@article{1085,
  abstract     = {Sex chromosomes evolve once recombination is halted between a homologous pair of chromosomes. The dominant model of sex chromosome evolution posits that recombination is suppressed between emerging X and Y chromosomes in order to resolve sexual conflict. Here we test this model using whole genome and transcriptome resequencing data in the guppy, a model for sexual selection with many Y-linked colour traits. We show that although the nascent Y chromosome encompasses nearly half of the linkage group, there has been no perceptible degradation of Y chromosome gene content or activity. Using replicate wild populations with differing levels of sexually antagonistic selection for colour, we also show that sexual selection leads to greater expansion of the non-recombining region and increased Y chromosome divergence. These results provide empirical support for longstanding models of sex chromosome catalysis, and suggest an important role for sexual selection and sexual conflict in genome evolution.},
  author       = {Wright, Alison and Darolti, Iulia and Bloch, Natasha and Oostra, Vicencio and Sandkam, Benjamin and Buechel, Séverine and Kolm, Niclas and Breden, Felix and Vicoso, Beatriz and Mank, Judith},
  issn         = {20411723},
  journal      = {Nature Communications},
  publisher    = {Nature Publishing Group},
  title        = {{Convergent recombination suppression suggests role of sexual selection in guppy sex chromosome formation}},
  doi          = {10.1038/ncomms14251},
  volume       = {8},
  year         = {2017},
}

@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},
}

@misc{5571,
  abstract     = {This folder contains all the data used in each of the main figures of "The genomic characterization of the t-haplotype, a mouse meiotic driver, highlights its complex history and specialized biology" (Kelemen, R., Vicoso, B.), as well as in the supplementary figures. 
},
  author       = {Vicoso, Beatriz},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Data for "The genomic characterization of the t-haplotype, a mouse meiotic driver, highlights its complex history and specialized biology"}},
  doi          = {10.15479/AT:ISTA:78},
  year         = {2017},
}

@misc{5572,
  abstract     = {Code described in the Supplementary Methods of "The genomic characterization of the t-haplotype, a mouse meiotic driver, highlights its complex history and specialized biology" (Kelemen, R., Vicoso, B.)},
  author       = {Vicoso, Beatriz},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Code for "The genomic characterization of the t-haplotype, a mouse meiotic driver, highlights its complex history and specialized biology"}},
  doi          = {10.15479/AT:ISTA:79 },
  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},
}

@article{1019,
  abstract     = {As a consequence of its difference in copy number between males and females, the X chromosome is subject to unique evolutionary forces and gene regulatory mechanisms. Previous studies of Drosophila melanogaster have shown that the expression of X-linked, testis-specific reporter genes is suppressed in the male germline. However, it is not known whether this phenomenon is restricted to testis-expressed genes or if it is a more general property of genes with tissue-specific expression, which are also underrepresented on the X chromosome. To test this, we compared the expression of three tissue-specific reporter genes (ovary, accessory gland and Malpighian tubule) inserted at various autosomal and X-chromosomal locations. In contrast to testis-specific reporter genes, we found no reduction of X-linked expression in any of the other tissues. In accessory gland and Malpighian tubule, we detected higher expression of the X-linked reporter genes, which suggests that they are at least partially dosage compensated. We found no difference in the tissue-specificity of X-linked and autosomal reporter genes. These findings indicate that, in general, the X chromosome is not a detrimental environment for tissue-specific gene expression and that the suppression of X-linked expression is limited to the male germline.},
  author       = {Argyridou, Eliza and Huylmans, Ann K and Königer, Annabella and Parsch, John},
  issn         = {0018067X},
  journal      = {Heredity},
  number       = {1},
  pages        = {27 -- 34},
  publisher    = {Nature Publishing Group},
  title        = {{X-linkage is not a general inhibitor of tissue-specific gene expression in Drosophila melanogaster}},
  doi          = {10.1038/hdy.2017.12},
  volume       = {119},
  year         = {2017},
}

