@article{10167, abstract = {Schistosomes, the human parasites responsible for snail fever, are female-heterogametic. Different parts of their ZW sex chromosomes have stopped recombining in distinct lineages, creating “evolutionary strata” of various ages. Although the Z-chromosome is well characterized at the genomic and molecular level, the W-chromosome has remained largely unstudied from an evolutionary perspective, as only a few W-linked genes have been detected outside of the model species Schistosoma mansoni. Here, we characterize the gene content and evolution of the W-chromosomes of S. mansoni and of the divergent species S. japonicum. We use a combined RNA/DNA k-mer based pipeline to assemble around 100 candidate W-specific transcripts in each of the species. About half of them map to known protein coding genes, the majority homologous to S. mansoni Z-linked genes. We perform an extended analysis of the evolutionary strata present in the two species (including characterizing a previously undetected young stratum in S. japonicum) to infer patterns of sequence and expression evolution of W-linked genes at different time points after recombination was lost. W-linked genes show evidence of degeneration, including high rates of protein evolution and reduced expression. Most are found in young lineage-specific strata, with only a few high expression ancestral W-genes remaining, consistent with the progressive erosion of nonrecombining regions. Among these, the splicing factor u2af2 stands out as a promising candidate for primary sex determination, opening new avenues for understanding the molecular basis of the reproductive biology of this group.}, author = {Elkrewi, Marwan N and Moldovan, Mikhail A. and Picard, Marion A L and Vicoso, Beatriz}, issn = {1537-1719}, journal = {Molecular Biology and Evolution}, keywords = {sex chromosomes, evolutionary strata, W-linked gene, sex determining gene, schistosome parasites}, publisher = {Oxford University Press }, title = {{Schistosome W-Linked genes inform temporal dynamics of sex chromosome evolution and suggest candidate for sex determination}}, doi = {10.1093/molbev/msab178}, year = {2021}, } @article{8099, abstract = {Sewall Wright developed FST for describing population differentiation and it has since been extended to many novel applications, including the detection of homomorphic sex chromosomes. However, there has been confusion regarding the expected estimate of FST for a fixed difference between the X‐ and Y‐chromosome when comparing males and females. Here, we attempt to resolve this confusion by contrasting two common FST estimators and explain why they yield different estimates when applied to the case of sex chromosomes. We show that this difference is true for many allele frequencies, but the situation characterized by fixed differences between the X‐ and Y‐chromosome is among the most extreme. To avoid additional confusion, we recommend that all authors using FST clearly state which estimator of FST their work uses.}, author = {Gammerdinger, William J and Toups, Melissa A and Vicoso, Beatriz}, issn = {1755-0998}, journal = {Molecular Ecology Resources}, number = {6}, pages = {1517--1525}, publisher = {Wiley}, title = {{Disagreement in FST estimators: A case study from sex chromosomes}}, doi = {10.1111/1755-0998.13210}, volume = {20}, year = {2020}, } @article{6089, abstract = {Pleiotropy is the well-established idea that a single mutation affects multiple phenotypes. If a mutation has opposite effects on fitness when expressed in different contexts, then genetic conflict arises. Pleiotropic conflict is expected to reduce the efficacy of selection by limiting the fixation of beneficial mutations through adaptation, and the removal of deleterious mutations through purifying selection. Although this has been widely discussed, in particular in the context of a putative “gender load,” it has yet to be systematically quantified. In this work, we empirically estimate to which extent different pleiotropic regimes impede the efficacy of selection in Drosophila melanogaster. We use whole-genome polymorphism data from a single African population and divergence data from D. simulans to estimate the fraction of adaptive fixations (α), the rate of adaptation (ωA), and the direction of selection (DoS). After controlling for confounding covariates, we find that the different pleiotropic regimes have a relatively small, but significant, effect on selection efficacy. Specifically, our results suggest that pleiotropic sexual antagonism may restrict the efficacy of selection, but that this conflict can be resolved by limiting the expression of genes to the sex where they are beneficial. Intermediate levels of pleiotropy across tissues and life stages can also lead to maladaptation in D. melanogaster, due to inefficient purifying selection combined with low frequency of mutations that confer a selective advantage. Thus, our study highlights the need to consider the efficacy of selection in the context of antagonistic pleiotropy, and of genetic conflict in general.}, author = {Fraisse, Christelle and Puixeu Sala, Gemma and Vicoso, Beatriz}, issn = {1537-1719}, journal = {Molecular biology and evolution}, number = {3}, pages = {500--515}, publisher = {Oxford University Press}, title = {{Pleiotropy modulates the efficacy of selection in drosophila melanogaster}}, doi = {10.1093/molbev/msy246}, volume = {36}, year = {2019}, } @misc{5586, abstract = {Input files and scripts from "Evolution of gene dosage on the Z-chromosome of schistosome parasites" by Picard M.A.L., et al (2018).