwin he showed that the to the then 30 at a right which it to the of the orchid the studies to (Darwin that with were by bees or and those with by or F. Darwin species of that he had to their After Darwin published his orchid suggested that was insects the through the large on the and by one of the two to the and (Darwin Darwin this by into the of C. but when he a into the it as The has a to 12 and Darwin that there must be a with a to its (Darwin In found a with a a was discovered and has been The book a major in and in as a completely our of and to literature on ecology. that has been on the of and has been or by this John it of the most books of all Darwin listed in the of (Darwin of publications that had since he published the first to this Darwin's On the and of (Darwin first as parts of the Journal of the Linnean Society of London (Freeman and only as a book in the (Darwin He was in the evolution of this and its for these include in which the another and The in most species which he were from or but he also from by and (Darwin included and including and and F. to or with their He did not study the of on their and he did not the that its Darwin later his book in a of studies on this (Darwin in 1 and and to and Darwin a Darwin (Darwin in the same as the of but it was a more substantial book by and Darwin was his and during the in part (Egerton that had in that the and all but he did not their or Darwin had read in 1839 2009). Darwin first the in the of when he on the of the them on but he had to the to and had on to other subjects by He returned to the on (Darwin and a and for this Darwin he had off in with his of the two of showing the to Darwin of the book He and to and to the to and also the to did not the that live in do not for further The remaining chapters the mechanisms of the and a few M. of had his of the of that and and had and that a of than not (Darwin to both botanists and and modern literature and these species as and Darwin's books, The of and in the and The of on of the Species are relevant to ecology since insects were the had been a in his and in this new book he those more Darwin the of for and and he the that had evolved in to some had and so that the were separated from the and did not Darwin to some and was by other botanists of field on which and had been about 15 years after it had been and and Darwin considered The of in Darwin's greatest work. Darwin the of his on its was on and there were and of had in the of though it some of in that he had been by and Darwin's at Darwin later the of this but not the with He the with in his (Darwin Charles Darwin in By John for the Linnean Society of A is also in the Darwin's book was The of through the of with on He had with this on 12 he had his for four and his Darwin later showed fields that had been covered with or with and some years but at the they were those were even though the fields had not been since the His thought that the of had those Darwin had in that could so he could believe that the of might also have an on He the and wrote a for the Society of which he read on 1 1837, and which was published in In the book he that are at and so do not see them at work, but if one one can find their of their He even that were on the had due to both the them and the that were He that which as with a the of the land, has all many through their (Darwin The or into their to a of or (Darwin but their can to or or more (Darwin The book in measurements and such as at was by to the on a in the course of a (Darwin their on the land, the in an excellent for the growth of and for of all (Darwin “It be whether there are many other which have so a part in the history of the world, as have these organized this book as in the field of the in such subjects as at the of the and ecology, and ecologists also have a for Darwin's book In Darwin's a of his (two which named and a new of Darwin's has or though not the ecology discussion and Darwin's are of ecological and His Journal of Researches 1839 and other Beagle were (Egerton the of his ecological was in the Origin, with contributions in other had first an ecological in the economy of nature (Egerton but since he species were so was his economy of In the first of the 1800s, developed a economy of nature (Egerton it the of an more was before that and Darwin's evolutionary ecology became a on which ecological sciences would be two decades after his his I Darwin and University of",
    url = "https://doi.org/10.1890/0012-9623-92.4.351",
    doi = "10.1890/0012-9623-92.4.351",
    openalex = "W2010067442",
    references = "doi105860choice413408, openalexw1501278615"
}

Birds are well known for occupying diverse feeding niches, and for having evolved diverse beak morphologies associated with dietary specialization. Birds that feed on hard seeds typically possess beaks that are both deep and wide, presumably because of selection for fracture avoidance, as suggested by prior studies. It follows then that birds that eat seeds of different size and hardness should vary in one or more aspects of beak morphology, including the histological organization of the rhamphotheca, the cellular interface that binds the rhamphotheca to the bone, and the organization of trabeculae in the beak. To explore this expectation we here investigate tissue organization in the rhamphotheca of the Java finch, a large granivorous bird, and describe interspecific differences in the trabecular organization of the beak across 11 species of Darwin's finches. We identify specializations in multiple layers of the horny beak, with the dermis anchored to the bone by Sharpey's fibers in those regions that are subjected to high stresses during biting. Moreover, the rhamphotheca is characterized by a tight dermo-epidermal junction through interdigitations of these two tissues. Herbst corpuscles are observed in high density in the dermis of the lateral aspect of the beak as observed in other birds. Finally, the trabecular organization of the beak in Darwin's finches appears most variable in regions involved most in food manipulation, with the density of trabeculae in the beak generally mirroring loading regimes imposed by different feeding habits and beak use in this clade.

@article{doi101111j14697580201201561x,
    author = "Genbrugge, Annelies and Adriaens, Dominique and Kegel, Barbara De and Brabant, Loes and Hoorebeke, Luc Van and Podos, Jeffrey and Dirckx, Joris and Aerts, Peter and Herrel, Anthony",
    title = "Structural tissue organization in the beak of J ava and D arwin's finches",
    year = "2012",
    journal = "Journal of Anatomy",
    abstract = "Birds are well known for occupying diverse feeding niches, and for having evolved diverse beak morphologies associated with dietary specialization. Birds that feed on hard seeds typically possess beaks that are both deep and wide, presumably because of selection for fracture avoidance, as suggested by prior studies. It follows then that birds that eat seeds of different size and hardness should vary in one or more aspects of beak morphology, including the histological organization of the rhamphotheca, the cellular interface that binds the rhamphotheca to the bone, and the organization of trabeculae in the beak. To explore this expectation we here investigate tissue organization in the rhamphotheca of the Java finch, a large granivorous bird, and describe interspecific differences in the trabecular organization of the beak across 11 species of Darwin's finches. We identify specializations in multiple layers of the horny beak, with the dermis anchored to the bone by Sharpey's fibers in those regions that are subjected to high stresses during biting. Moreover, the rhamphotheca is characterized by a tight dermo-epidermal junction through interdigitations of these two tissues. Herbst corpuscles are observed in high density in the dermis of the lateral aspect of the beak as observed in other birds. Finally, the trabecular organization of the beak in Darwin's finches appears most variable in regions involved most in food manipulation, with the density of trabeculae in the beak generally mirroring loading regimes imposed by different feeding habits and beak use in this clade.",
    url = "https://doi.org/10.1111/j.1469-7580.2012.01561.x",
    doi = "10.1111/j.1469-7580.2012.01561.x",
    openalex = "W2001141929",
    references = "doi101002jmor11023"
}

Biodiversity data derive from myriad sources stored in various formats on many distinct hardware and software platforms. An essential step towards understanding global patterns of biodiversity is to provide a standardized view of these heterogeneous data sources to improve interoperability. Fundamental to this advance are definitions of common terms. This paper describes the evolution and development of Darwin Core, a data standard for publishing and integrating biodiversity information. We focus on the categories of terms that define the standard, differences between simple and relational Darwin Core, how the standard has been implemented, and the community processes that are essential for maintenance and growth of the standard. We present case-study extensions of the Darwin Core into new research communities, including metagenomics and genetic resources. We close by showing how Darwin Core records are integrated to create new knowledge products documenting species distributions and changes due to environmental perturbations.

