Biology subjects

Alfaro, M. E.

Publications and source records attributed to Alfaro, M. E..

6 recordsLinked to original sources

bioRxiv2026

Unlocking a flexible set of phylogenetic models for discrete and continuous trait evolution using discretized stochastic diffusion

The practical utility of many modern phylogenetic comparative methods can depend on how accurately mathematical models capture the evolutionary process of traits. Boucher and Demery (2016) described a new quantitative trait model for testing hypotheses about constraint on phenotypic character evolution: Brownian motion with reflective limits. Since their analytic solution for the probability function under this bounded scenario was intractable for reasonably-sized trees, Boucher and Demery (2016) also identified a creative technique for computing the likelihood of their model. The basis of this method derives from the convergence of an equal-rates, symmetric, ordered Markov chain and continuous stochastic diffusion in the limit as the number of lattice states in the chain goes to{infty} (or, alternatively, as their widths decrease towards zero). We realized that this general approach had the potential to unlock a surprisingly large number of additional models for the phylogenetic comparative analysis of discrete and continuous trait data, and we explore several of these in the present article. Specifically, we examine application of this discretized diffusion approximation to the threshold model from evolutionary quantitative genetics, to a new "semi-threshold" trait evolution model, to a joint model where the rate of evolution for a continuous trait depends on the value of a co-evolving discrete character, along with a separate model where precisely the converse is true, and to a discrete-character-dependent multi-trend trended continuous trait evolution model. We conclude with some context for the origins of our article and discussion of other possible applications of this powerful approach.

evolutionary biology↗

bioRxiv2025

charisma: An R package to perform reproducible color characterization of digital images for biological studies

O_LIAdvances in digital imaging and software tools have provided increasingly accessible datasets and methods for analyzing color evolution. Despite the variety of computational packages available, most rely on color classification before running analyses. Previous methods to characterize color limit the ability to analyze large-scale image databases and are not always representative of biologically relevant color classes, which decrease the accuracy of downstream analyses. C_LIO_LIHere, we present charisma, an R package designed to characterize the distribution of distinct color classes in images suitable for large-scale studies of biological organisms. Here, we demonstrate the utility of our package through an analysis of color evolution in a sample of diverse and charismatic birds, tanagers, in the subfamily Thraupinae. C_LIO_LIWe show that charisma can quickly and accurately classify every pixel in an image and validate these results using pre-identified, canonical color swatches. We find that charisma color classifications are consistent with those made by color-pattern experts in the field. Applying charisma to tanager color evolution, we find that charisma outputs seamlessly integrate with downstream evolutionary analyses. C_LIO_LIOur results demonstrate that using charisma to manually curate and characterize colors in images provides a standardized, reliable, and reproducible framework for high-throughput color classification. C_LI Anonymized Data/Code for Peer ReviewO_LIAnalytic data/code for this manuscript can be found on the following Open Science Frame-work repo: https://osf.io/cqg59/overview?view_only=29c9786a338e48618fabbab2883937cc C_LIO_LIcharisma package GitHub repo: https://anonymous.4open.science/r/charisma-C87E/ C_LI

evolutionary biology↗

bioRxiv2024

A highly contiguous genome assembly for the Yellow Warbler (Setophaga petechia)

The Yellow Warbler (Setophaga petechia) is a small songbird in the New World Warbler family (Parulidae) that exhibits phenotypic and ecological differences across a widespread distribution and is important to Californias riparian habitat conservation. Here, we present a high-quality de novo genome assembly of a vouchered female Yellow Warbler from southern California. Using HiFi long-read and Omni-C proximity sequencing technologies, we generated a 1.22 Gb assembly including 687 scaffolds with a contig N50 of 6.80 Mb, scaffold N50 of 21.18 Mb, and a BUSCO completeness score of 96.0%. This highly contiguous genome assembly provides an essential resource for understanding the history of gene flow, divergence, and local adaptation and can inform conservation management of this charismatic bird species.

evolutionary biology↗

bioRxiv2021

Prolonged morphological expansion of spiny-rayed fishes following the end-Cretaceous

