Adaptive radiation

@misc{walls1942the4,
    author = "Walls, G. L",
    title = "The Vertebrate Eye and its Adaptive Radiation",
    year = "1942",
    howpublished = "Bloomfield Hills, Michigan, The Cranbrook Institute of Science",
    note = "talkorigins\_source = {true}; raw\_reference = {Walls, G. L., 1942, The Vertebrate Eye and its Adaptive Radiation: Bloomfield Hills, Michigan, The Cranbrook Institute of Science.}"
}

This book is the nineteenth bulletin of the Cranbrook Institute of Science, a massive tome with illustrations galore. The material deals with the various phases of the vertebrate eye. The first part is labeled "basic." It treats of light and its properties with especial reference to perception by an eye. The eye itself, the human eye, is then discussed and dissected from all points, starting with embryology, passing through the gross and microscopic anatomy, and finishing with the physiology of vision. This part is well written in plain language. The second part is the ecologic; in this are discussed the necessary adaptations that the visual apparatus has undergone and is still undergoing so that the parent organism may survive under various conditions. To the clinical ophthalmologist, much of this section will be entirely new and he will be surprised how much of this applies to his daily routine. The third

@article{doi101001jama194302840160064031,
    author = "WALLS, Gordon Lynn",
    title = "The Vertebrate Eye and Its Adaptive Radiation",
    year = "1943",
    journal = "Journal of the American Medical Association",
    abstract = {This book is the nineteenth bulletin of the Cranbrook Institute of Science, a massive tome with illustrations galore. The material deals with the various phases of the vertebrate eye. The first part is labeled "basic." It treats of light and its properties with especial reference to perception by an eye. The eye itself, the human eye, is then discussed and dissected from all points, starting with embryology, passing through the gross and microscopic anatomy, and finishing with the physiology of vision. This part is well written in plain language. The second part is the ecologic; in this are discussed the necessary adaptations that the visual apparatus has undergone and is still undergoing so that the parent organism may survive under various conditions. To the clinical ophthalmologist, much of this section will be entirely new and he will be surprised how much of this applies to his daily routine. The third},
    url = "https://doi.org/10.1001/jama.1943.02840160064031",
    doi = "10.1001/jama.1943.02840160064031",
    openalex = "W2024935827"
}

@article{doi1023071437897,
    author = "Merriman, Daniel and Walls, Gordon L.",
    title = "The Vertebrate Eye and Its Adaptive Radiation",
    year = "1943",
    journal = "Copeia",
    url = "https://doi.org/10.2307/1437897",
    doi = "10.2307/1437897",
    openalex = "W2318517747"
}

@inproceedings{cole1958sketches2,
    author = "Cole, L. C",
    title = "Sketches of general and comparative demography",
    year = "1958",
    booktitle = "Cold Spring Harbor Symposium on Quantitative Biology, v. 22, p. 1-15",
    note = "talkorigins\_source = {true}; raw\_reference = {Cole, L. C., 1958, Sketches of general and comparative demography: Cold Spring Harbor Symposium on Quantitative Biology, v. 22, p. 1-15.}"
}

@book{bowman1961morphological1,
    author = "Bowman, R. L",
    title = "Morphological differentiation and adaptation in the Galpagos finches",
    year = "1961",
    publisher = "University of California Publications in Zoology, v. 58, p. 326 pp.; University of California Press, Berkeley",
    note = "talkorigins\_source = {true}; raw\_reference = {Bowman, R. L., 1961, Morphological differentiation and adaptation in the Galpagos finches: University of California Publications in Zoology, v. 58, p. 326 pp.; University of California Press, Berkeley.}"
}

The right tibia of an ornithopod dinosaur has been found in supposed Willow Creek beds in the Two Medicine valley southeast of Browning, Montana. This is the first report of dinosaur bones from the formation on the east side of the Alberta syncline. The specimen is referred to Thescelosaurus? sp., but there is some suggestion of the earlier genus Camptosaurus.

@article{russell1968a,
    author = "Russell, Loris S.",
    title = "A dinosaur bone from Willow Creek beds in Montana",
    year = "1968",
    journal = "Canadian Journal of Earth Sciences",
    abstract = "The right tibia of an ornithopod dinosaur has been found in supposed Willow Creek beds in the Two Medicine valley southeast of Browning, Montana. This is the first report of dinosaur bones from the formation on the east side of the Alberta syncline. The specimen is referred to Thescelosaurus? sp., but there is some suggestion of the earlier genus Camptosaurus.",
    url = "https://doi.org/10.1139/e68-034",
    doi = "10.1139/e68-034",
    number = "2",
    pages = "327-329",
    volume = "5"
}

@article{brazzell1981comparative,
    author = "Brazzell, Jan F. and Gillespie, Mary K.",
    title = "Comparative Demography",
    year = "1981",
    journal = "Comparative Sociology",
    url = "https://doi.org/10.1163/156854281x00091",
    doi = "10.1163/156854281x00091",
    number = "3",
    openalex = "W4205299391",
    pages = "141-168",
    volume = "22"
}

@incollection{brazzell1982comparative,
    author = "Brazzell, Jan F. and Gillespie, Mary K.",
    title = "Comparative Demography",
    year = "1982",
    booktitle = "Comparative Sociological Research in the 1960s and 1970s",
    url = "https://doi.org/10.1163/9789004473942\_010",
    doi = "10.1163/9789004473942\_010",
    openalex = "W4298855657",
    pages = "141-168"
}

@incollection{ricklefs1983comparative,
    author = "Ricklefs, Robert E.",
    title = "Comparative Avian Demography",
    year = "1983",
    booktitle = "Current Ornithology",
    url = "https://doi.org/10.1007/978-1-4615-6781-3\_1",
    doi = "10.1007/978-1-4615-6781-3\_1",
    openalex = "W6573412",
    pages = "1-32",
    references = "doi1010160022519366901846, doi101086282461, doi101086282697, doi101086409052, doi101111j1474919x1947tb04155x, doi1015159781400881376, doi1023072828, doi1023072874"
}

Dinosaur extinction in Montana, Alberta, and Wyoming was a gradual process that began 7 million years before the end of the Cretaceous and accelerated rapidly in the final 0.3 million years of the Cretaceous, during the interval of apparent competition from rapidly evolving immigrating ungulates. This interval involves rapid reduction in both diversity and population density of dinosaurs. The last dinosaurs known are from a channel that contains teeth of Mantuan mammals, seven species of dinosaurs, and Paleocene pollen. The top of this channel is 1.3 meters above the likely position of the iridium anomaly, the Cretaceous/Tertiary boundary.

@article{sloan1986gradual,
    author = "Sloan, Robert E. and Rigby, J. Keith and Van Valen, Leigh M. and Gabriel, Diane",
    title = "Gradual Dinosaur Extinction and Simultaneous Ungulate Radiation in the Hell Creek Formation",
    year = "1986",
    journal = "Science",
    abstract = "Dinosaur extinction in Montana, Alberta, and Wyoming was a gradual process that began 7 million years before the end of the Cretaceous and accelerated rapidly in the final 0.3 million years of the Cretaceous, during the interval of apparent competition from rapidly evolving immigrating ungulates. This interval involves rapid reduction in both diversity and population density of dinosaurs. The last dinosaurs known are from a channel that contains teeth of Mantuan mammals, seven species of dinosaurs, and Paleocene pollen. The top of this channel is 1.3 meters above the likely position of the iridium anomaly, the Cretaceous/Tertiary boundary.",
    url = "https://doi.org/10.1126/science.232.4750.629",
    doi = "10.1126/science.232.4750.629",
    number = "4750",
    pages = "629-633",
    volume = "232"
}

@misc{sloan1986gradual3,
    author = "Sloan, R. E. et al",
    title = "Gradual dinosaur extinction and simultaneous ungulate radiation in the Hell Creek Formation",
    year = "1986",
    howpublished = "Science, v. 232, p. 629-633",
    note = "talkorigins\_source = {true}; raw\_reference = {Sloan, R. E. et al., 1986, Gradual dinosaur extinction and simultaneous ungulate radiation in the Hell Creek Formation: Science, v. 232, p. 629-633.}"
}

Are measurements of quantitative genetic variation useful for predicting long-term adaptive evolution? To answer this question, I focus on g max, the multivariate direction of greatest additive genetic variance within populations. Original data on threespine sticklebacks, together with published genetic measurements from other vertebrates, show that morphological differentiation between species has been biased in the direction of g max for at least four million years, despite evidence that natural selection is the cause of differentiation. This bias toward the direction of evolution tends to decay with time. Rate of morphological divergence between species is inversely proportional to θ, the angle between the direction of divergence and the direction of greatest genetic variation. The direction of greatest phenotypic variance is not identical with g max, but for these data is nearly as successful at predicting the direction of species divergence. I interpret the findings to mean that genetic variances and covariances constrain adaptive change in quantitative traits for reasonably long spans of time. An alternative hypothesis, however, cannot be ruled out: that morphological differentiation is biased in the direction g max because divergence and g max are both shaped by the same natural selection pressures. Either way, the results reveal that adaptive differentiation occurs principally along "genetic lines of least resistance."

@article{doi101111j155856461996tb03563x,
    author = "Schluter, Dolph",
    title = "ADAPTIVE RADIATION ALONG GENETIC LINES OF LEAST RESISTANCE",
    year = "1996",
    journal = "Evolution",
    abstract = {Are measurements of quantitative genetic variation useful for predicting long-term adaptive evolution? To answer this question, I focus on g max, the multivariate direction of greatest additive genetic variance within populations. Original data on threespine sticklebacks, together with published genetic measurements from other vertebrates, show that morphological differentiation between species has been biased in the direction of g max for at least four million years, despite evidence that natural selection is the cause of differentiation. This bias toward the direction of evolution tends to decay with time. Rate of morphological divergence between species is inversely proportional to θ, the angle between the direction of divergence and the direction of greatest genetic variation. The direction of greatest phenotypic variance is not identical with g max, but for these data is nearly as successful at predicting the direction of species divergence. I interpret the findings to mean that genetic variances and covariances constrain adaptive change in quantitative traits for reasonably long spans of time. An alternative hypothesis, however, cannot be ruled out: that morphological differentiation is biased in the direction g max because divergence and g max are both shaped by the same natural selection pressures. Either way, the results reveal that adaptive differentiation occurs principally along "genetic lines of least resistance."},
    url = "https://doi.org/10.1111/j.1558-5646.1996.tb03563.x",
    doi = "10.1111/j.1558-5646.1996.tb03563.x",
    openalex = "W1963703713",
    references = "doi1010160169534787900280, doi101086285404, doi1023074785"
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Adaptive radiation therapy is a closed-loop radiation treatment process where the treatment plan can be modified using a systematic feedback of measurements. Adaptive radiation therapy intends to improve radiation treatment by systematically monitoring treatment variations and incorporating them to re-optimize the treatment plan early on during the course of treatment. In this process, field margin and treatment dose can be routinely customized to each individual patient to achieve a safe dose escalation.

