Biology subjects

Jeffries, D. L.

Publications and source records attributed to Jeffries, D. L..

6 recordsLinked to original sources

bioRxiv2026

Recombination on 'non-recombining' sex chromosomes: empirical insights from the blackspotted stickleback

One hallmark of sex chromosome evolution is recombination suppression driven by inversions. The resulting non-recombining sex-linked regions accumulate deleterious mutations and functionally degenerate. The question therefore arises: why does selection not favor the reestablishment of recombination? Two (non-exclusive) explanations for this have been proposed: 1) selection to maintain linkage between the Primary Sex Determination Locus (PSDL) and sexually antagonistic loci - loci with alleles that are beneficial to one sex but detrimental to the other; and 2) the rarity of reversions - structural mutations that reverse the inversion that initially suppressed recombination. Empirical perspectives are sorely needed to evaluate the relevance of these models. Here, we characterised the intermediate stages of sex chromosome evolution in the blackspotted stickleback (Gasterosteus wheatlandi). We generated high-quality, phased assemblies and annotations for the X and Y chromosomes, as well as population-level sequencing. Using these data, we inferred distinct recombination loss events and their associated inversions. Most significantly, we find support from multiple lines of evidence for a [~]2 Mb recombination event that likely occurred via double crossover within an existing non-recombining inversion. This result highlights that rare recombination can occur within sex-linked inversions. Simulations suggest that such histories of gene flux may allow for a novel empirical framework, adapted from work on autosomal inversions, to infer evolutionary processes at work within sex-linked non-recombining regions and distinguish between models to explain the maintenance of recombination suppression on sex chromosomes. Significance StatementSex chromosomes have evolved countless times across eukaryotes and often lose the ability to recombine, causing them to degenerate over time. Why then, does recombination not restart to purge harmful mutations? By generating a high-quality genome assembly of the blackspotted stickleback, we discovered the strong empirical evidence of a sex chromosome undergoing a double-crossover event within a "non-recombining" region, which reset the degenerative process. This finding challenges the view that sex chromosome decay is a one-way street. Furthermore, using forward evolutionary simulations, we demonstrate that the genetic signatures left by such events could help identify the selective forces acting within non-recombining sex chromosomes, thereby explaining the maintenance of recombination suppression.

evolutionary biology↗

bioRxiv2026

Evolution of recombination suppression and sex determination on Y chromosomes of the plant genus Mercurialis

Understanding why sex chromosomes repeatedly evolve recombination suppression, gene loss, and repeat accumulation remains a central challenge in evolutionary genomics. Plant sex chromosomes may be particularly informative, because they have often evolved recently from hermaphroditic ancestors. We studied the sex-linked region of the dioecious annual Mercurialis annua using new long-read genome assemblies of an XX female and a YY male, a published female assembly, linkage maps, and population-genomic data from several Mercurialis species. We identify two discrete nested evolutionary strata on the Y chromosome of diploid M. annua. A young stratum was generated by a large inversion and shows little degeneration, whereas an older stratum nested within it exhibits substantial gene loss, transposable-element accumulation, insertion of paralogous gene copies, and elevated X-Y sequence divergence. These findings indicate that recombination suppression evolved in at least two stages, with a recent inversion expanding an older non-recombining region. Comparative analyses among several Mercurialis species further show that the extent of sex-linked differentiation varies markedly among them. We also identify APRR7 as the only gene showing consistent male-specific inheritance across the genus; this gene is a strong candidate master sex-determination gene. Together, our results refine the structure and gene content of the sex-linked region in M. annua and contribute to our understanding of the diversity of sex chromosomes in plants.

evolutionary biology↗

bioRxiv2023

A female heterogametic ZW sex-determination system in Acariformes

Sexual reproduction, while often associated with separate sexes, is an ancient and widespread feature of multicellular eukaryotes. While a diversity of sex-determination mechanisms exist, for many organisms, which of these mechanisms is used remains unknown. Exploring sex-determination mechanisms in Acariformes, among the oldest chelicerate clades, is intriguing due to its potential to unveil conserved sex-determination systems. This insight can have implications for understanding sex chromosome evolution and its broader impact on higher taxa.To identify the mechanism of sex determination in Acari, i.e., oribatid mites, we generated a high-quality chromosome-level genome assembly of Hermannia gibba (Koch, 1839) by combining PacBio HiFi and Hi-C sequencing. Coverage and allele-frequency analyses on pools of male and female individuals suggest a female-heterogametic ZW sex-determination system with little degeneration of the W chromosome. To date, this represents the only documented case of a ZW system in Acariformes. Further comparative studies in H. gibba will reveal how old the ZW system is and whether it exhibits conservation or polymorphism.

genomics↗

bioRxiv2022

Convergent recruitment of Amh as the sex determination gene in two lineages of stickleback fish

Sex chromosomes vary greatly in their age and levels of differentiation across the tree of life. This variation is largely due to the rates of sex chromosome turnover in different lineages; however, we still lack an explanation for why sex chromosomes are so conserved in some lineages (e.g. Mammals, Birds) but so labile in others (e.g. Fish, Amphibians). Here we add to the information on sex chromosomes in stickleback, a valuable model lineage for the study of sex chromosome evolution, by identifying the sex chromosome and a strong candidate for the master sex determination gene in the brook stickleback, Culaea inconstans. Using whole genome sequencing of wild-caught samples and a lab cross, we identify AmhY, a male specific duplication of the gene Amh, as the candidate master sex determination gene. AmhY resides on Chromosome 20 in C. inconstans and is likely a recent duplication, as both AmhY and the sex linked region of Chromosome 20 show little sequence divergence. Importantly, this duplicate AmhY represents the second independent duplication and recruitment of Amh as the sex determination gene in stickleback and the eighth example now known across teleosts. We discuss this convergence in the context of sex chromosome turnovers and the role that the Amh/AmhrII pathway, which is crucial for sex determination, may play in the evolution of sex chromosomes in teleosts.

