Biology subjects

Berv, J. S.

Publications and source records attributed to Berv, J. S..

7 recordsLinked to original sources

bioRxiv2026

bifrost: an R package for scalable inference of phylogenetic shifts in multivariate evolutionary dynamics

O_LIHigh-dimensional comparative datasets, including geometric morphometric landmarks, functional traits, and other large trait datasets, are increasingly common in biology. When these datasets include a large number of traits relative to the number of taxa, they pose significant challenges for phylogenetic comparative analysis. In addition, evolutionary dynamics are often heterogeneous across phylogenies, challenging researchers to develop tools that can localize and account for such variation when investigating hypotheses of evolutionary change. C_LIO_LIWe present bifrost, an R package for detecting and characterizing shifts in multivariate trait evolution across phylogenetic trees. bifrost implements a stepwise greedy search over alternative macroevolutionary regime configurations on a phylogeny. Candidate shifts are proposed and assessed at internal nodes, accelerated with parallel model fitting where possible, and aggregated sequentially when they exceed a user-defined information-criterion acceptance threshold. C_LIO_LIThe underlying model is a scalar-rate multivariate Brownian motion process fit by generalized least squares using mvMORPH::mvgls [1]. Our framework also provides support estimates for individual shifts using information-criterion weights. C_LIO_LIWe illustrate the workflow using a fossil-tip-dated phylogeny and high-dimensional landmark data for early bony fish jaws (32,508 scalar coordinate values), and discuss tuning, outputs, and limitations. bifrost extends existing phylogenetic comparative frameworks for evolutionary analysis and provides a scalable pipeline for exploring the phylogenetic natural history of large multivariate datasets. C_LI

evolutionary biology↗

bioRxiv2024

Skeletal trait measurements for thousands of bird species

Large comparative datasets of avian functional traits have been used to address a wide range of questions in ecology and evolution. To date, this work has been constrained by the limited availability of skeletal trait datasets that include extensive inter- and intra-specific sampling. We use computer vision to identify and measure bones from photographs of museum skeletal specimens to assemble an extensive dataset of functionally important skeletal elements in birds. The dataset spans 2,057 species of birds (Aves: Passeriformes) and includes measurements of 12 skeletal elements from 14,419 individuals. In addition to the trait values directly measured from photographs, we leverage the multi-dimensional nature of our dataset and known phylogenetic relationships of the species to impute missing data under an evolutionary model. To facilitate use of the dataset, the taxonomy has been reconciled with an existing comprehensive avian phylogeny and an additional dataset of external functional traits for all birds.

evolutionary biology↗

bioRxiv2024

Variable patterns of phenotypic evolution among canonical 'living fossil' lineages

Coelacanths, lungfishes, and holosteans represent three emblematic living fossil lineages, thought to be united by similar patterns of phenotypic change through time. While past studies suggest that diverse evolutionary patterns occur within these groups, it is unclear whether these reflect biological differences or arise from contrasting analytical approaches. Here, we examine these lineages under a common framework to assess variation in the evolution of discrete characters, and morphometric shape data, to test whether living fossils show comparable patterns of phenotypic evolution. Our results suggest different evolutionary modes occur, both among and within lineages, as a function of data type. For lungfishes, rates in discrete characters are highest in the Devonian and monotonically decline over time. Coelacanth rates show multiple early peaks followed by a decline toward the recent. Holostean rates show modest peaks but are broadly comparable over time. Patterns of body shape evolution also differ among clades, with strong support for declining rates over time for coelacanths but mixed evidence for similar dynamics in the other groups. Our results imply idiosyncratic processes of evolutionary change among traditional examples of living fossils and indicate a need to explicitly quantify patterns of change rather than apply informal, often qualitative, macroevolutionary classifications.

evolutionary biology↗

bioRxiv2023

The genomic landscape, causes, and consequences of extensive phylogenomic discordance in Old World mice and rats

A species tree is a central concept in evolutionary biology whereby a single branching phylogeny reflects relationships among species. However, the phylogenies of different genomic regions often differ from the species tree. Although tree discordance is often widespread in phylogenomic studies, we still lack a clear understanding of how variation in phylogenetic patterns is shaped by genome biology or the extent to which discordance may compromise comparative studies. We characterized patterns of phylogenomic discordance across the murine rodents (Old World mice and rats) - a large and ecologically diverse group that gave rise to the mouse and rat model systems. Combining new linked-read genome assemblies for seven murine species with eleven published rodent genomes, we first used ultra-conserved elements (UCEs) to infer a robust species tree. We then used whole genomes to examine finer-scale patterns of discordance and found that phylogenies built from proximate chromosomal regions had similar phylogenies. However, there was no relationship between tree similarity and local recombination rates in house mice, suggesting that genetic linkage influences phylogenetic patterns over deeper timescales. This signal may be independent of contemporary recombination landscapes. We also detected a strong influence of linked selection whereby purifying selection at UCEs led to less discordance, while genes experiencing positive selection showed more discordant and variable phylogenetic signals. Finally, we show that assuming a single species tree can result in high error rates when testing for positive selection under different models. Collectively, our results highlight the complex relationship between phylogenetic inference and genome biology and underscore how failure to account for this complexity can mislead comparative genomic studies.

