Diversification

Comparative studies of the relationship between two phenotypes, or between a phenotype and an environment, are frequently carried out by invalid statistical methods. Most regression, correlation, and contingency table methods, including nonparametric methods, assume that the points are drawn independently from a common distribution. When species are taken from a branching phylogeny, they are manifestly nonindependent. Use of a statistical method that assumes independence will cause overstatement of the significance in hypothesis tests. Some illustrative examples of these phenomena have been given, and limitations of previous proposals of ways to correct for the nonindependence have been discussed. A method of correcting for the phylogeny has been proposed. It requires that we know both the tree topology and the branch lengths, and that we be willing to allow the characters to be modeled by Brownian motion on a linear scale. Given these conditions, the phylogeny specifies a set of contrasts among species, contrasts that are statistically independent and can be used in regression or correlation studies. The considerable barriers to making practical use of this technique have been discussed.

@article{doi101086284325,
    author = "Felsenstein, Joseph",
    title = "Phylogenies and the Comparative Method",
    year = "1985",
    journal = "The American Naturalist",
    abstract = "Comparative studies of the relationship between two phenotypes, or between a phenotype and an environment, are frequently carried out by invalid statistical methods. Most regression, correlation, and contingency table methods, including nonparametric methods, assume that the points are drawn independently from a common distribution. When species are taken from a branching phylogeny, they are manifestly nonindependent. Use of a statistical method that assumes independence will cause overstatement of the significance in hypothesis tests. Some illustrative examples of these phenomena have been given, and limitations of previous proposals of ways to correct for the nonindependence have been discussed. A method of correcting for the phylogeny has been proposed. It requires that we know both the tree topology and the branch lengths, and that we be willing to allow the characters to be modeled by Brownian motion on a linear scale. Given these conditions, the phylogeny specifies a set of contrasts among species, contrasts that are statistically independent and can be used in regression or correlation studies. The considerable barriers to making practical use of this technique have been discussed.",
    url = "https://doi.org/10.1086/284325",
    doi = "10.1086/284325",
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We compare two major long-term diversifications of marine animal families that began during periods of low diversity but produced strikingly different numbers of phyla, classes, and orders. The first is the early-Paleozoic diversification (late Vendian-Ordovician; 182 MY duration) and the other the Mesozoic phase of the post-Paleozoic diversification (183 MY duration). The earlier diversification was associated with a great burst of morphological invention producing many phyla, classes, and orders and displaying high per taxon rates of family origination. The later diversification lacked novel morphologies recognized as phyla and classes, produced fewer orders, and displayed lower per taxon rates of family appearances. The chief difference between the diversifications appears to be that the earlier one proceeded from relatively narrow portions of adaptive space, whereas the latter proceeded from species widely scattered among adaptive zones and representing a variety of body plans. This difference is believed to explain the major differences in the products of these great radiations. Our data support those models that hold that evolutionary opportunity is a major factor in the outcome of evolutionary processes.

@article{doi101111j155856461987tb02459x,
    author = "Erwin, Douglas H. and Valentine, James W. and Sepkoski, J. John",
    title = "A COMPARATIVE STUDY OF DIVERSIFICATION EVENTS: THE EARLY PALEOZOIC VERSUS THE MESOZOIC",
    year = "1987",
    journal = "Evolution",
    abstract = "We compare two major long-term diversifications of marine animal families that began during periods of low diversity but produced strikingly different numbers of phyla, classes, and orders. The first is the early-Paleozoic diversification (late Vendian-Ordovician; 182 MY duration) and the other the Mesozoic phase of the post-Paleozoic diversification (183 MY duration). The earlier diversification was associated with a great burst of morphological invention producing many phyla, classes, and orders and displaying high per taxon rates of family origination. The later diversification lacked novel morphologies recognized as phyla and classes, produced fewer orders, and displayed lower per taxon rates of family appearances. The chief difference between the diversifications appears to be that the earlier one proceeded from relatively narrow portions of adaptive space, whereas the latter proceeded from species widely scattered among adaptive zones and representing a variety of body plans. This difference is believed to explain the major differences in the products of these great radiations. Our data support those models that hold that evolutionary opportunity is a major factor in the outcome of evolutionary processes.",
    url = "https://doi.org/10.1111/j.1558-5646.1987.tb02459.x",
    doi = "10.1111/j.1558-5646.1987.tb02459.x",
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Douglas H. Erwin, James W. Valentine, J. John Sepkoski, Jr., A Comparative Study of Diversification Events: The Early Paleozoic Versus the Mesozoic, Evolution, Vol. 41, No. 6 (Nov., 1987), pp. 1177-1186

@article{doi1023072409086,
    author = "Erwin, Douglas H. and Valentine, James W. and Sepkoski, J. John",
    title = "A Comparative Study of Diversification Events: The Early Paleozoic Versus the Mesozoic",
    year = "1987",
    journal = "Evolution",
    abstract = "Douglas H. Erwin, James W. Valentine, J. John Sepkoski, Jr., A Comparative Study of Diversification Events: The Early Paleozoic Versus the Mesozoic, Evolution, Vol. 41, No. 6 (Nov., 1987), pp. 1177-1186",
    url = "https://doi.org/10.2307/2409086",
    doi = "10.2307/2409086",
    openalex = "W4232440558"
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@misc{erwin1987a1,
    author = "Erwin, D. H. and Valentine, J. W. and Sepkoski, J. J",
    title = "A comparative study of diversification events",
    year = "1987",
    howpublished = "The early Paleozoic versus the Mesozoic: Evolution, v. 141, p. 1177-1186",
    note = "talkorigins\_source = {true}; raw\_reference = {Erwin, D. H., Valentine, J. W., and Sepkoski, J. J., 1987, A comparative study of diversification events: The early Paleozoic versus the Mesozoic: Evolution, v. 141, p. 1177-1186.}"
}

Simpson's postulate that rapid diversification follows entrance into a new "adaptive zone" is frequently invoked a posteriori for groups of unusual diversity. The postulate can be tested more rigorously by defining an adaptive zone according to ecological criteria, independent of particular groups of organisms. The adaptive-zone hypothesis predicts that if multiple lineages have invaded a new adaptive zone, they should be consistently more diverse than their (equally old) sister groups, when the latter retain the more primitive way of life. Higher-plant feeding among insects is an independently defined, repeatedly invaded adaptive zone, to which a profound acceleration of diversification rate has been attributed. We have quantified the evidence for this hypothesis by comparing sister groups and species diversity of as many phytophagous insect groups as current taxonomic evidence allows. A sign test showed significant association of diversification rate with the adoption of phytophagy. The possible artifactual bases for this trend are discussed and provisionally rejected. We discuss several possible biological explanations for the association, including models of phylogenesis either dependent on or independent of ecological role.

@article{doi101086284840,
    author = "Mitter, Charles and Farrell, Brian D. and Wiegmann, Brian M.",
    title = "The Phylogenetic Study of Adaptive Zones: Has Phytophagy Promoted Insect Diversification?",
    year = "1988",
    journal = "The American Naturalist",
    abstract = {Simpson's postulate that rapid diversification follows entrance into a new "adaptive zone" is frequently invoked a posteriori for groups of unusual diversity. The postulate can be tested more rigorously by defining an adaptive zone according to ecological criteria, independent of particular groups of organisms. The adaptive-zone hypothesis predicts that if multiple lineages have invaded a new adaptive zone, they should be consistently more diverse than their (equally old) sister groups, when the latter retain the more primitive way of life. Higher-plant feeding among insects is an independently defined, repeatedly invaded adaptive zone, to which a profound acceleration of diversification rate has been attributed. We have quantified the evidence for this hypothesis by comparing sister groups and species diversity of as many phytophagous insect groups as current taxonomic evidence allows. A sign test showed significant association of diversification rate with the adoption of phytophagy. The possible artifactual bases for this trend are discussed and provisionally rejected. We discuss several possible biological explanations for the association, including models of phylogenesis either dependent on or independent of ecological role.},
    url = "https://doi.org/10.1086/284840",
    doi = "10.1086/284840",
    openalex = "W2142973105",
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Abstract From Darwin onward, it has been second nature for evolutionary biologists to think comparatively because comparisons establish the generality of evolutionary phenomena. Do large genomes slow down development? What lifestyles select for large brains? Are extinction rates related to body size? These are all questions for the comparative method, and this book is about how such questions can be answered. The first chapter elaborates on suitable questions for the comparative approach and shows how it complements other approaches to problem-solving in evolution. The second chapter identifies the biological causes of similarity among closely related species for almost any observed character. The third chapter discusses methods for reconstructing phylogenetic trees and ancestral character states. The fourth chapter sets out to develop statistical tests that will determine whether different characters that exist in discrete states show evidence for correlated evolution. Chapter 5 turns to comparative analyses of continuously varying characters. Chapter 6 looks at allometry to exemplify the themes and methods discussed earlier, while the last chapter looks to future development of the comparative approach in both molecular and organismic biology.

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

@article{doi105860choice295104,
    title = "The comparative method in evolutionary biology",
    year = "1992",
    journal = "Choice Reviews Online",
    abstract = "The comparative method for studying adaptation why worry about phylogeny? reconstructing phylogenetic trees and ancestral character states comparative analysis of discrete data comparative analysis of continuous variables determining the form of comparative relationships.",
    url = "https://doi.org/10.5860/choice.29-5104",
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Paleoecologic study of invertebrate faunas from three successive Early Triassic seaways reveals that biotic recovery from the end-Permian mass extinction event was slow, and that full recovery did not occur until after the Early Triassic. Simple, cosmopolitan, opportunistic generalists, and low-diversity, low-complexity paleocommunities were characteristic of the entire Early Triassic in the Western USA. An increase in guild and taxonomic diversity was observed with the addition of several new higher taxa in the late Early Triassic (Spathian) to the almost exclusively molluscan faunas of the earlier Early Triassic (Nammalian). Potential “disaster forms” (the inarticulate brachiopod, Lingula, and the paper pecten, Claraia) dominated the earliest Early Triassic faunas (Griesbachian) and even occurred in the late Early Triassic (normal marine stromatolites). Comparison with data on faunas from the Permian and Triassic suggests that even the most diverse Early Triassic faunas (in the Spathian) were rather low in guild diversity and species richness. These characteristics of genera and paleocommunities in the Early Triassic may be typical of mass extinction aftermaths.

@article{doi101016003101829400093n,
    author = "Schubert, Jennifer K. and Bottjer, David J.",
    title = "Aftermath of the Permian-Triassic mass extinction event: Paleoecology of Lower Triassic carbonates in the western USA",
    year = "1995",
    journal = "Palaeogeography Palaeoclimatology Palaeoecology",
    abstract = "Paleoecologic study of invertebrate faunas from three successive Early Triassic seaways reveals that biotic recovery from the end-Permian mass extinction event was slow, and that full recovery did not occur until after the Early Triassic. Simple, cosmopolitan, opportunistic generalists, and low-diversity, low-complexity paleocommunities were characteristic of the entire Early Triassic in the Western USA. An increase in guild and taxonomic diversity was observed with the addition of several new higher taxa in the late Early Triassic (Spathian) to the almost exclusively molluscan faunas of the earlier Early Triassic (Nammalian). Potential “disaster forms” (the inarticulate brachiopod, Lingula, and the paper pecten, Claraia) dominated the earliest Early Triassic faunas (Griesbachian) and even occurred in the late Early Triassic (normal marine stromatolites). Comparison with data on faunas from the Permian and Triassic suggests that even the most diverse Early Triassic faunas (in the Spathian) were rather low in guild diversity and species richness. These characteristics of genera and paleocommunities in the Early Triassic may be typical of mass extinction aftermaths.",
    url = "https://doi.org/10.1016/0031-0182(94)00093-n",
    doi = "10.1016/0031-0182(94)00093-n",
    openalex = "W2061526312",
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Analysis of the fossil record of microbes, algae, fungi, protists, plants, and animals shows that the diversity of both marine and continental life increased exponentially since the end of the Precambrian. This diversification was interrupted by mass extinctions, the largest of which occurred in the Early Cambrian, Late Ordovician, Late Devonian, Late Permian, Early Triassic, Late Triassic, and end-Cretaceous. Most of these extinctions were experienced by both marine and continental organisms. As for the periodicity of mass extinctions, no support was found: Seven mass extinction peaks in the last 250 million years are spaced 20 to 60 million years apart.

@article{doi101126science7701342,
    author = "Benton, Michael J.",
    title = "Diversification and Extinction in the History of Life",
    year = "1995",
    journal = "Science",
    abstract = "Analysis of the fossil record of microbes, algae, fungi, protists, plants, and animals shows that the diversity of both marine and continental life increased exponentially since the end of the Precambrian. This diversification was interrupted by mass extinctions, the largest of which occurred in the Early Cambrian, Late Ordovician, Late Devonian, Late Permian, Early Triassic, Late Triassic, and end-Cretaceous. Most of these extinctions were experienced by both marine and continental organisms. As for the periodicity of mass extinctions, no support was found: Seven mass extinction peaks in the last 250 million years are spaced 20 to 60 million years apart.",
    url = "https://doi.org/10.1126/science.7701342",
    doi = "10.1126/science.7701342",
    openalex = "W2010154591",
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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",
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Comparative modeling predicts the three-dimensional structure of a given protein sequence (target) based primarily on its alignment to one or more proteins of known structure (templates). The prediction process consists of fold assignment, target-template alignment, model building, and model evaluation. The number of protein sequences that can be modeled and the accuracy of the predictions are increasing steadily because of the growth in the number of known protein structures and because of the improvements in the modeling software. Further advances are necessary in recognizing weak sequence-structure similarities, aligning sequences with structures, modeling of rigid body shifts, distortions, loops and side chains, as well as detecting errors in a model. Despite these problems, it is currently possible to model with useful accuracy significant parts of approximately one third of all known protein sequences. The use of individual comparative models in biology is already rewarding and increasingly widespread. A major new challenge for comparative modeling is the integration of it with the torrents of data from genome sequencing projects as well as from functional and structural genomics. In particular, there is a need to develop an automated, rapid, robust, sensitive, and accurate comparative modeling pipeline applicable to whole genomes. Such large-scale modeling is likely to encourage new kinds of applications for the many resulting models, based on their large number and completeness at the level of the family, organism, or functional network.

