cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.19316693
title: DatasetS3.csv from Adaptive changes of the autosomal part of the genome in a dioecious clade of <i>Silene</i>

description: The genus <i>Silene</i> brings many opportunities for the study of various processes involved in the evolution of dioecy and young sex chromosomes. Here we focus on a dioecious clade in <i>Silene</i> subgenus <i>Silene</i> and closely related species. This study provides improved support for monophyly of this clade (based on inclusion of further dioecious species) and a new estimate of its age (approxi. 2.3 million years). We observed a rise in adaptive evolution in the autosomal and pseudoautosomal parts of the genome on the branch where dioecy originated. This increase is not a result of the accumulation of sexually antagonistic genes in the pseudoautosomal region. It is also not caused by the coevolution of genes acting in mitochondria (despite the possibility that dioecy along this branch could have evolved from a nucleo-cytoplasmic male sterility-based system). After considering other possibilities, the most parsimonious explanation for the increase seen in the number of positively selected codons is the adaptive evolution of genes involved in the adaptation of the autosomal part of the genome to dioecy as described in Charnov's sex-allocation theory. As the observed coincidence cannot prove causality, studies in other dioecious clades are necessary to allow the forming of general conclusions.
DOI: 10.6084/m9.figshare.19316693.v1
title: DatasetS3.csv from Adaptive changes of the autosomal part of the genome in a dioecious clade of <i>Silene</i>

description: The genus <i>Silene</i> brings many opportunities for the study of various processes involved in the evolution of dioecy and young sex chromosomes. Here we focus on a dioecious clade in <i>Silene</i> subgenus <i>Silene</i> and closely related species. This study provides improved support for monophyly of this clade (based on inclusion of further dioecious species) and a new estimate of its age (approxi. 2.3 million years). We observed a rise in adaptive evolution in the autosomal and pseudoautosomal parts of the genome on the branch where dioecy originated. This increase is not a result of the accumulation of sexually antagonistic genes in the pseudoautosomal region. It is also not caused by the coevolution of genes acting in mitochondria (despite the possibility that dioecy along this branch could have evolved from a nucleo-cytoplasmic male sterility-based system). After considering other possibilities, the most parsimonious explanation for the increase seen in the number of positively selected codons is the adaptive evolution of genes involved in the adaptation of the autosomal part of the genome to dioecy as described in Charnov's sex-allocation theory. As the observed coincidence cannot prove causality, studies in other dioecious clades are necessary to allow the forming of general conclusions.
DOI: 10.6084/m9.figshare.19316696
title: Supplementary Table S3: List of all fifteen so far recognised species of the dioecious clade in subgenus Silene. from Adaptive changes of the autosomal part of the genome in a dioecious clade of <i>Silene</i>

description: The genus <i>Silene</i> brings many opportunities for the study of various processes involved in the evolution of dioecy and young sex chromosomes. Here we focus on a dioecious clade in <i>Silene</i> subgenus <i>Silene</i> and closely related species. This study provides improved support for monophyly of this clade (based on inclusion of further dioecious species) and a new estimate of its age (approxi. 2.3 million years). We observed a rise in adaptive evolution in the autosomal and pseudoautosomal parts of the genome on the branch where dioecy originated. This increase is not a result of the accumulation of sexually antagonistic genes in the pseudoautosomal region. It is also not caused by the coevolution of genes acting in mitochondria (despite the possibility that dioecy along this branch could have evolved from a nucleo-cytoplasmic male sterility-based system). After considering other possibilities, the most parsimonious explanation for the increase seen in the number of positively selected codons is the adaptive evolution of genes involved in the adaptation of the autosomal part of the genome to dioecy as described in Charnov's sex-allocation theory. As the observed coincidence cannot prove causality, studies in other dioecious clades are necessary to allow the forming of general conclusions.
DOI: 10.6084/m9.figshare.19316687
title: Supplementary Table S1: List of the accession numbers of the sequences that were used for the phylogenetic analyses. from Adaptive changes of the autosomal part of the genome in a dioecious clade of <i>Silene</i>

description: The genus <i>Silene</i> brings many opportunities for the study of various processes involved in the evolution of dioecy and young sex chromosomes. Here we focus on a dioecious clade in <i>Silene</i> subgenus <i>Silene</i> and closely related species. This study provides improved support for monophyly of this clade (based on inclusion of further dioecious species) and a new estimate of its age (approxi. 2.3 million years). We observed a rise in adaptive evolution in the autosomal and pseudoautosomal parts of the genome on the branch where dioecy originated. This increase is not a result of the accumulation of sexually antagonistic genes in the pseudoautosomal region. It is also not caused by the coevolution of genes acting in mitochondria (despite the possibility that dioecy along this branch could have evolved from a nucleo-cytoplasmic male sterility-based system). After considering other possibilities, the most parsimonious explanation for the increase seen in the number of positively selected codons is the adaptive evolution of genes involved in the adaptation of the autosomal part of the genome to dioecy as described in Charnov's sex-allocation theory. As the observed coincidence cannot prove causality, studies in other dioecious clades are necessary to allow the forming of general conclusions.
DOI: 10.6084/m9.figshare.19316696.v1
title: Supplementary Table S3: List of all fifteen so far recognised species of the dioecious clade in subgenus Silene. from Adaptive changes of the autosomal part of the genome in a dioecious clade of <i>Silene</i>

