Evolutionary theory

@misc{lamarck1809zoological24,
    author = "Lamarck, J. B",
    title = "Zoological Philosophy",
    year = "1809",
    howpublished = "Translated into English by H. Elliott, 1914. Macmillan \& Co., New York",
    note = "talkorigins\_source = {true}; raw\_reference = {Lamarck, J. B., 1809, Zoological Philosophy. Translated into English by H. Elliott, 1914. Macmillan \& Co., New York.}"
}

@misc{kellogg1907darwinism22,
    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.}"
}

We need scarcely add that the contemplation in natural science of a wider domain than the actual leads to a far better understanding of the actual.' (p. 267,The, Nature of the Physical World.)x PREFACE evolutionary theory was thus chiefly retrogressive, the mighty body of Mendelian researches throughout the world has evidently out- grown the fallacies with which it was at first fostered.As a pioneer of genetics he has done more than enough to expiate the rash polemics of his early writings.To treat Natural Selection as an agency based independently on its own foundations is not to mimimize its importance in the theory of evolution.On the contrary, as soon as we require to form opinions by other means than by comparison and analogy, such an indepen- dent deductive basis becomes a necessity.This necessity is particu- larly to be noted for mankind; since we have some knowledge of the structure of society, of human motives, and of the vital statistics of this species, the use of the deductive method can supply a more intimate knowledge of the evolutionary processes than is elsewhere possible.In addition it will be of importance for our subject to call) attention to several consequences of the principle of Natural Selection!which, since they do not consist in the adaptive modification of specific I forms, have necessarily escaped attention.The genetic phenomena of I dominance and linkage seem to offer examples of this class, the future ' investigation of which may add greatly to the scope of our subject.No efforts of mine could avail to make the book easy reading.I have endeavoured to assist the reader by giving short summaries at the ends of all chapters, except Chapter IV, which is summarized conjointly with Chapter V.Those who prefer to do so may regardChapter IV as a mathematical appendix to the corresponding part of the summary.The deductions respecting Man are strictly in- separable from the more general chapters, but have been placed together in a group commencing with Chapter VIII.I believe no one will be surprised that a large number of the points considered demand a far fuller, more rigorous, and more comprehensive treat- ment.It seems impossible that full justice should be done to the subject in this way, until there is built up a tradition of mathematical work devoted to biological problems, comparable to the researches upon which a mathematical physicist can draw in the resolution of special difficulties.

@book{doi105962bhltitle27468,
    author = "Fisher, Ronald Aylmer",
    title = "The genetical theory of natural selection",
    year = "1930",
    booktitle = "Clarendon Press eBooks",
    abstract = "We need scarcely add that the contemplation in natural science of a wider domain than the actual leads to a far better understanding of the actual.' (p. 267,The, Nature of the Physical World.)x PREFACE evolutionary theory was thus chiefly retrogressive, the mighty body of Mendelian researches throughout the world has evidently out- grown the fallacies with which it was at first fostered.As a pioneer of genetics he has done more than enough to expiate the rash polemics of his early writings.To treat Natural Selection as an agency based independently on its own foundations is not to mimimize its importance in the theory of evolution.On the contrary, as soon as we require to form opinions by other means than by comparison and analogy, such an indepen- dent deductive basis becomes a necessity.This necessity is particu- larly to be noted for mankind; since we have some knowledge of the structure of society, of human motives, and of the vital statistics of this species, the use of the deductive method can supply a more intimate knowledge of the evolutionary processes than is elsewhere possible.In addition it will be of importance for our subject to call) attention to several consequences of the principle of Natural Selection!which, since they do not consist in the adaptive modification of specific I forms, have necessarily escaped attention.The genetic phenomena of I dominance and linkage seem to offer examples of this class, the future ' investigation of which may add greatly to the scope of our subject.No efforts of mine could avail to make the book easy reading.I have endeavoured to assist the reader by giving short summaries at the ends of all chapters, except Chapter IV, which is summarized conjointly with Chapter V.Those who prefer to do so may regardChapter IV as a mathematical appendix to the corresponding part of the summary.The deductions respecting Man are strictly in- separable from the more general chapters, but have been placed together in a group commencing with Chapter VIII.I believe no one will be surprised that a large number of the points considered demand a far fuller, more rigorous, and more comprehensive treat- ment.It seems impossible that full justice should be done to the subject in this way, until there is built up a tradition of mathematical work devoted to biological problems, comparable to the researches upon which a mathematical physicist can draw in the resolution of special difficulties.",
    url = "https://doi.org/10.5962/bhl.title.27468",
    doi = "10.5962/bhl.title.27468",
    openalex = "W2004778468",
    references = "darwin2009the, doi101017cbo9780511693946006, doi101017cbo9780511702884, doi101038033529a0, doi101111j136523111908tb02141x, doi1023071929022, doi1023074345450, doi105962bhltitle121292, doi105962bhltitle61004, doi105962bhltitle87899, openalexw2163836228"
}

@book{lovejoy1936the28,
    author = "Lovejoy, A. D",
    title = "The Great Chain of Being",
    year = "1936",
    publisher = "Cambridge, Mass., Harvard University Press",
    note = "talkorigins\_source = {true}; raw\_reference = {Lovejoy, A. D., 1936, The Great Chain of Being: Cambridge, Mass., Harvard University Press.}"
}

@book{lack1947darwins23,
    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{haldane1949suggestions16,
    author = "Haldane, J. B. S",
    title = "Suggestions as to quantitative measurement of rates of evolution",
    year = "1949",
    howpublished = "Evolution, v. 3, p. 51-56",
    note = "talkorigins\_source = {true}; raw\_reference = {Haldane, J. B. S., 1949, Suggestions as to quantitative measurement of rates of evolution: Evolution, v. 3, p. 51-56.}"
}

@book{simpson1949the39,
    author = "Simpson, G. G",
    title = "The Meaning of Evolution",
    year = "1949",
    publisher = "New Haven, Conecticut, Yale University Press",
    note = "talkorigins\_source = {true}; raw\_reference = {Simpson, G. G., 1949, The Meaning of Evolution: New Haven, Conecticut, Yale University Press.}"
}

@article{doi101001jama195002910300087029,
    title = "Factors of Evolution:. The Theory of Stabilizing Selection",
    year = "1950",
    journal = "Journal of the American Medical Association",
    url = "https://doi.org/10.1001/jama.1950.02910300087029",
    doi = "10.1001/jama.1950.02910300087029",
    openalex = "W1504663309"
}

@misc{irvine1955apes19,
    author = "Irvine, W",
    title = "Apes, Angels, and Victorians",
    year = "1955",
    howpublished = "New York, McGraw-Hill",
    note = "talkorigins\_source = {true}; raw\_reference = {Irvine, W., 1955, Apes, Angels, and Victorians: New York, McGraw-Hill.}"
}

@misc{eiseley1958darwins5,
    author = "Eiseley, L. C",
    title = "Darwin's Century",
    year = "1958",
    howpublished = "Evolution and the Men Who Discovered It: New York, Doubleday",
    note = "talkorigins\_source = {true}; raw\_reference = {Eiseley, L. C., 1958, Darwin's Century: Evolution and the Men Who Discovered It: New York, Doubleday.}"
}

@book{glass1959the8,
    author = "Glass, B. O. and Strauss, W. L. and Jr",
    title = "The Forerunners of Darwin",
    year = "1959",
    publisher = "1745- 1859: Baltimore, Johns Hopkins Press",
    note = "talkorigins\_source = {true}; raw\_reference = {Glass, B. O., and Strauss, W. L., Jr., 1959, The Forerunners of Darwin: 1745- 1859: Baltimore, Johns Hopkins Press.}"
}

@inproceedings{lerner1959the25,
    author = "Lerner, I. M",
    title = "The concept of natural selection",
    year = "1959",
    booktitle = "A centennial view: Proceedings of the American Philosophical Society, v. 103, p. 173-182",
    note = "talkorigins\_source = {true}; raw\_reference = {Lerner, I. M., 1959, The concept of natural selection: A centennial view: Proceedings of the American Philosophical Society, v. 103, p. 173-182.}"
}

@book{millhauser1959just32,
    author = "Millhauser, M",
    title = "Just Before Darwin",
    year = "1959",
    publisher = "Robert Chambers and Vestiges: Middletown, Connecticut, Wesleyan University Press",
    note = "talkorigins\_source = {true}; raw\_reference = {Millhauser, M., 1959, Just Before Darwin: Robert Chambers and Vestiges: Middletown, Connecticut, Wesleyan University Press.}"
}

@misc{scriven1959explanation38,
    author = "Scriven, M",
    title = "Explanation and prediction in evolutionary theory",
    year = "1959",
    howpublished = "Science, v. 130, p. 477-482",
    note = "talkorigins\_source = {true}; raw\_reference = {Scriven, M., 1959, Explanation and prediction in evolutionary theory: Science, v. 130, p. 477-482.}"
}

@phdthesis{ross1962a36,
    author = "Ross, HH",
    title = "A Synthesis of Evolutionary Theory",
    year = "1962",
    publisher = "Englewood Cliffs, New Jersey, Prentice-Hall",
    note = "talkorigins\_source = {true}; raw\_reference = {Ross,, HH, 1962, A Synthesis of Evolutionary Theory: Englewood Cliffs, New Jersey, Prentice-Hall.}"
}

@misc{ehrilch1963the4,
    author = "Ehrilch, P. R. and Holm, R. W",
    title = "The process of evolution",
    year = "1963",
    howpublished = "New York, McGraw-Hill, 347 p",
    note = "talkorigins\_source = {true}; raw\_reference = {Ehrilch, P. R., and Holm, R. W., 1963, The process of evolution: New York, McGraw-Hill, 347 p.}"
}

@misc{gasking1967investigations7,
    author = "Gasking, E",
    title = "Investigations into Generation",
    year = "1967",
    howpublished = "1651-1828: London, Hutchinson",
    note = "talkorigins\_source = {true}; raw\_reference = {Gasking, E., 1967, Investigations into Generation: 1651-1828: London, Hutchinson.}"
}

@misc{moorehead1969darwin34,
    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{mckinney1971lamarck30,
    author = "McKinney, H. L",
    title = "Lamarck to Darwin",
    year = "1971",
    publisher = "Contributions to Evolutionary Biology, 1809-1859: Lawrence, Kansas, Coronado Press",
    note = "talkorigins\_source = {true}; raw\_reference = {McKinney, H. L., 1971, Lamarck to Darwin: Contributions to Evolutionary Biology, 1809-1859: Lawrence, Kansas, Coronado Press.}"
}

@misc{jukes1972evolutionary21,
    author = "Jukes, T. H. and Holmquist, W. R",
    title = "Evolutionary clocks; nonconstancy of rate in different species",
    year = "1972",
    howpublished = "Science, v. 177, p. 530-532",
    note = "talkorigins\_source = {true}; raw\_reference = {Jukes, T. H., and Holmquist, W. R., 1972, Evolutionary clocks; nonconstancy of rate in different species: Science, v. 177, p. 530-532.}"
}

@book{mckinney1972wallace31,
    author = "McKinney, H. L",
    title = "Wallace and Natural Selection",
    year = "1972",
    publisher = "New Haven, Connecticut, Yale University Press",
    note = "talkorigins\_source = {true}; raw\_reference = {McKinney, H. L., 1972, Wallace and Natural Selection: New Haven, Connecticut, Yale University Press.}"
}

@article{openalexw2145250129,
    author = "Valen, Leigh Van",
    title = "A NEW EVOLUTIONARY LAW.",
    year = "1973",
    journal = "Medical Entomology and Zoology",
    openalex = "W2145250129"
}

@misc{vanvalen1973a44,
    author = "Van Valen, L",
    title = "A new evolutionary law",
    year = "1973",
    howpublished = "Evolutionary Theory, v. 1, p. 1-30",
    note = "talkorigins\_source = {true}; raw\_reference = {Van Valen, L., 1973, A new evolutionary law: Evolutionary Theory, v. 1, p. 1-30.}"
}

@article{doi101111j155856461975tb00851x,
    author = "Felsenstein, Joseph",
    title = "THE GENETIC BASIS OF EVOLUTIONARY CHANGE",
    year = "1975",
    journal = "Evolution",
    url = "https://doi.org/10.1111/j.1558-5646.1975.tb00851.x",
    doi = "10.1111/j.1558-5646.1975.tb00851.x",
    openalex = "W1547248981"
}

@misc{maynardsmith1975the29,
    author = "Maynard Smith, J",
    title = "The Theory of Evolution [3rd ed.]",
    year = "1975",
    howpublished = "New York, Penguin",
    note = "talkorigins\_source = {true}; raw\_reference = {Maynard Smith, J., 1975, The Theory of Evolution [3rd ed.]: New York, Penguin.}"
}

@inproceedings{stanley1975a40,
    author = "Stanley, S. M",
    title = "A theory of evolution above the species level",
    year = "1975",
    booktitle = "Proceedings of the National Academy of Sciences, USA, v. 72, p. 646-650",
    note = "talkorigins\_source = {true}; raw\_reference = {Stanley, S. M., 1975, A theory of evolution above the species level: Proceedings of the National Academy of Sciences, USA, v. 72, p. 646-650.}"
}

@book{crossref1977patterns,
    title = "Patterns of Evolution as Illustrated by the Fossil Record",
    year = "1977",
    booktitle = "Developments in Palaeontology and Stratigraphy",
    url = "https://doi.org/10.1016/s0920-5446(08)x7012-8",
    doi = "10.1016/s0920-5446(08)x7012-8",
    openalex = "W563635432"
}

@book{gould1977eternal9,
    author = "Gould, S. J",
    title = "Eternal Metaphors of Paleontology, in Hallam, A., ed., Patterns of Evolution as Illustrated by the Fossil Record",
    year = "1977",
    publisher = "Amsterdam, Elsevier, p. 1-26",
    note = "talkorigins\_source = {true}; raw\_reference = {Gould, S. J., 1977, Eternal Metaphors of Paleontology, in Hallam, A., ed., Patterns of Evolution as Illustrated by the Fossil Record: Amsterdam, Elsevier, p. 1-26.}"
}

@misc{gould1977the15,
    author = "Gould, S. J. and Raup, D. M. and Sepkoski, J. J. and Schopf, T. J. M. and Simberloff, D. S",
    title = "The shape of evolution",
    year = "1977",
    howpublished = "A comparison of real and random clades: Paleobiology, v. 3, p. 23-40",
    note = "talkorigins\_source = {true}; raw\_reference = {Gould, S. J., Raup, D. M., Sepkoski, J. J., Schopf, T. J. M., and Simberloff, D. S., 1977, The shape of evolution: A comparison of real and random clades: Paleobiology, v. 3, p. 23-40.}"
}

@book{hallam1977patterns17,
    author = "Hallam, A",
    title = "Patterns of Evolution as Illustrated by the Fossil Record, 5 of Developments in Palaeontology and Stratigraphy",
    year = "1977",
    publisher = "Amsterdam, Elsevier",
    note = "talkorigins\_source = {true}; raw\_reference = {Hallam, A., 1977, Patterns of Evolution as Illustrated by the Fossil Record, 5 of Developments in Palaeontology and Stratigraphy: Amsterdam, Elsevier.}"
}

@book{hanson1977the18,
    author = "Hanson, E. D",
    title = "The Origin and Early Evolution of Animals",
    year = "1977",
    publisher = "Middletown, Connecticut, Wesleyan University Press",
    note = "talkorigins\_source = {true}; raw\_reference = {Hanson, E. D., 1977, The Origin and Early Evolution of Animals: Middletown, Connecticut, Wesleyan University Press.}"
}

@article{doi101038scientificamerican117998,
    author = "Kimura, Motoo",
    title = "The Neutral Theory of Molecular Evolution",
    year = "1979",
    journal = "Scientific American",
    url = "https://doi.org/10.1038/scientificamerican1179-98",
    doi = "10.1038/scientificamerican1179-98",
    openalex = "W2045391589"
}

@techreport{schwartz1979models37,
    author = "Schwartz, J. H. and Rollins, H. B",
    title = "Models and methodologies in evolutionary theory, 13 of Bulletin of Carnegie Museum of Natural History",
    year = "1979",
    howpublished = "Pittsburgh, Pa",
    note = "talkorigins\_source = {true}; raw\_reference = {Schwartz, J. H., and Rollins, H. B., 1979, Models and methodologies in evolutionary theory, 13 of Bulletin of Carnegie Museum of Natural History: Pittsburgh, Pa.}"
}

@misc{stanley1979macroevolution41,
    author = "Stanley, S. M",
    title = "Macroevolution",
    year = "1979",
    howpublished = "Pattern and Process: San Francisco, W.H. Freeman",
    note = "talkorigins\_source = {true}; raw\_reference = {Stanley, S. M., 1979, Macroevolution: Pattern and Process: San Francisco, W.H. Freeman.}"
}

@article{doi101007bf01731581,
    author = "Kimura, Motoo",
    title = "A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences",
    year = "1980",
    journal = "Journal of Molecular Evolution",
    url = "https://doi.org/10.1007/bf01731581",
    doi = "10.1007/bf01731581",
    openalex = "W2065461553",
    references = "doi101007bf01653945, doi101007bf01732067, doi101007bf01732340, doi101016b9781483232119500097, doi101016s0021925817401566, doi101038217624a0, doi101038267275a0, doi101038scientificamerican117998, doi101073pnas7172848, doi101126science1643881788"
}

@misc{lewin1980evolutionary26,
    author = "Lewin, R",
    title = "Evolutionary theory under fire",
    year = "1980",
    howpublished = "Science, v. 210, p. 883-887",
    note = "talkorigins\_source = {true}; raw\_reference = {Lewin, R., 1980, Evolutionary theory under fire: Science, v. 210, p. 883-887.}"
}

A theoretical approach to the analysis of historical factors (Raup 1972) in evolutionary morphology is presented which addresses transformational hypotheses about structural systems. This (structural) approach to testing historical hypotheses about phylogenetic constraints on form and function and structural and functional versatility involves (1) the reconstruction of nested sets of structural features in monophyletic taxa, (2) the use of general or emergent organizational properties of structural and functional systems (as opposed to uniquely derived morphological features), and (3) the comparative examination of the consequences for structural and functional diversity of these general features in related monophyletic taxa. Three examples of emergent organizational properties are considered: structural complexity, repetition of parts, and the decoupling of primitively constrained systems. Two classes of hypotheses about the evolution of design are proposed. Transformational hypotheses concern historical pathways of change in form as a consequence of general organizational features which are primitive for a lineage. Relational hypotheses involve correlations between structure-function networks primitive for a clade and morphological diversity both between and within terminal taxa. To the extent that transformational and relational hypotheses about form are corroborated, they provide evidence of underlying regularity in the transformation of organic design that may be a consequence of the hierarchical organization of structural and functional patterns in organisms.