@article{doi10108800319155421008,
    author = "Yan, Di and Vicini, Frank A. and Wong, John W. and Martínez, Álvaro",
    title = "Adaptive radiation therapy",
    year = "1997",
    journal = "Physics in Medicine and Biology",
    abstract = "Adaptive radiation therapy is a closed-loop radiation treatment process where the treatment plan can be modified using a systematic feedback of measurements. Adaptive radiation therapy intends to improve radiation treatment by systematically monitoring treatment variations and incorporating them to re-optimize the treatment plan early on during the course of treatment. In this process, field margin and treatment dose can be routinely customized to each individual patient to achieve a safe dose escalation.",
    url = "https://doi.org/10.1088/0031-9155/42/1/008",
    doi = "10.1088/0031-9155/42/1/008",
    openalex = "W1967172105",
    references = "doi1010160167814093902557, doi1010160360301685903669, doi1010160360301687902665, doi1010160360301689909723, doi101016036030169190172z, doi10108009553009214552071, doi10108800319155386001, doi10310902841868409136037, doi10310902841868709104364, openalexw2346397638"
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Comparative studies tend to differ from optimality and functionality studies in how they treat adaptation. While the comparative approach focuses on the origin and change of traits, optimality studies assume that adaptations are maintained at an optimum by stabilizing selection. This paper presents a model of adaptive evolution on a macroevolutionary time scale that includes the maintenance of traits at adaptive optima by stabilizing selection as the dominant evolutionary force. Interspecific variation is treated as variation in the position of adaptive optima. The model illustrates how phylogenetic constraints not only lead to correlations between phylogenetically related species, but also to imperfect adaptations. From this model, a statistical comparative method is derived that can be used to estimate the effect of a selective factor on adaptive optima in a way that would be consistent with an optimality study of adaptation to this factor. The method is illustrated with an analysis of dental evolution in fossil horses. The use of comparative methods to study evolutionary trends is also discussed.

@article{doi101111j155856461997tb01457x,
    author = "Hansen, Thomas F.",
    title = "STABILIZING SELECTION AND THE COMPARATIVE ANALYSIS OF ADAPTATION",
    year = "1997",
    journal = "Evolution",
    abstract = "Comparative studies tend to differ from optimality and functionality studies in how they treat adaptation. While the comparative approach focuses on the origin and change of traits, optimality studies assume that adaptations are maintained at an optimum by stabilizing selection. This paper presents a model of adaptive evolution on a macroevolutionary time scale that includes the maintenance of traits at adaptive optima by stabilizing selection as the dominant evolutionary force. Interspecific variation is treated as variation in the position of adaptive optima. The model illustrates how phylogenetic constraints not only lead to correlations between phylogenetically related species, but also to imperfect adaptations. From this model, a statistical comparative method is derived that can be used to estimate the effect of a selective factor on adaptive optima in a way that would be consistent with an optimality study of adaptation to this factor. The method is illustrated with an analysis of dental evolution in fossil horses. The use of comparative methods to study evolutionary trends is also discussed.",
    url = "https://doi.org/10.1111/j.1558-5646.1997.tb01457.x",
    doi = "10.1111/j.1558-5646.1997.tb01457.x",
    openalex = "W2328578724",
    references = "doi10100703064746897, doi101017s009483730001157x, doi101086286013, doi101093aesa383396, doi101111j1469185x1988tb00630x, doi101111j155856461979tb04694x, doi1023071446122, doi105860choice304997"
}

@article{doi10103827900,
    author = "Rainey, Paul B. and Travisano, Michael",
    title = "Adaptive radiation in a heterogeneous environment",
    year = "1998",
    journal = "Nature",
    url = "https://doi.org/10.1038/27900",
    doi = "10.1038/27900",
    openalex = "W1583030352",
    references = "doi1010160169534787900280, doi101017cbo9780511623387, doi101038scientificamerican0779122, doi101073pnas91156808, doi101086285289, doi101111j155856461982tb05068x, doi101126science7701342, doi1023071933500, doi1023072409350, doi1023072409372, doi1023074785, doi105860choice273873, doi105860choice332720, openalexw1493831303"
}

The vagaries of history lead to the prediction that repeated instances of evolutionary diversification will lead to disparate outcomes even if starting conditions are similar. We tested this proposition by examining the evolutionary radiation of Anolis lizards on the four islands of the Greater Antilles. Morphometric analyses indicate that the same set of habitat specialists, termed ecomorphs, occurs on all four islands. Although these similar assemblages could result from a single evolutionary origin of each ecomorph, followed by dispersal or vicariance, phylogenetic analysis indicates that the ecomorphs originated independently on each island. Thus, adaptive radiation in similar environments can overcome historical contingencies to produce strikingly similar evolutionary outcomes.

@article{doi101126science27953592115,
    author = "Losos, Jonathan B. and Jackman, Todd R. and Larson, Allan and de Queiroz, Kevin and Rodrı́guez-Schettino, Lourdes",
    title = "Contingency and Determinism in Replicated Adaptive Radiations of Island Lizards",
    year = "1998",
    journal = "Science",
    abstract = "The vagaries of history lead to the prediction that repeated instances of evolutionary diversification will lead to disparate outcomes even if starting conditions are similar. We tested this proposition by examining the evolutionary radiation of Anolis lizards on the four islands of the Greater Antilles. Morphometric analyses indicate that the same set of habitat specialists, termed ecomorphs, occurs on all four islands. Although these similar assemblages could result from a single evolutionary origin of each ecomorph, followed by dispersal or vicariance, phylogenetic analysis indicates that the ecomorphs originated independently on each island. Thus, adaptive radiation in similar environments can overcome historical contingencies to produce strikingly similar evolutionary outcomes.",
    url = "https://doi.org/10.1126/science.279.5359.2115",
    doi = "10.1126/science.279.5359.2115",
    openalex = "W2103549209",
    references = "doi101007bf02100115, doi101017cbo9780511608568, doi101017s0094837300011350, doi101093oso97801985464120010001, doi101093oxfordjournalsmolbeva025706, doi101111j155856461983tb05533x, doi1023071943062, doi1023072408332, doi105860choice273873, doi105860choice295104, openalexw2273605253"
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Preface List of Contributors Part I. Introduction: 1. Adaptive radiation and molecular evolution: concepts and research issues Thomas J. Givnish 2. Homoplasy in molecular vs. morphological data: the likelihood of correct phylogenetic inference Thomas J. Givnish, and Kenneth J. Sytsma Part II. Integrative Studies: 3. Adaptive radiation of the Hawaiian silversword alliance: congruence and conflict of phylogenetic evidence from molecular and non-molecular investigations Bruce G. Baldwin 4. The chronicle of marsupial evolution Mark S. Springer, John A. W. Kirsch, and Judd A. Chase 5. Evolutionary origins of phenotypic diversity in Daphnia John K. Colbourne, Paul D. N. Hebert, and Derek J. Taylor 6. Evolutionary trends in the ecology of New World monkeys inferred from a combined phylogenetic analysis of nuclear, mitochondrial, and morphological data Ines Horovitz, and Axel Meye 7. Adaptive radiation in the aquatic plant family Pontederiaceae: insights from phylogenetic analysis Spencer C. H. Barrett, and Sean W. Graham 8. Molecular evolution and adaptive radiation in Brocchinia (Bromeliaceae: Pitcairnioideae) atop tepuis of the Guayana Shield Thomas J. Givnish, Kenneth J. Sytsma, James F. Smith, William J. Hahn, David H. Benzing, and Elizabeth M. Burkhardt Part III. Convergence: 9. You aren't always what you eat: evolution of nectar-feeding among Old World fruitbats (Megachiroptera: Pteropodidae) John A. W. Kirsch, and Francois-Joseph Lapointe 10. Chloroplast DNA restriction sites and floral versus non-floral characters in the obligate twig epiphytes in subtribe Oncidiinae (Orchidaceae) Mark W. Chase, and Jeffrey D. Palmer 11. Adaptation, cladogenesis, and the evolution of habitat association in North American tiger beetles: a phylogenetic perspective Alfried P. Vogler Part IV. Rapid Radiations: 12. Molecular phylogenetic tests of sympatric speciation models in Lake Malawi cichlid fishes Peter N. Reinthal, and Axel Mey 13. A rapid adaptive radiation due to a key innovation in Aquilegia Scott Hodges 14. Origin and evolution of Argyranthemum (Asteraceae: Anthemideae) in Macaronesia Javier Francisco-Ortega, Daniel J. Crawford, Arnoldo Santos-Guerra, and Robert K. Jansen Part V. Reproductive Strategies: 15. Floral diversification, pollination biology, and molecular evolution in Platanthera (Orchidaceae) Jeffrey R. Hapeman, and Kenneth Inoue 16. Phylogenetic perspectives on the evolution of dioecy: adaptive radiation in the endemic Hawaiian genera Schiedea and Alsinodendron (Caryophyllaceae: Alsinoideae) Ann K. Sakai, Stephen G. Weller, Warren L. Wagner, and Pamela S. Soltis 17. Ecological and reproductive shifts in the diversification of the endemic Hawaiian Drosophila Michael P. Kambysellis, and Elysse M. Craddock Part VI. Character Divergence and Community Assembly: 18. History of ecological selection in sticklebacks - uniting experimental and phylogenetic approaches Eric B. Taylor, James D. McPhail, and Dalph Schluter 19. Phylogenetic studies of convergent adaptive radiations in Caribbean Anolis lizards Todd Jackman, Jonathan B. Losos, Allan Larson, and Kevin de Queiros Part VII. Macroevolutionary Patterns: 20. Molecular and morphological evolution during the post-Palaeozoic diversification of echinoids Andrew B. Smith, and D. T. J. Littlewood 21. How fast is speciation: molecular, geological and phylogenetic evidences from adaptive radiations of fish Amy R. McCune Index.