description: The genus <i>Silene</i> brings many opportunities for the study of various processes involved in the evolution of dioecy and young sex chromosomes. Here we focus on a dioecious clade in <i>Silene</i> subgenus <i>Silene</i> and closely related species. This study provides improved support for monophyly of this clade (based on inclusion of further dioecious species) and a new estimate of its age (approxi. 2.3 million years). We observed a rise in adaptive evolution in the autosomal and pseudoautosomal parts of the genome on the branch where dioecy originated. This increase is not a result of the accumulation of sexually antagonistic genes in the pseudoautosomal region. It is also not caused by the coevolution of genes acting in mitochondria (despite the possibility that dioecy along this branch could have evolved from a nucleo-cytoplasmic male sterility-based system). After considering other possibilities, the most parsimonious explanation for the increase seen in the number of positively selected codons is the adaptive evolution of genes involved in the adaptation of the autosomal part of the genome to dioecy as described in Charnov's sex-allocation theory. As the observed coincidence cannot prove causality, studies in other dioecious clades are necessary to allow the forming of general conclusions.
DOI: 10.6084/m9.figshare.19316699
title: Supplementary Dataset S1: Alignment of sequences used in phylogenetic analyses. The file also contains MrBayes block. from Adaptive changes of the autosomal part of the genome in a dioecious clade of <i>Silene</i>

description: The genus <i>Silene</i> brings many opportunities for the study of various processes involved in the evolution of dioecy and young sex chromosomes. Here we focus on a dioecious clade in <i>Silene</i> subgenus <i>Silene</i> and closely related species. This study provides improved support for monophyly of this clade (based on inclusion of further dioecious species) and a new estimate of its age (approxi. 2.3 million years). We observed a rise in adaptive evolution in the autosomal and pseudoautosomal parts of the genome on the branch where dioecy originated. This increase is not a result of the accumulation of sexually antagonistic genes in the pseudoautosomal region. It is also not caused by the coevolution of genes acting in mitochondria (despite the possibility that dioecy along this branch could have evolved from a nucleo-cytoplasmic male sterility-based system). After considering other possibilities, the most parsimonious explanation for the increase seen in the number of positively selected codons is the adaptive evolution of genes involved in the adaptation of the autosomal part of the genome to dioecy as described in Charnov's sex-allocation theory. As the observed coincidence cannot prove causality, studies in other dioecious clades are necessary to allow the forming of general conclusions.
DOI: 10.6084/m9.figshare.19316699.v1
title: Supplementary Dataset S1: Alignment of sequences used in phylogenetic analyses. The file also contains MrBayes block. from Adaptive changes of the autosomal part of the genome in a dioecious clade of <i>Silene</i>

description: The genus <i>Silene</i> brings many opportunities for the study of various processes involved in the evolution of dioecy and young sex chromosomes. Here we focus on a dioecious clade in <i>Silene</i> subgenus <i>Silene</i> and closely related species. This study provides improved support for monophyly of this clade (based on inclusion of further dioecious species) and a new estimate of its age (approxi. 2.3 million years). We observed a rise in adaptive evolution in the autosomal and pseudoautosomal parts of the genome on the branch where dioecy originated. This increase is not a result of the accumulation of sexually antagonistic genes in the pseudoautosomal region. It is also not caused by the coevolution of genes acting in mitochondria (despite the possibility that dioecy along this branch could have evolved from a nucleo-cytoplasmic male sterility-based system). After considering other possibilities, the most parsimonious explanation for the increase seen in the number of positively selected codons is the adaptive evolution of genes involved in the adaptation of the autosomal part of the genome to dioecy as described in Charnov's sex-allocation theory. As the observed coincidence cannot prove causality, studies in other dioecious clades are necessary to allow the forming of general conclusions.
DOI: 10.5519/qd.vtooozq2
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (1437 records)
DOI: 10.6084/m9.figshare.19316720
title: Table_S4_Genome_wide_windowed_partial_correlations.csv from Recombination landscape dimorphism and sex chromosome evolution in the dioecious plant <i>Rumex hastatulus</i>