@article{doi101371journalpone0029715,
    author = "Wieczorek, John and Bloom, David and Guralnick, Robert and Blum, Stan and Döring, Markus and Giovanni, Renato De and Robertson, Tim and Vieglais, Dave",
    title = "Darwin Core: An Evolving Community-Developed Biodiversity Data Standard",
    year = "2012",
    journal = "PLoS ONE",
    abstract = "Biodiversity data derive from myriad sources stored in various formats on many distinct hardware and software platforms. An essential step towards understanding global patterns of biodiversity is to provide a standardized view of these heterogeneous data sources to improve interoperability. Fundamental to this advance are definitions of common terms. This paper describes the evolution and development of Darwin Core, a data standard for publishing and integrating biodiversity information. We focus on the categories of terms that define the standard, differences between simple and relational Darwin Core, how the standard has been implemented, and the community processes that are essential for maintenance and growth of the standard. We present case-study extensions of the Darwin Core into new research communities, including metagenomics and genetic resources. We close by showing how Darwin Core records are integrated to create new knowledge products documenting species distributions and changes due to environmental perturbations.",
    url = "https://doi.org/10.1371/journal.pone.0029715",
    doi = "10.1371/journal.pone.0029715",
    openalex = "W2159327312"
}

BACKGROUND: A classical example of repeated speciation coupled with ecological diversification is the evolution of 14 closely related species of Darwin's (Galápagos) finches (Thraupidae, Passeriformes). Their adaptive radiation in the Galápagos archipelago took place in the last 2-3 million years and some of the molecular mechanisms that led to their diversification are now being elucidated. Here we report evolutionary analyses of genome of the large ground finch, Geospiza magnirostris. RESULTS: 13,291 protein-coding genes were predicted from a 991.0 Mb G. magnirostris genome assembly. We then defined gene orthology relationships and constructed whole genome alignments between the G. magnirostris and other vertebrate genomes. We estimate that 15% of genomic sequence is functionally constrained between G. magnirostris and zebra finch. Genic evolutionary rate comparisons indicate that similar selective pressures acted along the G. magnirostris and zebra finch lineages suggesting that historical effective population size values have been similar in both lineages. 21 otherwise highly conserved genes were identified that each show evidence for positive selection on amino acid changes in the Darwin's finch lineage. Two of these genes (Igf2r and Pou1f1) have been implicated in beak morphology changes in Darwin's finches. Five of 47 genes showing evidence of positive selection in early passerine evolution have cilia related functions, and may be examples of adaptively evolving reproductive proteins. CONCLUSIONS: These results provide insights into past evolutionary processes that have shaped G. magnirostris genes and its genome, and provide the necessary foundation upon which to build population genomics resources that will shed light on more contemporaneous adaptive and non-adaptive processes that have contributed to the evolution of the Darwin's finches.

@article{doi101186147121641495,
    author = "Rands, Chris M. and Darling, Aaron E. and Fujita, Matthew K. and Kong, Lesheng and Webster, Matthew T. and Clabaut, Céline and Emes, Richard D. and Heger, Andreas and Meader, Stephen and Hawkins, M. Brent and Eisen, Michael B. and Teiling, Clotilde and Affourtit, Jason P. and Boese, Benjamin and Grant, Peter R. and Grant, B. Rosemary and Eisen, Jonathan A. and Abzhanov, Arhat and Ponting, Chris P.",
    title = "Insights into the evolution of Darwin’s finches from comparative analysis of the Geospiza magnirostris genome sequence",
    year = "2013",
    journal = "BMC Genomics",
    abstract = "BACKGROUND: A classical example of repeated speciation coupled with ecological diversification is the evolution of 14 closely related species of Darwin's (Galápagos) finches (Thraupidae, Passeriformes). Their adaptive radiation in the Galápagos archipelago took place in the last 2-3 million years and some of the molecular mechanisms that led to their diversification are now being elucidated. Here we report evolutionary analyses of genome of the large ground finch, Geospiza magnirostris. RESULTS: 13,291 protein-coding genes were predicted from a 991.0 Mb G. magnirostris genome assembly. We then defined gene orthology relationships and constructed whole genome alignments between the G. magnirostris and other vertebrate genomes. We estimate that 15\% of genomic sequence is functionally constrained between G. magnirostris and zebra finch. Genic evolutionary rate comparisons indicate that similar selective pressures acted along the G. magnirostris and zebra finch lineages suggesting that historical effective population size values have been similar in both lineages. 21 otherwise highly conserved genes were identified that each show evidence for positive selection on amino acid changes in the Darwin's finch lineage. Two of these genes (Igf2r and Pou1f1) have been implicated in beak morphology changes in Darwin's finches. Five of 47 genes showing evidence of positive selection in early passerine evolution have cilia related functions, and may be examples of adaptively evolving reproductive proteins. CONCLUSIONS: These results provide insights into past evolutionary processes that have shaped G. magnirostris genes and its genome, and provide the necessary foundation upon which to build population genomics resources that will shed light on more contemporaneous adaptive and non-adaptive processes that have contributed to the evolution of the Darwin's finches.",
    url = "https://doi.org/10.1186/1471-2164-14-95",
    doi = "10.1186/1471-2164-14-95",
    openalex = "W2159252300",
    references = "doi101006jmbi20004042, doi10103875556, doi101038nature03154, doi10108010635150701472164, doi101093bioinformaticsbti1018, doi101093molbevmsi097, doi101093molbevmsm088, doi101098rstb20090321, doi101186147121055113, doi1023071223169"
}

The prevailing theory for the molecular basis of evolution involves genetic mutations that ultimately generate the heritable phenotypic variation on which natural selection acts. However, epigenetic transgenerational inheritance of phenotypic variation may also play an important role in evolutionary change. A growing number of studies have demonstrated the presence of epigenetic inheritance in a variety of different organisms that can persist for hundreds of generations. The possibility that epigenetic changes can accumulate over longer periods of evolutionary time has seldom been tested empirically. This study was designed to compare epigenetic changes among several closely related species of Darwin's finches, a well-known example of adaptive radiation. Erythrocyte DNA was obtained from five species of sympatric Darwin's finches that vary in phylogenetic relatedness. Genome-wide alterations in genetic mutations using copy number variation (CNV) were compared with epigenetic alterations associated with differential DNA methylation regions (epimutations). Epimutations were more common than genetic CNV mutations among the five species; furthermore, the number of epimutations increased monotonically with phylogenetic distance. Interestingly, the number of genetic CNV mutations did not consistently increase with phylogenetic distance. The number, chromosomal locations, regional clustering, and lack of overlap of epimutations and genetic mutations suggest that epigenetic changes are distinct and that they correlate with the evolutionary history of Darwin's finches. The potential functional significance of the epimutations was explored by comparing their locations on the genome to the location of evolutionarily important genes and cellular pathways in birds. Specific epimutations were associated with genes related to the bone morphogenic protein, toll receptor, and melanogenesis signaling pathways. Species-specific epimutations were significantly overrepresented in these pathways. As environmental factors are known to result in heritable changes in the epigenome, it is possible that epigenetic changes contribute to the molecular basis of the evolution of Darwin's finches.

