Felids

@techreport{matthew1910the1,
    author = "Matthew, W. D",
    title = "THe phylogeny of the Felidae",
    year = "1910",
    howpublished = "American Museum of Natural History Bulletin, v. 28, p. 289-316",
    note = "talkorigins\_source = {true}; raw\_reference = {Matthew, W. D., 1910, THe phylogeny of the Felidae: American Museum of Natural History Bulletin, v. 28, p. 289-316.}"
}

Journal Article The Phylogeny of Dogs Get access W. D. Matthew W. D. Matthew Search for other works by this author on: Oxford Academic Google Scholar Journal of Mammalogy, Volume 11, Issue 2, 9 May 1930, Pages 117–138, https://doi.org/10.2307/1374061 Published: 09 May 1930

@article{doi1023071374061,
    author = "Matthew, W. D.",
    title = "The Phylogeny of Dogs",
    year = "1930",
    journal = "Journal of Mammalogy",
    abstract = "Journal Article The Phylogeny of Dogs Get access W. D. Matthew W. D. Matthew Search for other works by this author on: Oxford Academic Google Scholar Journal of Mammalogy, Volume 11, Issue 2, 9 May 1930, Pages 117–138, https://doi.org/10.2307/1374061 Published: 09 May 1930",
    url = "https://doi.org/10.2307/1374061",
    doi = "10.2307/1374061",
    openalex = "W2043325306"
}

The auditory region of the North American fossil Felidae is described in detail. In the Oligocene Felidae the characters of this region, especially the foramina associated with the veins and arteries of the head, are like those of the modern Canidae rather than the Felidae. On the contrary, all of the middle Miocene (post-John Day) and later genera have typical felid characters in this part of the skull. This has profound significance for the phylogeny and major taxonomy of the family. If any of the species of Oligocene felids are ancestral to the modern forms, an evolution of both the venous and arterial system of the head as well as the auditory bulla must have taken place. This is quite possible, for not only is there theoretical support for it in the ontogeny of modern genera, but there are species that have characters linking the Paleofelides to the Neofelides. Nevertheless, postulating such an evolution is a radical step as it throws doubt upon the validity of the current superfamial classification of the Carnivora. This arrangement is based primarily on the homology of the two-chambered bulla, and the presence or absence of the postglenoid foramen. If, as this paper attempts to show, these structures are not homologous, but have evolved independently in the Viverridae and Felidae (and in other families), the categories Aeluroidea and Arctoidea of Flower (Feloidea and Canoidea of Simpson) have no phylogenetic significance, but are at best convenient divisions applicable to modern genera only.

@article{doi103133pp243g,
    author = "Hough, Jean",
    title = "Auditory region in North American fossil Felidae; its significance in phylogeny",
    year = "1953",
    journal = "USGS professional paper",
    abstract = "The auditory region of the North American fossil Felidae is described in detail. In the Oligocene Felidae the characters of this region, especially the foramina associated with the veins and arteries of the head, are like those of the modern Canidae rather than the Felidae. On the contrary, all of the middle Miocene (post-John Day) and later genera have typical felid characters in this part of the skull. This has profound significance for the phylogeny and major taxonomy of the family. If any of the species of Oligocene felids are ancestral to the modern forms, an evolution of both the venous and arterial system of the head as well as the auditory bulla must have taken place. This is quite possible, for not only is there theoretical support for it in the ontogeny of modern genera, but there are species that have characters linking the Paleofelides to the Neofelides. Nevertheless, postulating such an evolution is a radical step as it throws doubt upon the validity of the current superfamial classification of the Carnivora. This arrangement is based primarily on the homology of the two-chambered bulla, and the presence or absence of the postglenoid foramen. If, as this paper attempts to show, these structures are not homologous, but have evolved independently in the Viverridae and Felidae (and in other families), the categories Aeluroidea and Arctoidea of Flower (Feloidea and Canoidea of Simpson) have no phylogenetic significance, but are at best convenient divisions applicable to modern genera only.",
    url = "https://doi.org/10.3133/pp243g",
    doi = "10.3133/pp243g",
    openalex = "W1520885139",
    references = "doi1010970000505319400100000088, doi101111j146979981869tb07286x, doi1023071374061, doi1023072405524, openalexw2596252908, openalexw2809958608, openalexw609226402"
}

@article{doi101111j1469185x1966tb01624x,
    author = "Gould, Stephen Jay",
    title = "ALLOMETRY AND SIZE IN ONTOGENY AND PHYLOGENY",
    year = "1966",
    journal = "Biological reviews/Biological reviews of the Cambridge Philosophical Society",
    url = "https://doi.org/10.1111/j.1469-185x.1966.tb01624.x",
    doi = "10.1111/j.1469-185x.1966.tb01624.x",
    openalex = "W2082598566",
    references = "colbert1948evolution, doi101001jama196203050110085031, doi101007bf02982279, doi101038114895a0, doi101038137780b0, doi101038164820b0, doi101086280573, doi101093biomet371230, doi101111j155856461949tb00010x, doi101152physrev1947274511, doi1015159780691183978018, doi1023071538742, doi1023072405671, doi1023072527939, doi1023072532815, doi107312rens91062, doi107312simp93764, kermack1954a"
}

* *1. Prospectus * Part I: Recapitulation *2. The Analogistic Tradition from Anaximander to Bonnet * The Seeds of Recapitulation in Greek Science? * Ontogeny and Phylogeny in the Conflict of and Epigenesis: The Idyll of Charles Bonnet * Appendix: The Revolution in *3. Transcendental Origins, 1793--1860 * Naturphilosophie: An Expression of Developmentalism * Two Leading Recapitulationists among the Naturphilosophen: Oken and Meckel * Oken's Classification of Animals Linear Additions of Organs * J. F. Meckel's Sober Statement of the Same Principles * Serres and the French Transcendentalists * Recapitulation and the Theory of Developmental Arrests * Von Baer's Critique of Recapitulation * The Direction of Development and Classification of Animals * Von Baer and Naturphilosophie: What Is the Universal Direction of Development? * Louis Agassiz and the Threefold Parallelism *4. Evolutionary Triumph, 1859--1900 * Evolutionary Theory and Zoological Practice * Darwin and the Evolution of Von Baer' Laws * Evolution and the Mechanics of Recapitulation * Ernst Haeckel: Phylogeny as the Mechanical Cause of Ontogeny * The Mechanism of Recapitulation * The American Neo-Lamarckians: The Law of Acceleration as Evolution's Motor * Progressive Evolution by Acceleration * The Extent of Parallelism * Why Does Recapitulation Dominate the History of Life? * Alpheus Hyatt and Universal Acceleration * Lamarckism and the Memory Analogy * Recapitulation and Darwinism * Appendix: The Evolutionary Translation of von Baer's Laws *5. Pervasive Influence * Criminal Anthropology * Racism * Child Development * Primary Education * Freudian Psychoanalysis * Epilogue *6. Decline, Fall, and Generalization * A Clever Argument * An Empirical Critique * Organs or Ancestors: The Transformation of Haeckel's Heterochrony * Interpolations into Juvenile Stages * Introduction of Juvenile Features into the Adults of Descendants * What Had Become of von Baer's Critique? * Benign Neglect: Recapitulation and the Rise of Experimental Embryology * The Prior Assumptions of Recapitulation * Wilhelm His and His Physiological Embryology: A Preliminary Skirmish * Roux's Entwicklungsmechanik and the Biogenetic Low * Recapitulation and Substantive Issues in Experimental Embryology: The New Preformationism * Mendel's Resurrection, Haeckel's Fall, and the Generalization of Recapitulation * Part II: Heterocrony and Paedomorphosis *7. Heterochrony and the Parallel of Ontogeny and Phylogeny * Acceleration and Retardation * Confusion in and after Haeckel's Wake * Guidelines for a Resolution * The Reduction of de Beer's Categories of Heterochrony to Acceleration and Retardation * A Historical Paradox: The Supposed Dominance of Recapitulation * Dissociability and Heterochrony * Correlation and Disociability * Dissociation of the Three Processes * A Metric for Dissociation * Temporal Shift as a Mechanism of Dissociation * A Clock Model of Heterochrony * Appendix: A Note on the Multivariate Representation of Dissociation *8. The Ecological and Evolutionary Significance of Heterochrony * The Argument from Frequency * The Importance of Recapitulation * The Importance of Heterochronic Change: Selected Cases * Frequency of Paedomorphosis in the Origin of Higher Taxa * A Critique of the Classical Significance of Heterochrony * The Classical Arguments * Retrospective and Immediate Significance * Heterochrony, Ecology, and Life-History Strategies * The Potential Ease and Rapidity of Heterochronic Change * The Control of Metamorphosis in Insects * Amphibian Paedomorphosis and the Thyroid Gland *9. Progenesis and Neoteny Insect Progenesis * Prothetely and Metathetely * Paedogenesis (Parthenogenetic Progenesis) in Gall Midges and Beetles * Progenesis in Wingless, Parthenogenetic Aphids * Additional Cases of Progenesis with a Similar Ecological Basis * Neotenic Solitary Locusts: Are They an Exception to the Rule? * Amphibian Neoteny * The Ecological Determinants of Progenesis * Unstable Environments * Colonization * Parasites * Male Dispersal * Progenesis as an Adaptive Response to Pressures for Small Size * The Role of Heterochrony in Macroevolution: Contrasting Flexibilities for Progenesis and Neoteny * Progenesis * Neoteny * The Social Correlates of Neoteny in Higher Vertebrates *10. Retardation and Neoteny in Human Evolution * The Seeds of Neoteny * The Fetalization Theory of Louis Bolk * Bolk's Data * Bolk's Interpretation * Bolk's Evolutionary Theory * A Tradition of Argument * Retardation in Human Evolution * Morphology in the Matrix of Retardation * Of Enumeration * Of Prototypes * Of Correlation * The Adaptive Significance of Retarded Development *11. Epilogue * Notes * Bibliography * Glossary * Index

@book{openalexw2506868775,
    author = "Gould, Stephen Jay",
    title = "Ontogeny and Phylogeny",
    year = "1977",
    abstract = "* *1. Prospectus * Part I: Recapitulation *2. The Analogistic Tradition from Anaximander to Bonnet * The Seeds of Recapitulation in Greek Science? * Ontogeny and Phylogeny in the Conflict of and Epigenesis: The Idyll of Charles Bonnet * Appendix: The Revolution in *3. Transcendental Origins, 1793--1860 * Naturphilosophie: An Expression of Developmentalism * Two Leading Recapitulationists among the Naturphilosophen: Oken and Meckel * Oken's Classification of Animals Linear Additions of Organs * J. F. Meckel's Sober Statement of the Same Principles * Serres and the French Transcendentalists * Recapitulation and the Theory of Developmental Arrests * Von Baer's Critique of Recapitulation * The Direction of Development and Classification of Animals * Von Baer and Naturphilosophie: What Is the Universal Direction of Development? * Louis Agassiz and the Threefold Parallelism *4. Evolutionary Triumph, 1859--1900 * Evolutionary Theory and Zoological Practice * Darwin and the Evolution of Von Baer' Laws * Evolution and the Mechanics of Recapitulation * Ernst Haeckel: Phylogeny as the Mechanical Cause of Ontogeny * The Mechanism of Recapitulation * The American Neo-Lamarckians: The Law of Acceleration as Evolution's Motor * Progressive Evolution by Acceleration * The Extent of Parallelism * Why Does Recapitulation Dominate the History of Life? * Alpheus Hyatt and Universal Acceleration * Lamarckism and the Memory Analogy * Recapitulation and Darwinism * Appendix: The Evolutionary Translation of von Baer's Laws *5. Pervasive Influence * Criminal Anthropology * Racism * Child Development * Primary Education * Freudian Psychoanalysis * Epilogue *6. Decline, Fall, and Generalization * A Clever Argument * An Empirical Critique * Organs or Ancestors: The Transformation of Haeckel's Heterochrony * Interpolations into Juvenile Stages * Introduction of Juvenile Features into the Adults of Descendants * What Had Become of von Baer's Critique? * Benign Neglect: Recapitulation and the Rise of Experimental Embryology * The Prior Assumptions of Recapitulation * Wilhelm His and His Physiological Embryology: A Preliminary Skirmish * Roux's Entwicklungsmechanik and the Biogenetic Low * Recapitulation and Substantive Issues in Experimental Embryology: The New Preformationism * Mendel's Resurrection, Haeckel's Fall, and the Generalization of Recapitulation * Part II: Heterocrony and Paedomorphosis *7. Heterochrony and the Parallel of Ontogeny and Phylogeny * Acceleration and Retardation * Confusion in and after Haeckel's Wake * Guidelines for a Resolution * The Reduction of de Beer's Categories of Heterochrony to Acceleration and Retardation * A Historical Paradox: The Supposed Dominance of Recapitulation * Dissociability and Heterochrony * Correlation and Disociability * Dissociation of the Three Processes * A Metric for Dissociation * Temporal Shift as a Mechanism of Dissociation * A Clock Model of Heterochrony * Appendix: A Note on the Multivariate Representation of Dissociation *8. The Ecological and Evolutionary Significance of Heterochrony * The Argument from Frequency * The Importance of Recapitulation * The Importance of Heterochronic Change: Selected Cases * Frequency of Paedomorphosis in the Origin of Higher Taxa * A Critique of the Classical Significance of Heterochrony * The Classical Arguments * Retrospective and Immediate Significance * Heterochrony, Ecology, and Life-History Strategies * The Potential Ease and Rapidity of Heterochronic Change * The Control of Metamorphosis in Insects * Amphibian Paedomorphosis and the Thyroid Gland *9. Progenesis and Neoteny Insect Progenesis * Prothetely and Metathetely * Paedogenesis (Parthenogenetic Progenesis) in Gall Midges and Beetles * Progenesis in Wingless, Parthenogenetic Aphids * Additional Cases of Progenesis with a Similar Ecological Basis * Neotenic Solitary Locusts: Are They an Exception to the Rule? * Amphibian Neoteny * The Ecological Determinants of Progenesis * Unstable Environments * Colonization * Parasites * Male Dispersal * Progenesis as an Adaptive Response to Pressures for Small Size * The Role of Heterochrony in Macroevolution: Contrasting Flexibilities for Progenesis and Neoteny * Progenesis * Neoteny * The Social Correlates of Neoteny in Higher Vertebrates *10. Retardation and Neoteny in Human Evolution * The Seeds of Neoteny * The Fetalization Theory of Louis Bolk * Bolk's Data * Bolk's Interpretation * Bolk's Evolutionary Theory * A Tradition of Argument * Retardation in Human Evolution * Morphology in the Matrix of Retardation * Of Enumeration * Of Prototypes * Of Correlation * The Adaptive Significance of Retarded Development *11. Epilogue * Notes * Bibliography * Glossary * Index",
    openalex = "W2506868775",
    references = "doi101086409052, doi101146annureves08110177001045"
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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",
    openalex = "W2013410948",
    references = "doi101007bf01734359, doi101038290699a0, doi101038293057a0, doi101093sysbio274401, doi101111j155856461981tb04991x, doi101126science1864167892, doi101126science6407108, doi101146annureves14110183001525, openalexw191281502, openalexw3045142570"
}

Abstract- Several prominent cladists have questioned the importance of fossils in phylogenctic inference, and it is becoming increasingly popular to simply fit extinct forms, if they are considered at all, to a cladogram of Recent taxa. Gardiner's (1982) and Løvtrup's (1985) study of amniote phylogeny exemplifies this differential treatment, and we focused on that group of organisms to test the proposition that fossils cannot overturn a theory of relationships based only on the Recent biota. Our parsimony analysis of amniote phylogeny, special knowledge contributed by fossils being scrupulously avoided, led to the following best fitting classification, which is similar to the novel hypothesis Gardiner published: (lepidosaurs (turtles (mammals (birds, crocodiles)))). However, adding fossils resulted in a markedly different most parsimonious cladogram of the extant taxa: (mammals (turtles (lepidosaurs (birds, crocodiles)))). That classification is like the traditional hypothesis, and it provides a better fit to the stratigraphic record. To isolate the extinct taxa responsible for the latter classification, the data were successively partitioned with each phylogenetic analysis, and we concluded that: (1) the ingroup, not the outgroup, fossils were important; (2) synapsid, not reptile, fossils were pivotal; (3) certain synapsid fossils, not the earliest or latest, were responsible. The critical nature of the synapsid fossils seemed to lie in the particular combination of primitive and derived character slates they exhibited. Classifying those fossils, along with mammals, as the sister group to the lineage consisting of birds and crocodiles resulted in a relatively poor fit to data; one involving a 2-4 fold increase in evolutionary reversals! Thus, the importance of the critical fossils, collectively or individually, seems to reside in their relative primitive-ness, and the simplest explanation for their more conservative nature is that they have had less time to evolve. While fossils may be important in phylogenetic inference only under certain conditions, there is no compelling reason to prejudge their contribution. We urge systematists to evaluate fairly all of the available evidence.

