Dynamic Copy Number Evolution of X- and Y-Linked Ampliconic Genes in Human Populations

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  • Bioinformatics Research Centre (BiRC)

Ampliconic genes are multicopy, in majority found on sex-chromosomes and enriched for testis-expressed genes. While ampliconic genes have been associated with the emergence of hybrid incompatibilities, we know little about their copy number distribution and their turnover in human populations. Here we explore the evolution of human X- and Y-linked ampliconic genes by investigating copy number variation (CNV) and coding variation between populations using the Simons Genome Diversity Project. We develop a method to assess CNVs using the read-depth on modified X and Y chromosome targets containing only one repetition of each ampliconic gene. Our results reveal extensive standing variation in copy number both within and between human populations for several ampliconic genes. For the Y chromosome, we can infer multiple independent amplifications and losses of these gene copies even within closely related Y haplogroups, that diversified less than 50,000 years ago. Moreover, X and Y-linked ampliconic genes seem to have a faster amplification dynamic than autosomal multicopy genes. Looking at expression data from another study, we also find that XY-linked ampliconic genes with extensive copy number variation are significantly more expressed than genes with no copy number variation during meiotic sex-chromosome inactivation (for both X and Y) and post-meiotic sex chromosome repression (for the Y only). While we cannot rule out that the X-Y ampliconic genes are evolving neutrally, this study gives insights on the distribution of copy number within human populations, and demonstrates an extremely fast turnover in copy number of these regions.

Original languageEnglish
StateE-pub ahead of print - 16 May 2018

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