@article{doi101017s0094837300025495,
    author = "Lauder, George",
    title = "Form and function: structural analysis in evolutionary morphology",
    year = "1981",
    journal = "Paleobiology",
    abstract = "A theoretical approach to the analysis of historical factors (Raup 1972) in evolutionary morphology is presented which addresses transformational hypotheses about structural systems. This (structural) approach to testing historical hypotheses about phylogenetic constraints on form and function and structural and functional versatility involves (1) the reconstruction of nested sets of structural features in monophyletic taxa, (2) the use of general or emergent organizational properties of structural and functional systems (as opposed to uniquely derived morphological features), and (3) the comparative examination of the consequences for structural and functional diversity of these general features in related monophyletic taxa. Three examples of emergent organizational properties are considered: structural complexity, repetition of parts, and the decoupling of primitively constrained systems. Two classes of hypotheses about the evolution of design are proposed. Transformational hypotheses concern historical pathways of change in form as a consequence of general organizational features which are primitive for a lineage. Relational hypotheses involve correlations between structure-function networks primitive for a clade and morphological diversity both between and within terminal taxa. To the extent that transformational and relational hypotheses about form are corroborated, they provide evidence of underlying regularity in the transformation of organic design that may be a consequence of the hierarchical organization of structural and functional patterns in organisms.",
    url = "https://doi.org/10.1017/s0094837300025495",
    doi = "10.1017/s0094837300025495",
    openalex = "W2275850409",
    references = "doi101111j155856461965tb01720x, doi1023072412293, doi1023072412953, doi107312crac92306005, openalexw1869415094, openalexw2128666103"
}

@book{eldredge1981phylogenetic6,
    author = "Eldredge, N. and Cracraft, J",
    title = "Phylogenetic Patterns and the Evolutionary Process",
    year = "1981",
    publisher = "Method and Theory in Comparitive Biology: New York, Columbia University Press",
    note = "talkorigins\_source = {true}; raw\_reference = {Eldredge, N., and Cracraft, J., 1981, Phylogenetic Patterns and the Evolutionary Process: Method and Theory in Comparitive Biology: New York, Columbia University Press.}"
}

@misc{jaanusson1981functional20,
    author = "Jaanusson, V",
    title = "Functional thresholds in evolutionary progress",
    year = "1981",
    howpublished = "Lethaia, v. 14, p. 251-260",
    note = "talkorigins\_source = {true}; raw\_reference = {Jaanusson, V., 1981, Functional thresholds in evolutionary progress: Lethaia, v. 14, p. 251-260.}"
}

@misc{lewin1981no27,
    author = "Lewin, R",
    title = "No gap here in the fossil record",
    year = "1981",
    howpublished = "Science, v. 214, p. 645-646",
    note = "talkorigins\_source = {true}; raw\_reference = {Lewin, R., 1981, No gap here in the fossil record: Science, v. 214, p. 645-646.}"
}

@book{ospovat1981the35,
    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.}"
}

@phdthesis{stebbins1981is42,
    author = "Stebbins, G. L. and Ayala, F. J",
    title = "Is a New Evolutionary Synthesis Necessary?",
    year = "1981",
    publisher = "Science, v. 213, p. 967-971",
    note = "talkorigins\_source = {true}; raw\_reference = {Stebbins, G. L., and Ayala, F. J., 1981, Is a New Evolutionary Synthesis Necessary?: Science, v. 213, p. 967-971.}"
}

A new compilation of fossil data on invertebrate and vertebrate families indicates that four mass extinctions in the marine realm are statistically distinct from background extinction levels. These four occurred late in the Ordovician, Permian, Triassic, and Cretaceous periods. A fifth extinction event in the Devonian stands out from the background but is not statistically significant in these data. Background extinction rates appear to have declined since Cambrian time, which is consistent with the prediction that optimization of fitness should increase through evolutionary time.

@article{doi101126science21545391501,
    author = "Raup, David M. and Sepkoski, J. John",
    title = "Mass Extinctions in the Marine Fossil Record",
    year = "1982",
    journal = "Science",
    abstract = "A new compilation of fossil data on invertebrate and vertebrate families indicates that four mass extinctions in the marine realm are statistically distinct from background extinction levels. These four occurred late in the Ordovician, Permian, Triassic, and Cretaceous periods. A fifth extinction event in the Devonian stands out from the background but is not statistically significant in these data. Background extinction rates appear to have declined since Cambrian time, which is consistent with the prediction that optimization of fitness should increase through evolutionary time.",
    url = "https://doi.org/10.1126/science.215.4539.1501",
    doi = "10.1126/science.215.4539.1501",
    openalex = "W1976721572",
    references = "doi101017s009483730000511x, doi101017s0094837300006539, doi101130spe89p63, doi105281zenodo16226412, openalexw2335729143, openalexw2591197405, openalexw2596207362"
}

@article{doi1023071936778,
    author = "Lande, Russell",
    title = "A Quantitative Genetic Theory of Life History Evolution",
    year = "1982",
    journal = "Ecology",
    url = "https://doi.org/10.2307/1936778",
    doi = "10.2307/1936778",
    openalex = "W2089325551",
    references = "doi101001jama195002910300087029, doi101086404940, doi101111j146918091957tb01874x, doi101111j155856461980tb04817x"
}

@misc{gould1982darwinism10,
    author = "Gould, S. J",
    title = "Darwinism and the expansion of evolutionary theory",
    year = "1982",
    howpublished = "Science, v. 216, p. 380-387",
    note = "talkorigins\_source = {true}; raw\_reference = {Gould, S. J., 1982, Darwinism and the expansion of evolutionary theory: Science, v. 216, p. 380-387.}"
}

@article{sulloway1982darwin43,
    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.}"
}

With the aim of analyzing and interpreting data on DNA polymorphism obtained by DNA sequencing or restriction enzyme technique, a mathematical theory on the expected evolutionary relationship among DNA sequences (nucleons) sampled is developed under the assumption that the evolutionary change of nucleons is determined solely by mutation and random genetic drift. The statistical property of the number of nucleotide differences between randomly chosen nucleons and that of heterozygosity or nucleon diversity is investigated using this theory. These studies indicate that the estimates of the average number of nucleotide differences and nucleon diversity have a large variance, and a large part of this variance is due to stochastic factors. Therefore, increasing sample size does not help reduce the variance significantly The distribution of sample allele (nucleomorph) frequencies is also studied, and it is shown that a small number of samples are sufficient in order to know the distribution pattern.

@article{doi101093genetics1052437,
    author = "Tajima, Fumio",
    title = "EVOLUTIONARY RELATIONSHIP OF DNA SEQUENCES IN FINITE POPULATIONS",
    year = "1983",
    journal = "Genetics",
    abstract = "With the aim of analyzing and interpreting data on DNA polymorphism obtained by DNA sequencing or restriction enzyme technique, a mathematical theory on the expected evolutionary relationship among DNA sequences (nucleons) sampled is developed under the assumption that the evolutionary change of nucleons is determined solely by mutation and random genetic drift. The statistical property of the number of nucleotide differences between randomly chosen nucleons and that of heterozygosity or nucleon diversity is investigated using this theory. These studies indicate that the estimates of the average number of nucleotide differences and nucleon diversity have a large variance, and a large part of this variance is due to stochastic factors. Therefore, increasing sample size does not help reduce the variance significantly The distribution of sample allele (nucleomorph) frequencies is also studied, and it is shown that a small number of samples are sufficient in order to know the distribution pattern.",
    url = "https://doi.org/10.1093/genetics/105.2.437",
    doi = "10.1093/genetics/105.2.437",
    openalex = "W1928220195",
    references = "doi1010160040580972900354, doi1010160040580974900252, doi1010160040580975900209, doi101017s000186780003994x, doi101073pnas7763605, doi101093genetics1032287, doi101093genetics893583, doi101093genetics971145, doi101111j155856461983tb05528x, doi1023072408186"
}

Journal Article An Evolutionary Theory of Economic Change Get access An Evolutionary Theory of Economic Change. By Richard R. Nelson and Sidney G. Winter. (Cambridge, Massachusetts & London: Harvard University Press, 1982. Pp. xi +437. £17.50.) Brian J. Loasby Brian J. Loasby University of Stirling Search for other works by this author on: Oxford Academic Google Scholar The Economic Journal, Volume 93, Issue 371, 1 September 1983, Pages 652–654, https://doi.org/10.2307/2232409 Published: 01 September 1983

@article{doi1023072232409,
    author = "Loasby, Brian J. and Nelson, Richard R. and Winter, Sidney G.",
    title = "An Evolutionary Theory of Economic Change.",
    year = "1983",
    journal = "The Economic Journal",
    abstract = "Journal Article An Evolutionary Theory of Economic Change Get access An Evolutionary Theory of Economic Change. By Richard R. Nelson and Sidney G. Winter. (Cambridge, Massachusetts \& London: Harvard University Press, 1982. Pp. xi +437. £17.50.) Brian J. Loasby Brian J. Loasby University of Stirling Search for other works by this author on: Oxford Academic Google Scholar The Economic Journal, Volume 93, Issue 371, 1 September 1983, Pages 652–654, https://doi.org/10.2307/2232409 Published: 01 September 1983",
    url = "https://doi.org/10.2307/2232409",
    doi = "10.2307/2232409",
    openalex = "W2137358449"
}

@book{bowler1984evolution2,
    author = "Bowler, P. J",
    title = "Evolution",
    year = "1984",
    publisher = "The History of an Idea: Berkeley, University of California Press",
    note = "talkorigins\_source = {true}; raw\_reference = {Bowler, P. J., 1984, Evolution: The History of an Idea: Berkeley, University of California Press.}"
}

@misc{dodson1985the3,
    author = "Dodson, E. O",
    title = "The Theory of Evolution, in Encyclopedia Britannica [1st ed.]",
    year = "1985",
    howpublished = "Chicago, Illinois, Encyclopedia Britannica, Inc., v. 18, p. 981-1011",
    note = "talkorigins\_source = {true}; raw\_reference = {Dodson, E. O., 1985, The Theory of Evolution, in Encyclopedia Britannica [1st ed.]: Chicago, Illinois, Encyclopedia Britannica, Inc., v. 18, p. 981-1011.}"
}

Journal Article Mitochondrial DNA and two perspectives on evolutionary genetics Get access ALLAN C. WILSON, ALLAN C. WILSON 1Department of Biochemistry, University of California, Berkeley, California 94720, U.S.A Search for other works by this author on: Oxford Academic Google Scholar REBECCA L. CANN, REBECCA L. CANN 1Department of Biochemistry, University of California, Berkeley, California 94720, U.S.A2Howard Hughes Medical Institute, U426, University of California, San Francisco, California 94143, U.S.A Search for other works by this author on: Oxford Academic Google Scholar STEVEN M. CARR, STEVEN M. CARR 1Department of Biochemistry, University of California, Berkeley, California 94720, U.S.A3Wildlife Genetics Laboraiory, Department of Wildlge and Fisheries Sciences, Texas A & M University, College Station, Texas 77843, U.S.A Search for other works by this author on: Oxford Academic Google Scholar MATTHEW GEORGE, MATTHEW GEORGE 1Department of Biochemistry, University of California, Berkeley, California 94720, U.S.A4Department of Biochemistry, Howard University, Washington, DC 20059, U.S.A Search for other works by this author on: Oxford Academic Google Scholar ULF B. GYLLENSTEN, ULF B. GYLLENSTEN 1Department of Biochemistry, University of California, Berkeley, California 94720, U.S.A5Department of Clinical Genetics, Karolinska Hospital, Box 60500, S-104 01 Stockholm, Sweden Search for other works by this author on: Oxford Academic Google Scholar KATHLEEN M. HELM-BYCHOWSKI, KATHLEEN M. HELM-BYCHOWSKI 1Department of Biochemistry, University of California, Berkeley, California 94720, U.S.A Search for other works by this author on: Oxford Academic Google Scholar RUSSELL G. HIGUCHI, RUSSELL G. HIGUCHI 1Department of Biochemistry, University of California, Berkeley, California 94720, U.S.A Search for other works by this author on: Oxford Academic Google Scholar STEPHEN R. PALUMBI, STEPHEN R. PALUMBI 1Department of Biochemistry, University of California, Berkeley, California 94720, U.S.A6Department of Zoology, University of Hawaii, Honolulu, Hawaii 96822, U.S.A Search for other works by this author on: Oxford Academic Google Scholar ELLEN M. PRAGER, ELLEN M. PRAGER 1Department of Biochemistry, University of California, Berkeley, California 94720, U.S.A Search for other works by this author on: Oxford Academic Google Scholar RICHARD D. SAGE, RICHARD D. SAGE 1Department of Biochemistry, University of California, Berkeley, California 94720, U.S.A7Museum of Vertebrate Zoology, University of California, Berkeley, California 94720, U.S.A Search for other works by this author on: Oxford Academic Google Scholar... Show more MARK STONEKING MARK STONEKING 1Department of Biochemistry, University of California, Berkeley, California 94720, U.S.A Search for other works by this author on: Oxford Academic Google Scholar Biological Journal of the Linnean Society, Volume 26, Issue 4, December 1985, Pages 375–400, https://doi.org/10.1111/j.1095-8312.1985.tb02048.x Published: 28 June 2008 Article history Accepted: 01 July 1985 Published: 28 June 2008

@article{doi101111j109583121985tb02048x,
    author = "Wilson, Allan C. and Cann, Rebecca L. and Carr, Steven M. and George, Matthew and GYLLENSTEN, ULF B. and Helm‐Bychowski, Kathleen and Higuchi, Russell and Palumbi, Stephen R. and Prager, Ellen M. and Sage, Richard D. and Stoneking, Mark",
    title = "Mitochondrial DNA and two perspectives on evolutionary genetics",
    year = "1985",
    journal = "Biological Journal of the Linnean Society",
    abstract = "Journal Article Mitochondrial DNA and two perspectives on evolutionary genetics Get access ALLAN C. WILSON, ALLAN C. WILSON 1Department of Biochemistry, University of California, Berkeley, California 94720, U.S.A Search for other works by this author on: Oxford Academic Google Scholar REBECCA L. CANN, REBECCA L. CANN 1Department of Biochemistry, University of California, Berkeley, California 94720, U.S.A2Howard Hughes Medical Institute, U426, University of California, San Francisco, California 94143, U.S.A Search for other works by this author on: Oxford Academic Google Scholar STEVEN M. CARR, STEVEN M. CARR 1Department of Biochemistry, University of California, Berkeley, California 94720, U.S.A3Wildlife Genetics Laboraiory, Department of Wildlge and Fisheries Sciences, Texas A \& M University, College Station, Texas 77843, U.S.A Search for other works by this author on: Oxford Academic Google Scholar MATTHEW GEORGE, MATTHEW GEORGE 1Department of Biochemistry, University of California, Berkeley, California 94720, U.S.A4Department of Biochemistry, Howard University, Washington, DC 20059, U.S.A Search for other works by this author on: Oxford Academic Google Scholar ULF B. GYLLENSTEN, ULF B. GYLLENSTEN 1Department of Biochemistry, University of California, Berkeley, California 94720, U.S.A5Department of Clinical Genetics, Karolinska Hospital, Box 60500, S-104 01 Stockholm, Sweden Search for other works by this author on: Oxford Academic Google Scholar KATHLEEN M. HELM-BYCHOWSKI, KATHLEEN M. HELM-BYCHOWSKI 1Department of Biochemistry, University of California, Berkeley, California 94720, U.S.A Search for other works by this author on: Oxford Academic Google Scholar RUSSELL G. HIGUCHI, RUSSELL G. HIGUCHI 1Department of Biochemistry, University of California, Berkeley, California 94720, U.S.A Search for other works by this author on: Oxford Academic Google Scholar STEPHEN R. PALUMBI, STEPHEN R. PALUMBI 1Department of Biochemistry, University of California, Berkeley, California 94720, U.S.A6Department of Zoology, University of Hawaii, Honolulu, Hawaii 96822, U.S.A Search for other works by this author on: Oxford Academic Google Scholar ELLEN M. PRAGER, ELLEN M. PRAGER 1Department of Biochemistry, University of California, Berkeley, California 94720, U.S.A Search for other works by this author on: Oxford Academic Google Scholar RICHARD D. SAGE, RICHARD D. SAGE 1Department of Biochemistry, University of California, Berkeley, California 94720, U.S.A7Museum of Vertebrate Zoology, University of California, Berkeley, California 94720, U.S.A Search for other works by this author on: Oxford Academic Google Scholar... Show more MARK STONEKING MARK STONEKING 1Department of Biochemistry, University of California, Berkeley, California 94720, U.S.A Search for other works by this author on: Oxford Academic Google Scholar Biological Journal of the Linnean Society, Volume 26, Issue 4, December 1985, Pages 375–400, https://doi.org/10.1111/j.1095-8312.1985.tb02048.x Published: 28 June 2008 Article history Accepted: 01 July 1985 Published: 28 June 2008",
    url = "https://doi.org/10.1111/j.1095-8312.1985.tb02048.x",
    doi = "10.1111/j.1095-8312.1985.tb02048.x",
    openalex = "W2065697254",
    references = "doi101038202147a0, doi101073pnas504672, doi101073pnas581142, doi101111j155856461983tb05533x, doi101126science15838051200, doi1023071438156, doi1023072407274, doi107312simp93764, openalexw788933220, sarich1967immunological"
}

@phdthesis{beardsley1986fossil1,
    author = "Beardsley, T",
    title = "Fossil bird shakes evolutionary hypothesis",
    year = "1986",
    publisher = "Nature, v. 322, p. 677",
    note = "talkorigins\_source = {true}; raw\_reference = {Beardsley, T., 1986, Fossil bird shakes evolutionary hypothesis: Nature, v. 322, p. 677.}"
}

The small-subunit rRNA gene sequences of the flagellated protists Euglena gracilis and Trypanosoma brucei were determined and compared to those of other eukaryotes. A phylogenetic tree was constructed in which the earliest branching among the eukaryotes is represented by E. gracilis. The E. gracilis divergence far antedates a period of massive evolutionary radiation that gave rise to the plants, animals, fungi, and certain groups of protists such as ciliates and the acanthamoebae. The genetic diversity in this collection of eukaryotes is seen to exceed that displayed within either the eubacterial or the archaebacterial lines of descent.

