Biology subjects

Barrow, L. N.

Publications and source records attributed to Barrow, L. N..

11 recordsLinked to original sources

bioRxiv2026

Mapping frog genomic diversity on a continental scale

Genetic variation is a key component of population resilience and thus an essential tool for wildlife management. For most species, however, we lack information about their current range-wide genomic diversity and how historical and contemporary factors have shaped those patterns. To address these gaps, we built new georeferenced genomic datasets for 2,481 individuals from 46 frog species to develop a genomic diversity atlas representing 43% of species native to the United States and Canada. We identified geographic "hotspots" of high genomic diversity and "coldspots" of low genomic diversity across species and analyzed potential explanations for these patterns. Our results show that several species have their lowest diversity at northern latitudes, at range edges, or within fragmented populations, suggesting areas in need of careful monitoring. More than half (56.8%) of species exhibited a latitudinal gradient in genomic diversity, but we found little evidence for an association between genomic diversity and human disturbance. Furthermore, discordant latitudinal patterns among species suggest that a combination of factors, including range center-edge dynamics and range fragmentation, interact to produce variable diversity patterns. Our study provides a general framework for mapping range-wide genomic diversity of multiple species to support genetically informed biodiversity conservation.

evolutionary biology↗

bioRxiv2026

The Tangled History and Taxonomy of an Iconic Chorus Frog Complex Clarified using Genomic Analyses

Species represent a fundamental unit of biodiversity in evolutionary biology, but the nature of the speciation continuum and inadequate sampling of organisms with broad distributions provide substantial challenges to species delimitation. The Pacific Treefrog complex (Pseudacris regilla sensu lato) is an iconic but systematically poorly understood group of chorus frogs inhabiting a vast portion of western North America. Current studies tentatively recognize three species in this complex (P. hypochondriaca, P. regilla, P. sierra), but disagreement remains among morphological, mitochondrial, and nuclear genetic data. In this study, we used thorough geographic sampling and thousands of nuclear loci, along with an integrative, multi-method approach to clarify the phylogenetic relationships and divergence history of P. regilla s.l. lineages and recommend a new taxonomic arrangement for the group. Pseudacris regilla and P. sierra fall firmly within the "gray zone" of speciation, composing a combined "north" lineage. Based on the degree of congruence in inferences from our analyses and evidence for isolating mechanisms, we propose a two species taxonomy for this complex, recognizing the "north" lineage as P. regilla and retaining P. hypochondriaca as a species. Our study shows how extensive geographic sampling, high-throughput sequencing, and multiple analytical approaches can resolve systematic uncertainties in challenging species complexes.

evolutionary biology↗

bioRxiv2025

Parallel elevational replacement of hosts and parasites in a highly susceptible songbird genus

Elevational replacement distribution patterns underpin montane diversity and reflect the interaction of both biotic and abiotic pressures, but the degree to which parasites exhibit elevational zonation remains unclear. Investigating infection patterns in related host species across elevational gradients can reveal whether parasites and hosts show concordant patterns of elevational turnover, potentially due to shared historical and ecological factors. Here, we assessed patterns of elevational replacement in haemosporidian parasite assemblages that infect three congeneric songbird species: Bells vireo (Vireo bellii), gray vireo (V. vicinior), and plumbeous vireo (V. plumbeus), each of which breeds across distinct elevations and habitats in the southwestern United States. We screened a total of 248 individuals using cytochrome b PCR and microscopy. We identified 19 haemosporidian haplotypes, including eight novel lineages. We found that each of the three vireo species exhibited high haemosporidian prevalence (55.0-86.2%), with nearly all infections from the genus Haemoproteus (subgenus Parahaemoproteus). Haemosporidian assemblages varied across elevations; each sampled range of elevations harbored abundant, yet host-specific lineages with different environmental associations. Bells and plumbeous vireos, but not gray vireos, hosted several phylogenetically distinct, putative generalist lineages, likely reflecting spillover from more diverse local breeding bird communities. Repeated infections in individuals across breeding seasons, together with moderate parasitemia (x{square} {approx} 1%) suggest that these focal vireo species harbor chronic infections during their respective breeding seasons. These results demonstrate that elevational replacement patterns in avian hosts may be mirrored by their haemosporidian parasites, particularly among host-specialized lineages.

ecology↗

bioRxiv2025

Caudata macrogenetics: Species range size predicts intraspecific genetic variation in global salamanders