@article{doi101146annurevbiophys291291,
    author = "Martı́-Renom, Marc A. and Stuart, Ashley C. and Fiser, András and Sánchez, Roberto and Melo, Francisco and Săli, Andrej",
    title = "Comparative Protein Structure Modeling of Genes and Genomes",
    year = "2000",
    journal = "Annual Review of Biophysics and Biomolecular Structure",
    abstract = "Comparative modeling predicts the three-dimensional structure of a given protein sequence (target) based primarily on its alignment to one or more proteins of known structure (templates). The prediction process consists of fold assignment, target-template alignment, model building, and model evaluation. The number of protein sequences that can be modeled and the accuracy of the predictions are increasing steadily because of the growth in the number of known protein structures and because of the improvements in the modeling software. Further advances are necessary in recognizing weak sequence-structure similarities, aligning sequences with structures, modeling of rigid body shifts, distortions, loops and side chains, as well as detecting errors in a model. Despite these problems, it is currently possible to model with useful accuracy significant parts of approximately one third of all known protein sequences. The use of individual comparative models in biology is already rewarding and increasingly widespread. A major new challenge for comparative modeling is the integration of it with the torrents of data from genome sequencing projects as well as from functional and structural genomics. In particular, there is a need to develop an automated, rapid, robust, sensitive, and accurate comparative modeling pipeline applicable to whole genomes. Such large-scale modeling is likely to encourage new kinds of applications for the many resulting models, based on their large number and completeness at the level of the family, organism, or functional network.",
    url = "https://doi.org/10.1146/annurev.biophys.29.1.291",
    doi = "10.1146/annurev.biophys.29.1.291",
    openalex = "W2114520383",
    references = "doi1023072408678"
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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"
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The question is often raised whether it is statistically necessary to control for phylogenetic associations in comparative studies. To investigate this question, we explore the use of a measure of phylogenetic correlation, lambda, introduced by Pagel (1999), that normally varies between 0 (phylogenetic independence) and 1 (species' traits covary in direct proportion to their shared evolutionary history). Simulations show lambda to be a statistically powerful index for measuring whether data exhibit phylogenetic dependence or not and whether it has low rates of Type I error. Moreover, lambda is robust to incomplete phylogenetic information, which demonstrates that even partial information on phylogeny will improve the accuracy of phylogenetic analyses. To assess whether traits generally show phylogenetic associations, we present a quantitative review of 26 published phylogenetic comparative data sets. The data sets include 103 traits and were chosen from the ecological literature in which debate about the need for phylogenetic correction has been most acute. Eighty-eight percent of data sets contained at least one character that displayed significant phylogenetic dependence, and 60% of characters overall (pooled across studies) showed significant evidence of phylogenetic association. In 16% of tests, phylogenetic correlation could be neither supported nor rejected. However, most of these equivocal results were found in small phylogenies and probably reflect a lack of power. We suggest that the parameter lambda be routinely estimated when analyzing comparative data, since it can also be used simultaneously to adjust the phylogenetic correction in a manner that is optimal for the data set, and we present an example of how this may be done.

@article{doi101086343873,
    author = "Freckleton, Robert P. and Harvey, Paul and Pagel, Mark",
    title = "Phylogenetic Analysis and Comparative Data: A Test and Review of Evidence",
    year = "2002",
    journal = "The American Naturalist",
    abstract = "The question is often raised whether it is statistically necessary to control for phylogenetic associations in comparative studies. To investigate this question, we explore the use of a measure of phylogenetic correlation, lambda, introduced by Pagel (1999), that normally varies between 0 (phylogenetic independence) and 1 (species' traits covary in direct proportion to their shared evolutionary history). Simulations show lambda to be a statistically powerful index for measuring whether data exhibit phylogenetic dependence or not and whether it has low rates of Type I error. Moreover, lambda is robust to incomplete phylogenetic information, which demonstrates that even partial information on phylogeny will improve the accuracy of phylogenetic analyses. To assess whether traits generally show phylogenetic associations, we present a quantitative review of 26 published phylogenetic comparative data sets. The data sets include 103 traits and were chosen from the ecological literature in which debate about the need for phylogenetic correction has been most acute. Eighty-eight percent of data sets contained at least one character that displayed significant phylogenetic dependence, and 60\% of characters overall (pooled across studies) showed significant evidence of phylogenetic association. In 16\% of tests, phylogenetic correlation could be neither supported nor rejected. However, most of these equivocal results were found in small phylogenies and probably reflect a lack of power. We suggest that the parameter lambda be routinely estimated when analyzing comparative data, since it can also be used simultaneously to adjust the phylogenetic correction in a manner that is optimal for the data set, and we present an example of how this may be done.",
    url = "https://doi.org/10.1086/343873",
    doi = "10.1086/343873",
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Species radiations provide unique insights into evolutionary processes underlying species diversification and patterns of biodiversity. To compare plant diversification over a similar time period to the recent cichlid fish radiations, which are an order of magnitude faster than documented bird, arthropod, and plant radiations, we focus on the high-altitude flora of the Andes, which is the most species-rich of any tropical mountains. Because of the recent uplift of the northern Andes, the upland environments where much of this rich endemic flora is found have been available for colonization only since the late Pliocene or Pleistocene, 2-4 million years (Myr) ago. Using DNA sequence data we identify a monophyletic group within the genus Lupinus representing 81 species endemic to the Andes. The age of this clade is estimated to be 1.18-1.76 Myr, implying a diversification rate of 2.49-3.72 species per Myr. This exceeds previous estimates for plants, providing the most spectacular example of explosive plant species diversification documented to date. Furthermore, it suggests that the high cichlid diversification rates are not unique. Lack of key innovations associated with the Andean Lupinus clade suggests that diversification was driven by ecological opportunities afforded by the emergence of island-like habitats after Andean uplift. Data from other genera indicate that lupines are one of a set of similarly rapid Andean plant radiations, continental in scale and island-like in stimulus, suggesting that the high-elevation Andean flora provides a system that rivals other groups, including cichlids, for understanding rapid species diversification.

@article{doi101073pnas0601928103,
    author = "Hughes, Colin E. and Eastwood, Ruth J.",
    title = "Island radiation on a continental scale: Exceptional rates of plant diversification after uplift of the Andes",
    year = "2006",
    journal = "Proceedings of the National Academy of Sciences",
    abstract = "Species radiations provide unique insights into evolutionary processes underlying species diversification and patterns of biodiversity. To compare plant diversification over a similar time period to the recent cichlid fish radiations, which are an order of magnitude faster than documented bird, arthropod, and plant radiations, we focus on the high-altitude flora of the Andes, which is the most species-rich of any tropical mountains. Because of the recent uplift of the northern Andes, the upland environments where much of this rich endemic flora is found have been available for colonization only since the late Pliocene or Pleistocene, 2-4 million years (Myr) ago. Using DNA sequence data we identify a monophyletic group within the genus Lupinus representing 81 species endemic to the Andes. The age of this clade is estimated to be 1.18-1.76 Myr, implying a diversification rate of 2.49-3.72 species per Myr. This exceeds previous estimates for plants, providing the most spectacular example of explosive plant species diversification documented to date. Furthermore, it suggests that the high cichlid diversification rates are not unique. Lack of key innovations associated with the Andean Lupinus clade suggests that diversification was driven by ecological opportunities afforded by the emergence of island-like habitats after Andean uplift. Data from other genera indicate that lupines are one of a set of similarly rapid Andean plant radiations, continental in scale and island-like in stimulus, suggesting that the high-elevation Andean flora provides a system that rivals other groups, including cichlids, for understanding rapid species diversification.",
    url = "https://doi.org/10.1073/pnas.0601928103",
    doi = "10.1073/pnas.0601928103",
    openalex = "W2045366837",
    references = "doi101038nrg1316, doi101073pnas0506330102, doi101073pnas89178322, doi1011300016760620001121091uhotca23co2, doi1023072419593"
}

Evidence from both molecular phylogenies and the fossil record suggests that rates of species diversification often decline through time during evolutionary radiations. One proposed explanation for this pattern is ecological opportunity, whereby an initial abundance of resources and lack of potential competitors facilitate rapid diversification. This model predicts density-dependent declines in diversification rates, but has not been formally tested in any species-level radiation. Here we develop a new conceptual framework that distinguishes density dependence from alternative processes that also produce temporally declining diversification, and we demonstrate this approach using a new phylogeny of North American Dendroica wood warblers. We show that explosive lineage accumulation early in the history of this avian radiation is best explained by a density-dependent diversification process. Our results suggest that the tempo of wood warbler diversification was mediated by ecological interactions among species and that lineage and ecological diversification in this group are coupled, as predicted under the ecological opportunity model.

@article{doi101098rspb20080630,
    author = "Rabosky, Daniel L. and Lovette, Irby J.",
    title = "Density-dependent diversification in North American wood warblers",
    year = "2008",
    journal = "Proceedings of the Royal Society B Biological Sciences",
    abstract = "Evidence from both molecular phylogenies and the fossil record suggests that rates of species diversification often decline through time during evolutionary radiations. One proposed explanation for this pattern is ecological opportunity, whereby an initial abundance of resources and lack of potential competitors facilitate rapid diversification. This model predicts density-dependent declines in diversification rates, but has not been formally tested in any species-level radiation. Here we develop a new conceptual framework that distinguishes density dependence from alternative processes that also produce temporally declining diversification, and we demonstrate this approach using a new phylogeny of North American Dendroica wood warblers. We show that explosive lineage accumulation early in the history of this avian radiation is best explained by a density-dependent diversification process. Our results suggest that the tempo of wood warbler diversification was mediated by ecological interactions among species and that lineage and ecological diversification in this group are coupled, as predicted under the ecological opportunity model.",
    url = "https://doi.org/10.1098/rspb.2008.0630",
    doi = "10.1098/rspb.2008.0630",
    openalex = "W1999179318",
    references = "doi101017cbo9780511623387, doi101093bioinformaticsbtm538, doi101093oso97801985052350010001, doi101111j155856461987tb02459x, doi101186147121487214, doi101371journalpbio0040088, doi1023071931600, doi1023072405671, doi1023073071998, doi105860choice332720, doi107312simp93764"
}

George Gaylord Simpson famously postulated that much of life's diversity originated as adaptive radiations-more or less simultaneous divergences of numerous lines from a single ancestral adaptive type. However, identifying adaptive radiations has proven difficult due to a lack of broad-scale comparative datasets. Here, we use phylogenetic comparative data on body size and shape in a diversity of animal clades to test a key model of adaptive radiation, in which initially rapid morphological evolution is followed by relative stasis. We compared the fit of this model to both single selective peak and random walk models. We found little support for the early-burst model of adaptive radiation, whereas both other models, particularly that of selective peaks, were commonly supported. In addition, we found that the net rate of morphological evolution varied inversely with clade age. The youngest clades appear to evolve most rapidly because long-term change typically does not attain the amount of divergence predicted from rates measured over short time scales. Across our entire analysis, the dominant pattern was one of constraints shaping evolution continually through time rather than rapid evolution followed by stasis. We suggest that the classical model of adaptive radiation, where morphological evolution is initially rapid and slows through time, may be rare in comparative data.

@article{doi101111j15585646201001025x,
    author = "Harmon, Luke J. and Losos, Jonathan B. and Davies, T. Jonathan and Gillespie, Rosemary G. and Gittleman, John L. and Jennings, W. Bryan and Kozak, Kenneth H. and McPeek, Mark A. and Moreno-Roark, Franck and Near, Thomas J. and Purvis, Andy and Ricklefs, Robert E. and Schluter, Dolph and Schulte, James A. and Seehausen, Ole and Sidlauskas, Brian L. and Torres‐Carvajal, Omar and Weir, Jason T. and Mooers, Arne Ø.",
    title = "EARLY BURSTS OF BODY SIZE AND SHAPE EVOLUTION ARE RARE IN COMPARATIVE DATA",
    year = "2010",
    journal = "Evolution",
    abstract = "George Gaylord Simpson famously postulated that much of life's diversity originated as adaptive radiations-more or less simultaneous divergences of numerous lines from a single ancestral adaptive type. However, identifying adaptive radiations has proven difficult due to a lack of broad-scale comparative datasets. Here, we use phylogenetic comparative data on body size and shape in a diversity of animal clades to test a key model of adaptive radiation, in which initially rapid morphological evolution is followed by relative stasis. We compared the fit of this model to both single selective peak and random walk models. We found little support for the early-burst model of adaptive radiation, whereas both other models, particularly that of selective peaks, were commonly supported. In addition, we found that the net rate of morphological evolution varied inversely with clade age. The youngest clades appear to evolve most rapidly because long-term change typically does not attain the amount of divergence predicted from rates measured over short time scales. Across our entire analysis, the dominant pattern was one of constraints shaping evolution continually through time rather than rapid evolution followed by stasis. We suggest that the classical model of adaptive radiation, where morphological evolution is initially rapid and slows through time, may be rare in comparative data.",
    url = "https://doi.org/10.1111/j.1558-5646.2010.01025.x",
    doi = "10.1111/j.1558-5646.2010.01025.x",
    openalex = "W2151541130",
    references = "doi101007978940100585210, doi101017s009483730001280x, doi101023a1013311015886, doi101073pnas89178322, doi101086510633, doi101098rspb19990641, doi101098rspb20080630, doi101126science2224620159, doi1023072419593, doi102307jctvjsf433, doi105860choice455580, openalexw1973833797"
}

The pace of phenotypic diversification during adaptive radiation should decrease as ecological opportunity declines. We test this prediction using phylogenetic comparative analyses of a wide range of morphological traits in Greater Antillean Anolis lizards. We find that the rate of diversification along two important axes of Anolis radiation-body size and limb dimensions-decreased as opportunity declined, with opportunity quantified either as time elapsed in the radiation or as the diversity of competing anole lineages inferred to have been present on an island at different times in the past. Most previous studies of the ecological opportunity hypothesis have focused on the rate of species diversification; our results provide a complementary perspective, indicating that the rate of phenotypic diversification declines with decreasing opportunity in an adaptive radiation.