@article{doi101111j109600311988tb00514x,
    author = "Gauthier, Jacques and Kluge, Arnold G. and Rowe, Timothy",
    title = "AMNIOTE PHYLOGENY AND THE IMPORTANCE OF FOSSILS",
    year = "1988",
    journal = "Cladistics",
    abstract = "Abstract- Several prominent cladists have questioned the importance of fossils in phylogenctic inference, and it is becoming increasingly popular to simply fit extinct forms, if they are considered at all, to a cladogram of Recent taxa. Gardiner's (1982) and Løvtrup's (1985) study of amniote phylogeny exemplifies this differential treatment, and we focused on that group of organisms to test the proposition that fossils cannot overturn a theory of relationships based only on the Recent biota. Our parsimony analysis of amniote phylogeny, special knowledge contributed by fossils being scrupulously avoided, led to the following best fitting classification, which is similar to the novel hypothesis Gardiner published: (lepidosaurs (turtles (mammals (birds, crocodiles)))). However, adding fossils resulted in a markedly different most parsimonious cladogram of the extant taxa: (mammals (turtles (lepidosaurs (birds, crocodiles)))). That classification is like the traditional hypothesis, and it provides a better fit to the stratigraphic record. To isolate the extinct taxa responsible for the latter classification, the data were successively partitioned with each phylogenetic analysis, and we concluded that: (1) the ingroup, not the outgroup, fossils were important; (2) synapsid, not reptile, fossils were pivotal; (3) certain synapsid fossils, not the earliest or latest, were responsible. The critical nature of the synapsid fossils seemed to lie in the particular combination of primitive and derived character slates they exhibited. Classifying those fossils, along with mammals, as the sister group to the lineage consisting of birds and crocodiles resulted in a relatively poor fit to data; one involving a 2-4 fold increase in evolutionary reversals! Thus, the importance of the critical fossils, collectively or individually, seems to reside in their relative primitive-ness, and the simplest explanation for their more conservative nature is that they have had less time to evolve. While fossils may be important in phylogenetic inference only under certain conditions, there is no compelling reason to prejudge their contribution. We urge systematists to evaluate fairly all of the available evidence.",
    url = "https://doi.org/10.1111/j.1096-0031.1988.tb00514.x",
    doi = "10.1111/j.1096-0031.1988.tb00514.x",
    openalex = "W1978557909",
    references = "crossref1943the, currie1985cranial, doi101001jama194302840160064031, doi1010079781468488517, doi101007978146848851721, doi101016002555648290027x, doi1010160169534789901626, doi101016b9781483198279500198, doi101016b9781483231426500124, doi101017cbo9780511693281002, doi101038142004a0, doi10108002724634198810011708, doi101086628623, doi101093sysbio1811, doi101093sysbio33183, doi1010970000505319311100000026, doi101098rstb19830079, doi101111j109636421977tb01031x, doi101111j109636421985tb01796x, doi101146annureven10010165000525, doi1023071005355, doi1023071220820, doi1023071292217, doi1023071441916, doi1023072412407, doi1023072412685, doi1023072413134, doi1023072413259, doi1023072413454, doi1023072485224, doi105281zenodo16171435, doi10560219780801847806, doi105962bhltitle6408, doi105962bhltitle82144, openalexw1534787790, openalexw1534857865, openalexw2954279587, openalexw2983381470, openalexw3146596760, openalexw3184837389, openalexw575222456, roaf1943the"
}

Systematists and evolutionary geneticists don't often talk to each other, and they routinely dispaiage each other's work as being of little relevance to evolution. Systematists sometimes invoke the punctuationist argument that most evolutionary change does not occur by individual selection and hence that within-population phenomena are largely irrelevant to evolution. They sometimes make the pattern-cladist contention that evolutionary processes cannot be inferred from any observation about pattern, nor can any knowledge of evolutionary processes inform inferences about pattern. More frequently systematists feel, with considerable justification, that evolutionary geneticists have simply failed to concern themselves with morphological characters and data on differences between species. Evolutionary geneticists in turn dismiss the idea that studies comparing species anciently diverged, using morphological characters far removed from the level of the gene and using nonquantitative methods, can either be sound in their inferences of pattern or can shed much light on evolutionary processes. Changes in the methods of collecting and analyzing data are invalidating some of these views. Molecular data, such as nucleic acid sequences, give us observations at the gene level that are comparable across many species, and consideration of these data has drawn population geneticists across the species boundary. The availability of microcomputers and digitizers is leading to more quantitation of morphological data by systematists, and the field of

@article{doi101146annureves19110188002305,
    author = "Felsenstein, Joseph",
    title = "PHYLOGENIES AND QUANTITATIVE CHARACTERS",
    year = "1988",
    journal = "Annual Review of Ecology and Systematics",
    abstract = "Systematists and evolutionary geneticists don't often talk to each other, and they routinely dispaiage each other's work as being of little relevance to evolution. Systematists sometimes invoke the punctuationist argument that most evolutionary change does not occur by individual selection and hence that within-population phenomena are largely irrelevant to evolution. They sometimes make the pattern-cladist contention that evolutionary processes cannot be inferred from any observation about pattern, nor can any knowledge of evolutionary processes inform inferences about pattern. More frequently systematists feel, with considerable justification, that evolutionary geneticists have simply failed to concern themselves with morphological characters and data on differences between species. Evolutionary geneticists in turn dismiss the idea that studies comparing species anciently diverged, using morphological characters far removed from the level of the gene and using nonquantitative methods, can either be sound in their inferences of pattern or can shed much light on evolutionary processes. Changes in the methods of collecting and analyzing data are invalidating some of these views. Molecular data, such as nucleic acid sequences, give us observations at the gene level that are comparable across many species, and consideration of these data has drawn population geneticists across the species boundary. The availability of microcomputers and digitizers is leading to more quantitation of morphological data by systematists, and the field of",
    url = "https://doi.org/10.1146/annurev.es.19.110188.002305",
    doi = "10.1146/annurev.es.19.110188.002305",
    openalex = "W2110224102"
}

@incollection{doi101007978146130855319,
    author = "Wozencraft, W. Chris",
    title = "The Phylogeny of the Recent Carnivora",
    year = "1989",
    url = "https://doi.org/10.1007/978-1-4613-0855-3\_19",
    doi = "10.1007/978-1-4613-0855-3\_19",
    openalex = "W4211065429",
    references = "andgray1843list, doi101002jmor1051430103, doi10100797814684216682, doi1010160011747173900107, doi10108011035898309454564, doi101146annureven10010165000525, doi1023071441916, doi1023072992297, doi1023073280934, doi103133pp243g, doi105281zenodo18028696, openalexw1988829823"
}

@incollection{doi101007978147574716419,
    author = "Wozencraft, W. Chris",
    title = "The Phylogeny of the Recent Carnivora",
    year = "1989",
    url = "https://doi.org/10.1007/978-1-4757-4716-4\_19",
    doi = "10.1007/978-1-4757-4716-4\_19",
    openalex = "W1485845513",
    references = "doi103133pp243g"
}

@article{openalexw3199943451,
    author = "Felsenstein, Joe",
    title = "PHYLIP-Phylogeny inference package (Version 3.2)",
    year = "1989",
    journal = "Cladistics",
    openalex = "W3199943451"
}

@article{doi101098rspb19940006,
    title = "Detecting correlated evolution on phylogenies: a general method for the comparative analysis of discrete characters",
    year = "1994",
    journal = "Proceedings of the Royal Society B Biological Sciences",
    url = "https://doi.org/10.1098/rspb.1994.0006",
    doi = "10.1098/rspb.1994.0006",
    openalex = "W2134871125",
    references = "doi101098rstb19890106"
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Variable molecular sequences sampled from a population can be used to infer its dynamic history. Graphical methods are developed and applied to real data, illustrating ways of navigating through hypothesis space with two landmarks for reference: constant population size and exponentially growing population size.

@article{doi101098rstb19950087,
    author = "Nee, Sean and Holmes, Eddie C. and Rambaut, Andrew and Harvey, Paul",
    title = "Inferring population history from molecular phylogenies",
    year = "1995",
    journal = "Philosophical Transactions of the Royal Society B Biological Sciences",
    abstract = "Variable molecular sequences sampled from a population can be used to infer its dynamic history. Graphical methods are developed and applied to real data, illustrating ways of navigating through hypothesis space with two landmarks for reference: constant population size and exponentially growing population size.",
    url = "https://doi.org/10.1098/rstb.1995.0087",
    doi = "10.1098/rstb.1995.0087",
    openalex = "W1978546114"
}

Bruce G. Baldwin, Michael J. Sanderson, J. Mark Porter, Martin F. Wojciechowski, Christopher S. Campbell, Michael J. Donoghue, The its Region of Nuclear Ribosomal DNA: A Valuable Source of Evidence on Angiosperm Phylogeny, Annals of the Missouri Botanical Garden, Vol. 82, No. 2 (1995), pp. 247-277

@article{doi1023072399880,
    author = "Baldwin, Bruce G. and Sanderson, Michael J. and Porter, J. Mark and Wojciechowski, Martin F. and Campbell, Christopher S. and Donoghue, Michael J.",
    title = "The its Region of Nuclear Ribosomal DNA: A Valuable Source of Evidence on Angiosperm Phylogeny",
    year = "1995",
    journal = "Annals of the Missouri Botanical Garden",
    abstract = "Bruce G. Baldwin, Michael J. Sanderson, J. Mark Porter, Martin F. Wojciechowski, Christopher S. Campbell, Michael J. Donoghue, The its Region of Nuclear Ribosomal DNA: A Valuable Source of Evidence on Angiosperm Phylogeny, Annals of the Missouri Botanical Garden, Vol. 82, No. 2 (1995), pp. 247-277",
    url = "https://doi.org/10.2307/2399880",
    doi = "10.2307/2399880",
    openalex = "W2315674852",
    references = "doi101073pnas86239355, doi101093sysbio3817, doi1023072399846, doi1023072419070, doi105860choice392183"
}

@article{doi101006mpev19960085,
    author = "Masuda, Ryuichi and Lopez, Jose V. and Slattery, Jill Pecon and Yuhki, Naoya and O’Brien, Stephen J.",
    title = "Molecular Phylogeny of Mitochondrial Cytochrome b and 12S rRNA Sequences in the Felidae: Ocelot and Domestic Cat Lineages",
    year = "1996",
    journal = "Molecular Phylogenetics and Evolution",
    url = "https://doi.org/10.1006/mpev.1996.0085",
    doi = "10.1006/mpev.1996.0085",
    openalex = "W2066181980",
    references = "doi1010079781461523819, doi101007bf01731581, doi101038290457a0, doi101073pnas74125463, doi101073pnas86166196, doi101093oxfordjournalsmolbeva040454, doi10113719781611970319, doi1023072992540, openalexw2144634347, openalexw3199943451"
}

SEAVIEW and PHYLO_WIN are two graphic tools for X Windows-Unix computers dedicated to sequence alignment and molecular phylogenetics. SEAVIEW is a sequence alignment editor allowing manual or automatic alignment through an interface with CLUSTALW program. Alignment of large sequences with extensive length differences is made easier by a dot-plot-based routine. The PHYLO_WIN program allows phylogenetic tree building according to most usual methods (neighbor joining with numerous distance estimates, maximum parsimony, maximum likelihood), and a bootstrap analysis with any of them. Reconstructed trees can be drawn, edited, printed, stored, evaluated according to numerous criteria. Taxonomic species groups and sets of conserved regions can be defined by mouse and stored into sequence files, thus avoiding multiple data files. Both tools are entirely mouse driven. On-line help makes them easy to use. They are freely available by anonymous ftp at biom3.univ-lyon1.fr/pub/ mol_phylogeny or http:@acnuc.univ-lyon1.fr/, or by e-mail to galtier@biomserv.univ-lyon1.fr.