@article{doi101093gbeevu158,
    author = "Skinner, Michael K. and Gurerrero-Bosagna, Carlos and Haque, M. Muksitul and Nilsson, Eric and Koop, Jennifer A. H. and Knutie, Sarah A. and Clayton, Dale H.",
    title = "Epigenetics and the Evolution of Darwin’s Finches",
    year = "2014",
    journal = "Genome Biology and Evolution",
    abstract = "The prevailing theory for the molecular basis of evolution involves genetic mutations that ultimately generate the heritable phenotypic variation on which natural selection acts. However, epigenetic transgenerational inheritance of phenotypic variation may also play an important role in evolutionary change. A growing number of studies have demonstrated the presence of epigenetic inheritance in a variety of different organisms that can persist for hundreds of generations. The possibility that epigenetic changes can accumulate over longer periods of evolutionary time has seldom been tested empirically. This study was designed to compare epigenetic changes among several closely related species of Darwin's finches, a well-known example of adaptive radiation. Erythrocyte DNA was obtained from five species of sympatric Darwin's finches that vary in phylogenetic relatedness. Genome-wide alterations in genetic mutations using copy number variation (CNV) were compared with epigenetic alterations associated with differential DNA methylation regions (epimutations). Epimutations were more common than genetic CNV mutations among the five species; furthermore, the number of epimutations increased monotonically with phylogenetic distance. Interestingly, the number of genetic CNV mutations did not consistently increase with phylogenetic distance. The number, chromosomal locations, regional clustering, and lack of overlap of epimutations and genetic mutations suggest that epigenetic changes are distinct and that they correlate with the evolutionary history of Darwin's finches. The potential functional significance of the epimutations was explored by comparing their locations on the genome to the location of evolutionarily important genes and cellular pathways in birds. Specific epimutations were associated with genes related to the bone morphogenic protein, toll receptor, and melanogenesis signaling pathways. Species-specific epimutations were significantly overrepresented in these pathways. As environmental factors are known to result in heritable changes in the epigenome, it is possible that epigenetic changes contribute to the molecular basis of the evolution of Darwin's finches.",
    url = "https://doi.org/10.1093/gbe/evu158",
    doi = "10.1093/gbe/evu158",
    openalex = "W2113157204",
    references = "doi101186147121641495"
}

@article{doi101038nature14181,
    author = "Lamichhaney, Sangeet and Berglund, Jonas and Almén, Markus Sällman and Maqbool, Khurram and Grabherr, Manfred and Barrio, Álvaro Martínez and Promerová, Marta and Rubin, Carl‐Johan and Wang, Chao and Zamani, Neda and Grant, B. Rosemary and Grant, Peter R. and Webster, Matthew T. and Andersson, Leif",
    title = "Evolution of Darwin’s finches and their beaks revealed by genome sequencing",
    year = "2015",
    journal = "Nature",
    url = "https://doi.org/10.1038/nature14181",
    doi = "10.1038/nature14181",
    openalex = "W2070534356",
    references = "doi101038nature04843, doi101038nature11041, doi101126science1098095, doi101146annurevecolsys110512135800, doi101186147121641495, doi105860choice455580"
}

INTRODUCTION: In 1836, Charles Darwin returned to England with finches classified and seemingly showing little resemblance. However, subsequent examination by John Gould revealed 13 closely related species endemic to the Galápagos Islands. Despite initial confusion, and Darwin's overlooking to label these birds by island, some 100 years later they had become evolution's icon. The same could be said of Darwin's education and scientific pursuits, beginning in a rough, trial and error manner, lacking direction, but eventually benefitting from an unexpected opportunity that would lead to his theory of natural selection. CASE DESCRIPTION: This case study examines Darwin's way of learning and the reserve of courage and perseverance that he would need to see his treatise on evolution and natural selection published. To do this, themes from studying the "Nature of Science" are used to examine how Darwin's "way of knowing" advanced before and after his voyage upon HMS Beagle. Five themes from the "Nature of Science" were selected to illustrate Darwin's struggles and triumph: creating scientific knowledge is a human endeavor, such knowledge can explain an order and consistency in natural systems, knowledge comes from a scientist's way of knowing, is open to revision, and based on empirical evidence. DISCUSSION AND EVALUATION: The "Nature of Science" as applied to Charles Darwin is explored through the three above mentioned themes identified by the Next Generation Science Standards. Together, the themes help explain Darwin's way of knowing, from boyhood to manhood. This explanation helps humanize Darwin, allows students to see how he arrived at his theories, how the time taken to do so wore on his health and safety, and the risk Darwin had to weigh from their eventual publication. CONCLUSIONS: Each theme ends with a summary and related extension questions to draw students into the case, and facilitate inquiry. They relate Darwin's way of learning from the 1800s and his commitment to see his work published, to the learning environment of students today.

@article{doi101186s4006401630530,
    author = "Cohen, Joel I",
    title = "Exploring the nature of science through courage and purpose: a case study of Charles Darwin's way of knowing.",
    year = "2016",
    journal = "SpringerPlus",
    abstract = {INTRODUCTION: In 1836, Charles Darwin returned to England with finches classified and seemingly showing little resemblance. However, subsequent examination by John Gould revealed 13 closely related species endemic to the Galápagos Islands. Despite initial confusion, and Darwin's overlooking to label these birds by island, some 100 years later they had become evolution's icon. The same could be said of Darwin's education and scientific pursuits, beginning in a rough, trial and error manner, lacking direction, but eventually benefitting from an unexpected opportunity that would lead to his theory of natural selection. CASE DESCRIPTION: This case study examines Darwin's way of learning and the reserve of courage and perseverance that he would need to see his treatise on evolution and natural selection published. To do this, themes from studying the "Nature of Science" are used to examine how Darwin's "way of knowing" advanced before and after his voyage upon HMS Beagle. Five themes from the "Nature of Science" were selected to illustrate Darwin's struggles and triumph: creating scientific knowledge is a human endeavor, such knowledge can explain an order and consistency in natural systems, knowledge comes from a scientist's way of knowing, is open to revision, and based on empirical evidence. DISCUSSION AND EVALUATION: The "Nature of Science" as applied to Charles Darwin is explored through the three above mentioned themes identified by the Next Generation Science Standards. Together, the themes help explain Darwin's way of knowing, from boyhood to manhood. This explanation helps humanize Darwin, allows students to see how he arrived at his theories, how the time taken to do so wore on his health and safety, and the risk Darwin had to weigh from their eventual publication. CONCLUSIONS: Each theme ends with a summary and related extension questions to draw students into the case, and facilitate inquiry. They relate Darwin's way of learning from the 1800s and his commitment to see his work published, to the learning environment of students today.},
    url = "https://pmc.ncbi.nlm.nih.gov/articles/PMC5020019/",
    doi = "10.1186/s40064-016-3053-0",
    openalex = "W2518831623",
    pmcid = "PMC5020019",
    pmid = "27652105",
    references = "doi101007bf00132004, doi101017cbo9780511693106004, doi101017cbo9781139103831, doi101525abt20157772, doi105860choice453772, doi105962bhltitle25011, openalexw1492219581, openalexw179752181, openalexw242266841"
}

Abstract Darwin's finches have been the focus of intense study demonstrating how climatic fluctuations coupled with resource competition drive the evolution of a variety of bill sizes and shapes. The bill, as other peripheral surfaces, also plays an important role in thermoregulation in numerous bird species. The avian bill is vascularized, while limbs have specialized vasculature that facilitate heat loss or heat conservation (i.e. they are thermoregulatory windows). The Galápagos Islands, home to Darwin's finches, have a hot and relatively dry climate for approximately half of the year, during which thermoregulatory windows (i.e. surfaces) could be important for thermoregulation and the linked challenge of water balance. We hypothesized that Darwin's finch bills have evolved in part for their role in thermoregulation, possibly co‐opted, following adaptation for other functions, such as foraging. We predicted that bills of Darwin's finches are effective thermoregulatory windows, and that species differences in bill morphology, along with physiology and behaviour, lead to differences in thermoregulatory function. To test these hypotheses, we conducted a field study to assess heat exchange and microclimate use in three ground finch species and sympatric cactus finch (Geospiza spp.). We collected thermal images of free‐living birds during a hot and dry season and recorded microclimate data for each observation. We used individual thermographic data to model the contribution of bills, legs and bodies to overall heat balance and compared surface temperatures to those from dead birds to test physiological control of heat loss from these surfaces. We derived and compared species‐specific threshold environmental temperatures, which are indicative of a species’ thermally neutral temperature. In all species, the bill surface was an effective heat dissipater during naturally occurring warm temperatures. As expected, we found that finches controlled surface temperatures through physiology and that young birds had higher surface temperatures than adults. Larger bills contributed proportionally more to overall heat loss than smaller bills. We demonstrate here that related, sympatric species with different bill sizes exhibit different patterns in the use of these thermoregulatory structures, supporting a role for thermoregulation in the evolution and ecology of Darwin's finch morphology. A plain language summary is available for this article.