evolutionary biology↗

bioRxiv2020

Meiosis reveals the early steps in the evolution of a neo-XY sex chromosome pair in the African pygmy mouse Mus minutoides

Sex chromosomes of eutherian mammals are highly different in size and gene content, and share only a small region of homology (pseudoautosomal region, PAR). They are thought to have evolved through an addition-attrition cycle involving the addition of autosomal segments to sex chromosomes and their subsequent differentiation. The events that drive this process are difficult to investigate because sex chromosomes in most mammals are at a very advanced stage of differentiation. Here, we have taken advantage of a recent translocation of an autosome to both sex chromosomes in the African pygmy mouse Mus minutoides, which has restored a large segment of homology (neo-PAR). By studying meiotic sex chromosome behavior and identifying fully sex-linked genetic markers in the neo-PAR, we demonstrate that this region shows unequivocal signs of early sex-differentiation. First, synapsis and resolution of DNA damage intermediates are delayed in the neo-PAR during meiosis. Second, recombination is suppressed in a large portion of the neo-PAR. However, the inactivation process that characterizes sex chromosomes during meiosis does not extend to this region. Finally, the sex chromosomes show a dual mechanism of association at metaphase-I that involves the formation of a chiasma in the neo-PAR and the preservation of an ancestral achiasmate mode of association in the non-homologous segments. We show that the study of meiosis is crucial to apprehend the onset of sex chromosome differentiation, as it introduces structural and functional constrains to sex chromosome evolution. Synapsis and DNA repair dynamics are the first processes affected in the incipient differentiation of X and Y chromosomes, and they may be involved in accelerating their evolution. This provides one of the very first reports of early steps in neo-sex chromosome differentiation in mammals, and for the first time a cellular framework for the addition-attrition model of sex chromosome evolution. AUTHOR SUMMARYThe early steps in the evolution of sex chromosomes are particularly difficult to study. Cessation of recombination around the sex-determining locus is thought to initiate the differentiation of sex chromosomes. Several studies have investigated this process from a genetic point of view. However, the cellular context in which recombination arrest occurs has not been considered as an important factor. In this report, we show that meiosis, the cellular division in which pairing and recombination between chromosomes takes place, can affect the incipient differentiation of X and Y chromosomes. Combining cytogenetic and genomic approaches, we found that in the African pygmy mouse Mus minutoides, which has recently undergone a sex chromosome-autosome fusion, synapsis and DNA repair dynamics are altered along the newly added region of the sex chromosomes, likely interfering with recombination and thus contributing to the genetic isolation of a large segment of the Y chromosome. Therefore, the cellular events that occur during meiosis are crucial to understand the very early stages of sex chromosome differentiation. This can help to explain why sex chromosomes evolve very fast in some organisms while in others they have barely changed for million years.

genetics↗

bioRxiv2019

Mapping of multiple complementary sex determination loci in a parasitoid wasp

Sex determination has evolved in a variety of ways and can depend on environmental and genetic signals. A widespread form of genetic sex determination is haplodiploidy, where unfertilized, haploid eggs develop into males and fertilized diploid eggs into females. One of the molecular mechanisms underlying haplodiploidy in Hymenoptera, a large insect order comprising ants, bees and wasps, is known as complementary sex determination (CSD). In species with CSD, heterozygosity at one or several loci induces female development. Here, we identify the genomic regions putatively underlying multi-locus CSD in the parasitoid wasp Lysiphlebus fabarum using restriction-site associated DNA sequencing. By analysing segregation patterns at polymorphic sites among 331 diploid males and females, we identify four CSD candidate regions, all on different chromosomes. None of the candidate regions feature evidence for homology with the csd gene from the honeybee, the only species in which CSD has been characterized, suggesting that CSD in L. fabarum is regulated via a novel molecular mechanism. Moreover, no homology is shared between the candidate loci, in contrast to the idea that multi-locus CSD should emerge from duplications of an ancestral single-locus system. Taken together, our results suggest that the molecular mechanisms underlying CSD in Hymenoptera are not conserved between species, raising the question as to whether CSD may have evolved multiple times independently in the group.\n\nAuthor summaryThe genetic or environmental signals that govern whether an organism develops into a male or female differ across species, and understanding their evolution is a key aspect of biology. In this paper, we focus on complementary sex determination (CSD), a genetic sex determination system found in many species of bees, ants and wasps where heterozygosity at one or multiple genetic regions determines the sex of the individual. We identify multiple genetic regions in the parasitoid wasp species Lysiphlebus fabarum that are likely underlying CSD. We show that these candidate CSD regions share no similarity with each other and that they differ from the CSD region known in the honey bee, the only species with a well-characterized CSD system. Our results suggest a different molecular mechanism underlying CSD in the wasp and that multiple CSD regions do not necessarily arise from duplications as generally thought.

genomics↗