@article{doi101093bioinformatics126543,
    author = "Galtier, Nicolas and Gouy, Manolo and Gautier, Christian",
    title = "SEAVIEW and PHYLO\_WIN: two graphic tools for sequence alignment and molecular phylogeny",
    year = "1996",
    journal = "Computer applications in the biosciences",
    abstract = "SEAVIEW and PHYLO\_WIN are two graphic tools for X Windows-Unix computers dedicated to sequence alignment and molecular phylogenetics. SEAVIEW is a sequence alignment editor allowing manual or automatic alignment through an interface with CLUSTALW program. Alignment of large sequences with extensive length differences is made easier by a dot-plot-based routine. The PHYLO\_WIN program allows phylogenetic tree building according to most usual methods (neighbor joining with numerous distance estimates, maximum parsimony, maximum likelihood), and a bootstrap analysis with any of them. Reconstructed trees can be drawn, edited, printed, stored, evaluated according to numerous criteria. Taxonomic species groups and sets of conserved regions can be defined by mouse and stored into sequence files, thus avoiding multiple data files. Both tools are entirely mouse driven. On-line help makes them easy to use. They are freely available by anonymous ftp at biom3.univ-lyon1.fr/pub/ mol\_phylogeny or http:@acnuc.univ-lyon1.fr/, or by e-mail to galtier@biomserv.univ-lyon1.fr.",
    url = "https://doi.org/10.1093/bioinformatics/12.6.543",
    doi = "10.1093/bioinformatics/12.6.543",
    openalex = "W2149160071",
    references = "doi101007978140206754912413, doi101007bf02407308, doi101093oxfordjournalsmolbeva040343"
}

This article considers the statistical issues relevant to the comparative method in evolutionary biology. A generalized linear model (GLM) is presented for the analysis of comparative data, which can be used to address questions regarding the relationship between traits or between traits and environments, the rate of phenotypic evolution, the degree of phylogenetic effect, and the ancestral state of a character. Our approach thus emphasizes the similarity among evolutionary questions asked in comparative studies. We then discuss ways of specifying the sources of error involved in a comparative study (e.g., measurement error, error due to evolution along a phylogeny, error due to misspecification of a phylogeny) and show how the impact of these sources of error can be taken into account in a comparative analysis. In contrast to most existing phylogenetic comparative methods, our procedure offers substantial flexibility in the choice of microevolutionary assumptions underlying the statistical analysis, allowing researchers to choose assumptions that are most appropriate for their particular set of data and evolutionary question. In developing the approach, we also propose novel ways of incorporating within-species variation and/or measurement error into phylogenetic analyses, of estimating ancestral states, and of considering both continuous (quantitative) and categorical (qualitative or "state") characters in the same analysis.

@article{doi101086286013,
    author = "Martins, Emı́lia P. and Hansen, Thomas F.",
    title = "Phylogenies and the Comparative Method: A General Approach to Incorporating Phylogenetic Information into the Analysis of Interspecific Data",
    year = "1997",
    journal = "The American Naturalist",
    abstract = {This article considers the statistical issues relevant to the comparative method in evolutionary biology. A generalized linear model (GLM) is presented for the analysis of comparative data, which can be used to address questions regarding the relationship between traits or between traits and environments, the rate of phenotypic evolution, the degree of phylogenetic effect, and the ancestral state of a character. Our approach thus emphasizes the similarity among evolutionary questions asked in comparative studies. We then discuss ways of specifying the sources of error involved in a comparative study (e.g., measurement error, error due to evolution along a phylogeny, error due to misspecification of a phylogeny) and show how the impact of these sources of error can be taken into account in a comparative analysis. In contrast to most existing phylogenetic comparative methods, our procedure offers substantial flexibility in the choice of microevolutionary assumptions underlying the statistical analysis, allowing researchers to choose assumptions that are most appropriate for their particular set of data and evolutionary question. In developing the approach, we also propose novel ways of incorporating within-species variation and/or measurement error into phylogenetic analyses, of estimating ancestral states, and of considering both continuous (quantitative) and categorical (qualitative or "state") characters in the same analysis.},
    url = "https://doi.org/10.1086/286013",
    doi = "10.1086/286013",
    openalex = "W1963617394",
    references = "doi10100703872725509, doi101086284325, doi101093sysbio41118, doi101098rstb19890106, doi101111j155856461949tb00004x, doi101111j155856461976tb00911x, doi101111j155856461985tb05699x, doi101111j155856461996tb03914x, doi1023072290548, doi1023072992183, doi105860choice295104, openalexw63174745"
}

@article{doi101023a1001761008817,
    author = "Kurtzman, Cletus P. and Robnett, Christie J.",
    title = "Identification and phylogeny of ascomycetous yeasts from analysis of nuclear large subunit (26S) ribosomal DNA partial sequences",
    year = "1998",
    journal = "Antonie van Leeuwenhoek",
    url = "https://doi.org/10.1023/a:1001761008817",
    doi = "10.1023/a:1001761008817",
    openalex = "W1868830645",
    references = "doi101007978140206754912413, doi101093sysbio422182, doi1023072992540"
}

The ® eld of ge om etric m orphom etrics is relatively new (see Books tein, 1991; R ohlf and M arcus, 1993) and has show n very rap id pro gress over the last few years.A s m igh t be exp ected du rin g a period of rapid develop m en t, there can be technical problem s in som e of the p ioneerin g studies as biologists attem p t to apply the new tools.It is only now becom ing clear how the new techniques shou ld be com bined in order to carry out com prehens ive analyses of real data sets.Bookstein (1996b) gave a list of recom m en dations for such ap plications, and Bo okstein (1996a) gave severa l com prehen sive exam ples of m orphom etric analyses.However, these accounts do no t address som e of the typ es of ap plications that are of p articular in tere st in sy stem atic b io lo g y.B o o k st ein (1 9 9 4) p o in t e d ou t problem s w ith usin g ge om etric m orphom etric methods in the usual characterbased cladistic studies.He em phasized that m orphom etrics cann ot sup ply hom ologou s sh ap e characters.The purp ose of this note is to com m ent about som e recent ap plications of m orphom etric m ethods in sy stem atic biolog y.This note is p articularly concerned w ith the morphom etric methods used by Zelditch et al. (1992Zelditch et al. (, 1993Zelditch et al. (, 1995)), Sw idersk i (1993), Fink and Zeld itch (1995), and Zelditch and Fink (1995).The se m ethods were also used by Burke et al. (1996).For conven ience, these studies w ill be referred to usin g the acrony m Z& F. In these studies the authors investigated the use of partial warp s (Bookstein, 1991) as variables in ontogenetic and taxonom ic studies.They were im pressed by their observation that differen ces in p artia l warp s scores (R ohlf, 1993b) corre sponded to sh ape differen ces

@article{doi101080106351598261094,
    author = "Rohlf, F. James",
    title = "On Applications of Geometric Morphometrics to Studies of Ontogeny and Phylogeny",
    year = "1998",
    journal = "Systematic Biology",
    abstract = "The ® eld of ge om etric m orphom etrics is relatively new (see Books tein, 1991; R ohlf and M arcus, 1993) and has show n very rap id pro gress over the last few years.A s m igh t be exp ected du rin g a period of rapid develop m en t, there can be technical problem s in som e of the p ioneerin g studies as biologists attem p t to apply the new tools.It is only now becom ing clear how the new techniques shou ld be com bined in order to carry out com prehens ive analyses of real data sets.Bookstein (1996b) gave a list of recom m en dations for such ap plications, and Bo okstein (1996a) gave severa l com prehen sive exam ples of m orphom etric analyses.However, these accounts do no t address som e of the typ es of ap plications that are of p articular in tere st in sy stem atic b io lo g y.B o o k st ein (1 9 9 4) p o in t e d ou t problem s w ith usin g ge om etric m orphom etric methods in the usual characterbased cladistic studies.He em phasized that m orphom etrics cann ot sup ply hom ologou s sh ap e characters.The purp ose of this note is to com m ent about som e recent ap plications of m orphom etric m ethods in sy stem atic biolog y.This note is p articularly concerned w ith the morphom etric methods used by Zelditch et al. (1992Zelditch et al. (, 1993Zelditch et al. (, 1995)), Sw idersk i (1993), Fink and Zeld itch (1995), and Zelditch and Fink (1995).The se m ethods were also used by Burke et al. (1996).For conven ience, these studies w ill be referred to usin g the acrony m Z\& F. In these studies the authors investigated the use of partial warp s (Bookstein, 1991) as variables in ontogenetic and taxonom ic studies.They were im pressed by their observation that differen ces in p artia l warp s scores (R ohlf, 1993b) corre sponded to sh ape differen ces",
    url = "https://doi.org/10.1080/106351598261094",
    doi = "10.1080/106351598261094",
    openalex = "W2155970995",
    references = "doi101017cbo9780511529870"
}

Phylogenies reconstructed from gene sequences can be used to investigate the tempo and mode of species diversification. Here we develop and use new statistical methods to infer past patterns of speciation and extinction from molecular phylogenies. Specifically, we test the null hypothesis that per-lineage speciation and extinction rates have remained constant through time. Rejection of this hypothesis may provide evidence for evolutionary events such as adaptive radiations or key adaptations. In contrast to previous approaches, our methods are robust to incomplete taxon sampling and are conservative with respect to extinction. Using simulation we investigate, first, the adverse effects of failing to take incomplete sampling into account and, second, the power and reliability of our tests. When applied to published phylogenies our tests suggest that, in some cases, speciation rates have decreased through time.

@article{doi101098rspb20001278,
    author = "Pybus, Oliver G. and Harvey, Paul",
    title = "Testing macro–evolutionary models using incomplete molecular phylogenies",
    year = "2000",
    journal = "Proceedings of the Royal Society B Biological Sciences",
    abstract = "Phylogenies reconstructed from gene sequences can be used to investigate the tempo and mode of species diversification. Here we develop and use new statistical methods to infer past patterns of speciation and extinction from molecular phylogenies. Specifically, we test the null hypothesis that per-lineage speciation and extinction rates have remained constant through time. Rejection of this hypothesis may provide evidence for evolutionary events such as adaptive radiations or key adaptations. In contrast to previous approaches, our methods are robust to incomplete taxon sampling and are conservative with respect to extinction. Using simulation we investigate, first, the adverse effects of failing to take incomplete sampling into account and, second, the power and reliability of our tests. When applied to published phylogenies our tests suggest that, in some cases, speciation rates have decreased through time.",
    url = "https://doi.org/10.1098/rspb.2000.1278",
    doi = "10.1098/rspb.2000.1278",
    openalex = "W2118610143",
    references = "doi101086627905"
}

The phylogeny of the Felidae is reconstructed using a total evidence approach combining sequences from 12S rRNA, 16S rRNA, NADH-5, and cytochrome b genes with morphological and karyological characters. The 1504-character data set generated two equally parsimonious trees (CI = 0.413, 1795 steps) of which a strict consensus revealed one polytomy in the placement of the bay cat group. The tree supports several traditional groupings such as the genera Panthera and Lynx and the ocelot group of small South American felids, and it provides additional resolution of relationships within and among the major felid lineages. Combining phylogenetic, distributional, and ecological data indicates that vicariant speciation has played a relatively minor role in the diversification of the felids (approximately 26% of events), while sympatric speciation has been more important than expected on theoretical grounds (approximately 51.8% of events), although postspeciation dispersal may have blurred the boundaries between sympatric, parapatric, and peripheral isolate modes. An examination of ecological changes on the felid tree shows repeated patterns of resource partitioning in time (activity patterns), space (preferred habitat type), and food (as measured by body size) among closely related species. The rapid diversification of the cats thus appears to have been associated more with ecological than with geological separation.

@article{doi101111j109600312000tb00354x,
    author = "Mattern, Michelle and McLennan, Deborah A.",
    title = "Phylogeny and Speciation of Felids",
    year = "2000",
    journal = "Cladistics",
    abstract = "The phylogeny of the Felidae is reconstructed using a total evidence approach combining sequences from 12S rRNA, 16S rRNA, NADH-5, and cytochrome b genes with morphological and karyological characters. The 1504-character data set generated two equally parsimonious trees (CI = 0.413, 1795 steps) of which a strict consensus revealed one polytomy in the placement of the bay cat group. The tree supports several traditional groupings such as the genera Panthera and Lynx and the ocelot group of small South American felids, and it provides additional resolution of relationships within and among the major felid lineages. Combining phylogenetic, distributional, and ecological data indicates that vicariant speciation has played a relatively minor role in the diversification of the felids (approximately 26\% of events), while sympatric speciation has been more important than expected on theoretical grounds (approximately 51.8\% of events), although postspeciation dispersal may have blurred the boundaries between sympatric, parapatric, and peripheral isolate modes. An examination of ecological changes on the felid tree shows repeated patterns of resource partitioning in time (activity patterns), space (preferred habitat type), and food (as measured by body size) among closely related species. The rapid diversification of the cats thus appears to have been associated more with ecological than with geological separation.",
    url = "https://doi.org/10.1111/j.1096-0031.2000.tb00354.x",
    doi = "10.1111/j.1096-0031.2000.tb00354.x",
    openalex = "W2088764137",
    references = "doi101007978140206754912413, doi101038260204c0, doi101086282070, doi101086282505, doi101126science185414527, doi101146annureven10010165000525, doi101353book59141, doi1023072485224, doi104159harvard9780674865327, doi105860choice392183"
}

MacClade is a computer program, with accompanying manual, that provides theory and tools for the graphic and interactive analysis of molecular and morphological data, phylogeny, and character evolution. Systematists and other evolutionary biologists can use its flexible tools to analyse phylogeny and character evolution, yet its ease of use allows beginning students to grasp phylogenetic principles in an interactive environment.

@article{doi105860choice392183,
    title = "MacClade 4.0: analysis of phylogeny and character evolution",
    year = "2001",
    journal = "Choice Reviews Online",
    abstract = "MacClade is a computer program, with accompanying manual, that provides theory and tools for the graphic and interactive analysis of molecular and morphological data, phylogeny, and character evolution. Systematists and other evolutionary biologists can use its flexible tools to analyse phylogeny and character evolution, yet its ease of use allows beginning students to grasp phylogenetic principles in an interactive environment.",
    url = "https://doi.org/10.5860/choice.39-2183",
    doi = "10.5860/choice.39-2183",
    openalex = "W1522592213"
}

▪ Abstract As better phylogenetic hypotheses become available for many groups of organisms, studies in community ecology can be informed by knowledge of the evolutionary relationships among coexisting species. We note three primary approaches to integrating phylogenetic information into studies of community organization: 1. examining the phylogenetic structure of community assemblages, 2. exploring the phylogenetic basis of community niche structure, and 3. adding a community context to studies of trait evolution and biogeography. We recognize a common pattern of phylogenetic conservatism in ecological character and highlight the challenges of using phylogenies of partial lineages. We also review phylogenetic approaches to three emergent properties of communities: species diversity, relative abundance distributions, and range sizes. Methodological advances in phylogenetic supertree construction, character reconstruction, null models for community assembly and character evolution, and metrics of community phylogenetic structure underlie the recent progress in these areas. We highlight the potential for community ecologists to benefit from phylogenetic knowledge and suggest several avenues for future research.