@article{doi1023072419593,
    author = "Gottlieb, L. D. and Givnish, Thomas J. and Sytsma, Kenneth J.",
    title = "Molecular Evolution and Adaptive Radiation.",
    year = "1998",
    journal = "Systematic Botany",
    abstract = "Preface List of Contributors Part I. Introduction: 1. Adaptive radiation and molecular evolution: concepts and research issues Thomas J. Givnish 2. Homoplasy in molecular vs. morphological data: the likelihood of correct phylogenetic inference Thomas J. Givnish, and Kenneth J. Sytsma Part II. Integrative Studies: 3. Adaptive radiation of the Hawaiian silversword alliance: congruence and conflict of phylogenetic evidence from molecular and non-molecular investigations Bruce G. Baldwin 4. The chronicle of marsupial evolution Mark S. Springer, John A. W. Kirsch, and Judd A. Chase 5. Evolutionary origins of phenotypic diversity in Daphnia John K. Colbourne, Paul D. N. Hebert, and Derek J. Taylor 6. Evolutionary trends in the ecology of New World monkeys inferred from a combined phylogenetic analysis of nuclear, mitochondrial, and morphological data Ines Horovitz, and Axel Meye 7. Adaptive radiation in the aquatic plant family Pontederiaceae: insights from phylogenetic analysis Spencer C. H. Barrett, and Sean W. Graham 8. Molecular evolution and adaptive radiation in Brocchinia (Bromeliaceae: Pitcairnioideae) atop tepuis of the Guayana Shield Thomas J. Givnish, Kenneth J. Sytsma, James F. Smith, William J. Hahn, David H. Benzing, and Elizabeth M. Burkhardt Part III. Convergence: 9. You aren't always what you eat: evolution of nectar-feeding among Old World fruitbats (Megachiroptera: Pteropodidae) John A. W. Kirsch, and Francois-Joseph Lapointe 10. Chloroplast DNA restriction sites and floral versus non-floral characters in the obligate twig epiphytes in subtribe Oncidiinae (Orchidaceae) Mark W. Chase, and Jeffrey D. Palmer 11. Adaptation, cladogenesis, and the evolution of habitat association in North American tiger beetles: a phylogenetic perspective Alfried P. Vogler Part IV. Rapid Radiations: 12. Molecular phylogenetic tests of sympatric speciation models in Lake Malawi cichlid fishes Peter N. Reinthal, and Axel Mey 13. A rapid adaptive radiation due to a key innovation in Aquilegia Scott Hodges 14. Origin and evolution of Argyranthemum (Asteraceae: Anthemideae) in Macaronesia Javier Francisco-Ortega, Daniel J. Crawford, Arnoldo Santos-Guerra, and Robert K. Jansen Part V. Reproductive Strategies: 15. Floral diversification, pollination biology, and molecular evolution in Platanthera (Orchidaceae) Jeffrey R. Hapeman, and Kenneth Inoue 16. Phylogenetic perspectives on the evolution of dioecy: adaptive radiation in the endemic Hawaiian genera Schiedea and Alsinodendron (Caryophyllaceae: Alsinoideae) Ann K. Sakai, Stephen G. Weller, Warren L. Wagner, and Pamela S. Soltis 17. Ecological and reproductive shifts in the diversification of the endemic Hawaiian Drosophila Michael P. Kambysellis, and Elysse M. Craddock Part VI. Character Divergence and Community Assembly: 18. History of ecological selection in sticklebacks - uniting experimental and phylogenetic approaches Eric B. Taylor, James D. McPhail, and Dalph Schluter 19. Phylogenetic studies of convergent adaptive radiations in Caribbean Anolis lizards Todd Jackman, Jonathan B. Losos, Allan Larson, and Kevin de Queiros Part VII. Macroevolutionary Patterns: 20. Molecular and morphological evolution during the post-Palaeozoic diversification of echinoids Andrew B. Smith, and D. T. J. Littlewood 21. How fast is speciation: molecular, geological and phylogenetic evidences from adaptive radiations of fish Amy R. McCune Index.",
    url = "https://doi.org/10.2307/2419593",
    doi = "10.2307/2419593",
    openalex = "W2052217453"
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Abstract Adaptive radiation is a spectacular feature of evolution. It is also widespread, more so than the list of familiar cases, including the Galapagos finches, the cichlid fishes of East African lakes, and the Hawaiian silversword alliance, alone would suggest. Much of life’s diversity, perhaps even most of it, has arisen during similar episodes of speciation and phenotypic and ecological divergence. My main goal in this book is to assess how far we have come in understanding the causes of this remarkable process. Before I began the book I held the naive notion that my years of study on the Galapagos finches, where my fascination with adaptive radiation began, on African and American finches, and more recently on fishes of postglacial lakes, had taught me enough about adaptive radiation that my task would involve little more than writing down all I knew before I forgot it. As the book got underway the limits of my knowledge became distressingly apparent, and I now feel I learned most of its contents along the way. Here I aim to put the results of many studies together to ask whether they conform or contra st with the dominant ‘ecological’ theory of adaptive radiation that was formulated in the first half of the last century.

@book{doi101093oso97801985052350010001,
    author = "Schluter, Dolph",
    title = "The Ecology of Adaptive Radiation",
    year = "2000",
    abstract = "Abstract Adaptive radiation is a spectacular feature of evolution. It is also widespread, more so than the list of familiar cases, including the Galapagos finches, the cichlid fishes of East African lakes, and the Hawaiian silversword alliance, alone would suggest. Much of life’s diversity, perhaps even most of it, has arisen during similar episodes of speciation and phenotypic and ecological divergence. My main goal in this book is to assess how far we have come in understanding the causes of this remarkable process. Before I began the book I held the naive notion that my years of study on the Galapagos finches, where my fascination with adaptive radiation began, on African and American finches, and more recently on fishes of postglacial lakes, had taught me enough about adaptive radiation that my task would involve little more than writing down all I knew before I forgot it. As the book got underway the limits of my knowledge became distressingly apparent, and I now feel I learned most of its contents along the way. Here I aim to put the results of many studies together to ask whether they conform or contra st with the dominant ‘ecological’ theory of adaptive radiation that was formulated in the first half of the last century.",
    url = "https://doi.org/10.1093/oso/9780198505235.001.0001",
    doi = "10.1093/oso/9780198505235.001.0001",
    openalex = "W1603923763"
}

Abstract Before the Evolutionary Synthesis, ‘phylogenetic inertia’ was associated with theories of orthogenesis, which claimed that organisms possessed an endogenous perfecting principle. The concept in the modern literature dates to Simpson (1944), who used ‘evolutionary inertia’ as a description of pattern in the fossil record. Wilson (1975) used ‘phylogenetic inertia’ to describe population-level or organismal properties that can affect the course of evolution in response to selection. Many current authors now view phylogenetic inertia as an alternative hypothesis to adaptation by natural selection when attempting to explain interspecific variation, covariation or lack thereof in phenotypic traits. Some phylogenetic comparative methods have been claimed to allow quantification and testing of phylogenetic inertia. Although some existing methods do allow valid tests of whether related species tend to resemble each other, which we term ‘phylogenetic signal’, this is simply pattern recognition and does not imply any underlying process. Moreover, comparative data sets generally do not include information that would allow rigorous inferences concerning causal processes underlying such patterns. The concept of phylogenetic inertia needs to be defined and studied with as much care as ‘adaptation’.

@article{doi101046j14209101200200472x,
    author = "Blomberg, Simon P. and Garland, Theodore",
    title = "Tempo and mode in evolution: phylogenetic inertia, adaptation and comparative methods",
    year = "2002",
    journal = "Journal of Evolutionary Biology",
    abstract = "Abstract Before the Evolutionary Synthesis, ‘phylogenetic inertia’ was associated with theories of orthogenesis, which claimed that organisms possessed an endogenous perfecting principle. The concept in the modern literature dates to Simpson (1944), who used ‘evolutionary inertia’ as a description of pattern in the fossil record. Wilson (1975) used ‘phylogenetic inertia’ to describe population-level or organismal properties that can affect the course of evolution in response to selection. Many current authors now view phylogenetic inertia as an alternative hypothesis to adaptation by natural selection when attempting to explain interspecific variation, covariation or lack thereof in phenotypic traits. Some phylogenetic comparative methods have been claimed to allow quantification and testing of phylogenetic inertia. Although some existing methods do allow valid tests of whether related species tend to resemble each other, which we term ‘phylogenetic signal’, this is simply pattern recognition and does not imply any underlying process. Moreover, comparative data sets generally do not include information that would allow rigorous inferences concerning causal processes underlying such patterns. The concept of phylogenetic inertia needs to be defined and studied with as much care as ‘adaptation’.",
    url = "https://doi.org/10.1046/j.1420-9101.2002.00472.x",
    doi = "10.1046/j.1420-9101.2002.00472.x",
    openalex = "W2152910720",
    references = "doi101086303327, doi101086physzool67430163866, doi101093aesa383396, doi101111j001438202001tb00731x, doi107312simp92414"
}