@article{doi1011111365243512990,
    author = "Tattersall, Glenn J. and Chaves, Jaime A. and Danner, Raymond M.",
    title = "Thermoregulatory windows in Darwin's finches",
    year = "2017",
    journal = "Functional Ecology",
    abstract = "Abstract Darwin's finches have been the focus of intense study demonstrating how climatic fluctuations coupled with resource competition drive the evolution of a variety of bill sizes and shapes. The bill, as other peripheral surfaces, also plays an important role in thermoregulation in numerous bird species. The avian bill is vascularized, while limbs have specialized vasculature that facilitate heat loss or heat conservation (i.e. they are thermoregulatory windows). The Galápagos Islands, home to Darwin's finches, have a hot and relatively dry climate for approximately half of the year, during which thermoregulatory windows (i.e. surfaces) could be important for thermoregulation and the linked challenge of water balance. We hypothesized that Darwin's finch bills have evolved in part for their role in thermoregulation, possibly co‐opted, following adaptation for other functions, such as foraging. We predicted that bills of Darwin's finches are effective thermoregulatory windows, and that species differences in bill morphology, along with physiology and behaviour, lead to differences in thermoregulatory function. To test these hypotheses, we conducted a field study to assess heat exchange and microclimate use in three ground finch species and sympatric cactus finch (Geospiza spp.). We collected thermal images of free‐living birds during a hot and dry season and recorded microclimate data for each observation. We used individual thermographic data to model the contribution of bills, legs and bodies to overall heat balance and compared surface temperatures to those from dead birds to test physiological control of heat loss from these surfaces. We derived and compared species‐specific threshold environmental temperatures, which are indicative of a species’ thermally neutral temperature. In all species, the bill surface was an effective heat dissipater during naturally occurring warm temperatures. As expected, we found that finches controlled surface temperatures through physiology and that young birds had higher surface temperatures than adults. Larger bills contributed proportionally more to overall heat loss than smaller bills. We demonstrate here that related, sympatric species with different bill sizes exhibit different patterns in the use of these thermoregulatory structures, supporting a role for thermoregulation in the evolution and ecology of Darwin's finch morphology. A plain language summary is available for this article.",
    url = "https://doi.org/10.1111/1365-2435.12990",
    doi = "10.1111/1365-2435.12990",
    openalex = "W2757630438",
    references = "doi101002jmor11023"
}

Proliferative leg skin lesions have been described in wild finches in Europe although there have been no large-scale studies of their aetiology or epizootiology to date. Firstly, disease surveillance, utilising public reporting of observations of live wild finches was conducted in Great Britain (GB) and showed proliferative leg skin lesions in chaffinches (Fringilla coelebs) to be widespread. Seasonal variation was observed, with a peak during the winter months. Secondly, pathological investigations were performed on a sample of 39 chaffinches, four bullfinches (Pyrrhula pyrrhula), one greenfinch (Chloris chloris) and one goldfinch (Carduelis carduelis) with proliferative leg skin lesions and detected Cnemidocoptes sp. mites in 91% (41/45) of affected finches and from all species examined. Fringilla coelebs papillomavirus (FcPV1) PCR was positive in 74% (23/31) of birds tested: a 394 base pair sequence was derived from 20 of these birds, from all examined species, with 100% identity to reference genomes. Both mites and FcPV1 DNA were detected in 71% (20/28) of birds tested for both pathogens. Histopathological examination of lesions did not discriminate the relative importance of mite or FcPV1 infection as their cause. Development of techniques to localise FcPV1 within lesions is required to elucidate the pathological significance of FcPV1 DNA detection.

@article{doi101038s4159801832255y,
    author = "Lawson, Becki and Robinson, Robert A. and Fernández, Julia Rodríguez-Ramos and John, Shinto K. and Benı́tez, Laura and Tolf, Conny and Risely, Kate and Toms, Mike P. and Cunningham, Andrew A. and Williams, Richard",
    title = "Spatio-temporal dynamics and aetiology of proliferative leg skin lesions in wild British finches",
    year = "2018",
    journal = "Scientific Reports",
    abstract = "Proliferative leg skin lesions have been described in wild finches in Europe although there have been no large-scale studies of their aetiology or epizootiology to date. Firstly, disease surveillance, utilising public reporting of observations of live wild finches was conducted in Great Britain (GB) and showed proliferative leg skin lesions in chaffinches (Fringilla coelebs) to be widespread. Seasonal variation was observed, with a peak during the winter months. Secondly, pathological investigations were performed on a sample of 39 chaffinches, four bullfinches (Pyrrhula pyrrhula), one greenfinch (Chloris chloris) and one goldfinch (Carduelis carduelis) with proliferative leg skin lesions and detected Cnemidocoptes sp. mites in 91\% (41/45) of affected finches and from all species examined. Fringilla coelebs papillomavirus (FcPV1) PCR was positive in 74\% (23/31) of birds tested: a 394 base pair sequence was derived from 20 of these birds, from all examined species, with 100\% identity to reference genomes. Both mites and FcPV1 DNA were detected in 71\% (20/28) of birds tested for both pathogens. Histopathological examination of lesions did not discriminate the relative importance of mite or FcPV1 infection as their cause. Development of techniques to localise FcPV1 within lesions is required to elucidate the pathological significance of FcPV1 DNA detection.",
    url = "https://doi.org/10.1038/s41598-018-32255-y",
    doi = "10.1038/s41598-018-32255-y",
    openalex = "W2894444060",
    references = "doi1016379685021411reg1"
}

@article{doi101007s10592019011753,
    author = "Farrington, Heather L. and Lawson, Lucinda P. and Petren, Kenneth",
    title = "Predicting population extinctions in Darwin’s finches",
    year = "2019",
    journal = "Conservation Genetics",
    url = "https://doi.org/10.1007/s10592-019-01175-3",
    doi = "10.1007/s10592-019-01175-3",
    openalex = "W2928137517",
    references = "doi1010079780387981413, doi101016jtree200608009, doi101073pnas0403809101, doi101093bioinformaticsbts460, doi101093genetics14442001, doi101093oxfordjournalsjhereda111627, doi101098rstb20090316, doi101111j109583121991tb00548x, doi101111j14718286200501155x, doi105751es00650090205"
}

; a species of Darwin's finch) during a dry year on San Cristóbal Island. We quantified nest building, egg laying and hatching, and fledging in an urban and nonurban area and characterized the anthropogenic debris in nests. We also documented mortalities including nest trash-related deaths and whether anthropogenic materials directly led to entanglement- or ingestion-related nest mortalities. Overall, urban finches built more nests, laid more eggs, and produced more fledglings than nonurban finches. However, every nest in the urban area contained anthropogenic material, which resulted in 18% nestling mortality while nonurban nests had no anthropogenic debris. Our study showed that urban living has trade-offs: urban birds have overall higher nesting success during a dry year than nonurban birds, but urban birds can suffer mortality from anthropogenic-related nest-materials. These results suggest that despite potential costs, finches benefit overall from urban living and urbanization may buffer the effects of limited resource availability in the Galápagos Islands.

