Spurley, W. J. | bioRxiv Science

bioRxiv2025

Comparative Patterns of Variation on the X Chromosome and Autosomes: The Role of the Breeding Sex Ratio

In many populations, unequal numbers of females and males reproduce each generation. This imbalance in the breeding sex ratio (BSR) shapes patterns of genetic variation on the sex chromosomes and the autosomes in distinct ways. Despite recognition of this phenomenon, effects of the BSR on some aspects of variation remain unclear, especially for populations with non-equilibrium demographic histories. To address this gap in the field, we used coalescent simulations to examine relative patterns of variation at X-linked loci and autosomal loci in populations spanning the range of BSR with historical changes in population size. Shifts in BSR away from 1:1 reduce nucleotide diversity and the number of unique haplotypes and increase linkage disequilibrium and the frequency of the most common haplotype, with contrasting effects on X-linked loci and autosomal loci. Strong population bottlenecks transform relationships between the BSR, the site frequency spectrum, and linkage disequilibrium while relationships between the BSR, nucleotide diversity, and haplotype characteristics are broadly conserved. Our findings indicate that evolutionary interpretations of variation on the X chromosome should consider the combined effects of the BSR and demographic history. The genomic signatures we report could be used to reconstruct these fundamental population parameters from genomic data in natural populations. Significance StatementThe breeding sex ratio is a fundamental evolutionary parameter, but genomic analyses routinely assume it is 1:1. Our research characterizes the relationships between the breeding sex ratio and multiple facets of genomic variation and shows how these relationships change in the context of dynamic demographic histories. In doing so, we provide increasingly realistic expectations for patterns of X-linked and autosomal variation in population genomic datasets collected from natural populations.

evolutionary biology↗

bioRxiv2021

Substrate, temperature, and geographical patterns among nearly 2,000 natural yeast isolates

Yeasts have broad importance as industrially and clinically relevant microbes and as powerful models for fundamental research, but we are only beginning to understand the roles yeasts play in natural ecosystems. Yeast ecology is often more difficult to study compared to other, more abundant microbes, but growing collections of natural yeast isolates are beginning to shed light on fundamental ecological questions. Here we used environmental sampling and isolation to assemble a dataset of 1,962 isolates collected from throughout the contiguous United States of America (USA) and Alaska, which were then used to uncover geographic patterns, along with substrate and temperature associations among yeast taxa. We found some taxa, including the common yeasts Torulaspora delbrueckii and Saccharomyces paradoxus, to be repeatedly isolated from multiple sampled regions of the US, and we classify these as broadly distributed cosmopolitan yeasts. A number of yeast taxon - substrate associations were identified, some of which were novel and some of which support previously reported associations. Further, we found a strong effect of isolation temperature on the phyla of yeasts recovered, as well as for many species. We speculate that substrate and isolation temperature associations reflect the ecological diversity of and niche partitioning by yeast taxa. Take AwayO_LIAnalysis of environmental metadata of nearly 2,000 yeast isolates. C_LIO_LIIndividual yeast taxa associate with specific substrates and plant genera. C_LIO_LIOptimal yeast isolation temperature differs depending on taxonomic rank. C_LIO_LISubstrate type and isolation temperatures affect isolated yeast diversity. C_LI

ecology↗