Biology subjects

Nash, W. J.

Publications and source records attributed to Nash, W. J..

6 recordsLinked to original sources

bioRxiv2026

Over-representation of sperm-associated deleterious mutations across wild and ex situ cheetah (Acinonyx jubatus) populations

As purifying selection becomes less effective and inbreeding increases, small populations frequently develop an increased load of genome-wide deleterious mutations. Reflecting this pattern, deleterious mutations in genes associated with fertility and immunity have previously been identified in the cheetah (Acinonyx jubatus), which has had a low effective population size for at least the last 10,000 years. However, the distribution of deleterious mutations across cheetah populations is currently unknown. Here, we analysed novel whole genome resequencing data from 30 ex situ and 9 wild cheetahs. We investigated variation in genetic diversity, genomic measures of inbreeding, and the distribution of deleterious mutations across cheetah populations. South Sudanese and Tanzanian cheetahs showed higher inbreeding and realized load, while Namibian cheetahs had a higher proportion of population-specific deleterious mutations. Genes containing high- or moderate-impact deleterious mutations were significantly enriched for sperm-related functions, highlighting putative causative loci associated with poor sperm quality in cheetahs. Similar levels of genetic diversity and inbreeding were observed in ex situ cheetahs compared to their wild counterparts, providing empirical evidence of the efficacy of captive breeding programmes in maintaining genetic variation in ex situ populations.

genomics↗

bioRxiv2026

Sexual selection purges mutation load, but not overall genetic diversity in populations, decreasing vulnerability to extinction

Theory suggests sexual selection will enhance population viability by purging deleterious alleles. However, direct genomic evidence for this fundamental idea is scarce and contradictory. We combined long-term experimental evolution with whole-genome re-sequencing to directly test how sexual selection affects mutation load, genomic divergence and extinction risk in Tribolium castaneum. After 156 generations, populations evolving under strong sexual selection carried substantially fewer deleterious alleles than populations under weak sexual selection, based on both individual-level estimates of missense and nonsense variants and population-level Rxy analyses, indicating more efficient purging of deleterious alleles. In contrast, nucleotide diversity and runs of homozygosity were similar across treatments, indicating that purging was targeted at deleterious variation, and that reduced mutation load in populations under strong sexual selection was not explained by demographic effects. Importantly, population-level mutation load estimates provided best explained extinction risk under inbreeding, directly linking sexual selection to purging and population viability for the first time. Genome scans of high and low sexual selection populations revealed peaks of divergence, enriched for genes involved in courtship, sex discrimination, and seminal fluid proteins. Our results provide direct genomic evidence that sexual selection can reduce mutation load without eroding standing genetic diversity and thus adaptive potential, while driving adaptive divergence in reproductive traits. This beneficial purging may help explain the widespread prevalence of sexual reproduction in nature despite inherent costs and have important ramifications as to how we manage populations of conservation concern. Significance StatementA long standing and unconfirmed prediction is that sexual selection can improve population health by biasing reproduction away from individuals with high deleterious mutation load. However, direct genomic evidence is lacking, and the indirect data available are scant and contradictory. Now, using whole-genome resequencing of experimental evolved beetle populations, we show that populations evolving under stronger sexual selection carry fewer deleterious mutations and, importantly, are less vulnerable to extinction. Our results provide the first direct genomic support for this long-debated evolutionary process that may help explain the widespread prevalence of sexual reproduction in nature. Our findings also highlight the importance of allowing sexual selection to act in populations of conservation concern.

evolutionary biology↗

bioRxiv2025

Divergent selection on dispersal targets chemosensory and neuronal genes in Tribolium castaneum

Dispersal is key to the life history, ecology and evolution of many organisms, and important in pest invasiveness. However, the genetic architecture underlying variation in dispersal behaviour remains poorly understood outside of a few model species. We investigated the genomic basis of dispersal using artificial selection on replicated lines of Tribolium castaneum, a flour beetle, an emergent model system, and an economically important agricultural pest. Combining whole-genome resequencing with population-level genotype-phenotype association analysis, we identify genomic regions associated with selection on dispersal. Identified candidate genes were significantly enriched for functions related to neuronal structure and function, as well as chemosensory behaviour and mating, suggesting that variation in dispersal is mediated by neural and chemosensory pathways. Our results demonstrate that dispersal propensity has a polygenic basis and support an interaction between dispersal and mating ecology in this system. These findings contribute to a deeper understanding of the genetic mechanisms driving dispersal evolution of dispersal and its role in shaping eco-evolutionary dynamics.

