Biology subjects

Vicoso, B.

Publications and source records attributed to Vicoso, B..

12 recordsLinked to original sources

bioRxiv2026

Single-nucleus transcriptomics and phosphoproteomics identify misregulated sperm components in mice carrying a selfish supergene

The t-haplotype is a selfish variant of the mouse chromosome 17. It reaches 90-100% transmission rates in heterozygous (+/t) males through a poison-antidote system that disables sperm carrying the homologous (+) haplotype. While several poisons and one antidote have been identified, how these mediate drive, and what additional molecular players are involved, is not fully understood. Here, we characterized patterns of gene expression throughout spermatogenesis in +/t versus +/+ males using single nucleus RNA sequencing. Genes differentially expressed in early spermatogenesis, when poisons are likely to be expressed, were enriched for key regulators of sperm motility. These included dyneins, which provide the motor function of sperm flagella, and protein phosphatase 1 (PP1) complex genes, which regulate protein activity through dephosphorylation. Phosphoproteomics of +/t versus +/+ testes revealed changes in phosphorylation levels of several spermatogenesis proteins, supporting a contribution of dysregulated phosphorylation to the biology of the t-haplotype. In particular, the PP1 component PPP1CC2 itself showed significantly decreased phosphorylation in +/t testes. Further, we found that dyneins located on both the t-haplotype and the corresponding standard version of chromosome 17 have undergone large increases in spermatocyte expression in the house mouse lineage. We argue that this may result from an ongoing arms race between the homologs for transmission rates. Together, these results extend our understanding of the molecular changes associated with the t-haplotype, and highlight the value of integrating various OMICS approaches to investigate the mechanisms and evolutionary consequences of transmission distortion.

evolutionary biology↗

bioRxiv2026

A single locus carrying modified oogenesis genes underlies the switch to asexuality in Artemia brine shrimp

Transitions from sexual to asexual reproduction are well-documented across different taxa. However, despite extensive efforts, the regulatory changes underlying the emergence of asexuality remain largely undiscovered in the majority of species studied. Artemia brine shrimp have multiple closely related sexual and obligate parthenogenetic lineages, making them a promising model for addressing this question. While earlier work suggested that asexuals use a modified meiosis, and inferred a likely role for the Z-chromosome in its transmission, no master regulator or genetic changes have been put forward as the root causes for the shift. Here, we generate single-nucleus RNAseq data of the female reproductive system of individuals from the Aibi lake population of Artemia parthenogenetica and its closely related obligate sexual species Artemia sp. Kazakhstan. We identify the germline cell clusters in the female reproductive system and perform differential expression analysis to infer substantial transcriptional differences at genes putatively involved in cell cycle and oocyte development between the meiotic cells of the two species. Additionally, we use whole-genome sequencing of 32 individuals from two backcrossing experiments to narrow down the genomic regions associated with the transmission of asexuality to an 8 megabase region of the Z chromosome. Within the identified regions, two adjacent genes with known functions in oogenesis, ITPR and USP8, show differential expression and genetic differentiation between sexuals and asexuals, making them promising candidate drivers of asexuality in this species. Significance statementWhile most animals reproduce sexually, many do not, and why and how these shifts occur remains an open question. This paper presents a systematic investigation of the molecular changes that underlie the transition from sexual to asexual reproduction in brine shrimp. We combine multiple computational and experimental approaches to look for differences between close sexual and asexual lineages. We find that a subset of meiotic germ cells is regulated differently in the two, and that two important oogenesis genes are the likely drivers of asexuality. This work is unique in providing an in-depth characterization of the combined genetic and regulatory changes underlying this key transition in reproductive modes.

evolutionary biology↗

bioRxiv2026

Is faster-X adaptation due to large-effect mutations? An empirical test of a new theory

