Inference of gorilla demographic and selective history from whole-genome sequence data

Kimberly F. McManus, Joanna L. Kelley, Shiya Song, Krishna R. Veeramah, August E. Woerner, Laurie S. Stevison, Oliver A. Ryder, Great Ape Genome Project, Jeffrey M. Kidd, Jeffrey D. Wall, Carlos D. Bustamante, Michael F. Hammer

Research output: Contribution to journalArticle

26 Scopus citations

Abstract

Although population-level genomic sequence data have been gathered extensively for humans, similar data from our closest living relatives are just beginning to emerge. Examination of genomic variation within great apes offers many opportunities to increase our understanding of the forces that have differentially shaped the evolutionary history of hominid taxa. Here, we expand upon the work of the Great Ape Genome Project by analyzing medium to high coverage whole-genome sequences from 14 western lowland gorillas (Gorilla gorilla gorilla), 2 eastern lowland gorillas (G. beringei graueri), and a single Cross River individual (G. gorilla diehli). We infer that the ancestors of western and eastern lowland gorillas diverged from a common ancestor approximately 261 ka, and that the ancestors of the Cross River population diverged from the western lowland gorilla lineage approximately 68 ka. Using a diffusion approximation approach to model the genome-wide site frequency spectrum, we infer a history of western lowland gorillas that includes an ancestral population expansion of 1.4-fold around 970 ka and a recent 5.6-fold contraction in population size 23 ka. The lattermay correspond to amajor reduction in African equatorial forests around the Last GlacialMaximum.We also analyze patterns of variation among western lowland gorillas to identify several genomic regions with strong signatures of recent selective sweeps. We find that processes related to taste, pancreatic and saliva secretion, sodium ion transmembrane transport, and cardiac muscle function are overrepresented in genomic regions predicted to have experienced recent positive selection.

Original languageEnglish (US)
Pages (from-to)600-612
Number of pages13
JournalMolecular biology and evolution
Volume32
Issue number3
DOIs
StatePublished - 2015

Keywords

  • Genomics
  • Gorillas
  • Great apes
  • Natural selection

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Molecular Biology
  • Genetics

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    McManus, K. F., Kelley, J. L., Song, S., Veeramah, K. R., Woerner, A. E., Stevison, L. S., Ryder, O. A., Project, G. A. G., Kidd, J. M., Wall, J. D., Bustamante, C. D., & Hammer, M. F. (2015). Inference of gorilla demographic and selective history from whole-genome sequence data. Molecular biology and evolution, 32(3), 600-612. https://doi.org/10.1093/molbev/msu394