Inference of Adaptive Shifts for Multivariate Correlated Traits

Bastide, Paul; Ané, Cécile; Robin, Stéphane; Mariadassou, Mahendra

doi:10.1101/146191

Cited by 40 publications

(102 citation statements)

References 53 publications

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“…Some studies have previously indicated difficulties and intrinsic issues of many of the presently proposed methods for automatically detecting regime shifts of phenotypic traits in phylogenies (e.g. Adams & Collyer, 2018; Bastide et al ., 2018), many of which assume evolution under a non-uniform Ornstein-Uhlenbeck [OU] process (although methods that assume other models/processes are also available; e.g. Rabosky, 2014; Castiglione et al ., 2017, 2019).…”

Section: Methodsmentioning

confidence: 99%

Crocodylomorph cranial shape evolution and its relationship with body size and ecology

Godoy

2019

Preprint

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Crocodylomorpha, which includes living crocodylians and their extinct relatives, has a rich fossil record, extending back for more than 200 million years. Unlike modern semi-aquatic crocodylians, extinct crocodylomorphs exhibited more varied lifestyles, ranging from marine to fully terrestrial forms. This ecological diversity was mirrored by a remarkable morphological disparity, particularly in terms of cranial morphology, which seems to be closely associated with ecological roles in the group. Here, I use geometric morphometrics to comprehensively investigate cranial shape variation and disparity in Crocodylomorpha. I quantitatively assess the relationship between cranial shape and ecology (i.e. terrestrial, aquatic, and semi-aquatic lifestyles), as well as possible allometric shape changes. I also characterise patterns of cranial shape evolution and identify regime shifts. I found a strong link between shape and size, and a significant influence of ecology on the observed shape variation. Terrestrial taxa, particularly notosuchians, have significantly higher disparity, and shifts to more longirostrine regimes are associated with large-bodied aquatic or semi-aquatic species. This demonstrates an intricate relationship between cranial shape, body size and lifestyle in crocodylomorph evolutionary history. Additionally, disparity-through-time analyses were highly sensitive to different phylogenetic hypotheses, suggesting the description of overall patterns among distinct trees. For crocodylomorphs, most results agree in an early peak during the Early Jurassic and another in the middle of the Cretaceous, followed by nearly continuous decline until today. Since only crown-group members survived through the Cenozoic, this decrease in disparity was likely the result of habitat loss, which narrowed down the range of crocodylomorph lifestyles.

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Section: Methodsmentioning

confidence: 99%

Crocodylomorph cranial shape evolution and its relationship with body size and ecology

Godoy

2019

Preprint

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“…Even with the AICc correction, SURFACE may still over fit the number of optima, and it has attracted criticism for its unreasonable assumption of no evolutionary correlation among PC axes (Adams and Collyer 2017). In light of the potential issues with the SURFACE analysis, we also used Phylogenet-icEM (Bastide et al 2018) to identify optima on the MCC phylogeny a posteriori, and included that model in the mv-MORPH analysis. This newer likelihood method uses an ex-pectation maximization algorithm (multivariate OU model, or scOU) to estimate the shift positions without assuming uncorrelated axes (Bastide et al 2018).…”

Section: Evolutionary Model Selectionmentioning

confidence: 99%

“…In light of the potential issues with the SURFACE analysis, we also used Phylogenet-icEM (Bastide et al 2018) to identify optima on the MCC phylogeny a posteriori, and included that model in the mv-MORPH analysis. This newer likelihood method uses an ex-pectation maximization algorithm (multivariate OU model, or scOU) to estimate the shift positions without assuming uncorrelated axes (Bastide et al 2018). We compare the optima identified in the SURFACE and PhylogeneticEM analyses in the results.…”

Section: Evolutionary Model Selectionmentioning

confidence: 99%

Ancient and contingent body shape diversification in a hyperdiverse continental fish radiation

Burns

Sidlauskas

2019

Evolution

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The characiform fishes of the Neotropics and Africa radiated remarkably in ecomorphology, but the macroevolutionary processes responsible for their biodiversity remain unexplored, and the degree to which their continental diversification parallels classic adaptive radiations remains untested. We reconstruct their diversification using a new fossil‐calibrated molecular phylogeny, dietary information, and geometric morphometrics. Though body shape diversified early in a manner consistent with an ancient continental adaptive radiation, trophic shifts did not always coincide with shape changes. With the notable exception of piscivores, lineages that converged in diet did not converge closely in body shape. Shifts in habitat or other variables likely influenced body shape evolution in addition to changes in diet, and the clade's history departs from many classic adaptive radiations in lakes or on islands, in which trophic convergence drives morphological convergence. The contrast between the Neotropical radiation's exhaustive exploration of morphospace and the more restrained diversification in Africa suggests a major role for contingency in characiform evolution, with the presence of cypriniform competitors in the Old World, but not the New, providing one possible explanation. Our results depict the clearest ecomorphological reconstruction to date for Characiformes and set the stage for studies further elucidating the processes underlying its diversification.

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“…However, there has been a recent expansion of the types of evolutionary dynamics that can be modeled, including bounded explorations of traitspace (Boucher and Démery 2016), trajectories punctuated by rapid bursts of change (Landis and Schraiber 2017) and macroevolutionary landscapes that can represent directional and disruptive selection (Boucher et al 2017). Complex OUM models capable of detecting heterogeneities in evolutionary processes across clades have also been developed (Beaulieu et al 2012; Ingram and Mahler 2013; Khabbazian et al 2016; Bastide et al 2018). Nonetheless, there have been few attempts at comparing the fit of non-uniform OUM processes to the expanded repertoire of uniform models now available.…”

Section: Discussionmentioning

confidence: 99%

“…This method allowed us to identify an OUMVAZ model describing a four-peak adaptive landscape which attained almost absolute AICc weight. This approach is a promising way to mitigate the overfitting tendencies of SURFACE while generating more biologically realistic models, especially as other methods to fit OUM models without specifying the location of regime shifts cannot be applied to non-ultrametric trees (e.g., Khabbazian et al 2016; Bastide et al 2018).…”

Section: Discussionmentioning

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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Inference of Adaptive Shifts for Multivariate Correlated Traits

Cited by 40 publications

References 53 publications

Crocodylomorph cranial shape evolution and its relationship with body size and ecology

Crocodylomorph cranial shape evolution and its relationship with body size and ecology

Ancient and contingent body shape diversification in a hyperdiverse continental fish radiation

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

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