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

Genetics
Elise A LucotteMikkel H Schierup

Abstract

Ampliconic genes are multicopy, with the 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 < 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 X- and Y-linked ampliconic genes with extensive CNV are significantly more expressed than g...Continue Reading

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Citations

Oct 24, 2019·Proceedings. Biological Sciences·Cécile CourretAmanda M Larracuente
May 7, 2020·Genome Biology and Evolution·Rahulsimham VegesnaKateryna D Makova
Nov 2, 2019·Nature Ecology & Evolution·Doris BachtrogRyan Bracewell
Mar 25, 2021·The Journal of Heredity·Thea F RogersAlison E Wright
Jun 13, 2021·Genome Biology and Evolution·James J LewisStephen H Montgomery
Jul 25, 2021·Genome Research·Wesley A BrashearWilliam J Murphy
Sep 15, 2021·Molecular Biology and Evolution·Kevin R BredemeyerWilliam J Murphy

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Methods Mentioned

BETA
the

Software Mentioned

pysam
GATK
SnpEff
AMPLICONIC
Lastz
SAMtools
BWA
chimp
BLAST ( Basic Local Alignment Search Tool
R

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