Total evidence phylogeny and evolutionary timescale for Australian faunivorous marsupials (Dasyuromorphia)

Kealy, Shimona; Beck, Robin M. D.

doi:10.1186/s12862-017-1090-0

Cited by 59 publications

(112 citation statements)

References 165 publications

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“…Because we found that the evolutionary rates of morphological characters largely determine the impact of model mismatch on TED analyses, we estimated site rates from empirical datasets that have been compiled for the purpose of TED. Among the six empirical datasets examined (Beck and Lee 2014;Close, et al 2016;Herrera and Davolos 2016;Kealy and Beck 2017;Lee 2016;Ronquist, et al 2012a), we found that the vast majority of the morphological characters evolve under near-optimal evolutionary rates (0.01 to about 0.5 per root-tip distance), while none or fewer than 5% of characters have a rate which is higher than 2.0 ( Fig. 9).…”

Section: Evolutionary Rates In Empirical Datasetsmentioning

confidence: 72%

“…The six empirical studies that we have chosen to estimate evolutionary rates of their morphological partitions might or might not reflect a random sample. We focussed on studies that used datasets chosen specifically for the purpose of TED (Beck and Lee 2014;Herrera and Davolos 2016;Kealy and Beck 2017;Lee 2016;Ronquist, et al 2012a), including both presumably well-behaved datasets and some for which the authors of the study suspected a low performance of TED (based mostly on comparisons with the fossil record of a group). It remains to be shown whether morphological datasets in general contain only few fastevolving characters; this at least seems likely, given that morphologists often mostly choose slow characters which are believed to be more informative for phylogenetic reconstruction due to low levels of homoplasy.…”

Section: Mismatch Of the Markov Model Is Mostly Unproblematic In Totamentioning

confidence: 99%

“…In order to validate our simulation results, we estimated evolutionary rates of morphological characters from six empirical dataset that have been compiled for totalevidence dating. The chosen datasets cover insects (Ronquist, et al 2012a), fishes (Close, et al 2016), and four different mammal groups (Beck and Lee 2014;Herrera and Davolos 2016;Kealy and Beck 2017;Lee 2016). We estimated evolutionary rates of each character individually in R (R Core Team 2014) using the function "ACE" from the "ape" package (Paradis, et al 2004) under the equal rates model.…”

Section: Estimating Evolutionary Rates In Empirical Datasetsmentioning

confidence: 99%

“…This function takes a fully resolved rooted tree and a character matrix as input. For all datasets except for Beck and Lee (2014), we used one of the publicly available trees: a maximum clade credibility tree (Kealy and Beck 2017), a maximum sampled-ancestor clade credibility tree (Close, et al 2016), a maximum likelihood tree (Herrera and Davolos 2016), or the tree with the highest likelihood from a set of Bayesian posterior trees (Lee 2016;Ronquist, et al 2012a). An appropriate tree was not available for the Beck and Lee (2014) study; we thus re-run their Bayesian analysis with the same settings and selected the tree with the highest likelihood.…”

Section: Estimating Evolutionary Rates In Empirical Datasetsmentioning

confidence: 99%

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Mismatch of the morphology model is mostly unproblematic in total-evidence dating: insights from an extensive simulation study

Klopfstein

Ryer

Coiro

et al. 2019

Preprint

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Calibrating the molecular clock is the most contentious step in every dating analysis, but the emerging total-evidence dating approach promises increased objectivity. It combines molecular and morphological data of extant and fossil taxa in a Bayesian framework.Information about absolute node ages stems from the inferred fossil placements and associated branch lengths, under the assumption of a morphological clock. We here use computer simulations to assess the impact of mismatch of the morphology model, such as misspecification of character states and transition rates, non-stationarity of the evolutionary process, and extensive variation of evolutionary rates among branches. Comparisons with published datasets suggest that, at least for evolutionary rates typically observed in discrete morphological characters, the total-evidence dating framework is surprisingly robust to these factors. We show that even with relatively low numbers of morphological characters sampled, extensive model mismatch is mostly irrelevant for the performance of the method.The only exception we found are cases of highly asymmetric state frequencies and thus transition rates, but these can be accounted for by appropriate morphology models. In contrast, we find that the temporal scope of fossil sampling has a major impact on divergence time estimates, with the time signal quickly eroding if only rather young fossils are included in an analysis. Our results suggest that total-evidence dating might work even without a good understanding of morphological evolution and that study design should instead focus on an adequate sampling of all relevant fossils, even those with highly incomplete preservation.

