The 82nd Annual Meeting of the American Association of Physical Anthropologists (2013)


Whole genome DNA sequence analysis of the kinda baboon (Papio kindae)

JEFFREY ROGERS1, JANE PHILLIPS-CONROY2, CLIFFORD J. JOLLY3, DAVID RIO DEIROS1, MUTHUSWAMY RAVEENDRAN1, GLORIA L. FAWCETT1, KIM WORLEY1, DONNA M. MUZNY1 and RICHARD A. GIBBS1.

1Human Genome Sequencing Center, Baylor College of Medicine, 2Dept. of Anatomy and Neurobiology, Washington University School of Medicine, 3Dept. of Anthropology, New York University

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The goal of this study is to compare the complete genome sequences of wild-caught kinda baboons (Papio kindae) with equivalent sequences from all other species of Papio, as well as with other primates. As part of a larger multi-disciplinary field study, 76 kinda baboons in the vicinity of Chunga within Kafue National Park, Zambia were captured, bled and released. Blood samples (clots, buffy coats and whole blood) were frozen in the field, and transported to the US. DNA was extracted using standard methods. We then used the Illumina Hi-Seq platform to generate an average of 40x whole genome sequence coverage (approximately 120 gigabases of paired-end sequence reads) for each of three kinda individuals. To facilitate identification of variants and perform other comparisons, the kinda baboon sequence reads were mapped to the available baboon reference genome, a draft whole genome assembly from an olive baboon (Papio anubis) that was sequenced using a combination of Illumina, Roche 454 and Sanger platforms and assembled using CABOG, Altas-Link and Atlas-Gapfill. Genomic comparisons among baboon species indicate substantial genetic differentiation at several levels. Pairwise sequence divergence across our sample of 15 individuals representing six Papio species ranges from 0.29% to 0.49%. Single base differences outnumber small indels more than 4:1. This presentation will summarize the amount and type of genetic differences between kinda baboons and other baboons. We will also describe within-species genetic variation in P. kindae and the other baboon species.

This work is funded by NSF grant BCS-1029451 and NIH grant U54-HG003273.

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