A widespread observation in molecular evolution is that X-linked genes evolve faster--and often adapt faster--than autosomal genes. Three main ideas have been put forward to explain "faster-X" adaptation. The first is that new beneficial mutations are typically partially recessive with respect to fitness, leading to more efficient selection in hemizygous males. The second is that sex differences in recombination, or sex differences in variance in reproductive success, enhance the effective population size on the X chromosome relative to autosomes. Both ideas have limitations: the first conflicts with theories of dominance, in which beneficial mutations are proposed to be partially dominant, while the second only applies to some taxa. Here we tested a third, newly-proposed theory, in which mutations with large "scaled phenotypic effects" (i.e., large effects relative to the distance to a phenotypic optimum) experience more positive selection on the X. Specifically, we used three proxies for scaled phenotypic effects--amino-acid dissimilarity, sequence conservation, and gene age--and estimated X and autosomal rates of adaptation of nonsynonymous mutations across effect-size classes. We did this in three lineages with a well-documented faster-X: Drosophila melanogaster, Mus musculus, and Homo sapiens. As expected, we found that large-effect mutations were more likely to be under purifying selection and less likely to be under positive selection than small-effect mutations. However, contrary to the new theory, faster-X adaptation was not enriched among large-effect mutations. Overall, our results highlight an unresolved gap between patterns of sex chromosome evolution and theories of dominance, and the need for more direct empirical data on the dominance of new beneficial mutations. Significance statementIn many species, genes on the X chromosome undergo more adaptation than autosomal genes, but it is not clear why this pattern of "faster-X" occurs. One possibility is that recessive beneficial mutations drive the effect, but theories of dominance propose instead that beneficial mutations should be dominant. Meanwhile, alternative explanations (e.g., sex differences in recombination or sex differences in variance in reproductive success) can only apply to some taxa. Here we tested a new idea, which proposes that the effect is driven by mutations with large effects. However, data from fruit flies, humans and mice did not provide support for the new theory. Our work highlights an unresolved gap between patterns of sex chromosome evolution and theories of dominance.

evolutionary biology↗

bioRxiv2026

Out with the Old: Contrasting Histone Marks are Associated with Dosage Compensation on the Ancient and New Z of a Moth with Complex Sex Chromosomes

Sex chromosome differentiation is often accompanied by the evolution of dosage compensation (DC) mechanisms that balance gene expression between autosomes and sex chromosomes, and consequently between the sexes. ZW systems were traditionally thought to exhibit only partial DC, but recent studies in Lepidoptera, Artemia franciscana, and Apalone spinifera suggest a diverse range of compensation strategies, challenging traditional assumptions. While DC often involves chromatin-level regulation, the specific mechanisms in most ZW systems are still poorly understood. To explore these gaps, we generated a genome assembly of Cameraria ohridella (horse-chestnut leaf miner moth, Gracillidae), and combined transcriptomic data from two tissues with CUT&Tag epigenomic profiling targeting both active (H4K16ac, H3K4me3) and repressive (H3K27me3) chromatin marks. Our findings reveal a highly dynamic landscape of sex chromosome evolution in C. ohridella, including the ancestral Z (AncZ), a NeoZ1 formed by fusion of AncZ with an autosome, and a NeoZ2 that likely arose via the fusion of another autosome to the W chromosome. We uncover distinct dosage compensation (DC) patterns across ancestral and neo-sex chromosome regions. On the Ancestral Z, DC involves repression of gene expression in males (ZZ), with a depletion of the active histone mark H4K16ac being observed in this region. In contrast, NeoZ1 regions show upregulation of gene expression in the heterogametic sex (ZW), accompanied by enrichment of H4K16ac. Together, our findings underscore the dynamic nature of sex chromosome evolution and reveal variation in dosage compensation strategies across the Z chromosome, where the NeoZ1 appears to evolve entirely new, Drosophila-like mechanisms rather than co-opting the existing Nematode-like mechanisms of AncZ. We performed simulations that suggest that cooption of ancient DC mechanisms on a neo-sex chromosome is expected when it acts through up-regulation in the heterogametic sex but not when it involves downregulation in the homogametic sex, providing a framework for understanding the different patterns observed between Drosophila and Lepidoptera neo sex chromosomes.