AimGenetic diversity contains valuable information about ecological and evolutionary aspects of species. Intraspecific genetic variation is shaped by species natural history traits and by characteristics of geography and climate within their ranges. Amphibians are of ecological and conservation interest because of their global distribution, deep history, trait diversity, and roles within ecological communities. Here, we studied genetic variation within salamanders to investigate predictors of nucleotide diversity and spatial patterns of genetic differentiation. LocationGlobal. Time PeriodPresent. Major Taxa StudiedSalamanders. MethodsWe repurposed mitochondrial DNA sequences and ecological data from open-access databases for 220 salamander species. We calculated nucleotide diversity ({pi}) and tested for isolation by distance (IBD) and isolation by environment (IBE). We analyzed these three variables with random forest and phylogenetic comparative methods using 28 predictors expected to be associated with genetic variation. ResultsWe recovered 8,108 Cytb sequences with their associated geographic coordinates, of which 7,007 sequences were manually curated by us. Range size, lineage age, and sample size were important predictors of genetic variation. We found higher diversity in regions including the Neotropics and central-eastern Europe. The absence of phylogenetic signal in {pi}, IBD, and IBE suggests that genetic variation is shaped by local ecological and geographical factors rather than by shared ancestry. Main ConclusionsOur finding of range size as an important predictor aligns with theoretical expectations that species with larger ranges tend to harbor more genetic diversity. Furthermore, lineage age being an important predictor is in line with the clade-age hypothesis, in which species with longer divergence times have higher genetic diversity because they have had more time to accumulate genetic variation. Our results underscore the importance of integrating spatial data into macrogenetic studies, providing valuable information for future studies and conservation strategies targeting regions with high or low genetic diversity.

evolutionary biology↗

bioRxiv2023

Machine learning and phylogenetic models identify predictors of genetic variation in Neotropical amphibians

AimIntraspecific genetic variation is key for adaptation and survival in changing environments and is known to be influenced by many factors, including population size, migration, and life history traits. We investigated genetic variation within Neotropical amphibian species to provide insights into how natural history traits, phylogeny, climatic, and geographic characteristics influence intraspecific diversity. LocationNeotropics. TaxonAmphibians. MethodsWe assembled datasets using open-access databases for natural history traits, genetic sequences, phylogenetic trees, climatic, and geographic data. For each species, we calculated overall nucleotide diversity ({pi}) and tested for isolation by distance (IBD) and isolation by environment (IBE). We then identified predictors of {pi}, IBD, and IBE using Random Forest (RF) regression or RF classification. To incorporate phylogenetic relationships, we fitted phylogenetic generalized linear mixed models (PGLMMs) to predict {pi}, IBD, and IBE. ResultsWe compiled 4,052 mitochondrial DNA sequences from 256 amphibian species (230 frogs and 26 salamanders), georeferencing 2,477 sequences from 176 species that were not linked to occurrence data. RF regressions and PGLMMs were congruent in identifying range size and precipitation ({sigma}) as the most important predictors of {pi}. RF classification and PGLMMs identified minimum elevation as an important predictor of IBD, and maximum latitude and precipitation ({sigma}) as the best predictors of IBE. Main conclusionsThis study unified machine learning and phylogenetic methods and identified predictors of genetic variation in Neotropical amphibians. This approach was valuable to determine which predictors were congruent between methods. We found that species with small ranges or living in zones with less variable precipitation tended to have low genetic diversity. We also showed that Western Mesoamerica, Andes, and Atlantic Forest biogeographic units harbor high diversity across many species that should be prioritized for protection. These results could play a key role in the development of conservation strategies for Neotropical amphibians.

evolutionary biology↗

bioRxiv2022

Predictors of genomic diversity within North American squamates

Comparisons of intraspecific genetic diversity across species can reveal the roles of geography, ecology, and life history in shaping biodiversity. The wide availability of mitochondrial DNA (mtDNA) sequences in open-access databases makes this marker practical for conducting analyses across several species in a common framework, but patterns may not be representative of overall species diversity. Here, we gather new and existing mtDNA sequences and genome-wide nuclear data (genotyping-by-sequencing; GBS) for 30 North American squamate species sampled in the Southeastern and Southwestern United States. We estimated mtDNA nucleotide diversity for two mtDNA genes, COI (22 species alignments; average 16 sequences) and cytb (22 species; average 58 sequences), as well as nuclear heterozygosity and nucleotide diversity from GBS data for 118 individuals (30 species; four individuals and 6,820-44,309 loci per species). We showed that nuclear genomic diversity estimates were highly consistent across individuals for some species, while other species showed large differences depending on the locality sampled. Range size was positively correlated with both cytb diversity (Phylogenetically Independent Contrasts: R2 = 0.31, p = 0.007) and GBS diversity (R2 = 0.21; p = 0.006), while other predictors differed across the top models for each dataset. Mitochondrial and nuclear diversity estimates were not correlated within species, although sampling differences in the data available made these datasets difficult to compare. Further study of mtDNA and nuclear diversity sampled across species ranges is needed to evaluate the roles of geography and life history in structuring diversity across a variety of taxonomic groups.