@article{doi101073pnas8351383,
    author = "Sogin, M L and Elwood, Hille J. and Gunderson, John H.",
    title = "Evolutionary diversity of eukaryotic small-subunit rRNA genes.",
    year = "1986",
    journal = "Proceedings of the National Academy of Sciences",
    abstract = "The small-subunit rRNA gene sequences of the flagellated protists Euglena gracilis and Trypanosoma brucei were determined and compared to those of other eukaryotes. A phylogenetic tree was constructed in which the earliest branching among the eukaryotes is represented by E. gracilis. The E. gracilis divergence far antedates a period of massive evolutionary radiation that gave rise to the plants, animals, fungi, and certain groups of protists such as ciliates and the acanthamoebae. The genetic diversity in this collection of eukaryotes is seen to exceed that displayed within either the eubacterial or the archaebacterial lines of descent.",
    url = "https://doi.org/10.1073/pnas.83.5.1383",
    doi = "10.1073/pnas.83.5.1383",
    openalex = "W2062738309"
}

@misc{monastersky1986reining33,
    author = "Monastersky, R",
    title = "Reining in a runaway theory",
    year = "1986",
    howpublished = "Science News, v. 130, p. 374",
    note = "talkorigins\_source = {true}; raw\_reference = {Monastersky, R., 1986, Reining in a runaway theory: Science News, v. 130, p. 374.}"
}

@book{doi107312nei92038,
    author = "Nei, Masatoshi",
    title = "Molecular Evolutionary Genetics",
    year = "1987",
    booktitle = "Columbia University Press eBooks",
    url = "https://doi.org/10.7312/nei-92038",
    doi = "10.7312/nei-92038",
    openalex = "W93588716"
}

@misc{gould1987asymmetry14,
    author = "Gould, S. J. and Gilinsky, N. L. and German, R. Z",
    title = "Asymmetry of lineages and the directions of evolutionary time",
    year = "1987",
    howpublished = "Science, v. 236, p. 1437-1441",
    note = "talkorigins\_source = {true}; raw\_reference = {Gould, S. J., Gilinsky, N. L., and German, R. Z., 1987, Asymmetry of lineages and the directions of evolutionary time: Science, v. 236, p. 1437-1441.}"
}

@misc{gould1987bushes12,
    author = "Gould, S. J",
    title = "Bushes all the way down",
    year = "1987",
    howpublished = "Natural History Magazine, v. 96 (June), p. 12-19",
    note = "talkorigins\_source = {true}; raw\_reference = {Gould, S. J., 1987, Bushes all the way down: Natural History Magazine, v. 96 (June), p. 12-19.}"
}

@misc{gould1987lifes11,
    author = "Gould, S. J",
    title = "Life's little joke",
    year = "1987",
    howpublished = "Natural History Magazine, v. 96 (April), p. 16- 25",
    note = "talkorigins\_source = {true}; raw\_reference = {Gould, S. J., 1987, Life's little joke: Natural History Magazine, v. 96 (April), p. 16- 25.}"
}

@article{doi101007978146847862422,
    author = "Smith, John Maynard",
    title = "Evolution and the Theory of Games",
    year = "1988",
    url = "https://doi.org/10.1007/978-1-4684-7862-4\_22",
    doi = "10.1007/978-1-4684-7862-4\_22",
    openalex = "W1960351623",
    references = "doi101038246015a0, doi101038254463b0, doi105962bhltitle27468, openalexw175750636"
}

@misc{gould1988a13,
    author = "Gould, S. J",
    title = "A web of tales",
    year = "1988",
    howpublished = "Natural History Magazine, v. 97 (October), p. 16-23",
    note = "talkorigins\_source = {true}; raw\_reference = {Gould, S. J., 1988, A web of tales: Natural History Magazine, v. 97 (October), p. 16-23.}"
}

Abstract Contemporary mate preferences can provide important clues to human reproductive history. Little is known about which characteristics people value in potential mates. Five predictions were made about sex differences in human mate preferences based on evolutionary conceptions of parental investment, sexual selection, human reproductive capacity, and sexual asymmetries regarding certainty of paternity versus maternity. The predictions centered on how each sex valued earning capacity, ambition— industriousness, youth, physical attractiveness, and chastity. Predictions were tested in data from 37 samples drawn from 33 countries located on six continents and five islands (total N = 10,047). For 27 countries, demographic data on actual age at marriage provided a validity check on questionnaire data. Females were found to value cues to resource acquisition in potential mates more highly than males. Characteristics signaling reproductive capacity were valued more by males than by females. These sex differences may reflect different evolutionary selection pressures on human males and females; they provide powerful cross-cultural evidence of current sex differences in reproductive strategies. Discussion focuses on proximate mechanisms underlying mate preferences, consequences for human intrasexual competition, and the limitations of this study.

@article{doi101017s0140525x00023992,
    author = "Buss, David M.",
    title = "Sex differences in human mate preferences: Evolutionary hypotheses tested in 37 cultures",
    year = "1989",
    journal = "Behavioral and Brain Sciences",
    abstract = "Abstract Contemporary mate preferences can provide important clues to human reproductive history. Little is known about which characteristics people value in potential mates. Five predictions were made about sex differences in human mate preferences based on evolutionary conceptions of parental investment, sexual selection, human reproductive capacity, and sexual asymmetries regarding certainty of paternity versus maternity. The predictions centered on how each sex valued earning capacity, ambition— industriousness, youth, physical attractiveness, and chastity. Predictions were tested in data from 37 samples drawn from 33 countries located on six continents and five islands (total N = 10,047). For 27 countries, demographic data on actual age at marriage provided a validity check on questionnaire data. Females were found to value cues to resource acquisition in potential mates more highly than males. Characteristics signaling reproductive capacity were valued more by males than by females. These sex differences may reflect different evolutionary selection pressures on human males and females; they provide powerful cross-cultural evidence of current sex differences in reproductive strategies. Discussion focuses on proximate mechanisms underlying mate preferences, consequences for human intrasexual competition, and the limitations of this study.",
    url = "https://doi.org/10.1017/s0140525x00023992",
    doi = "10.1017/s0140525x00023992",
    openalex = "W2157338817",
    references = "doi101007978146847862422, doi1010160022519364900384, doi1010160022519366901846, doi1010160162309582900279, doi1010160162309583900274, doi101016s0065260122x00026, doi101017cbo9780511806292, doi101017s0140525x00010128, doi10103711774000, doi10103712293000, doi101038246015a0, doi101038369716c0, doi101086284064, doi101111j155856461957tb02911x, doi101126science327542, doi1011425786, doi1011770022022190211001, doi101537ase188722495, doi1023072393017, doi1023072412191, doi1023072485224, doi1023072576242, doi1023075530, doi102307582242, doi1043249781315129266, doi10432497813151292667, doi1043249781410606266, doi105962bhltitle27468, doi105962bhltitle59991, doi105962bhltitle82303, openalexw1649242647, openalexw2000871817"
}

Journal Article The Evolutionary Significance of Phenotypic Plasticity: Phenotypic sources of variation among organisms can be described by developmental switches and reaction norms Get access Stephen C. Stearns Stephen C. Stearns Search for other works by this author on: Oxford Academic Google Scholar BioScience, Volume 39, Issue 7, July/August 1989, Pages 436–445, https://doi.org/10.2307/1311135 Published: 01 August 1989

@article{doi1023071311135,
    author = "Stearns, Stephen C.",
    title = "The Evolutionary Significance of Phenotypic Plasticity",
    year = "1989",
    journal = "BioScience",
    abstract = "Journal Article The Evolutionary Significance of Phenotypic Plasticity: Phenotypic sources of variation among organisms can be described by developmental switches and reaction norms Get access Stephen C. Stearns Stephen C. Stearns Search for other works by this author on: Oxford Academic Google Scholar BioScience, Volume 39, Issue 7, July/August 1989, Pages 436–445, https://doi.org/10.2307/1311135 Published: 01 August 1989",
    url = "https://doi.org/10.2307/1311135",
    doi = "10.2307/1311135",
    openalex = "W2058670567",
    references = "doi101001jama195002910300087029, doi1015159780691224244, doi1023071439305, doi1023072389364, openalexw1635425035"
}

Abstract From Darwin onward, it has been second nature for evolutionary biologists to think comparatively because comparisons establish the generality of evolutionary phenomena. Do large genomes slow down development? What lifestyles select for large brains? Are extinction rates related to body size? These are all questions for the comparative method, and this book is about how such questions can be answered. The first chapter elaborates on suitable questions for the comparative approach and shows how it complements other approaches to problem-solving in evolution. The second chapter identifies the biological causes of similarity among closely related species for almost any observed character. The third chapter discusses methods for reconstructing phylogenetic trees and ancestral character states. The fourth chapter sets out to develop statistical tests that will determine whether different characters that exist in discrete states show evidence for correlated evolution. Chapter 5 turns to comparative analyses of continuously varying characters. Chapter 6 looks at allometry to exemplify the themes and methods discussed earlier, while the last chapter looks to future development of the comparative approach in both molecular and organismic biology.

@book{doi101093oso97801985464120010001,
    author = "Harvey, Paul and Pagel, Mark",
    title = "The Comparative Method in Evolutionary Biology",
    year = "1991",
    abstract = "Abstract From Darwin onward, it has been second nature for evolutionary biologists to think comparatively because comparisons establish the generality of evolutionary phenomena. Do large genomes slow down development? What lifestyles select for large brains? Are extinction rates related to body size? These are all questions for the comparative method, and this book is about how such questions can be answered. The first chapter elaborates on suitable questions for the comparative approach and shows how it complements other approaches to problem-solving in evolution. The second chapter identifies the biological causes of similarity among closely related species for almost any observed character. The third chapter discusses methods for reconstructing phylogenetic trees and ancestral character states. The fourth chapter sets out to develop statistical tests that will determine whether different characters that exist in discrete states show evidence for correlated evolution. Chapter 5 turns to comparative analyses of continuously varying characters. Chapter 6 looks at allometry to exemplify the themes and methods discussed earlier, while the last chapter looks to future development of the comparative approach in both molecular and organismic biology.",
    url = "https://doi.org/10.1093/oso/9780198546412.001.0001",
    doi = "10.1093/oso/9780198546412.001.0001",
    openalex = "W4388245928"
}

Our understanding of evolution is built on a Darwinian tripod of three fundamental observations: (1) living organisms are units of organization that reproduce; (2) individuals differ from one another, and some of their differences are inherited, and (3) in a population, individuals enjoy differing degrees of reproductive success based at least in part on these heritable differences. This differential reproduction is what is meant by natural selection.

@incollection{goldsmith1991evolutionary,
    author = "Goldsmith, Timothy H",
    title = "Evolutionary Theory Since Darwin",
    year = "1991",
    booktitle = "The Biological Roots of Human Nature",
    abstract = "Our understanding of evolution is built on a Darwinian tripod of three fundamental observations: (1) living organisms are units of organization that reproduce; (2) individuals differ from one another, and some of their differences are inherited, and (3) in a population, individuals enjoy differing degrees of reproductive success based at least in part on these heritable differences. This differential reproduction is what is meant by natural selection.",
    url = "https://doi.org/10.1093/oso/9780195062885.003.0003",
    doi = "10.1093/oso/9780195062885.003.0003",
    openalex = "W4388079806",
    pages = "23-45"
}

The comparative method for studying adaptation why worry about phylogeny? reconstructing phylogenetic trees and ancestral character states comparative analysis of discrete data comparative analysis of continuous variables determining the form of comparative relationships.

@article{doi105860choice295104,
    title = "The comparative method in evolutionary biology",
    year = "1992",
    journal = "Choice Reviews Online",
    abstract = "The comparative method for studying adaptation why worry about phylogeny? reconstructing phylogenetic trees and ancestral character states comparative analysis of discrete data comparative analysis of continuous variables determining the form of comparative relationships.",
    url = "https://doi.org/10.5860/choice.29-5104",
    doi = "10.5860/choice.29-5104",
    openalex = "W1488393970"
}

A phylogenetic framework inferred from comparisons of small subunit ribosomal RNA sequences describes the evolutionary origin and early branching patterns of the kingdom Animalia. Maximum likelihood analyses show the animal lineage is monophyletic and includes choanoflagellates. Within the metazoan assemblage, the divergence of sponges is followed by the Ctenophora, the Cnidaria plus the placozoan Trichoplax adhaerens, and finally by an unresolved polychotomy of bilateral animal phyla. From these data, it was inferred that animals and fungi share a unique evolutionary history and that their last common ancestor was a flagellated protist similar to extant choanoflagellates.

@article{doi101126science8469985,
    author = "Wainright, Patricia O. and Hinkle, Gregory and Sogin, Mitchell L. and Stickel, Shawn K.",
    title = "Monophyletic Origins of the Metazoa: an Evolutionary Link with Fungi",
    year = "1993",
    journal = "Science",
    abstract = "A phylogenetic framework inferred from comparisons of small subunit ribosomal RNA sequences describes the evolutionary origin and early branching patterns of the kingdom Animalia. Maximum likelihood analyses show the animal lineage is monophyletic and includes choanoflagellates. Within the metazoan assemblage, the divergence of sponges is followed by the Ctenophora, the Cnidaria plus the placozoan Trichoplax adhaerens, and finally by an unresolved polychotomy of bilateral animal phyla. From these data, it was inferred that animals and fungi share a unique evolutionary history and that their last common ancestor was a flagellated protist similar to extant choanoflagellates.",
    url = "https://doi.org/10.1126/science.8469985",
    doi = "10.1126/science.8469985",
    openalex = "W2034733986",
    references = "doi101126science3277277, openalexw2076004673"
}

Introduction. Basal Groups. Monera (bacteria blue-green algae). Fungi.Algae. Animals: Invertebrates. Protozoa. Porifera. Coelenterata. Mollusca: Amphineura and Monoplacophora. Mollusca: Gastropoda. Mollusca: Cephalopoda (Nautiloidea). Mollusca: Cephalopoda (Pre-Jurassic Ammonoidea). Mollusca: Cephalopoda (Ammonoidea: Phylloceratina, Lytoceratina, Ammonitina, Ancyloceratina). Mollusca: Cephalopoda (Coleoidea). Mollusca: Rostroconchia, Scaphopoda, and Bivalvia. Mollusca: incertae sedis. Annelida. Arthropoda (Trilobita). Arthropoda (Aglaspidida, Chelicerata, Pycnogonida). Arthropoda (Crustacea, excluding Ostracoda). Arthropoda (Crustacea: Ostracoda). Arthropoda (Euthycarcinoidea and Myriapoda). Arthropoda (Hexapoda: Insecta). Brachiopoda. Phoronida. Bryozoa. Echinodermata. Basal deuterostomes (chaetognaths, hemichordates, calcichordates, cephalochordates, and tunicates). Graptolithina. Problematica. Miscellania. Animals: Vertebrates. Conodonta. Agnatha. Placodermi. Acanthodii. Chondrichthyes. Osteichthyes: basal actinopterygians. Osteichthyes: Teleostei. Osteichthyes: Sarcopterygii. Amphibian-grade Tetrapoda. Reptilia. Aves. Mammalia. Plants. Bryophyta. Pteridophyta. Gymnospermophyta. Magnoliophyta (Angiospermae). Index.

@book{openalexw1599677799,
    author = "Benton, Michael J.",
    title = "The fossil record 2",
    year = "1993",
    abstract = "Introduction. Basal Groups. Monera (bacteria blue-green algae). Fungi.Algae. Animals: Invertebrates. Protozoa. Porifera. Coelenterata. Mollusca: Amphineura and Monoplacophora. Mollusca: Gastropoda. Mollusca: Cephalopoda (Nautiloidea). Mollusca: Cephalopoda (Pre-Jurassic Ammonoidea). Mollusca: Cephalopoda (Ammonoidea: Phylloceratina, Lytoceratina, Ammonitina, Ancyloceratina). Mollusca: Cephalopoda (Coleoidea). Mollusca: Rostroconchia, Scaphopoda, and Bivalvia. Mollusca: incertae sedis. Annelida. Arthropoda (Trilobita). Arthropoda (Aglaspidida, Chelicerata, Pycnogonida). Arthropoda (Crustacea, excluding Ostracoda). Arthropoda (Crustacea: Ostracoda). Arthropoda (Euthycarcinoidea and Myriapoda). Arthropoda (Hexapoda: Insecta). Brachiopoda. Phoronida. Bryozoa. Echinodermata. Basal deuterostomes (chaetognaths, hemichordates, calcichordates, cephalochordates, and tunicates). Graptolithina. Problematica. Miscellania. Animals: Vertebrates. Conodonta. Agnatha. Placodermi. Acanthodii. Chondrichthyes. Osteichthyes: basal actinopterygians. Osteichthyes: Teleostei. Osteichthyes: Sarcopterygii. Amphibian-grade Tetrapoda. Reptilia. Aves. Mammalia. Plants. Bryophyta. Pteridophyta. Gymnospermophyta. Magnoliophyta (Angiospermae). Index.",
    openalex = "W1599677799"
}

@book{doi1010079781461523819,
    author = "Avise, John C.",
    title = "Molecular Markers, Natural History and Evolution",
    year = "1994",
    url = "https://doi.org/10.1007/978-1-4615-2381-9",
    doi = "10.1007/978-1-4615-2381-9",
    openalex = "W2037882155"
}

We report a new transformation, the LogDet, that is consistent for sequences with differing nucleotide composition and that have arisen under simple but asymmetric stochastic models of evolution. This transformation is required because existing methods tend to group sequences on the basis of their nucleotide composition, irrespective of their evolutionary history. This effect of differing nucleotide frequencies is illustrated by using a tree-selection criterion on a simple distance measure defined solely on the basis of base composition, independent of the actual sequences. The new LogDet transformation uses determinants of the observed divergence matrices and works because multiplication of determinants (real numbers) is commutative, whereas multiplication of matrices is not,except in special symmetric cases. The use of determinants thus allows more general models of evolution with a symmetric rates of nucleotide change. The transformation is illustrated on a theoretical data set (where existing methods select the wrong tree) and with three biological data sets: chloroplasts, birds/mammals (nuclear), and honeybees (mitochondrial). The LogDet transformation reinforces the logical distinction between transformations on the data and tree-selection criteria. The overall conclusions from this study are that irregular A,C,G,T compositions are an important and possible general cause of patterns that can mislead tree-reconstruction methods, even when high bootstrap values are obtained. Consequently, many published studies may need to be reexamined.