@misc{9861,
  abstract     = {As a consequence of its difference in copy number between males and females, the X chromosome is subject to unique evolutionary forces and gene regulatory mechanisms. Previous studies of Drosophila melanogaster have shown that the expression of X-linked, testis-specific reporter genes is suppressed in the male germline. However, it is not known whether this phenomenon is restricted to testis-expressed genes or if it is a more general property of genes with tissue-specific expression, which are also underrepresented on the X chromosome. To test this, we compared the expression of three tissue-specific reporter genes (ovary, accessory gland and Malpighian tubule) inserted at various autosomal and X-chromosomal locations. In contrast to testis-specific reporter genes, we found no reduction of X-linked expression in any of the other tissues. In accessory gland and Malpighian tubule, we detected higher expression of the X-linked reporter genes, which suggests that they are at least partially dosage compensated. We found no difference in the tissue-specificity of X-linked and autosomal reporter genes. These findings indicate that, in general, the X chromosome is not a detrimental environment for tissue-specific gene expression and that the suppression of X-linked expression is limited to the male germline.},
  author       = {Argyridou, Eliza and Huylmans, Ann K and Königer, Annabella and Parsch, John},
  publisher    = {Dryad},
  title        = {{Data from: X-linkage is not a general inhibitor of tissue-specific gene expression in Drosophila melanogaster}},
  doi          = {10.5061/dryad.02f6r},
  year         = {2017},
}

@article{1158,
  abstract     = {Speciation results from the progressive accumulation of mutations that decrease the probability of mating between parental populations or reduce the fitness of hybrids—the so-called species barriers. The speciation genomic literature, however, is mainly a collection of case studies, each with its own approach and specificities, such that a global view of the gradual process of evolution from one to two species is currently lacking. Of primary importance is the prevalence of gene flow between diverging entities, which is central in most species concepts and has been widely discussed in recent years. Here, we explore the continuum of speciation thanks to a comparative analysis of genomic data from 61 pairs of populations/species of animals with variable levels of divergence. Gene flow between diverging gene pools is assessed under an approximate Bayesian computation (ABC) framework. We show that the intermediate "grey zone" of speciation, in which taxonomy is often controversial, spans from 0.5% to 2% of net synonymous divergence, irrespective of species life history traits or ecology. Thanks to appropriate modeling of among-locus variation in genetic drift and introgression rate, we clarify the status of the majority of ambiguous cases and uncover a number of cryptic species. Our analysis also reveals the high incidence in animals of semi-isolated species (when some but not all loci are affected by barriers to gene flow) and highlights the intrinsic difficulty, both statistical and conceptual, of delineating species in the grey zone of speciation.},
  author       = {Roux, Camille and Fraisse, Christelle and Romiguier, Jonathan and Anciaux, Youann and Galtier, Nicolas and Bierne, Nicolas},
  journal      = {PLoS Biology},
  number       = {12},
  publisher    = {Public Library of Science},
  title        = {{Shedding light on the grey zone of speciation along a continuum of genomic divergence}},
  doi          = {10.1371/journal.pbio.2000234},
  volume       = {14},
  year         = {2016},
}

@article{1329,
  abstract     = {Daphnia species have become models for ecological genomics and exhibit interesting features, such as high phenotypic plasticity and a densely packed genome with many lineage-specific genes. They are also cyclic parthenogenetic, with alternating asexual and sexual cycles and environmental sex determination. Here, we present a de novo transcriptome assembly of over 32,000 D. galeata genes and use it to investigate gene expression in females and spontaneously produced males of two clonal lines derived from lakes in Germany and the Czech Republic. We find that only a low percentage (18%) of genes shows sex-biased expression and that there are many more female-biased gene (FBG) than male-biased gene (MBG). Furthermore, FBGs tend to be more conserved between species than MBGs in both sequence and expression. These patterns may be a consequence of cyclic parthenogenesis leading to a relaxation of purifying selection on MBGs. The two clonal lines show considerable differences in both number and identity of sex-biased genes, suggesting that they may have reproductive strategies differing in their investment in sexual reproduction. Orthologs of key genes in the sex determination and juvenile hormone pathways, which are thought to be important for the transition from asexual to sexual reproduction, are present in D. galeata and highly conserved among Daphnia species.},
  author       = {Huylmans, Ann K and López Ezquerra, Alberto and Parsch, John and Cordellier, Mathilde},
  journal      = {Genome Biology and Evolution},
  number       = {10},
  pages        = {3120 -- 3139},
  publisher    = {Oxford University Press},
  title        = {{De novo transcriptome assembly and sex-biased gene expression in the cyclical parthenogenetic Daphnia galeata}},
  doi          = {10.1093/gbe/evw221},
  volume       = {8},
  year         = {2016},
}

