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Genetics. 2016 Jun;203(2):699-714. doi: 10.1534/genetics.116.187492. Epub 2016 Apr 20.

Efficient Genome-Wide Sequencing and Low-Coverage Pedigree Analysis from Noninvasively Collected Samples.

Author information

1
Department of Evolutionary Anthropology, Duke University, Durham, North Carolina.
2
Graduate Program in Computational Biology and Bioinformatics, Duke University, Durham, North Carolina.
3
Department of Biology, Duke University, Durham, North Carolina.
4
Cognitive Ethology Laboratory, German Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany Department of Biology, University of Konstanz, 78457 Konstanz, Germany Department of Migration and Immuno-Ecology, Max Planck Institute for Ornithology, 82319 Radolfzell, Germany.
5
Department of Molecular and Cell Biology, University of Cape Town, 7700 Cape Town, South Africa.
6
Institute for Human Genetics, University of California, San Francisco, California 94143.
7
Department of Evolutionary Anthropology, Duke University, Durham, North Carolina Department of Biology, Duke University, Durham, North Carolina Institute of Primate Research, National Museums of Kenya, Nairobi, Kenya.
8
Department of Statistical Science, Duke University, Durham, North Carolina Department of Mathematics, Duke University, Durham, North Carolina Department of Computer Science, Duke University, Durham, North Carolina.
9
Department of Biostatistics, University of Michigan, Ann Arbor, Michigan Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan 48109 jt5@duke.edu xzhousph@umich.edu.
10
Department of Evolutionary Anthropology, Duke University, Durham, North Carolina Department of Biology, Duke University, Durham, North Carolina Institute of Primate Research, National Museums of Kenya, Nairobi, Kenya Duke University Population Research Institute, Duke University, Durham, North Carolina 27708 jt5@duke.edu xzhousph@umich.edu.

Abstract

Research on the genetics of natural populations was revolutionized in the 1990s by methods for genotyping noninvasively collected samples. However, these methods have remained largely unchanged for the past 20 years and lag far behind the genomics era. To close this gap, here we report an optimized laboratory protocol for genome-wide capture of endogenous DNA from noninvasively collected samples, coupled with a novel computational approach to reconstruct pedigree links from the resulting low-coverage data. We validated both methods using fecal samples from 62 wild baboons, including 48 from an independently constructed extended pedigree. We enriched fecal-derived DNA samples up to 40-fold for endogenous baboon DNA and reconstructed near-perfect pedigree relationships even with extremely low-coverage sequencing. We anticipate that these methods will be broadly applicable to the many research systems for which only noninvasive samples are available. The lab protocol and software ("WHODAD") are freely available at www.tung-lab.org/protocols-and-software.html and www.xzlab.org/software.html, respectively.

KEYWORDS:

baboons; capture-based enrichment; genome resequencing; noninvasive samples; paternity analysis; pedigree

PMID:
27098910
PMCID:
PMC4896188
DOI:
10.1534/genetics.116.187492
[Indexed for MEDLINE]
Free PMC Article

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