@article{doi101002ece37360,
    author = "Harvey, Johanna A. and Chernicky, Kiley and Simons, Shelby and Verrett, Taylor B. and Chaves, Jaime A. and Knutie, Sarah A.",
    title = "Urban living influences the nesting success of Darwin’s finches in the Galápagos Islands",
    year = "2021",
    journal = "Ecology and Evolution",
    abstract = "; a species of Darwin's finch) during a dry year on San Cristóbal Island. We quantified nest building, egg laying and hatching, and fledging in an urban and nonurban area and characterized the anthropogenic debris in nests. We also documented mortalities including nest trash-related deaths and whether anthropogenic materials directly led to entanglement- or ingestion-related nest mortalities. Overall, urban finches built more nests, laid more eggs, and produced more fledglings than nonurban finches. However, every nest in the urban area contained anthropogenic material, which resulted in 18\% nestling mortality while nonurban nests had no anthropogenic debris. Our study showed that urban living has trade-offs: urban birds have overall higher nesting success during a dry year than nonurban birds, but urban birds can suffer mortality from anthropogenic-related nest-materials. These results suggest that despite potential costs, finches benefit overall from urban living and urbanization may buffer the effects of limited resource availability in the Galápagos Islands.",
    url = "https://doi.org/10.1002/ece3.7360",
    doi = "10.1002/ece3.7360",
    openalex = "W3139007008",
    references = "doi101017s0959270919000285"
}

Significance Genomes contain signatures of past gene exchange between species. However, genomic data are not available for many organisms. For these, morphology may substitute for genes, as exemplified by Darwin’s finches on the Galápagos island of Floreana. In 1835, Darwin and companions collected seven specimens of a uniquely large form of Geospiza magnirostris that became extinct in the next few decades. A surviving population of Geospiza fortis shows evidence of hybridization in a pronounced skew in the distribution of beak size in the direction of the absent G. magnirostris. The genetic and morphological residuum of an extinct species in an extant one has implications for its future evolution, as well as for conservation programs of reintroduction in extinction-depleted communities.

@article{doi101073pnas2107434118,
    author = "Grant, Peter R. and Grant, B. Rosemary",
    title = "Morphological ghosts of introgression in Darwin’s finch populations",
    year = "2021",
    journal = "Proceedings of the National Academy of Sciences",
    abstract = "Significance Genomes contain signatures of past gene exchange between species. However, genomic data are not available for many organisms. For these, morphology may substitute for genes, as exemplified by Darwin’s finches on the Galápagos island of Floreana. In 1835, Darwin and companions collected seven specimens of a uniquely large form of Geospiza magnirostris that became extinct in the next few decades. A surviving population of Geospiza fortis shows evidence of hybridization in a pronounced skew in the distribution of beak size in the direction of the absent G. magnirostris. The genetic and morphological residuum of an extinct species in an extant one has implications for its future evolution, as well as for conservation programs of reintroduction in extinction-depleted communities.",
    url = "https://doi.org/10.1073/pnas.2107434118",
    doi = "10.1073/pnas.2107434118",
    openalex = "W3186186215",
    references = "doi101007s10592019011753, doi101016jtree200401003, doi101017cbo9780511808999, doi101038nature14181, doi101038ncomms14363, doi101098rstb20090316, doi101111eva12367, doi101111j155856461995tb05971x, doi101126science1070315, doi101146annurevecolsys27183, doi104159harvard9780674865327, doi105860choice401529"
}

Abstract Oceanic archipelagos comprise multiple disparate environments over small geographic areas and are isolated from other biotas. These conditions have led to some of the most spectacular adaptive radiations, which have been key to our understanding of evolution, and offer a unique chance to characterise the genomic basis underlying rapid and pronounced phenotypic changes. Repeated patterns of evolutionary change in plants on oceanic archipelagos, i.e. the plant island syndrome, include changes in leaf morphology, acquisition of perennial life-style, and change of ploidy. Here, we describe the genome of the critically endangered and Galápagos endemic Scalesia atractyloides Arnot., obtaining a chromosome-resolved 3.2-Gbp assembly with 43,093 candidate gene models. Using a combination of fossil transposable elements, k -mer spectra analyses and orthologue assignment, we identify the two ancestral subgenomes and date their divergence and the polyploidization event, concluding that the ancestor of all Scalesia species on the Galápagos was an allotetraploid. There are a comparable number of genes and transposable elements across the two subgenomes, and while their synteny has been mostly conserved, we find multiple inversions that may have facilitated adaptation. We identify clear signatures of selection across genes associated with vascular development, life-growth, adaptation to salinity and changes in flowering time, thus finding compelling evidence for a genomic basis of island syndrome in Darwin’s giant daisy radiation. This work advances understanding of factors influencing subgenome divergence in polyploid genomes, and characterizes the quick and pronounced genomic changes in a specular and diverse radiation of an iconic island plant radiation.

@misc{doi10110120220126477903,
    author = "Cerca, José and Petersen, Bent and Lázaro-Guevara, José M. and Rivera‐Colón, Angel G. and Birkeland, Siri and Vizueta, Joel and Li, Siyu and Loureiro, João and Kosawang, Chatchai and Jaramillo, Patricia and Rivas‐Torres, Gonzalo and Fernández‐Mazuecos, Mario and Vargas, Pablo and McCauley, Ross A. and Petersen, Gitte and Santos‐Bay, Luisa and Wales, Nathan and Catchen, Julian and Machado, Daniel and Nowak, Michael and Suh, Alexander and Sinha, Neelima and Nielsen, Lene Rostgaard and Seberg, Ole and Gilbert, M. Thomas P. and Leebens-Mack, James H. and Rieseberg, Loren H. and Martin, Michael D.",
    title = "The genomic basis of the plant island syndrome in Darwin’s giant daisies",
    year = "2022",
    booktitle = "bioRxiv (Cold Spring Harbor Laboratory)",
    abstract = "Abstract Oceanic archipelagos comprise multiple disparate environments over small geographic areas and are isolated from other biotas. These conditions have led to some of the most spectacular adaptive radiations, which have been key to our understanding of evolution, and offer a unique chance to characterise the genomic basis underlying rapid and pronounced phenotypic changes. Repeated patterns of evolutionary change in plants on oceanic archipelagos, i.e. the plant island syndrome, include changes in leaf morphology, acquisition of perennial life-style, and change of ploidy. Here, we describe the genome of the critically endangered and Galápagos endemic Scalesia atractyloides Arnot., obtaining a chromosome-resolved 3.2-Gbp assembly with 43,093 candidate gene models. Using a combination of fossil transposable elements, k -mer spectra analyses and orthologue assignment, we identify the two ancestral subgenomes and date their divergence and the polyploidization event, concluding that the ancestor of all Scalesia species on the Galápagos was an allotetraploid. There are a comparable number of genes and transposable elements across the two subgenomes, and while their synteny has been mostly conserved, we find multiple inversions that may have facilitated adaptation. We identify clear signatures of selection across genes associated with vascular development, life-growth, adaptation to salinity and changes in flowering time, thus finding compelling evidence for a genomic basis of island syndrome in Darwin’s giant daisy radiation. This work advances understanding of factors influencing subgenome divergence in polyploid genomes, and characterizes the quick and pronounced genomic changes in a specular and diverse radiation of an iconic island plant radiation.",
    url = "https://doi.org/10.1101/2022.01.26.477903",
    doi = "10.1101/2022.01.26.477903",
    openalex = "W4210684169",
    references = "doi1012685bauhinia1687"
}