@article{doi101093oxfordjournalsmolbeva040136,
    author = "Lockhart, Peter J. and Steel, Mike and Hendy, Michael D. and Penny, David",
    title = "Recovering evolutionary trees under a more realistic model of sequence evolution.",
    year = "1994",
    journal = "Molecular Biology and Evolution",
    abstract = "We report a new transformation, the LogDet, that is consistent for sequences with differing nucleotide composition and that have arisen under simple but asymmetric stochastic models of evolution. This transformation is required because existing methods tend to group sequences on the basis of their nucleotide composition, irrespective of their evolutionary history. This effect of differing nucleotide frequencies is illustrated by using a tree-selection criterion on a simple distance measure defined solely on the basis of base composition, independent of the actual sequences. The new LogDet transformation uses determinants of the observed divergence matrices and works because multiplication of determinants (real numbers) is commutative, whereas multiplication of matrices is not,except in special symmetric cases. The use of determinants thus allows more general models of evolution with a symmetric rates of nucleotide change. The transformation is illustrated on a theoretical data set (where existing methods select the wrong tree) and with three biological data sets: chloroplasts, birds/mammals (nuclear), and honeybees (mitochondrial). The LogDet transformation reinforces the logical distinction between transformations on the data and tree-selection criteria. The overall conclusions from this study are that irregular A,C,G,T compositions are an important and possible general cause of patterns that can mislead tree-reconstruction methods, even when high bootstrap values are obtained. Consequently, many published studies may need to be reexamined.",
    url = "https://doi.org/10.1093/oxfordjournals.molbev.a040136",
    doi = "10.1093/oxfordjournals.molbev.a040136",
    openalex = "W2162443218",
    references = "doi101093oxfordjournalsmolbeva040752, doi101093oxfordjournalsmolbeva040771, doi101126science3277277"
}

@article{crossref1995systematics,
    title = "Systematics and the fossil record: documenting evolutionary patterns",
    year = "1995",
    journal = "Choice Reviews Online",
    url = "https://doi.org/10.5860/choice.32-3881",
    doi = "10.5860/choice.32-3881",
    number = "07",
    openalex = "W626899126",
    pages = "32-3881-32-3881",
    volume = "32"
}

@article{doi101006mpev19980495,
    author = "Goodman, Morris and Porter, Calvin A. and Czelusniak, John and Page, Scott L. and Schneider, Horacio and Shoshani, Jeheskel and Gunnell, Gregg F. and Groves, Colin P.",
    title = "Toward a Phylogenetic Classification of Primates Based on DNA Evidence Complemented by Fossil Evidence",
    year = "1998",
    journal = "Molecular Phylogenetics and Evolution",
    url = "https://doi.org/10.1006/mpev.1998.0495",
    doi = "10.1006/mpev.1998.0495",
    openalex = "W2058993504",
    references = "crossref1995systematics, doi102110pec9504, doi102110pec9554, doi1023071375443, doi1023072412685, doi1043249781315081083, doi105281zenodo18028696, doi105860choice323881, doi105860choice352112, openalexw1964182146"
}

@article{doi10103844766,
    author = "Pagel, Mark",
    title = "Inferring the historical patterns of biological evolution",
    year = "1999",
    journal = "Nature",
    url = "https://doi.org/10.1038/44766",
    doi = "10.1038/44766",
    openalex = "W2114525641",
    references = "doi101016s0092867400803104, doi10103818872, doi101038366223a0, doi101038384055a0, doi101086284325, doi101086286013, doi101093oso97801985464120010001, doi101093sysbio41118, doi101098rspb19940006, doi101111j146364091997tb00423x, doi101126science2740904, doi101126science2765313734, doi101128mr5122212711987, doi1015159781503621534, doi1023072407154, doi1023072485224, doi105860choice295104, rambaut1998estimating"
}

@book{doi102307jctvjsf433,
    author = "Gould, Stephen Jay",
    title = "The Structure of Evolutionary Theory",
    year = "2002",
    booktitle = "Harvard University Press eBooks",
    url = "https://doi.org/10.2307/j.ctvjsf433",
    doi = "10.2307/j.ctvjsf433",
    openalex = "W4300925890"
}

* *1. Defining and Revising the Structure of Evolutionary Theory * Part I: The History of Darwinian Logic and Debate *2. The Essence of Darwinism and the Basis of Modern Orthodoxy: An Exegesis of the Origin of Species *3. Seeds of Hierarchy *4. Internalism and Laws of Form: Pre-Darwinian Alternatives to Functionalism *5. The Fruitful Facets of Galton's Polyhedron: Channels and Saltations in Post-Darwinian Formalism *6. Pattern and Progress on the Geological Stage *7. The Modern Synthesis as a Limited Consensus * Part II: Towards a Revised and Expanded Evolutionary Theory *8. Species as Individuals in the Hierarchical Theory of Selection *9. Punctuated Equilibrium and the Validation of Macroevolutionary Theory *10. The Integration of Constraint and Adaptation (Structure and Function) in Ontogeny and Phylogeny: Historical Constraints and the Evolution of Development *11. The Integration of Constraint and Adaptation (Structure and Function) in Ontogeny and Phylogeny: Structural Constraints, Spandrels, and the Centrality of Exaptation in Macroevolution *12. Tiers of Time and Trials of Extrapolationism, With an Epilog on the Interaction of General Theory and Contingent History * Bibliography * Index

@article{doi105860choice396411,
    author = "Gould, Stephen Jay",
    title = "The structure of evolutionary theory",
    year = "2002",
    journal = "Choice Reviews Online",
    abstract = "* *1. Defining and Revising the Structure of Evolutionary Theory * Part I: The History of Darwinian Logic and Debate *2. The Essence of Darwinism and the Basis of Modern Orthodoxy: An Exegesis of the Origin of Species *3. Seeds of Hierarchy *4. Internalism and Laws of Form: Pre-Darwinian Alternatives to Functionalism *5. The Fruitful Facets of Galton's Polyhedron: Channels and Saltations in Post-Darwinian Formalism *6. Pattern and Progress on the Geological Stage *7. The Modern Synthesis as a Limited Consensus * Part II: Towards a Revised and Expanded Evolutionary Theory *8. Species as Individuals in the Hierarchical Theory of Selection *9. Punctuated Equilibrium and the Validation of Macroevolutionary Theory *10. The Integration of Constraint and Adaptation (Structure and Function) in Ontogeny and Phylogeny: Historical Constraints and the Evolution of Development *11. The Integration of Constraint and Adaptation (Structure and Function) in Ontogeny and Phylogeny: Structural Constraints, Spandrels, and the Centrality of Exaptation in Macroevolution *12. Tiers of Time and Trials of Extrapolationism, With an Epilog on the Interaction of General Theory and Contingent History * Bibliography * Index",
    url = "https://doi.org/10.5860/choice.39-6411",
    doi = "10.5860/choice.39-6411",
    openalex = "W1539968307"
}

Epidemiological observations have led to the hypothesis that the risk of developing some chronic noncommunicable diseases in adulthood is influenced not only by genetic and adult life-style factors but also by environmental factors acting in early life. Research in evolutionary biology, developmental biology, and animal and human physiology provides support for this idea and suggests that environmental processes influencing the propensity to disease in adulthood operate during the periconceptual, fetal, and infant phases of life. This "developmental origins of health and disease" concept may have important biological, medical, and socioeconomic implications.

@article{doi101126science1095292,
    author = "Gluckman, Peter D. and Hanson, Mark A.",
    title = "Living with the Past: Evolution, Development, and Patterns of Disease",
    year = "2004",
    journal = "Science",
    abstract = {Epidemiological observations have led to the hypothesis that the risk of developing some chronic noncommunicable diseases in adulthood is influenced not only by genetic and adult life-style factors but also by environmental factors acting in early life. Research in evolutionary biology, developmental biology, and animal and human physiology provides support for this idea and suggests that environmental processes influencing the propensity to disease in adulthood operate during the periconceptual, fetal, and infant phases of life. This "developmental origins of health and disease" concept may have important biological, medical, and socioeconomic implications.},
    url = "https://doi.org/10.1126/science.1095292",
    doi = "10.1126/science.1095292",
    openalex = "W2125089843",
    references = "doi105694j132653771958tb86500x"
}

The evolutionary history of a set of taxa is usually represented by a phylogenetic tree, and this model has greatly facilitated the discussion and testing of hypotheses. However, it is well known that more complex evolutionary scenarios are poorly described by such models. Further, even when evolution proceeds in a tree-like manner, analysis of the data may not be best served by using methods that enforce a tree structure but rather by a richer visualization of the data to evaluate its properties, at least as an essential first step. Thus, phylogenetic networks should be employed when reticulate events such as hybridization, horizontal gene transfer, recombination, or gene duplication and loss are believed to be involved, and, even in the absence of such events, phylogenetic networks have a useful role to play. This article reviews the terminology used for phylogenetic networks and covers both split networks and reticulate networks, how they are defined, and how they can be interpreted. Additionally, the article outlines the beginnings of a comprehensive statistical framework for applying split network methods. We show how split networks can represent confidence sets of trees and introduce a conservative statistical test for whether the conflicting signal in a network is treelike. Finally, this article describes a new program, SplitsTree4, an interactive and comprehensive tool for inferring different types of phylogenetic networks from sequences, distances, and trees.

@article{doi101093molbevmsj030,
    author = "Huson, Daniel H. and Bryant, David",
    title = "Application of Phylogenetic Networks in Evolutionary Studies",
    year = "2005",
    journal = "Molecular Biology and Evolution",
    abstract = "The evolutionary history of a set of taxa is usually represented by a phylogenetic tree, and this model has greatly facilitated the discussion and testing of hypotheses. However, it is well known that more complex evolutionary scenarios are poorly described by such models. Further, even when evolution proceeds in a tree-like manner, analysis of the data may not be best served by using methods that enforce a tree structure but rather by a richer visualization of the data to evaluate its properties, at least as an essential first step. Thus, phylogenetic networks should be employed when reticulate events such as hybridization, horizontal gene transfer, recombination, or gene duplication and loss are believed to be involved, and, even in the absence of such events, phylogenetic networks have a useful role to play. This article reviews the terminology used for phylogenetic networks and covers both split networks and reticulate networks, how they are defined, and how they can be interpreted. Additionally, the article outlines the beginnings of a comprehensive statistical framework for applying split network methods. We show how split networks can represent confidence sets of trees and introduce a conservative statistical test for whether the conflicting signal in a network is treelike. Finally, this article describes a new program, SplitsTree4, an interactive and comprehensive tool for inferring different types of phylogenetic networks from sequences, distances, and trees.",
    url = "https://doi.org/10.1093/molbev/msj030",
    doi = "10.1093/molbev/msj030",
    openalex = "W2055298722",
    references = "doi101016s0169534700020267, doi101038nrg929, doi10108010635150390235520, doi101093bioinformaticsbtg180, doi101093molbevmsi111, doi101093sysbio463523, doi101111j155856461985tb00420x"
}

Bats make up more than 20% of extant mammals, yet their evolutionary history is largely unknown because of a limited fossil record and conflicting or incomplete phylogenies. Here, we present a highly resolved molecular phylogeny for all extant bat families. Our results support the hypothesis that megabats are nested among four major microbat lineages, which originated in the early Eocene [52 to 50 million years ago (Mya)], coincident with a significant global rise in temperature, increase in plant diversity and abundance, and the zenith of Tertiary insect diversity. Our data suggest that bats originated in Laurasia, possibly in North America, and that three of the major microbat lineages are Laurasian in origin, whereas the fourth is Gondwanan. Combining principles of ghost lineage analysis with molecular divergence dates, we estimate that the bat fossil record underestimates (unrepresented basal branch length, UBBL) first occurrences by, on average, 73% and that the sum of missing fossil history is 61%.

@article{doi101126science1105113,
    author = "Teeling, Emma C. and Springer, Mark S. and Madsen, Ole and Bates, Paul J. J. and O’Brien, Stephen J. and Murphy, William J.",
    title = "A Molecular Phylogeny for Bats Illuminates Biogeography and the Fossil Record",
    year = "2005",
    journal = "Science",
    abstract = "Bats make up more than 20\% of extant mammals, yet their evolutionary history is largely unknown because of a limited fossil record and conflicting or incomplete phylogenies. Here, we present a highly resolved molecular phylogeny for all extant bat families. Our results support the hypothesis that megabats are nested among four major microbat lineages, which originated in the early Eocene [52 to 50 million years ago (Mya)], coincident with a significant global rise in temperature, increase in plant diversity and abundance, and the zenith of Tertiary insect diversity. Our data suggest that bats originated in Laurasia, possibly in North America, and that three of the major microbat lineages are Laurasian in origin, whereas the fourth is Gondwanan. Combining principles of ghost lineage analysis with molecular divergence dates, we estimate that the bat fossil record underestimates (unrepresented basal branch length, UBBL) first occurrences by, on average, 73\% and that the sum of missing fossil history is 61\%.",
    url = "https://doi.org/10.1126/science.1105113",
    doi = "10.1126/science.1105113",
    openalex = "W1997655974",
    references = "doi101007bf01454359, doi101017cbo9780511529924, doi10103835003188, doi10103835055536, doi101073pnas0334222100, doi101073pnas111551998, doi101126science1067179, doi101126science11536548, doi101126science15437541333, doi101126science28454232153, doi1023071223169"
}

Biomedical science has little considered the relevance of life history theory and evolutionary and ecological developmental biology to clinical medicine. However, the observations that early life influences can alter later disease risk--the "developmental origins of health and disease" (DOHaD) paradigm--have led to a recognition that these perspectives can inform our understanding of human biology. We propose that the DOHaD phenomenon can be considered as a subset of the broader processes of developmental plasticity by which organisms adapt to their environment during their life course. Such adaptive processes allow genotypic variation to be preserved through transient environmental changes. Cues for plasticity operate particularly during early development; they may affect a single organ or system, but generally they induce integrated adjustments in the mature phenotype, a process underpinned by epigenetic mechanisms and influenced by prediction of the mature environment. In mammals, an adverse intrauterine environment results in an integrated suite of responses, suggesting the involvement of a few key regulatory genes, that resets the developmental trajectory in expectation of poor postnatal conditions. Mismatch between the anticipated and the actual mature environment exposes the organism to risk of adverse consequences-the greater the mismatch, the greater the risk. For humans, prediction is inaccurate for many individuals because of changes in the postnatal environment toward energy-dense nutrition and low energy expenditure, contributing to the epidemic of chronic noncommunicable disease. This view of human disease from the perspectives of life history biology and evolutionary theory offers new approaches to prevention, diagnosis and intervention.

@article{doi101002ajhb20590,
    author = "Gluckman, Peter D. and Hanson, Mark A. and Beedle, Alan S.",
    title = "Early life events and their consequences for later disease: A life history and evolutionary perspective",
    year = "2006",
    journal = "American Journal of Human Biology",
    abstract = {Biomedical science has little considered the relevance of life history theory and evolutionary and ecological developmental biology to clinical medicine. However, the observations that early life influences can alter later disease risk--the "developmental origins of health and disease" (DOHaD) paradigm--have led to a recognition that these perspectives can inform our understanding of human biology. We propose that the DOHaD phenomenon can be considered as a subset of the broader processes of developmental plasticity by which organisms adapt to their environment during their life course. Such adaptive processes allow genotypic variation to be preserved through transient environmental changes. Cues for plasticity operate particularly during early development; they may affect a single organ or system, but generally they induce integrated adjustments in the mature phenotype, a process underpinned by epigenetic mechanisms and influenced by prediction of the mature environment. In mammals, an adverse intrauterine environment results in an integrated suite of responses, suggesting the involvement of a few key regulatory genes, that resets the developmental trajectory in expectation of poor postnatal conditions. Mismatch between the anticipated and the actual mature environment exposes the organism to risk of adverse consequences-the greater the mismatch, the greater the risk. For humans, prediction is inaccurate for many individuals because of changes in the postnatal environment toward energy-dense nutrition and low energy expenditure, contributing to the epidemic of chronic noncommunicable disease. This view of human disease from the perspectives of life history biology and evolutionary theory offers new approaches to prevention, diagnosis and intervention.},
    url = "https://doi.org/10.1002/ajhb.20590",
    doi = "10.1002/ajhb.20590",
    openalex = "W2050014967",
    references = "doi105694j132653771958tb86500x"
}

The evolutionary dynamics underlying the latitudinal gradient in biodiversity have been controversial for over a century. Using a spatially explicit approach that incorporates not only origination and extinction but immigration, a global analysis of genera and subgenera of marine bivalves over the past 11 million years supports an "out of the tropics" model, in which taxa preferentially originate in the tropics and expand toward the poles without losing their tropical presence. The tropics are thus both a cradle and a museum of biodiversity, contrary to the conceptual dichotomy dominant since 1974; a tropical diversity crisis would thus have profound evolutionary effects at all latitudes.

