Biology subjects

Martin, B. S.

Publications and source records attributed to Martin, B. S..

6 recordsLinked to original sources

bioRxiv2026

Comprehensive Phylogenomic Inference of Eucalypts Reveals Taxonomic Limits through Gene Tree Concordance

Speciation can be a slow process for long-lived organisms with large populations due to persistent incomplete lineage sorting, while hybridisation can further obscure species boundaries through admixture. In eucalypts, there is tremendous morphological and environmental variation with almost a thousand described species, subspecies, and hybrid taxa falling into multiple subgenera and intermediate sections. Multilocus molecular studies have generated concatenated species trees supporting deeper divergence between the Corymbia + Blakella + Angophora clade with the rest of eucalypts. However, the proportion of gene trees that recover the concatenated tree topology, including the taxonomic relationships among individual subgenera and sections, remains underappreciated. In this study, we assessed the predictive power of current eucalypt taxonomy - represented as a concatenated tree - in explaining topological variation across gene trees. To do this, we first extracted 1,187 BUSCO loci from short-read data of 701 samples representing roughly 500 described species using CAPTUS. We then inferred individual gene trees and a concatenated species tree using IQ-TREE2. Finally, we calculated the concordance factors for every described subgenus and section on the concatenated tree, and developed a taxonomic consistency test that tracks the taxonomic placement of each sample across gene trees. We show that, even though most taxonomic groups are monophyletic on the concatenated tree with 100% bootstrap support, several groups exhibit very low concordance, indicating that most gene trees do not recover their relationships as represented by the concatenated tree. These results highlight important considerations for current eucalypt taxonomic classification and provide a phylogenomic inference pipeline that can be applied not only to future eucalypt studies, but also to other evolutionarily complex groups of taxa.

evolutionary biology↗

bioRxiv2026

Conserved covariance structure underlies 60 million years of morphological diversification in primates

Evolvability, the capacity of populations to respond to selection, is shaped by the structure and amount of variation transmitted from generation to generation. Whether the heritable covariance structure itself remains stable or evolves rapidly is a central, yet unresolved, question in phenotypic evolution. Competing hypotheses suggest that trait covariation may be constrained by developmental and genetic architectures or, alternatively, reshaped by persistent directional selection. Here, we test whether covariance structure and evolvability are stable over macroevolutionary timescales by applying a comparative evolutionary quantitative genetics framework on primates. We quantified cranial variation using over ten thousand specimens representing 309 species and compared phenotypic covariance matrices for 57 genera within a Bayesian framework. Our results show that despite extensive morphological divergence, primates show remarkably conserved patterns of variation, modular organization, and capacity to respond to selection. Reconstruction of selection gradients across the primate radiation revealed that selection was highly structured, with preferential directions aligned with major axes of cranial variation. These results suggest that the stability of evolvability does not reflect evolutionary stasis, but rather emerges from the alignment between conserved developmental architecture and selection. Our findings demonstrate that covariance structure and the evolutionary potential it provides can persist over deep evolutionary timescales, providing a mechanistic framework for understanding how developmental systems shape the trajectories of major radiations.

evolutionary biology↗

bioRxiv2024

A Global Assessment of Plant-Mite Mutualism and its Ecological Drivers

Mutualisms are mediated by adaptive traits of interacting organisms and play a central role in the ecology and evolution of species. Thousands of plant species possess tiny structures called "domatia" that house mites which protect plants from pests, yet these traits remain woefully understudied. Here we release a worldwide database of species with mite domatia and provide the first evaluation of the phylogenetic and geographic distribution of this mutualistic trait. With >2,500 additions based on digital herbarium scans and published reports, we increased the number of known species with domatia by 27% and, importantly, documented their absence in >4,000 species. We show that mite domatia likely evolved hundreds of times among flowering plants, occurring in an estimated [~]10% of woody species representing over a quarter of all angiosperm families. Contrary to classic hypotheses about the evolutionary drivers of mutualism, we find that mite domatia evolved more frequently in temperate regions and in deciduous lineages; this pattern is concordant with a large-scale geographic transition from predominantly ant-based plant defense mutualisms in the tropics to mite-based defense mutualisms in temperate climates. Our data also reveal a previously undescribed pattern of evolutionary convergence in domatia morphology, with tuft-form domatia more likely to evolve in dry temperate habitats and pit domatia were more likely to evolve in wet tropical environments. We have shown climate-associated drivers of mite domatia evolution, demonstrating their utility and power as an evolutionarily replicated system for the study of plant defense mutualisms.