evolutionary biology↗

bioRxiv2025

Causes and consequences of sex-chromosome turnovers in Diptera

Sex-chromosome systems are highly variable across animals, but how they transition from one to another is not well understood. Diptera have undergone multiple sex-chromosome turnovers and expansions while maintaining their general chromosomal content, which makes them an ideal clade to study such transitions. We analysed more than 100 dipteran whole-genome assemblies and identified 4 new lineages that underwent sex-chromosome turnover (in addition to the 5 previously reported). We find the majority of turnovers happened in the group Schizophora, which tend to have fewer genes on the F element (the chromosome homologous to the ancestral insect X chromosome) than lower dipterans, a factor previously hypothesized to facilitate turnover. Most derived X chromosomes have higher GC content than autosomes, consistent with a high prevalence of male-achiasmy in Diptera. In addition, an excess of gene movement out of the X is detected for most of these new X chromosomes, and many of these moved genes have high testis expression in Drosophila, suggesting that out-of-X gene movement contributes to the long-term demasculinization of X chromosomes.

evolutionary biology↗

bioRxiv2025

A re-evaluation of Muller's sheltering hypothesis for the evolution of sex chromosome gene content

The first influential hypothesis for sex chromosome evolution was proposed in 1914 by H. J. Muller, who argued that once recombination was suppressed between the X and Y chromosomes, Y-linked genes become "sheltered" from selection, leading to accumulation of recessive loss-of-function (LOF) mutations and decay of Y-linked genes. The hypothesis fell out of favour in the 1970s because early mathematical models failed to support it and data on the dominance of lethal mutations were viewed as incompatible with the hypothesis. We reevaluate the main arguments against Mullers hypothesis and find that they do not conclusively exclude a role for sheltering in sex chromosome evolution. By relaxing restrictive assumptions of earlier models, we show that sheltering promotes fixation of LOF mutations with sexually dimorphic fitness effects, resulting in decay of X-linked genes that are exclusively expressed by males and Y-linked genes that are primarily, though not necessarily exclusively, expressed by females. We further show that drift and other processes contributing to Y degeneration (i.e., selective interference and regulatory evolution) expand conditions of Y-linked gene loss by sheltering. The actual contribution of sheltering to sex chromosome evolution hinges upon the distribution of dominance and sex-specific fitness effects of LOF mutations, which we discuss.

evolutionary biology↗

bioRxiv2024

The Draparnaldia genome: alternative mechanisms for multicellularity and terrestrialization in green plants

Green plants contain two algal lineages: Streptophyte algae that diverged into land plants and Chlorophyte algae that are mostly aquatic. Draparnaldia is a Chlorophyte alga morphologically resembling mosses and living in both, the aquatic and terrestrial habitats. Because of its complex morphology and terrestrial adaptations, Draparnaldia can provide new insights into the evolution of multicellularity and terrestrialization in green plants. To develop Draparnaldia into a model, we de novo sequenced its genome and transcriptomes, and profiled its phytohormone repertoire. We found that 1) Expanded gene families in Draparnaldia with respect to unicellular Chlamydomonas are linked to multicellularity and abiotic stresses. 2) Draparnaldias terrestrial adaptations are reflected at both the morphological and molecular levels. 3) Draparnaldia synthesizes most of the phytohormones used by land plants to thrive in terrestrial habitats. All of this makes Draparnaldia a powerful model to uncover and study alternative evolutionary trajectories towards multicellularity and terrestrialization in plants.

evolutionary biology↗

bioRxiv2024

Recurrent sex chromosome turn-over in termites

Termites, together with cockroaches, belong to the Blattodea. They possess an XX/XY sex determination system which has evolved from an XX/X0 system present in other Blattodean species such as cockroaches and wood roaches. Little is currently known about the sex chromosomes of termites, their gene content, or their evolution. We here investigate the X chromosome of multiple termite species and compare them to the X chromosome of cockroaches using genomic and transcriptomic data. We find that the X chromosome of the termite Macrotermes natalensis is large and differentiated showing hall marks of sex chromosome evolution such as dosage compensation, while this does not seem to be the case in the other two termite species investigated here where sex chromosomes are probably evolutionary young. Furthermore, that X chromosome in M. natalensis is different from the X chromosome found in the cockroach Blattella germanica indicating at least one, potentially multiple, sex chromosome turn-over events during termite evolution.