Spiny-rayed fishes (Acanthomorpha) dominate modern marine habitats and comprise more than a quarter of all living vertebrate species1-3. It is believed that this dominance resulted from explosive lineage and phenotypic diversification coincident with the Cretaceous-Paleogene (K-Pg) mass-extinction event4. It remains unclear, however, if living acanthomorph diversity is the result of a punctuated burst or gradual accumulation of diversity following the K-Pg. We assess these hypotheses with a time-calibrated phylogeny inferred using ultraconserved elements from a sampling of species that represent over 91% of all acanthomorph families, as well as an extensive body shape dataset of extant species. Our results indicate that several million years after the end-Cretaceous, acanthomorphs underwent a prolonged and significant expansion of morphological disparity primarily driven by changes in body elongation, and that acanthomorph lineages containing the bulk of the living species diversity originated throughout the Cenozoic. These acanthomorph lineages radiated into distinct regions of morphospace and retained their iconic phenotypes, including a large group of laterally compressed reef fishes, fast-swimming open-ocean predators, bottom-dwelling flatfishes, seahorses, and pufferfishes. The evolutionary success of spiny-rayed fishes is the culmination of a post K-Pg adaptive radiation in which rates of lineage diversification were decoupled from periods of high phenotypic disparity.

evolutionary biology↗

bioRxiv2018

A target enrichment bait set for studying relationships among ostariophysan fishes

O_LITarget enrichment of conserved nuclear loci has helped reconstruct evolutionary relationships among a wide variety of species. While there are preexisting bait sets to enrich a few hundred loci across all fishes or a thousand loci from acanthomorph fishes, no bait set exists to enrich large numbers (>1000 loci) of ultraconserved nuclear loci from ostariophysans, the second largest actinopterygian superorder.\nC_LIO_LIIn this manuscript, we describe how we designed a bait set to enrich 2,708 ultraconserved nuclear loci from ostariophysan fishes by combining an existing genome assembly with low coverage sequence data collected from two ostariophysan lineages.\nC_LIO_LIWe perform a series of enrichment experiments using this bait set across the ostariophysan Tree of Life, from the deepest splits among the major groups (>150 MYA) to more recent divergence events that have occured during the last 50 million years.\nC_LIO_LIOur results demonstrate that the bait set we designed is useful for addressing phylogenetic questions from the origin of crown ostariophysans to more recent divergence events, and our in silico results suggest that this bait set may be useful for addressing evolutionary questions in closely related groups of fishes, like Clupeiformes.\nC_LI

evolutionary biology↗

bioRxiv2018

Lack of signal for the impact of venom gene diversity on speciation rates in cone snails

Understanding why some groups of organisms are more diverse than others is a central goal in macroevolution. Evolvability, or lineages intrinsic capacity for evolutionary change, is thought to influence disparities in species diversity across taxa. Over macroevolutionary time scales, clades that exhibit high evolvability are expected to have higher speciation rates. Cone snails (family: Conidae, >900 spp.) provide a unique opportunity to test this prediction because their venom genes can be used to characterize differences in evolvability between clades. Cone snails are carnivorous, use prey-specific venom (conotoxins) to capture prey, and the genes that encode venom are known and diversify through gene duplication. Theory predicts that higher gene diversity confers a greater potential to generate novel phenotypes for specialization and adaptation. Therefore, if conotoxin gene diversity gives rise to varying levels of evolvability, conotoxin gene diversity should be coupled with macroevolutionary speciation rates. We applied exon capture techniques to recover phylogenetic markers and conotoxin loci across 314 species, the largest venom discovery effort in a single study. We paired a reconstructed timetree using 12 fossil calibrations with species-specific estimates of conotoxin gene diversity and used trait-dependent diversification methods to test the impact of evolvability on diversification patterns. Surprisingly, did not detect any signal for the relationship between conotoxin gene diversity and speciation rates, suggesting that venom evolution may not be the rate-limiting factor controlling diversification dynamics in Conidae. Comparative analyses showed some signal for the impact of diet and larval dispersal strategy on diversification patterns, though whether or not we detected a signal depended on the dataset and the method. If our results remain true with increased sampling in future studies, they suggest that the rapid evolution of Conidae venom may cause other factors to become more critical to diversification, such as ecological opportunity or traits that promote isolation among lineages.

evolutionary biology↗