@article{doi101146annurevecolsys33010802150448,
    author = "Webb, Campbell O. and Ackerly, David D. and McPeek, Mark A. and Donoghue, Michael J.",
    title = "Phylogenies and Community Ecology",
    year = "2002",
    journal = "Annual Review of Ecology and Systematics",
    abstract = "▪ Abstract As better phylogenetic hypotheses become available for many groups of organisms, studies in community ecology can be informed by knowledge of the evolutionary relationships among coexisting species. We note three primary approaches to integrating phylogenetic information into studies of community organization: 1. examining the phylogenetic structure of community assemblages, 2. exploring the phylogenetic basis of community niche structure, and 3. adding a community context to studies of trait evolution and biogeography. We recognize a common pattern of phylogenetic conservatism in ecological character and highlight the challenges of using phylogenies of partial lineages. We also review phylogenetic approaches to three emergent properties of communities: species diversity, relative abundance distributions, and range sizes. Methodological advances in phylogenetic supertree construction, character reconstruction, null models for community assembly and character evolution, and metrics of community phylogenetic structure underlie the recent progress in these areas. We highlight the potential for community ecologists to benefit from phylogenetic knowledge and suggest several avenues for future research.",
    url = "https://doi.org/10.1146/annurev.ecolsys.33.010802.150448",
    doi = "10.1146/annurev.ecolsys.33.010802.150448",
    openalex = "W2109628725",
    references = "doi10100797814615696881, doi101007978303487527124, doi101007bf02806171, doi101016s0169534701021619, doi101038363342a0, doi10108010292389509380518, doi101086282106, doi101086282505, doi101086284325, doi101086285258, doi101086285357, doi101086627905, doi101093oso97801985052350010001, doi101093oso97801985464120010001, doi101093oxfordjournalsmolbeva003974, doi101093oxfordjournalsmolbeva025892, doi101098rstb19950125, doi101111j001438202001tb00826x, doi101111j109583122001tb01368x, doi101126science20343871299, doi101126science2354785167, doi101126science2785338692, doi101126science27953592115, doi101126science28554311265, doi101146annurevecolsys311343, doi1015159781400881376, doi1023071446122, doi1023071939377, doi1023072412182, doi1023072413039, doi1023072485224, doi1023073071998, doi1023073544421, doi1023075503, doi102307jctv1nzfgj7, doi105860choice295104, doi105860choice375647, doi105860choice392183, openalexw2273605253, openalexw3035987306"
}

@article{doi101038nature02053,
    author = "Rokas, Antonis and Williams, Barry L. and King, Nicole and Carroll, Sean B.",
    title = "Genome-scale approaches to resolving incongruence in molecular phylogenies",
    year = "2003",
    journal = "Nature",
    url = "https://doi.org/10.1038/nature02053",
    doi = "10.1038/nature02053",
    openalex = "W2068225247",
    references = "doi10103835054550, doi101038387489a0, doi101093sysbio463523, doi101126science28454232129, doi1014601phytopatholmediterr14998u129"
}

The muroid rodents are the largest superfamily of mammals, containing nearly one third of all mammal species. We report on a phylogenetic study comprising 53 genera sequenced for four nuclear genes, GHR, BRCA1, RAG1, and c-myc, totaling up to 6400 nucleotides. Most relationships among the subfamilies are resolved. All four genes yield nearly identical phylogenies, differing only in five key regions, four of which may represent particularly rapid radiations. Support is very strong for a fundamental division of the mole rats of the subfamilies Spalacinae and Rhizomyinae from all other muroids. Among the other "core" muroids, a rapid radiation led to at least four distinct lineages: Asian Calomyscus, an African clade of at least four endemic subfamilies, including the diverse Nesomyinae of Madagascar, a hamster clade with maximum diversity in the New World, and an Old World clade including gerbils and the diverse Old World mice and rats (Murinae). The Deomyinae, recently removed from the Murinae, is well supported as the sister group to the gerbils (Gerbillinae). Four key regions appear to represent rapid radiations and, despite a large amount of sequence data, remain poorly resolved: the base of the "core" muroids, among the five cricetid (hamster) subfamilies, within a large clade of Sigmodontinae endemic to South America, and among major geographic lineages of Old World Murinae. Because of the detailed taxon sampling within the Murinae, we are able to refine the fossil calibration of a rate-smoothed molecular clock and apply this clock to date key events in muroid evolution. We calculate rate differences among the gene regions and relate those differences to relative contribution of each gene to the support for various nodes. The among-gene variance in support is greatest for the shortest branches. We present a revised classification for this largest but most unsettled mammalian superfamily.

@article{doi10108010635150490468701,
    author = "Steppan, Scott J. and Adkins, Ronald M. and Anderson, Joel",
    title = "Phylogeny and Divergence-Date Estimates of Rapid Radiations in Muroid Rodents Based on Multiple Nuclear Genes",
    year = "2004",
    journal = "Systematic Biology",
    abstract = {The muroid rodents are the largest superfamily of mammals, containing nearly one third of all mammal species. We report on a phylogenetic study comprising 53 genera sequenced for four nuclear genes, GHR, BRCA1, RAG1, and c-myc, totaling up to 6400 nucleotides. Most relationships among the subfamilies are resolved. All four genes yield nearly identical phylogenies, differing only in five key regions, four of which may represent particularly rapid radiations. Support is very strong for a fundamental division of the mole rats of the subfamilies Spalacinae and Rhizomyinae from all other muroids. Among the other "core" muroids, a rapid radiation led to at least four distinct lineages: Asian Calomyscus, an African clade of at least four endemic subfamilies, including the diverse Nesomyinae of Madagascar, a hamster clade with maximum diversity in the New World, and an Old World clade including gerbils and the diverse Old World mice and rats (Murinae). The Deomyinae, recently removed from the Murinae, is well supported as the sister group to the gerbils (Gerbillinae). Four key regions appear to represent rapid radiations and, despite a large amount of sequence data, remain poorly resolved: the base of the "core" muroids, among the five cricetid (hamster) subfamilies, within a large clade of Sigmodontinae endemic to South America, and among major geographic lineages of Old World Murinae. Because of the detailed taxon sampling within the Murinae, we are able to refine the fossil calibration of a rate-smoothed molecular clock and apply this clock to date key events in muroid evolution. We calculate rate differences among the gene regions and relate those differences to relative contribution of each gene to the support for various nodes. The among-gene variance in support is greatest for the shortest branches. We present a revised classification for this largest but most unsettled mammalian superfamily.},
    url = "https://doi.org/10.1080/10635150490468701",
    doi = "10.1080/10635150490468701",
    openalex = "W2164341121"
}

Biologists frequently attempt to infer the character states at ancestral nodes of a phylogeny from the distribution of traits observed in contemporary organisms. Because phylogenies are normally inferences from data, it is desirable to account for the uncertainty in estimates of the tree and its branch lengths when making inferences about ancestral states or other comparative parameters. Here we present a general Bayesian approach for testing comparative hypotheses across statistically justified samples of phylogenies, focusing on the specific issue of reconstructing ancestral states. The method uses Markov chain Monte Carlo techniques for sampling phylogenetic trees and for investigating the parameters of a statistical model of trait evolution. We describe how to combine information about the uncertainty of the phylogeny with uncertainty in the estimate of the ancestral state. Our approach does not constrain the sample of trees only to those that contain the ancestral node or nodes of interest, and we show how to reconstruct ancestral states of uncertain nodes using a most-recent-common-ancestor approach. We illustrate the methods with data on ribonuclease evolution in the Artiodactyla. Software implementing the methods (BayesMultiState) is available from the authors.

@article{doi10108010635150490522232,
    author = "Pagel, Mark and Meade, Andrew and Barker, Daniel",
    title = "Bayesian Estimation of Ancestral Character States on Phylogenies",
    year = "2004",
    journal = "Systematic Biology",
    abstract = "Biologists frequently attempt to infer the character states at ancestral nodes of a phylogeny from the distribution of traits observed in contemporary organisms. Because phylogenies are normally inferences from data, it is desirable to account for the uncertainty in estimates of the tree and its branch lengths when making inferences about ancestral states or other comparative parameters. Here we present a general Bayesian approach for testing comparative hypotheses across statistically justified samples of phylogenies, focusing on the specific issue of reconstructing ancestral states. The method uses Markov chain Monte Carlo techniques for sampling phylogenetic trees and for investigating the parameters of a statistical model of trait evolution. We describe how to combine information about the uncertainty of the phylogeny with uncertainty in the estimate of the ancestral state. Our approach does not constrain the sample of trees only to those that contain the ancestral node or nodes of interest, and we show how to reconstruct ancestral states of uncertain nodes using a most-recent-common-ancestor approach. We illustrate the methods with data on ribonuclease evolution in the Artiodactyla. Software implementing the methods (BayesMultiState) is available from the authors.",
    url = "https://doi.org/10.1080/10635150490522232",
    doi = "10.1080/10635150490522232",
    openalex = "W2096484952",
    references = "doi10103844766, doi101080106351501753462876, doi101111j146364091997tb00423x"
}

The cat family Felidae was used as a species tree to assess the phylogenetic performance of genes, and their embedded SINE elements, within the nonrecombining region of the Y chromosome (NRY). Genomic segments from single-copy X-Y homologs SMCY, UBE1Y, and ZFY (3,604 bp) were amplified in 36 species of cat. These genes are located within the X-degenerate region of the NRY and are thought to be molecular "fossils" that ceased conventional recombination with the X chromosome early within the placental mammal evolution. The pattern and tempo of evolution at these three genes is significant in light of the recent, rapid evolution of the family over approximately 12 Myr and provides exceptional support for each of the eight recognized felid lineages, as well as clear diagnostic substitutions identifying nearly all species. Bootstrap support and Bayesian posterior probabilities are uniformly high for defining each of the eight monophyletic lineages. Further, the preferential use of specific target-site motifs facilitating SINE insertion is empirically supported by sequence analyses of SINEs embedded within the three genes. Target-site insertion is thought to explain the contradiction between intron phylogeny and results of the SMCY SINE phylogeny that unites distantly related species. Overall, our data suggest X-degenerate genes within the NRY are singularly powerful markers and offer a valuable patrilineal perspective in species evolution.

@article{doi101093molbevmsh241,
    author = "Pecon‐Slattery, Jill and Wilkerson, Alison J. Pearks and Murphy, William J. and O’Brien, Stephen J.",
    title = "Phylogenetic Assessment of Introns and SINEs Within the Y Chromosome Using the Cat Family Felidae As a Species Tree",
    year = "2004",
    journal = "Molecular Biology and Evolution",
    abstract = {The cat family Felidae was used as a species tree to assess the phylogenetic performance of genes, and their embedded SINE elements, within the nonrecombining region of the Y chromosome (NRY). Genomic segments from single-copy X-Y homologs SMCY, UBE1Y, and ZFY (3,604 bp) were amplified in 36 species of cat. These genes are located within the X-degenerate region of the NRY and are thought to be molecular "fossils" that ceased conventional recombination with the X chromosome early within the placental mammal evolution. The pattern and tempo of evolution at these three genes is significant in light of the recent, rapid evolution of the family over approximately 12 Myr and provides exceptional support for each of the eight recognized felid lineages, as well as clear diagnostic substitutions identifying nearly all species. Bootstrap support and Bayesian posterior probabilities are uniformly high for defining each of the eight monophyletic lineages. Further, the preferential use of specific target-site motifs facilitating SINE insertion is empirically supported by sequence analyses of SINEs embedded within the three genes. Target-site insertion is thought to explain the contradiction between intron phylogeny and results of the SMCY SINE phylogeny that unites distantly related species. Overall, our data suggest X-degenerate genes within the NRY are singularly powerful markers and offer a valuable patrilineal perspective in species evolution.},
    url = "https://doi.org/10.1093/molbev/msh241",
    doi = "10.1093/molbev/msh241",
    openalex = "W2148153874",
    references = "doi101038nature01722, doi101073pnas0334222100, doi10108010635150290069913, doi101093bioinformatics149817, doi101093bioinformatics178754, doi101093nar25244876, doi101126science1998119, doi101126science2785338675, doi101126science2865441964, openalexw3217097258"
}

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

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

Taxonomic revision by molecular phylogeny is needed to categorize members of the genus Echinococcus (Cestoda: Taeniidae). We have reconstructed the phylogenetic relationships of E. oligarthrus, E. vogeli, E. multilocularis, E. shiquicus, E. equinus, E. ortleppi, E. granulosus sensu stricto and 3 genotypes of E. granulosus sensu lato (G6, G7 and G8) from their complete mitochondrial genomes. Maximum likelihood and partitioned Bayesian analyses using concatenated data sets of nucleotide and amino acid sequences depicted phylogenetic trees with the same topology. The 3 E. granulosus genotypes corresponding to the camel, pig, and cervid strains were monophyletic, and their high level of genetic similarity supported taxonomic species unification of these genotypes into E. canadensis. Sister species relationships were confirmed between E. ortleppi and E. canadensis, and between E. multilocularis and E. shiquicus, regardless of the analytical approach employed. The basal positions of the phylogenetic tree were occupied by the neotropical endemic species, E. oligarthrus and E. vogeli, whose definitive hosts are derived from carnivores that immigrated from North America after the formation of the Panamanian land bridge. Host-parasite co-evolution comparisons suggest that the ancestral homeland of Echinococcus was North America or Asia, depending on whether the ancestral definitive hosts were canids or felids.

@article{doi101017s0031182006001934,
    author = "Nakao, Miki and McManus, Donald P. and Schantz, Peter M. and Craig, Philip S. and Ito, Akira",
    title = "A molecular phylogeny of the genus Echinococcus inferred from complete mitochondrial genomes",
    year = "2006",
    journal = "Parasitology",
    abstract = "Taxonomic revision by molecular phylogeny is needed to categorize members of the genus Echinococcus (Cestoda: Taeniidae). We have reconstructed the phylogenetic relationships of E. oligarthrus, E. vogeli, E. multilocularis, E. shiquicus, E. equinus, E. ortleppi, E. granulosus sensu stricto and 3 genotypes of E. granulosus sensu lato (G6, G7 and G8) from their complete mitochondrial genomes. Maximum likelihood and partitioned Bayesian analyses using concatenated data sets of nucleotide and amino acid sequences depicted phylogenetic trees with the same topology. The 3 E. granulosus genotypes corresponding to the camel, pig, and cervid strains were monophyletic, and their high level of genetic similarity supported taxonomic species unification of these genotypes into E. canadensis. Sister species relationships were confirmed between E. ortleppi and E. canadensis, and between E. multilocularis and E. shiquicus, regardless of the analytical approach employed. The basal positions of the phylogenetic tree were occupied by the neotropical endemic species, E. oligarthrus and E. vogeli, whose definitive hosts are derived from carnivores that immigrated from North America after the formation of the Panamanian land bridge. Host-parasite co-evolution comparisons suggest that the ancestral homeland of Echinococcus was North America or Asia, depending on whether the ancestral definitive hosts were canids or felids.",
    url = "https://doi.org/10.1017/s0031182006001934",
    doi = "10.1017/s0031182006001934",
    openalex = "W2160073440",
    references = "doi101073pnas972111359, doi101126science1122277"
}

It is now well known that incomplete lineage sorting can cause serious difficulties for phylogenetic inference, but little attention has been paid to methods that attempt to overcome these difficulties by explicitly considering the processes that produce them. Here we explore approaches to phylogenetic inference designed to consider retention and sorting of ancestral polymorphism. We examine how the reconstructability of a species (or population) phylogeny is affected by (a) the number of loci used to estimate the phylogeny and (b) the number of individuals sampled per species. Even in difficult cases with considerable incomplete lineage sorting (times between divergences less than 1 N(e) generations), we found the reconstructed species trees matched the "true" species trees in at least three out of five partitions, as long as a reasonable number of individuals per species were sampled. We also studied the tradeoff between sampling more loci versus more individuals. Although increasing the number of loci gives more accurate trees for a given sampling effort with deeper species trees (e.g., total depth of 10 N(e) generations), sampling more individuals often gives better results than sampling more loci with shallower species trees (e.g., depth = 1 N(e)). Taken together, these results demonstrate that gene sequences retain enough signal to achieve an accurate estimate of phylogeny despite widespread incomplete lineage sorting. Continued improvement in our methods to reconstruct phylogeny near the species level will require a shift to a compound model that considers not only nucleotide or character state substitutions, but also the population genetics processes of lineage sorting. [Coalescence; divergence; population; speciation.].

