A Nonstationary Markov Model Detects Directional Evolution in Hymenopteran Morphology

Klopfstein, Seraina; Vilhelmsen, Lars; Ronquist, Fredrik

doi:10.1093/sysbio/syv052

Cited by 66 publications

(78 citation statements)

References 85 publications

(118 reference statements)

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“…It is ironic that, whereas the lack of consistency was in the past supposed to be the main argument to abandon parsimony, the development of many new models is now made with no concern whatsoever for whether the model results in statistically consistent estimations (e.g. Klopfstein et al., ; Wright et al., ; Pyron, ). And (with the exception of Yang, , p. 176) no Bayesian has expressed any concern in print with examples showing that the standard form of Bayesian analysis (i.e.…”

Section: Discussionmentioning

confidence: 99%

Weighted parsimony outperforms other methods of phylogenetic inference under models appropriate for morphology

2017

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One of the lasting controversies in phylogenetic inference is the degree to which specific evolutionary models should influence the choice of methods. Model‐based approaches to phylogenetic inference (likelihood, Bayesian) are defended on the premise that without explicit statistical models there is no science, and parsimony is defended on the grounds that it provides the best rationalization of the data, while refraining from assigning specific probabilities to trees or character‐state reconstructions. Authors who favour model‐based approaches often focus on the statistical properties of the methods and models themselves, but this is of only limited use in deciding the best method for phylogenetic inference—such decision also requires considering the conditions of evolution that prevail in nature. Another approach is to compare the performance of parsimony and model‐based methods in simulations, which traditionally have been used to defend the use of models of evolution for DNA sequences. Some recent papers, however, have promoted the use of model‐based approaches to phylogenetic inference for discrete morphological data as well. These papers simulated data under models already known to be unfavourable to parsimony, and modelled morphological evolution as if it evolved just like DNA, with probabilities of change for all characters changing in concert along tree branches. The present paper discusses these issues, showing that under reasonable and less restrictive models of evolution for discrete characters, equally weighted parsimony performs as well or better than model‐based methods, and that parsimony under implied weights clearly outperforms all other methods.

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Section: Discussionmentioning

confidence: 99%

Weighted parsimony outperforms other methods of phylogenetic inference under models appropriate for morphology

2017

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“…all-rates-different) using model selection metrics (Leslie et al, 2013;Goldberg et al, 2017;Sauquet et al, 2017). However, fewer efforts have attempted to model and test the intriguing possibility of unidirectional and more generally nonstationary directional discrete trait evolution (including irreversible evolution or 'Dollo's law'; Alekseyenko et al, 2008;Goldberg & Igi c, 2008;Klopfstein et al, 2015;Leslie et al, 2015). Importantly, these questions may also take the fossil record into account (Hunt, 2012;Slater et al, 2012).…”

Section: What Are the Tempo And Mode Of Morphological Evolution In Anmentioning

confidence: 99%

Key questions and challenges in angiosperm macroevolution

2018

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Contents Summary 1170 I. Introduction 1170 II. Six key questions 1172 III. Three key challenges 1177 IV. Conclusions 1181 Acknowledgements 1182 References 1183 SUMMARY: The origin and rapid diversification of angiosperms (flowering plants) represent one of the most intriguing topics in evolutionary biology. Despite considerable progress made in complementary fields over the last two decades (paleobotany, phylogenetics, ecology, evo-devo, genomics), many important questions remain. For instance, what has been the impact of mass extinctions on angiosperm diversification? Are the angiosperms an adaptive radiation? Has morphological evolution in angiosperms been gradual or pulsed? We propose that the recent and ongoing revolution in macroevolutionary methods provides an unprecedented opportunity to explore long-standing questions that probably hold important clues to understand present-day biodiversity. We present six key questions that explore the origin and diversification of angiosperms. We also identify three key challenges to address these questions: (1) the development of new integrative models that include diversification, multiple intrinsic and environmental traits, biogeography and the fossil record all at once, whilst accounting for sampling bias and heterogeneity of macroevolutionary processes through time and among lineages; (2) the need for large and standardized synthetic databases of morphological variation; and (3) continuous effort on sampling the fossil record, but with a revolution in current paleobotanical practice.

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“…Analyses were performed under the symmetric model. Many morphological character systems follow a directional pattern across parts of the tree of life, be it due to positive selection or biased starting conditions (Gould 1996;Klopfstein, et al 2015). To mimic increasing levels of directionality, we varied the proportion of characters in the dataset that followed a non-stationary pattern between zero and one by adjusting the state frequencies at the root.…”

Section: Morphology Model and Model Mismatchmentioning

confidence: 99%

“…Second, Lewis (2001) suggested a way to account for asymmetry in state frequencies and thus in transition rates, an improvement that only recently started to attract attention (Klopfstein and Spasojevic 2019;Wright, et al 2016). Furthermore, it is straightforward to incorporate non-stationarity and thus directional evolutionary patterns by introducing separate state frequencies at the root (Klopfstein, et al 2015). Other types of model mismatch might be more difficult to overcome, such as pronounced heterotachy (Goloboff, et al in press) or non-homogeneity of the evolutionary process (Jayaswal, et al 2011;Jermiin, et al 2008).…”

Section: Introductionmentioning

confidence: 99%

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

Klopfstein

Ryer

Coiro

et al. 2019

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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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A Nonstationary Markov Model Detects Directional Evolution in Hymenopteran Morphology

Cited by 66 publications

References 85 publications

Weighted parsimony outperforms other methods of phylogenetic inference under models appropriate for morphology

Weighted parsimony outperforms other methods of phylogenetic inference under models appropriate for morphology

Key questions and challenges in angiosperm macroevolution

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

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