@article{doi101126science1130880,
    author = "Jablonski, David and Roy, Kaustuv and Valentine, James W.",
    title = "Out of the Tropics: Evolutionary Dynamics of the Latitudinal Diversity Gradient",
    year = "2006",
    journal = "Science",
    abstract = {The evolutionary dynamics underlying the latitudinal gradient in biodiversity have been controversial for over a century. Using a spatially explicit approach that incorporates not only origination and extinction but immigration, a global analysis of genera and subgenera of marine bivalves over the past 11 million years supports an "out of the tropics" model, in which taxa preferentially originate in the tropics and expand toward the poles without losing their tropical presence. The tropics are thus both a cradle and a museum of biodiversity, contrary to the conceptual dichotomy dominant since 1974; a tropical diversity crisis would thus have profound evolutionary effects at all latitudes.},
    url = "https://doi.org/10.1126/science.1130880",
    doi = "10.1126/science.1130880",
    openalex = "W2147544980",
    references = "darlington1959area, doi1010160169534794901635, doi101016jtree200409011, doi101017cbo9780511623387, doi10103835012228, doi101086381004, doi101093oso97801985052350010001, doi101146annurevecolsys34012103144032, doi1016660094837320050310192meam20co2, doi101890038006, doi1023072389612, doi105860choice332720"
}

Ecological changes in the phenology and distribution of plants and animals are occurring in all well-studied marine, freshwater, and terrestrial groups. These observed changes are heavily biased in the directions predicted from global warming and have been linked to local or regional climate change through correlations between climate and biological variation, field and laboratory experiments, and physiological research. Range-restricted species, particularly polar and mountaintop species, show severe range contractions and have been the first groups in which entire species have gone extinct due to recent climate change. Tropical coral reefs and amphibians have been most negatively affected. Predator-prey and plant-insect interactions have been disrupted when interacting species have responded differently to warming. Evolutionary adaptations to warmer conditions have occurred in the interiors of species' ranges, and resource use and dispersal have evolved rapidly at expanding range margins. Observed genetic shifts modulate local effects of climate change, but there is little evidence that they will mitigate negative effects at the species level.

@article{doi101146annurevecolsys37091305110100,
    author = "Parmesan, Camille",
    title = "Ecological and Evolutionary Responses to Recent Climate Change",
    year = "2006",
    journal = "Annual Review of Ecology Evolution and Systematics",
    abstract = "Ecological changes in the phenology and distribution of plants and animals are occurring in all well-studied marine, freshwater, and terrestrial groups. These observed changes are heavily biased in the directions predicted from global warming and have been linked to local or regional climate change through correlations between climate and biological variation, field and laboratory experiments, and physiological research. Range-restricted species, particularly polar and mountaintop species, show severe range contractions and have been the first groups in which entire species have gone extinct due to recent climate change. Tropical coral reefs and amphibians have been most negatively affected. Predator-prey and plant-insect interactions have been disrupted when interacting species have responded differently to warming. Evolutionary adaptations to warmer conditions have occurred in the interiors of species' ranges, and resource use and dispersal have evolved rapidly at expanding range margins. Observed genetic shifts modulate local effects of climate change, but there is little evidence that they will mitigate negative effects at the species level.",
    url = "https://doi.org/10.1146/annurev.ecolsys.37.091305.110100",
    doi = "10.1146/annurev.ecolsys.37.091305.110100",
    openalex = "W2135858501",
    references = "doi1010160169534794902488, doi10103835079180, doi101038369448a0, doi101038382146a0, doi101038386698a0, doi101038nature01286, doi101038nature04095, doi101038nature04246, doi101071mf99078, doi101093aesa492190, doi101126science28954872068, doi101126science2925517673, doi1023071939337, doi1023071940431, doi105860choice301495, openalexw1500291103, openalexw2151235472"
}

@article{doi101016jcell200806030,
    author = "Carroll, Sean B.",
    title = "Evo-Devo and an Expanding Evolutionary Synthesis: A Genetic Theory of Morphological Evolution",
    year = "2008",
    journal = "Cell",
    url = "https://doi.org/10.1016/j.cell.2008.06.030",
    doi = "10.1016/j.cell.2008.06.030",
    openalex = "W2171193618",
    references = "doi1010079783642866593, doi101016b9781483227344500176, doi101038276565a0, doi101038376479a0, doi10103841710, doi101038nature02415, doi101038nature03158, doi101038nrg2063, doi101086406830, doi101111j001438202000tb00544x, doi101111j15585646200700105x, doi101126science1090005, doi101126science1107239, doi101126science147365368, doi101126science7892602, doi101242dev1212333, doi101371journalpbio0030245, doi105860choice395182, openalexw591049712, openalexw614012683"
}

@incollection{doi10100797814020965011,
    author = "Favareau, Donald",
    title = "Introduction: An Evolutionary History of Biosemiotics",
    year = "2009",
    booktitle = "Biosemiotics/Biosemiotics. Bookseries",
    url = "https://doi.org/10.1007/978-1-4020-9650-1\_1",
    doi = "10.1007/978-1-4020-9650-1\_1",
    openalex = "W2098182790",
    references = "doi101007978140209650112"
}

@article{doi101038nrg3028,
    author = "Danchin, Étienne and Charmantier, Anne and Champagne, Frances A. and Mesoudi, Alex and Pujol, Benoît and Blanchet, Simon",
    title = "Beyond DNA: integrating inclusive inheritance into an extended theory of evolution",
    year = "2011",
    journal = "Nature Reviews Genetics",
    url = "https://doi.org/10.1038/nrg3028",
    doi = "10.1038/nrg3028",
    openalex = "W2162016759",
    references = "doi101002evan10110, doi101016jtree200603015, doi101017s0140525x06009083, doi101038374227a0, doi101098rstb20061998, doi101111j15585646201001012x, doi1043249781315801889, doi107551mitpress97802625136780010001"
}

Biological systems that perform multiple tasks face a fundamental trade-off: A given phenotype cannot be optimal at all tasks. Here we ask how trade-offs affect the range of phenotypes found in nature. Using the Pareto front concept from economics and engineering, we find that best-trade-off phenotypes are weighted averages of archetypes--phenotypes specialized for single tasks. For two tasks, phenotypes fall on the line connecting the two archetypes, which could explain linear trait correlations, allometric relationships, as well as bacterial gene-expression patterns. For three tasks, phenotypes fall within a triangle in phenotype space, whose vertices are the archetypes, as evident in morphological studies, including on Darwin's finches. Tasks can be inferred from measured phenotypes based on the behavior of organisms nearest the archetypes.

@article{doi101126science1217405,
    author = "Shoval, Oren and Sheftel, Hila and Shinar, Guy and Hart, Yuval and Ramote, Omer and Mayo, Avi and Dekel, E. and Kavanagh, Kathryn D. and Alon, Uri",
    title = "Evolutionary Trade-Offs, Pareto Optimality, and the Geometry of Phenotype Space",
    year = "2012",
    journal = "Science",
    abstract = "Biological systems that perform multiple tasks face a fundamental trade-off: A given phenotype cannot be optimal at all tasks. Here we ask how trade-offs affect the range of phenotypes found in nature. Using the Pareto front concept from economics and engineering, we find that best-trade-off phenotypes are weighted averages of archetypes--phenotypes specialized for single tasks. For two tasks, phenotypes fall on the line connecting the two archetypes, which could explain linear trait correlations, allometric relationships, as well as bacterial gene-expression patterns. For three tasks, phenotypes fall within a triangle in phenotype space, whose vertices are the archetypes, as evident in morphological studies, including on Darwin's finches. Tasks can be inferred from measured phenotypes based on the behavior of organisms nearest the archetypes.",
    url = "https://doi.org/10.1126/science.1217405",
    doi = "10.1126/science.1217405",
    openalex = "W2010025771",
    references = "doi101098rstb19870030, openalexw1869415094"
}

Work in our laboratory is supported by grants BIO2008-00090 from the Spanish Ministry of Science and Innovation and KBBE-227258 (BIOHYPO), HEALTH-F3-2011-282004 (EVOTAR), and HEALTH-F3-2010-241476 (PAR) from European Union.

@article{doi103389fmicb201200001,
    author = "Martínez, José Luis",
    title = "Natural Antibiotic Resistance and Contamination by Antibiotic Resistance Determinants: The Two Ages in the Evolution of Resistance to Antimicrobials",
    year = "2012",
    journal = "Frontiers in Microbiology",
    abstract = "Work in our laboratory is supported by grants BIO2008-00090 from the Spanish Ministry of Science and Innovation and KBBE-227258 (BIOHYPO), HEALTH-F3-2011-282004 (EVOTAR), and HEALTH-F3-2010-241476 (PAR) from European Union.",
    url = "https://doi.org/10.3389/fmicb.2012.00001",
    doi = "10.3389/fmicb.2012.00001",
    openalex = "W2026352429",
    references = "doi101017s0094837300004310, doi101128mmbr0001610, doi103929ethzb000667478"
}

I summarize marine studies on plastic versus adaptive responses to global change. Due to the lack of time series, this review focuses largely on the potential for adaptive evolution in marine animals and plants. The approaches were mainly synchronic comparisons of phenotypically divergent populations, substituting spatial contrasts in temperature or CO2 environments for temporal changes, or in assessments of adaptive genetic diversity within populations for traits important under global change. The available literature is biased towards gastropods, crustaceans, cnidarians and macroalgae. Focal traits were mostly environmental tolerances, which correspond to phenotypic buffering, a plasticity type that maintains a functional phenotype despite external disturbance. Almost all studies address coastal species that are already today exposed to fluctuations in temperature, pH and oxygen levels. Recommendations for future research include (i) initiation and analyses of observational and experimental temporal studies encompassing diverse phenotypic traits (including diapausing cues, dispersal traits, reproductive timing, morphology) (ii) quantification of nongenetic trans-generational effects along with components of additive genetic variance (iii) adaptive changes in microbe-host associations under the holobiont model in response to global change (iv) evolution of plasticity patterns under increasingly fluctuating environments and extreme conditions and (v) joint consideration of demography and evolutionary adaptation in evolutionary rescue approaches.

@article{doi101111eva12109,
    author = "Reusch, Thorsten B. H.",
    title = "Climate change in the oceans: evolutionary versus phenotypically plastic responses of marine animals and plants",
    year = "2013",
    journal = "Evolutionary Applications",
    abstract = "I summarize marine studies on plastic versus adaptive responses to global change. Due to the lack of time series, this review focuses largely on the potential for adaptive evolution in marine animals and plants. The approaches were mainly synchronic comparisons of phenotypically divergent populations, substituting spatial contrasts in temperature or CO2 environments for temporal changes, or in assessments of adaptive genetic diversity within populations for traits important under global change. The available literature is biased towards gastropods, crustaceans, cnidarians and macroalgae. Focal traits were mostly environmental tolerances, which correspond to phenotypic buffering, a plasticity type that maintains a functional phenotype despite external disturbance. Almost all studies address coastal species that are already today exposed to fluctuations in temperature, pH and oxygen levels. Recommendations for future research include (i) initiation and analyses of observational and experimental temporal studies encompassing diverse phenotypic traits (including diapausing cues, dispersal traits, reproductive timing, morphology) (ii) quantification of nongenetic trans-generational effects along with components of additive genetic variance (iii) adaptive changes in microbe-host associations under the holobiont model in response to global change (iv) evolution of plasticity patterns under increasingly fluctuating environments and extreme conditions and (v) joint consideration of demography and evolutionary adaptation in evolutionary rescue approaches.",
    url = "https://doi.org/10.1111/eva.12109",
    doi = "10.1111/eva.12109",
    openalex = "W2071187584",
    references = "doi107551mitpress97802625136780010001"
}

Evolutionary responses are required for tree populations to be able to track climate change. Results of 250 years of common garden experiments show that most forest trees have evolved local adaptation, as evidenced by the adaptive differentiation of populations in quantitative traits, reflecting environmental conditions of population origins. On the basis of the patterns of quantitative variation for 19 adaptation-related traits studied in 59 tree species (mostly temperate and boreal species from the Northern hemisphere), we found that genetic differentiation between populations and clinal variation along environmental gradients were very common (respectively, 90% and 78% of cases). Thus, responding to climate change will likely require that the quantitative traits of populations again match their environments. We examine what kind of information is needed for evaluating the potential to respond, and what information is already available. We review the genetic models related to selection responses, and what is known currently about the genetic basis of the traits. We address special problems to be found at the range margins, and highlight the need for more modeling to understand specific issues at southern and northern margins. We need new common garden experiments for less known species. For extensively studied species, new experiments are needed outside the current ranges. Improving genomic information will allow better prediction of responses. Competitive and other interactions within species and interactions between species deserve more consideration. Despite the long generation times, the strong background in quantitative genetics and growing genomic resources make forest trees useful species for climate change research. The greatest adaptive response is expected when populations are large, have high genetic variability, selection is strong, and there is ecological opportunity for establishment of better adapted genotypes.

@article{doi101111gcb12181,
    author = "Alberto, Florian and Aitken, Sally N. and Alı́a, Ricardo and González‐Martínez, Santiago C. and Hänninen, Heikki and Kremer, Antoine and Lefèvre, François and Lenormand, Thomas and Yeaman, Sam and Whetten, Ross and Savolainen, Outi",
    title = "Potential for evolutionary responses to climate change – evidence from tree populations",
    year = "2013",
    journal = "Global Change Biology",
    abstract = "Evolutionary responses are required for tree populations to be able to track climate change. Results of 250 years of common garden experiments show that most forest trees have evolved local adaptation, as evidenced by the adaptive differentiation of populations in quantitative traits, reflecting environmental conditions of population origins. On the basis of the patterns of quantitative variation for 19 adaptation-related traits studied in 59 tree species (mostly temperate and boreal species from the Northern hemisphere), we found that genetic differentiation between populations and clinal variation along environmental gradients were very common (respectively, 90\% and 78\% of cases). Thus, responding to climate change will likely require that the quantitative traits of populations again match their environments. We examine what kind of information is needed for evaluating the potential to respond, and what information is already available. We review the genetic models related to selection responses, and what is known currently about the genetic basis of the traits. We address special problems to be found at the range margins, and highlight the need for more modeling to understand specific issues at southern and northern margins. We need new common garden experiments for less known species. For extensively studied species, new experiments are needed outside the current ranges. Improving genomic information will allow better prediction of responses. Competitive and other interactions within species and interactions between species deserve more consideration. Despite the long generation times, the strong background in quantitative genetics and growing genomic resources make forest trees useful species for climate change research. The greatest adaptive response is expected when populations are large, have high genetic variability, selection is strong, and there is ecological opportunity for establishment of better adapted genotypes.",
    url = "https://doi.org/10.1111/gcb.12181",
    doi = "10.1111/gcb.12181",
    openalex = "W2152279961",
    references = "doi101111j00221112200400433x, doi101111j14209101200701445x"
}

Uncertainties surrounding the evolutionary origin of the epipelagic fish family Scombridae (tunas and mackerels) are symptomatic of the difficulties in resolving suprafamilial relationships within Percomorpha, a hyperdiverse teleost radiation that contains approximately 17,000 species placed in 13 ill-defined orders and 269 families. Here we find that scombrids share a common ancestry with 14 families based on (i) bioinformatic analyses using partial mitochondrial and nuclear gene sequences from all percomorphs deposited in GenBank (10,733 sequences) and (ii) subsequent mitogenomic analysis based on 57 species from those targeted 15 families and 67 outgroup taxa. Morphological heterogeneity among these 15 families is so extraordinary that they have been placed in six different perciform suborders. However, members of the 15 families are either coastal or oceanic pelagic in their ecology with diverse modes of life, suggesting that they represent a previously undetected adaptive radiation in the pelagic realm. Time-calibrated phylogenies imply that scombrids originated from a deep-ocean ancestor and began to radiate after the end-Cretaceous when large predatory epipelagic fishes were selective victims of the Cretaceous-Paleogene mass extinction. We name this clade of open-ocean fishes containing Scombridae "Pelagia" in reference to the common habitat preference that links the 15 families.

@article{doi101371journalpone0073535,
    author = "Miya, Masaki and Friedman, Matt and Satoh, Takashi and Takeshima, Hirohiko and Sado, Tetsuya and Iwasaki, Wataru and Yamanoue, Yusuke and Nakatani, Masanori and Mabuchi, Kohji and Inoue, Jun and Poulsen, Jan Yde and Fukunaga, Tsukasa and Sato, Yukuto and Nishida, Mutsumi",
    title = "Evolutionary Origin of the Scombridae (Tunas and Mackerels): Members of a Paleogene Adaptive Radiation with 14 Other Pelagic Fish Families",
    year = "2013",
    journal = "PLoS ONE",
    abstract = {Uncertainties surrounding the evolutionary origin of the epipelagic fish family Scombridae (tunas and mackerels) are symptomatic of the difficulties in resolving suprafamilial relationships within Percomorpha, a hyperdiverse teleost radiation that contains approximately 17,000 species placed in 13 ill-defined orders and 269 families. Here we find that scombrids share a common ancestry with 14 families based on (i) bioinformatic analyses using partial mitochondrial and nuclear gene sequences from all percomorphs deposited in GenBank (10,733 sequences) and (ii) subsequent mitogenomic analysis based on 57 species from those targeted 15 families and 67 outgroup taxa. Morphological heterogeneity among these 15 families is so extraordinary that they have been placed in six different perciform suborders. However, members of the 15 families are either coastal or oceanic pelagic in their ecology with diverse modes of life, suggesting that they represent a previously undetected adaptive radiation in the pelagic realm. Time-calibrated phylogenies imply that scombrids originated from a deep-ocean ancestor and began to radiate after the end-Cretaceous when large predatory epipelagic fishes were selective victims of the Cretaceous-Paleogene mass extinction. We name this clade of open-ocean fishes containing Scombridae "Pelagia" in reference to the common habitat preference that links the 15 families.},
    url = "https://doi.org/10.1371/journal.pone.0073535",
    doi = "10.1371/journal.pone.0073535",
    openalex = "W2087061078",
    references = "doi101111j14754983201201165x"
}

In the era of the extended evolutionary synthesis, which no longer considers natural selection as the only leading factor of evolution, it is meaningful to revisit the legacy of biologists who discussed the role of alternative factors. Here we analyze the evolutionary views of Sergei Meyen (1935-1987), a paleobotanist who argued that the theory of evolution should incorporate a "nomothetical" approach which infers the laws of morphogenesis (i.e., form generation) from the observed patterns of variation in living organisms and in the fossil records. Meyen developed a theory of "repeated polymorphic sets" (RPSs), which he applied consistently to describe inter-organism variation in populations, intra-organism variation of metameric organs, variation of abnormalities, heterotopy, changes during embryo development, and inter-species variation within evolutionary lineages. The notion of RPS assumes the active nature of organisms that possess hidden morphogenic and behavioral capacities. Meyen's theory is compatible with Darwin's natural selection; however, Meyen emphasized the importance of other forms of selection (e.g., selection of developmental trajectories, habitats, and behaviors) in choosing specific elements from the RPS. Finally, Meyen developed a new typological concept of time, where time represents variability (i.e., change) of real objects such as living organisms or geological formations.