@article{doi10108010635150500354928,
    author = "Maddison, Wayne P. and Knowles, L. Lacey",
    title = "Inferring Phylogeny Despite Incomplete Lineage Sorting",
    year = "2006",
    journal = "Systematic Biology",
    abstract = {It is now well known that incomplete lineage sorting can cause serious difficulties for phylogenetic inference, but little attention has been paid to methods that attempt to overcome these difficulties by explicitly considering the processes that produce them. Here we explore approaches to phylogenetic inference designed to consider retention and sorting of ancestral polymorphism. We examine how the reconstructability of a species (or population) phylogeny is affected by (a) the number of loci used to estimate the phylogeny and (b) the number of individuals sampled per species. Even in difficult cases with considerable incomplete lineage sorting (times between divergences less than 1 N(e) generations), we found the reconstructed species trees matched the "true" species trees in at least three out of five partitions, as long as a reasonable number of individuals per species were sampled. We also studied the tradeoff between sampling more loci versus more individuals. Although increasing the number of loci gives more accurate trees for a given sampling effort with deeper species trees (e.g., total depth of 10 N(e) generations), sampling more individuals often gives better results than sampling more loci with shallower species trees (e.g., depth = 1 N(e)). Taken together, these results demonstrate that gene sequences retain enough signal to achieve an accurate estimate of phylogeny despite widespread incomplete lineage sorting. Continued improvement in our methods to reconstruct phylogeny near the species level will require a shift to a compound model that considers not only nucleotide or character state substitutions, but also the population genetics processes of lineage sorting. [Coalescence; divergence; population; speciation.].},
    url = "https://doi.org/10.1080/10635150500354928",
    doi = "10.1080/10635150500354928",
    openalex = "W2128252278",
    references = "doi101146annureven10010165000525, doi1023072419070"
}

The importance of geographic isolation in speciation has been debated since the 19th century. Since the beginning of the 20th century, the consensus has been that most speciation involves divergence in allopatry. This consensus was based largely on decades of observations by naturalists and verbal arguments against speciation without isolation. Recent attempts to quantify the importance of allopatric versus sympatric speciation using comparative methods called "age-range correlation" (ARC) suggest that allopatric speciation is more common than sympatric speciation. However, very few taxa have been studied and there are concerns about the adequacy of the methods. We propose methodological improvements including changes in the way overlap between clades is quantified and Monte Carlo methods to test the null hypothesis of no relationship between phylogenetic relatedness and geographic range overlap. We analyze 14 clades of mammals, chosen because of the availability of data and the consensus among mammalogists that speciation is routinely allopatric. Although data from a few clades clearly indicate allopatric speciation, divergence with gene flow is plausible in others and many results are inconclusive. The relative rarity of significant correlations between phylogenetic distance and range overlap may have three distinct causes: (1) post-speciation range changes, (2) relative rarity of range overlap, and (3) a mixture of geographic modes of speciation. Our results support skepticism about ARC's power for inferring the biogeography of speciation. Yet, even if few clades provide clear signals, meta-analytic approaches such as ARC may set bounds on the prevalence of alternative modes of speciation.

@article{doi101111j001438202006tb01140x,
    author = "Fitzpatrick, Benjamin M. and Turelli, Michael",
    title = "THE GEOGRAPHY OF MAMMALIAN SPECIATION: MIXED SIGNALS FROM PHYLOGENIES AND RANGE MAPS",
    year = "2006",
    journal = "Evolution",
    abstract = {The importance of geographic isolation in speciation has been debated since the 19th century. Since the beginning of the 20th century, the consensus has been that most speciation involves divergence in allopatry. This consensus was based largely on decades of observations by naturalists and verbal arguments against speciation without isolation. Recent attempts to quantify the importance of allopatric versus sympatric speciation using comparative methods called "age-range correlation" (ARC) suggest that allopatric speciation is more common than sympatric speciation. However, very few taxa have been studied and there are concerns about the adequacy of the methods. We propose methodological improvements including changes in the way overlap between clades is quantified and Monte Carlo methods to test the null hypothesis of no relationship between phylogenetic relatedness and geographic range overlap. We analyze 14 clades of mammals, chosen because of the availability of data and the consensus among mammalogists that speciation is routinely allopatric. Although data from a few clades clearly indicate allopatric speciation, divergence with gene flow is plausible in others and many results are inconclusive. The relative rarity of significant correlations between phylogenetic distance and range overlap may have three distinct causes: (1) post-speciation range changes, (2) relative rarity of range overlap, and (3) a mixture of geographic modes of speciation. Our results support skepticism about ARC's power for inferring the biogeography of speciation. Yet, even if few clades provide clear signals, meta-analytic approaches such as ARC may set bounds on the prevalence of alternative modes of speciation.},
    url = "https://doi.org/10.1111/j.0014-3820.2006.tb01140.x",
    doi = "10.1111/j.0014-3820.2006.tb01140.x",
    openalex = "W2175331942",
    references = "doi101007bf00125354, doi101086282771, doi101086284325, doi101093bioinformatics149817, doi101111j109600312000tb00354x, doi1023073669094, doi102307jctvjsf433, doi104159harvard9780674865327, doi105860choice396411, doi105962bhltitle59991, openalexw1840956397, openalexw3217097258"
}

Modern felid species descend from relatively recent (<11 million years ago) divergence and speciation events that produced successful predatory carnivores worldwide but that have confounded taxonomic classifications. A highly resolved molecular phylogeny with divergence dates for all living cat species, derived from autosomal, X-linked, Y-linked, and mitochondrial gene segments (22,789 base pairs) and 16 fossil calibrations define eight principal lineages produced through at least 10 intercontinental migrations facilitated by sea-level fluctuations. A ghost lineage analysis indicates that available felid fossils underestimate (i.e., unrepresented basal branch length) first occurrence by an average of 76%, revealing a low representation of felid lineages in paleontological remains. The phylogenetic performance of distinct gene classes showed that Y-chromosome segments are appreciably more informative than mitochondrial DNA, X-linked, or autosomal genes in resolving the rapid Felidae species radiation.

@article{doi101126science1122277,
    author = "Johnson, Warren E. and Eizirik, Eduardo and Pecon‐Slattery, Jill and Murphy, William J. and Antunes, Agostinho and Teeling, Emma C. and O’Brien, Stephen J.",
    title = "The Late Miocene Radiation of Modern Felidae: A Genetic Assessment",
    year = "2006",
    journal = "Science",
    abstract = "Modern felid species descend from relatively recent (<11 million years ago) divergence and speciation events that produced successful predatory carnivores worldwide but that have confounded taxonomic classifications. A highly resolved molecular phylogeny with divergence dates for all living cat species, derived from autosomal, X-linked, Y-linked, and mitochondrial gene segments (22,789 base pairs) and 16 fossil calibrations define eight principal lineages produced through at least 10 intercontinental migrations facilitated by sea-level fluctuations. A ghost lineage analysis indicates that available felid fossils underestimate (i.e., unrepresented basal branch length) first occurrence by an average of 76\%, revealing a low representation of felid lineages in paleontological remains. The phylogenetic performance of distinct gene classes showed that Y-chromosome segments are appreciably more informative than mitochondrial DNA, X-linked, or autosomal genes in resolving the rapid Felidae species radiation.",
    url = "https://doi.org/10.1126/science.1122277",
    doi = "10.1126/science.1122277",
    openalex = "W2101139153",
    references = "doi1010079781475747164, doi101007bf00163806, doi101038nature02053, doi101093molbevmsg050, doi101093molbevmsh241, doi101098rstb20031394, doi101111j109600312000tb00354x, doi101126science1105113, doi101126science23547931156, doi101353book59141, doi105860choice355657, openalexw604002547"
}

@article{doi101016jympev200710019,
    author = "Pagès, Marie and Calvignac‐Spencer, Sébastien and Klein, Catherine J. and Paris, Mathilde and Hughes, Sandrine and Hänni, Catherine",
    title = "Combined analysis of fourteen nuclear genes refines the Ursidae phylogeny",
    year = "2007",
    journal = "Molecular Phylogenetics and Evolution",
    url = "https://doi.org/10.1016/j.ympev.2007.10.019",
    doi = "10.1016/j.ympev.2007.10.019",
    openalex = "W1997402834",
    references = "doi101093molbevmsh241"
}

The ongoing generation of prodigious amounts of genomic sequence data from myriad vertebrates is providing unparalleled opportunities for establishing definitive phylogenetic relationships among species. The size and complexities of such comparative sequence data sets not only allow smaller and more difficult branches to be resolved but also present unique challenges, including large computational requirements and the negative consequences of systematic biases. To explore these issues and to clarify the phylogenetic relationships among mammals, we have analyzed a large data set of over 60 megabase pairs (Mb) of high-quality genomic sequence, which we generated from 41 mammals and 3 other vertebrates. All sequences are orthologous to a 1.9-Mb region of the human genome that encompasses the cystic fibrosis transmembrane conductance regulator gene (CFTR). To understand the characteristics and challenges associated with phylogenetic analyses of such a large data set, we partitioned the sequence data in several ways and utilized maximum likelihood, maximum parsimony, and Neighbor-Joining algorithms, implemented in parallel on Linux clusters. These studies yielded well-supported phylogenetic trees, largely confirming other recent molecular phylogenetic analyses. Our results provide support for rooting the placental mammal tree between Atlantogenata (Xenarthra and Afrotheria) and Boreoeutheria (Euarchontoglires and Laurasiatheria), illustrate the difficulty in resolving some branches even with large amounts of data (e.g., in the case of Laurasiatheria), and demonstrate the valuable role that very large comparative sequence data sets can play in refining our understanding of the evolutionary relationships of vertebrates.

@article{doi101093molbevmsn104,
    author = "Prasad, Arjun and Allard, Marc W. and Program, NISC Comparative Sequencing and Green, Eric D.",
    title = "Confirming the Phylogeny of Mammals by Use of Large Comparative Sequence Data Sets",
    year = "2008",
    journal = "Molecular Biology and Evolution",
    abstract = "The ongoing generation of prodigious amounts of genomic sequence data from myriad vertebrates is providing unparalleled opportunities for establishing definitive phylogenetic relationships among species. The size and complexities of such comparative sequence data sets not only allow smaller and more difficult branches to be resolved but also present unique challenges, including large computational requirements and the negative consequences of systematic biases. To explore these issues and to clarify the phylogenetic relationships among mammals, we have analyzed a large data set of over 60 megabase pairs (Mb) of high-quality genomic sequence, which we generated from 41 mammals and 3 other vertebrates. All sequences are orthologous to a 1.9-Mb region of the human genome that encompasses the cystic fibrosis transmembrane conductance regulator gene (CFTR). To understand the characteristics and challenges associated with phylogenetic analyses of such a large data set, we partitioned the sequence data in several ways and utilized maximum likelihood, maximum parsimony, and Neighbor-Joining algorithms, implemented in parallel on Linux clusters. These studies yielded well-supported phylogenetic trees, largely confirming other recent molecular phylogenetic analyses. Our results provide support for rooting the placental mammal tree between Atlantogenata (Xenarthra and Afrotheria) and Boreoeutheria (Euarchontoglires and Laurasiatheria), illustrate the difficulty in resolving some branches even with large amounts of data (e.g., in the case of Laurasiatheria), and demonstrate the valuable role that very large comparative sequence data sets can play in refining our understanding of the evolutionary relationships of vertebrates.",
    url = "https://doi.org/10.1093/molbev/msn104",
    doi = "10.1093/molbev/msn104",
    openalex = "W2051254500",
    references = "doi101093molbevmsh241"
}

BACKGROUND: Adaptive radiation, the evolution of ecological and phenotypic diversity from a common ancestor, is a central concept in evolutionary biology and characterizes the evolutionary histories of many groups of organisms. One such group is the Mustelidae, the most species-rich family within the mammalian order Carnivora, encompassing 59 species classified into 22 genera. Extant mustelids display extensive ecomorphological diversity, with different lineages having evolved into an array of adaptive zones, from fossorial badgers to semi-aquatic otters. Mustelids are also widely distributed, with multiple genera found on different continents. As with other groups that have undergone adaptive radiation, resolving the phylogenetic history of mustelids presents a number of challenges because ecomorphological convergence may potentially confound morphologically based phylogenetic inferences, and because adaptive radiations often include one or more periods of rapid cladogenesis that require a large amount of data to resolve. RESULTS: We constructed a nearly complete generic-level phylogeny of the Mustelidae using a data matrix comprising 22 gene segments (approximately 12,000 base pairs) analyzed with maximum parsimony, maximum likelihood and Bayesian inference methods. We show that mustelids are consistently resolved with high nodal support into four major clades and three monotypic lineages. Using Bayesian dating techniques, we provide evidence that mustelids underwent two bursts of diversification that coincide with major paleoenvironmental and biotic changes that occurred during the Neogene and correspond with similar bursts of cladogenesis in other vertebrate groups. Biogeographical analyses indicate that most of the extant diversity of mustelids originated in Eurasia and mustelids have colonized Africa, North America and South America on multiple occasions. CONCLUSION: Combined with information from the fossil record, our phylogenetic and dating analyses suggest that mustelid diversification may have been spurred by a combination of faunal turnover events and diversification at lower trophic levels, ultimately caused by climatically driven environmental changes. Our biogeographic analyses show Eurasia as the center of origin of mustelid diversity and that mustelids in Africa, North America and South America have been assembled over time largely via dispersal, which has important implications for understanding the ecology of mustelid communities.