evolutionary biology↗

bioRxiv2024

Evidence of a Slower-Z effect in Schistosoma japonicum

Sex-linked and autosomal loci experience different selective pressures and evolutionary dynamics. X (or Z) chromosomes are often hemizygous, as Y (or W) chromosomes often degenerate. Such hemizygous regions can be under greater efficacy of selection, as recessive mutations are immediately exposed to selection in the heterogametic sex (the so-called Faster-X or Faster-Z effect). However, in young non-recombining regions, Y/W chromosomes often have many functional genes, and many X/Z-linked loci are therefore diploid. The sheltering of recessive mutations on the X/Z by the Y/W homolog is expected to drive a Slower-X (Slower-Z) effect for diploid X/Z loci, i.e. a reduction in the efficacy of selection. While the Faster-X effect has been studied extensively, much less is known empirically about the evolutionary dynamics of diploid X or Z chromosomes. Here, we took advantage of published population genomic data in the female-heterogametic human parasite Schistosoma japonicum to characterize the gene content and diversity levels of the diploid and hemizygous regions of the Z chromosome. We used different metrics of selective pressures acting on genes to test for differences in the efficacy of selection in hemizygous and diploid Z regions, relative to autosomes. We found consistent patterns suggesting reduced Ne, and reduced efficacy of purifying selection, on both hemizygous and diploid Z regions. Moreover, relaxed selection was particularly pronounced for female-biased genes on the diploid Z, as predicted by Slower-Z theory.

evolutionary biology↗

bioRxiv2023

The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome.

Many insects carry an ancient X chromosome - the Drosophila Muller element F - that likely predates their origin. Interestingly, the X has undergone turnover in multiple fly species (Diptera) after being conserved for more than 450 MY. The long evolutionary distance between Diptera and other sequenced insect clades makes it difficult to infer what could have contributed to this sudden increase in rate of turnover. Here, we produce the first genome and transcriptome of a long overlooked sister-order to Diptera: Mecoptera. We compare the scorpionfly Panorpa cognata X-chromosome gene content, expression, and structure, to that of several dipteran species as well as more distantly-related insect orders (Orthoptera and Blattodea). We find high conservation of gene content between the mecopteran X and the dipteran Muller F element, as well as several shared biological features, such as the presence of dosage compensation and a low amount of genetic diversity, consistent with a low recombination rate. However, the two homologous X chromosomes differ strikingly in their size and number of genes they carry. Our results therefore support a common ancestry of the mecopteran and ancestral dipteran X chromosomes, and suggest that Muller element F shrank in size and gene content after the split of Diptera and Mecoptera, which may have contributed to its turnover in dipteran insects.

evolutionary biology↗

bioRxiv2023

The X chromosome of insects predates the origin of Class Insecta

Sex chromosomes have evolved independently multiple times, but why some are conserved for more than 100 million years whereas others turnover rapidly remains an open question. Here, we examine the homology of sex chromosomes across nine orders of insects, plus the outgroup springtails. We find that the X chromosome is shared among all insect orders and springtails; the only exception is in the Lepidoptera, which has lost the X and now has a ZZ/ZW sex chromosome system. Therefore, the ancestral insect X chromosome has persisted for more than 450 million years - the oldest known sex chromosome to date. Further, we suggest that the shrinking of gene content the Dipteran X chromosome has allowed for a burst of sex-chromosome turnover that is absent from other speciose insect orders.

evolutionary biology↗

bioRxiv2022

ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp

Eurasian brine shrimp (genus Artemia) have closely related sexual and asexual lineages of parthenogenetic females, which produce rare males at low frequencies. Although they are known to have ZW chromosomes, these are not well characterized, and it is unclear whether they are shared across the clade. Furthermore, the underlying genetic architecture of the transmission of asexuality, which can occur when rare males mate with closely related sexual females, is not well understood. We produced a chromosome-level assembly for the Eurasian species A. sinica and characterized in detail the pair of sex chromosomes of this species. We combined this with short-read genomic data for the sexual species A. sp. Kazakhstan and several lineages of A. parthenogenetica, allowing us to perform a first in-depth characterization of sex-chromosome evolution across the genus. We identified a small differentiated region of the ZW pair that is shared by all sexual and asexual lineages, supporting the shared ancestry of the sex chromosomes. We also inferred that recombination suppression has spread to larger sections of the chromosome independently in the American and Eurasian lineages. Finally, we took advantage of a rare male, which we backcrossed to sexual females, to explore the genetic basis of asexuality. Our results suggest that parthenogenesis may be partly controlled by a locus on the Z chromosome, highlighting the interplay between sex determination and asexuality.

evolutionary biology↗