Title : Efficient genome-wide sequencing and low coverage pedigree analysis from non-1 invasively collected samples

47 Research on the genetics of natural populations was revolutionized in the 1990’s 48 by methods for genotyping non-invasively collected samples. However, these methods 49 have remained largely unchanged for the past 20 years and lag far behind the genomics 50 era. To close this gap, here we report an optimized laboratory protocol for genome-wide 51 capture of endogenous DNA from non-invasively collected samples, coupled with a 52 novel computational approach to reconstruct pedigree links from the resulting low53 coverage data. We validated both methods using fecal samples from 62 wild baboons, 54 including 48 from an independently constructed extended pedigree. We enriched fecal55 derived DNA samples up to 40-fold for endogenous baboon DNA, and reconstructed 56 near-perfect pedigree relationships even with extremely low-coverage sequencing. We 57 anticipate that these methods will be broadly applicable to the many research systems 58 for which only non-invasive samples are available. The lab protocol and software 59 (“WHODAD”) are freely available at www.tung-lab.org/protocols and 60 www.xzlab.org/software, respectively. 61