Data from: Genomic-scale capture and sequencing of endogenous DNA from feces

Genomic-level analyses of DNA from non-invasive sources would facilitate
powerful conservation and evolutionary studies in natural populations of
endangered and otherwise elusive species. However, the typical low
quantity and poor quality of DNA that is extracted from non-invasive
samples have generally precluded such work. Here we apply a modified DNA
capture protocol that, when used in combination with massively-parallel
sequencing technology, facilitates efficient and highly-accurate
resequencing of megabases of specified nuclear genomic regions from fecal
DNA samples. We validated our approach by comparing genetic variants
identified from corresponding fecal and blood DNA samples of six western
chimpanzees (Pan troglodytes verus) across more than 1.5 megabases of
chromosome 21, chromosome X, and the complete mitochondrial genome. Our
results suggest that it is now feasible to conduct genomic studies in
natural populations for which constraints on invasive sampling have
otherwise long been a barrier. The data we collected also provided an
opportunity to examine western chimpanzee genetic diversity at
unprecedented scale. Despite high mitochondrial genome diversity (pi =
0.585%), western chimpanzees have a low ratio (0.42) of X chromosomal (pi
= 0.034%) to autosomal (chromosome 21 pi = 0.081%) sequence diversity, a
pattern that may reflect an unusual demographic history of this
subspecies.