description: There is growing evidence from diverse taxa for sex differences in the genomic landscape of recombination, but the causes and consequences of these differences remain poorly understood. Strong recombination landscape dimorphism between the sexes could have important implications for the dynamics of sex chromosome evolution because low recombination in the heterogametic sex can favour the spread of sexually antagonistic alleles. Here, we present a sex-specific linkage map and revised genome assembly of <i>Rumex hastatulus</i> and provide the first evidence and characterization of sex differences in recombination landscape in a dioecious plant. We present data on significant sex differences in recombination, with regions of very low recombination in males covering over half of the genome. This pattern is evident on both sex chromosomes and autosomes, suggesting that pre-existing differences in recombination may have contributed to sex chromosome formation and divergence. Our analysis of segregation distortion suggests that haploid selection due to pollen competition occurs disproportionately in regions with low male recombination. We hypothesize that sex differences in the recombination landscape have contributed to the formation of a large heteromorphic pair of sex chromosomes in <i>R. hastatulus</i>, but more comparative analyses of recombination will be important to investigate this hypothesis further.This article is part of the theme issue ‘Sex determination, sex chromosome evolution, and the role of sexual differentiation in land plants’.
DOI: 10.6084/m9.figshare.19316720.v1
title: Table_S4_Genome_wide_windowed_partial_correlations.csv from Recombination landscape dimorphism and sex chromosome evolution in the dioecious plant <i>Rumex hastatulus</i>

description: There is growing evidence from diverse taxa for sex differences in the genomic landscape of recombination, but the causes and consequences of these differences remain poorly understood. Strong recombination landscape dimorphism between the sexes could have important implications for the dynamics of sex chromosome evolution because low recombination in the heterogametic sex can favour the spread of sexually antagonistic alleles. Here, we present a sex-specific linkage map and revised genome assembly of <i>Rumex hastatulus</i> and provide the first evidence and characterization of sex differences in recombination landscape in a dioecious plant. We present data on significant sex differences in recombination, with regions of very low recombination in males covering over half of the genome. This pattern is evident on both sex chromosomes and autosomes, suggesting that pre-existing differences in recombination may have contributed to sex chromosome formation and divergence. Our analysis of segregation distortion suggests that haploid selection due to pollen competition occurs disproportionately in regions with low male recombination. We hypothesize that sex differences in the recombination landscape have contributed to the formation of a large heteromorphic pair of sex chromosomes in <i>R. hastatulus</i>, but more comparative analyses of recombination will be important to investigate this hypothesis further.This article is part of the theme issue ‘Sex determination, sex chromosome evolution, and the role of sexual differentiation in land plants’.
DOI: 10.6084/m9.figshare.19316726
title: Table_S7_linear_model results.xlsx from Recombination landscape dimorphism and sex chromosome evolution in the dioecious plant <i>Rumex hastatulus</i>

description: There is growing evidence from diverse taxa for sex differences in the genomic landscape of recombination, but the causes and consequences of these differences remain poorly understood. Strong recombination landscape dimorphism between the sexes could have important implications for the dynamics of sex chromosome evolution because low recombination in the heterogametic sex can favour the spread of sexually antagonistic alleles. Here, we present a sex-specific linkage map and revised genome assembly of <i>Rumex hastatulus</i> and provide the first evidence and characterization of sex differences in recombination landscape in a dioecious plant. We present data on significant sex differences in recombination, with regions of very low recombination in males covering over half of the genome. This pattern is evident on both sex chromosomes and autosomes, suggesting that pre-existing differences in recombination may have contributed to sex chromosome formation and divergence. Our analysis of segregation distortion suggests that haploid selection due to pollen competition occurs disproportionately in regions with low male recombination. We hypothesize that sex differences in the recombination landscape have contributed to the formation of a large heteromorphic pair of sex chromosomes in <i>R. hastatulus</i>, but more comparative analyses of recombination will be important to investigate this hypothesis further.This article is part of the theme issue ‘Sex determination, sex chromosome evolution, and the role of sexual differentiation in land plants’.
DOI: 10.6084/m9.figshare.19316729
title: Table_S2_Genotypes_for_all_markers.csv from Recombination landscape dimorphism and sex chromosome evolution in the dioecious plant <i>Rumex hastatulus</i>