@article{doi101111j15585646201001026x,
    author = "Mahler, D. Luke and Revell, Liam J. and Glor, Richard E. and Losos, Jonathan B.",
    title = "ECOLOGICAL OPPORTUNITY AND THE RATE OF MORPHOLOGICAL EVOLUTION IN THE DIVERSIFICATION OF GREATER ANTILLEAN ANOLES",
    year = "2010",
    journal = "Evolution",
    abstract = "The pace of phenotypic diversification during adaptive radiation should decrease as ecological opportunity declines. We test this prediction using phylogenetic comparative analyses of a wide range of morphological traits in Greater Antillean Anolis lizards. We find that the rate of diversification along two important axes of Anolis radiation-body size and limb dimensions-decreased as opportunity declined, with opportunity quantified either as time elapsed in the radiation or as the diversity of competing anole lineages inferred to have been present on an island at different times in the past. Most previous studies of the ecological opportunity hypothesis have focused on the rate of species diversification; our results provide a complementary perspective, indicating that the rate of phenotypic diversification declines with decreasing opportunity in an adaptive radiation.",
    url = "https://doi.org/10.1111/j.1558-5646.2010.01026.x",
    doi = "10.1111/j.1558-5646.2010.01026.x",
    openalex = "W1538212908",
    references = "doi101017cbo9780511608551, doi101017s009483730001280x, doi101038nature07893, doi101086282070, doi101086284325, doi101093biomet762297, doi101093oso97801985052350010001, doi101109tac19741100705, doi101111j14209101201002029x, doi101111j155856461987tb02459x, doi101126science1157966, doi10118614712105788, doi101186147121487214, doi1023073802723, doi105860choice273873, openalexw1558456135"
}

Summary 1. Here, I present a new, multifunctional phylogenetics package, phytools, for the R statistical computing environment. 2. The focus of the package is on methods for phylogenetic comparative biology; however, it also includes tools for tree inference, phylogeny input/output, plotting, manipulation and several other tasks. 3. I describe and tabulate the major methods implemented in phytools, and in addition provide some demonstration of its use in the form of two illustrative examples. 4. Finally, I conclude by briefly describing an active web‐log that I use to document present and future developments for phytools. I also note other web resources for phylogenetics in the R computational environment.

@article{doi101111j2041210x201100169x,
    author = "Revell, Liam J.",
    title = "phytools: an R package for phylogenetic comparative biology (and other things)",
    year = "2011",
    journal = "Methods in Ecology and Evolution",
    abstract = "Summary 1. Here, I present a new, multifunctional phylogenetics package, phytools, for the R statistical computing environment. 2. The focus of the package is on methods for phylogenetic comparative biology; however, it also includes tools for tree inference, phylogeny input/output, plotting, manipulation and several other tasks. 3. I describe and tabulate the major methods implemented in phytools, and in addition provide some demonstration of its use in the form of two illustrative examples. 4. Finally, I conclude by briefly describing an active web‐log that I use to document present and future developments for phytools. I also note other web resources for phylogenetics in the R computational environment.",
    url = "https://doi.org/10.1111/j.2041-210x.2011.00169.x",
    doi = "10.1111/j.2041-210x.2011.00169.x",
    openalex = "W1605984840",
    references = "doi1010179781316276259010, doi10103844766, doi10108010635150802302427, doi101086284325, doi101086343873, doi101086383584, doi101086660020, doi101093bioinformaticsbtg412, doi101093bioinformaticsbtq706, doi101093oso97801985464120010001, doi101111j001438202003tb00285x, doi101111j15585646201001026x, doi10118614712105788, doi105860choice295104, openalexw1549853756, openalexw229097380"
}

Previous analyses of relations, divergence times, and diversification patterns among extant mammalian families have relied on supertree methods and local molecular clocks. We constructed a molecular supermatrix for mammalian families and analyzed these data with likelihood-based methods and relaxed molecular clocks. Phylogenetic analyses resulted in a robust phylogeny with better resolution than phylogenies from supertree methods. Relaxed clock analyses support the long-fuse model of diversification and highlight the importance of including multiple fossil calibrations that are spread across the tree. Molecular time trees and diversification analyses suggest important roles for the Cretaceous Terrestrial Revolution and Cretaceous-Paleogene (KPg) mass extinction in opening up ecospace that promoted interordinal and intraordinal diversification, respectively. By contrast, diversification analyses provide no support for the hypothesis concerning the delayed rise of present-day mammals during the Eocene Period.

@article{doi101126science1211028,
    author = "Meredith, Robert W. and Janečka, Jan E. and Gatesy, John and Ryder, Oliver A. and Fisher, Colleen A. and Teeling, Emma C. and Goodbla, Alisha and Eizirik, Eduardo and Simão, Taiz L. L. and Stadler, Tanja and Rabosky, Daniel L. and Honeycutt, Rodney L. and Flynn, John J. and Ingram, Colleen M. and Steiner, Cynthia and Williams, Tiffani L. and Robinson, Terence J. and Burk-Herrick, Angela and Westerman, Michael and Ayoub, Nadia A. and Springer, Mark S. and Murphy, William J.",
    title = "Impacts of the Cretaceous Terrestrial Revolution and KPg Extinction on Mammal Diversification",
    year = "2011",
    journal = "Science",
    abstract = "Previous analyses of relations, divergence times, and diversification patterns among extant mammalian families have relied on supertree methods and local molecular clocks. We constructed a molecular supermatrix for mammalian families and analyzed these data with likelihood-based methods and relaxed molecular clocks. Phylogenetic analyses resulted in a robust phylogeny with better resolution than phylogenies from supertree methods. Relaxed clock analyses support the long-fuse model of diversification and highlight the importance of including multiple fossil calibrations that are spread across the tree. Molecular time trees and diversification analyses suggest important roles for the Cretaceous Terrestrial Revolution and Cretaceous-Paleogene (KPg) mass extinction in opening up ecospace that promoted interordinal and intraordinal diversification, respectively. By contrast, diversification analyses provide no support for the hypothesis concerning the delayed rise of present-day mammals during the Eocene Period.",
    url = "https://doi.org/10.1126/science.1211028",
    doi = "10.1126/science.1211028",
    openalex = "W2140803428",
    references = "doi101016jtree200610002, doi101023a1011317930838, doi101038381226a0, doi101038nature05634, doi101038nature09705, doi101038nature10291, doi101073pnas0334222100, doi101073pnas1016876108, doi101093sysbiosyp031, doi101101gr5918807, doi101126science1067179, doi101353book59141"
}

BACKGROUND: Development of phylogenetic methods that do not rely on fossils for the study of evolutionary processes through time have revolutionized the field of evolutionary biology and resulted in an unprecedented expansion of our knowledge about the tree of life. These methods have helped to shed light on the macroevolution of many taxonomic groups such as the placentals (Mammalia). However, despite the increase of studies addressing the diversification patterns of organisms, no synthesis has addressed the case of the most diversified mammalian clade: the Rodentia. RESULTS: Here we present a rodent maximum likelihood phylogeny inferred from a molecular supermatrix. It is based on 11 mitochondrial and nuclear genes that covers 1,265 species, i.e., respectively 56% and 81% of the known specific and generic rodent diversity. The inferred topology recovered all Rodentia clades proposed by recent molecular works. A relaxed molecular clock dating approach provided a time framework for speciation events. We found that the Myomorpha clade shows a greater degree of variation in diversification rates than Sciuroidea, Caviomorpha, Castorimorpha and Anomaluromorpha. We identified a number of shifts in diversification rates within the major clades: two in Castorimorpha, three in Ctenohystrica, 6 within the squirrel-related clade and 24 in the Myomorpha clade. The majority of these shifts occurred within the most recent familial rodent radiations: the Cricetidae and Muridae clades. Using the topological imbalances and the time line we discuss the potential role of different diversification factors that might have shaped the rodents radiation. CONCLUSIONS: The present glimpse on the diversification pattern of rodents can be used for further comparative meta-analyses. Muroid lineages have a greater degree of variation in their diversification rates than any other rodent group. Different topological signatures suggest distinct diversification processes among rodent lineages. In particular, Muroidea and Sciuroidea display widespread distribution and have undergone evolutionary and adaptive radiation on most of the continents. Our results show that rodents experienced shifts in diversification rate regularly through the Tertiary, but at different periods for each clade. A comparison between the rodent fossil record and our results suggest that extinction led to the loss of diversification signal for most of the Paleogene nodes.

@article{doi101186147121481288,
    author = "Fabre, Pierre‐Henri and Hautier, Lionel and Dimitrov, Dimitar and Douzery, Emmanuel",
    title = "A glimpse on the pattern of rodent diversification: a phylogenetic approach",
    year = "2012",
    journal = "BMC Evolutionary Biology",
    abstract = "BACKGROUND: Development of phylogenetic methods that do not rely on fossils for the study of evolutionary processes through time have revolutionized the field of evolutionary biology and resulted in an unprecedented expansion of our knowledge about the tree of life. These methods have helped to shed light on the macroevolution of many taxonomic groups such as the placentals (Mammalia). However, despite the increase of studies addressing the diversification patterns of organisms, no synthesis has addressed the case of the most diversified mammalian clade: the Rodentia. RESULTS: Here we present a rodent maximum likelihood phylogeny inferred from a molecular supermatrix. It is based on 11 mitochondrial and nuclear genes that covers 1,265 species, i.e., respectively 56\% and 81\% of the known specific and generic rodent diversity. The inferred topology recovered all Rodentia clades proposed by recent molecular works. A relaxed molecular clock dating approach provided a time framework for speciation events. We found that the Myomorpha clade shows a greater degree of variation in diversification rates than Sciuroidea, Caviomorpha, Castorimorpha and Anomaluromorpha. We identified a number of shifts in diversification rates within the major clades: two in Castorimorpha, three in Ctenohystrica, 6 within the squirrel-related clade and 24 in the Myomorpha clade. The majority of these shifts occurred within the most recent familial rodent radiations: the Cricetidae and Muridae clades. Using the topological imbalances and the time line we discuss the potential role of different diversification factors that might have shaped the rodents radiation. CONCLUSIONS: The present glimpse on the diversification pattern of rodents can be used for further comparative meta-analyses. Muroid lineages have a greater degree of variation in their diversification rates than any other rodent group. Different topological signatures suggest distinct diversification processes among rodent lineages. In particular, Muroidea and Sciuroidea display widespread distribution and have undergone evolutionary and adaptive radiation on most of the continents. Our results show that rodents experienced shifts in diversification rate regularly through the Tertiary, but at different periods for each clade. A comparison between the rodent fossil record and our results suggest that extinction led to the loss of diversification signal for most of the Paleogene nodes.",
    url = "https://doi.org/10.1186/1471-2148-12-88",
    doi = "10.1186/1471-2148-12-88",
    openalex = "W2044886350",
    references = "doi101007bf01734359, doi101016jympev200910033, doi101016s0022283605803602, doi101093bioinformatics149817, doi101093bioinformaticsbtl446, doi101093nargkh340, doi101093oxfordjournalsmolbeva026334, doi101093oxfordjournalsmolbeva040023, doi101111j155856461985tb00420x, doi101126science1156963, doi101186147121487214, doi1023072408678"
}

Why some clades are more species-rich than others is a central question in macroevolution. Most hypotheses explaining exceptionally diverse clades involve the emergence of an ecological opportunity caused by a major biogeographic transition or evolution of a key innovation. The radiation of muroid rodents is an ideal model for testing theories of diversification rates in relation to biogeography and ecological opportunity because the group is exceptionally species-rich (comprising nearly one-third of all mammal species), it is ecologically diverse, and it has colonized every major landmass except New Zealand and Antarctica, thus providing multiple replicate radiations. We present an extension of the conventional ecological opportunity model to include a geographic incumbency effect, develop the largest muroid phylogeny to date, and use this phylogeny to test the new model. The nearly 300-species phylogeny based on four nuclear genes is robustly resolved throughout. Consistent with the fossil record, we identified Eurasia as the most likely origin of the group and reconstructed five to seven colonizations of Africa, five of North America, four of Southeast Asia, two of South America, two of Sahul, one of Madagascar, and eight to ten recolonizations of Eurasia. We accounted for incomplete taxon sampling by using multiple statistical methods and identified three corroborated regions of the tree with significant shifts in diversification rates. In several cases, higher rates were associated with the first colonization of a continental area, but most colonizations were not followed by bursts of speciation. We found strong evidence for diversification consistent with the ecological opportunity model (initial burst followed by density-dependent slowdown) in the first colonization of South America and partial support for this model in the first colonization of Sahul. Primary colonizers appear to inhibit the ultimate diversity of secondary colonizers, a pattern of incumbency that is consistent with ecological opportunity, but they did not inhibit initial diversification rates of secondary colonizers. These results indicate that ecological opportunity may be a general but weak process in muroids and one that requires specific circumstances to lead to an adaptive radiation. The total land area, length of time between colonizations, and rank of colonizations did not influence the diversification rates of primary colonizers. Models currently employed to test ecological opportunity do a poor job of explaining muroid diversity. In addition, the various rate-shift metrics identified different clades, suggesting that caution should be used when only one is applied, and we discuss which methods are most appropriate to address different questions of diversification.