}, author = {Vicoso, Beatriz}, keywords = {schistosoma, Z-chromosome, gene expression}, publisher = {Institute of Science and Technology Austria}, title = {{Input files and scripts from "Evolution of gene dosage on the Z-chromosome of schistosome parasites" by Picard M.A.L., et al (2018)}}, doi = {10.15479/AT:ISTA:109}, year = {2018}, } @article{131, abstract = {XY systems usually show chromosome-wide compensation of X-linked genes, while in many ZW systems, compensation is restricted to a minority of dosage-sensitive genes. Why such differences arose is still unclear. Here, we combine comparative genomics, transcriptomics and proteomics to obtain a complete overview of the evolution of gene dosage on the Z-chromosome of Schistosoma parasites. We compare the Z-chromosome gene content of African (Schistosoma mansoni and S. haematobium) and Asian (S. japonicum) schistosomes and describe lineage-specific evolutionary strata. We use these to assess gene expression evolution following sex-linkage. The resulting patterns suggest a reduction in expression of Z-linked genes in females, combined with upregulation of the Z in both sexes, in line with the first step of Ohno’s classic model of dosage compensation evolution. Quantitative proteomics suggest that post-transcriptional mechanisms do not play a major role in balancing the expression of Z-linked genes. }, author = {Picard, Marion A and Cosseau, Celine and Ferré, Sabrina and Quack, Thomas and Grevelding, Christoph and Couté, Yohann and Vicoso, Beatriz}, journal = {eLife}, publisher = {eLife Sciences Publications}, title = {{Evolution of gene dosage on the Z-chromosome of schistosome parasites}}, doi = {10.7554/eLife.35684}, volume = {7}, year = {2018}, } @misc{7163, abstract = {The de novo genome assemblies generated for this study, and the associated metadata.}, author = {Fraisse, Christelle}, publisher = {Institute of Science and Technology Austria}, title = {{Supplementary Files for "The deep conservation of the Lepidoptera Z chromosome suggests a non canonical origin of the W"}}, doi = {10.15479/AT:ISTA:7163}, year = {2017}, } @article{614, abstract = {Moths and butterflies (Lepidoptera) usually have a pair of differentiated WZ sex chromosomes. However, in most lineages outside of the division Ditrysia, as well as in the sister order Trichoptera, females lack a W chromosome. The W is therefore thought to have been acquired secondarily. Here we compare the genomes of three Lepidoptera species (one Dytrisia and two non-Dytrisia) to test three models accounting for the origin of the W: (1) a Z-autosome fusion; (2) a sex chromosome turnover; and (3) a non-canonical mechanism (e.g., through the recruitment of a B chromosome). We show that the gene content of the Z is highly conserved across Lepidoptera (rejecting a sex chromosome turnover) and that very few genes moved onto the Z in the common ancestor of the Ditrysia (arguing against a Z-autosome fusion). Our comparative genomics analysis therefore supports the secondary acquisition of the Lepidoptera W by a non-canonical mechanism, and it confirms the extreme stability of well-differentiated sex chromosomes.}, author = {Fraisse, Christelle and Picard, Marion A and Vicoso, Beatriz}, issn = {20411723}, journal = {Nature Communications}, number = {1}, publisher = {Nature Publishing Group}, title = {{The deep conservation of the Lepidoptera Z chromosome suggests a non canonical origin of the W}}, doi = {10.1038/s41467-017-01663-5}, volume = {8}, year = {2017}, } @article{945, abstract = {While chromosome-wide dosage compensation of the X chromosome has been found in many species, studies in ZW clades have indicated that compensation of the Z is more localized and/or incomplete. In the ZW Lepidoptera, some species show complete compensation of the Z chromosome, while others lack full equalization, but what drives these inconsistencies is unclear. Here, we compare patterns of male and female gene expression on the Z chromosome of two closely related butterfly species, Papilio xuthus and Papilio machaon, and in multiple tissues of two moths species, Plodia interpunctella and Bombyx mori, which were previously found to differ in the extent to which they equalize Z-linked gene expression between the sexes. We find that, while some species and tissues seem to have incomplete dosage compensation, this is in fact due to the accumulation of male-biased genes and the depletion of female-biased genes on the Z chromosome. Once this is accounted for, the Z chromosome is fully compensated in all four species, through the up-regulation of Z expression in females and in some cases additional down-regulation in males. We further find that both sex-biased genes and Z-linked genes have increased rates of expression divergence in this clade, and that this can lead to fast shifts in patterns of gene expression even between closely related species. Taken together, these results show that the uneven distribution of sex-biased genes on sex chromosomes can confound conclusions about dosage compensation and that Z chromosome-wide dosage compensation is not only possible but ubiquitous among Lepidoptera.}, author = {Huylmans, Ann K and Macon, Ariana and Vicoso, Beatriz}, issn = {07374038}, journal = {Molecular Biology and Evolution}, number = {10}, pages = {2637 -- 2649}, publisher = {Oxford University Press}, title = {{Global dosage compensation is ubiquitous in Lepidoptera, but counteracted by the masculinization of the Z chromosome}}, doi = {10.1093/molbev/msx190}, volume = {34}, year = {2017}, }