genomics↗

bioRxiv2020

Predicting intraspecific diversity with machine learning: Challenges and prospects for integrating traits, geography, and genetic data

The growing availability of genetic datasets, in combination with machine learning frameworks, offer great potential to answer long-standing questions in ecology and evolution. One such question has intrigued population geneticists, biogeographers, and conservation biologists: What determines intraspecific genetic diversity? This question is challenging to answer because many factors may influence genetic variation, including life history traits, historical influences, and geography, and the relative importance of these factors varies across taxonomic and geographic scales. Furthermore, interpreting the influence of numerous, potentially correlated variables is difficult with traditional statistical approaches. To address these challenges, we combined repurposed data with machine learning and investigated predictors of genetic diversity, focusing on Nearctic amphibians as a case study. We aggregated species traits, range characteristics, and >42,000 genetic sequences for 299 species using open-access scripts and various databases. After identifying important predictors of nucleotide diversity with random forest regression, we conducted follow-up analyses to examine the roles of phylogenetic history, geography, and demographic processes on intraspecific diversity. Although life history traits were not important predictors for this dataset, we found significant phylogenetic signal in genetic diversity within amphibians. We also found that salamander species at northern latitudes contain lower genetic diversity. Data repurposing and machine learning provide valuable tools for detecting patterns with relevance for conservation, but concerted efforts are needed to compile meaningful datasets with greater utility for understanding global biodiversity.

evolutionary biology↗

bioRxiv2020

Detecting turnover among complex communities using null models: A case study with sky-island haemosporidian parasites

Turnover in species composition between sites, or beta diversity, is a critical component of species diversity that is typically influenced by geography, environment, and biotic interactions. Quantifying turnover is particularly challenging, however, in multi-host, multi-parasite assemblages where undersampling is unavoidable, resulting in inflated estimates of turnover and uncertainty about its spatial scale. We developed and implemented a framework using null models to test for community turnover in avian haemosporidian communities of three sky islands in the southwestern United States. We screened 776 birds for haemosporidian parasites from three genera (Parahaemoproteus, Plasmodium, and Leucocytozoon) by amplifying and sequencing a mitochondrial DNA barcode. We detected infections in 280 birds (36.1%), sequenced 357 infections, and found a total of 99 parasite haplotypes. When compared to communities simulated from a regional pool, we observed more unique, single-mountain haplotypes and fewer haplotypes shared among three mountain ranges than expected, indicating that haemosporidian communities differ to some degree among adjacent mountain ranges. These results were robust even after pruning datasets to include only identical sets of host species, and they were consistent for two of the three haemosporidian genera. The two more distant mountain ranges were more similar to each other than the one located centrally, suggesting that the differences we detected were due to stochastic colonization-extirpation dynamics. These results demonstrate that avian haemosporidian communities of temperate-zone forests differ on relatively fine spatial scales associated with adjacent sky-islands. Null models are essential tools for detecting turnover in complex, undersampled, and poorly known systems.

ecology↗

bioRxiv2018

Deeply conserved susceptibility in a multi-host, multi-parasite system

Variation in susceptibility is ubiquitous in multi-host, multi-parasite assemblages, and can have profound implications for ecology and evolution. The extent to which susceptibility is phylogenetically conserved among hosts is poorly understood and has rarely been appropriately tested. We screened for haemosporidian parasites in 3983 birds representing 40 families and 523 species, spanning ~4500 meters elevation in the tropical Andes. To quantify the influence of host phylogeny on infection status, we applied Bayesian phylogenetic multilevel models that included a suite of environmental, spatial, temporal, life history, and ecological predictors. We found evidence of deeply-conserved susceptibility across the avian tree; host phylogeny explained substantial variation in infection rate, and results were robust to phylogenetic uncertainty. Our study suggests that susceptibility is governed, in part, by conserved, latent aspects of anti-parasite defense. This demonstrates the importance of deep phylogeny for understanding the outcomes of present-day ecological interactions.\n\nStatement of authorshipLNB, SMM, NM, and CCW designed the study; SMM, SCG, HLL, HS, TV, JDW, and CCW collected the data; LNB and NM analyzed the data; LNB, NM, and CCW wrote the paper with input from all authors.\n\nData accessibility statementSpecimen information is available from the Arctos database (arctosdb.org) and in supplementary tables (Appendix S1). Files used for analysis will be archived in Dryad. DOI: XXX.