@article{doi10118617417007610,
    author = "Koepfli, Klaus‐Peter and Deere, Kerry A and Slater, Graham J. and Begg, Colleen and Begg, Keith S. and Grassman, Lon I. and Lucherini, Mauro and Veron, Géraldine and Wayne, Robert K.",
    title = "Multigene phylogeny of the Mustelidae: Resolving relationships, tempo and biogeographic history of a mammalian adaptive radiation",
    year = "2008",
    journal = "BMC Biology",
    abstract = "BACKGROUND: Adaptive radiation, the evolution of ecological and phenotypic diversity from a common ancestor, is a central concept in evolutionary biology and characterizes the evolutionary histories of many groups of organisms. One such group is the Mustelidae, the most species-rich family within the mammalian order Carnivora, encompassing 59 species classified into 22 genera. Extant mustelids display extensive ecomorphological diversity, with different lineages having evolved into an array of adaptive zones, from fossorial badgers to semi-aquatic otters. Mustelids are also widely distributed, with multiple genera found on different continents. As with other groups that have undergone adaptive radiation, resolving the phylogenetic history of mustelids presents a number of challenges because ecomorphological convergence may potentially confound morphologically based phylogenetic inferences, and because adaptive radiations often include one or more periods of rapid cladogenesis that require a large amount of data to resolve. RESULTS: We constructed a nearly complete generic-level phylogeny of the Mustelidae using a data matrix comprising 22 gene segments (approximately 12,000 base pairs) analyzed with maximum parsimony, maximum likelihood and Bayesian inference methods. We show that mustelids are consistently resolved with high nodal support into four major clades and three monotypic lineages. Using Bayesian dating techniques, we provide evidence that mustelids underwent two bursts of diversification that coincide with major paleoenvironmental and biotic changes that occurred during the Neogene and correspond with similar bursts of cladogenesis in other vertebrate groups. Biogeographical analyses indicate that most of the extant diversity of mustelids originated in Eurasia and mustelids have colonized Africa, North America and South America on multiple occasions. CONCLUSION: Combined with information from the fossil record, our phylogenetic and dating analyses suggest that mustelid diversification may have been spurred by a combination of faunal turnover events and diversification at lower trophic levels, ultimately caused by climatically driven environmental changes. Our biogeographic analyses show Eurasia as the center of origin of mustelid diversity and that mustelids in Africa, North America and South America have been assembled over time largely via dispersal, which has important implications for understanding the ecology of mustelid communities.",
    url = "https://doi.org/10.1186/1741-7007-6-10",
    doi = "10.1186/1741-7007-6-10",
    openalex = "W1969810115",
    references = "doi101093oso97801985771880010001, doi101126science1122277"
}

@article{doi101016jympev200910033,
    author = "Agnarsson, Ingi and Kuntner, Matjaž and May‐Collado, Laura J.",
    title = "Dogs, cats, and kin: A molecular species-level phylogeny of Carnivora",
    year = "2009",
    journal = "Molecular Phylogenetics and Evolution",
    url = "https://doi.org/10.1016/j.ympev.2009.10.033",
    doi = "10.1016/j.ympev.2009.10.033",
    openalex = "W2037909707",
    references = "doi101006mpev19960085, doi101007bf00160154, doi101016s0022519305801043, doi101017s0952836904005242, doi10108010635150490522304, doi101086284325, doi101093bioinformatics149817, doi101093bioinformatics178754, doi101093oso97801985464120010001, doi101111j109600312000tb00354x, doi105860choice295104, doi105962bhltitle59991, openalexw2611511275"
}

Picante is a package for the R statistical language and environment written in R and C, released under a GPL v2 open-source license, and freely available on the web (http://picante.r-forge.r-project.org) and from CRAN (http://cran.r-project.org).

@article{doi101093bioinformaticsbtq166,
    author = "Kembel, Steven W. and Cowan, Peter D. and Helmus, Matthew R. and Cornwell, William K. and Morlon, Hélène and Ackerly, David D. and Blomberg, Simon P. and Webb, Campbell O.",
    title = "Picante: R tools for integrating phylogenies and ecology",
    year = "2010",
    journal = "Bioinformatics",
    abstract = "Picante is a package for the R statistical language and environment written in R and C, released under a GPL v2 open-source license, and freely available on the web (http://picante.r-forge.r-project.org) and from CRAN (http://cran.r-project.org).",
    url = "https://doi.org/10.1093/bioinformatics/btq166",
    doi = "10.1093/bioinformatics/btq166",
    openalex = "W2133360663",
    references = "doi1010160006320792912013, doi101046j14610248200100230x, doi101093bioinformaticsbtg412, doi101111j001438202003tb00285x, doi101111j14610248200901314x, doi101146annurevecolsys33010802150448"
}

A complete explanation of the diversity of animal colour patterns requires an understanding of both the developmental mechanisms generating them and their adaptive value. However, only two previous studies, which involved computer-generated evolving prey, have attempted to make this link. This study examines variation in the camouflage patterns displayed on the flanks of many felids. After controlling for the effects of shared ancestry using a fully resolved molecular phylogeny, this study shows how phenotypes from plausible felid coat pattern generation mechanisms relate to ecology. We found that likelihood of patterning and pattern attributes, such as complexity and irregularity, were related to felids' habitats, arboreality and nocturnality. Our analysis also indicates that disruptive selection is a likely explanation for the prevalence of melanistic forms in Felidae. Furthermore, we show that there is little phylogenetic signal in the visual appearance of felid patterning, indicating that camouflage adapts to ecology over relatively short time scales. Our method could be applied to any taxon with colour patterns that can reasonably be matched to reaction-diffusion and similar models, where the kinetics of the reaction between two or more initially randomly dispersed morphogens determines the outcome of pattern development.

@article{doi101098rspb20101734,
    author = "Allen, William L. and Cuthill, Innes C. and Scott‐Samuel, Nicholas E. and Baddeley, Roland",
    title = "Why the leopard got its spots: relating pattern development to ecology in felids",
    year = "2010",
    journal = "Proceedings of the Royal Society B Biological Sciences",
    abstract = "A complete explanation of the diversity of animal colour patterns requires an understanding of both the developmental mechanisms generating them and their adaptive value. However, only two previous studies, which involved computer-generated evolving prey, have attempted to make this link. This study examines variation in the camouflage patterns displayed on the flanks of many felids. After controlling for the effects of shared ancestry using a fully resolved molecular phylogeny, this study shows how phenotypes from plausible felid coat pattern generation mechanisms relate to ecology. We found that likelihood of patterning and pattern attributes, such as complexity and irregularity, were related to felids' habitats, arboreality and nocturnality. Our analysis also indicates that disruptive selection is a likely explanation for the prevalence of melanistic forms in Felidae. Furthermore, we show that there is little phylogenetic signal in the visual appearance of felid patterning, indicating that camouflage adapts to ecology over relatively short time scales. Our method could be applied to any taxon with colour patterns that can reasonably be matched to reaction-diffusion and similar models, where the kinetics of the reaction between two or more initially randomly dispersed morphogens determines the outcome of pattern development.",
    url = "https://doi.org/10.1098/rspb.2010.1734",
    doi = "10.1098/rspb.2010.1734",
    openalex = "W2147027233",
    references = "doi101007b98869, doi10103844766, doi101086343873, doi101093bioinformaticsbtg412, doi101098rstb19890106, doi101111j143903101963tb01161x, doi101353book59141, doi1023072285423, doi1023072937121, doi105860choice392183"
}

The phylogeny and taxonomy of mammalian species were originally based upon shared or derived morphological characteristics. However, genetic analyses have more recently played an increasingly important role in confirming existing or establishing often radically different mammalian groupings and phylogenies. The two most commonly used genetic loci in species identification are the cytochrome oxidase I gene (COI) and the cytochrome b gene (cyt b). For the first time this study provides a detailed comparison of the effectiveness of these two loci in reconstructing the phylogeny of mammals at different levels of the taxonomic hierarchy in order to provide a basis for standardizing methodologies in the future. Interspecific and intraspecific variation is assessed and for the first time, to our knowledge, statistical confidence is applied to sequence comparisons. Comparison of the DNA sequences of 217 mammalian species reveals that cyt b more accurately reconstructs their phylogeny and known relationships between species based on other molecular and morphological analyses at Super Order, Order, Family and generic levels. Cyt b correctly assigned 95.85% of mammal species to Super Order, 94.31% to Order and 98.16% to Family compared to 78.34%, 93.36% and 96.93% respectively for COI. Cyt b also gives better resolution when separating species based on sequence data. Using a Kimura 2-parameter p-distance (x100) threshold of 1.5-2.5, cyt b gives a better resolution for separating species with a lower false positive rate and higher positive predictive value than those of COI.

@article{doi101371journalpone0014156,
    author = "Tobe, Shanan S. and Kitchener, Andrew C. and Linacre, Adrian",
    title = "Reconstructing Mammalian Phylogenies: A Detailed Comparison of the Cytochrome b and Cytochrome Oxidase Subunit I Mitochondrial Genes",
    year = "2010",
    journal = "PLoS ONE",
    abstract = "The phylogeny and taxonomy of mammalian species were originally based upon shared or derived morphological characteristics. However, genetic analyses have more recently played an increasingly important role in confirming existing or establishing often radically different mammalian groupings and phylogenies. The two most commonly used genetic loci in species identification are the cytochrome oxidase I gene (COI) and the cytochrome b gene (cyt b). For the first time this study provides a detailed comparison of the effectiveness of these two loci in reconstructing the phylogeny of mammals at different levels of the taxonomic hierarchy in order to provide a basis for standardizing methodologies in the future. Interspecific and intraspecific variation is assessed and for the first time, to our knowledge, statistical confidence is applied to sequence comparisons. Comparison of the DNA sequences of 217 mammalian species reveals that cyt b more accurately reconstructs their phylogeny and known relationships between species based on other molecular and morphological analyses at Super Order, Order, Family and generic levels. Cyt b correctly assigned 95.85\% of mammal species to Super Order, 94.31\% to Order and 98.16\% to Family compared to 78.34\%, 93.36\% and 96.93\% respectively for COI. Cyt b also gives better resolution when separating species based on sequence data. Using a Kimura 2-parameter p-distance (x100) threshold of 1.5-2.5, cyt b gives a better resolution for separating species with a lower false positive rate and higher positive predictive value than those of COI.",
    url = "https://doi.org/10.1371/journal.pone.0014156",
    doi = "10.1371/journal.pone.0014156",
    openalex = "W2100621850",
    references = "doi101016jympev200910033"
}

The molecular clock provides a powerful way to estimate species divergence times. If information on some species divergence times is available from the fossil or geological record, it can be used to calibrate a phylogeny and estimate divergence times for all nodes in the tree. The Bayesian method provides a natural framework to incorporate different sources of information concerning divergence times, such as information in the fossil and molecular data. Current models of sequence evolution are intractable in a Bayesian setting, and Markov chain Monte Carlo (MCMC) is used to generate the posterior distribution of divergence times and evolutionary rates. This method is computationally expensive, as it involves the repeated calculation of the likelihood function. Here, we explore the use of Taylor expansion to approximate the likelihood during MCMC iteration. The approximation is much faster than conventional likelihood calculation. However, the approximation is expected to be poor when the proposed parameters are far from the likelihood peak. We explore the use of parameter transforms (square root, logarithm, and arcsine) to improve the approximation to the likelihood curve. We found that the new methods, particularly the arcsine-based transform, provided very good approximations under relaxed clock models and also under the global clock model when the global clock is not seriously violated. The approximation is poorer for analysis under the global clock when the global clock is seriously wrong and should thus not be used. The results suggest that the approximate method may be useful for Bayesian dating analysis using large data sets.

@article{doi101093molbevmsr045,
    author = "dos Reis, Mario and Yang, Zu-Xing",
    title = "Approximate Likelihood Calculation on a Phylogeny for Bayesian Estimation of Divergence Times",
    year = "2011",
    journal = "Molecular Biology and Evolution",
    abstract = "The molecular clock provides a powerful way to estimate species divergence times. If information on some species divergence times is available from the fossil or geological record, it can be used to calibrate a phylogeny and estimate divergence times for all nodes in the tree. The Bayesian method provides a natural framework to incorporate different sources of information concerning divergence times, such as information in the fossil and molecular data. Current models of sequence evolution are intractable in a Bayesian setting, and Markov chain Monte Carlo (MCMC) is used to generate the posterior distribution of divergence times and evolutionary rates. This method is computationally expensive, as it involves the repeated calculation of the likelihood function. Here, we explore the use of Taylor expansion to approximate the likelihood during MCMC iteration. The approximation is much faster than conventional likelihood calculation. However, the approximation is expected to be poor when the proposed parameters are far from the likelihood peak. We explore the use of parameter transforms (square root, logarithm, and arcsine) to improve the approximation to the likelihood curve. We found that the new methods, particularly the arcsine-based transform, provided very good approximations under relaxed clock models and also under the global clock model when the global clock is not seriously violated. The approximation is poorer for analysis under the global clock when the global clock is seriously wrong and should thus not be used. The results suggest that the approximate method may be useful for Bayesian dating analysis using large data sets.",
    url = "https://doi.org/10.1093/molbev/msr045",
    doi = "10.1093/molbev/msr045",
    openalex = "W2131633033",
    references = "doi101126science1122277"
}

Despite their obvious utility, detailed species-level phylogenies are lacking for many groups, including several major mammalian lineages such as bats. Here we provide a cytochrome b genealogy of over 50% of bat species (648 terminal taxa). Based on prior analyzes of related mammal groups, cytb emerges as a particularly reliable phylogenetic marker, and given that our results are broadly congruent with prior knowledge, the phylogeny should be a useful tool for comparative analyzes. Nevertheless, we stress that a single-gene analysis of such a large and old group cannot be interpreted as more than a crude estimate of the bat species tree. Analysis of the full dataset supports the traditional division of bats into macro- and microchiroptera, but not the recently proposed division into Yinpterochiroptera and Yangochiroptera. However, our results only weakly reject the former and strongly support the latter group, and furthermore, a time calibrated analysis of a pruned dataset where most included taxa have the entire 1140bp cytb sequence finds monophyletic Yinpterochiroptera. Most bat families and many higher level groups are supported, however, relationships among families are in general weakly supported, as are many of the deeper nodes of the tree. The exceptions are in most cases apparently due to the misplacement of species with little available data, while in a few cases the results suggest putative problems with current classification, such as the non-monophyly of Mormoopidae. We provide this phylogenetic hypothesis, and an analysis of divergence times, as tools for evolutionary and ecological studies that will be useful until more inclusive studies using multiple loci become available.

