TY - JOUR T1 - Efficient genome-wide sequencing and low coverage pedigree analysis from non-invasively collected samples JF - bioRxiv DO - 10.1101/029520 SP - 029520 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 Y1 - 2015/01/01 UR - http://biorxiv.org/content/early/2015/10/21/029520.abstract N2 - 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. ER -