Biology subjects

Slater, G. J.

Publications and source records attributed to Slater, G. J..

7 recordsLinked to original sources

bioRxiv2026

Beyond the Panglossian paradigm: adaptation, constraint, and anuran functional trait evolution.

Recognizing patterns in functional trait evolution is a necessary step in testing macroevolutionary questions. Quantification of these patterns and interpretation of their generative processes relies on an ever-expanding suite of comparative approaches, but current methods oversimplify the process-to-pattern mapping. This simplification may promote binary classifications of patterns and their drivers, such as adaptive versus non-adaptive or constrained versus unconstrained. A potentially more robust and evolutionarily informative alternative is to fit an expanded suite of evolutionary models at different levels of taxonomic or ecological resolution to reveal how evolutionary drivers imprint simultaneously on observed patterns of trait evolution. Here, we perform a clade-wide analysis of functional trait evolution across Anura (frogs and toads). Focusing on three functionally important traits, we quantify the relative fit of random, directional, and bounded models at the intra- and inter-microhabitat levels to explore how changes in trait function across microhabitats translate into different evolutionary regimes. We recover heterogeneous regime-level distributions of model support that imply complex underlying evolutionary dynamics, while also revealing methodological biases and model identifiability issues. These findings underscore the need to develop more robust tools for evolutionary model fitting and advance beyond binary frameworks for interpreting evolutionary processes.

evolutionary biology↗

bioRxiv2024

Bayesian Least-Squares Supertrees (BLeSS): flexible inference of large time-calibrated phylogenies

AO_SCPLOWBSTRACTC_SCPLOWTime-calibrated phylogenies are key to macroevolutionary hypothesis testing and parameter inference, but their estimation is difficult when the number of tips is large. Despite its attractive properties, the joint Bayesian inference of topology and divergence times remains computationally prohibitive for large supermatrices. Historically, supertrees represented a popular alternative to supermatrix-based phylogenetic methods, but most of the existing supertree techniques do not accommodate branch lengths or topological uncertainty, rendering them unfit to supply input for modern comparative methods. Here, we present Bayesian Least-Squares Supertrees (BLeSS), a new approach that takes a profile of time trees with partially overlapping leaf sets as its input, and returns the joint posterior distribution of supertree topologies and divergence times as its output. Building upon the earlier exponential error model and average consensus techniques, BLeSS transforms the profile into path-length distance matrices, computes their arithmetic average, and uses MCMC to sample time-calibrated supertrees according to their least-squares fit to the average distance matrix. We provide a fast, flexible, and validated implementation of BLeSS in the program RevBayes, and test its performance using a comprehensive set of simulations. We show that the method performs well across a wide range of conditions, including variation in missing data treatment and the steepness of the error function. Finally, we apply BLeSS to an empirical dataset comprising 33 time trees for 260 species of carnivorans, illustrating its ability to recover well-supported clades and plausible node ages, and discuss how the method can best be used in practice, outlining possible extensions and performance boosts.

evolutionary biology↗

bioRxiv2022

Bayesian prediction of multivariate ecology from phenotypic data yields novel insights into the diets of extant and extinct taxa

Morphology often reflects ecology, enabling the prediction of ecological roles for taxa that lack direct observations such as fossils. In comparative analyses, ecological traits, like diet, are often treated as categorical, which may aid prediction and simplify analyses but ignores the multivariate nature of ecological niches. Futhermore, methods for quantifying and predicting multivariate ecology remain rare. Here, we ranked the relative importance of 13 food items for a sample of 88 extant carnivoran mammals, and then used Bayesian multilevel modeling to assess whether those rankings could be predicted from dental morphology and body size. Traditional diet categories fail to capture the true multivariate nature of carnivoran diets, but Bayesian regression models derived from living taxa have good predictive accuracy for importance ranks. Using our models to predict the importance of individual food items, the multivariate dietary niche, and the nearest extant analogs for a set of data-deficient extant and extinct carnivoran species confirms long-standing ideas for some taxa, but yields new insights about the fundamental dietary niches of others. Our approach provides a promising alternative to traditional dietary classifications. Importantly, this approach need not be limited to diet, but serves as a general framework for predicting multivariate ecology from phenotypic traits.

evolutionary biology↗

bioRxiv2022

Topographically distinct adaptive landscapes for skulls, skeletons, and size explain the dietary adaptive radiation of Carnivora (Mammalia)

