Demographic Histories and Patterns of Linkage Disequilibrium in Chinese and Indian Rhesus Macaques
Ryan D. Hernandez1,
Melissa J. Hubisz2,
David A. Wheeler3,
David G. Smith4,5,
Betsy Ferguson6,7,
Jeffrey Rogers8,
Lynne Nazareth3,
Amit Indap1,
Traci Bourquin3,
John McPherson3,
Donna Muzny3,
Richard Gibbs3,
Rasmus Nielsen9 and
Carlos D. Bustamante1*
1 Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14850, USA.
2 Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA.
3 Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA.
4 Department of Anthropology, Davis, CA, USA.
5 California National Primate Research Center, Davis, CA, USA.
6 Genetics Research and Informatics Program, Oregon National Primate Research Center, Oregon Health and Sciences University, Beaverton, OR 97006, USA.
7 Washington National Primate Research Center, University of Washington, Seattle, WA 98195, USA.
8 Department of Genetics, Southwest Foundation for Biomedical Research, and Southwest National Primate Research Center, San Antonio, TX 78227, USA.
9 Center for Comparative Genomics, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100 Kbh Ø, Denmark.
|
Fig. 2. (A) The marginal frequency spectrum of derived mutations for each population (shown as expected proportions in a subsample of 10 chromosomes by integrating over possible configurations of observed and missing data, with the total number of SNPs in parentheses) and the expected distribution under the standard neutral model (SNM) of constant size. (B) A "topographical map" of the joint site-frequency spectrum for the two populations, with darker tones representing frequency pairs with few SNPs, and lighter tones representing frequency pairs with many SNPs.
[View Larger Version of this Image (34K GIF file)]
|
|
|
Fig. 3. (A) The distribution of FST between Indian and Chinese rhesus, calculated with the average pairwise-difference across each nonoverlapping window (13). (B) STRUCTURE results. Individuals are represented by vertical lines, and sorted by their amount of Chinese ancestry (black vertical line separates animals with Indian and Chinese origins). Colors correspond to the proportion of an individual's ancestry attributable to a given population (blue, Indian; red, Chinese). (C) Principal component 1 (PC1) and PC2 separate Indian from Chinese individuals. PC2 also isolates a single Chinese individual [corresponding to an individual sampled from Suzhou and shown as the fourth individual from the right in (B)].
[View Larger Version of this Image (13K GIF file)]
|
|
|
Fig. 4. The decay of LD for Indian and Chinese rhesus macaques versus European and African humans (n = 9 for all samples), along with the decay of LD for 1000 neutral simulations of our inferred demographic history for rhesus macaque. Human data are from three ENCODE regions orthologous to the rhesus data (13, 21).
[View Larger Version of this Image (46K GIF file)]
|
|
