Abstract Sex chromosomes often evolve through successive recombination arrests, forming evolutionary strata. Accurately describing these strata, their boundaries and history is crucial for studying sex chromosome evolution, but this can be very challenging, particularly in young sex chromosomes where X–Y or Z–W divergence is low or in highly rearranged sex chromosomes where strata are divided into pieces. Standard approaches to distinguish recently evolved strata involve combining signals from dS, Fst and gene-by-gene phylogenies, all of which can be noisy. Here, we propose a new method that uses the proportion of allele topologies observed on sex-linked genes between at least a pair of sister species, obtained from reconstructed X and Y sequences aligned to the same reference, along with an outgroup to infer ancestral alleles, with flexibility in the reconstruction pipeline. We implement a change-point analysis to objectively identify transitions in these proportions. Our method both delimitates strata and infers whether their evolutionary history is shared or convergent between species. We illustrate and test this method on Silene and Artemia species. Our new method is reliable and robust, globally confirming previous findings known for some of these species. The method is also sensitive, refining those previous findings and identifying regions that were not previously reported. We finally illustrate how this approach can inform scenarios that retrace the history of sex chromosomes in these species. Overall, this approach presents a tool that can be widely used and that complement existing methods to study sex chromosomes.
Abstract This study explores the evolutionary origins of class I and II fumarases across the tree of life, focusing on the prevalence and phylogenetic patterns of their enzymes. Using a dataset of ∼21,000 complete proteomes and MMseqs2 easy-search against known fumarase sequences, we identified representative sequences for each class and constructed phylogenetic trees. Class I fumarases are found primarily in bacteria and in several eukaryotic groups, including Protozoa, SAR, and algae, with absence in fungi and archaea and low presence in plants and animals. Their patchy distribution and absence in archaea suggest horizontal gene transfer from bacteria to eukaryotes. Class II fumarases are ubiquitously distributed across bacteria, archaea, and eukaryotes. Phylogenetic and genetic analyzes suggest a closer relationship between eukaryotic class II fumarases and bacterial homologs (particularly Alphaproteobacteria) compared to archaea. These results support the hypothesis that class II fumarase originated early on in bacteria and was then inherited by vertical gene transfer by eukaryotes. Analysis of protein sequences and structures for both classes demonstrates high evolutionary conservation, consistent with their essential catalytic function. Fumarases, TCA cycle enzymes, have been implicated in DNA damage response in numerous organisms, in all domains of life. These enzymes have also been shown to be dual targeted to mitochondria and the cytosol/nucleus in eukaryotes. We have examined how these two functions are linked to the evolution of fumarases and concluded that the extramitochondrial functions and subcellular localization of fumarases were determined much later in evolution. We conclude that metabolic signaling and its specific metabolites may provide the driving force for the fumarases' dual function, dual targeting, and interaction with different entities in the cell.
Abstract As one of the earliest domesticated and most globally ubiquitous livestock, pigs (Sus scrofa) have undergone profound environmental adaptation while following human expansion across diverse bioclimatic zones. Despite their evolutionary significance, the genomic mechanisms enabling pigs to thrive in disparate ecological settings remain poorly understood. Here, we present a comprehensive global analysis using a dataset of 1,151 pig genome sequences representing 146 distinct populations. By integrating three complementary genotype–environment association (GEA) frameworks including redundancy analysis (RDA), BayPass, and latent factor mixed models (LFMM), we identified genomic regions and candidate genes associated with environmental variation. Our analysis detected several candidate genes associated with high-altitude adaptation, particularly those involved in ultraviolet radiation response. By integrating lung single-cell RNA sequencing analysis (scRNA) from high-altitude and commercial breeds, we identified ASXL1 as a candidate gene potentially involved in high-altitude adaptation. Meanwhile, scRNA revealed candidate regulatory pathways, including the NOTCH signaling pathway, that were overlooked by traditional GEA methods, suggesting the complex regulatory landscape of physiological adaptation. Together, this study integrates large-scale population genomics and scRNA to provide insights into the genetic associations and regulatory landscapes potentially contributing to environmental adaptation in domestic pigs, advancing our understanding of livestock evolutionary responses to diverse ecological conditions.
Abstract The genus Procapra, comprising the Mongolian gazelle (MG, Procapra gutturosa), Przewalski's gazelle (PG, Procapra przewalskii), and Tibetan gazelle (TG, Procapra picticaudata), has experienced substantial range contractions and population declines due to anthropogenic disturbance and habitat degradation. Effective conservation of these species requires a clearer understanding of how distinct demographic histories have shaped their current evolutionary potential and genetic risks. Here, we assembled chromosome-level genomes for all three Procapra species and conducted population genomic analyses using whole-genome resequencing data from 93 individuals. Our findings show that MG underwent substantial historical population expansion and retained the highest genetic diversity and lowest levels of inbreeding. In contrast, TG currently has a relatively large census size, but its historically small effective population size may have contributed to elevated inbreeding and reduced genetic diversity. Despite having the smallest census size among the three species, PG retained intermediate genetic diversity, consistent with its historically larger effective population size, whereas severe contemporary habitat fragmentation is associated with elevated inbreeding and a pronounced demographic decline. Collectively, our results demonstrate that census size alone does not reliably predict genetic risk in closely related Procapra species and highlight the importance of demographic history in shaping evolutionary potential and species-specific conservation needs. Given the escalating anthropogenic fragmentation affecting PG, targeted conservation actions are urgently needed to limit further inbreeding and erosion of genetic diversity and to safeguard its long-term viability.