@article{doi101093sysbiosyt050,
    author = "Schenk, John J. and Rowe, Kevin C. and Steppan, Scott J.",
    title = "Ecological Opportunity and Incumbency in the Diversification of Repeated Continental Colonizations by Muroid Rodents",
    year = "2013",
    journal = "Systematic Biology",
    abstract = "Why some clades are more species-rich than others is a central question in macroevolution. Most hypotheses explaining exceptionally diverse clades involve the emergence of an ecological opportunity caused by a major biogeographic transition or evolution of a key innovation. The radiation of muroid rodents is an ideal model for testing theories of diversification rates in relation to biogeography and ecological opportunity because the group is exceptionally species-rich (comprising nearly one-third of all mammal species), it is ecologically diverse, and it has colonized every major landmass except New Zealand and Antarctica, thus providing multiple replicate radiations. We present an extension of the conventional ecological opportunity model to include a geographic incumbency effect, develop the largest muroid phylogeny to date, and use this phylogeny to test the new model. The nearly 300-species phylogeny based on four nuclear genes is robustly resolved throughout. Consistent with the fossil record, we identified Eurasia as the most likely origin of the group and reconstructed five to seven colonizations of Africa, five of North America, four of Southeast Asia, two of South America, two of Sahul, one of Madagascar, and eight to ten recolonizations of Eurasia. We accounted for incomplete taxon sampling by using multiple statistical methods and identified three corroborated regions of the tree with significant shifts in diversification rates. In several cases, higher rates were associated with the first colonization of a continental area, but most colonizations were not followed by bursts of speciation. We found strong evidence for diversification consistent with the ecological opportunity model (initial burst followed by density-dependent slowdown) in the first colonization of South America and partial support for this model in the first colonization of Sahul. Primary colonizers appear to inhibit the ultimate diversity of secondary colonizers, a pattern of incumbency that is consistent with ecological opportunity, but they did not inhibit initial diversification rates of secondary colonizers. These results indicate that ecological opportunity may be a general but weak process in muroids and one that requires specific circumstances to lead to an adaptive radiation. The total land area, length of time between colonizations, and rank of colonizations did not influence the diversification rates of primary colonizers. Models currently employed to test ecological opportunity do a poor job of explaining muroid diversity. In addition, the various rate-shift metrics identified different clades, suggesting that caution should be used when only one is applied, and we discuss which methods are most appropriate to address different questions of diversification.",
    url = "https://doi.org/10.1093/sysbio/syt050",
    doi = "10.1093/sysbio/syt050",
    openalex = "W2101475581",
    references = "doi101007bf01734359, doi10108001621459199510476572, doi101093bioinformatics149817, doi101093bioinformatics178754, doi101093bioinformaticsbtg180, doi101093bioinformaticsbtg412, doi101093bioinformaticsbtl446, doi101109gce20105676129, doi101109tac19741100705, doi101111j155856461947tb01340x, doi101186147121481288, doi101186147121487214"
}

Reconstructing the origin and evolution of land plants and their algal relatives is a fundamental problem in plant phylogenetics, and is essential for understanding how critical adaptations arose, including the embryo, vascular tissue, seeds, and flowers. Despite advances in molecular systematics, some hypotheses of relationships remain weakly resolved. Inferring deep phylogenies with bouts of rapid diversification can be problematic; however, genome-scale data should significantly increase the number of informative characters for analyses. Recent phylogenomic reconstructions focused on the major divergences of plants have resulted in promising but inconsistent results. One limitation is sparse taxon sampling, likely resulting from the difficulty and cost of data generation. To address this limitation, transcriptome data for 92 streptophyte taxa were generated and analyzed along with 11 published plant genome sequences. Phylogenetic reconstructions were conducted using up to 852 nuclear genes and 1,701,170 aligned sites. Sixty-nine analyses were performed to test the robustness of phylogenetic inferences to permutations of the data matrix or to phylogenetic method, including supermatrix, supertree, and coalescent-based approaches, maximum-likelihood and Bayesian methods, partitioned and unpartitioned analyses, and amino acid versus DNA alignments. Among other results, we find robust support for a sister-group relationship between land plants and one group of streptophyte green algae, the Zygnematophyceae. Strong and robust support for a clade comprising liverworts and mosses is inconsistent with a widely accepted view of early land plant evolution, and suggests that phylogenetic hypotheses used to understand the evolution of fundamental plant traits should be reevaluated.

@article{doi101073pnas1323926111,
    author = "Wickett, Norman J. and Mirarab, Siavash and Nguyen, Nam and Warnow, Tandy and Carpenter, Eric and Matasci, Naim and Ayyampalayam, Saravanaraj and Barker, Michael S. and Burleigh, J. Gordon and Gitzendanner, Matthew A. and Ruhfel, Brad R. and Wafula, Eric and Der, Joshua P. and Graham, Sean W. and Mathews, Sarah and Melkonian, Michael and Soltis, Pamela S. and Soltis, Pamela S. and Miles, Nicholas W. and Rothfels, Carl J. and Pokorny, Lisa and Shaw, A. Jonathan and DeGironimo, Lisa and Stevenson, Dennis and Surek, Barbara and Villarreal, Juan Carlos and Roure, Béatrice and Philippe, Hervé and dePamphilis, Claude W. and Chen, Tao and Deyholos, Michael K. and Baucom, Regina S. and Kutchan, Toni M. and Augustin, Megan M. and Wang, Jun and Zhang, Yong and Tian, Zhijian and Yan, Zhixiang and Wu, Xiaolei and Sun, Xiao and Wong, Gane Ka‐Shu and Leebens-Mack, James",
    title = "Phylotranscriptomic analysis of the origin and early diversification of land plants",
    year = "2014",
    journal = "Proceedings of the National Academy of Sciences",
    abstract = "Reconstructing the origin and evolution of land plants and their algal relatives is a fundamental problem in plant phylogenetics, and is essential for understanding how critical adaptations arose, including the embryo, vascular tissue, seeds, and flowers. Despite advances in molecular systematics, some hypotheses of relationships remain weakly resolved. Inferring deep phylogenies with bouts of rapid diversification can be problematic; however, genome-scale data should significantly increase the number of informative characters for analyses. Recent phylogenomic reconstructions focused on the major divergences of plants have resulted in promising but inconsistent results. One limitation is sparse taxon sampling, likely resulting from the difficulty and cost of data generation. To address this limitation, transcriptome data for 92 streptophyte taxa were generated and analyzed along with 11 published plant genome sequences. Phylogenetic reconstructions were conducted using up to 852 nuclear genes and 1,701,170 aligned sites. Sixty-nine analyses were performed to test the robustness of phylogenetic inferences to permutations of the data matrix or to phylogenetic method, including supermatrix, supertree, and coalescent-based approaches, maximum-likelihood and Bayesian methods, partitioned and unpartitioned analyses, and amino acid versus DNA alignments. Among other results, we find robust support for a sister-group relationship between land plants and one group of streptophyte green algae, the Zygnematophyceae. Strong and robust support for a clade comprising liverworts and mosses is inconsistent with a widely accepted view of early land plant evolution, and suggests that phylogenetic hypotheses used to understand the evolution of fundamental plant traits should be reevaluated.",
    url = "https://doi.org/10.1073/pnas.1323926111",
    doi = "10.1073/pnas.1323926111",
    openalex = "W2013277649",
    references = "doi101016jtree200901009, doi101016s0022283605803602, doi10103837918, doi101046j109583392003t01100158x, doi101093bioinformatics83275, doi101093bioinformaticsbtl446, doi101093sysbio463523, doi101093sysbiosyt022, doi101111boj12385, doi101111j10958339200900996x, doi101111j10960031200800217x, doi1011861471214811104, doi101371journalpcbi1002195, doi1023072346830, openalexw3148514506"
}

Estimating rates of speciation and extinction, and understanding how and why they vary over evolutionary time, geographical space and species groups, is a key to understanding how ecological and evolutionary processes generate biological diversity. Such inferences will increasingly benefit from phylogenetic approaches given the ever-accelerating rates of genetic sequencing. In the last few years, models designed to understand diversification from phylogenetic data have advanced significantly. Here, I review these approaches and what they have revealed about diversification in the natural world. I focus on key distinctions between different models, and I clarify the conclusions that can be drawn from each model. I identify promising areas for future research. A major challenge ahead is to develop models that more explicitly take into account ecology, in particular the interaction of species with each other and with their environment. This will not only improve our understanding of diversification; it will also present a new perspective to the use of phylogenies in community ecology, the science of interaction networks and conservation biology, and might shift the current focus in ecology on equilibrium biodiversity theories to non-equilibrium theories recognising the crucial role of history.

@article{doi101111ele12251,
    author = "Morlon, Hélène",
    title = "Phylogenetic approaches for studying diversification",
    year = "2014",
    journal = "Ecology Letters",
    abstract = "Estimating rates of speciation and extinction, and understanding how and why they vary over evolutionary time, geographical space and species groups, is a key to understanding how ecological and evolutionary processes generate biological diversity. Such inferences will increasingly benefit from phylogenetic approaches given the ever-accelerating rates of genetic sequencing. In the last few years, models designed to understand diversification from phylogenetic data have advanced significantly. Here, I review these approaches and what they have revealed about diversification in the natural world. I focus on key distinctions between different models, and I clarify the conclusions that can be drawn from each model. I identify promising areas for future research. A major challenge ahead is to develop models that more explicitly take into account ecology, in particular the interaction of species with each other and with their environment. This will not only improve our understanding of diversification; it will also present a new perspective to the use of phylogenies in community ecology, the science of interaction networks and conservation biology, and might shift the current focus in ecology on equilibrium biodiversity theories to non-equilibrium theories recognising the crucial role of history.",
    url = "https://doi.org/10.1111/ele.12251",
    doi = "10.1111/ele.12251",
    openalex = "W2098713714",
    references = "doi101086660020, doi101371journalpbio1001775"
}

Genomic data are rapidly resolving the tree of living species calibrated to time, the timetree of life, which will provide a framework for research in diverse fields of science. Previous analyses of taxonomically restricted timetrees have found a decline in the rate of diversification in many groups of organisms, often attributed to ecological interactions among species. Here, we have synthesized a global timetree of life from 2,274 studies representing 50,632 species and examined the pattern and rate of diversification as well as the timing of speciation. We found that species diversity has been mostly expanding overall and in many smaller groups of species, and that the rate of diversification in eukaryotes has been mostly constant. We also identified, and avoided, potential biases that may have influenced previous analyses of diversification including low levels of taxon sampling, small clade size, and the inclusion of stem branches in clade analyses. We found consistency in time-to-speciation among plants and animals, ∼2 My, as measured by intervals of crown and stem species times. Together, this clock-like change at different levels suggests that speciation and diversification are processes dominated by random events and that adaptive change is largely a separate process.

@article{doi101093molbevmsv037,
    author = "Hedges, S. Blair and Marin, Julie and Suleski, Michael and Paymer, Madeline and Kumar, Sudhir",
    title = "Tree of Life Reveals Clock-Like Speciation and Diversification",
    year = "2015",
    journal = "Molecular Biology and Evolution",
    abstract = "Genomic data are rapidly resolving the tree of living species calibrated to time, the timetree of life, which will provide a framework for research in diverse fields of science. Previous analyses of taxonomically restricted timetrees have found a decline in the rate of diversification in many groups of organisms, often attributed to ecological interactions among species. Here, we have synthesized a global timetree of life from 2,274 studies representing 50,632 species and examined the pattern and rate of diversification as well as the timing of speciation. We found that species diversity has been mostly expanding overall and in many smaller groups of species, and that the rate of diversification in eukaryotes has been mostly constant. We also identified, and avoided, potential biases that may have influenced previous analyses of diversification including low levels of taxon sampling, small clade size, and the inclusion of stem branches in clade analyses. We found consistency in time-to-speciation among plants and animals, ∼2 My, as measured by intervals of crown and stem species times. Together, this clock-like change at different levels suggests that speciation and diversification are processes dominated by random events and that adaptive change is largely a separate process.",
    url = "https://doi.org/10.1093/molbev/msv037",
    doi = "10.1093/molbev/msv037",
    openalex = "W2117260150",
    references = "doi101007s116920129171x, doi101016b9781483227344500176, doi101017s0094837300008186, doi101038217624a0, doi101038nature05634, doi101038nature11631, doi101073pnas1213199109, doi101093oso97801951358480010001, doi101093oso97801995350330010001, doi101111j1365294x201105239x, doi101126science1194442, doi101126science1211028, doi101126science2785338692, doi101130001676061952631117haaoet20co2, doi101146annurevecolsys110512135800, doi101159000452856, doi101371journalpone0089543"
}

Phylogenetic relationships in Rosaceae have long been problematic because of frequent hybridisation, apomixis and presumed rapid radiation, and their historical diversification has not been clarified. With 87 genera representing all subfamilies and tribes of Rosaceae and six of the other eight families of Rosales (outgroups), we analysed 130 newly sequenced plastomes together with 12 from GenBank in an attempt to reconstruct deep relationships and reveal temporal diversification of this family. Our results highlight the importance of improving sequence alignment and the use of appropriate substitution models in plastid phylogenomics. Three subfamilies and 16 tribes (as previously delimited) were strongly supported as monophyletic, and their relationships were fully resolved and strongly supported at most nodes. Rosaceae were estimated to have originated during the Late Cretaceous with evidence for rapid diversification events during several geological periods. The major lineages rapidly diversified in warm and wet habits during the Late Cretaceous, and the rapid diversification of genera from the early Oligocene onwards occurred in colder and drier environments. Plastid phylogenomics offers new and important insights into deep phylogenetic relationships and the diversification history of Rosaceae. The robust phylogenetic backbone and time estimates we provide establish a framework for future comparative studies on rosaceous evolution.

