Biology subjects

Vance, S. E.

Publications and source records attributed to Vance, S. E..

4 recordsLinked to original sources

bioRxiv2026

Rethink the Sink: Urban cores act as leaky sinks to maintain regional gene flow in coyotes

Urbanization is an accelerating evolutionary force, yet the patterns and drivers of urban gene flow remain largely obscured. This leaves a critical gap in testing the interplay between demographic and genetic models of urban connectivity. Specifically: the urban fragmentation model, where structural barriers restrict gene flow and drive genetic drift; the urban facilitation model, where permeable matrices enhance functional connectivity; and the urban sink hypothesis, a demographic model where high mortality creates unsustainable population sinks. We used high-resolution RAD-capture data to conduct landscape genomics and gene flow analyses to resolve these models and investigate contemporary evolution in urban coyotes (Canis latrans) across the greater Los Angeles, CA, USA metropolitan area. By incorporating fine-scale environmental, social-ecological, and historical variables of the built environment, we rigorously assessed how urban heterogeneity shapes intra-city evolutionary dynamics. We found weak population structure, heavily influenced by family groups. There was extensive landscape permeability and gene flow across the study area including across four major highways. We also identified heavily asymmetric gene flow from exurban source populations into the urban core, supporting the urban sink paradigm. However, rather than acting as a genetic dead-end, the urban matrix showed striking functional heterogeneity: one urban core functioned as a 'genetic sponge,' absorbing unique transient alleles from multiple surrounding sources, and both urban cores operated as permeable 'leaky sinks,' exporting critical gene flow to other populations. Consequently, urban demographic sinks can simultaneously act as vital genetic bridges. Our findings reject a pure urban fragmentation model while demonstrating that demographic sink dynamics and genetic facilitation are not mutually exclusive. This demonstrates that high-turnover urban sinks can buffer regional biodiversity against genetic erosion, highlighting the need to prioritize matrix permeability and inter-patch connectivity in urban conservation strategies.

evolutionary biology↗

bioRxiv2026

Habituation drives elevated antimicrobial resistance, functional, and compositional shifts in the black bear gut microbiome

Wildlife habituation across the globe poses threats to human and animal safety and alters regular ecological function, yet the wildlife, environmental, and public health ramifications are poorly characterized. The gut microbiome is a valuable proxy for these factors as it influences host health, is affected by anthropogenic exposure, and may contribute to the environmental spread of virulence factors. Despite their importance, wildlife gut microbiomes are largely uncharacterized, both in composition and function. We characterized American black bear (Ursus americanus) gut microbiomes across a spectrum of lifestyles including wild (conflict-free), habituated (conflict-prone), and captive individuals. 16S rRNA gene sequencing was used for compositional analyses and whole genome short-read sequencing (WGS) was performed on a subset of bears to investigate microbiome function and virulence factors. We found that habituated, wild, and captive bears have unique gut microbiome compositions that are indicative of their respective lifestyles. In particular, captive bears are enriched in carnivory-associated taxa and habituated bears in inflammatory taxa. WGS reveals wild bears have increased fungi and soil-associated bacteria, as well as higher proportions of unclassified reads. Habituated bears have significantly increased levels of antimicrobial resistance genes, and captive bears are enriched in enterotoxins. Our results demonstrate previously undescribed wildlife physiological and One Health consequences of habituation.

ecology↗

bioRxiv2024

Reference-free Structural Variant Detection inMicrobiomes via Long-read Coassembly Graphs

Bacterial genome dynamics are vital for understanding the mechanisms underlying microbial adaptation, growth, and their broader impact on host phenotype. Structural variants (SVs), genomic alterations of 10 base pairs or more, play a pivotal role in driving evolutionary processes and maintaining genomic heterogeneity within bacterial populations. While SV detection in isolate genomes is relatively straightforward, metagenomes present broader challenges due to absence of clear reference genomes and presence of mixed strains. In response, our proposed method rhea, forgoes reference genomes and metagenome-assembled genomes (MAGs) by encompassing a single metagenome coassembly graph constructed from all samples in a series. The log fold change in graph coverage between subsequent samples is then calculated to call SVs that are thriving or declining throughout the series. We show rhea to outperform existing methods for SV and horizontal gene transfer (HGT) detection in two simulated mock metagenomes, which is particularly noticeable as the simulated reads diverge from reference genomes and an increase in strain diversity is incorporated. We additionally demonstrate use cases for rhea on series metagenomic data of environmental and fermented food microbiomes to detect specific sequence alterations between subsequent time and temperature samples, suggesting host advantage. Our innovative approach leverages raw read patterns rather than references or MAGs to include all sequencing reads in analysis, and thus provide versatility in studying SVs across diverse and poorly characterized microbial communities for more comprehensive insights into microbial genome dynamics.

bioinformatics↗

bioRxiv2021

A screen of covalent inhibitors in Mycobacterium tuberculosis identifies serine hydrolases involved in lipid metabolism as potential therapeutic targets

The increasing incidence of antibiotic-resistant Mycobacterium tuberculosis infections is a global health threat necessitating the development of new antibiotics. Serine hydrolases (SHs) are a promising class of targets because of their importance for the synthesis of the mycobacterial cell envelope. We screened a library of small molecules containing serine-reactive electrophiles and identified narrow spectrum inhibitors of M. tuberculous growth. Using these lead molecules, we performed competitive activity-based protein profiling and identified multiple SH targets, including enzymes with uncharacterized functions. Lipidomic analyses of compound-treated cultures revealed an accumulation of free lipids and a substantial decrease in lipooligosaccharides, linking SH inhibition to defects in cell envelope biogenesis. Mutant analysis revealed a path to resistance via the synthesis of mycocerates, but not through mutations to target enzymes. Our results suggest that simultaneous inhibition of multiple SH enzymes is likely to be an effective therapeutic strategy for the treatment of M. tuberculosis infections.

microbiology↗