The primary rationale for the use of phylogenetically based statistical methods is that phylogenetic signal, the tendency for related species to resemble each other, is ubiquitous. Whether this assertion is true for a given trait in a given lineage is an empirical question, but general tools for detecting and quantifying phylogenetic signal are inadequately developed. We present new methods for continuous-valued characters that can be implemented with either phylogenetically independent contrasts or generalized least-squares models. First, a simple randomization procedure allows one to test the null hypothesis of no pattern of similarity among relatives. The test demonstrates correct Type I error rate at a nominal alpha = 0.05 and good power (0.8) for simulated datasets with 20 or more species. Second, we derive a descriptive statistic, K, which allows valid comparisons of the amount of phylogenetic signal across traits and trees. Third, we provide two biologically motivated branch-length transformations, one based on the Ornstein-Uhlenbeck (OU) model of stabilizing selection, the other based on a new model in which character evolution can accelerate or decelerate (ACDC) in rate (e.g., as may occur during or after an adaptive radiation). Maximum likelihood estimation of the OU (d) and ACDC (g) parameters can serve as tests for phylogenetic signal because an estimate of d or g near zero implies that a phylogeny with little hierarchical structure (a star) offers a good fit to the data. Transformations that improve the fit of a tree to comparative data will increase power to detect phylogenetic signal and may also be preferable for further comparative analyses, such as of correlated character evolution. Application of the methods to data from the literature revealed that, for trees with 20 or more species, 92% of traits exhibited significant phylogenetic signal (randomization test), including behavioral and ecological ones that are thought to be relatively evolutionarily malleable (e.g., highly adaptive) and/or subject to relatively strong environmental (nongenetic) effects or high levels of measurement error. Irrespective of sample size, most traits (but not body size, on average) showed less signal than expected given the topology, branch lengths, and a Brownian motion model of evolution (i.e., K was less than one), which may be attributed to adaptation and/or measurement error in the broad sense (including errors in estimates of phenotypes, branch lengths, and topology). Analysis of variance of log K for all 121 traits (from 35 trees) indicated that behavioral traits exhibit lower signal than body size, morphological, life-history, or physiological traits. In addition, physiological traits (corrected for body size) showed less signal than did body size itself. For trees with 20 or more species, the estimated OU (25% of traits) and/or ACDC (40%) transformation parameter differed significantly from both zero and unity, indicating that a hierarchical tree with less (or occasionally more) structure than the original better fit the data and so could be preferred for comparative analyses.

@article{doi101111j001438202003tb00285x,
    author = "Blomberg, Simon P. and Garland, Theodore and Ives, Anthony R.",
    title = "TESTING FOR PHYLOGENETIC SIGNAL IN COMPARATIVE DATA: BEHAVIORAL TRAITS ARE MORE LABILE",
    year = "2003",
    journal = "Evolution",
    abstract = "The primary rationale for the use of phylogenetically based statistical methods is that phylogenetic signal, the tendency for related species to resemble each other, is ubiquitous. Whether this assertion is true for a given trait in a given lineage is an empirical question, but general tools for detecting and quantifying phylogenetic signal are inadequately developed. We present new methods for continuous-valued characters that can be implemented with either phylogenetically independent contrasts or generalized least-squares models. First, a simple randomization procedure allows one to test the null hypothesis of no pattern of similarity among relatives. The test demonstrates correct Type I error rate at a nominal alpha = 0.05 and good power (0.8) for simulated datasets with 20 or more species. Second, we derive a descriptive statistic, K, which allows valid comparisons of the amount of phylogenetic signal across traits and trees. Third, we provide two biologically motivated branch-length transformations, one based on the Ornstein-Uhlenbeck (OU) model of stabilizing selection, the other based on a new model in which character evolution can accelerate or decelerate (ACDC) in rate (e.g., as may occur during or after an adaptive radiation). Maximum likelihood estimation of the OU (d) and ACDC (g) parameters can serve as tests for phylogenetic signal because an estimate of d or g near zero implies that a phylogeny with little hierarchical structure (a star) offers a good fit to the data. Transformations that improve the fit of a tree to comparative data will increase power to detect phylogenetic signal and may also be preferable for further comparative analyses, such as of correlated character evolution. Application of the methods to data from the literature revealed that, for trees with 20 or more species, 92\% of traits exhibited significant phylogenetic signal (randomization test), including behavioral and ecological ones that are thought to be relatively evolutionarily malleable (e.g., highly adaptive) and/or subject to relatively strong environmental (nongenetic) effects or high levels of measurement error. Irrespective of sample size, most traits (but not body size, on average) showed less signal than expected given the topology, branch lengths, and a Brownian motion model of evolution (i.e., K was less than one), which may be attributed to adaptation and/or measurement error in the broad sense (including errors in estimates of phenotypes, branch lengths, and topology). Analysis of variance of log K for all 121 traits (from 35 trees) indicated that behavioral traits exhibit lower signal than body size, morphological, life-history, or physiological traits. In addition, physiological traits (corrected for body size) showed less signal than did body size itself. For trees with 20 or more species, the estimated OU (25\% of traits) and/or ACDC (40\%) transformation parameter differed significantly from both zero and unity, indicating that a hierarchical tree with less (or occasionally more) structure than the original better fit the data and so could be preferred for comparative analyses.",
    url = "https://doi.org/10.1111/j.0014-3820.2003.tb00285.x",
    doi = "10.1111/j.0014-3820.2003.tb00285.x",
    openalex = "W1990221500",
    references = "doi1010079781489945419, doi1010160164070486900273, doi10103844766, doi101086284325, doi101086286013, doi101086303327, doi101086343873, doi101086physzool67430163866, doi101093auk1002507, doi101093oso97801985464120010001, doi101093sysbio41118, doi101098rstb19890106, doi101111j001438202000tb00026x, doi101111j001438202001tb00731x, doi1023072412182, doi102307jctt1xp3v3r, doi104159harvard9780674865327, doi105860choice295104, doi105860choice304983, openalexw1550375751, openalexw1558456135"
}

@article{doi101016jtree200401003,
    author = "Seehausen, Ole",
    title = "Hybridization and adaptive radiation",
    year = "2004",
    journal = "Trends in Ecology \& Evolution",
    url = "https://doi.org/10.1016/j.tree.2004.01.003",
    doi = "10.1016/j.tree.2004.01.003",
    openalex = "W2055997230",
    references = "doi101016s0169534700020267, doi101038347550a0, doi101038sjhdy6886170, doi101046j1365294x200101216x, doi101093oso97801950997440010001, doi101093oso97801985052350010001, doi101098rspb19990641, doi101111j155856461981tb04864x, doi101126science27753331808, doi101126science27953592115, doi101146annurevecolsys281359, doi101146annureves16110185000553, doi101579004474472912, doi104159harvard9780674865327, doi105860choice350883"
}

The African cichlid fish radiations are the most diverse extant animal radiations and provide a unique system to test predictions of speciation and adaptive radiation theory. The past few years have seen major advances in the phylogenetics, evolutionary biogeography and ecology of cichlid fish. Most of this work has concentrated on the most diverse radiations. Unfortunately, a large number of small radiations and 'non-radiations' have been overlooked, potentially limiting the contribution of the cichlid system to our understanding of speciation and adaptive radiation. I have reviewed the literature to identify 33 intralacustrine radiations and 76 failed radiations. For as many as possible I collected information on lake size, age and phylogenetic relationships. I use these data to address two questions: (i) whether the rate of speciation and the resulting species richness are related to temporal and spatial variation in ecological opportunity and (ii) whether the likelihood of undergoing adaptive radiation is similar for different African cichlid lineages. The former is a key prediction of the ecological theory of adaptive radiation that has been presumed true but remains untested for cichlid radiations. The second is based on the hypothesis that the propensity of cichlids to radiate is due to a key evolutionary innovation shared by all African cichlids. The evidence suggests that speciation rate declines through time as niches get filled up during adaptive radiation: young radiations and early stages of old radiations are characterized by high rates of speciation, whereas at least 0.5 Myr into a radiation speciation becomes a lot less frequent. The number of species in cichlid radiations increases with lake size, supporting the prediction that species diversity increases with habitat heterogeneity, but also with opportunity for isolation by distance. Finally, the data suggest that the propensity to radiate within lakes is a derived property that evolved during the evolutionary history of some African cichlids, and the appearance of which does not coincide with the appearance of proposed key innovations in morphology and life history.

@article{doi101098rspb20063539,
    author = "Seehausen, Ole",
    title = "African cichlid fish: a model system in adaptive radiation research",
    year = "2006",
    journal = "Proceedings of the Royal Society B Biological Sciences",
    abstract = "The African cichlid fish radiations are the most diverse extant animal radiations and provide a unique system to test predictions of speciation and adaptive radiation theory. The past few years have seen major advances in the phylogenetics, evolutionary biogeography and ecology of cichlid fish. Most of this work has concentrated on the most diverse radiations. Unfortunately, a large number of small radiations and 'non-radiations' have been overlooked, potentially limiting the contribution of the cichlid system to our understanding of speciation and adaptive radiation. I have reviewed the literature to identify 33 intralacustrine radiations and 76 failed radiations. For as many as possible I collected information on lake size, age and phylogenetic relationships. I use these data to address two questions: (i) whether the rate of speciation and the resulting species richness are related to temporal and spatial variation in ecological opportunity and (ii) whether the likelihood of undergoing adaptive radiation is similar for different African cichlid lineages. The former is a key prediction of the ecological theory of adaptive radiation that has been presumed true but remains untested for cichlid radiations. The second is based on the hypothesis that the propensity of cichlids to radiate is due to a key evolutionary innovation shared by all African cichlids. The evidence suggests that speciation rate declines through time as niches get filled up during adaptive radiation: young radiations and early stages of old radiations are characterized by high rates of speciation, whereas at least 0.5 Myr into a radiation speciation becomes a lot less frequent. The number of species in cichlid radiations increases with lake size, supporting the prediction that species diversity increases with habitat heterogeneity, but also with opportunity for isolation by distance. Finally, the data suggest that the propensity to radiate within lakes is a derived property that evolved during the evolutionary history of some African cichlids, and the appearance of which does not coincide with the appearance of proposed key innovations in morphology and life history.",
    url = "https://doi.org/10.1098/rspb.2006.3539",
    doi = "10.1098/rspb.2006.3539",
    openalex = "W2097509699",
    references = "doi101038nrg1316, doi101073pnas0506330102"
}

Biologists have long been fascinated by the exceptionally high diversity displayed by some evolutionary groups. Adaptive radiation in such clades is not only spectacular, but is also an extremely complex process influenced by a variety of ecological, genetic, and developmental factors and strongly dependent on historical contingencies. Using modeling approaches, we identify 10 general patterns concerning the temporal, spatial, and genetic/morphological properties of adaptive radiation. Some of these are strongly supported by empirical work, whereas for others, empirical support is more tentative. In almost all cases, more data are needed. Future progress in our understanding of adaptive radiation will be most successful if theoretical and empirical approaches are integrated, as has happened in other areas of evolutionary biology.

