Analytical advances alleviate model misspecification in non-Brownian multivariate comparative methods

Evolution, Journal Year: 2023, Volume and Issue: 78(3), P. 389 - 400

Published: Oct. 28, 2023

Abstract Adams and Collyer argue that contemporary multivariate (Gaussian) phylogenetic comparative methods are prone to favouring more complex models of evolution sometimes rotation invariance can be an issue. Here we dissect the concept point out that, depending on understanding, this issue with any method relies numerical instead analytical estimation approaches. We relate ongoing discussion concerning principal component analysis. Contrary what found, do not observe a bias against simpler Brownian motion process in simulations when use new, improved, likelihood evaluation algorithm employed by mvSLOUCH, which allows for studying much larger phylogenies model setups.

Language: Английский

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The macroevolutionary adaptive landscape: more than a metaphor?

Evolution, Journal Year: 2024, Volume and Issue: 78(4), P. 792 - 795

Published: Jan. 24, 2024

Language: Английский

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Detecting diversifying selection for a trait from within and between-species genotypes and phenotypes

Journal of Evolutionary Biology, Journal Year: 2024, Volume and Issue: 37(12), P. 1538 - 1550

Published: July 12, 2024

Abstract To quantify selection acting on a trait, methods have been developed using either within or between-species variation. However, within-species variation do not integrate the changes at macro-evolutionary scale. Conversely, current usually discard variation, thus accounting for processes micro-evolutionary The main goal of this study is to define neutrality index quantitative by combining within- and This integrates nucleotide polymorphism divergence normalizing trait As such, it does require estimation population size nor time speciation normalization. Our can be used seek deviation from null model neutral evolution, test diversifying selection. Applied brain mass body mammalian scale, we show that under Finally, our sensitive assumption sizes, mutation rates generation are constant across phylogeny, automatically adjust it.

Language: Английский

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Blouch: Bayesian Linear Ornstein-Uhlenbeck Models for Comparative Hypotheses

Systematic Biology, Journal Year: 2024, Volume and Issue: unknown

Published: July 19, 2024

Abstract Abstract.—Relationships among species in the tree of life can complicate comparative methods and testing adaptive hypotheses. Models based on Ornstein-Uhlenbeck process permit hypotheses about adaptation to be tested by allowing traits either evolve toward fixed optima (e.g., regimes or niches) track continuously changing that influenced other traits. These models allow estimation effects both phylogenetic inertia—resistance due any source—on trait evolution, an approach known as “adaptation-inertia” framework. However, previous applications this framework, most approaches suggested deal with issue non-independence, are a maximum likelihood approach, thus it is difficult include information prior biological knowledge analysis, which affect resulting inferences. Here, I present Blouch, (Bayesian Linear for Comparative Hypotheses), fits allometric continuous evolution Bayesian framework predictors incorporates measurement error. first briefly discuss implemented then new these provided This includes advantages assigning biologically meaningful priors when compared non-Bayesian approaches, varying (intercepts slopes), multilevel modeling. Validations simulated data show good performance recovering true evolutionary parameters all models. To demonstrate workflow Blouch empirical dataset, test hypothesis relatively larger antlers larger-bodied deer result more intense sexual selection comes along their tendency live breeding groups. While results groups have antlers, living smallest appear different steeper scaling pattern antler size body than contrary findings may argue type selective pressures govern optimum

Language: Английский

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Pappus phenotypes and flight performance across evolutionary history in the daisy family

Annals of Botany, Journal Year: 2024, Volume and Issue: 134(5), P. 863 - 876

Published: July 30, 2024

Abstract Background and Aims Diversity in pappus shapes size Asteraceae suggests an adaptive response to dispersion challenges adjusting diaspores optimal phenotypic configurations. Here, by analysing the relationship among pappus–cypsela relationships, flight performance types evolutionary context, we evaluate role of natural selection acting on evolution diaspore configuration at a macro-ecological scale daisy family. Methods To link relationships with collected published data these traits from 82 species. This allowed us translate morphometric for 150 species represented fully resolved backbone phylogeny Through ancestral reconstructions model selection, assessed whether was associated constrained different types. Additionally, evaluated, through phylogenetic regressions, exhibited allometric relationships. Results The setose type had highest performances most probable state Stepwise changes independently led multiple instances loss reduction performance. Flight best modelled as five regimes specific which correspond configurations that are distinct Conclusions Evolutionary modelling main factor proceeded towards optima, often overcoming constraints imposed favouring certain directions. With perspective is process driving observed patterns, various biotic abiotic suggested principal drivers transitions along space time family history. results also allow discussion historical context.