SUMMARY The Galápagos Islands are a prime example of a natural laboratory for the study of evolutionary radiations. While much attention has been devoted to iconic species like Darwin’s finches 1–4, the islands offer an equally unique but often overlooked opportunity for plant radiations 5. Yet, compared to their animal counterparts, our understanding of the patterns and processes underpinning Galápagos plant radiations remains relatively limited 6,7. We present evidence of the early stages of a radiation in prickly-pear cactus (Opuntia, Cactaceae), a plant lineage widespread across the archipelago. Phylogenomic and population genomic analyses show that notwithstanding overall low genetic differentiation across populations, there is marked geographic structure that is broadly consistent with current taxonomy and the dynamic paleogeography of the Galápagos. Because such low genetic differentiation stands in stark contrast to the exceptional eco-phenotypic diversity displayed by cacti across islands, it is plausible that phenotypic plasticity precedes genetic divergence and is the source of adaptive evolution, or that introgression between populations facilitates local adaptation. Models of population relationships including admixture indicate that gene flow is common between certain islands, likely facilitated by dispersal via animals known to feed on Opuntia flowers, fruits, and seeds across the archipelago. Scans of genetic differentiation between populations reveal candidate loci associated with seed traits and environmental stressors, suggesting that a combination of biotic interactions and abiotic pressures due to the harsh conditions characterizing island life in a volcanic, equatorial archipelago may underlie the diversification of prickly-pear cacti. Considered in concert, these results are relevant to both the mechanisms of plant eco-phenotypic differentiation and the evolutionary history and conservation of the Galápagos biota.

@misc{doi10110120231003560736,
    author = "Zapata, Felipe and Cerca, José and McCarney, Dana and Henriquez, Claudia L. and Tiamiyu, Bashir B. and McCormack, John E. and Reckling, Kelsey R. and Chaves, Jaime A. and Rivas‐Torres, Gonzalo",
    title = "Darwin’s Overlooked Radiation: genomic evidence points to the early stages of a radiation in the Galápagos prickly pear cactus (Opuntia, Cactaceae)",
    year = "2023",
    booktitle = "bioRxiv (Cold Spring Harbor Laboratory)",
    abstract = "SUMMARY The Galápagos Islands are a prime example of a natural laboratory for the study of evolutionary radiations. While much attention has been devoted to iconic species like Darwin’s finches 1–4, the islands offer an equally unique but often overlooked opportunity for plant radiations 5. Yet, compared to their animal counterparts, our understanding of the patterns and processes underpinning Galápagos plant radiations remains relatively limited 6,7. We present evidence of the early stages of a radiation in prickly-pear cactus (Opuntia, Cactaceae), a plant lineage widespread across the archipelago. Phylogenomic and population genomic analyses show that notwithstanding overall low genetic differentiation across populations, there is marked geographic structure that is broadly consistent with current taxonomy and the dynamic paleogeography of the Galápagos. Because such low genetic differentiation stands in stark contrast to the exceptional eco-phenotypic diversity displayed by cacti across islands, it is plausible that phenotypic plasticity precedes genetic divergence and is the source of adaptive evolution, or that introgression between populations facilitates local adaptation. Models of population relationships including admixture indicate that gene flow is common between certain islands, likely facilitated by dispersal via animals known to feed on Opuntia flowers, fruits, and seeds across the archipelago. Scans of genetic differentiation between populations reveal candidate loci associated with seed traits and environmental stressors, suggesting that a combination of biotic interactions and abiotic pressures due to the harsh conditions characterizing island life in a volcanic, equatorial archipelago may underlie the diversification of prickly-pear cacti. Considered in concert, these results are relevant to both the mechanisms of plant eco-phenotypic differentiation and the evolutionary history and conservation of the Galápagos biota.",
    url = "https://doi.org/10.1101/2023.10.03.560736",
    doi = "10.1101/2023.10.03.560736",
    openalex = "W4387381159",
    references = "doi1012685bauhinia1687"
}

Abstract Charles Darwin's research during the second voyage of HMS Beagle is examined within the context of Charles Lyell's ideas on crustal movement. Darwin's pre-voyage training is summarized and the impact on his own subsequent theorizing of his commitment early in the voyage to a Lyellian theoretical framework is analysed. Two sites studied by Darwin which he interpreted as strong support for Lyell's theory of vertical crustal mobility are examined: the first is Signal Post Hill in the Cape Verdes, visited in 1832; the second is Agua de la Zorra in Argentina, visited in 1835. Darwin's work at both sites was key to his first theory of globally-balanced elevation and subsidence as an explanation for the structure and distribution of coral reefs. The case is made that both sites are of international geoheritage importance and that their protection should be assured with enhanced access and interpretation.

@article{doi101144sp5432022217,
    author = "Chancellor, Gordon",
    title = "Signal Post Hill and Agua de la Zorra: two geological sites studied by Charles Darwin on the Beagle voyage and their contributions to geoheritage",
    year = "2023",
    journal = "Geological Society London Special Publications",
    abstract = "Abstract Charles Darwin's research during the second voyage of HMS Beagle is examined within the context of Charles Lyell's ideas on crustal movement. Darwin's pre-voyage training is summarized and the impact on his own subsequent theorizing of his commitment early in the voyage to a Lyellian theoretical framework is analysed. Two sites studied by Darwin which he interpreted as strong support for Lyell's theory of vertical crustal mobility are examined: the first is Signal Post Hill in the Cape Verdes, visited in 1832; the second is Agua de la Zorra in Argentina, visited in 1835. Darwin's work at both sites was key to his first theory of globally-balanced elevation and subsidence as an explanation for the structure and distribution of coral reefs. The case is made that both sites are of international geoheritage importance and that their protection should be assured with enhanced access and interpretation.",
    url = "https://doi.org/10.1144/sp543-2022-217",
    doi = "10.1144/sp543-2022-217",
    openalex = "W4380669138",
    references = "doi105860choice413408"
}

Abstract In the Galápagos Islands, much attention has been devoted to the radiation of iconic species like Darwin’s finches, yet the Galápagos Islands offer an overlooked but equally remarkable opportunity for investigating plant radiations. Using a combination of genomic and phenotypic data, we present evidence of the early stages of a radiation in prickly pear cactus (Opuntia), a lineage widespread across the archipelago. We show that despite extensive ecophenotypic variation, there is limited genomic differentiation, consistent with the hypothesis that Opuntia is in the early stages of the diversification process. Phylogenomic and population genomic analyses show that notwithstanding low genetic differentiation across islands, there is marked geographical structure that is broadly consistent with the palaeogeography of the Galápagos. Because low genetic differentiation stands in stark contrast to the exceptional eco-phenotypic diversity displayed by cacti, it is plausible that the genetic architecture of phenotypic divergence mismatches our genomic sequencing, that phenotypic plasticity precedes genetic divergence and is the source of adaptive evolution, or that introgression influences local adaptation. Models of population relationships including admixture indicate that gene flow is common, probably facilitated by dispersal via animals known to feed on Opuntia flowers, fruits, and seeds. Because the prickly pear cacti of the Galápagos are a radiation in the making, they provide an exciting opportunity to investigate the interplay between ecological and genomic mechanisms promoting diversification.