@article{doi101371currentsrrn1212,
    author = "Agnarsson, Ingi and Zambrana‐Torrelio, Carlos and Flores-Saldana, Nadia Paola and May‐Collado, Laura J.",
    title = "A time-calibrated species-level phylogeny of bats (Chiroptera, Mammalia)",
    year = "2011",
    journal = "PLoS Currents",
    abstract = "Despite their obvious utility, detailed species-level phylogenies are lacking for many groups, including several major mammalian lineages such as bats. Here we provide a cytochrome b genealogy of over 50\% of bat species (648 terminal taxa). Based on prior analyzes of related mammal groups, cytb emerges as a particularly reliable phylogenetic marker, and given that our results are broadly congruent with prior knowledge, the phylogeny should be a useful tool for comparative analyzes. Nevertheless, we stress that a single-gene analysis of such a large and old group cannot be interpreted as more than a crude estimate of the bat species tree. Analysis of the full dataset supports the traditional division of bats into macro- and microchiroptera, but not the recently proposed division into Yinpterochiroptera and Yangochiroptera. However, our results only weakly reject the former and strongly support the latter group, and furthermore, a time calibrated analysis of a pruned dataset where most included taxa have the entire 1140bp cytb sequence finds monophyletic Yinpterochiroptera. Most bat families and many higher level groups are supported, however, relationships among families are in general weakly supported, as are many of the deeper nodes of the tree. The exceptions are in most cases apparently due to the misplacement of species with little available data, while in a few cases the results suggest putative problems with current classification, such as the non-monophyly of Mormoopidae. We provide this phylogenetic hypothesis, and an analysis of divergence times, as tools for evolutionary and ecological studies that will be useful until more inclusive studies using multiple loci become available.",
    url = "https://doi.org/10.1371/currents.rrn1212",
    doi = "10.1371/currents.rrn1212",
    openalex = "W2073591031",
    references = "doi101016jympev200910033"
}

Comparative genomic analyses of primates offer considerable potential to define and understand the processes that mold, shape, and transform the human genome. However, primate taxonomy is both complex and controversial, with marginal unifying consensus of the evolutionary hierarchy of extant primate species. Here we provide new genomic sequence (~8 Mb) from 186 primates representing 61 (~90%) of the described genera, and we include outgroup species from Dermoptera, Scandentia, and Lagomorpha. The resultant phylogeny is exceptionally robust and illuminates events in primate evolution from ancient to recent, clarifying numerous taxonomic controversies and providing new data on human evolution. Ongoing speciation, reticulate evolution, ancient relic lineages, unequal rates of evolution, and disparate distributions of insertions/deletions among the reconstructed primate lineages are uncovered. Our resolution of the primate phylogeny provides an essential evolutionary framework with far-reaching applications including: human selection and adaptation, global emergence of zoonotic diseases, mammalian comparative genomics, primate taxonomy, and conservation of endangered species.

@article{doi101371journalpgen1001342,
    author = "Perelman, Polina L. and Johnson, Warren E. and Roos, Christian and Seuánez, Héctor N. and Horvath, Julie E. and Moreira, Miguel A. M. and Kessing, Bailey and Pontius, Joan and Roelke, Melody E. and Rumpler, Y. and Schneider, Maria Paula Cruz and Silva, Artur and O’Brien, Stephen J. and Pecon‐Slattery, Jill",
    title = "A Molecular Phylogeny of Living Primates",
    year = "2011",
    journal = "PLoS Genetics",
    abstract = "Comparative genomic analyses of primates offer considerable potential to define and understand the processes that mold, shape, and transform the human genome. However, primate taxonomy is both complex and controversial, with marginal unifying consensus of the evolutionary hierarchy of extant primate species. Here we provide new genomic sequence (\textasciitilde 8 Mb) from 186 primates representing 61 (\textasciitilde 90\%) of the described genera, and we include outgroup species from Dermoptera, Scandentia, and Lagomorpha. The resultant phylogeny is exceptionally robust and illuminates events in primate evolution from ancient to recent, clarifying numerous taxonomic controversies and providing new data on human evolution. Ongoing speciation, reticulate evolution, ancient relic lineages, unequal rates of evolution, and disparate distributions of insertions/deletions among the reconstructed primate lineages are uncovered. Our resolution of the primate phylogeny provides an essential evolutionary framework with far-reaching applications including: human selection and adaptation, global emergence of zoonotic diseases, mammalian comparative genomics, primate taxonomy, and conservation of endangered species.",
    url = "https://doi.org/10.1371/journal.pgen.1001342",
    doi = "10.1371/journal.pgen.1001342",
    openalex = "W2144820135",
    references = "doi10103835054550, doi10108010635150701472164, doi101093bibbbn013, doi101093molbevmsh241, doi101126science1122277, doi101353book59141"
}

Bone morphology of the cats (Mammalia: Felidae) is influenced by many factors, including locomotor mode, body size, hunting methods, prey size and phylogeny. Here, we investigate the shape of the proximal and distal humeral epiphyses in extant species of the felids, based on two-dimensional landmark configurations. Geometric morphometric techniques were used to describe shape differences in the context of phylogeny, allometry and locomotion. The influence of these factors on epiphyseal shape was assessed using Principal Component Analysis, Linear Discriminant functions and multivariate regression. Phylogenetic Generalised Least Squares was used to examine the association between size or locomotion and humeral epiphyseal shape, after taking a phylogenetic error term into account. Results show marked differences in epiphyseal shape between felid lineages, with a relatively large phylogenetic influence. Additionally, the adaptive influences of size and locomotion are demonstrated, and their influence is independent of phylogeny in most, but not all, cases. Several features of epiphyseal shape are common to the largest terrestrial felids, including a relative reduction in the surface area of the humeral head and increased robusticity of structures that provide attachment for joint-stabilising muscles, including the medial epicondyle and the greater and lesser tubercles. This increased robusticity is a functional response to the increased loading forces placed on the joints due to large body mass.

@article{doi101002jmor20084,
    author = "Walmsley, A. D. and Elton, Sarah and Louys, Julien and Bishop, Laura C. and Meloro, Carlo",
    title = "Humeral epiphyseal shape in the felidae: The influence of phylogeny, allometry, and locomotion",
    year = "2012",
    journal = "Journal of Morphology",
    abstract = "Bone morphology of the cats (Mammalia: Felidae) is influenced by many factors, including locomotor mode, body size, hunting methods, prey size and phylogeny. Here, we investigate the shape of the proximal and distal humeral epiphyses in extant species of the felids, based on two-dimensional landmark configurations. Geometric morphometric techniques were used to describe shape differences in the context of phylogeny, allometry and locomotion. The influence of these factors on epiphyseal shape was assessed using Principal Component Analysis, Linear Discriminant functions and multivariate regression. Phylogenetic Generalised Least Squares was used to examine the association between size or locomotion and humeral epiphyseal shape, after taking a phylogenetic error term into account. Results show marked differences in epiphyseal shape between felid lineages, with a relatively large phylogenetic influence. Additionally, the adaptive influences of size and locomotion are demonstrated, and their influence is independent of phylogeny in most, but not all, cases. Several features of epiphyseal shape are common to the largest terrestrial felids, including a relative reduction in the surface area of the humeral head and increased robusticity of structures that provide attachment for joint-stabilising muscles, including the medial epicondyle and the greater and lesser tubercles. This increased robusticity is a functional response to the increased loading forces placed on the joints due to large body mass.",
    url = "https://doi.org/10.1002/jmor.20084",
    doi = "10.1002/jmor.20084",
    openalex = "W2095297834",
    references = "doi1010079781475790832, doi101016c20100662092, doi101080106351599260526, doi10108011250000409356545, doi101086286013, doi101111j001438202001tb00731x, doi101126science1122277, doi1023072532725, doi1023072534038, doi105860choice483867"
}

@misc{christiansen2014phylogeny,
    author = "Christiansen, C",
    title = "Phylogeny of the sabertoothed felids (Carnivora: Felidae: Machairodontinae) (project)",
    year = "2014",
    booktitle = "MorphoBank datasets",
    url = "https://doi.org/10.7934/p681",
    doi = "10.7934/p681",
    openalex = "W2907140659"
}

@misc{doi107934p681,
    author = "Christiansen, C",
    title = "Phylogeny of the sabertoothed felids (Carnivora: Felidae: Machairodontinae) (project)",
    year = "2014",
    booktitle = "MorphoBank datasets",
    url = "https://doi.org/10.7934/p681",
    doi = "10.7934/p681",
    openalex = "W2907140659"
}

The evolution of body mass is a fundamental topic in evolutionary biology, because it is closely linked to manifold life history and ecological traits and is readily estimable for many extinct taxa. In this study, we examine patterns of body mass evolution in Felidae (Placentalia, Carnivora) to assess the effects of phylogeny, mode of evolution, and the relationship between body mass and prey choice in this charismatic mammalian clade. Our data set includes 39 extant and 26 extinct taxa, with published body mass data supplemented by estimates based on condylobasal length. These data were run through 'SURFACE' and 'bayou' to test for patterns of body mass evolution and convergence between taxa. Body masses of felids are significantly different among prey choice groupings (small, mixed and large). We find that body mass evolution in cats is strongly influenced by phylogeny, but different patterns emerged depending on inclusion of extinct taxa and assumptions about branch lengths. A single Ornstein-Uhlenbeck optimum best explains the distribution of body masses when first-occurrence data were used for the fossil taxa. However, when mean occurrence dates or last known occurrence dates were used, two selective optima for felid body mass were recovered in most analyses: a small optimum around 5 kg and a large one around 100 kg. Across living and extinct cats, we infer repeated evolutionary convergences towards both of these optima, but, likely due to biased extinction of large taxa, our results shift to supporting a Brownian motion model when only extant taxa are included in analyses.

@article{doi101111jeb12671,
    author = "Cuff, Andrew R. and Randau, Marcela and Head, Jason J. and Hutchinson, John R. and Pierce, Stephanie E. and Goswami, Anjali",
    title = "Big cat, small cat: reconstructing body size evolution in living and extinct Felidae",
    year = "2015",
    journal = "Journal of Evolutionary Biology",
    abstract = "The evolution of body mass is a fundamental topic in evolutionary biology, because it is closely linked to manifold life history and ecological traits and is readily estimable for many extinct taxa. In this study, we examine patterns of body mass evolution in Felidae (Placentalia, Carnivora) to assess the effects of phylogeny, mode of evolution, and the relationship between body mass and prey choice in this charismatic mammalian clade. Our data set includes 39 extant and 26 extinct taxa, with published body mass data supplemented by estimates based on condylobasal length. These data were run through 'SURFACE' and 'bayou' to test for patterns of body mass evolution and convergence between taxa. Body masses of felids are significantly different among prey choice groupings (small, mixed and large). We find that body mass evolution in cats is strongly influenced by phylogeny, but different patterns emerged depending on inclusion of extinct taxa and assumptions about branch lengths. A single Ornstein-Uhlenbeck optimum best explains the distribution of body masses when first-occurrence data were used for the fossil taxa. However, when mean occurrence dates or last known occurrence dates were used, two selective optima for felid body mass were recovered in most analyses: a small optimum around 5 kg and a large one around 100 kg. Across living and extinct cats, we infer repeated evolutionary convergences towards both of these optima, but, likely due to biased extinction of large taxa, our results shift to supporting a Brownian motion model when only extant taxa are included in analyses.",
    url = "https://doi.org/10.1111/jeb.12671",
    doi = "10.1111/jeb.12671",
    openalex = "W2136520319",
    references = "doi10103846266, doi101093bioinformaticsbtm538, doi101093bioinformaticsbtq166, doi101111j001438202003tb00285x, doi101111j155856461973tb05912x, doi101111j15585646201001025x, doi101126science1122277, doi101643004585112002002117020co2, doi105860choice483867, doi107208chicago97802265182370010001"
}

Mammalian carnivores adhere to two different feeding strategies relative to their body masses. Large carnivores prey on animals that are the same size or larger than themselves, whereas small carnivores prey on smaller vertebrates and invertebrates. The Eurasian lynx (Lynx lynx) falls in between these two categories. Lynx descend from larger forms that were probably large prey specialists, but during the Pleistocene became predators of small prey. The modern Eurasian lynx may be an evolutionary reversal toward specializing in large prey again. We hypothesized that the musculoskeletal anatomy of lynx should show traits for catching large prey. To test our hypothesis, we dissected the forelimb muscles of six Eurasian lynx individuals and compared our findings to results published for other felids. We measured the bones and compared their dimensions to the published material. Our material displayed a well-developed pectoral girdle musculature with some uniquely extensive muscle attachments. The upper arm musculature resembled that of the pantherine felids and probably the extinct sabertooths, and also the muscles responsible for supination and pronation were similar to those in large cats. The muscles controlling the pollex were well-developed. However, skeletal indices were similar to those of small prey predators. Our findings show that lynx possess the topographic pattern of muscle origin and insertion like in large felids. J. Morphol. 277:753-765, 2016. © 2016 Wiley Periodicals, Inc.

@article{doi101002jmor20532,
    author = "Viranta, Suvi and Lommi, Hanna and Holmala, Katja and Laakkonen, Juha",
    title = "Musculoskeletal anatomy of the Eurasian lynx, Lynx lynx (Carnivora: Felidae) forelimb: Adaptations to capture large prey?",
    year = "2016",
    journal = "Journal of Morphology",
    abstract = "Mammalian carnivores adhere to two different feeding strategies relative to their body masses. Large carnivores prey on animals that are the same size or larger than themselves, whereas small carnivores prey on smaller vertebrates and invertebrates. The Eurasian lynx (Lynx lynx) falls in between these two categories. Lynx descend from larger forms that were probably large prey specialists, but during the Pleistocene became predators of small prey. The modern Eurasian lynx may be an evolutionary reversal toward specializing in large prey again. We hypothesized that the musculoskeletal anatomy of lynx should show traits for catching large prey. To test our hypothesis, we dissected the forelimb muscles of six Eurasian lynx individuals and compared our findings to results published for other felids. We measured the bones and compared their dimensions to the published material. Our material displayed a well-developed pectoral girdle musculature with some uniquely extensive muscle attachments. The upper arm musculature resembled that of the pantherine felids and probably the extinct sabertooths, and also the muscles responsible for supination and pronation were similar to those in large cats. The muscles controlling the pollex were well-developed. However, skeletal indices were similar to those of small prey predators. Our findings show that lynx possess the topographic pattern of muscle origin and insertion like in large felids. J. Morphol. 277:753-765, 2016. © 2016 Wiley Periodicals, Inc.",
    url = "https://doi.org/10.1002/jmor.20532",
    doi = "10.1002/jmor.20532",
    openalex = "W2301964202",
    references = "doi101002jmor20303"
}

@article{doi101007s1312701603044,
    author = "Randau, Marcela and Cuff, Andrew R. and Hutchinson, John R. and Pierce, Stephanie E. and Goswami, Anjali",
    title = "Regional differentiation of felid vertebral column evolution: a study of 3D shape trajectories",
    year = "2016",
    journal = "Organisms Diversity \& Evolution",
    url = "https://doi.org/10.1007/s13127-016-0304-4",
    doi = "10.1007/s13127-016-0304-4",
    openalex = "W2535389874",
    references = "doi101002jmor20084, doi101007s116920099055x, doi10103846266, doi101086284325, doi101093bioinformaticsbtg412, doi101093sysbio423265, doi1011112041210x12035, doi101111j1469185x1966tb01624x, doi101111zoj12403, doi101371journalpone0085574, doi104404hystrix2416283, doi105860choice431300, doi107208chicago97802265182370010001"
}

Members of the mammalian family Felidae (extant and extinct cats) are grossly phenotypically similar, but display a 300-fold range in body size, from less than 1 kg to more than 300 kg. In addition to differences in body mass, felid species show dietary and locomotory specializations that correlate to skull and limb osteological measurements, such as shape or cross-sectional area. However, ecological correlates to the axial skeleton are yet untested. Here, we build on previous studies of the biomechanical and morphological evolution of the felid appendicular skeleton by conducting a quantitative analysis of morphology and allometry in the presacral vertebral column across extant cats. Our results demonstrate that vertebral columns of arboreal, scansorial and terrestrial felids significantly differ in morphology, specifically in the lumbar region, while no distinction based on dietary specialization was found. Body size significantly influences vertebral morphology, with clear regionalization of allometry along the vertebral column, suggesting that anterior (cervicals and thoracics) and posterior (lumbar) vertebrae may be independently subjected to distinct selection pressures.

