The 84th Annual Meeting of the American Association of Physical Anthropologists (2015)


Exomic copy number variation in the macaques

TIMOTHY H. WEBSTER1 and BRENDA J. BRADLEY1,2.

1Department of Anthropology, Yale University, 2Department of Anthropology, The George Washington University

March 28, 2015 , Gateway Ballroom 2/3/4/5 Add to calendar

A large portion of the genome contains regions that exhibit both intra- and interspecific variation in copy number. These copy number variants (CNVs) can significantly impact phenotypic variation through dosage effects on gene expression and neofunctionalization of duplicated genes, suggesting that CNVs may have played a major role in primate evolution. To better understand the extent and potential role of copy number variation in the evolution of the genus Macaca, we sequenced the exomes of six individuals representing five species of macaques – M. fascicularis, M. fuscata, M. mulatta, M. nigra, and M. thibetana – including two populations of M. mulatta. We targeted the coding region of the genome using NimbleGen SeqCap v2.0 human capture probes (44.1 mb coverage) and sequenced the exomes on a single lane of an Illumina Hiseq 2000. We mapped reads to the rhesus macaque (Macaca mulatta) draft genome assembly (rhemac2) and then called CNVs using CoNIFER, which calls variants based on the normalized relative copy number of each exon in each sample based on read depth and coverage. We identified 216 variants among the six individuals and found that CNVs were nonrandomly distributed throughout the genome. In particular, 37% of CNVs overlapped with segmental duplications in the rhesus genome assembly, and another 17% were in regions flanking segmental duplications. CNVs fell into a small number of functional categories, including a highly significant enrichment for olfactory receptor genes. Our results have implications for understanding structural variation in primates and molecular evolution in the macaques.