@article{doi101093evolinneankzae021,
    author = "Zapata, Felipe and Cerca, José and McCarney, Dana and Henriquez, Claudia L. and Tiamiyu, Bashir B. and McCormack, John E. and Reckling, Kelsey R. and Chaves, Jaime A. and Rivas‐Torres, Gonzalo",
    title = "Darwin’s overlooked radiation: genomic evidence points to the early stages of a radiation in the Galápagos prickly pear cactus (Opuntia: Cactaceae)",
    year = "2024",
    journal = "Evolutionary Journal of the Linnean Society",
    abstract = "Abstract In the Galápagos Islands, much attention has been devoted to the radiation of iconic species like Darwin’s finches, yet the Galápagos Islands offer an overlooked but equally remarkable opportunity for investigating plant radiations. Using a combination of genomic and phenotypic data, we present evidence of the early stages of a radiation in prickly pear cactus (Opuntia), a lineage widespread across the archipelago. We show that despite extensive ecophenotypic variation, there is limited genomic differentiation, consistent with the hypothesis that Opuntia is in the early stages of the diversification process. Phylogenomic and population genomic analyses show that notwithstanding low genetic differentiation across islands, there is marked geographical structure that is broadly consistent with the palaeogeography of the Galápagos. Because low genetic differentiation stands in stark contrast to the exceptional eco-phenotypic diversity displayed by cacti, it is plausible that the genetic architecture of phenotypic divergence mismatches our genomic sequencing, that phenotypic plasticity precedes genetic divergence and is the source of adaptive evolution, or that introgression influences local adaptation. Models of population relationships including admixture indicate that gene flow is common, probably facilitated by dispersal via animals known to feed on Opuntia flowers, fruits, and seeds. Because the prickly pear cacti of the Galápagos are a radiation in the making, they provide an exciting opportunity to investigate the interplay between ecological and genomic mechanisms promoting diversification.",
    url = "https://doi.org/10.1093/evolinnean/kzae021",
    doi = "10.1093/evolinnean/kzae021",
    openalex = "W4402208166",
    references = "doi1012685bauhinia1687"
}

Abstract The Galapagos finches represent a rapid radiation of birds across the remote oceanic archipelago that vary morphologically, behaviourally, and genetically. The level of diversity and rapid rate of speciation have created taxonomic difficulties in resolving phylogenetic relationships. While much of the phylogeny has recently been clarified with modern genomic methods, some of the diversity has been overlooked by under-sampling across islands within presumed species. The woodpecker finch, Camarhynchus pallidus Sclater and Salvin, 1870, represents one such lineage, as all three recognized subspecies have never been fully phylogenetically assessed in regard to their species’ status and relationship with their close sister-species, the mangrove finch (C. heliobates; Snodgrass and Heller 1901). Using genetic and genomic tools, along with morphological analyses, we show that the San Cristobal woodpecker finch (C. p. striatipecta; Swarth 1931) is genetically distinct and paraphyletic with the mangrove finch, compared to all other woodpecker finch subspecies. Given these results we propose that the San Cristobal woodpecker finch be prioritized for further research, as our results hint that it should be given full species’ status as Camarhynchus striatipecta Swarth, 1931.

@article{doi101093zoolinneanzlae163,
    author = "Lawson, Lucinda P. and Nemeth, Erwin and Dvorak, Michael and Cunninghame, Francesca and Feßl, Birgit and Mueller, Jakob C. and Mosquera, Denis and Wendelin, Beate and Petren, Kenneth",
    title = "A hidden finch from the Galapagos Islands: a genetically and morphologically distinctive woodpecker finch from San Cristobal Island",
    year = "2024",
    journal = "Zoological Journal of the Linnean Society",
    abstract = "Abstract The Galapagos finches represent a rapid radiation of birds across the remote oceanic archipelago that vary morphologically, behaviourally, and genetically. The level of diversity and rapid rate of speciation have created taxonomic difficulties in resolving phylogenetic relationships. While much of the phylogeny has recently been clarified with modern genomic methods, some of the diversity has been overlooked by under-sampling across islands within presumed species. The woodpecker finch, Camarhynchus pallidus Sclater and Salvin, 1870, represents one such lineage, as all three recognized subspecies have never been fully phylogenetically assessed in regard to their species’ status and relationship with their close sister-species, the mangrove finch (C. heliobates; Snodgrass and Heller 1901). Using genetic and genomic tools, along with morphological analyses, we show that the San Cristobal woodpecker finch (C. p. striatipecta; Swarth 1931) is genetically distinct and paraphyletic with the mangrove finch, compared to all other woodpecker finch subspecies. Given these results we propose that the San Cristobal woodpecker finch be prioritized for further research, as our results hint that it should be given full species’ status as Camarhynchus striatipecta Swarth, 1931.",
    url = "https://doi.org/10.1093/zoolinnean/zlae163",
    doi = "10.1093/zoolinnean/zlae163",
    openalex = "W4405469568",
    references = "doi101007s10592019011753"
}

Abstract Spermatozoa may provide insights into the evolutionary history, reproductive isolation, and mating systems of species. Here we combine sperm and genomic data to conduct the first comparative analysis of sperm differentiation among Darwin’s finches, an iconic adaptive radiation with considerable gene flow across species borders. All eight study species had the typical form of songbird spermatozoa, but shorter than most other species in the Thraupidae family. There was no detectable differentiation in sperm length among four ground finch species (Geospiza) and two tree finch species (Camarhynchus). In both genera, autosomal single nucleotide polymorphisms (SNPs) revealed signatures of genetic admixture. The grey warbler-finch Certhidea fusca and the vegetarian finch Platyspiza crassirostris had significantly shorter sperm than the sister genera Geospiza and Camarhynchus from which they diverged about 0.90 and 0.43 Mya, respectively. The largest intergeneric divergences in sperm length were of the same magnitude as divergences observed within the speciation continuum in other songbirds over similar time spans. Relatively high among-male variation in sperm length indicates a moderate-to-low level of extrapair paternity and a divergence rate in sperm length that is lower than in more promiscuous songbirds. We conclude that sperm size evolution is too slow to drive prezygotic isolation in this radiation.

@article{doi101093biolinneanblaf103,
    author = "Lifjeld, Jan T. and García‐del‐Rey, Eduardo and Grønstøl, Gaute and Valle, Carlos A. and Leder, Erica H.",
    title = "Weak sperm differentiation in Darwin’s finches",
    year = "2025",
    journal = "Biological Journal of the Linnean Society",
    abstract = "Abstract Spermatozoa may provide insights into the evolutionary history, reproductive isolation, and mating systems of species. Here we combine sperm and genomic data to conduct the first comparative analysis of sperm differentiation among Darwin’s finches, an iconic adaptive radiation with considerable gene flow across species borders. All eight study species had the typical form of songbird spermatozoa, but shorter than most other species in the Thraupidae family. There was no detectable differentiation in sperm length among four ground finch species (Geospiza) and two tree finch species (Camarhynchus). In both genera, autosomal single nucleotide polymorphisms (SNPs) revealed signatures of genetic admixture. The grey warbler-finch Certhidea fusca and the vegetarian finch Platyspiza crassirostris had significantly shorter sperm than the sister genera Geospiza and Camarhynchus from which they diverged about 0.90 and 0.43 Mya, respectively. The largest intergeneric divergences in sperm length were of the same magnitude as divergences observed within the speciation continuum in other songbirds over similar time spans. Relatively high among-male variation in sperm length indicates a moderate-to-low level of extrapair paternity and a divergence rate in sperm length that is lower than in more promiscuous songbirds. We conclude that sperm size evolution is too slow to drive prezygotic isolation in this radiation.",
    url = "https://doi.org/10.1093/biolinnean/blaf103",
    doi = "10.1093/biolinnean/blaf103",
    openalex = "W4415269237",
    references = "doi101073pnas2107434118"
}