@misc{9862,
  author       = {Roux, Camille and Fraisse, Christelle and Romiguier, Jonathan and Anciaux, Youann and Galtier, Nicolas and Bierne, Nicolas},
  publisher    = {Public Library of Science},
  title        = {{Simulation study to test the robustness of ABC in face of recent times of divergence}},
  doi          = {10.1371/journal.pbio.2000234.s016},
  year         = {2016},
}

@misc{9863,
  author       = {Roux, Camille and Fraisse, Christelle and Romiguier, Jonathan and Anciaux, Youann and Galtier, Nicolas and Bierne, Nicolas},
  publisher    = {Public Library of Science},
  title        = {{Accessions of surveyed individuals, geographic locations and summary statistics}},
  doi          = {10.1371/journal.pbio.2000234.s017},
  year         = {2016},
}

@article{1513,
  abstract     = {Insects of the order Hemiptera (true bugs) use a wide range of mechanisms of sex determination, including genetic sex determination, paternal genome elimination, and haplodiploidy. Genetic sex determination, the prevalent mode, is generally controlled by a pair of XY sex chromosomes or by an XX/X0 system, but different configurations that include additional sex chromosomes are also present. Although this diversity of sex determining systems has been extensively studied at the cytogenetic level, only the X chromosome of the model pea aphid Acyrthosiphon pisum has been analyzed at the genomic level, and little is known about X chromosome biology in the rest of the order.

In this study, we take advantage of published DNA- and RNA-seq data from three additional Hemiptera species to perform a comparative analysis of the gene content and expression of the X chromosome throughout this clade. We find that, despite showing evidence of dosage compensation, the X chromosomes of these species show female-biased expression, and a deficit of male-biased genes, in direct contrast to the pea aphid X. We further detect an excess of shared gene content between these very distant species, suggesting that despite the diversity of sex determining systems, the same chromosomal element is used as the X throughout a large portion of the order. },
  author       = {Pal, Arka and Vicoso, Beatriz},
  journal      = {Genome Biology and Evolution},
  number       = {12},
  pages        = {3259 -- 3268},
  publisher    = {Oxford University Press},
  title        = {{The X chromosome of hemipteran insects: Conservation, dosage compensation and sex-biased expression}},
  doi          = {10.1093/gbe/evv215},
  volume       = {7},
  year         = {2015},
}

@article{1577,
  abstract     = {Contrary to the pattern seen in mammalian sex chromosomes, where most Y-linked genes have X-linked homologs, the Drosophila X and Y chromosomes appear to be unrelated. Most of the Y-linked genes have autosomal paralogs, so autosome-to-Y transposition must be the main source of Drosophila Y-linked genes. Here we show how these genes were acquired. We found a previously unidentified gene (flagrante delicto Y, FDY) that originated from a recent duplication of the autosomal gene vig2 to the Y chromosome of Drosophila melanogaster. Four contiguous genes were duplicated along with vig2, but they became pseudogenes through the accumulation of deletions and transposable element insertions, whereas FDY remained functional, acquired testis-specific expression, and now accounts for ∼20% of the vig2-like mRNA in testis. FDY is absent in the closest relatives of D. melanogaster, and DNA sequence divergence indicates that the duplication to the Y chromosome occurred ∼2 million years ago. Thus, FDY provides a snapshot of the early stages of the establishment of a Y-linked gene and demonstrates how the Drosophila Y has been accumulating autosomal genes.},
  author       = {Carvalho, Antonio and Vicoso, Beatriz and Russo, Claudia and Swenor, Bonnielin and Clark, Andrew},
  journal      = {PNAS},
  number       = {40},
  pages        = {12450 -- 12455},
  publisher    = {National Academy of Sciences},
  title        = {{Birth of a new gene on the Y chromosome of Drosophila melanogaster}},
  doi          = {10.1073/pnas.1516543112},
  volume       = {112},
  year         = {2015},
}