Biology subjects

Wilcox, J. J. S.

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

3 recordsLinked to original sources

bioRxiv2026

Genomic Architecture, Differentiation, and Adaptation in Three Large Falcons

Recent chromosomal rearrangements and divergence in large falcon species make them excellent foci for studies on evolution and genomic architecture. Here, we use high-coverage (44-74X) whole genome resequencing with 10X Genomics Linked-Reads to assess patterns of genomic divergence in peregrine, saker, and gyrfalcons and we link these to chromosomal type and chromosomal rearrangements. We first use admixture analysis and cross-coalescent MSMC2 to demonstrate distinct species boundaries between the large falcons and retrace their demography. We assessed genomic landscapes in terms of recombination rate, nucleotide diversity ({pi}), Tajimas D, autozygosity and Fst between saker and gyrfalcons: {pi} had higher values on smaller chromosomes and Fst had higher values on larger chromosomes. Recombination rate concealed other chromosome type effects on {pi} and Tajimas D but largely explained variation in Fst. We find 39 selective sweeps--some shared--across the falcons. However, only five candidate genes--mostly housekeeping genes--were implicated as targets of balancing selection across all falcons, with 4 of these shared between Hierofalco and three shared across all the falcons. Occurrence of selective sweeps and balancing selection were not enriched by chromosome type or in the context of chromosome fusions. Overall, our findings provide insights into divergence and adaptation in large falcons, and demonstrate an association of genomic architecture and chromosomal fusions with all population genomic indicators and metrics of differentiation between species. Significance StatementFalcons are culturally and commercially important birds that have undergone recent chromosomal rearrangement, providing a natural system for studies on chromosomal heterogeneities and evolution. By analyzing genomic variation across three large falcon species, we show that chromosome type and chromosomal fusions structure patterns of recombination, diversity, and divergence. Our findings highlight the importance of underlying genomic architecture to common forms of evolutionary inference and call attention to the role of chromosomal fusions in shaping falcon evolution.

genomics↗

bioRxiv2025

Characterizing Bacterial and Archaeal Microbiomes of Urban Long-Tailed Macaques in Singapore

Animal microbiomes are sources of ecological responsiveness in the face of environmental change, and may serve as modulators and indicators of adaptability and stress in the face of emerging ecological perturbations. Baseline characterizations of non-human primate microbiomes will be important to applied and theoretical applications of microbiome research. Long-tailed macaques (Macaca fasciularis) are among the most ubiquitous primates, they live in close association with humans, and are a common model organism in biomedical research. Here, we use 16S amplicon metabarcoding of the V4 hypervariable region to provide baseline information on taxonomic and inferred functional variation in the prokaryotic (Archaea and Eubacteria) assemblies of oral and gut microbiomes of urban long-tailed macaques in Singapore. Oral microbiomes showed the most pronounced community structure at lower taxonomic levels, particularly ASVs. Gut microbiomes, in contrast, showed the most pronounced community structure at higher taxonomic levels, particularly phyla. Gut microbiomes showed clear groupings based on relative abundances of Proteobacteria, Firmicutes, and Bacteroidetes. Gut microbiome community composition was almost entirely explained by the Proteobacteria:Firmicutes ratio and this metric explained twice as much inferred functional variation as the more traditional Firmicutes:Bacteroidetes ratio. Archaeal communities in both oral and gut communities were dominated by methanogens. These were the only archaea found in the gut, but ammonia-oxidizing archaea were consistent constituents of oral microbiome assemblies as well. Ultimately, our findings imply distinct microbiome composition in Singapores urban macaques relative to reports from non-urban conspecifics.

microbiology↗

bioRxiv2024

Identification of 5mC within heterogenous tissue using de-novo somatic mutations

Tissues represent a fundamental evolutionary interface at the junction of genotype and phenotype. Indeed, gene regulation often occurs at the tissue level and manifests itself through tissue-specific epigenetic modifications. Studies investigating tissue epigenetics are limited by access to pure tissues. Tissues not only differ epigenetically, they are also subject to genetic differentiation through somatic mutations. As somatic mutations follow predictable patterns of inheritance, the application of population genomic approaches to inter- and intra-tissue variation could allow for the efficient detection of epigenetic modifications, even when tissue samples are convoluted. Here, we present an approach that uses de-novo somatic mutations to deconvolute 5mC methylation patterns through analysis of shifts in tissue-specific allele frequencies. We use simulations and bisulfite sequencing data to show that somatic mutations are common and detectable in next-generation sequencing data. We then use changes in mutation frequencies to accurately derive the proportional tissue of origin along a gradient of in silico subsamples of mixed-tissue bisulfite reads. We confirm that mixed tissues bias estimates of methylation levels and prevent detection of methylation differences at high levels of mixture. Our derived estimates of tissue contamination allow for unbiased and accurate deconvolution of mixed-tissue methylations in CpG and non-CpG context. We are ultimately able to recover 15-30% of differentially-methylated sites, and approximately 40-90% of differentially-methylated CpG islands and gene bodies in any cytosine context at contamination levels up to 90%. Our findings highlight the utility of population genomic approaches across scales, and expand the accessibility of epigenetics studies within evolutionary biology.

genomics↗