Whether the work and thought of Charles Darwin can be more accurately described as reductionist or holist remains a strangely unresolved question to this day. Darwin is a legitimate heir to two distinct intellectual traditions: romantic natural philosophy of Von Humboldt and Goethe (with a significant inspiration drawn from Kant) and Victorian natural science of Herschel and Lyell. While Darwin's focus on uncovering evolutionary mechanisms (and, crucially, demonstration that a single type of mechanism - natural selection - explains much of the incredible diversity of living forms) induces many scholars to consider him an epitome of scientific reductionism, there appear to be equal grounds to regard this titan of science as thorougly holistic in his approach to life's history on our planet. Was Darwin, then, a reductionist or a holist? Perhaps there is another way to answer this question (or even better, another way to ask it): is it possible one can be reductionist and holist? Namely, contrary to eminently reductionist early and classical Modern Syntheses in evolutionary biology, both Darwin's original body of work and many today's developments in evolutionary biology, subsumed unter the label of Extended Synthesis - centered on shifting tempo and mode of evolution, punctuated equilibria, hierarchical multilevel selection, ecological-evolutionary-developmental (eco-evo-devo) feedback integration, phenotypic plasticity, and, last but not least, recent works by W. Ford Doolittle and others attempting to unify the Gaia hypothesis of James Lovelock and Lynn Margulis with evolution by natural selection and evolutionary worldview in general - seem to offer us a glimpse of complex multidimensional landscapes underlying biology as we know it (and, through continuing astrobiological reasearch, potentially also biology as we do not know it). All of this could be but a foretaste of a promising direction in our scientific and philosophical endeavor to understand life - one transcending the classical dichotomy of reductionism vs. holism, not without resonance with great philosophical traditions seeking the Union of Opposites.

@article{doi105937bpa2502007j,
    author = "Janković, Srdja",
    title = "Charles Darwin: Reductionist, holist, or both?",
    year = "2025",
    journal = "Belgrade Philosophical Annual",
    abstract = "Whether the work and thought of Charles Darwin can be more accurately described as reductionist or holist remains a strangely unresolved question to this day. Darwin is a legitimate heir to two distinct intellectual traditions: romantic natural philosophy of Von Humboldt and Goethe (with a significant inspiration drawn from Kant) and Victorian natural science of Herschel and Lyell. While Darwin's focus on uncovering evolutionary mechanisms (and, crucially, demonstration that a single type of mechanism - natural selection - explains much of the incredible diversity of living forms) induces many scholars to consider him an epitome of scientific reductionism, there appear to be equal grounds to regard this titan of science as thorougly holistic in his approach to life's history on our planet. Was Darwin, then, a reductionist or a holist? Perhaps there is another way to answer this question (or even better, another way to ask it): is it possible one can be reductionist and holist? Namely, contrary to eminently reductionist early and classical Modern Syntheses in evolutionary biology, both Darwin's original body of work and many today's developments in evolutionary biology, subsumed unter the label of Extended Synthesis - centered on shifting tempo and mode of evolution, punctuated equilibria, hierarchical multilevel selection, ecological-evolutionary-developmental (eco-evo-devo) feedback integration, phenotypic plasticity, and, last but not least, recent works by W. Ford Doolittle and others attempting to unify the Gaia hypothesis of James Lovelock and Lynn Margulis with evolution by natural selection and evolutionary worldview in general - seem to offer us a glimpse of complex multidimensional landscapes underlying biology as we know it (and, through continuing astrobiological reasearch, potentially also biology as we do not know it). All of this could be but a foretaste of a promising direction in our scientific and philosophical endeavor to understand life - one transcending the classical dichotomy of reductionism vs. holism, not without resonance with great philosophical traditions seeking the Union of Opposites.",
    url = "https://doi.org/10.5937/bpa2502007j",
    doi = "10.5937/bpa2502007j",
    openalex = "W7117688748",
    references = "doi101186s4006401630530"
}

Abstract Background: Morphogenesis depends on spatial and temporal coordination of signaling pathways, yet the colocalization of proteins across pathways remains poorly understood. Here we examine cellular and histological localization of regulatory proteins forming core craniofacial developmental pathways during beak morphogenesis of the zebra finch (Taeniopygia guttata). Results: We present an atlas of spatiotemporal coexpression of β-catenin, Bmp4, CaM, Dkk3, Fgf8, Ihh, Tgfβ2, and Wnt4 across embryonic stages HH29-42 revealing both established and novel patterns of expression. Overall, in the earliest stages (HH29-32), most proteins show broad and overlapping expression across epithelial and mesenchymal tissues. By stage HH36, expression becomes increasingly compartmentalized, with pronounced differentiation among tissue types. Notably, at later stages, proteins showed tissue-specific distributions in boundary versus core regions of chondrogenic and osteogenic domains indicating coordinated cross-pathway patterning during cartilage and bone formation. Conclusions: Osteogenesis in the zebra finch beak is organized by coordinated signaling between boundary-associated cells and differentiating cores, with cross-pathway feedback establishing bone and cartilage differentiation while maintaining boundaries. Our results corroborated core elements of craniofacial signaling dynamics, while revealing unexpected subcellular localization for several proteins that showed regulatory complexity not captured by prior transcript-level maps. This atlas provides a protein-level baseline for comparative and mechanistic studies of beak morphogenesis.

@article{doi106489820251217695020,
    author = "Duckworth, Renée A. and Britton, Sarah and Lee, Cody and Chenard, Kathryn C. and Badyaev, Alexander V.",
    title = "Spatial and temporal coordination of signaling pathways in tissue differentiation: developmental atlas of protein expression during zebra finch beak maturation",
    year = "2025",
    journal = "bioRxiv (Cold Spring Harbor Laboratory)",
    abstract = "Abstract Background: Morphogenesis depends on spatial and temporal coordination of signaling pathways, yet the colocalization of proteins across pathways remains poorly understood. Here we examine cellular and histological localization of regulatory proteins forming core craniofacial developmental pathways during beak morphogenesis of the zebra finch (Taeniopygia guttata). Results: We present an atlas of spatiotemporal coexpression of β-catenin, Bmp4, CaM, Dkk3, Fgf8, Ihh, Tgfβ2, and Wnt4 across embryonic stages HH29-42 revealing both established and novel patterns of expression. Overall, in the earliest stages (HH29-32), most proteins show broad and overlapping expression across epithelial and mesenchymal tissues. By stage HH36, expression becomes increasingly compartmentalized, with pronounced differentiation among tissue types. Notably, at later stages, proteins showed tissue-specific distributions in boundary versus core regions of chondrogenic and osteogenic domains indicating coordinated cross-pathway patterning during cartilage and bone formation. Conclusions: Osteogenesis in the zebra finch beak is organized by coordinated signaling between boundary-associated cells and differentiating cores, with cross-pathway feedback establishing bone and cartilage differentiation while maintaining boundaries. Our results corroborated core elements of craniofacial signaling dynamics, while revealing unexpected subcellular localization for several proteins that showed regulatory complexity not captured by prior transcript-level maps. This atlas provides a protein-level baseline for comparative and mechanistic studies of beak morphogenesis.",
    url = "https://doi.org/10.64898/2025.12.17.695020",
    doi = "10.64898/2025.12.17.695020",
    openalex = "W4417451350",
    references = "doi101101pdbemo119"
}