These authors contributed equally to this work.
Genomic-scale capture and sequencing of endogenous DNA from feces
Article first published online: 3 NOV 2010
© 2010 Blackwell Publishing Ltd
Volume 19, Issue 24, pages 5332–5344, December 2010
How to Cite
PERRY, G. H., MARIONI, J. C., MELSTED, P. and GILAD, Y. (2010), Genomic-scale capture and sequencing of endogenous DNA from feces. Molecular Ecology, 19: 5332–5344. doi: 10.1111/j.1365-294X.2010.04888.x
Data deposition: All sequence data have been deposited at the National Center for Biotechnology Information short read archive (http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi) as study no. SRA012374.
- Issue published online: 6 DEC 2010
- Article first published online: 3 NOV 2010
- Received 22 June 2010; revision received 1 September 2010; accepted 7 September 2010
- conservation genomics;
- molecular ecology;
- non-invasive sampling;
- population genetics
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 (π = 0.585%), western chimpanzees have a low ratio (0.42) of X chromosomal (π = 0.034%) to autosomal (chromosome 21 π = 0.081%) sequence diversity, a pattern that may reflect an unusual demographic history of this subspecies.