ecology↗

bioRxiv2024

Stochastic Character Mapping of Continuous Traits on Phlyogenies

AO_SCPLOWBSTRACTC_SCPLOWFossilized organisms only represent a small fraction of Earths evolutionary history, motivating "ancestral state reconstruction" techniques for inferring unobserved phenotypes of evolving lineages based on measurements of their relatives. Stochastic character mapping has emerged as a particularly powerful approach in this regard, allowing researchers to sample histories of discrete variables on phylogenies and better account for the inherent uncertainty of reconstructed ancestral states. Here, we generalize this procedure to work with continuous variables by developing an efficient algorithm for sampling evolutionary histories under Brownian Motion, implemented in a new R package contsimmap. To demonstrate potential applications of these "continuous stochastic character maps", we develop a pipeline for inferring relationships between rates of continuous trait evolution and continuously-varying factors (e.g., body size, generation time)--a difficult statistical problem for which relatively few methods are available. After verifying this novel pipelines performance on simulated data, we use it to show that smaller eucalypt trees tend to exhibit higher rates of flower and leaf trait evolution overall, aligning with well-established predictions based on life history theory as well as empirical patterns in other systems. Ultimately, continuous stochastic character mapping is a valuable new tool for analyzing macroevolutionary data, enabling rigorous yet flexible investigation of complex evolutionary dynamics involving continuous traits and/or continuous variables hypothesized to affect evolutionary processes.

evolutionary biology↗

bioRxiv2022

Modeling the Evolution of Rates of Continuous Trait Evolution

AO_SCPLOWBSTRACTC_SCPLOWRates of phenotypic evolution vary markedly across the tree of life, from the accelerated evolution apparent in adaptive radiations to the remarkable evolutionary stasis exhibited by so-called "living fossils". Such rate variation has important consequences for large-scale evolutionary dynamics, generating vast disparities in phenotypic diversity across space, time, and taxa. Despite this, most methods for estimating trait evolution rates assume rates vary deterministically with respect to some variable of interest or change infrequently during a clades history. These assumptions may cause underfitting of trait evolution models and mislead hypothesis testing. Here, we develop a new trait evolution model that allows rates to vary gradually and stochastically across a clade. Further, we extend this model to accommodate generally decreasing or increasing rates over time, allowing for flexible modeling of "early/late bursts" of trait evolution. We implement a Bayesian method, termed "evolving rates" (evorates for short), to efficiently fit this model to comparative data. Through simulation, we demonstrate that evorates can reliably infer both how and in which lineages trait evolution rates varied during a clades history. We apply this method to body size evolution in cetaceans, recovering substantial support for an overall slowdown in body size evolution over time with recent bursts among some oceanic dolphins and relative stasis among beaked whales of the genus Mesoplodon. These results unify and expand on previous research, demonstrating the empirical utility of evorates.

evolutionary biology↗

bioRxiv2022

Distilling complex evolutionary histories with shiftPlot

Phylogenies form the backbone of many modern comparative methods and are integral components of contemporary science communication. Recent years have seen drastic increases in both the size and complexity of phylogenetic data as computational resources and genetic/trait databases expand. Graphical representations of these massive phylogenetic datasets push against the limits of legibility, often veering closer to artwork than scientific figures optimized to communicate results. While attractive scientific illustrations are certainly a laudable goal, researchers may want to opt for simpler representations to communicate results more concisely. Here, we introduce a new R package, shiftPlot, which implements methods for simplifying and plotting phylogenetic comparative data on discrete traits. Specifically, shiftPlot automatically finds and collapses clades exhibiting the same character state, effectively creating smaller phylogenies that may be more legibly rendered on standard page sizes. Further, these visualizations more clearly communicate evolutionary dynamics by emphasizing state shifts over tip states. While there are undoubtedly situations where this graphical approach will not be suitable (e.g., continuous traits), we believe shiftPlot will prove useful for modern researchers faced with the task of communicating the results of complex phylogenetic analyses.

evolutionary biology↗