ArticleGenome biology and evolution2013
Detecting evolutionary strata on the human x chromosome in the absence of gametologous y-linked sequences.
Article in Genome biology and evolution, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed.
- Article
- Sharks and rays have the oldest vertebrate sex chromosome with unique sex determination mechanisms.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Evolutionarily new genes in humans with disease phenotypes reveal functional enrichment patterns shaped by adaptive innovation and sexual selection.Genome research · 2025Article
- Evolutionary divergence between homologous X-Y chromosome genes shapes sex-biased biology.Nature ecology & evolution · 2025Article
- Evolution and regulation of animal sex chromosomes.Nature reviews. Genetics · 2025Review
- Evolutionarily new genes in humans with disease phenotypes reveal functional enrichment patterns shaped by adaptive innovation and sexual selection.bioRxiv : the preprint server for biology · 2024Article
- Imprinted X chromosome inactivation at the gamete-to-embryo transition.Molecular cell · 2024Article
- Evolutionarily new genes in humans with disease phenotypes reveal functional enrichment patterns shaped by adaptive innovation and sexual selection.Research square · 2023Article
- Parallel Evolution of Sex-Linked Genes across XX/XY and ZZ/ZW Sex Chromosome Systems in the FrogGenes · 2023Article
- Genomic and demographic processes differentially influence genetic variation across the human X chromosome.PloS one · 2023Article
- Evolutionary dynamics of pseudoautosomal region 1 in humans and great apes.Genome biology · 2022Article
- Dosage sensitivity and exon shuffling shape the landscape of polymorphic duplicates in Drosophila and humans.Nature ecology & evolution · 2022Article
- The Many Faces of G Protein-Coupled Receptor 143, an Atypical Intracellular Receptor.Frontiers in molecular biosciences · 2022Review
- Article
- Reference genome and transcriptome informed by the sex chromosome complement of the sample increase ability to detect sex differences in gene expression from RNA-Seq data.Biology of sex differences · 2020Article
- Genome assembly of the basket willow, Salix viminalis, reveals earliest stages of sex chromosome expansion.BMC biology · 2020Article
- The Evolution of Unusually Small Amelogenin Genes in Cetaceans; Pseudogenization, X-Y Gene Conversion, and Feeding Strategy.Journal of molecular evolution · 2020Article
- Deciphering Ancestral Sex Chromosome Turnovers Based on Analysis of Male Mutation Bias.Genome biology and evolution · 2019Article
- Escape From X-Chromosome Inactivation: An Evolutionary Perspective.Frontiers in cell and developmental biology · 2019Review
- Sex-chromosome dosage effects on gene expression in humans.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
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3 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Mammalian sex chromosomes arose from a pair of homologous autosomes that differentiated into the X and Y chromosomes following a series of recombination suppression events between the X and Y. The stepwise recombination suppressions from the distal long arm to the distal short arm of the chromosomes are reflected as regions with distinct X-Y divergence, referred to as evolutionary strata on the X. All current methods for stratum detection depend on X-Y comparisons but are severely limited by the paucity of X-Y gametologs. We have developed an integrative method that combines a top-down, recursive segmentation algorithm with a bottom-up, agglomerative clustering algorithm to decipher compositionally distinct regions on the X, which reflect regions of unique X-Y divergence. In application to human X chromosome, our method correctly classified a concatenated set of 35 previously assayed X-linked gene sequences by evolutionary strata. We then extended our analysis, applying this method to the entire sequence of the human X chromosome, in an effort to define stratum boundaries. The boundaries of more recently formed strata on X-added region, namely the fourth and fifth strata, have been defined by previous studies and are recapitulated with our method. The older strata, from the first up to the third stratum, have remained poorly resolved due to paucity of X-Y gametologs. By analyzing the entire X sequence, our method identified seven evolutionary strata in these ancient regions, where only three could previously be assayed, thus demonstrating the robustness of our method in detecting the evolutionary strata.
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