@article{doi101016jbiosystems201406008,
    author = "Sharov, Alexei A and Igamberdiev, Abir U",
    title = "Inferring directions of evolution from patterns of variation: the legacy of Sergei Meyen.",
    year = "2014",
    journal = "Bio Systems",
    abstract = {In the era of the extended evolutionary synthesis, which no longer considers natural selection as the only leading factor of evolution, it is meaningful to revisit the legacy of biologists who discussed the role of alternative factors. Here we analyze the evolutionary views of Sergei Meyen (1935-1987), a paleobotanist who argued that the theory of evolution should incorporate a "nomothetical" approach which infers the laws of morphogenesis (i.e., form generation) from the observed patterns of variation in living organisms and in the fossil records. Meyen developed a theory of "repeated polymorphic sets" (RPSs), which he applied consistently to describe inter-organism variation in populations, intra-organism variation of metameric organs, variation of abnormalities, heterotopy, changes during embryo development, and inter-species variation within evolutionary lineages. The notion of RPS assumes the active nature of organisms that possess hidden morphogenic and behavioral capacities. Meyen's theory is compatible with Darwin's natural selection; however, Meyen emphasized the importance of other forms of selection (e.g., selection of developmental trajectories, habitats, and behaviors) in choosing specific elements from the RPS. Finally, Meyen developed a new typological concept of time, where time represents variability (i.e., change) of real objects such as living organisms or geological formations.},
    url = "https://pmc.ncbi.nlm.nih.gov/articles/PMC4254149/",
    doi = "10.1016/j.biosystems.2014.06.008",
    openalex = "W2018299764",
    pmcid = "PMC4254149",
    pmid = "25072709",
    references = "doi101001jama195002910300087029, doi101086276408, doi101126science1130880, doi101126science1483671754, doi1015159780691183978018, doi101890039000, doi105694j132653771958tb86500x, doi105962bhltitle27468, doi107551mitpress97802625136780010001, openalexw1869415094"
}

@article{doi101038514161a,
    author = "Laland, Kevin N. and Uller, Tobias and Feldman, Marc and Sterelny, Kim and Müller, Gerd B. and Moczek, Armin P. and Jablonka, Eva and Odling‐Smee, John and Wray, Gregory A. and Hoekstra, Hopi E. and Futuyma, Douglas J. and Lenski, Richard E. and Mackay, Trudy F. C. and Schluter, Dolph and Strassmann, Joan E.",
    title = "Does evolutionary theory need a rethink?",
    year = "2014",
    journal = "Nature",
    url = "https://doi.org/10.1038/514161a",
    doi = "10.1038/514161a",
    openalex = "W1991285543",
    references = "doi107551mitpress97802625136780010001, openalexw135071171"
}

@article{doi101038nrg3982,
    author = "Gilbert, Scott F. and Bosch, Thomas C. G. and Ledón‐Rettig, Cristina C.",
    title = "Eco-Evo-Devo: developmental symbiosis and developmental plasticity as evolutionary agents",
    year = "2015",
    journal = "Nature Reviews Genetics",
    url = "https://doi.org/10.1038/nrg3982",
    doi = "10.1038/nrg3982",
    openalex = "W2219314901",
    references = "doi101146annurevmarine120709142753, doi107551mitpress97802625136780010001"
}

Scientific activities take place within the structured sets of ideas and assumptions that define a field and its practices. The conceptual framework of evolutionary biology emerged with the Modern Synthesis in the early twentieth century and has since expanded into a highly successful research program to explore the processes of diversification and adaptation. Nonetheless, the ability of that framework satisfactorily to accommodate the rapid advances in developmental biology, genomics and ecology has been questioned. We review some of these arguments, focusing on literatures (evo-devo, developmental plasticity, inclusive inheritance and niche construction) whose implications for evolution can be interpreted in two ways—one that preserves the internal structure of contemporary evolutionary theory and one that points towards an alternative conceptual framework. The latter, which we label the 'extended evolutionary synthesis' (EES), retains the fundaments of evolutionary theory, but differs in its emphasis on the role of constructive processes in development and evolution, and reciprocal portrayals of causation. In the EES, developmental processes, operating through developmental bias, inclusive inheritance and niche construction, share responsibility for the direction and rate of evolution, the origin of character variation and organism-environment complementarity. We spell out the structure, core assumptions and novel predictions of the EES, and show how it can be deployed to stimulate and advance research in those fields that study or use evolutionary biology.

@article{doi101098rspb20151019,
    author = "Laland, Kevin N. and Uller, Tobias and Feldman, Marcus W. and Sterelny, Kim and Müller, Gerd B. and Moczek, Armin P. and Jablonka, Eva and Odling‐Smee, John",
    title = "The extended evolutionary synthesis: its structure, assumptions and predictions",
    year = "2015",
    journal = "Proceedings of the Royal Society B Biological Sciences",
    abstract = "Scientific activities take place within the structured sets of ideas and assumptions that define a field and its practices. The conceptual framework of evolutionary biology emerged with the Modern Synthesis in the early twentieth century and has since expanded into a highly successful research program to explore the processes of diversification and adaptation. Nonetheless, the ability of that framework satisfactorily to accommodate the rapid advances in developmental biology, genomics and ecology has been questioned. We review some of these arguments, focusing on literatures (evo-devo, developmental plasticity, inclusive inheritance and niche construction) whose implications for evolution can be interpreted in two ways—one that preserves the internal structure of contemporary evolutionary theory and one that points towards an alternative conceptual framework. The latter, which we label the 'extended evolutionary synthesis' (EES), retains the fundaments of evolutionary theory, but differs in its emphasis on the role of constructive processes in development and evolution, and reciprocal portrayals of causation. In the EES, developmental processes, operating through developmental bias, inclusive inheritance and niche construction, share responsibility for the direction and rate of evolution, the origin of character variation and organism-environment complementarity. We spell out the structure, core assumptions and novel predictions of the EES, and show how it can be deployed to stimulate and advance research in those fields that study or use evolutionary biology.",
    url = "https://doi.org/10.1098/rspb.2015.1019",
    doi = "10.1098/rspb.2015.1019",
    openalex = "W2103794982",
    references = "doi101001jama195002910300087029, doi101002jezb21081, doi101017cbo9780511621123, doi101038218525a0, doi10106313050879, doi101086346135, doi101093auk1002507, doi101093oso97801951223430010001, doi101111j155856461982tb05068x, doi101126science1113832, doi101146annureves01110170000245, doi1015159780691209418, doi1015159781400847266, doi1023071367778, doi1023072260026, doi102307jctvjsf433, doi102307jctvx5wbbh, doi105860choice364478, doi105860choice396411, doi105962bhltitle27468, doi107208chicago97802263088830010001, doi107551mitpress97802625136780010001, openalexw2080618944, openalexw227636185"
}

Dating the tree of life is a core endeavor in evolutionary biology. Rates of evolution are fundamental to nearly every evolutionary model and process. Rates need dates. There is much debate on the most appropriate and reasonable ways in which to date the tree of life, and recent work has highlighted some confusions and complexities that can be avoided. Whether phylogenetic trees are dated after they have been established, or as part of the process of tree finding, practitioners need to know which calibrations to use. We emphasize the importance of identifying crown (not stem) fossils, levels of confidence in their attribution to the crown, current chronostratigraphic precision, the primacy of the host geological formation and asymmetric confidence intervals. Here we present calibrations for 88 key nodes across the phylogeny of animals, ranging from the root of Metazoa to the last common ancestor of Homo sapiens. Close attention to detail is constantly required: for example, the classic bird-mammal date (base of crown Amniota) has often been given as 310-315 Ma; the 2014 international time scale indicates a minimum age of 318 Ma.

@article{doi1026879424,
    author = "Benton, Michael J. and Donoghue, PCJ and Vinther, Jakob and Asher, RJ and Friedman, Mary M. and Near, Thomas J.",
    title = "Constraints on the timescale of animal evolutionary history",
    year = "2015",
    journal = "Palaeontologia Electronica",
    abstract = "Dating the tree of life is a core endeavor in evolutionary biology. Rates of evolution are fundamental to nearly every evolutionary model and process. Rates need dates. There is much debate on the most appropriate and reasonable ways in which to date the tree of life, and recent work has highlighted some confusions and complexities that can be avoided. Whether phylogenetic trees are dated after they have been established, or as part of the process of tree finding, practitioners need to know which calibrations to use. We emphasize the importance of identifying crown (not stem) fossils, levels of confidence in their attribution to the crown, current chronostratigraphic precision, the primacy of the host geological formation and asymmetric confidence intervals. Here we present calibrations for 88 key nodes across the phylogeny of animals, ranging from the root of Metazoa to the last common ancestor of Homo sapiens. Close attention to detail is constantly required: for example, the classic bird-mammal date (base of crown Amniota) has often been given as 310-315 Ma; the 2014 international time scale indicates a minimum age of 318 Ma.",
    url = "https://doi.org/10.26879/424",
    doi = "10.26879/424",
    openalex = "W1962669040",
    references = "doi10100703064746897, doi101007978146139246016, doi101007bf02101694, doi101016b9780126709506500187, doi101016b9780444594259000196, doi101016b9780444594259000202, doi101016b9780444594259000214, doi101016b9780444594259000238, doi101016b9780444594259000287, doi101016jpalaeo200703046, doi101016jpalwor200911007, doi101016s0301926899000777, doi101016s096098220900431x, doi101017s0006323199005472, doi101017s0016756811000720, doi101017s1464793102006103, doi101017s1464793105006779, doi101017s1477201906002008, doi101023a1018471324332, doi101038377720a0, doi101038nature01264, doi101038nature03150, doi101038nature05634, doi101038nature06134, doi101038nature06277, doi101038nature06614, doi101038nature07855, doi101038nature08322, doi101038nature09810, doi101038nature09864, doi101038nature10291, doi101038nature13718, doi101073pnas1010350107, doi101073pnas1110395108, doi101073pnas9794469, doi10108002724634198110011886, doi10108002724634199710010948, doi10108002724634199810011114, doi10108010635150590950326, doi10108010635150600755396, doi10108010635150701397635, doi101098rstb19790006, doi101098rstb19990489, doi101111j109636421995tb00932x, doi101111j10963642200600293x, doi101111j1469185x1999tb00046x, doi101111j1469185x200900094x, doi101111j1469185x201200220x, doi101111j14754983201001019x, doi101111j14754983201201165x, doi101111pala12125, doi101111zoj12111, doi101126science1157704, doi101139e87124, doi1011861471214813208, doi1012060003009020062970001tatol20co2, doi1012066231, doi101242dev066712, doi101371journalpone0009586, doi101643004585112002002053220co2, doi1016660022336020030770822mbatho20co2, doi102307jctt1xp3v3r, doi105252g2010n4a1, doi105281zenodo18028696, doi105860choice320949, doi105860choice355657, doi105860choice405235, doi105860choice432801, doi105860choice503272, doi107312kiel11918, gardiner1989interrelationships, openalexw2898156694, openalexw78894702"
}

Multigene and genomic data sets have become commonplace in the field of phylogenetics, but many existing tools are not designed for such data sets, which often makes the analysis time-consuming and tedious. Here, we present PhyloSuite, a (cross-platform, open-source, stand-alone Python graphical user interface) user-friendly workflow desktop platform dedicated to streamlining molecular sequence data management and evolutionary phylogenetics studies. It uses a plugin-based system that integrates several phylogenetic and bioinformatic tools, thereby streamlining the entire procedure, from data acquisition to phylogenetic tree annotation (in combination with iTOL). It has the following features: (a) point-and-click and drag-and-drop graphical user interface; (b) a workplace to manage and organize molecular sequence data and results of analyses; (c) GenBank entry extraction and comparative statistics; and (d) a phylogenetic workflow with batch processing capability, comprising sequence alignment (mafft and macse), alignment optimization (trimAl, HmmCleaner and Gblocks), data set concatenation, best partitioning scheme and best evolutionary model selection (PartitionFinder and modelfinder), and phylogenetic inference (MrBayes and iq-tree). PhyloSuite is designed for both beginners and experienced researchers, allowing the former to quick-start their way into phylogenetic analysis, and the latter to conduct, store and manage their work in a streamlined way, and spend more time investigating scientific questions instead of wasting it on transferring files from one software program to another.

@article{doi1011111755099813096,
    author = "Zhang, Dong and Gao, Fangluan and Jakovlić, Ivan and Zou, Hong and Zhang, Jin and Li, Wen X. and Wang, Gui T.",
    title = "PhyloSuite: An integrated and scalable desktop platform for streamlined molecular sequence data management and evolutionary phylogenetics studies",
    year = "2019",
    journal = "Molecular Ecology Resources",
    abstract = "Multigene and genomic data sets have become commonplace in the field of phylogenetics, but many existing tools are not designed for such data sets, which often makes the analysis time-consuming and tedious. Here, we present PhyloSuite, a (cross-platform, open-source, stand-alone Python graphical user interface) user-friendly workflow desktop platform dedicated to streamlining molecular sequence data management and evolutionary phylogenetics studies. It uses a plugin-based system that integrates several phylogenetic and bioinformatic tools, thereby streamlining the entire procedure, from data acquisition to phylogenetic tree annotation (in combination with iTOL). It has the following features: (a) point-and-click and drag-and-drop graphical user interface; (b) a workplace to manage and organize molecular sequence data and results of analyses; (c) GenBank entry extraction and comparative statistics; and (d) a phylogenetic workflow with batch processing capability, comprising sequence alignment (mafft and macse), alignment optimization (trimAl, HmmCleaner and Gblocks), data set concatenation, best partitioning scheme and best evolutionary model selection (PartitionFinder and modelfinder), and phylogenetic inference (MrBayes and iq-tree). PhyloSuite is designed for both beginners and experienced researchers, allowing the former to quick-start their way into phylogenetic analysis, and the latter to conduct, store and manage their work in a streamlined way, and spend more time investigating scientific questions instead of wasting it on transferring files from one software program to another.",
    url = "https://doi.org/10.1111/1755-0998.13096",
    doi = "10.1111/1755-0998.13096",
    openalex = "W2979811825",
    references = "doi101016jtree200901009, doi101038nmeth4285, doi10108010635150701472164, doi101093bioinformaticsbtp348, doi101093bioinformaticsbts199, doi101093molbevmst010, doi101093sysbiosys029"
}

Elaboration of Bayesian phylogenetic inference methods has continued at pace in recent years with major new advances in nearly all aspects of the joint modelling of evolutionary data. It is increasingly appreciated that some evolutionary questions can only be adequately answered by combining evidence from multiple independent sources of data, including genome sequences, sampling dates, phenotypic data, radiocarbon dates, fossil occurrences, and biogeographic range information among others. Including all relevant data into a single joint model is very challenging both conceptually and computationally. Advanced computational software packages that allow robust development of compatible (sub-)models which can be composed into a full model hierarchy have played a key role in these developments. Developing such software frameworks is increasingly a major scientific activity in its own right, and comes with specific challenges, from practical software design, development and engineering challenges to statistical and conceptual modelling challenges. BEAST 2 is one such computational software platform, and was first announced over 4 years ago. Here we describe a series of major new developments in the BEAST 2 core platform and model hierarchy that have occurred since the first release of the software, culminating in the recent 2.5 release.

@article{doi101371journalpcbi1006650,
    author = "Bouckaert, Remco and Vaughan, Timothy G. and Barido‐Sottani, Joëlle and Duchêne, Sebastián and Fourment, Mathieu and Gavryushkina, Alexandra and Heled, Joseph and Jones, Graham and Kühnert, Denise and Maio, Nicola De and Matschiner, Michael and Mendes, Fábio K. and Müller, Nicola F. and Ogilvie, Huw A. and du Plessis, Louis and Popinga, Alex and Rambaut, Andrew and Rasmussen, David A. and Siveroni, Igor and Suchard, Marc A. and Wu, Chieh‐Hsi and Xie, Dong and Zhang, Chi and Stadler, Tanja and Drummond, Alexei J.",
    title = "BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis",
    year = "2019",
    journal = "PLoS Computational Biology",
    abstract = "Elaboration of Bayesian phylogenetic inference methods has continued at pace in recent years with major new advances in nearly all aspects of the joint modelling of evolutionary data. It is increasingly appreciated that some evolutionary questions can only be adequately answered by combining evidence from multiple independent sources of data, including genome sequences, sampling dates, phenotypic data, radiocarbon dates, fossil occurrences, and biogeographic range information among others. Including all relevant data into a single joint model is very challenging both conceptually and computationally. Advanced computational software packages that allow robust development of compatible (sub-)models which can be composed into a full model hierarchy have played a key role in these developments. Developing such software frameworks is increasingly a major scientific activity in its own right, and comes with specific challenges, from practical software design, development and engineering challenges to statistical and conceptual modelling challenges. BEAST 2 is one such computational software platform, and was first announced over 4 years ago. Here we describe a series of major new developments in the BEAST 2 core platform and model hierarchy that have occurred since the first release of the software, culminating in the recent 2.5 release.",
    url = "https://doi.org/10.1371/journal.pcbi.1006650",
    doi = "10.1371/journal.pcbi.1006650",
    openalex = "W2901954177",
    references = "doi101016jtree200901009, doi101038nature10231, doi101038nature13726, doi101073pnas1319091111, doi101073pnas89178322, doi101080106351501753462876, doi101093acprofoso97801985670280010001, doi101093genetics1551431, doi101093molbevmsp274, doi101093sysbiosyq085, doi101093sysbiosyr047, doi101093sysbiosyv080, doi101093vevey016, doi101098rspa19270118, doi101186147121487214, doi101186s1286201708906, doi1012019780429258411, doi101371journalpbio0040088, doi101371journalpcbi1003537"
}

@incollection{doi101007978303065536513,
    author = "Granovitch, Andrei I.",
    title = "Natural Selection, Morphoprocess and a Logical Field of Evolutionary Concepts",
    year = "2021",
    booktitle = "Evolutionary Biology/Evolutionary biology",
    url = "https://doi.org/10.1007/978-3-030-65536-5\_13",
    doi = "10.1007/978-3-030-65536-5\_13",
    openalex = "W3134657069",
    references = "doi101016jbiosystems201406008, doi101016jtree200611004, doi101038nrm2632, doi10106313050879, doi101093genetics16297, doi101093genetics286491, doi101093oso97801951223430010001, doi101098rstb19520012, doi101111j155856461975tb00851x, doi1015159781400820108, openalexw2624262714"
}

@incollection{doi10100797830306553656,
    author = "Ochoa, Carlos",
    title = "The Origins of Theoretical Developmental Genetics: Reinterpreting William Bateson’s Role in the History of Evolutionary Thought",
    year = "2021",
    booktitle = "Evolutionary Biology/Evolutionary biology",
    url = "https://doi.org/10.1007/978-3-030-65536-5\_6",
    doi = "10.1007/978-3-030-65536-5\_6",
    openalex = "W3133716585",
    references = "doi101007978303065536513"
}

@article{doi101016jbiosystems2021104454,
    author = "Igamberdiev, Abir U.",
    title = "The drawbridge of nature: Evolutionary complexification as a generation and novel interpretation of coding systems",
    year = "2021",
    journal = "Biosystems",
    url = "https://doi.org/10.1016/j.biosystems.2021.104454",
    doi = "10.1016/j.biosystems.2021.104454",
    openalex = "W3171803253",
    references = "doi101016jbiosystems2019104063, doi101016jbiosystems2020104279"
}

The Modern Synthesis (or "Neo-Darwinism"), which arose out of the reconciliation of Darwin's theory of natural selection and Mendel's research on genetics, remains the foundation of evolutionary theory. However, since its inception, it has been a lightning rod for criticism, which has ranged from minor quibbles to complete dismissal. Among the most famous of the critics was Stephen Jay Gould, who, in 1980, proclaimed that the Modern Synthesis was "effectively dead." Gould and others claimed that the action of natural selection on random mutations was insufficient on its own to explain patterns of macroevolutionary diversity and divergence, and that new processes were required to explain findings from the fossil record. In 1982, Charlesworth, Lande, and Slatkin published a response to this critique in Evolution, in which they argued that Neo-Darwinism was indeed sufficient to explain macroevolutionary patterns. In this Perspective for the 75th Anniversary of the Society for the Study of Evolution, we review Charlesworth et al. in its historical context and provide modern support for their arguments. We emphasize the importance of microevolutionary processes in the study of macroevolutionary patterns. Ultimately, we conclude that punctuated equilibrium did not represent a major revolution in evolutionary biology - although debate on this point stimulated significant research and furthered the field - and that Neo-Darwinism is alive and well.