@article{doi101126science1157966,
    author = "Gavrilets, Sergey and Losos, Jonathan B.",
    title = "Adaptive Radiation: Contrasting Theory with Data",
    year = "2009",
    journal = "Science",
    abstract = "Biologists have long been fascinated by the exceptionally high diversity displayed by some evolutionary groups. Adaptive radiation in such clades is not only spectacular, but is also an extremely complex process influenced by a variety of ecological, genetic, and developmental factors and strongly dependent on historical contingencies. Using modeling approaches, we identify 10 general patterns concerning the temporal, spatial, and genetic/morphological properties of adaptive radiation. Some of these are strongly supported by empirical work, whereas for others, empirical support is more tentative. In almost all cases, more data are needed. Future progress in our understanding of adaptive radiation will be most successful if theoretical and empirical approaches are integrated, as has happened in other areas of evolutionary biology.",
    url = "https://doi.org/10.1126/science.1157966",
    doi = "10.1126/science.1157966",
    openalex = "W1968716653",
    references = "doi101016jtree200401003, doi101038nature07285, doi101073pnas0506330102, doi101093oso97801985052350010001, doi101098rspb20080630, doi101111j15585646200800317x, doi101146annurevecolsys281129, doi101146annurevecolsys33010802150448, doi101146annurevecolsys36102803095431, doi1015159780691187051, doi1023072405671, doi1023072407738, doi104159harvard9780674865327, doi105860choice455580, doi107312simp93764"
}

Adaptive radiation refers to diversification from an ancestral species that produces descendants adapted to use a great variety of distinct ecological niches. In this review, I examine two aspects of adaptive radiation: first, that it results from ecological opportunity and, second, that it is deterministic in terms of its outcome and evolutionary trajectory. Ecological opportunity is usually a prerequisite for adaptive radiation, although in some cases, radiation can occur in the absence of preexisting opportunity. Nonetheless, many clades fail to radiate although seemingly in the presence of ecological opportunity; until methods are developed to identify and quantify ecological opportunity, the concept will have little predictive utility in understanding a priori when a clade might be expected to radiate. Although predicted by theory, replicated adaptive radiations occur only rarely, usually in closely related and poorly dispersing taxa found in the same region on islands or in lakes. Contingencies of a variety of types may usually preclude close similarity in the outcome of evolutionary diversification in other situations. Whether radiations usually unfold in the same general sequence is unclear because of the unreliability of methods requiring phylogenetic reconstruction of ancestral events. The synthesis of ecological, phylogenetic, experimental, and genomic advances promises to make the coming years a golden age for the study of adaptive radiation; natural history data, however, will always be crucial to understanding the forces shaping adaptation and evolutionary diversification.

@article{doi101086652433,
    author = "Losos, Jonathan B.",
    title = "Adaptive Radiation, Ecological Opportunity, and Evolutionary Determinism",
    year = "2010",
    journal = "The American Naturalist",
    abstract = "Adaptive radiation refers to diversification from an ancestral species that produces descendants adapted to use a great variety of distinct ecological niches. In this review, I examine two aspects of adaptive radiation: first, that it results from ecological opportunity and, second, that it is deterministic in terms of its outcome and evolutionary trajectory. Ecological opportunity is usually a prerequisite for adaptive radiation, although in some cases, radiation can occur in the absence of preexisting opportunity. Nonetheless, many clades fail to radiate although seemingly in the presence of ecological opportunity; until methods are developed to identify and quantify ecological opportunity, the concept will have little predictive utility in understanding a priori when a clade might be expected to radiate. Although predicted by theory, replicated adaptive radiations occur only rarely, usually in closely related and poorly dispersing taxa found in the same region on islands or in lakes. Contingencies of a variety of types may usually preclude close similarity in the outcome of evolutionary diversification in other situations. Whether radiations usually unfold in the same general sequence is unclear because of the unreliability of methods requiring phylogenetic reconstruction of ancestral events. The synthesis of ecological, phylogenetic, experimental, and genomic advances promises to make the coming years a golden age for the study of adaptive radiation; natural history data, however, will always be crucial to understanding the forces shaping adaptation and evolutionary diversification.",
    url = "https://doi.org/10.1086/652433",
    doi = "10.1086/652433",
    openalex = "W2148362488",
    references = "doi101038nature04843, doi101038nature07893, doi101038nrg1316, doi101073pnas101092598, doi10108010292389509380518, doi101086284196, doi101098rspb20080630, doi101111j15585646200800317x, doi101111j15585646201001026x, doi101126science1098095, doi1023072412953, doi105860choice415285"
}

@incollection{crossref2013adaptive,
    title = "Adaptive Demography",
    year = "2013",
    booktitle = "The Fire Ants",
    url = "https://doi.org/10.2307/j.ctv1dp0txz.34",
    doi = "10.2307/j.ctv1dp0txz.34",
    openalex = "W4239753217",
    pages = "295-303"
}

@article{kapralov2013molecular,
    author = "Kapralov, Maxim V. and Votintseva, Antonina A. and Filatov, Dmitry A.",
    title = "Molecular Adaptation during a Rapid Adaptive Radiation",
    year = "2013",
    journal = "Molecular Biology and Evolution",
    url = "https://doi.org/10.1093/molbev/mst013",
    doi = "10.1093/molbev/mst013",
    number = "5",
    openalex = "W2099176711",
    pages = "1051-1059",
    volume = "30",
    references = "doi101016s0022283605803602, doi101093bioinformatics149817, doi101093bioinformaticsbtg180, doi101093bioinformaticsbtm404, doi101093molbevmsm088, doi101093molbevmsm092, doi101093molbevmsn083, doi101111j251761611995tb02031x, doi105962bhltitle59991, doi105962bhltitle82303"
}

Cichlid fishes are famous for large, diverse and replicated adaptive radiations in the Great Lakes of East Africa. To understand the molecular mechanisms underlying cichlid phenotypic diversity, we sequenced the genomes and transcriptomes of five lineages of African cichlids: the Nile tilapia (Oreochromis niloticus), an ancestral lineage with low diversity; and four members of the East African lineage: Neolamprologus brichardi/pulcher (older radiation, Lake Tanganyika), Metriaclima zebra (recent radiation, Lake Malawi), Pundamilia nyererei (very recent radiation, Lake Victoria), and Astatotilapia burtoni (riverine species around Lake Tanganyika). We found an excess of gene duplications in the East African lineage compared to tilapia and other teleosts, an abundance of non-coding element divergence, accelerated coding sequence evolution, expression divergence associated with transposable element insertions, and regulation by novel microRNAs. In addition, we analysed sequence data from sixty individuals representing six closely related species from Lake Victoria, and show genome-wide diversifying selection on coding and regulatory variants, some of which were recruited from ancient polymorphisms. We conclude that a number of molecular mechanisms shaped East African cichlid genomes, and that amassing of standing variation during periods of relaxed purifying selection may have been important in facilitating subsequent evolutionary diversification.

@article{doi101038nature13726,
    author = "Brawand, David and Wagner, Catherine E. and Li, Yang and Malinsky, Milan and Keller, Irene and Fan, Shaohua and Simakov, Oleg and Ng, Alvin Yu Jin and Lim, Zhi Wei and Bezault, Étienne and Turner-Maier, Jason and Johnson, Jeremy and Alcazar, Rosa and Noh, Hyun Ji and Russell, Pamela and Aken, Bronwen and Alföldi, Jessica and Amemiya, Chris T. and Azzouzi, Naoual and Baroiller, Jean‐François and Barloy-Hubler, Frédérique and Berlin, Aaron and Bloomquist, Ryan F. and Carleton, Karen L. and Conte, Matthew A. and D'Cotta, Hélèna and Eshel, Orly and Gaffney, Leslie and Galibert, Francis and Gante, Hugo F. and Gnerre, Sante and Greuter, Lucie and Guyon, Richard and Haddad, Natalie S. and Haerty, Wilfried and Harris, H. and Hofmann, Hans A. and Hourlier, Thibaut and Hulata, Gideon and Jaffe, David B. and Lara, Marcia and Lee, Alison and MacCallum, Iain and Mwaiko, Salome and Nikaido, Masato and Nishihara, Hidenori and Ozouf‐Costaz, Catherine and Penman, David J. and Przybylski, Dariusz and Rakotomanga, Michaëlle and Renn, Suzy C. P. and Ribeiro, Filipe J. and Ron, Micha and Salzburger, Walter and Sánchez‐Pulido, Luis and Santos, M. Emília and Searle, Steve and Sharpe, Ted and Swofford, Ross and Tan, Frederick J. and Williams, Louise and Young, Sarah and Yin, Shuangye and Okada, Norihiro and Kocher, Thomas D. and Miska, Eric A. and Lander, Eric S. and Venkatesh, Byrappa and Fernald, Russell D. and Meyer, Axel and Ponting, Chris P. and Streelman, J. Todd and Lindblad‐Toh, Kerstin and Seehausen, Ole and Palma, Federica Di",
    title = "The genomic substrate for adaptive radiation in African cichlid fish",
    year = "2014",
    journal = "Nature",
    abstract = "Cichlid fishes are famous for large, diverse and replicated adaptive radiations in the Great Lakes of East Africa. To understand the molecular mechanisms underlying cichlid phenotypic diversity, we sequenced the genomes and transcriptomes of five lineages of African cichlids: the Nile tilapia (Oreochromis niloticus), an ancestral lineage with low diversity; and four members of the East African lineage: Neolamprologus brichardi/pulcher (older radiation, Lake Tanganyika), Metriaclima zebra (recent radiation, Lake Malawi), Pundamilia nyererei (very recent radiation, Lake Victoria), and Astatotilapia burtoni (riverine species around Lake Tanganyika). We found an excess of gene duplications in the East African lineage compared to tilapia and other teleosts, an abundance of non-coding element divergence, accelerated coding sequence evolution, expression divergence associated with transposable element insertions, and regulation by novel microRNAs. In addition, we analysed sequence data from sixty individuals representing six closely related species from Lake Victoria, and show genome-wide diversifying selection on coding and regulatory variants, some of which were recruited from ancient polymorphisms. We conclude that a number of molecular mechanisms shaped East African cichlid genomes, and that amassing of standing variation during periods of relaxed purifying selection may have been important in facilitating subsequent evolutionary diversification.",
    url = "https://doi.org/10.1038/nature13726",
    doi = "10.1038/nature13726",
    openalex = "W2165933771",
    references = "doi10100703064746897, doi101016jtree200709008, doi101038nature10842, doi101038nature10944, doi101038nrg1316, doi101038nrg3079, doi101093aesa383396, doi101111j15585646200800450x, doi101126science27352781091, doi101126science29054941151, doi1043249780203509104"
}