evolutionary biology↗

bioRxiv2018

Genomic sequence capture of haemosporidian parasites: Methods and prospects for enhanced study of host-parasite evolution

Avian malaria and related haemosporidians (Plasmodium, [Para]Haemoproteus, and Leucocytoozoon) represent an exciting multi-host, multi-parasite system in ecology and evolution. Global research in this field accelerated after 1) the publication in 2000 of PCR protocols to sequence a haemosporidian mitochondrial (mtDNA) barcode, and 2) the development in 2009 of an open-access database to document the geographic and host ranges of parasite mtDNA haplotypes. Isolating haemosporidian nuclear DNA from bird hosts, however, has been technically challenging, slowing the transition to genomic-scale sequencing techniques. We extend a recently-developed sequence capture method to obtain hundreds of haemosporidian nuclear loci from wild bird samples, which typically have low levels of infection, or parasitemia. We tested 51 infected birds from Peru and New Mexico and evaluated locus recovery in light of variation in parasitemia, divergence from reference sequences, and pooling strategies. Our method was successful for samples with parasitemia as low as [~]0.03% (3 of 10,000 blood cells infected) and mtDNA divergence as high as 15.9% (one Leucocytozoon sample), and using the most cost-effective pooling strategy tested. Phylogenetic relationships estimated with >300 nuclear loci were well resolved, providing substantial improvement over the mtDNA barcode. We provide protocols for sample preparation and sequence capture including custom probe kit sequences, and describe our bioinformatics pipeline using aTRAM 2.0, PHYLUCE, and custom Perl and Python scripts. This approach can be applied to the tens of thousands of avian samples that have already been screened for haemosporidians, and greatly improve our understanding of parasite speciation, biogeography, and evolutionary dynamics.

genomics↗

bioRxiv2018

Ecology, Not Distance, Explains Community Composition in Parasites of Sky-Island Audubon’s Warblers

O_LIHaemosporidian parasites of birds are ubiquitous in terrestrial ecosystems, but their coevolutionary dynamics remain poorly understood. If species turnover in parasites occurs at a finer scale than species turnover in hosts, widespread hosts would encounter diverse parasites and potentially diversify as a result. Previous studies have shown that some wide-ranging hosts encounter varied haemosporidian communities throughout their range, and vice-versa. However, it remains difficult to test spatial patterns of diversity in this complex multi-host multi-parasite system because it remains inadequately surveyed.\nC_LIO_LIWe sought to understand how and why a community of avian haemosporidian parasites varies in abundance and composition across an array of eight sky islands in southwestern North America. We tested whether bird community composition, aspects of the environment, or geographic distance explain parasite species turnover in a widespread, generalist host.\nC_LIO_LIWe sampled 178 Audubons Warblers (Setophaga auduboni) along elevational transects in eight mountain ranges and screened them for haemosporidian mtDNA. We tested predictors of infection using generalized linear models (GLMs) and we tested predictors of bird- and parasite-community dissimilarity using generalized dissimilarity modeling (GDM).\nC_LIO_LIPredictors of infection differed by genus: Parahaemoproteus was predicted by elevation and climate, Leucocytozoon varied idiosyncratically among mountain ranges, and Plasmodium was unpredictable, but rare. Parasite species turnover was nearly three-fold higher than bird species turnover and was predicted by elevation, climate, and bird community composition, but not by geographic distance.\nC_LIO_LIHaemosporidian communities vary strikingly at spatial scales of hundreds of kilometers, across which the bird community varies only subtly. The finer spatial scale of turnover among parasites species implies that their ranges tend to be smaller than those of their hosts. Avian host species should encounter different parasite species in different parts of their ranges, resulting in spatially varying selection on host immune systems. Furthermore, the fact that parasite turnover was predicted by bird turnover implies that different species within a host community affect each others parasites, potentially facilitating indirect antagonistic effects.\nC_LI

ecology↗