Abstract
Chromosomal rearrangements, which shuffle DNA across the genome, are an
important source of divergence across taxa that can modify gene expression and
function. Using a paired-end read approach with Illumina sequence data for
archaic humans, I identify changes in genome structure that occurred recently
in human evolution. Hundreds of rearrangements indicate genomic trafficking
between the sex chromosomes and autosomes, raising the possibility of
sex-specific changes. Additionally, genes adjacent to genome structure changes
in Neanderthals are associated with testis-specific expression, consistent with
evolutionary theory that new genes commonly form with expression in the testes.
I identify one case of new-gene creation through transposition from the Y
chromosome to chromosome 10 that combines the 5' end of the testis-specific
gene Fank1 with previously untranscribed sequence. This new transcript
experienced copy number expansion in archaic genomes, indicating rapid genomic
change. Finally, loci containing genome structure changes show diminished rates
of introgression from Neanderthals into modern humans, consistent with the
hypothesis that rearrangements serve as barriers to gene flow during
hybridization. Together, these results suggest that this previously
unidentified source of genomic variation has important biological consequences
in human evolution.
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