@article{doi101111zoj12403,
    author = "Randau, Marcela and Goswami, Anjali and Hutchinson, John R. and Cuff, Andrew R. and Pierce, Stephanie E.",
    title = "Cryptic complexity in felid vertebral evolution: shape differentiation and allometry of the axial skeleton",
    year = "2016",
    journal = "Zoological Journal of the Linnean Society",
    abstract = "Members of the mammalian family Felidae (extant and extinct cats) are grossly phenotypically similar, but display a 300-fold range in body size, from less than 1 kg to more than 300 kg. In addition to differences in body mass, felid species show dietary and locomotory specializations that correlate to skull and limb osteological measurements, such as shape or cross-sectional area. However, ecological correlates to the axial skeleton are yet untested. Here, we build on previous studies of the biomechanical and morphological evolution of the felid appendicular skeleton by conducting a quantitative analysis of morphology and allometry in the presacral vertebral column across extant cats. Our results demonstrate that vertebral columns of arboreal, scansorial and terrestrial felids significantly differ in morphology, specifically in the lumbar region, while no distinction based on dietary specialization was found. Body size significantly influences vertebral morphology, with clear regionalization of allometry along the vertebral column, suggesting that anterior (cervicals and thoracics) and posterior (lumbar) vertebrae may be independently subjected to distinct selection pressures.",
    url = "https://doi.org/10.1111/zoj.12403",
    doi = "10.1111/zoj.12403",
    openalex = "W2301353392",
    references = "doi101002jmor20084, doi101086284325, doi101086286013, doi101093bioinformaticsbtg412, doi101093sysbio423265, doi101093sysbiosyt053, doi101111j15585646200900804x, doi101111j2041210x201100153x, doi101111jeb12671, doi101126science2740914, doi105860choice483867, openalexw2183707334, openalexw2611511275"
}

Morphological integration and modularity, which describe the relationships among morphological attributes and reflect genetic, developmental, and functional interactions, have been hypothesized to be major influences on trait responses to selection and thus morphological evolution. The mammalian presacral vertebral column shows little variation in vertebral count and therefore specialization for function occurs primarily through modification of vertebral shape. However, vertebral shape has been suggested to be under strong control from developmental canalization, although this has never been explicitly tested. Here, we assess hypotheses of developmental modules in the vertebrae of felids to determine whether developmental interactions are a primary influence on vertebral modularity. Additionally, we analyze the magnitudes of both intravertebral integration and disparity to evaluate if level of integration varies along the vertebral column and, if so, whether integration and disparity are associated. Our results confirm the hypothesis of vertebral developmental modularity, with most presacral vertebrae displaying two modules. Exceptions are concentrated in the boundaries among traditional and functional regions, suggesting that intravertebral modularity may reflect larger-scale modularity of the felid vertebral column. We further demonstrate that overall integration and disparity are highest in posterior vertebrae, thus providing an empirical example of integration potentially promoting greater morphological responses to selection.

@article{doi101111ede12218,
    author = "Randau, Marcela and Goswami, Anjali",
    title = "Unravelling intravertebral integration, modularity and disparity in Felidae (Mammalia)",
    year = "2017",
    journal = "Evolution \& Development",
    abstract = "Morphological integration and modularity, which describe the relationships among morphological attributes and reflect genetic, developmental, and functional interactions, have been hypothesized to be major influences on trait responses to selection and thus morphological evolution. The mammalian presacral vertebral column shows little variation in vertebral count and therefore specialization for function occurs primarily through modification of vertebral shape. However, vertebral shape has been suggested to be under strong control from developmental canalization, although this has never been explicitly tested. Here, we assess hypotheses of developmental modules in the vertebrae of felids to determine whether developmental interactions are a primary influence on vertebral modularity. Additionally, we analyze the magnitudes of both intravertebral integration and disparity to evaluate if level of integration varies along the vertebral column and, if so, whether integration and disparity are associated. Our results confirm the hypothesis of vertebral developmental modularity, with most presacral vertebrae displaying two modules. Exceptions are concentrated in the boundaries among traditional and functional regions, suggesting that intravertebral modularity may reflect larger-scale modularity of the felid vertebral column. We further demonstrate that overall integration and disparity are highest in posterior vertebrae, thus providing an empirical example of integration potentially promoting greater morphological responses to selection.",
    url = "https://doi.org/10.1111/ede.12218",
    doi = "10.1111/ede.12218",
    openalex = "W2615000196",
    references = "doi101007s1312701603044, doi101111zoj12403"
}

Within carnivorans, cats show comparatively little disparity in overall morphology, with species differing mainly in body size. However, detailed shape analyses of individual osteological structures, such as limbs or skulls, have shown that felids display significant morphological differences that correlate with their observed ecological and behavioural ranges. Recently, these shape analyses have been extended to the felid axial skeleton. Results demonstrate a functionally-partitioned vertebral column, with regions varying greatly in level of correlation between shape and ecology. Moreover, a clear distinction is evident between a phylogenetically-constrained neck region and a selection-responsive posterior spine. Here, we test whether this regionalisation of function reflected in vertebral column shape is also translated into varying levels of phenotypic integration between this structure and most other skeletal elements. We accomplish this comparison by performing pairwise tests of integration between vertebral and other osteological units, quantified with 3D geometric morphometric data and analysed both with and without phylogenetic correction. To our knowledge, this is the first study to test for integration across a comprehensive sample of whole-skeleton elements. Our results show that, prior to corrections, strong covariation is present between vertebrae across the vertebral column and all other elements, with the exception of the femur. However, most of these significant correlations disappear after correcting for phylogeny, which is a significant influence on cranial and limb morphology of felids and other carnivorans. Our results thus suggest that the vertebral column of cats displays relative independence from other skeletal elements and may represent several distinct evolutionary morphological modules.

@article{doi101007s1169201794436,
    author = "Randau, Marcela and Goswami, Anjali",
    title = "Shape Covariation (or the Lack Thereof) Between Vertebrae and Other Skeletal Traits in Felids: The Whole is Not Always Greater than the Sum of Parts",
    year = "2018",
    journal = "Evolutionary Biology",
    abstract = "Within carnivorans, cats show comparatively little disparity in overall morphology, with species differing mainly in body size. However, detailed shape analyses of individual osteological structures, such as limbs or skulls, have shown that felids display significant morphological differences that correlate with their observed ecological and behavioural ranges. Recently, these shape analyses have been extended to the felid axial skeleton. Results demonstrate a functionally-partitioned vertebral column, with regions varying greatly in level of correlation between shape and ecology. Moreover, a clear distinction is evident between a phylogenetically-constrained neck region and a selection-responsive posterior spine. Here, we test whether this regionalisation of function reflected in vertebral column shape is also translated into varying levels of phenotypic integration between this structure and most other skeletal elements. We accomplish this comparison by performing pairwise tests of integration between vertebral and other osteological units, quantified with 3D geometric morphometric data and analysed both with and without phylogenetic correction. To our knowledge, this is the first study to test for integration across a comprehensive sample of whole-skeleton elements. Our results show that, prior to corrections, strong covariation is present between vertebrae across the vertebral column and all other elements, with the exception of the femur. However, most of these significant correlations disappear after correcting for phylogeny, which is a significant influence on cranial and limb morphology of felids and other carnivorans. Our results thus suggest that the vertebral column of cats displays relative independence from other skeletal elements and may represent several distinct evolutionary morphological modules.",
    url = "https://doi.org/10.1007/s11692-017-9443-6",
    doi = "10.1007/s11692-017-9443-6",
    openalex = "W2783273734",
    references = "doi101007s1312701603044, doi101111evo12566, doi101111jeb12671, doi101111zoj12403, doi1011861471214814129, doi101371journalpone0085574, doi10166612001"
}

Since the early 2000s, a revival of a felid relationship for barbourofeline sabretooths has become popular due to recent discoveries of fragmentary fossils from Africa. According to this view, barbourofelines trace their common ancestor with felids through shared similarities in dental morphology going back to the early Miocene of Africa and Europe. However, whether or not such an idea is represented in the basicranial morphology, a conservative area of high importance in family-level relationships, is yet to be tested. A nearly complete skull of Oriensmilus liupanensis gen. and sp. nov. from the middle Miocene Tongxin Basin of northern China represents the most primitive known barbourofeline with an intact basicranial region, affording an opportunity to re-examine the relationship of felids and nimravines. We also present an update on East Asian records of barbourofelines. The new skull of Oriensmilus possesses a suite of characters shared with nimravines, such as the lack of an ossified (entotympanic) bullar floor, absence of an intrabullar septum, lack of a ventral promontorial process of the petrosal, presence of a small rostral entotympanic on the dorsal side of the caudal entotympanic, and a distinct caudal entry of the internal carotid artery and nerve that pierces the caudal entotympanic at the junction of the ossified and unossified caudal entotympanics. The absence of an ossified bullar floor in O. liupanensis and its presence in those from the middle Miocene of Sansan, France thus help to bracket the transition of this character, which must have happened in the early part of the middle Miocene. Spatial relationships between bullar construction and the middle ear configuration of the carotid artery in Oriensmilus strongly resemble those in nimravines but are distinctly different from felids and other basal feliforms. Despite the attractive notion that early barbourofelines arose from a Miocene ancestor that also gave rise to felids, the basicranial evidence argues against this view.http://zoobank.org/urn:http://lsid:zoobank.org:pub:2DE98DBC-4D02-4E18-9788-0B0D8587E73F

@article{doi1010801477201920191691066,
    author = "Wang, Xiaoming and White, Stuart C. and Guan, Jian",
    title = "A new genus and species of sabretooth, Oriensmilus liupanensis (Barbourofelinae, Nimravidae, Carnivora), from the middle Miocene of China suggests barbourofelines are nimravids, not felids",
    year = "2020",
    journal = "Journal of Systematic Palaeontology",
    abstract = "Since the early 2000s, a revival of a felid relationship for barbourofeline sabretooths has become popular due to recent discoveries of fragmentary fossils from Africa. According to this view, barbourofelines trace their common ancestor with felids through shared similarities in dental morphology going back to the early Miocene of Africa and Europe. However, whether or not such an idea is represented in the basicranial morphology, a conservative area of high importance in family-level relationships, is yet to be tested. A nearly complete skull of Oriensmilus liupanensis gen. and sp. nov. from the middle Miocene Tongxin Basin of northern China represents the most primitive known barbourofeline with an intact basicranial region, affording an opportunity to re-examine the relationship of felids and nimravines. We also present an update on East Asian records of barbourofelines. The new skull of Oriensmilus possesses a suite of characters shared with nimravines, such as the lack of an ossified (entotympanic) bullar floor, absence of an intrabullar septum, lack of a ventral promontorial process of the petrosal, presence of a small rostral entotympanic on the dorsal side of the caudal entotympanic, and a distinct caudal entry of the internal carotid artery and nerve that pierces the caudal entotympanic at the junction of the ossified and unossified caudal entotympanics. The absence of an ossified bullar floor in O. liupanensis and its presence in those from the middle Miocene of Sansan, France thus help to bracket the transition of this character, which must have happened in the early part of the middle Miocene. Spatial relationships between bullar construction and the middle ear configuration of the carotid artery in Oriensmilus strongly resemble those in nimravines but are distinctly different from felids and other basal feliforms. Despite the attractive notion that early barbourofelines arose from a Miocene ancestor that also gave rise to felids, the basicranial evidence argues against this view.http://zoobank.org/urn:http://lsid:zoobank.org:pub:2DE98DBC-4D02-4E18-9788-0B0D8587E73F",
    url = "https://doi.org/10.1080/14772019.2019.1691066",
    doi = "10.1080/14772019.2019.1691066",
    openalex = "W3000580878",
    references = "doi101111jeb12671, doi103133pp243g"
}

Abstract The pampas cat Leopardus colocola has been subject to conflicting classifications over the years. Currently, one polytypic species with seven subspecies is recognized, but integrative taxonomic study for this debated group has never been done. Here, we combine the broadest morphological coverage of the pampas cat to date with molecular data and ecological niche models to clarify its species composition and test the validity of recently proposed subspecies. The multiple lines of evidence derived from morphology, molecular, biogeography and climatic niche datasets converged on the recognition of five monotypic species: L. braccatus, L. colocola, L. garleppi (including thomasi, budini, steinbachi, crespoi and wolffsohni as synonyms), L. munoai and L. pajeros (including crucina as synonym). These five species are morphologically diagnosable based on skin and skull traits, have evolved in distinct climatic niche spaces and were recovered in molecular species delimitation. Contrary to previous taxonomic arrangements, we do not recognize subspecies in pampas cats. To objectively define the two most controversial species, we designate neotypes for L. colocola and L. pajeros. The diversification of pampas cats is associated with Middle Pleistocene glaciations, but additional genetic samples from the central Andean region are still needed to conclusively reconstruct its evolutionary history.

@article{doi101093zoolinneanzlaa043,
    author = "do Nascimento, Fábio Oliveira and Cheng, Jilong and Feijó, Anderson",
    title = "Taxonomic revision of the pampas cat Leopardus colocola complex (Carnivora: Felidae): an integrative approach",
    year = "2020",
    journal = "Zoological Journal of the Linnean Society",
    abstract = "Abstract The pampas cat Leopardus colocola has been subject to conflicting classifications over the years. Currently, one polytypic species with seven subspecies is recognized, but integrative taxonomic study for this debated group has never been done. Here, we combine the broadest morphological coverage of the pampas cat to date with molecular data and ecological niche models to clarify its species composition and test the validity of recently proposed subspecies. The multiple lines of evidence derived from morphology, molecular, biogeography and climatic niche datasets converged on the recognition of five monotypic species: L. braccatus, L. colocola, L. garleppi (including thomasi, budini, steinbachi, crespoi and wolffsohni as synonyms), L. munoai and L. pajeros (including crucina as synonym). These five species are morphologically diagnosable based on skin and skull traits, have evolved in distinct climatic niche spaces and were recovered in molecular species delimitation. Contrary to previous taxonomic arrangements, we do not recognize subspecies in pampas cats. To objectively define the two most controversial species, we designate neotypes for L. colocola and L. pajeros. The diversification of pampas cats is associated with Middle Pleistocene glaciations, but additional genetic samples from the central Andean region are still needed to conclusively reconstruct its evolutionary history.",
    url = "https://doi.org/10.1093/zoolinnean/zlaa043",
    doi = "10.1093/zoolinnean/zlaa043",
    openalex = "W3031127939",
    references = "doi101006mpev19960085, doi101093molbevmsh241"
}