@article{doi101111evo14268,
    author = "Hancock, Zachary B. and Lehmberg, Emma S. and Bradburd, Gideon S.",
    title = "Neo‐darwinism still haunts evolutionary theory: A modern perspective on Charlesworth, Lande, and Slatkin (1982)",
    year = "2021",
    journal = "Evolution",
    abstract = {The Modern Synthesis (or "Neo-Darwinism"), which arose out of the reconciliation of Darwin's theory of natural selection and Mendel's research on genetics, remains the foundation of evolutionary theory. However, since its inception, it has been a lightning rod for criticism, which has ranged from minor quibbles to complete dismissal. Among the most famous of the critics was Stephen Jay Gould, who, in 1980, proclaimed that the Modern Synthesis was "effectively dead." Gould and others claimed that the action of natural selection on random mutations was insufficient on its own to explain patterns of macroevolutionary diversity and divergence, and that new processes were required to explain findings from the fossil record. In 1982, Charlesworth, Lande, and Slatkin published a response to this critique in Evolution, in which they argued that Neo-Darwinism was indeed sufficient to explain macroevolutionary patterns. In this Perspective for the 75th Anniversary of the Society for the Study of Evolution, we review Charlesworth et al. in its historical context and provide modern support for their arguments. We emphasize the importance of microevolutionary processes in the study of macroevolutionary patterns. Ultimately, we conclude that punctuated equilibrium did not represent a major revolution in evolutionary biology - although debate on this point stimulated significant research and furthered the field - and that Neo-Darwinism is alive and well.},
    url = "https://doi.org/10.1111/evo.14268",
    doi = "10.1111/evo.14268",
    openalex = "W3163859581",
    references = "doi101016jtree200611004, doi101016jtree200901009, doi101017s0094837300005224, doi101093sysbio463523, doi101111j001438202006tb01143x, doi101111j00221112200400433x, doi101128mmbr0001610, doi101146annureves01110170000245, doi1023071438156, doi1023072485224"
}

@incollection{doi10100797830310478319,
    author = "Granovitch, Andrei I.",
    title = "The Morphoprocess and the Diversity of Evolutionary Mechanisms of Metastable Structures",
    year = "2022",
    booktitle = "Evolutionary Biology/Evolutionary biology",
    url = "https://doi.org/10.1007/978-3-031-04783-1\_9",
    doi = "10.1007/978-3-031-04783-1\_9",
    openalex = "W4285188686",
    references = "doi101007978303065536513"
}

@article{doi101016jbiosystems2022104706,
    author = "Olovnikov, A. M.",
    title = "Eco-crossover, or environmentally regulated crossing-over, and natural selection are two irreplaceable drivers of adaptive evolution: Eco-crossover hypothesis",
    year = "2022",
    journal = "Biosystems",
    url = "https://doi.org/10.1016/j.biosystems.2022.104706",
    doi = "10.1016/j.biosystems.2022.104706",
    openalex = "W4281478058",
    references = "doi101007bf02984069, doi101016jbiosystems201406008, doi101016jmolcel201806034, doi101016jygeno201601008, doi101017s0094837300005224, doi101038227561a0, doi101038366223a0, doi101038s415800200243y, doi101073pnas1508347112, doi101093auk1002507, doi1015252embj2018100836, doi1023071437764"
}

@article{doi101016jbiosystems2022104719,
    author = "Shklovskiy-Kordi, Nikita E. and Matsuno, Koichiro and Marijuán, Pedro C. and Lgamberdiev, Abir U",
    title = "Editorial: Fundamental principles of biological computation: From molecular computing to evolutionary complexity",
    year = "2022",
    journal = "Biosystems",
    url = "https://doi.org/10.1016/j.biosystems.2022.104719",
    doi = "10.1016/j.biosystems.2022.104719",
    openalex = "W4281989749",
    references = "doi101016jbiosystems2022104712"
}

@article{doi101016jbiosystems2022104779,
    author = "Cottam, Ron and Iurato, Giuseppe and Igamberdiev, Abir U.",
    title = "Fundamentals of evolutionary transformations in biological systems",
    year = "2022",
    journal = "Biosystems",
    url = "https://doi.org/10.1016/j.biosystems.2022.104779",
    doi = "10.1016/j.biosystems.2022.104779",
    openalex = "W4295166759",
    references = "doi101016jbiosystems2021104567, doi101016jbiosystems2022104706"
}

Abstract The goal-directedness of biological evolution is realized via the anticipatory achievement of the final state of the system that corresponds to the condition of its perfection in self-maintenance and in adaptability. In the course of individual development, a biological system maximizes its power via synergistic effects and becomes able to perform external work most efficiently. In this state, defined as stasis, robust self-maintaining configurations act as attractors resistant to external and internal perturbations. This corresponds to the local energy–time constraints that most efficiently fit the integral optimization of the whole system. In evolution, major evolutionary transitions that establish new states of stasis are achieved via codepoiesis, a process in which the undecided statements of existing coding systems form the basis for the evolutionary unfolding of the system by assigning new values to them. The genetic fixation of this macroevolutionary process leads to new programmes of individual development representing the process of natural computation. The phenomenon of complexification in evolution represents a metasystem transition that results in maximization of a system’s power and in the ability to increase external work performed by the system.

@article{doi101093biolinneanblac093,
    author = "Igamberdiev, Abir U.",
    title = "Overcoming the limits of natural computation in biological evolution toward the maximization of system efficiency",
    year = "2022",
    journal = "Biological Journal of the Linnean Society",
    abstract = "Abstract The goal-directedness of biological evolution is realized via the anticipatory achievement of the final state of the system that corresponds to the condition of its perfection in self-maintenance and in adaptability. In the course of individual development, a biological system maximizes its power via synergistic effects and becomes able to perform external work most efficiently. In this state, defined as stasis, robust self-maintaining configurations act as attractors resistant to external and internal perturbations. This corresponds to the local energy–time constraints that most efficiently fit the integral optimization of the whole system. In evolution, major evolutionary transitions that establish new states of stasis are achieved via codepoiesis, a process in which the undecided statements of existing coding systems form the basis for the evolutionary unfolding of the system by assigning new values to them. The genetic fixation of this macroevolutionary process leads to new programmes of individual development representing the process of natural computation. The phenomenon of complexification in evolution represents a metasystem transition that results in maximization of a system’s power and in the ability to increase external work performed by the system.",
    url = "https://doi.org/10.1093/biolinnean/blac093",
    doi = "10.1093/biolinnean/blac093",
    openalex = "W4296816592",
    references = "doi1010160022519373901987, doi1010160303264774900318, doi101016jbiosystems201406008, doi101016jbiosystems2022104706, doi101017s0094837300004310, doi101038nrn2787, doi101073pnas86147, doi101086276408, doi1023072103745, doi1023072412825, doi105860choice294505, openalexw1556913189"
}

Pioneer naturalists such as Whewell, Lyell, Humboldt, Darwin and Wallace acknowledged the interactions between ecological and evolutionary forces, as well as the roles of continental movement, mountain formation and climate variations, in shaping biodiversity patterns. Recent developments in computer modelling and paleo‐environmental reconstruction have made it possible for scientists to study in silico how biodiversity emerges from eco‐evolutionary and environmental dynamic processes and their interactions. Simulating emergent biodiversity enables the experimentation of multiple interconnected hypotheses in a largely fragmented scientific landscape, with the final objective of successfully approximating natural mechanisms (i.e. hypothetical spatio–temporally unrestricted generalizations that hold across multiple empirical biodiversity patterns). This new interdisciplinary approach opens unprecedented scientific pathways, facilitating the communication and contemplation of causal implications of complex eco‐evolutionary and environmental interactions. In this review I provide a comprehensive overview of the available population‐based spatially explicit mechanistic eco‐evolutionary models (MEEMs) that rely on paleo‐environmental reconstructions, critically discussing their relevance and limitations for our understanding of biodiversity. To achieve this, I first introduce diverse biodiversity models and contextualize MEEMs. Second, I define MEEMs and synthesize the major insights from studies using MEEMs combined with deep‐time environmental dynamics (> 0.1 Ma). Lastly, I discuss the challenges and perspectives of solving long‐standing biodiversity enigmas by coupling eco‐evolutionary mechanisms with deep‐time environmental dynamics. Studies show that linking dynamic environments and eco‐evolutionary processes is necessary to reproduce multiple large‐scale biodiversity patterns simultaneously. Mechanisms related to adaptations (e.g. niche evolution), dispersal abilities and other eco‐evolutionary interactions (e.g. those resulting in speciation or extinction events) show universal importance, although their signatures across spatial and temporal scales remain largely unknown. Investigations with MEEMS spanning multiple levels of complexity in space and time foster interdisciplinary cooperation across the natural sciences and show promise for solving some of the enigmas in Earth's biodiversity.

@article{doi101111ecog06132,
    author = "Hagen, Oskar",
    title = "Coupling eco‐evolutionary mechanisms with deep‐time environmental dynamics to understand biodiversity patterns",
    year = "2022",
    journal = "Ecography",
    abstract = "Pioneer naturalists such as Whewell, Lyell, Humboldt, Darwin and Wallace acknowledged the interactions between ecological and evolutionary forces, as well as the roles of continental movement, mountain formation and climate variations, in shaping biodiversity patterns. Recent developments in computer modelling and paleo‐environmental reconstruction have made it possible for scientists to study in silico how biodiversity emerges from eco‐evolutionary and environmental dynamic processes and their interactions. Simulating emergent biodiversity enables the experimentation of multiple interconnected hypotheses in a largely fragmented scientific landscape, with the final objective of successfully approximating natural mechanisms (i.e. hypothetical spatio–temporally unrestricted generalizations that hold across multiple empirical biodiversity patterns). This new interdisciplinary approach opens unprecedented scientific pathways, facilitating the communication and contemplation of causal implications of complex eco‐evolutionary and environmental interactions. In this review I provide a comprehensive overview of the available population‐based spatially explicit mechanistic eco‐evolutionary models (MEEMs) that rely on paleo‐environmental reconstructions, critically discussing their relevance and limitations for our understanding of biodiversity. To achieve this, I first introduce diverse biodiversity models and contextualize MEEMs. Second, I define MEEMs and synthesize the major insights from studies using MEEMs combined with deep‐time environmental dynamics (> 0.1 Ma). Lastly, I discuss the challenges and perspectives of solving long‐standing biodiversity enigmas by coupling eco‐evolutionary mechanisms with deep‐time environmental dynamics. Studies show that linking dynamic environments and eco‐evolutionary processes is necessary to reproduce multiple large‐scale biodiversity patterns simultaneously. Mechanisms related to adaptations (e.g. niche evolution), dispersal abilities and other eco‐evolutionary interactions (e.g. those resulting in speciation or extinction events) show universal importance, although their signatures across spatial and temporal scales remain largely unknown. Investigations with MEEMS spanning multiple levels of complexity in space and time foster interdisciplinary cooperation across the natural sciences and show promise for solving some of the enigmas in Earth's biodiversity.",
    url = "https://doi.org/10.1111/ecog.06132",
    doi = "10.1111/ecog.06132",
    openalex = "W4288050970",
    references = "doi101111ecog05778, doi101111evo14407"
}

Successful fundamental theories are built on verifiable principles that include measurable variables. This paper shows that Darwin’s inclusive theory is built on such principles and follows their rocky road into modern operational theories. Besides reproduction, variation, and heredity, Darwin’s conditions of diversification also include the potential for exponential (geometric) population growth and its necessarily limited nature. The Struggle for Existence (Malthus Doctrine), the Principles of Natural Selection, Competitive Exclusion (Rule of Similar Checks), and Divergence are mere deductions from these conditions. The dynamic system theory of robust coexistence, the theory of adaptive dynamics, and the extended theory of evolution all assume Darwin’s inclusive principles as essentials. Incorporating the feedbacks controlling population growth and the tradeoffs between fitness components into the core of evolutionary theory leads to the conclusion that diversification is a fundamental, inherent feature of life and provides laws that support the determination of the expected direction of evolution in any particular case.

@misc{doi1032942osfiouh3jq,
    author = "Pásztor, Líz and Meszéna, Géza",
    title = "Stable laws in a changing world The structure of evolutionary theories over the centuries",
    year = "2022",
    abstract = "Successful fundamental theories are built on verifiable principles that include measurable variables. This paper shows that Darwin’s inclusive theory is built on such principles and follows their rocky road into modern operational theories. Besides reproduction, variation, and heredity, Darwin’s conditions of diversification also include the potential for exponential (geometric) population growth and its necessarily limited nature. The Struggle for Existence (Malthus Doctrine), the Principles of Natural Selection, Competitive Exclusion (Rule of Similar Checks), and Divergence are mere deductions from these conditions. The dynamic system theory of robust coexistence, the theory of adaptive dynamics, and the extended theory of evolution all assume Darwin’s inclusive principles as essentials. Incorporating the feedbacks controlling population growth and the tradeoffs between fitness components into the core of evolutionary theory leads to the conclusion that diversification is a fundamental, inherent feature of life and provides laws that support the determination of the expected direction of evolution in any particular case.",
    url = "https://doi.org/10.32942/osf.io/uh3jq",
    doi = "10.32942/osf.io/uh3jq",
    openalex = "W4297539941",
    references = "doi101007978303122028911"
}

This book is reflecting upon core theories in evolutionary biology in a historical and contemporary context. It uses biological models to do so.

@book{doi1010079783031220289,
    author = "Dickins, Thomas E. and Dickins, Benjamin",
    title = "Evolutionary Biology: Contemporary and Historical Reflections Upon Core Theory",
    year = "2023",
    booktitle = "Evolutionary Biology/Evolutionary biology",
    abstract = "This book is reflecting upon core theories in evolutionary biology in a historical and contemporary context. It uses biological models to do so.",
    url = "https://doi.org/10.1007/978-3-031-22028-9",
    doi = "10.1007/978-3-031-22028-9",
    openalex = "W4360981572",
    references = "doi101007978303122028911"
}

@incollection{doi101007978303122028911,
    author = "Svensson, Erik",
    title = "The Structure of Evolutionary Theory: Beyond Neo-Darwinism, Neo-Lamarckism and Biased Historical Narratives About the Modern Synthesis",
    year = "2023",
    booktitle = "Evolutionary Biology/Evolutionary biology",
    url = "https://doi.org/10.1007/978-3-031-22028-9\_11",
    doi = "10.1007/978-3-031-22028-9\_11",
    openalex = "W4360982005",
    references = "doi101007s1206400000046, doi101016jtree200709008, doi101017s0080456800012163, doi101017s0094837300004310, doi101093genetics16297, doi101093oso97801951223430010001, doi101098rspb19790086, doi101111evo14268, doi1015159781400847266, doi102307jctvjsf433, doi104159harvard9780674865327, doi105962bhltitle27468"
}

@incollection{doi10100797830313030438,
    author = "Gefaell, Juan and Alejandro, Cristián",
    title = "Incommensurability in Evolutionary Biology: The Extended Evolutionary Synthesis Controversy",
    year = "2023",
    booktitle = "Interdisciplinary evolution research",
    url = "https://doi.org/10.1007/978-3-031-30304-3\_8",
    doi = "10.1007/978-3-031-30304-3\_8",
    openalex = "W4380342996",
    references = "doi101007978303122028911"
}

The origin of life remains one of the greatest enigmas in science. The immense leap in complexity between prebiotic soup and cellular life challenges historically "chemistry-forward" and "biology-backwards" approaches. Evolution must have bridged this gap in complexity, so understanding factors that influence evolutionary outcomes is critical for exploring life's emergence. Here, we review insights from ecology and evolution and their application throughout abiogenesis. In particular, we discuss how ecological and evolutionary constraints shape the evolution of biological innovation. We propose an "eco-evolutionary" approach, which is agnostic towards particular chemistries or environments and instead explores the several ways that an evolvable system may emerge and gain complexity.

