PT  - JOURNAL ARTICLE
AU  - Noah Snyder-Mackler
AU  - William H. Majoros
AU  - Michael L. Yuan
AU  - Amanda O. Shaver
AU  - Jacob B. Gordon
AU  - Gisela H. Kopp
AU  - Stephen A. Schlebusch
AU  - Jeffrey D. Wall
AU  - Susan C. Alberts
AU  - Sayan Mukherjee
AU  - Xiang Zhou
AU  - Jenny Tung
TI  - Efficient genome-wide sequencing and low coverage pedigree analysis from non-invasively collected samples
AID  - 10.1101/029520
DP  - 2015 Jan 01
TA  - bioRxiv
PG  - 029520
4099  - http://biorxiv.org/content/early/2015/10/21/029520.short
4100  - http://biorxiv.org/content/early/2015/10/21/029520.full
AB  - Research on the genetics of natural populations was revolutionized in the 1990’s by methods for genotyping non-invasively 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 non-invasively 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 non-invasive samples are available. The lab protocol and software (“WHODAD”) are freely available at www.tung-lab.org/protocols and www.xzlab.org/software, respectively.