description: There is growing evidence from diverse taxa for sex differences in the genomic landscape of recombination, but the causes and consequences of these differences remain poorly understood. Strong recombination landscape dimorphism between the sexes could have important implications for the dynamics of sex chromosome evolution because low recombination in the heterogametic sex can favour the spread of sexually antagonistic alleles. Here, we present a sex-specific linkage map and revised genome assembly of <i>Rumex hastatulus</i> and provide the first evidence and characterization of sex differences in recombination landscape in a dioecious plant. We present data on significant sex differences in recombination, with regions of very low recombination in males covering over half of the genome. This pattern is evident on both sex chromosomes and autosomes, suggesting that pre-existing differences in recombination may have contributed to sex chromosome formation and divergence. Our analysis of segregation distortion suggests that haploid selection due to pollen competition occurs disproportionately in regions with low male recombination. We hypothesize that sex differences in the recombination landscape have contributed to the formation of a large heteromorphic pair of sex chromosomes in <i>R. hastatulus</i>, but more comparative analyses of recombination will be important to investigate this hypothesis further.This article is part of the theme issue ‘Sex determination, sex chromosome evolution, and the role of sexual differentiation in land plants’.
DOI: 10.6084/m9.figshare.19316726.v1
title: Table_S7_linear_model results.xlsx from Recombination landscape dimorphism and sex chromosome evolution in the dioecious plant <i>Rumex hastatulus</i>

description: There is growing evidence from diverse taxa for sex differences in the genomic landscape of recombination, but the causes and consequences of these differences remain poorly understood. Strong recombination landscape dimorphism between the sexes could have important implications for the dynamics of sex chromosome evolution because low recombination in the heterogametic sex can favour the spread of sexually antagonistic alleles. Here, we present a sex-specific linkage map and revised genome assembly of <i>Rumex hastatulus</i> and provide the first evidence and characterization of sex differences in recombination landscape in a dioecious plant. We present data on significant sex differences in recombination, with regions of very low recombination in males covering over half of the genome. This pattern is evident on both sex chromosomes and autosomes, suggesting that pre-existing differences in recombination may have contributed to sex chromosome formation and divergence. Our analysis of segregation distortion suggests that haploid selection due to pollen competition occurs disproportionately in regions with low male recombination. We hypothesize that sex differences in the recombination landscape have contributed to the formation of a large heteromorphic pair of sex chromosomes in <i>R. hastatulus</i>, but more comparative analyses of recombination will be important to investigate this hypothesis further.This article is part of the theme issue ‘Sex determination, sex chromosome evolution, and the role of sexual differentiation in land plants’.
DOI: 10.6084/m9.figshare.19316729.v1
title: Table_S2_Genotypes_for_all_markers.csv from Recombination landscape dimorphism and sex chromosome evolution in the dioecious plant <i>Rumex hastatulus</i>

description: There is growing evidence from diverse taxa for sex differences in the genomic landscape of recombination, but the causes and consequences of these differences remain poorly understood. Strong recombination landscape dimorphism between the sexes could have important implications for the dynamics of sex chromosome evolution because low recombination in the heterogametic sex can favour the spread of sexually antagonistic alleles. Here, we present a sex-specific linkage map and revised genome assembly of <i>Rumex hastatulus</i> and provide the first evidence and characterization of sex differences in recombination landscape in a dioecious plant. We present data on significant sex differences in recombination, with regions of very low recombination in males covering over half of the genome. This pattern is evident on both sex chromosomes and autosomes, suggesting that pre-existing differences in recombination may have contributed to sex chromosome formation and divergence. Our analysis of segregation distortion suggests that haploid selection due to pollen competition occurs disproportionately in regions with low male recombination. We hypothesize that sex differences in the recombination landscape have contributed to the formation of a large heteromorphic pair of sex chromosomes in <i>R. hastatulus</i>, but more comparative analyses of recombination will be important to investigate this hypothesis further.This article is part of the theme issue ‘Sex determination, sex chromosome evolution, and the role of sexual differentiation in land plants’.
DOI: 10.6084/m9.figshare.19316732
title: Table_S5_all_chromosomes_windowed_partial_correlations.csv from Recombination landscape dimorphism and sex chromosome evolution in the dioecious plant <i>Rumex hastatulus</i>

description: There is growing evidence from diverse taxa for sex differences in the genomic landscape of recombination, but the causes and consequences of these differences remain poorly understood. Strong recombination landscape dimorphism between the sexes could have important implications for the dynamics of sex chromosome evolution because low recombination in the heterogametic sex can favour the spread of sexually antagonistic alleles. Here, we present a sex-specific linkage map and revised genome assembly of <i>Rumex hastatulus</i> and provide the first evidence and characterization of sex differences in recombination landscape in a dioecious plant. We present data on significant sex differences in recombination, with regions of very low recombination in males covering over half of the genome. This pattern is evident on both sex chromosomes and autosomes, suggesting that pre-existing differences in recombination may have contributed to sex chromosome formation and divergence. Our analysis of segregation distortion suggests that haploid selection due to pollen competition occurs disproportionately in regions with low male recombination. We hypothesize that sex differences in the recombination landscape have contributed to the formation of a large heteromorphic pair of sex chromosomes in <i>R. hastatulus</i>, but more comparative analyses of recombination will be important to investigate this hypothesis further.This article is part of the theme issue ‘Sex determination, sex chromosome evolution, and the role of sexual differentiation in land plants’.