Due to its special geological history, the New Caledonian Archipelago is a mosaic of soil types, and in combination with climatic conditions this results in a heterogeneous environment across relatively small distances. A group of over 20 endemic species of Diospyros (Ebenaceae) has rapidly and recently radiated on the archipelago after a single long-distance dispersal event. Most of the Diospyros species in the radiating group are morphologically and ecologically well differentiated, but they exhibit low levels of DNA variability. To investigate the processes that shaped the diversification of this group we employed restriction site associated DNA sequencing (RADseq). Over 8400 filtered SNPs generally confirm species delimitations and produce a well-supported phylogenetic tree. Our analyses document local introgression, but only a limited potential for gene flow over longer distances. The phylogenetic relationships point to an early regional clustering among populations and species, indicating that allopatric speciation with respect to macrohabitat (i.e., climatic conditions) may have had a role in the initial differentiation within the group. A later, more rapid radiation involved divergence with respect to microhabitat (i.e., soil preference). Several sister species in the group show a parallel divergence in edaphic preference. Searches for genomic regions that are systematically differentiated in this replicated phenotypic divergence pointed to loci potentially involved in ion binding and cellular transport. These loci appear meaningful in the context of adaptations to soil types that differ in heavy-metal and mineral content. Identical nucleotide changes affected only two of these loci, indicating that introgression may have played a limited role in their evolution. Our results suggest that both allopatric diversification and (parapatric) ecological divergence shaped successive rounds of speciation in the Diospyros radiation on New Caledonia.

@article{doi101093sysbiosyv076,
    author = "Paun, Ovidiu and Turner, Barbara and Trucchi, Emiliano and Munzinger, Jérôme and Chase, Mark W. and Samuel, Rosabelle",
    title = "Processes Driving the Adaptive Radiation of a Tropical Tree (Diospyros, Ebenaceae) in New Caledonia, a Biodiversity Hotspot",
    year = "2015",
    journal = "Systematic Biology",
    abstract = "Due to its special geological history, the New Caledonian Archipelago is a mosaic of soil types, and in combination with climatic conditions this results in a heterogeneous environment across relatively small distances. A group of over 20 endemic species of Diospyros (Ebenaceae) has rapidly and recently radiated on the archipelago after a single long-distance dispersal event. Most of the Diospyros species in the radiating group are morphologically and ecologically well differentiated, but they exhibit low levels of DNA variability. To investigate the processes that shaped the diversification of this group we employed restriction site associated DNA sequencing (RADseq). Over 8400 filtered SNPs generally confirm species delimitations and produce a well-supported phylogenetic tree. Our analyses document local introgression, but only a limited potential for gene flow over longer distances. The phylogenetic relationships point to an early regional clustering among populations and species, indicating that allopatric speciation with respect to macrohabitat (i.e., climatic conditions) may have had a role in the initial differentiation within the group. A later, more rapid radiation involved divergence with respect to microhabitat (i.e., soil preference). Several sister species in the group show a parallel divergence in edaphic preference. Searches for genomic regions that are systematically differentiated in this replicated phenotypic divergence pointed to loci potentially involved in ion binding and cellular transport. These loci appear meaningful in the context of adaptations to soil types that differ in heavy-metal and mineral content. Identical nucleotide changes affected only two of these loci, indicating that introgression may have played a limited role in their evolution. Our results suggest that both allopatric diversification and (parapatric) ecological divergence shaped successive rounds of speciation in the Diospyros radiation on New Caledonia.",
    url = "https://doi.org/10.1093/sysbio/syv076",
    doi = "10.1093/sysbio/syv076",
    openalex = "W2179433510",
    references = "doi101007s1268601195487, doi10103835002501, doi101038nmeth2109, doi101093bioinformaticsbtu033, doi101093genetics1552945, doi101093molbevmss075, doi101109gce20105676129, doi101111j1365294x200502553x, doi101111j14718286200501155x, kapralov2013molecular, openalexw3217097258"
}

The process of adaptive radiation—the proliferation of species from a single ancestor and diversification into many ecologically different forms—has been of great interest to evolutionary biologists since Darwin. Since the middle of the last century, ecological opportunity has been invoked as a potential key to understanding when and how adaptive radiation occurs. Interest in the topic of ecological opportunity has accelerated as research on adaptive radiation has experienced a resurgence, fueled in part by advances in phylogenetic approaches to studying evolutionary diversification. Nonetheless, what the term actually means, much less how it mechanistically leads to adaptive diversification, is currently debated; whether the term has any predictive value or is a heuristic useful only for post hoc explanation also remains unclear. Recent recognition that evolutionary change can occur rapidly and on a timescale commensurate with ecological processes suggests that it is time to synthesize ecological and evolutionary approaches to the study of community assembly and evolutionary diversification.

@article{doi101146annurevecolsys121415032254,
    author = "Stroud, James T. and Losos, Jonathan B.",
    title = "Ecological Opportunity and Adaptive Radiation",
    year = "2016",
    journal = "Annual Review of Ecology Evolution and Systematics",
    abstract = "The process of adaptive radiation—the proliferation of species from a single ancestor and diversification into many ecologically different forms—has been of great interest to evolutionary biologists since Darwin. Since the middle of the last century, ecological opportunity has been invoked as a potential key to understanding when and how adaptive radiation occurs. Interest in the topic of ecological opportunity has accelerated as research on adaptive radiation has experienced a resurgence, fueled in part by advances in phylogenetic approaches to studying evolutionary diversification. Nonetheless, what the term actually means, much less how it mechanistically leads to adaptive diversification, is currently debated; whether the term has any predictive value or is a heuristic useful only for post hoc explanation also remains unclear. Recent recognition that evolutionary change can occur rapidly and on a timescale commensurate with ecological processes suggests that it is time to synthesize ecological and evolutionary approaches to the study of community assembly and evolutionary diversification.",
    url = "https://doi.org/10.1146/annurev-ecolsys-121415-032254",
    doi = "10.1146/annurev-ecolsys-121415-032254",
    openalex = "W2327977699",
    references = "doi101007978146124018114, doi101016jcub201311063, doi101016jearscirev201004001, doi101038nature13726, doi101038ncomms5087, doi101038ngeo1475, doi101073pnas1302642110, doi101086282505, doi101086284196, doi101093behecoart058, doi101093oso97801951223430010001, doi101093oso97801985052350010001, doi101093sysbiosyt050, doi101098rspb20080630, doi101111j14209101201002029x, doi101111j14698137200601864x, doi101111j155856461964tb01674x, doi101111j15585646200800317x, doi101111j15585646201001026x, doi101111nph13230, doi101126sciadv1400253, doi101126science1161833, doi101146annurevearth271463, doi101146annurevecolsys281129, doi101146annurevecolsys33010802150448, doi101146annurevecolsys39110707173447, doi101371journalpone0089543, doi1015159780691224244, doi1015159781400847266, doi1023072412953, doi1023073545850, doi104159harvard9780674865327, doi105860choice485062"
}

Speciation events often occur in rapid bursts of diversification, but the ecological and genetic factors that promote these radiations are still much debated. Using whole transcriptomes from all 13 species in the ecologically and reproductively diverse wild tomato clade (Solanum sect. Lycopersicon), we infer the species phylogeny and patterns of genetic diversity in this group. Despite widespread phylogenetic discordance due to the sorting of ancestral variation, we date the origin of this radiation to approximately 2.5 million years ago and find evidence for at least three sources of adaptive genetic variation that fuel diversification. First, we detect introgression both historically between early-branching lineages and recently between individual populations, at specific loci whose functions indicate likely adaptive benefits. Second, we find evidence of lineage-specific de novo evolution for many genes, including loci involved in the production of red fruit color. Finally, using a "PhyloGWAS" approach, we detect environment-specific sorting of ancestral variation among populations that come from different species but share common environmental conditions. Estimated across the whole clade, small but substantial and approximately equal fractions of the euchromatic portion of the genome are inferred to contribute to each of these three sources of adaptive genetic variation. These results indicate that multiple genetic sources can promote rapid diversification and speciation in response to new ecological opportunity, in agreement with our emerging phylogenomic understanding of the complexity of both ancient and recent species radiations.

@article{doi101371journalpbio1002379,
    author = "Pease, James B. and Haak, David C. and Hahn, Matthew W. and Moyle, Leonie C.",
    title = "Phylogenomics Reveals Three Sources of Adaptive Variation during a Rapid Radiation",
    year = "2016",
    journal = "PLoS Biology",
    abstract = {Speciation events often occur in rapid bursts of diversification, but the ecological and genetic factors that promote these radiations are still much debated. Using whole transcriptomes from all 13 species in the ecologically and reproductively diverse wild tomato clade (Solanum sect. Lycopersicon), we infer the species phylogeny and patterns of genetic diversity in this group. Despite widespread phylogenetic discordance due to the sorting of ancestral variation, we date the origin of this radiation to approximately 2.5 million years ago and find evidence for at least three sources of adaptive genetic variation that fuel diversification. First, we detect introgression both historically between early-branching lineages and recently between individual populations, at specific loci whose functions indicate likely adaptive benefits. Second, we find evidence of lineage-specific de novo evolution for many genes, including loci involved in the production of red fruit color. Finally, using a "PhyloGWAS" approach, we detect environment-specific sorting of ancestral variation among populations that come from different species but share common environmental conditions. Estimated across the whole clade, small but substantial and approximately equal fractions of the euchromatic portion of the genome are inferred to contribute to each of these three sources of adaptive genetic variation. These results indicate that multiple genetic sources can promote rapid diversification and speciation in response to new ecological opportunity, in agreement with our emerging phylogenomic understanding of the complexity of both ancient and recent species radiations.},
    url = "https://doi.org/10.1371/journal.pbio.1002379",
    doi = "10.1371/journal.pbio.1002379",
    openalex = "W2272393905",
    references = "doi101038nature10158, doi101038nature11119, doi101038nature13726, doi101093bioinformatics182337, doi101093bioinformaticsbtp352, doi101093bioinformaticsbts635, doi101093bioinformaticsbtu033, doi101093jxberf068, doi101093molbevmsm088, doi101093oso97801985052350010001, doi101111mec12415, doi101126science1157966, doi101126science1188021, doi101126science1194585, doi101146annurevecolsys110512135800, doi101146annurevecolsys39110707173447"
}

Understanding why some evolutionary lineages generate exceptionally high species diversity is an important goal in evolutionary biology. Haplochromine cichlid fishes of Africa's Lake Victoria region encompass >700 diverse species that all evolved in the last 150,000 years. How this 'Lake Victoria Region Superflock' could evolve on such rapid timescales is an enduring question. Here, we demonstrate that hybridization between two divergent lineages facilitated this process by providing genetic variation that subsequently became recombined and sorted into many new species. Notably, the hybridization event generated exceptional allelic variation at an opsin gene known to be involved in adaptation and speciation. More generally, differentiation between new species is accentuated around variants that were fixed differences between the parental lineages, and that now appear in many new combinations in the radiation species. We conclude that hybridization between divergent lineages, when coincident with ecological opportunity, may facilitate rapid and extensive adaptive radiation.

