The soft explosive model of placental mammal evolution

Phillips, Matthew J.; Fruciano, Carmelo

doi:10.1186/s12862-018-1218-x

Cited by 39 publications

(35 citation statements)

References 67 publications

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“…2019 ). Furthermore, parallel changes in substitution rate have been inferred in empirical data ( Phillips 2016 ; Phillips and Fruciano 2018 ). Our simulations are also fair in that the same conditions are applied across all methods, and differential performance under these conditions is informative of relative merits of alternative algorithms and calibration strategies.…”

Section: Discussionmentioning

confidence: 94%

Performance of A Priori and A Posteriori Calibration Strategies in Divergence Time Estimation

Beavan

Donoghue

Beaumont

et al. 2020

Genome Biology and Evolution

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Relaxed molecular clock methods allow the use of genomic data to estimate divergence times across the tree of life. This is most commonly achieved in Bayesian analyses where the molecular clock is calibrated a priori through the integration of fossil information. Alternatively, fossil calibrations can be used a posteriori, to transform previously estimated relative divergence times that were inferred without considering fossil information, into absolute divergence times. However, as branch length is the product of the rate of evolution and the duration in time of the considered branch, the extent to which a posteriori-calibrated, relative divergence time methods can disambiguate time and rate, is unclear. Here, we use forward evolutionary simulations and compare a priori and a posteriori calibration strategies using different molecular clock methods and models. Specifically, we compare three Bayesian methods, the strict clock, uncorrelated clock and autocorrelated clock, and the non-Bayesian algorithm implemented in RelTime. We simulate phylogenies with multiple, independent substitution rate changes and show that correct timescales cannot be inferred without the use of calibrations. Under our simulation conditions, a posteriori calibration strategies almost invariably inferred incorrect rate changes and divergence times. The a priori integration of fossil calibrations is fundamental in these cases to improve the accuracy of the estimated divergence times. Relative divergence times and absolute timescales derived by calibrating relative timescales to geological time a posteriori, appear to be less reliable than a priori calibrated, timescales.

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Section: Discussionmentioning

confidence: 94%

Performance of A Priori and A Posteriori Calibration Strategies in Divergence Time Estimation

Beavan

Donoghue

Beaumont

et al. 2020

Genome Biology and Evolution

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“…Reports of pre‐Cretaceous angiosperms do not offer serious support for older molecular dates, and most are clearly erroneous. These results, like those involving other taxa such as placental mammals (Phillips & Fruciano, ), underline the need to investigate whether current molecular methods have inherent biases that are responsible for conflicts of this type with the fossil record.…”

Section: Discussionmentioning

confidence: 99%

How deep is the conflict between molecular and fossil evidence on the age of angiosperms?

2019

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Summary The timing of the origin of angiosperms is a hotly debated topic in plant evolution. Molecular dating analyses that consistently retrieve pre‐Cretaceous ages for crown‐group angiosperms have eroded confidence in the fossil record, which indicates a radiation and possibly also origin in the Early Cretaceous. Here, we evaluate paleobotanical evidence on the age of the angiosperms, showing how fossils provide crucial data for clarifying the situation. Pollen floras document a Northern Gondwanan appearance of monosulcate angiosperms in the Valanginian and subsequent poleward spread of monosulcates and tricolpate eudicots, accelerating in the Albian. The sequence of pollen types agrees with molecular phylogenetic inferences on the course of pollen evolution, but it conflicts strongly with Triassic and early Jurassic molecular ages, and the discrepancy is difficult to explain by geographic or taphonomic biases. Critical scrutiny shows that supposed pre‐Cretaceous angiosperms either represent other plant groups or lack features that might confidently assign them to the angiosperms. However, the record may allow the Late Jurassic existence of ecologically restricted angiosperms, like those seen in the basal ANITA grade. Finally, we examine recently recognized biases in molecular dating and argue that a thoughtful integration of fossil and molecular evidence could help resolve these conflicts.

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“…A phylogenetic study of mammals combining molecular sequence data and morphological characters for extant and fossil taxa, found only a single placental ancestor crossing the KPB (O'Leary et al, 2013; but see Springer et al, 2013;dos Reis et al, 2014). Others have argued that diversification of Placentalia followed a "soft explosive" model, with a few lineages crossing the KPB followed by rapid ordinal level Paleocene radiation (Phillips, 2015;Phillips and Fruciano, 2018). Recent time-calibrated phylogenies for birds showed the age of Neoaves to also be close to the KPB (Jarvis et al, 2014;Claramunt and Cracraft, 2015;Prum et al, 2015), with rapid post-KPB http://mc.manuscriptcentral.com/systbiol PHYLOGENOMIC COMPLEXITY AND POLYPLOIDY IN LEGUMES 9 divergence represented by a hard polytomy (Suh, 2016).…”

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confidence: 99%

The Origin of the Legumes is a Complex Paleopolyploid Phylogenomic Tangle Closely Associated with the Cretaceous–Paleogene (K–Pg) Mass Extinction Event

et al. 2020

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The consequences of the Cretaceous-Paleogene (K-Pg) boundary (KPB) mass extinction for the evolution of plant diversity remain poorly understood, even though evolutionary turnover of plant lineages at the KPB is central to understanding assembly of the Cenozoic biota. The apparent concentration of whole genome duplication (WGD) events around the KPB may have played a role in survival and subsequent diversification of plant lineages. To gain new insights into the origins of Cenozoic biodiversity, we examine the origin and early evolution of the globally diverse legume family (Leguminosae or Fabaceae). Legumes are ecologically (co-)dominant across many vegetation types, and the fossil record suggests that they rose to such prominence after the KPB in parallel with several well-studied animal clades including Placentalia and Neoaves. Furthermore, multiple WGD events are hypothesized to have occurred early in legume evolution. Using a recently inferred phylogenomic framework, we investigate the placement of WGDs during early legume evolution using gene tree reconciliation methods, gene count data and phylogenetic supernetwork reconstruction. Using 20 fossil calibrations we estimate a revised timeline of legume evolution based on 36 nuclear genes selected as informative and evolving in an approximately clock-like fashion. To establish the timing of WGDs we also date duplication nodes in gene trees. Results suggest either a pan-legume WGD event on the stem lineage of the family, or an allopolyploid event involving (some of) the earliest lineages within the crown group, with additional nested WGDs subtending subfamilies Papilionoideae and Detarioideae. Gene tree reconciliation methods that do not account for allopolyploidy may be misleading in inferring an earlier WGD event at the time of divergence of the two parental lineages of the polyploid, suggesting that the allopolyploid scenario is more likely. We show that the crown age of the legumes dates to the Maastrichtian or early Paleocene and that, apart from the Detarioideae WGD, paleopolyploidy occurred close to the KPB. We conclude that the early evolution of the legumes followed a complex history, in which multiple auto- and/or allopolyploidy events coincided with rapid diversification and in association with the mass extinction event at the KPB, ultimately underpinning the evolutionary success of the Leguminosae in the Cenozoic.

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The soft explosive model of placental mammal evolution

Cited by 39 publications

References 67 publications

Performance of A Priori and A Posteriori Calibration Strategies in Divergence Time Estimation

Performance of A Priori and A Posteriori Calibration Strategies in Divergence Time Estimation

How deep is the conflict between molecular and fossil evidence on the age of angiosperms?

The Origin of the Legumes is a Complex Paleopolyploid Phylogenomic Tangle Closely Associated with the Cretaceous–Paleogene (K–Pg) Mass Extinction Event

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