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Section: Evolutionary Rates In Empirical Datasetsmentioning

confidence: 72%

Section: Mismatch Of the Markov Model Is Mostly Unproblematic In Totamentioning

confidence: 99%

Section: Estimating Evolutionary Rates In Empirical Datasetsmentioning

confidence: 99%

Section: Estimating Evolutionary Rates In Empirical Datasetsmentioning

confidence: 99%

See 2 more Smart Citations

Mismatch of the morphology model is mostly unproblematic in total-evidence dating: insights from an extensive simulation study

Klopfstein

Ryer

Coiro

et al. 2019

Preprint

View full text Add to dashboard Cite

show abstract

“…Time-calibration was performed using a newly gathered dataset of both tip and node dates (SI File 3). Combining constraints on both tip and node ages has been found to outperform the use of either approach individually (O’Reilly and Donoghue 2016; Kealy and Beck 2017), and is particularly useful in our case as sampling of fossil terminals did not seek to represent the earliest members of lineages (Püschel et al 2020). We sought to identify the most precise stratigraphic duration for all terminals, when possible down to the biozone, although period or age levels were used when occurrences were insufficiently constrained.…”

Section: Methodsmentioning

confidence: 99%

A Total-Evidence Dated Phylogeny of Echinoids and the Evolution of Body Size across Adaptive Landscape

Koch

Thompson

2020

Preprint

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12Several unique properties of echinoids (sea urchins) make them useful for exploring 13 macroevolutionary dynamics, including their remarkable fossil record that can be incorporated 14 into explicit phylogenetic hypotheses. However, this potential cannot be exploited without a 15 robust resolution of the echinoid tree of life. We revisit the phylogeny of crown group 16 Echinoidea using both the largest phylogenomic dataset compiled for the clade, as well as a 17 large-scale morphological matrix with a dense fossil sampling. We also gather a new 18 compendium of both tip and node age constraints, allowing us to combine phylogenomic, 19 morphological and stratigraphic data using a total-evidence dating approach. For this, we 20 develop a novel method for subsampling phylogenomic datasets that selects loci with high 21 phylogenetic signal, low systematic biases and enhanced clock-like behavior. Our approach 22 restructure much of the higher-level phylogeny of echinoids, and demonstrates that combining 23 different data sources increases topological accuracy. We are able to resolve multiple alleged 24 conflicts between molecular and morphological datasets, such as the position of Echinothurioida 25 and Echinoneoida, as well as unravelling the relationships between sand dollars and their closest 26 relatives. We then use this topology to trace the evolutionary history of echinoid body size 27 through more than 270 million years, revealing a complex pattern of convergent evolution to 28 stable peaks in macroevolutionary adaptive landscape. Our efforts show how combining 29 phylogenomic and paleontological evidence offers new ways of exploring evolutionary forces 30 operating across deep timescales.31 32

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Evolution and Development of the Atrial Septum

Jensen

Wang

Moorman

2018

The Anatomical Record

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The complete division of the atrial cavity by a septum, resulting in a left and right atrium, is found in many amphibians and all amniotes (reptiles, birds, and mammals). Surprisingly, it is only in eutherian, or placental, mammals that full atrial septation necessitates addition from a second septum. The high incidence of incomplete closure of the atrial septum in human, so‐called probe patency, suggests this manner of closure is inefficient. We review the evolution and development of the atrial septum to understand the peculiar means of forming the atrial septum in eutherian mammals. The most primitive atrial septum is found in lungfishes and comprises a myocardial component with a mesenchymal cap on its leading edge, reminiscent to the primary atrial septum of embryonic mammals before closure of the primary foramen. In reptiles, birds, and mammals, the primary foramen is closed by the mesenchymal tissues of the atrioventricular cushions, the dorsal mesenchymal protrusion, and the mesenchymal cap. These tissues are also found in lungfishes. The closure of the primary foramen is preceded by the development of secondary perforations in the septal myocardium. In all amniotes, with the exception of eutherian mammals, the secondary perforations do not coalesce to a secondary foramen. Instead, the secondary perforations persist and are sealed by myocardial and endocardial growth after birth or hatching. We suggest that the error‐prone secondary foramen allows large volumes of oxygen‐rich blood to reach the cardiac left side, needed to sustain the growth of the extraordinary large offspring that characterizes eutherian mammals. Anat Rec, 302:32–48, 2019. © 2018 The Authors. The Anatomical Record published by Wiley Periodicals, Inc. on behalf of American Association of Anatomists.

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Total evidence phylogeny and evolutionary timescale for Australian faunivorous marsupials (Dasyuromorphia)

Cited by 59 publications

References 165 publications

Mismatch of the morphology model is mostly unproblematic in total-evidence dating: insights from an extensive simulation study

Mismatch of the morphology model is mostly unproblematic in total-evidence dating: insights from an extensive simulation study

A Total-Evidence Dated Phylogeny of Echinoids and the Evolution of Body Size across Adaptive Landscape

Evolution and Development of the Atrial Septum

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