@article{doi101038ncomms14363,
    author = "Meier, Joana I. and Marques, David A. and Mwaiko, Salome and Wagner, Catherine E. and Excoffier, Laurent and Seehausen, Ole",
    title = "Ancient hybridization fuels rapid cichlid fish adaptive radiations",
    year = "2017",
    journal = "Nature Communications",
    abstract = "Understanding why some evolutionary lineages generate exceptionally high species diversity is an important goal in evolutionary biology. Haplochromine cichlid fishes of Africa's Lake Victoria region encompass >700 diverse species that all evolved in the last 150,000 years. How this 'Lake Victoria Region Superflock' could evolve on such rapid timescales is an enduring question. Here, we demonstrate that hybridization between two divergent lineages facilitated this process by providing genetic variation that subsequently became recombined and sorted into many new species. Notably, the hybridization event generated exceptional allelic variation at an opsin gene known to be involved in adaptation and speciation. More generally, differentiation between new species is accentuated around variants that were fixed differences between the parental lineages, and that now appear in many new combinations in the radiation species. We conclude that hybridization between divergent lineages, when coincident with ecological opportunity, may facilitate rapid and extensive adaptive radiation.",
    url = "https://doi.org/10.1038/ncomms14363",
    doi = "10.1038/ncomms14363",
    openalex = "W2587197905",
    references = "doi101016jtree200401003, doi101038nature05706, doi101038nature13726, doi101038nmeth1923, doi101073pnas86166196, doi101093bioinformaticsbtl446, doi101093bioinformaticsbtr330, doi101111j14209101201202599x, doi101111j155856461954tb01504x, doi101111j17550998201002847x, doi101111mec12354, doi101126science1188021, doi101126science29054941151, doi101371journalpcbi1003537, doi1014601phytopatholmediterr14998u129, doi101579004474472912"
}

The subtribe Espeletiinae (Asteraceae), endemic to the high-elevations in the Northern Andes, exhibits an exceptional diversity of species, growth-forms, and reproductive strategies. This complex of 140 species includes large trees, dichotomous trees, shrubs and the extraordinary giant caulescent rosettes, considered as a classic example of adaptation in tropical high-elevation ecosystems. The subtribe has also long been recognized as a prominent case of adaptive radiation, but the understanding of its evolution has been hampered by a lack of phylogenetic resolution. Herein, we produce the first fully resolved phylogeny of all morphological groups of Espeletiinae, using whole plastomes and about a million nuclear nucleotides obtained with an original de novo assembly procedure without reference genome, and analyzed with traditional and coalescent-based approaches that consider the possible impact of incomplete lineage sorting and hybridization on phylogenetic inference. We show that the diversification of Espeletiinae started from a rosette ancestor about 2.3 Ma, after the final uplift of the Northern Andes. This was followed by two independent radiations in the Colombian and Venezuelan Andes, with a few trans-cordilleran dispersal events among low-elevation tree lineages but none among high-elevation rosettes. We demonstrate complex scenarios of morphological change in Espeletiinae, usually implying the convergent evolution of growth-forms with frequent loss/gains of various traits. For instance, caulescent rosettes evolved independently in both countries, likely as convergent adaptations to life in tropical high-elevation habitats. Tree growth-forms evolved independently three times from the repeated colonization of lower elevations by high-elevation rosette ancestors. The rate of morphological diversification increased during the early phase of the radiation, after which it decreased steadily towards the present. On the other hand, the rate of species diversification in the best-sampled Venezuelan radiation was on average very high (3.1 spp/My), with significant rate variation among growth-forms (much higher in polycarpic caulescent rosettes). Our results point out a scenario where both adaptive morphological evolution and geographical isolation due to Pleistocene climatic oscillations triggered an exceptionally rapid radiation for a continental plant group.

@article{doi101093sysbiosyy022,
    author = "Pouchon, Charles and Fernández, Ángel and Nassar, Jafet M. and Boyer, Frédéric and Aubert, S. and Lavergne, Sébastien and Mavárez, Jesús",
    title = "Phylogenomic Analysis of the Explosive Adaptive Radiation of the Espeletia Complex (Asteraceae) in the Tropical Andes",
    year = "2018",
    journal = "Systematic Biology",
    abstract = "The subtribe Espeletiinae (Asteraceae), endemic to the high-elevations in the Northern Andes, exhibits an exceptional diversity of species, growth-forms, and reproductive strategies. This complex of 140 species includes large trees, dichotomous trees, shrubs and the extraordinary giant caulescent rosettes, considered as a classic example of adaptation in tropical high-elevation ecosystems. The subtribe has also long been recognized as a prominent case of adaptive radiation, but the understanding of its evolution has been hampered by a lack of phylogenetic resolution. Herein, we produce the first fully resolved phylogeny of all morphological groups of Espeletiinae, using whole plastomes and about a million nuclear nucleotides obtained with an original de novo assembly procedure without reference genome, and analyzed with traditional and coalescent-based approaches that consider the possible impact of incomplete lineage sorting and hybridization on phylogenetic inference. We show that the diversification of Espeletiinae started from a rosette ancestor about 2.3 Ma, after the final uplift of the Northern Andes. This was followed by two independent radiations in the Colombian and Venezuelan Andes, with a few trans-cordilleran dispersal events among low-elevation tree lineages but none among high-elevation rosettes. We demonstrate complex scenarios of morphological change in Espeletiinae, usually implying the convergent evolution of growth-forms with frequent loss/gains of various traits. For instance, caulescent rosettes evolved independently in both countries, likely as convergent adaptations to life in tropical high-elevation habitats. Tree growth-forms evolved independently three times from the repeated colonization of lower elevations by high-elevation rosette ancestors. The rate of morphological diversification increased during the early phase of the radiation, after which it decreased steadily towards the present. On the other hand, the rate of species diversification in the best-sampled Venezuelan radiation was on average very high (3.1 spp/My), with significant rate variation among growth-forms (much higher in polycarpic caulescent rosettes). Our results point out a scenario where both adaptive morphological evolution and geographical isolation due to Pleistocene climatic oscillations triggered an exceptionally rapid radiation for a continental plant group.",
    url = "https://doi.org/10.1093/sysbio/syy022",
    doi = "10.1093/sysbio/syy022",
    openalex = "W2794322919",
    references = "doi101038ncomms12384"
}

The adaptive radiation of cichlid fishes in East African Lake Malawi encompasses over 500 species that are believed to have evolved within the last 800,000 years from a common founder population. It has been proposed that hybridization between ancestral lineages can provide the genetic raw material to fuel such exceptionally high diversification rates, and evidence for this has recently been presented for the Lake Victoria region cichlid superflock. Here, we report that Lake Malawi cichlid genomes also show evidence of hybridization between two lineages that split 3-4 Ma, today represented by Lake Victoria cichlids and the riverine Astatotilapia sp. "ruaha blue." The two ancestries in Malawi cichlid genomes are present in large blocks of several kilobases, but there is little variation in this pattern between Malawi cichlid species, suggesting that the large-scale mosaic structure of the genomes was largely established prior to the radiation. Nevertheless, tens of thousands of polymorphic variants apparently derived from the hybridization are interspersed in the genomes. These loci show a striking excess of differentiation across ecological subgroups in the Lake Malawi cichlid assemblage, and parental alleles sort differentially into benthic and pelagic Malawi cichlid lineages, consistent with strong differential selection on these loci during species divergence. Furthermore, these loci are enriched for genes involved in immune response and vision, including opsin genes previously identified as important for speciation. Our results reinforce the role of ancestral hybridization in explosive diversification by demonstrating its significance in one of the largest recent vertebrate adaptive radiations.

