Efficient Genome-Wide Sequencing and Low-Coverage Pedigree Analysis from Noninvasively Collected Samples

Area of Science:

• Population Genetics
• Genomics
• Conservation Biology

Background:

• Genotyping non-invasively collected samples revolutionized population genetics in the 1990s.
• Existing methods have not kept pace with the genomics era, limiting their application.
• There is a need for updated protocols to analyze endogenous DNA from non-invasive samples.

Purpose of the Study:

• To develop and validate an optimized laboratory protocol for genome-wide DNA capture from non-invasive samples.
• To create a novel computational approach for reconstructing pedigrees from low-coverage sequencing data.
• To improve the analysis of genetic data from wild populations using non-invasive sampling.

Main Methods:

• Optimized laboratory protocol for genome-wide capture of endogenous DNA.
• Novel computational approach (WHODAD) for pedigree reconstruction.
• Validation using fecal samples from 62 wild baboons with an existing pedigree.

Main Results:

• Enriched fecal-derived DNA samples up to 40-fold for endogenous baboon DNA.
• Reconstructed near-perfect pedigree relationships with extremely low-coverage sequencing.
• Demonstrated broad applicability of the methods for non-invasive genetic studies.

Conclusions:

• The developed methods significantly advance the analysis of non-invasively collected samples in population genetics.
• These tools enable accurate pedigree reconstruction, even with limited DNA and low sequencing coverage.
• The protocol and software are freely available, facilitating wider research application.