@article{doi101111nph14461,
    author = "Zhang, Shudong and Jin, Jian‐Jun and Chen, Siyun and Chase, Mark W. and Soltis, Pamela S. and Li, Hongtao and Yang, Jun‐Bo and D, Li and Yi, Ting‐Shuang",
    title = "Diversification of Rosaceae since the Late Cretaceous based on plastid phylogenomics",
    year = "2017",
    journal = "New Phytologist",
    abstract = "Phylogenetic relationships in Rosaceae have long been problematic because of frequent hybridisation, apomixis and presumed rapid radiation, and their historical diversification has not been clarified. With 87 genera representing all subfamilies and tribes of Rosaceae and six of the other eight families of Rosales (outgroups), we analysed 130 newly sequenced plastomes together with 12 from GenBank in an attempt to reconstruct deep relationships and reveal temporal diversification of this family. Our results highlight the importance of improving sequence alignment and the use of appropriate substitution models in plastid phylogenomics. Three subfamilies and 16 tribes (as previously delimited) were strongly supported as monophyletic, and their relationships were fully resolved and strongly supported at most nodes. Rosaceae were estimated to have originated during the Late Cretaceous with evidence for rapid diversification events during several geological periods. The major lineages rapidly diversified in warm and wet habits during the Late Cretaceous, and the rapid diversification of genera from the early Oligocene onwards occurred in colder and drier environments. Plastid phylogenomics offers new and important insights into deep phylogenetic relationships and the diversification history of Rosaceae. The robust phylogenetic backbone and time estimates we provide establish a framework for future comparative studies on rosaceous evolution.",
    url = "https://doi.org/10.1111/nph.14461",
    doi = "10.1111/nph.14461",
    openalex = "W2586653158",
    references = "doi10108010635150490522304, doi10108010635150701472164, doi101093bioinformaticsbtg412, doi101093bioinformaticsbtl446, doi101093bioinformaticsbts199, doi101093nargki198, doi101093oxfordjournalsmolbeva026334, doi101111boj12385, doi101126science1059412, doi101371journalpcbi1003537"
}

We combined new sequence data for more than 300 muroid rodent species with our previously published sequences for up to five nuclear and one mitochondrial genes to generate the most widely and densely sampled hypothesis of evolutionary relationships across Muroidea. An exhaustive screening procedure for publically available sequences was implemented to avoid the propagation of taxonomic errors that are common to supermatrix studies. The combined data set of carefully screened sequences derived from all available sequences on GenBank with our new data resulted in a robust maximum likelihood phylogeny for 900 of the approximately 1,620 muroids. Several regions that were equivocally resolved in previous studies are now more decisively resolved, and we estimated a chronogram using 28 fossil calibrations for the most integrated age and topological estimates to date. The results were used to update muroid classification and highlight questions needing additional data. We also compared the results of multigene supermatrix studies like this one with the principal published supertrees and concluded that the latter are unreliable for any comparative study in muroids. In addition, we explored diversification patterns as an explanation for why muroid rodents represent one of the most species-rich groups of mammals by detecting evidence for increasing net diversification rates through time across the muroid tree. We suggest the observation of increasing rates may be due to a combination of parallel increases in rate across clades and high average extinction rates. Five increased diversification-rate-shifts were inferred, suggesting that multiple, but perhaps not independent, events have led to the remarkable species diversity in the superfamily. Our results provide a phylogenetic framework for comparative studies that is not highly dependent upon the signal from any one gene.

@article{doi101371journalpone0183070,
    author = "Steppan, Scott J. and Schenk, John J.",
    title = "Muroid rodent phylogenetics: 900-species tree reveals increasing diversification rates",
    year = "2017",
    journal = "PLoS ONE",
    abstract = "We combined new sequence data for more than 300 muroid rodent species with our previously published sequences for up to five nuclear and one mitochondrial genes to generate the most widely and densely sampled hypothesis of evolutionary relationships across Muroidea. An exhaustive screening procedure for publically available sequences was implemented to avoid the propagation of taxonomic errors that are common to supermatrix studies. The combined data set of carefully screened sequences derived from all available sequences on GenBank with our new data resulted in a robust maximum likelihood phylogeny for 900 of the approximately 1,620 muroids. Several regions that were equivocally resolved in previous studies are now more decisively resolved, and we estimated a chronogram using 28 fossil calibrations for the most integrated age and topological estimates to date. The results were used to update muroid classification and highlight questions needing additional data. We also compared the results of multigene supermatrix studies like this one with the principal published supertrees and concluded that the latter are unreliable for any comparative study in muroids. In addition, we explored diversification patterns as an explanation for why muroid rodents represent one of the most species-rich groups of mammals by detecting evidence for increasing net diversification rates through time across the muroid tree. We suggest the observation of increasing rates may be due to a combination of parallel increases in rate across clades and high average extinction rates. Five increased diversification-rate-shifts were inferred, suggesting that multiple, but perhaps not independent, events have led to the remarkable species diversity in the superfamily. Our results provide a phylogenetic framework for comparative studies that is not highly dependent upon the signal from any one gene.",
    url = "https://doi.org/10.1371/journal.pone.0183070",
    doi = "10.1371/journal.pone.0183070",
    openalex = "W2749303980",
    references = "doi101038nature05634, doi101093bioinformatics149817, doi101093bioinformaticsbtg180, doi101093bioinformaticsbtg412, doi101093bioinformaticsbtl446, doi101093sysbiosyt050, doi101109gce20105676129, doi101109tac19741100705, doi101111evo12681, doi101111jeb12937, doi101159000452856, doi101186147121481288, doi101186147121487214, doi105860choice441281"
}

Abstract Aim To determine the historical dynamics of colonization and whether the relative timing of colonization predicts diversification rate in the species‐rich, murine rodent communities of Indo‐Australia. Location Indo‐Australian Archipelago including the Sunda shelf of continental Asia, Sahul shelf of continental Australia, the Philippines and Wallacea of Indonesia. Taxon Order Rodentia, Family Muridae. Methods We used a fossil‐calibrated molecular phylogeny and Bayesian biogeographical modelling to infer the frequency and temporal sequence of biogeographical transitions among Sunda, Sahul, the Philippines and Wallacea. We estimated diversification rates for each colonizing lineage using a method‐of‐moments estimator of net diversification and Bayesian mixture model estimates of diversification rate shifts. Results We identified 17 biogeographical transitions, including nine originating from Sunda, seven originating from Sulawesi and broader Wallacea and one originating from Sahul. Wallacea was colonized eight times, the Phillipines five times, Sunda twice and Sahul twice. Net diversification rates ranged from 0.2 to 2.12 species/lineage/My with higher rates in secondary and later colonizers than primary colonizers. The highest rates were in the genus Rattus and their closest relatives, irrespective of colonization history. Main Conclusions Our inferences from murines demonstrate once again the substantial role of islands as sources of species diversity in terrestrial vertebrates of the IAA with most speciation events occurring on islands. Sulawesi and broader Wallacea have been a major source of colonists for both island and continental systems. Crossings of Wallace's Line were more common than subsequent transitions across Lydekker's Line to the east. While speciation following colonization of oceanic archipelagos and large islands is consistent with adaptive radiation theory and ideas regarding ecological opportunity, we did not observe a strong signal of incumbency effects. Rather, subsequent colonists of landmasses radiated unhindered by previous radiations.

@article{doi101111jbi13720,
    author = "Rowe, Kevin C. and Achmadi, Anang S. and Fabre, Pierre‐Henri and Schenk, John J. and Steppan, Scott J. and Esselstyn, Jacob A.",
    title = "Oceanic islands of Wallacea as a source for dispersal and diversification of murine rodents",
    year = "2019",
    journal = "Journal of Biogeography",
    abstract = "Abstract Aim To determine the historical dynamics of colonization and whether the relative timing of colonization predicts diversification rate in the species‐rich, murine rodent communities of Indo‐Australia. Location Indo‐Australian Archipelago including the Sunda shelf of continental Asia, Sahul shelf of continental Australia, the Philippines and Wallacea of Indonesia. Taxon Order Rodentia, Family Muridae. Methods We used a fossil‐calibrated molecular phylogeny and Bayesian biogeographical modelling to infer the frequency and temporal sequence of biogeographical transitions among Sunda, Sahul, the Philippines and Wallacea. We estimated diversification rates for each colonizing lineage using a method‐of‐moments estimator of net diversification and Bayesian mixture model estimates of diversification rate shifts. Results We identified 17 biogeographical transitions, including nine originating from Sunda, seven originating from Sulawesi and broader Wallacea and one originating from Sahul. Wallacea was colonized eight times, the Phillipines five times, Sunda twice and Sahul twice. Net diversification rates ranged from 0.2 to 2.12 species/lineage/My with higher rates in secondary and later colonizers than primary colonizers. The highest rates were in the genus Rattus and their closest relatives, irrespective of colonization history. Main Conclusions Our inferences from murines demonstrate once again the substantial role of islands as sources of species diversity in terrestrial vertebrates of the IAA with most speciation events occurring on islands. Sulawesi and broader Wallacea have been a major source of colonists for both island and continental systems. Crossings of Wallace's Line were more common than subsequent transitions across Lydekker's Line to the east. While speciation following colonization of oceanic archipelagos and large islands is consistent with adaptive radiation theory and ideas regarding ecological opportunity, we did not observe a strong signal of incumbency effects. Rather, subsequent colonists of landmasses radiated unhindered by previous radiations.",
    url = "https://doi.org/10.1111/jbi.13720",
    doi = "10.1111/jbi.13720",
    openalex = "W2978697075",
    references = "doi101086665996, doi101371journalpone0183070"
}

We sequenced the genome of the highly heterozygous almond Prunus dulcis cv. Texas combining short- and long-read sequencing. We obtained a genome assembly totaling 227.6 Mb of the estimated almond genome size of 238 Mb, of which 91% is anchored to eight pseudomolecules corresponding to its haploid chromosome complement, and annotated 27 969 protein-coding genes and 6747 non-coding transcripts. By phylogenomic comparison with the genomes of 16 additional close and distant species we estimated that almond and peach (Prunus persica) diverged around 5.88 million years ago. These two genomes are highly syntenic and show a high degree of sequence conservation (20 nucleotide substitutions per kb). However, they also exhibit a high number of presence/absence variants, many attributable to the movement of transposable elements (TEs). Transposable elements have generated an important number of presence/absence variants between almond and peach, and we show that the recent history of TE movement seems markedly different between them. Transposable elements may also be at the origin of important phenotypic differences between both species, and in particular for the sweet kernel phenotype, a key agronomic and domestication character for almond. Here we show that in sweet almond cultivars, highly methylated TE insertions surround a gene involved in the biosynthesis of amygdalin, whose reduced expression has been correlated with the sweet almond phenotype. Altogether, our results suggest a key role of TEs in the recent history and diversification of almond and its close relative peach.