@article{doi101093molbevmsz294,
    author = "Svardal, Hannes and Quah, Fu Xiang and Malinsky, Milan and Ngatunga, Benjamin P. and Miska, Eric A. and Salzburger, Walter and Genner, Martin J. and Turner, George F. and Durbin, Richard",
    title = "Ancestral Hybridization Facilitated Species Diversification in the Lake Malawi Cichlid Fish Adaptive Radiation",
    year = "2019",
    journal = "Molecular Biology and Evolution",
    abstract = {The adaptive radiation of cichlid fishes in East African Lake Malawi encompasses over 500 species that are believed to have evolved within the last 800,000 years from a common founder population. It has been proposed that hybridization between ancestral lineages can provide the genetic raw material to fuel such exceptionally high diversification rates, and evidence for this has recently been presented for the Lake Victoria region cichlid superflock. Here, we report that Lake Malawi cichlid genomes also show evidence of hybridization between two lineages that split 3-4 Ma, today represented by Lake Victoria cichlids and the riverine Astatotilapia sp. "ruaha blue." The two ancestries in Malawi cichlid genomes are present in large blocks of several kilobases, but there is little variation in this pattern between Malawi cichlid species, suggesting that the large-scale mosaic structure of the genomes was largely established prior to the radiation. Nevertheless, tens of thousands of polymorphic variants apparently derived from the hybridization are interspersed in the genomes. These loci show a striking excess of differentiation across ecological subgroups in the Lake Malawi cichlid assemblage, and parental alleles sort differentially into benthic and pelagic Malawi cichlid lineages, consistent with strong differential selection on these loci during species divergence. Furthermore, these loci are enriched for genes involved in immune response and vision, including opsin genes previously identified as important for speciation. Our results reinforce the role of ancestral hybridization in explosive diversification by demonstrating its significance in one of the largest recent vertebrate adaptive radiations.},
    url = "https://doi.org/10.1093/molbev/msz294",
    doi = "10.1093/molbev/msz294",
    openalex = "W2994857231",
    references = "doi101038s415590180717x, doi101038s4157601800439"
}

A key outcome of evolution by natural selection is adaptation. Since the beginning of the age of genetics, evolutionary biologists have focused on the evolution of nuclear genes as the basis for adaptation. Changes to the mitochondrial genome were long viewed as the result of drift and unimportant to organism fitness. New theory and empirical observations, however, are implicating changes in mitochondrial function as a central component of adaptation related to temperature, oxygen pressure, and diet. Novel mitochondrial function underlying adaptive evolution is a product of interacting mitochondrial and nuclear genes to create changes to the electron transport system, and variation in mitochondrial genotypes has been found to play a key role in such adaptive evolution of eukaryotes. Evidence is emerging that changes in mitochondrial function resulting from mitonuclear coevolution underlie key evolutionary innovations associated with major adaptive radiations including the transition from terrestrial locomotion to flight. I discuss the empirical evidence that supports a key role for mitonuclear coevolution in adaptation and adaptive radiation and the implications for fundamental ideas in ecology and evolution.

@incollection{hill2019adaptation,
    author = "Hill, Geoffrey E.",
    title = "Adaptation and adaptive radiation",
    year = "2019",
    booktitle = "Mitonuclear Ecology",
    abstract = "A key outcome of evolution by natural selection is adaptation. Since the beginning of the age of genetics, evolutionary biologists have focused on the evolution of nuclear genes as the basis for adaptation. Changes to the mitochondrial genome were long viewed as the result of drift and unimportant to organism fitness. New theory and empirical observations, however, are implicating changes in mitochondrial function as a central component of adaptation related to temperature, oxygen pressure, and diet. Novel mitochondrial function underlying adaptive evolution is a product of interacting mitochondrial and nuclear genes to create changes to the electron transport system, and variation in mitochondrial genotypes has been found to play a key role in such adaptive evolution of eukaryotes. Evidence is emerging that changes in mitochondrial function resulting from mitonuclear coevolution underlie key evolutionary innovations associated with major adaptive radiations including the transition from terrestrial locomotion to flight. I discuss the empirical evidence that supports a key role for mitonuclear coevolution in adaptation and adaptive radiation and the implications for fundamental ideas in ecology and evolution.",
    url = "https://doi.org/10.1093/oso/9780198818250.003.0009",
    doi = "10.1093/oso/9780198818250.003.0009",
    openalex = "W2950118603",
    pages = "199-243"
}

Adaptive radiation is an evolutionary process that has been promulgated in some clades as an explanation for species richness and disparity in morphological forms across ecological gradients. Studies designed to elucidate the mechanisms and causes of adaptive radiation have largely focused on animal systems, but plant clades have tremendous potential to answer elusive questions regarding adaptive radiations. The goals of this review are to (1) produce a synthetic understanding of adaptive radiations through studies that have investigated plants systems, (2) critically reflect on contemporary studies to highlight how approaches have been successful as well as limiting, and (3) outline gaps in our understanding of adaptive radiations while emphasizing that plants have ideal characteristics to answer future questions. Thirty-five adaptive radiation clades are highlighted, of which several are supported with multiple lines of evidence, such as the Hawaiian silverswords, Hawaiian lobeliads, and columbines. Plant adaptive radiation examples are commonly insular, diversified in the Miocene or Pliocene, are associated with dispersal-mediated ecological opportunities, are polyploids, and have experienced hybridization. From those studies, a general model of plant insular adaptive radiation is proposed. The limitations of the current reliance on phylogenetic comparative approaches to detect adaptive radiations are considered, and an integrative approach that includes phylogenetics, genomics, and evolutionary ecology is advocated. The review concludes with a call for additional studies that are needed before we are to fully understand adaptive radiations, and they include the following: (1) how do biological interactions influence adaptive radiations, (2) what role does environmental change play in generating ecological opportunity, (3) how does genetic evolution drive adaptive radiation, (4) do models adequately explain the adaptive radiation process, (5) what is the role of hybridization, and (6) why do some groups not undergo adaptive radiation after ecological opportunity?

@article{doi101086713445,
    author = "Schenk, John J.",
    title = "The Next Generation of Adaptive Radiation Studies in Plants",
    year = "2021",
    journal = "International Journal of Plant Sciences",
    abstract = "Adaptive radiation is an evolutionary process that has been promulgated in some clades as an explanation for species richness and disparity in morphological forms across ecological gradients. Studies designed to elucidate the mechanisms and causes of adaptive radiation have largely focused on animal systems, but plant clades have tremendous potential to answer elusive questions regarding adaptive radiations. The goals of this review are to (1) produce a synthetic understanding of adaptive radiations through studies that have investigated plants systems, (2) critically reflect on contemporary studies to highlight how approaches have been successful as well as limiting, and (3) outline gaps in our understanding of adaptive radiations while emphasizing that plants have ideal characteristics to answer future questions. Thirty-five adaptive radiation clades are highlighted, of which several are supported with multiple lines of evidence, such as the Hawaiian silverswords, Hawaiian lobeliads, and columbines. Plant adaptive radiation examples are commonly insular, diversified in the Miocene or Pliocene, are associated with dispersal-mediated ecological opportunities, are polyploids, and have experienced hybridization. From those studies, a general model of plant insular adaptive radiation is proposed. The limitations of the current reliance on phylogenetic comparative approaches to detect adaptive radiations are considered, and an integrative approach that includes phylogenetics, genomics, and evolutionary ecology is advocated. The review concludes with a call for additional studies that are needed before we are to fully understand adaptive radiations, and they include the following: (1) how do biological interactions influence adaptive radiations, (2) what role does environmental change play in generating ecological opportunity, (3) how does genetic evolution drive adaptive radiation, (4) do models adequately explain the adaptive radiation process, (5) what is the role of hybridization, and (6) why do some groups not undergo adaptive radiation after ecological opportunity?",
    url = "https://doi.org/10.1086/713445",
    doi = "10.1086/713445",
    openalex = "W3126856616",
    references = "doi101016jtree200401003, doi10103827900, doi10103844766, doi101038nrg3095, doi101093bioinformaticsbtm538, doi101111j001438202003tb00285x, doi101126science1086949, doi101126science1090228, doi101146annureves18110187001321, doi1023072411924, kapralov2013molecular"
}

Adaptive radiations are rich laboratories for exploring, testing, and understanding key theories in evolution and ecology because they offer spectacular displays of speciation and ecological adaptation. Particular challenges to the study of adaptive radiation include high levels of species richness, rapid speciation, and gene flow between species. Over the last decade, high-throughput sequencing technologies and access to population genomic data have lessened these challenges by enabling the analysis of samples from many individual organisms at whole-genome scales. Here we review how population genomic data have facilitated our knowledge of adaptive radiation in five key areas: (1) phylogenetics, (2) hybridization, (3) timing and rates of diversification, (4) the genomic basis of trait evolution, and (5) the role of genome structure in divergence. We review current knowledge in each area, highlight outstanding questions, and focus on methods that facilitate detection of complex patterns in the divergence and demography of populations through time. It is clear that population genomic data are revolutionising the ability to reconstruct evolutionary history in rapidly diversifying clades. Additionally, studies are increasingly emphasising the central role of gene flow, re-use of standing genetic variation during adaptation, and structural genomic elements as facilitators of the speciation process in adaptive radiations. We highlight hybridization-and the hypothesized processes by which it shapes diversification-and questions seeking to bridge the divide between microevolutionary and macroevolutionary processes as rich areas for future study. Overall, access to population genomic data has facilitated an exciting era in adaptive radiation research, with implications for deeper understanding of fundamental evolutionary processes across the tree of life.

@article{doi101111mec17574,
    author = "Combrink, Lucia L. and Golcher‐Benavides, Jimena and Lewanski, Alexander L. and Rick, Jessica A. and Rosenthal, William C. and Wagner, Catherine E.",
    title = "Population Genomics of Adaptive Radiation",
    year = "2024",
    journal = "Molecular Ecology",
    abstract = "Adaptive radiations are rich laboratories for exploring, testing, and understanding key theories in evolution and ecology because they offer spectacular displays of speciation and ecological adaptation. Particular challenges to the study of adaptive radiation include high levels of species richness, rapid speciation, and gene flow between species. Over the last decade, high-throughput sequencing technologies and access to population genomic data have lessened these challenges by enabling the analysis of samples from many individual organisms at whole-genome scales. Here we review how population genomic data have facilitated our knowledge of adaptive radiation in five key areas: (1) phylogenetics, (2) hybridization, (3) timing and rates of diversification, (4) the genomic basis of trait evolution, and (5) the role of genome structure in divergence. We review current knowledge in each area, highlight outstanding questions, and focus on methods that facilitate detection of complex patterns in the divergence and demography of populations through time. It is clear that population genomic data are revolutionising the ability to reconstruct evolutionary history in rapidly diversifying clades. Additionally, studies are increasingly emphasising the central role of gene flow, re-use of standing genetic variation during adaptation, and structural genomic elements as facilitators of the speciation process in adaptive radiations. We highlight hybridization-and the hypothesized processes by which it shapes diversification-and questions seeking to bridge the divide between microevolutionary and macroevolutionary processes as rich areas for future study. Overall, access to population genomic data has facilitated an exciting era in adaptive radiation research, with implications for deeper understanding of fundamental evolutionary processes across the tree of life.",
    url = "https://doi.org/10.1111/mec.17574",
    doi = "10.1111/mec.17574",
    openalex = "W4405759961",
    references = "doi101086713445"
}