Language: Английский

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Challenges and advances in measuring phenotypic convergence

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2022, Volume and Issue: unknown

Published: Oct. 21, 2022

ABSTRACT Tests of phenotypic convergence can provide evidence adaptive evolution, and the popularity such studies has grown in recent years due to development novel, quantitative methods for identifying measuring convergence. These include commonly applied C 1– 4 measures Stayton (2015), which measure morphological distances between lineages, Ornstein-Uhlenbeck (OU) evolutionary model-fitting analyses, test whether lineages convergently evolved toward peaks. We performance -measures other under various scenarios reveal a critical issue with -measures: they often misidentify divergent as convergent. address this by developing novel measures— Ct 4-measures—that at specific points time, minimizing possibility misidentifying taxa are most appropriate when focal same or similar geologic ages (e.g., extant taxa), meaning that lineages’ histories considerable overlap time. Beyond -measures, we find all influenced position space, outliers statistically more likely be measured strongly convergent chance. Further, mimic researchers assess using OU models priori regime assignments classifying ecological traits), multiple-regime phenotypically assigned shared selective outperform simpler models. This highlights model support these should not assumed always reflect among regime. Our new 4-measures an improved comparative tool, but emphasize available imperfect, recognize limitations use multiple lines inferring

Language: Английский

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The impact of tip age distribution on reconstructing trait evolution using phylogenetic comparative methods

Published: July 27, 2024

Collecting data for use in constructing phylogenies is a valuable but time- and resource-consuming pursuit. As result, indicators of the potential value including certain species phylogeny priori could prove useful when planning this stage research. Here, we used simulation approach to investigate whether there are trends ability phylogenetic comparative methods recover correct model trait evolution based on characteristics phylogeny. First, multiple diversification rates simulate containing varying proportions fossil extant tips. We then simulated single across each using continuous models. compared fit incorrect models traits. This quantitative evaluation allows us discern tip associated with identifying Our results indicate that inclusion fossils can be highly beneficial reconstructing histories (e.g., Ornstein-Uhlenbeck ACDC) not others Brownian motion). In fact, many cases, increasing proportion dataset far more beneficial, perhaps resource-efficient, than number taxa dataset. corroborate previous findings tips vastly improve reconstruction histories, also show effect often stronger older fossils.

Language: Английский

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Evaluating the Performance of Widely Used Phylogenetic Models for Gene Expression Evolution

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Feb. 10, 2023

Phylogenetic comparative methods are increasingly used to test hypotheses about the evolutionary processes that drive divergence in gene expression among species. However, it is unknown whether distributional assumptions of phylogenetic models designed for quantitative phenotypic traits realistic data and importantly, reliability conclusions studies may depend on well-described by chosen model. To evaluate this, we first fit several trait evolution 8 previously published datasets, comprising a total 54,774 genes with 145,927 unique gene-tissue combinations. Using developed approach, then assessed how well best model set described an absolute (not just relative) sense. First, find Ornstein-Uhlenbeck models, which values constrained around optimum, were preferred 66% Second, 61% combinations, was found perform well; rest be performing poorly at least one statistics examined. Third, when simple do not well, this appears typically consequence failing fully account heterogeneity rate evolution. We advocate assessment performance should become routine component studies; doing so can improve inferences inspire development novel models.

Language: Английский

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TraitTrainR: Accelerating large-scale simulation under models of continuous trait evolution

Bioinformatics Advances, Journal Year: 2024, Volume and Issue: 5(1)

Published: Dec. 9, 2024

Abstract Motivation The scale and scope of comparative trait data are expanding at unprecedented rates, recent advances in evolutionary modeling simulation sometimes struggle to match this pace. Well-organized flexible applications for conducting large-scale simulations evolution hold promise context understanding models more so our ability confidently estimate them with real sampled from nature. Results We introduce TraitTrainR, an R package designed facilitate efficient, under complex continuous evolution. TraitTrainR employs several output formats, supports popular transformations, accommodates multi-trait evolution, exhibits flexibility defining input parameter space model stacking. Moreover, permits measurement error, allowing investigation its potential impacts on inference. envision a wealth we demonstrate one such example by examining the problem selection three empirical phylogenetic case studies. Collectively, these demonstrations applying explore problems underscores utility broader addressing key questions, including those related experimental design statistical power, biology. Availability implementation is developed 4.4.0 freely available https://github.com/radamsRHA/TraitTrainR/, which includes detailed documentation, quick-start guides, step-by-step tutorial.

Language: Английский

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The beak shape variation of Neotropical passerines is explained more by body size than diet

Biological Journal of the Linnean Society, Journal Year: 2024, Volume and Issue: 144(1)

Published: Dec. 1, 2024

Abstract Beak morphology in birds is often linked to diet. In this study, we aimed analyse whether diet or other drivers, such as allometry species relatedness, explain the morphological beak variation of Neotropical passerines and there are specific predictors for shape two passerine suborders, Oscines Suboscines. We analysed measurements (length, width, depth) response variables body size, diet, phylogenetic distance predictor variables. After controlling which had major impact on beack shape, length depth exhibited significant differences across categories between suborders. Compared with Oscines, Suboscines more influenced by probably owing niche conservatism. Our findings suggest an adaptive convergence suborders Neotropics, driven mainly allometric constraints rather than trophic niche.

Language: Английский

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