AO_SCPLOWBSTRACTC_SCPLOWModels of adaptive radiation were originally developed to explain the early, rapid appearance of distinct modes of life within diversifying clades. Phylogenetic tests of this hypothesis have yielded limited support for temporally declining rates of phenotypic evolution across diverse clades, but the concept of an adaptive landscape that links form to fitness, while also crucial to these models, has received more limited attention. Using methods that assess the temporal accumulation of morphological variation and estimate the topography of the underlying adaptive landscape, I found evidence of an early partitioning of mandibulo-dental morphological variation in Carnivora (Mammalia) that occurs on an adaptive landscape with multiple peaks, consistent with classic ideas about adaptive radiation. Although strong support for this mode of adaptive radiation is present in traits related to diet, its signal is not present in body mass data or for traits related to locomotor behavior and substrate use. These findings suggest that adaptive radiations may occur along some axes of ecomorphological variation without leaving a signal in others and that their dynamics are more complex than simple univariate tests might suggest.

evolutionary biology↗

bioRxiv2020

A Total-Group Phylogenetic Metatree for Cetacea and the Importance of Fossil Data in Diversification Analyses

AO_SCPLOWBSTRACTC_SCPLOWPhylogenetic trees provide a powerful framework for testing macroevolutionary hypotheses, but it is becoming increasingly apparent that inferences derived from extant species alone can be highly misleading. Trees incorporating living and extinct taxa are are needed to address fundamental questions about the origins of diversity and disparity but it has proved challenging to generate robust, species-rich phylogenies that include large numbers of fossil taxa. As a result, most studies of diversification dynamics continue to rely on molecular phylogenies. Here, we extend and apply a recently developed meta-analytic approach for synthesizing previously published phylogenetic studies to infer a well-resolved set of species level, time-scaled phylogenetic hypotheses for extinct and extant cetaceans (whales, dolphins and allies). Our trees extend sampling from the [~] 90 extant species to over 400 living and extinct species, and therefore allow for more robust inference of macroevolutionary dynamics. While the diversification scenarios we recover are broadly concordant with those inferred from molecular phylogenies they differ in critical ways, most notably in the relative contributions of extinction and speciation rate shifts in driving rapid radiations. Supertrees are often viewed as poor substitute for phylogenies inferred directly from character data but the metatree pipeline overcomes many of the past criticisms leveled at these approaches. Meta-analytic phylogenies provide the most immediate route for integrating fossils into macroevolutionary analyses, the results of which range from untrustworthy to nonsensical without them.

evolutionary biology↗

bioRxiv2018

Hierarchy, Morphology, and Adaptive Radiation: a Test of Osborn’s Law in the Carnivora

AO_SCPLOWBSTRACTC_SCPLOWHenry Fairfield Osborns law of adaptive radiation was intended to explain the early proliferation of morphological and functional variation in diversifying clades. Yet, despite much theoretical development and empirical testing, questions remain regarding the taxonomic levels at which adaptive radiation occurs, the traits involved, and its frequency across the tree of life. Here, we evaluate support for this \"early burst\" model of adaptive radiation in 14 ecomorphological traits plus body mass for the extant mammalian order Carnivora. Strong support for an early burst adaptive radiation is recovered for molar grinding area, a key proxy for diet. However, we find no evidence for early burst-like dynamics in body mass or multivariate trait data, suggesting a decoupling of evolutionary modes among traits driven by dietary specialization. Furthermore, the signal of an early burst is only recovered for Carnivora, and not in family-level clades. The lack of support for the early burst model of morphological adaptive radiation in previous phylogenetic studies may be a consequence of focusing on the wrong traits at the wrong taxonomic levels. Osborns law predicted that adaptive radiation should be hierarchically structured, and the search for its signature and understanding of its prevalence will require a renewed focus on functional traits and their evolution over higher-level clades.

evolutionary biology↗

bioRxiv2018

Inferring Species Trees Using Integrative Models of Species Evolution

Evolutionary models account for either population- or species-level processes, but usually not both. We introduce a new model, the FBD-MSC, which makes it possible for the first time to integrate both the genealogical and fossilization phenomena, by means of the multispecies coalescent (MSC) and the fossilized birth-death (FBD) processes. Using this model, we reconstruct the phylogeny representing all extant and many fossil Caninae, recovering both the relative and absolute time of speciation events. We quantify known inaccuracy issues with divergence time estimates using the popular strategy of concatenating molecular alignments, and show that the FBD-MSC solves them. Our new integrative method and empirical results advance the paradigm and practice of probabilistic total evidence analyses in evolutionary biology.

evolutionary biology↗