@article{doi101111tpj14538,
    author = "Alioto, Tyler and Alexiou, Konstantinos G. and Bardil, Amélie and Barteri, Fabio and Castanera, Raúl and Cruz, Fernando and Dhingra, Amit and Duval, Henri and i Martí, Á. Fernández and Frías, Leonor and Galán, Beatriz and Garcı́a, José L. and Howad, Werner and Gómez‐Garrido, Jèssica and Gut, Marta and Julca, Irene and Morata, Jordi and Puigdomènech, Pere and Ribeca, Paolo and Cabetas, María José Rubio and Vlasova, Anna and Wirthensohn, M. and García-Más, Jordi and Gabaldón, Toni and Casacuberta, Josep and Arús, Pere",
    title = "Transposons played a major role in the diversification between the closely related almond and peach genomes: results from the almond genome sequence",
    year = "2019",
    journal = "The Plant Journal",
    abstract = "We sequenced the genome of the highly heterozygous almond Prunus dulcis cv. Texas combining short- and long-read sequencing. We obtained a genome assembly totaling 227.6 Mb of the estimated almond genome size of 238 Mb, of which 91\% is anchored to eight pseudomolecules corresponding to its haploid chromosome complement, and annotated 27 969 protein-coding genes and 6747 non-coding transcripts. By phylogenomic comparison with the genomes of 16 additional close and distant species we estimated that almond and peach (Prunus persica) diverged around 5.88 million years ago. These two genomes are highly syntenic and show a high degree of sequence conservation (20 nucleotide substitutions per kb). However, they also exhibit a high number of presence/absence variants, many attributable to the movement of transposable elements (TEs). Transposable elements have generated an important number of presence/absence variants between almond and peach, and we show that the recent history of TE movement seems markedly different between them. Transposable elements may also be at the origin of important phenotypic differences between both species, and in particular for the sweet kernel phenotype, a key agronomic and domestication character for almond. Here we show that in sweet almond cultivars, highly methylated TE insertions surround a gene involved in the biosynthesis of amygdalin, whose reduced expression has been correlated with the sweet almond phenotype. Altogether, our results suggest a key role of TEs in the recent history and diversification of almond and its close relative peach.",
    url = "https://doi.org/10.1111/tpj.14538",
    doi = "10.1111/tpj.14538",
    openalex = "W2974873635",
    references = "doi101016s0022283605803602, doi101038nbt3122, doi10108010635150390235520, doi101093bioinformaticsbtp324, doi101093bioinformaticsbtq033, doi101093bioinformaticsbts635, doi101093bioinformaticsbtu170, doi101093bioinformaticsbtv351, doi101093nargkh340, doi101093sysbiosyq010, doi101111nph14461"
}

Abstract The foods consumed by animals reflect their adaptations and ecological roles, which makes diet an important trait for ecological, evolutionary, and paleobiological research. Rodents are the most species‐rich order of mammals and are also ecologically diverse, consuming a wide range of foods. To relate form with function, and to study diversification in the context of diet and feeding, researchers should follow classification schemes that capture diet composition. We evaluated existing diet datasets for mammals as well as previous classification schemes developed for rodents. To propose a suitable categorical scheme, we defined splits within plant‐eating and animal‐eating rodents, aiming to capture the intrinsic differences in diet composition in terms of the accessibility, nutrient content, and digestibility of various food items. Our proposal includes eight categories (Carnivore, Folivore, Frugivore, Granivore, Omnivore, Specialist Herbivore, Unknown, and Vermivore) in which species can be assigned with information from species accounts and field guides. To avoid ambiguity, we provide examples and detailed criteria for each diet category. For biologically tractable comparative research, we ask researchers to use our diet categories for rodent species. The categories can also be applied at other taxonomic levels or to different populations, sexes, or ontogenetic stages. We call for further study of the natural history of small mammals and the uptake of primary data into open databases.

@article{doi101111mam12214,
    author = "Arregoitia, Luis D. Verde and D’Elía, Guillermo",
    title = "Classifying rodent diets for comparative research",
    year = "2020",
    journal = "Mammal Review",
    abstract = "Abstract The foods consumed by animals reflect their adaptations and ecological roles, which makes diet an important trait for ecological, evolutionary, and paleobiological research. Rodents are the most species‐rich order of mammals and are also ecologically diverse, consuming a wide range of foods. To relate form with function, and to study diversification in the context of diet and feeding, researchers should follow classification schemes that capture diet composition. We evaluated existing diet datasets for mammals as well as previous classification schemes developed for rodents. To propose a suitable categorical scheme, we defined splits within plant‐eating and animal‐eating rodents, aiming to capture the intrinsic differences in diet composition in terms of the accessibility, nutrient content, and digestibility of various food items. Our proposal includes eight categories (Carnivore, Folivore, Frugivore, Granivore, Omnivore, Specialist Herbivore, Unknown, and Vermivore) in which species can be assigned with information from species accounts and field guides. To avoid ambiguity, we provide examples and detailed criteria for each diet category. For biologically tractable comparative research, we ask researchers to use our diet categories for rodent species. The categories can also be applied at other taxonomic levels or to different populations, sexes, or ontogenetic stages. We call for further study of the natural history of small mammals and the uptake of primary data into open databases.",
    url = "https://doi.org/10.1111/mam.12214",
    doi = "10.1111/mam.12214",
    openalex = "W3080274445",
    references = "doi101016jtree201905008, doi101093jmammalgyy179, doi101111jeb12937"
}

BACKGROUND: Chloroplast (cp) genome information would facilitate the development and utilization of Taxodium resources. However, cp genome characteristics of Taxodium were poorly understood. RESULTS: We determined the complete cp genome sequences of T. distichum, T. mucronatum, and T. ascendens. The cp genomes are 131,947 bp to 132,613 bp in length, encode 120 genes with the same order, and lack typical inverted repeat (IR) regions. The longest small IR, a 282 bp trnQ-containing IR, were involved in the formation of isomers. Comparative analysis of the 3 cp genomes showed that 91.57% of the indels resulted in the periodic variation of tandem repeat (TR) motifs and 72.46% single nucleotide polymorphisms (SNPs) located closely to TRs, suggesting a relationship between TRs and mutational dynamics. Eleven hypervariable regions were identified as candidates for DNA barcode development. Hypothetical cp open reading frame 1(Ycf1) was the only one gene that has an indel in coding DNA sequence, and the indel is composed of a long TR. When extended to cupressophytes, ycf1 genes have undergone a universal insertion of TRs accompanied by extreme length expansion. Meanwhile, ycf1 also located in rearrangement endpoints of cupressophyte cp genomes. All these characteristics highlight the important role of repeats in the evolution of cp genomes. CONCLUSIONS: This study added new evidence for the role of repeats in the dynamics mechanism of cp genome mutation and rearrangement. Moreover, the information of TRs and hypervariable regions would provide reliable molecular resources for future research focusing on the infrageneric taxa identification, phylogenetic resolution, population structure and biodiversity for the genus Taxodium and Cupressophytes.

@article{doi101186s1286402065321,
    author = "Duan, Hao and Guo, Jinbo and Xuan, Lei and Wang, Ziyang and Li, Mingzhi and Yin, Yunlong and Yang, Ying",
    title = "Comparative chloroplast genomics of the genus Taxodium",
    year = "2020",
    journal = "BMC Genomics",
    abstract = "BACKGROUND: Chloroplast (cp) genome information would facilitate the development and utilization of Taxodium resources. However, cp genome characteristics of Taxodium were poorly understood. RESULTS: We determined the complete cp genome sequences of T. distichum, T. mucronatum, and T. ascendens. The cp genomes are 131,947 bp to 132,613 bp in length, encode 120 genes with the same order, and lack typical inverted repeat (IR) regions. The longest small IR, a 282 bp trnQ-containing IR, were involved in the formation of isomers. Comparative analysis of the 3 cp genomes showed that 91.57\% of the indels resulted in the periodic variation of tandem repeat (TR) motifs and 72.46\% single nucleotide polymorphisms (SNPs) located closely to TRs, suggesting a relationship between TRs and mutational dynamics. Eleven hypervariable regions were identified as candidates for DNA barcode development. Hypothetical cp open reading frame 1(Ycf1) was the only one gene that has an indel in coding DNA sequence, and the indel is composed of a long TR. When extended to cupressophytes, ycf1 genes have undergone a universal insertion of TRs accompanied by extreme length expansion. Meanwhile, ycf1 also located in rearrangement endpoints of cupressophyte cp genomes. All these characteristics highlight the important role of repeats in the evolution of cp genomes. CONCLUSIONS: This study added new evidence for the role of repeats in the dynamics mechanism of cp genome mutation and rearrangement. Moreover, the information of TRs and hypervariable regions would provide reliable molecular resources for future research focusing on the infrageneric taxa identification, phylogenetic resolution, population structure and biodiversity for the genus Taxodium and Cupressophytes.",
    url = "https://doi.org/10.1186/s12864-020-6532-1",
    doi = "10.1186/s12864-020-6532-1",
    openalex = "W3013176840",
    references = "doi101038s4143801901711"
}

Among crop fruit trees, the apricot (Prunus armeniaca) provides an excellent model to study divergence and adaptation processes. Here, we obtain nearly 600 Armeniaca apricot genomes and four high-quality assemblies anchored on genetic maps. Chinese and European apricots form two differentiated gene pools with high genetic diversity, resulting from independent domestication events from distinct wild Central Asian populations, and with subsequent gene flow. A relatively low proportion of the genome is affected by selection. Different genomic regions show footprints of selection in European and Chinese cultivated apricots, despite convergent phenotypic traits, with predicted functions in both groups involved in the perennial life cycle, fruit quality and disease resistance. Selection footprints appear more abundant in European apricots, with a hotspot on chromosome 4, while admixture is more pervasive in Chinese cultivated apricots. Our study provides clues to the biology of selected traits and targets for fruit tree research and breeding.

@article{doi101038s41467021242836,
    author = "Groppi, Alexis and Liu, Shuo and Cornille, Amandine and Decroocq, Stéphane and Bui, Quynh Trang and Tricon, David and Cruaud, Corinne and Arribat, Sandrine and Belser, Caroline and Marande, William and Salse, Jérôme and Huneau, Cécile and Rodde, Nathalie and Rhalloussi, Wassim and Cauet, Stéphane and Istace, Benjamin and Denis, Erwan and Carrère, Sébastien and Audergon, Jean-Marc and Roch, Guillaume and Lambert, Patrick and Zhebentyayeva, Tetyana and Liu, Weisheng and Bouchez, Olivier and Lopez‐Roques, Céline and Serre, Rémy-Félix and Debuchy, Robert and Tran, Joseph and Wincker, Patrick and Chen, Xilong and Pétriacq, Pierre and Barré, Aurélien and Nikolski, Macha and Aury, Jean‐Marc and Abbott, Albert G. and Giraud, Tatiana and Decroocq, Véronique",
    title = "Population genomics of apricots unravels domestication history and adaptive events",
    year = "2021",
    journal = "Nature Communications",
    abstract = "Among crop fruit trees, the apricot (Prunus armeniaca) provides an excellent model to study divergence and adaptation processes. Here, we obtain nearly 600 Armeniaca apricot genomes and four high-quality assemblies anchored on genetic maps. Chinese and European apricots form two differentiated gene pools with high genetic diversity, resulting from independent domestication events from distinct wild Central Asian populations, and with subsequent gene flow. A relatively low proportion of the genome is affected by selection. Different genomic regions show footprints of selection in European and Chinese cultivated apricots, despite convergent phenotypic traits, with predicted functions in both groups involved in the perennial life cycle, fruit quality and disease resistance. Selection footprints appear more abundant in European apricots, with a hotspot on chromosome 4, while admixture is more pervasive in Chinese cultivated apricots. Our study provides clues to the biology of selected traits and targets for fruit tree research and breeding.",
    url = "https://doi.org/10.1038/s41467-021-24283-6",
    doi = "10.1038/s41467-021-24283-6",
    openalex = "W3176721616",
    references = "doi101111tpj14538"
}

Abstract Species of Rheum have high medicinal value, with the center of diversity in the Qinghai–Tibet Plateau (QTP) and adjacent regions. However, phylogenetic relationships of Rheum are still unclear due to fragment markers providing insufficient informative loci. Here, we sequenced and annotated plastomes of nine Rheum species, and compared the genome structure among the novel nine species along with three published species. Comparative analyses revealed that plastomes of Rheum share a relatively conserved structure. Five highly divergent regions (accD, ccsA, matK, ndhF, and ndhH) can be used as valuable molecular markers for further species delimitation and population genetic studies. Twenty‐two accessions representing 17 species were used for phylogenetic analysis, which generated a robust phylogenetic tree and revealed two major clades within Rheum. Phylogenetic results showed that glasshouse structures and cushions of Rheum are results of parallel evolution during adaptation to similar environments. Inconsistent tree topology between concatenated and coalescent methods was detected, implying that incomplete lineage sorting and hybridization may have occurred in the evolutionary history of Rheum. Divergence time estimation based on two fossil calibrations and three secondary calibrations revealed a Miocene to middle Oligocene origin of Rheum. Our study provides valuable genomic resources for the medicinally important genus Rheum, while gaining helpful insights into its systematics and evolution.

@article{doi101111jse12814,
    author = "Zhang, Huajie and Zhang, Xu and Landis, Jacob B. and Sun, Yanxia and Sun, Jiao and Kuang, Tianhui and Li, Lijuan and Tiamiyu, Bashir B. and Deng, Tao and Sun, Hang and Wang, Hengchang",
    title = "Phylogenomic and comparative analyses of Rheum (Polygonaceae, Polygonoideae)",
    year = "2021",
    journal = "Journal of Systematics and Evolution",
    abstract = "Abstract Species of Rheum have high medicinal value, with the center of diversity in the Qinghai–Tibet Plateau (QTP) and adjacent regions. However, phylogenetic relationships of Rheum are still unclear due to fragment markers providing insufficient informative loci. Here, we sequenced and annotated plastomes of nine Rheum species, and compared the genome structure among the novel nine species along with three published species. Comparative analyses revealed that plastomes of Rheum share a relatively conserved structure. Five highly divergent regions (accD, ccsA, matK, ndhF, and ndhH) can be used as valuable molecular markers for further species delimitation and population genetic studies. Twenty‐two accessions representing 17 species were used for phylogenetic analysis, which generated a robust phylogenetic tree and revealed two major clades within Rheum. Phylogenetic results showed that glasshouse structures and cushions of Rheum are results of parallel evolution during adaptation to similar environments. Inconsistent tree topology between concatenated and coalescent methods was detected, implying that incomplete lineage sorting and hybridization may have occurred in the evolutionary history of Rheum. Divergence time estimation based on two fossil calibrations and three secondary calibrations revealed a Miocene to middle Oligocene origin of Rheum. Our study provides valuable genomic resources for the medicinally important genus Rheum, while gaining helpful insights into its systematics and evolution.",
    url = "https://doi.org/10.1111/jse.12814",
    doi = "10.1111/jse.12814",
    openalex = "W3211885230",
    references = "doi101016jympev201812023"
}

Phylogenomic evidence from an increasing number of studies has demonstrated that different data sets and analytical approaches often reconstruct strongly supported but conflicting relationships. In this study, 785 single-copy nuclear genes and 75 complete plastomes were used to infer the phylogenetic relationships and estimate the historical biogeography of the apple genus Malus sensu lato, an economically important lineage disjunctly distributed in the Northern Hemisphere and involved in known and suspected hybridization and allopolyploidy events. The nuclear phylogeny recovered the monophyly of Malus s.l. (including Docynia); however, the genus was supported to be biphyletic in the plastid phylogeny. An ancient chloroplast capture event in the Eocene in western North America best explains the cytonuclear discordance. Our conflict analysis demonstrated that ILS, hybridization, and allopolyploidy could explain the widespread nuclear gene tree discordance. One deep hybridization event (Malus doumeri) and one recent event (Malus coronaria) were detected in Malus s.l. Furthermore, our historical biogeographic analysis integrating living and fossil data supported a widespread East Asian-western North American origin of Malus s.l. in the Eocene, followed by several extinction and dispersal events in the Northern Hemisphere. We also propose a general workflow for assessing phylogenomic discordance and biogeographic analysis using deep genome skimming data sets.