evolutionary biology↗

bioRxiv2023

The pace of mitochondrial molecular evolution varies with seasonal migration distance

Animals that engage in long-distance seasonal migration experience strong selective pressures on their metabolic performance and life history, with potential consequences for molecular evolution. Species with slow life histories typically show lower rates of synonymous substitution (dS) than "fast" species. Previous work has suggested that long-distance seasonal migrants have a slower life history strategy than short-distance migrants, raising the possibility that rates of molecular evolution may covary with migration distance. Additionally, long-distance migrants may face strong selection on metabolically important mitochondrial genes owing to their long-distance flights. Using over 1000 mitochondrial genomes, we assessed the relationship between migration distance and mitochondrial molecular evolution in 39 boreal-breeding migratory bird species. We show that migration distance correlates negatively with dS, suggesting that the slow life history associated with long-distance migration is reflected in rates of molecular evolution. Mitochondrial genes in every study species exhibited evidence of purifying selection, but the strength of selection was greater in short-distance migrants, contrary to our predictions. This result may indicate selection for cold tolerance on mitochondrial evolution among species overwintering at high latitudes. Our study demonstrates that the pervasive correlation between life history and molecular evolutionary rates exists in the context of differential adaptations to seasonality.

evolutionary biology↗

bioRxiv2022

Molecular early burst associated with the diversification of birds at the K-Pg boundary

Complex patterns of genome and life-history evolution associated with the end-Cretaceous (K- Pg) mass extinction event limit our understanding of the early evolutionary history of crown group birds [1-9]. Here, we assess molecular heterogeneity across living birds using a technique enabling inferred sequence substitution models to transition across the history of a clade [10]. Our approach identifies distinct and contrasting regimes of molecular evolution across exons, introns, untranslated regions, and mitochondrial genomes. Up to fifteen shifts in the mode of avian molecular evolution map to rapidly diversifying clades near the Cretaceous-Palaeogene boundary, demonstrating a burst of genomic disparity early in the evolutionary history of crown birds [11-13]. Using simulation and machine learning techniques, we show that shifts in developmental mode [14] or adult body mass [4] best explain transitions in the mode of nucleotide substitution. These patterns are related, in turn, to macroevolutionary shifts in the allometric scaling relationship between basal metabolic rate and body mass [15, 16]. In agreement with theoretical predictions, this scaling relationship appears to have weakened across the end-Cretaceous transition. Overall, our study provides evidence that the Chicxulub bolide impact [17] triggered integrated patterns of evolution across avian genomes, physiology, and life history that structured the evolutionary potential of modern birds.

evolutionary biology↗

bioRxiv2019

Genomic phylogeography of the White Crowned Manakin Pseudopipra pipra (Aves: Pipridae) illuminates a continental-scale radiation out of the Andes

The complex landscape history of the Neotropics has generated opportunities for population isolation and diversification that place this region among the most species-rich in the world. Detailed phylogeographic studies are required to uncover the biogeographic histories of Neotropical taxa, to identify evolutionary correlates of diversity, and to reveal patterns of genetic connectivity, disjunction, and potential differentiation among lineages from different areas of endemism. The White-crowned Manakin (Pseudopipra pipra) is a small suboscine passerine bird that is broadly distributed through the subtropical rainforests of Central America, the lower montane cloud forests of the Andes from Colombia to central Peru, the lowlands of Amazonia and the Guianas, and the Atlantic forest of southeast Brazil. Pseudopipra is currently recognized as a single, polytypic biological species. We studied the effect of the Neotropical landscape on genetic and phenotypic differentiation within this species using genomic data derived from double digest restriction site associated DNA sequencing (ddRAD), and mitochondrial DNA. Most of the genetic breakpoints we identify among populations coincide with physical barriers to gene flow previously associated with avian areas of endemism. The phylogenetic relationships among these populations imply a novel pattern of Andean origination for this group, with subsequent diversification into the Amazonian lowlands. Our analysis of genomic admixture and gene flow reveals a complex history of introgression between some western Amazonian populations. These reticulate processes confound our application of standard concatenated and coalescent phylogenetic methods and raise the question of whether a lineage in the western Napo area of endemism should be considered a hybrid species. Lastly, analysis of variation in vocal and plumage phenotypes in the context of our phylogeny supports the hypothesis that Pseudopipra is a species-complex composed of at least 8, and perhaps up to 17 distinct species which have arisen in the last [~]2.5 Ma.

evolutionary biology↗