@article{doi101093evolutqpad195,
    author = "Kalambokidis, Maria and Travisano, Michael",
    title = "The eco-evolutionary origins of life",
    year = "2023",
    journal = "Evolution",
    abstract = {The origin of life remains one of the greatest enigmas in science. The immense leap in complexity between prebiotic soup and cellular life challenges historically "chemistry-forward" and "biology-backwards" approaches. Evolution must have bridged this gap in complexity, so understanding factors that influence evolutionary outcomes is critical for exploring life's emergence. Here, we review insights from ecology and evolution and their application throughout abiogenesis. In particular, we discuss how ecological and evolutionary constraints shape the evolution of biological innovation. We propose an "eco-evolutionary" approach, which is agnostic towards particular chemistries or environments and instead explores the several ways that an evolvable system may emerge and gain complexity.},
    url = "https://doi.org/10.1093/evolut/qpad195",
    doi = "10.1093/evolut/qpad195",
    openalex = "W4388410145",
    references = "doi101007978303122028911"
}

Traditionally defined as the science of the living, or as the field that beyond anatomical structure and bodily form studies functional organization and behaviour, physiology has long been excluded from evolutionary research. The main reason for this exclusion is that physiology has a presential and futuristic outlook on life, while evolutionary theory is traditionally defined as the study of natural history. In this paper, I re-evaluate these classic science divisions and situate physiology within the history of the evolutionary sciences, as well as within debates on the Extended Evolutionary Synthesis and the need for a Third Way of Evolution. I then briefly point out how evolutionary physiology in particular contributes to research on function, causation, teleonomy, agency and cognition.

@article{doi101113jp284410,
    author = "Gontier, Nathalie",
    title = "Situating physiology within evolutionary theory",
    year = "2023",
    journal = "The Journal of Physiology",
    abstract = "Traditionally defined as the science of the living, or as the field that beyond anatomical structure and bodily form studies functional organization and behaviour, physiology has long been excluded from evolutionary research. The main reason for this exclusion is that physiology has a presential and futuristic outlook on life, while evolutionary theory is traditionally defined as the study of natural history. In this paper, I re-evaluate these classic science divisions and situate physiology within the history of the evolutionary sciences, as well as within debates on the Extended Evolutionary Synthesis and the need for a Third Way of Evolution. I then briefly point out how evolutionary physiology in particular contributes to research on function, causation, teleonomy, agency and cognition.",
    url = "https://doi.org/10.1113/jp284410",
    doi = "10.1113/jp284410",
    openalex = "W4387050144",
    references = "doi101093biolinneanblac093"
}

This essay attempts to combine some recent theoretical results in (bio)semiotics on arbitrariness, semiotic fitting, umwelt, choice, and extended theory of evolution into a more coherent whole. The proposed model describes a living being through its subjectivity and the ability to create meaning, which are often overlooked in models based on replicability. The concept of the umwelt is divided into two – the synchronic umwelt and the distributed or diachronic umwelt. For the latter, a new term ‘umweb’ is introduced. A mechanism of evolution is described in which arbitrary relating followed by semiotic fitting is somewhat analogous to the neo-Darwinian mechanism of random mutations followed by natural selection. The paper proceeds to discuss the alternativity and coexistence of these two radically different ways of evolution and learning.

@article{doi1012697sss202351108,
    author = "Kull, Kalevi",
    title = "Further considerations on semiosis in evolution: Arbitrarity plus semiotic fitting, and/or mutability plus natural selection",
    year = "2023",
    journal = "Sign Systems Studies",
    abstract = "This essay attempts to combine some recent theoretical results in (bio)semiotics on arbitrariness, semiotic fitting, umwelt, choice, and extended theory of evolution into a more coherent whole. The proposed model describes a living being through its subjectivity and the ability to create meaning, which are often overlooked in models based on replicability. The concept of the umwelt is divided into two – the synchronic umwelt and the distributed or diachronic umwelt. For the latter, a new term ‘umweb’ is introduced. A mechanism of evolution is described in which arbitrary relating followed by semiotic fitting is somewhat analogous to the neo-Darwinian mechanism of random mutations followed by natural selection. The paper proceeds to discuss the alternativity and coexistence of these two radically different ways of evolution and learning.",
    url = "https://doi.org/10.12697/sss.2023.51.1.08",
    doi = "10.12697/sss.2023.51.1.08",
    openalex = "W4378233472",
    references = "doi101007978303122028911"
}

@article{doi101016jbiosystems2024105383,
    author = "Melkikh, Alexey V.",
    title = "The problem of evolutionary directionality 50 years following the works of Sergei Meyen",
    year = "2024",
    journal = "Biosystems",
    url = "https://doi.org/10.1016/j.biosystems.2024.105383",
    doi = "10.1016/j.biosystems.2024.105383",
    openalex = "W4405531738",
    references = "doi101007bf02983073, doi101016jbiosystems201406008, doi101016jplrev201307001, doi101038s41467018054455, doi101038s41586021042696, doi101073pnas0500398102, doi101073pnas1120658109, doi101096fj201500083, doi101126science13434891501, doi101186gb20131410r115, openalexw4207021716"
}

If there is a questionable element in the theory of evolution, it is likely the randomness of mutations, which is seen as the primary source of evolutionary change. The idea that errors in DNA sequences are the source of species change does not seem acceptable to many scientists and philosophers. According to them, adaptive evolution, which suggests that some mutations occur purposefully, is possible. Both views seem scientifically supportable. However, science typically excludes purposes, especially due to their implications of the supernatural. So, the philosophical problem here concerns which metaphysical framework would better explain a natural world in which purposes are at work, assuming that adaptive evolution is real. In this article, I propose panpsychism as a candidate for such an explanation. Although panpsychism is a well-known metaphysical view, it has rarely been associated with evolution. Panpsychism simply states that all actual natural entities possess some form of mentality that is intrinsic to matter. Mentality must be present at the most fundamental level of existence to manifest in any higher-level form. This idea of panpsychism that mentality develops gradually is already compatible with the traditional view of evolution that species change slowly and incrementally by small steps. Nevertheless the adaptive evolution hypothesis demands more. The idea that organisms can alter their own DNA in response to environmental conditions implies that this process occurs voluntarily in a controlled manner. However, adaptation does not always occur voluntarily, and such an understanding becomes difficult to accept as it attributes higher-level cognitive functions, such as choosing, will, and decision-making, to cells and molecules. Thus, a more naturalistic approach is needed. Panpsychism can take many forms such as dualistic panpsychism or idealistic panpsychism. I suggest dual-aspect panpsychism as a wholly naturalistic version of this concept. Accordingly, mentality and physicality are two aspects of the same thing or stuff. Just as there is no mental causation from the mental to the physical, there is no physical causation from the physical to the mental. There are processes or events that manifest as physical happenings when observed from the outside and as mental happenings when experienced from the inside. Along with an interpretation of dual-aspect panpsychism that is compatible with physicalism, when we accept that the most plausible way to extend mentality to all actual entities is to think of it as intentionality, it may become even more easier to situate adaptive evolution within a naturalistic framework. Non-random mutations do not occur as mental acts of choice but arise from the organism’s behavior being about or directed towards selective environmental conditions for the purpose of ensuring survival. The article consists of two main parts. The first part seeks to establish the possibility that some mutations may not be random on a scientific-philosophical basis. The second part aims to show the compatibility of this possibility with dual-aspect panpsychism. As a result, it is hoped that an acceptable interpretation of evolutionary theory, combined with a naturalistic interpretation of panpsychism, will result in a fruitful synthesis that explains the seemingly purposeful actions of cells and organisms.

@article{doi1014395hid1521378,
    author = "ONUR, Ferhat",
    title = "A Panpsychist Interpretation of Evolutionary Theory",
    year = "2024",
    journal = "Hitit İlahiyat Dergisi",
    abstract = "If there is a questionable element in the theory of evolution, it is likely the randomness of mutations, which is seen as the primary source of evolutionary change. The idea that errors in DNA sequences are the source of species change does not seem acceptable to many scientists and philosophers. According to them, adaptive evolution, which suggests that some mutations occur purposefully, is possible. Both views seem scientifically supportable. However, science typically excludes purposes, especially due to their implications of the supernatural. So, the philosophical problem here concerns which metaphysical framework would better explain a natural world in which purposes are at work, assuming that adaptive evolution is real. In this article, I propose panpsychism as a candidate for such an explanation. Although panpsychism is a well-known metaphysical view, it has rarely been associated with evolution. Panpsychism simply states that all actual natural entities possess some form of mentality that is intrinsic to matter. Mentality must be present at the most fundamental level of existence to manifest in any higher-level form. This idea of panpsychism that mentality develops gradually is already compatible with the traditional view of evolution that species change slowly and incrementally by small steps. Nevertheless the adaptive evolution hypothesis demands more. The idea that organisms can alter their own DNA in response to environmental conditions implies that this process occurs voluntarily in a controlled manner. However, adaptation does not always occur voluntarily, and such an understanding becomes difficult to accept as it attributes higher-level cognitive functions, such as choosing, will, and decision-making, to cells and molecules. Thus, a more naturalistic approach is needed. Panpsychism can take many forms such as dualistic panpsychism or idealistic panpsychism. I suggest dual-aspect panpsychism as a wholly naturalistic version of this concept. Accordingly, mentality and physicality are two aspects of the same thing or stuff. Just as there is no mental causation from the mental to the physical, there is no physical causation from the physical to the mental. There are processes or events that manifest as physical happenings when observed from the outside and as mental happenings when experienced from the inside. Along with an interpretation of dual-aspect panpsychism that is compatible with physicalism, when we accept that the most plausible way to extend mentality to all actual entities is to think of it as intentionality, it may become even more easier to situate adaptive evolution within a naturalistic framework. Non-random mutations do not occur as mental acts of choice but arise from the organism’s behavior being about or directed towards selective environmental conditions for the purpose of ensuring survival. The article consists of two main parts. The first part seeks to establish the possibility that some mutations may not be random on a scientific-philosophical basis. The second part aims to show the compatibility of this possibility with dual-aspect panpsychism. As a result, it is hoped that an acceptable interpretation of evolutionary theory, combined with a naturalistic interpretation of panpsychism, will result in a fruitful synthesis that explains the seemingly purposeful actions of cells and organisms.",
    url = "https://doi.org/10.14395/hid.1521378",
    doi = "10.14395/hid.1521378",
    openalex = "W4405793730",
    references = "doi101007978303122028911"
}

Evolutionary biology was previously considered a historical science with predictions about evolutionary trajectories believed to be near impossible. The development of high throughput sequencing and data analysis technologies has challenged this belief, and provided an abundance of data that yields novel insights into evolutionary processes. Evolutionary predictions are now increasingly being used to develop fundamental knowledge of evolving systems and/or to demonstrate evolutionary control. Here we investigate the factors that make evolutionary repeatability more or less likely to increase the accuracy of evolutionary predictions. We identify outstanding questions and provide a potential starting point to determine how evolutionary repeatability is affected by genetic relatedness.

@article{doi103389fevo20241335452,
    author = "Pearless, Stella M. and Freed, Nikki E.",
    title = "Unravelling the factors of evolutionary repeatability: insights and perspectives on predictability in evolutionary biology",
    year = "2024",
    journal = "Frontiers in Ecology and Evolution",
    abstract = "Evolutionary biology was previously considered a historical science with predictions about evolutionary trajectories believed to be near impossible. The development of high throughput sequencing and data analysis technologies has challenged this belief, and provided an abundance of data that yields novel insights into evolutionary processes. Evolutionary predictions are now increasingly being used to develop fundamental knowledge of evolving systems and/or to demonstrate evolutionary control. Here we investigate the factors that make evolutionary repeatability more or less likely to increase the accuracy of evolutionary predictions. We identify outstanding questions and provide a potential starting point to determine how evolutionary repeatability is affected by genetic relatedness.",
    url = "https://doi.org/10.3389/fevo.2024.1335452",
    doi = "10.3389/fevo.2024.1335452",
    openalex = "W4395036902",
    references = "doi101038nature04742, doi101038nrg2626, doi101038nrmicro3380, doi101093genetics14841667, doi101093oso97801985464120010001, doi101111evo14268, doi101111j1469185x201100216x, doi101126science959840, doi105860choice273873, doi105962bhltitle68064, doi107312simp92414"
}

Efim Liberman (1925-2011) introduced in 1972 the idea of natural computation realized internally by living systems. He considered the physical principles employed by living systems as essential constraints that limit the computational process occurring in the course of adaptation, morphogenesis, and neural activity. The most general limits determined by the physical fundamental constants are universal for all nature. However, the more specific constraints are intrinsic to each biological system and can be overcome in the course of the evolutionary process. We discuss the roles of biological macromolecules, particularly the cytoskeleton, in shaping the actualization patterns formed in the internal measurement process occurring in living systems. Cytoskeletal rearrangements determine cellular, morphogenetic, and perceptive transformations in living systems and participate in the combinatorial genetic events that lead to evolutionary transformations. The operation of neurons is based on the transmission of signals via the cytoskeleton, where the digital output is generated that can be decoded through a reflexive action of the perceiving agent. It is concluded that the principles of natural computation formulated by Liberman represent the most fundamental feature of living beings and form the basis for the general theory of biological systems, with essential consequences for understanding metabolic closure, morphogenesis, evolution, and consciousness.

@article{doi101016jbiosystems2025105451,
    author = "Igamberdiev, Abir U. and Shklovskiy-Kordi, Nikita E.",
    title = "Physical limits of natural computation as the biological constraints of morphogenesis, evolution, and consciousness: On the 100th anniversary of Efim Liberman (1925–2011)",
    year = "2025",
    journal = "Biosystems",
    abstract = "Efim Liberman (1925-2011) introduced in 1972 the idea of natural computation realized internally by living systems. He considered the physical principles employed by living systems as essential constraints that limit the computational process occurring in the course of adaptation, morphogenesis, and neural activity. The most general limits determined by the physical fundamental constants are universal for all nature. However, the more specific constraints are intrinsic to each biological system and can be overcome in the course of the evolutionary process. We discuss the roles of biological macromolecules, particularly the cytoskeleton, in shaping the actualization patterns formed in the internal measurement process occurring in living systems. Cytoskeletal rearrangements determine cellular, morphogenetic, and perceptive transformations in living systems and participate in the combinatorial genetic events that lead to evolutionary transformations. The operation of neurons is based on the transmission of signals via the cytoskeleton, where the digital output is generated that can be decoded through a reflexive action of the perceiving agent. It is concluded that the principles of natural computation formulated by Liberman represent the most fundamental feature of living beings and form the basis for the general theory of biological systems, with essential consequences for understanding metabolic closure, morphogenesis, evolution, and consciousness.",
    url = "https://doi.org/10.1016/j.biosystems.2025.105451",
    doi = "10.1016/j.biosystems.2025.105451",
    openalex = "W4408252251",
    references = "doi101016jbiosystems2022104706, doi101093biolinneanblac093, doi101093biolinneanblad037"
}

This review explores agency, behavior intrinsic to an organism and initiated by it, as it relates to the development of multicellular organisms and its evolution. We ask how agential behaviors contribute to and change concomitantly with evolutionary transitions from unicellularity to multicellularity, including evolution of animals from their closest unicellular antecedents. We consider the relation of organizational properties to the agency of multicellular organisms and conclude, surprisingly, that it is not as strict as it is for individual cells. The main reasons are previously unacknowledged morphogenetic inherencies of multicellular matter and the capacity of development to amplify and partition functionalities of constituent cells. These modalities generate novel phenotypic enablements that enhance the scope of agential behavior. We discuss experimental approaches to distinguish between agency and evolved, stereotypical behaviors of organisms, including purposeful actions. We argue that evolved complexities of animal development make it unsuitable for exploring single-cell-to-multicellular transformations in agency experimentally. We focus our attention instead on agency in the life cycles of social bacteria and amoebae, and in the transitions between multicellular and unicellular states in cancer. Finally, we discuss mathematical representations of incompletely specified dynamical systems and how they may be used to characterize biological autonomy and agency.

@article{doi101086735964,
    author = "Newman, Stuart A. and Benítez, Mariana and Bhat, Ramray and Glimm, Tilmann and Kumar, K. Vijay and Nanjundiah, Vidyanand and Nicholson, Daniel J. and Sarkar, Sahotra",
    title = "Agency in the Evolutionary Transition to Multicellularity",
    year = "2025",
    journal = "The Quarterly Review of Biology",
    abstract = "This review explores agency, behavior intrinsic to an organism and initiated by it, as it relates to the development of multicellular organisms and its evolution. We ask how agential behaviors contribute to and change concomitantly with evolutionary transitions from unicellularity to multicellularity, including evolution of animals from their closest unicellular antecedents. We consider the relation of organizational properties to the agency of multicellular organisms and conclude, surprisingly, that it is not as strict as it is for individual cells. The main reasons are previously unacknowledged morphogenetic inherencies of multicellular matter and the capacity of development to amplify and partition functionalities of constituent cells. These modalities generate novel phenotypic enablements that enhance the scope of agential behavior. We discuss experimental approaches to distinguish between agency and evolved, stereotypical behaviors of organisms, including purposeful actions. We argue that evolved complexities of animal development make it unsuitable for exploring single-cell-to-multicellular transformations in agency experimentally. We focus our attention instead on agency in the life cycles of social bacteria and amoebae, and in the transitions between multicellular and unicellular states in cancer. Finally, we discuss mathematical representations of incompletely specified dynamical systems and how they may be used to characterize biological autonomy and agency.",
    url = "https://doi.org/10.1086/735964",
    doi = "10.1086/735964",
    openalex = "W4410763737",
    references = "doi101007s13752024004717, doi1010179781108616751"
}

@article{doi101093evolutqpaf036,
    author = "Bailey, Nick",
    title = "Steps toward a unified “evolutionary genomics”",
    year = "2025",
    journal = "Evolution",
    url = "https://doi.org/10.1093/evolut/qpaf036",
    doi = "10.1093/evolut/qpaf036",
    openalex = "W4407796936",
    references = "doi101007978303122028911"
}