@article{doi101111jipb13246,
    author = "Liu, Binbin and Ren, Chen and Kwak, Myounghai and Hodel, Richard G.J. and Xu, Chao and He, Jian and Zhou, Wenbin and Huang, Chien‐Hsun and Mā, Hong and Qian, Guan‐Ze and De‐Yuan, Hong and Wen, Jun",
    title = "Phylogenomic conflict analyses in the apple genus Malus s.l. reveal widespread hybridization and allopolyploidy driving diversification, with insights into the complex biogeographic history in the Northern Hemisphere",
    year = "2022",
    journal = "Journal of Integrative Plant Biology",
    abstract = "Phylogenomic evidence from an increasing number of studies has demonstrated that different data sets and analytical approaches often reconstruct strongly supported but conflicting relationships. In this study, 785 single-copy nuclear genes and 75 complete plastomes were used to infer the phylogenetic relationships and estimate the historical biogeography of the apple genus Malus sensu lato, an economically important lineage disjunctly distributed in the Northern Hemisphere and involved in known and suspected hybridization and allopolyploidy events. The nuclear phylogeny recovered the monophyly of Malus s.l. (including Docynia); however, the genus was supported to be biphyletic in the plastid phylogeny. An ancient chloroplast capture event in the Eocene in western North America best explains the cytonuclear discordance. Our conflict analysis demonstrated that ILS, hybridization, and allopolyploidy could explain the widespread nuclear gene tree discordance. One deep hybridization event (Malus doumeri) and one recent event (Malus coronaria) were detected in Malus s.l. Furthermore, our historical biogeographic analysis integrating living and fossil data supported a widespread East Asian-western North American origin of Malus s.l. in the Eocene, followed by several extinction and dispersal events in the Northern Hemisphere. We also propose a general workflow for assessing phylogenomic discordance and biogeographic analysis using deep genome skimming data sets.",
    url = "https://doi.org/10.1111/jipb.13246",
    doi = "10.1111/jipb.13246",
    openalex = "W4221042877",
    references = "doi101016jympev2020106784, doi10103835075035, doi101093bioinformaticsbtl446, doi101093bioinformaticsbtp348, doi101093bioinformaticsbtu033, doi101093molbevmsaa015, doi101093molbevmsw260, doi101093sysbiosyy032, doi101111nph14461, doi101126science1059412, doi101126science23547931156, doi101371journalpbio0040088"
}

BACKGROUND: The Peucedanum genus is the backbone member of Apiaceae, with many economically and medically important plants. Although the previous studies on Peucedanum provide us with a good research basis, there are still unclear phylogenetic relationships and many taxonomic problems in Peucedanum, and a robust phylogenetic framework of this genus still has not been obtained, which severely hampers the improvement and revision of taxonomic system for this genus. The plastid genomes possessing more variable characters have potential for reconstructing a robust phylogeny in plants. RESULTS: In the current study, we newly sequenced and assembled seven Peucedanum plastid genomes. Together with five previously published plastid genomes of Peucedanum, we performed a comprehensively comparative analyses for this genus. Twelve Peucedanum plastomes were similar in terms of genome structure, codon bias, RNA editing sites, and SSRs, but varied in genome size, gene content and arrangement, and border of SC/IR. Fifteen mutation hotspot regions were identified among plastid genomes that can serve as candidate DNA barcodes for species identification in Peucedanum. Our phylogenetic analyses based on plastid genomes generated a phylogeny with high supports and resolutions for Peucedanum that robustly supported the non-monophyly of genus Peucedanum. CONCLUSION: The plastid genomes of Peucedanum showed both conservation and diversity. The plastid genome data were efficient and powerful for improving the supports and resolutions of phylogeny for the complex Peucedanum genus. In summary, our study provides new sights into the plastid genome evolution, taxonomy, and phylogeny for Peucedanum species.

@article{doi101186s1287002203488x,
    author = "Liu, Chang‐Kun and Lei, Jia-Qing and Jiang, Qiu‐Ping and Zhou, Song‐Dong and He, Xing‐Jin",
    title = "The complete plastomes of seven Peucedanum plants: comparative and phylogenetic analyses for the Peucedanum genus",
    year = "2022",
    journal = "BMC Plant Biology",
    abstract = "BACKGROUND: The Peucedanum genus is the backbone member of Apiaceae, with many economically and medically important plants. Although the previous studies on Peucedanum provide us with a good research basis, there are still unclear phylogenetic relationships and many taxonomic problems in Peucedanum, and a robust phylogenetic framework of this genus still has not been obtained, which severely hampers the improvement and revision of taxonomic system for this genus. The plastid genomes possessing more variable characters have potential for reconstructing a robust phylogeny in plants. RESULTS: In the current study, we newly sequenced and assembled seven Peucedanum plastid genomes. Together with five previously published plastid genomes of Peucedanum, we performed a comprehensively comparative analyses for this genus. Twelve Peucedanum plastomes were similar in terms of genome structure, codon bias, RNA editing sites, and SSRs, but varied in genome size, gene content and arrangement, and border of SC/IR. Fifteen mutation hotspot regions were identified among plastid genomes that can serve as candidate DNA barcodes for species identification in Peucedanum. Our phylogenetic analyses based on plastid genomes generated a phylogeny with high supports and resolutions for Peucedanum that robustly supported the non-monophyly of genus Peucedanum. CONCLUSION: The plastid genomes of Peucedanum showed both conservation and diversity. The plastid genome data were efficient and powerful for improving the supports and resolutions of phylogeny for the complex Peucedanum genus. In summary, our study provides new sights into the plastid genome evolution, taxonomy, and phylogeny for Peucedanum species.",
    url = "https://doi.org/10.1186/s12870-022-03488-x",
    doi = "10.1186/s12870-022-03488-x",
    openalex = "W4220865946",
    references = "doi101016jympev2021107183"
}

, including the Middle Miocene Climate Optimum (MMCO), the late Miocene global cooling, as well as the successive uplift of the Qinghai-Tibet Plateau (QTP) and the strengthening of the monsoon climate in East Asia during the late Miocene and the Pliocene. This case study suggests that the unique geological and climatic events in the Neogene of East Asia, in particular the uplift of QTP and the enhancement of monsoonal climate, may have played an essential role in formation of uneven distribution of plant diversity in the Northern Hemisphere.

@article{doi101016jpld202307009,
    author = "Zhou, Nian and Miao, Ke and Liu, Chang‐Kun and Jia, Lin‐Bo and Hu, Jinjin and Huang, Yong‐Jiang and Ji, Yunheng",
    title = "Historical biogeography and evolutionary diversification of Lilium (Liliaceae): New insights from plastome phylogenomics",
    year = "2023",
    journal = "Plant Diversity",
    abstract = ", including the Middle Miocene Climate Optimum (MMCO), the late Miocene global cooling, as well as the successive uplift of the Qinghai-Tibet Plateau (QTP) and the strengthening of the monsoon climate in East Asia during the late Miocene and the Pliocene. This case study suggests that the unique geological and climatic events in the Neogene of East Asia, in particular the uplift of QTP and the enhancement of monsoonal climate, may have played an essential role in formation of uneven distribution of plant diversity in the Northern Hemisphere.",
    url = "https://doi.org/10.1016/j.pld.2023.07.009",
    doi = "10.1016/j.pld.2023.07.009",
    openalex = "W4385545178",
    references = "doi101016jympev2021107183, doi101126sciadvabg0625"
}

Maleae is one of the most widespread tribes of Rosaceae and includes several important fruit crops and ornamental plants. We used nuclear genes from 62 transcriptomes/genomes, including 26 newly generated transcriptomes, to reconstruct a well-supported phylogeny and study the evolution of fruit and leaf morphology and the possible effect of whole genome duplication (WGD). Our phylogeny recovered 11 well-supported clades and supported the monophyly of most genera (except Malus, Sorbus, and Pourthiaea) with at least two sampled species. A WGD was located to the most recent common ancestor (MRCA) of Maleae and dated to c. 54 million years ago (Ma) near the Early Eocene Climatic Optimum, supporting Gillenieae (x = 9) being a parental lineage of Maleae (x = 17) and including duplicate regulatory genes related to the origin of the fleshy pome fruit. Whole genome duplication-derived paralogs that are retained in specific lineages but lost in others are predicted to function in development, metabolism, and other processes. An upshift of diversification and innovations of fruit and leaf morphologies occurred at the MRCA of the Malinae subtribe, coinciding with the Eocene-Oligocene transition (c. 34 Ma), following a lag from the time of the WGD event. Our results provide new insights into the Maleae phylogeny, its rapid diversification, and morphological and molecular evolution.

@article{doi101111nph19175,
    author = "Zhang, Lin and Morales‐Briones, Diego F. and Li, Yujie and Zhang, Guojin and Zhang, Taikui and Huang, Chien‐Hsun and Guo, Peng and Zhang, Kaiming and Wang, Yihan and Wang, Hongwei and Shang, Fude and Mā, Hong",
    title = "Phylogenomics insights into gene evolution, rapid species diversification, and morphological innovation of the apple tribe (Maleae, Rosaceae)",
    year = "2023",
    journal = "New Phytologist",
    abstract = "Maleae is one of the most widespread tribes of Rosaceae and includes several important fruit crops and ornamental plants. We used nuclear genes from 62 transcriptomes/genomes, including 26 newly generated transcriptomes, to reconstruct a well-supported phylogeny and study the evolution of fruit and leaf morphology and the possible effect of whole genome duplication (WGD). Our phylogeny recovered 11 well-supported clades and supported the monophyly of most genera (except Malus, Sorbus, and Pourthiaea) with at least two sampled species. A WGD was located to the most recent common ancestor (MRCA) of Maleae and dated to c. 54 million years ago (Ma) near the Early Eocene Climatic Optimum, supporting Gillenieae (x = 9) being a parental lineage of Maleae (x = 17) and including duplicate regulatory genes related to the origin of the fleshy pome fruit. Whole genome duplication-derived paralogs that are retained in specific lineages but lost in others are predicted to function in development, metabolism, and other processes. An upshift of diversification and innovations of fruit and leaf morphologies occurred at the MRCA of the Malinae subtribe, coinciding with the Eocene-Oligocene transition (c. 34 Ma), following a lag from the time of the WGD event. Our results provide new insights into the Maleae phylogeny, its rapid diversification, and morphological and molecular evolution.",
    url = "https://doi.org/10.1111/nph.19175",
    doi = "10.1111/nph.19175",
    openalex = "W4385564326",
    references = "doi101111jipb13246"
}

BACKGROUND: The Ferula genus encompasses 180-185 species and is one of the largest genera in Apiaceae, with many of Ferula species possessing important medical value. The previous studies provided more information for Ferula, but its infrageneric relationships are still confusing. In addition, its genetic basis of its adaptive evolution remains poorly understood. Plastid genomes with more variable sites have the potential to reconstruct robust phylogeny in plants and investigate the adaptive evolution of plants. Although chloroplast genomes have been reported within the Ferula genus, few studies have been conducted using chloroplast genomes, especially for endemic species in China. RESULTS: Comprehensively comparative analyses of 22 newly sequenced and assembled plastomes indicated that these plastomes had highly conserved genome structure, gene number, codon usage, and repeats type and distribution, but varied in plastomes size, GC content, and the SC/IR boundaries. Thirteen mutation hotspot regions were detected and they would serve as the promising DNA barcodes candidates for species identification in Ferula and related genera. Phylogenomic analyses with high supports and resolutions showed that Talassia transiliensis and Soranthus meyeri were nested in the Ferula genus, and thus they should be transferred into the Ferula genus. Our phylogenies also indicated the monophyly of subgenera Sinoferula and subgenera Narthex in Ferula genus. Twelve genes with significant posterior probabilities for codon sites were identified in the positively selective analysis, and their function may relate to the photosystem II, ATP subunit, and NADH dehydrogenase. Most of them might play an important role to help Ferula species adapt to high-temperatures, strong-light, and drought habitats. CONCLUSION: Plastome data is powerful and efficient to improve the support and resolution of the complicated Ferula phylogeny. Twelve genes with significant posterior probabilities for codon sites were helpful for Ferula to adapt to the harsh environment. Overall, our study supplies a new perspective for comprehending the phylogeny and evolution of Ferula.

