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

Abstract

Research on the genetics of natural populations was revolutionized in the 1990s by methods for genotyping noninvasivelycollected samples. However, these methods have remained largely unchanged for the past 20 years and lag far behind the genomicsera. To close this gap, here we report an optimized laboratory protocol for genome-wide capture of endogenous DNA fromnoninvasively 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 independentlyconstructed extended pedigree. We enriched fecal-derived DNA samples up to 40-fold for endogenous baboon DNA andreconstructed near-perfect pedigree relationships even with extremely low-coverage sequencing. We anticipate that these methodswill be broadly applicable to the many research systems for which only noninvasive samples are available