evolutionary biology↗

bioRxiv2025

Effects of a temperate heatwave on diel rhythms of insect activity: a comparison across habitats

O_LIThe increasing frequency and intensity of heatwave events in temperate climates threatens to alter behavioural rhythms of ectothermic animals, such as insects. However, it is poorly understood how heatwaves affect daily activity patterns of insects, and whether shaded microclimates can moderate these responses. C_LIO_LIWe investigated impacts of a heatwave on the diel profile of insect activity, comparing effects across open, tree-covered and hedged habitats. Using yellow pan traps, insect activity was monitored from 07:00 to 19:00 on ten non-consecutive days, including two during a heatwave. C_LIO_LIInsect counts exhibited a unimodal relationship with temperature. C_LIO_LIDuring heatwave days, open habitat exhibited a significant ([~]81.9%) reduction in counts compared to two non-heatwave field-days, one before and one after the heatwave. Smaller, non-significant reductions were observed in the tree-covered (38.3%) and hedged (17.8%) habitats. C_LIO_LIThe diel activity profile on non-heatwave days approximated to a unimodal relationship, with GLMM-estimated counts peaking around 15:00; by contrast, heatwave days exhibited a bimodal profile, with predicted counts highest in the morning and evening. C_LIO_LISuch heatwave-induced deformations of activity patterns, modelled as interactions between heatwave and time-of-day, were significant across all three habitat types. C_LIO_LIThe findings suggest that temperate heatwaves can markedly decrease insect activity levels, and that whilst shade-providing vegetational features may reduce this effect, diel patterns of activity are affected landscape-wide. As heatwaves become more frequent, preservation of trees and hedges in temperate landscapes is likely crucial to support resilience of insect activity and wider ecosystem functioning. C_LI

ecology↗

bioRxiv2024

Gene pseudogenization in fertility-associated genes in cheetah (Acinonyx jubatus), a species with long-term low effective population size

The ongoing global biodiversity crisis is placing an increasing number of mammalian populations at risk of decline. Species that have survived severe historic bottlenecks, such as the cheetah (Acinonyx jubatus) exhibit symptoms of inbreeding depression including reproductive and developmental defects. Although it has long been suggested that such defects stem from an accumulation of weakly deleterious mutations, the implications of such mutations leading to pseudogenization has not been assessed. Here, we use comparative analysis of eight felid genomes to better understand the impacts of deleterious mutations in the cheetah. We find novel pseudogenization events specific to the cheetah. Through careful curation, we identify 89 genes with previously unreported premature termination codons that likely affect gene function, 65 of which are caused by point mutations. With the addition of population data, we find 22 PTCs fixed in wild populations, four of which (DEFB116, ARL13A, CFAP119 and NC5TD4) are also found in a more recent reference genome. Mutations within three of these genes are linked with sterility, including azoospermia, which is common in cheetahs. Our results highlight the power of comparative genomic approaches for the discovery of novel causative variants in declining species.

genomics↗

bioRxiv2018

Mate choice and gene expression signatures associated with nutritional adaptation in the medfly (Ceratitis capitata)

Evolutionary responses to nutrition are key to understanding host shifts and the potential for reproductive isolation. Previously, experimental evolution was used to describe responses of the medfly (Ceratitis capitata) to divergent larval diets. Within 30 generations there was divergence in larval development time, egg to adult survival and adaptation in adult body size. In this study, the gene expression signatures associated with these changes were examined, using mRNA-seq on males following 60 generations of nutritional selection. Variation in gene expression was also validated using qRT-PCR. The results showed observed an over-representation of differential expression in metabolism, oxidative phosphorylation and proteolysis genes. In addition, at generations 60 and 90, we tested whether these evolved patterns (differences in gene expression) were associated with mate choice. We found evidence for assortative mating by diet at generation 60, but not in mating tests within and between replicate lines at generation 90. Hence, there was no consistent evidence for assortative mating by diet, which emphasises the importance of replicate tests of evolutionary responses over time. Overall, the study provides the first genome-wide survey of the putative mechanisms underpinning evolved responses to nutritional adaptation.

evolutionary biology↗