@article{doi101186s12870022040274,
    author = "Qin, Huan-Huan and Cai, Jing and Liu, Chang‐Kun and Zhou, Ren-Xiu and Price, Megan and Zhou, Song‐Dong and He, Xing‐Jin",
    title = "The plastid genome of twenty-two species from Ferula, Talassia, and Soranthus: comparative analysis, phylogenetic implications, and adaptive evolution",
    year = "2023",
    journal = "BMC Plant Biology",
    abstract = "BACKGROUND: The Ferula genus encompasses 180-185 species and is one of the largest genera in Apiaceae, with many of Ferula species possessing important medical value. The previous studies provided more information for Ferula, but its infrageneric relationships are still confusing. In addition, its genetic basis of its adaptive evolution remains poorly understood. Plastid genomes with more variable sites have the potential to reconstruct robust phylogeny in plants and investigate the adaptive evolution of plants. Although chloroplast genomes have been reported within the Ferula genus, few studies have been conducted using chloroplast genomes, especially for endemic species in China. RESULTS: Comprehensively comparative analyses of 22 newly sequenced and assembled plastomes indicated that these plastomes had highly conserved genome structure, gene number, codon usage, and repeats type and distribution, but varied in plastomes size, GC content, and the SC/IR boundaries. Thirteen mutation hotspot regions were detected and they would serve as the promising DNA barcodes candidates for species identification in Ferula and related genera. Phylogenomic analyses with high supports and resolutions showed that Talassia transiliensis and Soranthus meyeri were nested in the Ferula genus, and thus they should be transferred into the Ferula genus. Our phylogenies also indicated the monophyly of subgenera Sinoferula and subgenera Narthex in Ferula genus. Twelve genes with significant posterior probabilities for codon sites were identified in the positively selective analysis, and their function may relate to the photosystem II, ATP subunit, and NADH dehydrogenase. Most of them might play an important role to help Ferula species adapt to high-temperatures, strong-light, and drought habitats. CONCLUSION: Plastome data is powerful and efficient to improve the support and resolution of the complicated Ferula phylogeny. Twelve genes with significant posterior probabilities for codon sites were helpful for Ferula to adapt to the harsh environment. Overall, our study supplies a new perspective for comprehending the phylogeny and evolution of Ferula.",
    url = "https://doi.org/10.1186/s12870-022-04027-4",
    doi = "10.1186/s12870-022-04027-4",
    openalex = "W4313559928",
    references = "doi101016jympev2021107183"
}

BACKGROUND: Pueraria is an edible and medicinal raw material, which is of great value to the pharmaceutical and food industries. Nonetheless, due to morphological diversity and complex domestication history, the classification of Pueraria plants is ambiguous. As the varieties on the market are mixed, the species are difficult to distinguish, and their morphological characteristics are similar to the physical and chemical properties. It is difficult to accurately identify them by traditional identification methods. Chloroplast (cp) genomes are widely used in species identification and phylogenetic studies to achieve accurate identification of medicinal plants, and can also provide more reference information for phylogenetic studies. Based on interspecific and intraspecific sampling, the cp genomes of eight species or varieties of Pueraria plants were examined in this study. RESULTS: The study unveiled that the cp genome size varied from 151,555 to 153,668 base pairs (bp), with the total GC content ranging from 35.4 to 37.0%. Moreover, it was discerned that the cp genome contained between 128 and 135 genes. Comparative analysis indicated that the highest number of Simple Sequence Repeats (SSRs) was identified in P. montana and P. alopecuroides, with a preponderance of these SSRs being rich in Adenine (A) and Thymine (T) nucleotides. Complete comparison and sliding window analysis of the cp genome established that the non-coding region exhibited greater sequence differences than the coding region, and that the large single copy (LSC) region demonstrated higher nucleotide polymorphism levels. Fourteen highly variable loci such as rpoB,ycf1,rbcL,trnF-GAA-trnL,psbC-psbD, and ycf4-cemA were detected as potential molecular markers for Pueraria species identification. Moreover, the phylogenetic tree demonstrated that other Pueraria species had the most distant relationship with Haymondia wallichii and Toxicopueraria peduncularis, thereby offering fresh perspectives into the species classification of Pueraria. The molecular clock analysis results indicate that the divergence time of Pueraria may occur at ∼6.46 Ma. It is speculated that the cold climate may be the cause of Pueraria species diversity and promote the radiation of the genus. CONCLUSION: This research provides theoretical backing and serves as a reference point for the identification and taxonomical classification of Pueraria species. The findings will prove beneficial in future studies on the preservation of medicinal resources, phylogenetic relationships, and genetic engineering of Pueraria plants.

@article{doi101186s12870024059059,
    author = "Hai, Yonglin and Huang, Xianjun and Sun, Hanzhu and Sun, Jing and Li, Jian and Zhang, Yunta and Qian, Yan and Wu, Jingjing and Yang, Yongcheng and Xia, Conglong",
    title = "Comparative analysis of the complete chloroplast genome of Pueraria provides insights for species identification, phylogenetic relationships, and taxonomy",
    year = "2024",
    journal = "BMC Plant Biology",
    abstract = "BACKGROUND: Pueraria is an edible and medicinal raw material, which is of great value to the pharmaceutical and food industries. Nonetheless, due to morphological diversity and complex domestication history, the classification of Pueraria plants is ambiguous. As the varieties on the market are mixed, the species are difficult to distinguish, and their morphological characteristics are similar to the physical and chemical properties. It is difficult to accurately identify them by traditional identification methods. Chloroplast (cp) genomes are widely used in species identification and phylogenetic studies to achieve accurate identification of medicinal plants, and can also provide more reference information for phylogenetic studies. Based on interspecific and intraspecific sampling, the cp genomes of eight species or varieties of Pueraria plants were examined in this study. RESULTS: The study unveiled that the cp genome size varied from 151,555 to 153,668 base pairs (bp), with the total GC content ranging from 35.4 to 37.0\%. Moreover, it was discerned that the cp genome contained between 128 and 135 genes. Comparative analysis indicated that the highest number of Simple Sequence Repeats (SSRs) was identified in P. montana and P. alopecuroides, with a preponderance of these SSRs being rich in Adenine (A) and Thymine (T) nucleotides. Complete comparison and sliding window analysis of the cp genome established that the non-coding region exhibited greater sequence differences than the coding region, and that the large single copy (LSC) region demonstrated higher nucleotide polymorphism levels. Fourteen highly variable loci such as rpoB,ycf1,rbcL,trnF-GAA-trnL,psbC-psbD, and ycf4-cemA were detected as potential molecular markers for Pueraria species identification. Moreover, the phylogenetic tree demonstrated that other Pueraria species had the most distant relationship with Haymondia wallichii and Toxicopueraria peduncularis, thereby offering fresh perspectives into the species classification of Pueraria. The molecular clock analysis results indicate that the divergence time of Pueraria may occur at ∼6.46 Ma. It is speculated that the cold climate may be the cause of Pueraria species diversity and promote the radiation of the genus. CONCLUSION: This research provides theoretical backing and serves as a reference point for the identification and taxonomical classification of Pueraria species. The findings will prove beneficial in future studies on the preservation of medicinal resources, phylogenetic relationships, and genetic engineering of Pueraria plants.",
    url = "https://doi.org/10.1186/s12870-024-05905-9",
    doi = "10.1186/s12870-024-05905-9",
    openalex = "W4405597070",
    references = "doi101038s4143801901711"
}

Phylogenetic comparative methods comprise the general endeavor of using an estimated phylogenetic tree (or set of trees) to make secondary inferences: about trait evolution, diversification dynamics, biogeography, community ecology, and a wide range of other phenomena or processes. Over the past ten years or so, the phytools R package has grown to become an important research tool for phylogenetic comparative analysis. phytools is a diverse contributed R library now consisting of hundreds of different functions covering a variety of methods and purposes in phylogenetic biology. As of the time of writing, phytools included functionality for fitting models of trait evolution, for reconstructing ancestral states, for studying diversification on trees, and for visualizing phylogenies, comparative data, and fitted models, as well numerous other tasks related to phylogenetic biology. Here, I describe some significant features of and recent updates to phytools, while also illustrating several popular workflows of the phytools computational software.

@article{doi107717peerj16505,
    author = "Revell, Liam J.",
    title = "phytools 2.0: an updated R ecosystem for phylogenetic comparative methods (and other things)",
    year = "2024",
    journal = "PeerJ",
    abstract = "Phylogenetic comparative methods comprise the general endeavor of using an estimated phylogenetic tree (or set of trees) to make secondary inferences: about trait evolution, diversification dynamics, biogeography, community ecology, and a wide range of other phenomena or processes. Over the past ten years or so, the phytools R package has grown to become an important research tool for phylogenetic comparative analysis. phytools is a diverse contributed R library now consisting of hundreds of different functions covering a variety of methods and purposes in phylogenetic biology. As of the time of writing, phytools included functionality for fitting models of trait evolution, for reconstructing ancestral states, for studying diversification on trees, and for visualizing phylogenies, comparative data, and fitted models, as well numerous other tasks related to phylogenetic biology. Here, I describe some significant features of and recent updates to phytools, while also illustrating several popular workflows of the phytools computational software.",
    url = "https://doi.org/10.7717/peerj.16505",
    doi = "10.7717/peerj.16505",
    openalex = "W4390608966",
    references = "doi1010079780387217062, doi1010079781441903181, doi10103844766, doi101038nature10516, doi10108010635150802302427, doi101086284325, doi101093bioinformaticsbtg412, doi101093bioinformaticsbty633, doi101093oso97801985464120010001, doi101093sysbiosyt034, doi101093sysbiosyw022, doi1011112041210x12420, doi101111j001438202003tb00285x, doi101111j15585646201001026x, doi101111j2041210x201100169x, doi10118614712105788, doi101371journalpone0089543, doi1023073802723"
}

Interferons (IFNs) are central regulators of innate antiviral immunity, acting through conserved signalling pathways to induce a diverse repertoire of interferon-stimulated genes (ISGs). IFNs have been identified across all lineages of jawed vertebrates, while related antiviral strategies in invertebrates rely on different systems. However, antiviral integrated pathways based on secreted factors analogous to IFN, and using homologous signalling modules, have been reported in Arthropods and Molluscs. This review examines the evolutionary origin, regulation, and functional diversification of ISGs, with an emphasis on fish research. Comparative analyses across vertebrates have revealed a conserved core set of ISGs inherited from the last common ancestor of fish and tetrapods, alongside extensive lineage-specific expansions driven by host-pathogen arms races. In teleost fish, whole-genome duplication events have further shaped ISG repertoires through differential paralog retention, loss, and neo/sub-functionalization. Beyond classical IFN-dependent induction, a subset of ISGs can be activated directly by viral infection, perhaps reflecting remnants of primordial cell-autonomous antiviral responses. Functional redundancy among ISGs underpins the robustness of the IFN system. Finally, the review highlights how recognition of self versus non-self RNA-exemplified by CpG-targeting mechanisms mediated by ZAP-has shaped both viral genomes and ISG sequence evolution. The IFN system as a highly integrated network whose comparative study across vertebrates offers critical insights into antiviral defence and host-virus co-evolution.

@article{doi101016jbj2026100987,
    author = "Collet, Bertrand and Boudinot, Pierre",
    title = "Evolutionary Conservation, Expansion and Diversification of Interferon stimulated genes (ISG) in Vertebrates: insights from fish.",
    year = "2026",
    journal = "Biomedical journal",
    abstract = "Interferons (IFNs) are central regulators of innate antiviral immunity, acting through conserved signalling pathways to induce a diverse repertoire of interferon-stimulated genes (ISGs). IFNs have been identified across all lineages of jawed vertebrates, while related antiviral strategies in invertebrates rely on different systems. However, antiviral integrated pathways based on secreted factors analogous to IFN, and using homologous signalling modules, have been reported in Arthropods and Molluscs. This review examines the evolutionary origin, regulation, and functional diversification of ISGs, with an emphasis on fish research. Comparative analyses across vertebrates have revealed a conserved core set of ISGs inherited from the last common ancestor of fish and tetrapods, alongside extensive lineage-specific expansions driven by host-pathogen arms races. In teleost fish, whole-genome duplication events have further shaped ISG repertoires through differential paralog retention, loss, and neo/sub-functionalization. Beyond classical IFN-dependent induction, a subset of ISGs can be activated directly by viral infection, perhaps reflecting remnants of primordial cell-autonomous antiviral responses. Functional redundancy among ISGs underpins the robustness of the IFN system. Finally, the review highlights how recognition of self versus non-self RNA-exemplified by CpG-targeting mechanisms mediated by ZAP-has shaped both viral genomes and ISG sequence evolution. The IFN system as a highly integrated network whose comparative study across vertebrates offers critical insights into antiviral defence and host-virus co-evolution.",
    url = "https://pubmed.ncbi.nlm.nih.gov/42055280/",
    doi = "10.1016/j.bj.2026.100987",
    openalex = "W7156106042",
    pmid = "42055280",
    references = "doi1010160022283687906899, doi101016jimmuni201903025, doi101038nature09907, doi101038nature11247, doi101038nature17164, doi101038nature19840, doi101038nri1604, doi101038nri2314, doi101146annurevbiochem671227, doi101146annurevimmunol032713120231"
}