The impact of phylogenetic dating method on interpreting trait evolution: a case study of Cretaceous–Palaeogene eutherian body-size evolution

Halliday, Thomas J. D.; Goswami, A.

doi:10.1098/rsbl.2016.0051

Cited by 19 publications

(22 citation statements)

References 24 publications

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“…While there was considerable variation in the statistical test output parameters, generally there was much less variation in the significance of the results, regardless of the tree topology or time‐scaling method used (Tables and ). This outcome contrasts with the conclusions of many recent studies which have highlighted that the choice of tree‐scaling method can be a major source of uncertainty in phylogenetic comparative analyses (Bapst ; Halliday & Goswami ; Soul & Friedman ).…”

Section: Discussioncontrasting

confidence: 90%

Archosauromorph extinction selectivity during the Triassic–Jurassic mass extinction

et al. 2018

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Many traits have been linked to extinction risk among modern vertebrates, including mode of life and body size. However, previous work has indicated there is little evidence that body size, or any other trait, was selective during past mass extinctions. Here, we investigate the impact of the Triassic–Jurassic mass extinction on early Archosauromorpha (basal dinosaurs, crocodylomorphs and their relatives) by focusing on body size and other life history traits. We built several new archosauromorph maximum‐likelihood supertrees, incorporating uncertainty in phylogenetic relationships. These supertrees were then employed as a framework to test whether extinction had a phylogenetic signal during the Triassic–Jurassic mass extinction, and whether species with certain traits were more or less likely to go extinct. We find evidence for phylogenetic signal in extinction, in that taxa were more likely to become extinct if a close relative also did. However, there is no correlation between extinction and body size, or any other tested trait. These conclusions add to previous findings that body size, and other traits, were not subject to selection during mass extinctions in closely‐related clades, although the phylogenetic signal in extinction indicates that selection may have acted on traits not investigated here.

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Section: Discussioncontrasting

confidence: 90%

Archosauromorph extinction selectivity during the Triassic–Jurassic mass extinction

et al. 2018

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“…The end‐Cretaceous cataclysm that killed off non‐avian dinosaurs and many other vertebrates about 66 million years ago provided placental mammals with a unique opportunity to thrive (Wible et al., ; O'Leary et al., ). Some 10 million years into the Paleogene, placental mammals had already displayed a clear increase in taxonomic and ecological diversity, as well as in evolutionary rates, in contrast to their end‐Cretaceous relatives (Alroy, ; Slater, ; Grossnickle & Newham, ; Halliday & Goswami, ,b; Halliday et al., ). This extrinsic environmental change definitively opened new ecological opportunities for placental mammals; however, intrinsic aspects of placental mammals likely played a role in their success as well (Wilson, ).…”

Section: Introductionmentioning

confidence: 99%

Virtual endocranial and inner ear endocasts of the Paleocene ‘condylarth’ Chriacus: new insight into the neurosensory system and evolution of early placental mammals

et al. 2019

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The end‐Cretaceous mass extinction allowed placental mammals to diversify ecologically and taxonomically as they filled ecological niches once occupied by non‐avian dinosaurs and more basal mammals. Little is known, however, about how the neurosensory systems of mammals changed after the extinction, and what role these systems played in mammalian diversification. We here use high‐resolution computed tomography (CT) scanning to describe the endocranial and inner ear endocasts of two species, Chriacus pelvidens and Chriacus baldwini, which belong to a cluster of ‘archaic’ placental mammals called ‘arctocyonid condylarths’ that thrived during the ca. 10 million years after the extinction (the Paleocene Epoch), but whose relationships to extant placentals are poorly understood. The endocasts provide new insight into the paleobiology of the long‐mysterious ‘arctocyonids’, and suggest that Chriacus was an animal with an encephalization quotient (EQ) range of 0.12–0.41, which probably relied more on its sense of smell than vision, because the olfactory bulbs are proportionally large but the neocortex and petrosal lobules are less developed. Agility scores, estimated from the dimensions of the semicircular canals of the inner ear, indicate that Chriacus was slow to moderately agile, and its hearing capabilities, estimated from cochlear dimensions, suggest similarities with the extant aardvark. Chriacus shares many brain features with other Paleocene mammals, such as a small lissencephalic brain, large olfactory bulbs and small petrosal lobules, which are likely plesiomorphic for Placentalia. The inner ear of Chriacus also shares derived characteristics of the elliptical and spherical recesses with extinct species that belong to Euungulata, the extant placental group that includes artiodactyls and perissodactyls. This lends key evidence to the hypothesized close relationship between Chriacus and the extant ungulate groups, and demonstrates that neurosensory features can provide important insight into both the paleobiology and relationships of early placental mammals.

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“…There have been studies on the effect on downstream analyses of several of the features that are more acute in phylogenies of fossil taxa than those of extant groups (e.g. uncertain divergence dates (Bapst ; Halliday & Goswami ), missing character data causing tree misspecification (Stone ) and a higher proportion of soft polytomies (Garland & Diaz‐Uriarte ; Housworth & Martins ; Davis et al . )).…”

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confidence: 99%

Bias in phylogenetic measurements of extinction and a case study of end‐Permian tetrapods

Soul

Friedman

2017

Palaeontology

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Extinction risk in the modern world and extinction in the geological past are often linked to aspects of life history or other facets of biology that are phylogenetically conserved within clades. These links can result in phylogenetic clustering of extinction, a measurement comparable across different clades and time periods that can be made in the absence of detailed trait data. This phylogenetic approach is particularly suitable for vertebrate taxa, which often have fragmentary fossil records, but robust, cladistically-inferred trees. Here we use simulations to investigate the adequacy of measures of phylogenetic clustering of extinction when applied to phylogenies of fossil taxa while assuming a Brownian motion model of trait evolution. We characterize expected biases under a variety of evolutionary and analytical scenarios. Recovery of accurate estimates of extinction clustering depends heavily on the sampling rate, and results can be highly variable across topologies. Clustering is often underestimated at low sampling rates, whereas at high sampling rates it is always overestimated. Sampling rate dictates which cladogram timescaling method will produce the most accurate results, as well as how much of a bias ancestor-descendant pairs introduce. We illustrate this approach by applying two phylogenetic metrics of extinction clustering (Fritz and Purvis's D and Moran's I) to three tetrapod clades across an interval including the Permo-Triassic mass extinction event. These groups consistently show phylogenetic clustering of extinction, unrelated to change in other quantitative metrics such as taxonomic diversity or extinction intensity.

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The impact of phylogenetic dating method on interpreting trait evolution: a case study of Cretaceous–Palaeogene eutherian body-size evolution

Cited by 19 publications

References 24 publications

Archosauromorph extinction selectivity during the Triassic–Jurassic mass extinction

Archosauromorph extinction selectivity during the Triassic–Jurassic mass extinction

Virtual endocranial and inner ear endocasts of the Paleocene ‘condylarth’ Chriacus: new insight into the neurosensory system and evolution of early placental mammals

Bias in phylogenetic measurements of extinction and a case study of end‐Permian tetrapods

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