Genome-scale evolution in local populations of wild chimpanzees

Area of Science:

• Genomics
• Evolutionary Biology
• Conservation Genetics

Background:

• Analyzing genome-scale evolution in endangered animals is challenging due to limited high-quality genetic samples.
• Novel, field-friendly, and cost-effective genetic techniques are needed for studying large, endangered species.

Purpose of the Study:

• To conduct an exome-wide analysis of wild chimpanzees (Pan troglodytes) to develop population discrimination techniques.
• To explore the application of cost-effective, human-derived exome-capture baits for non-human primate genomics.
• To investigate genetic diversity, mutation loads, and gene divergence at the population level.

Main Methods:

• Noninvasive DNA extraction from fecal samples using the lysis-buffer storage method.
• Exome-capture sequencing utilizing cost-effective human-designed baits.
• Multivariate analysis for population discrimination and geographical origin identification.
• Analysis of exome-wide heterozygosity, nonsynonymous-synonymous substitution ratios, and pseudogene annotation.

Main Results:

• Effective discrimination of local chimpanzee populations and identification of geographical origins.
• Negative correlation between exome-wide heterozygosity and genome-wide nonsynonymous-synonymous substitution ratios, indicating local mutation loads.
• Revealed functional diversity and protein-coding gene divergence, including population-specific and shared segregating pseudogenes.
• Identified shared pseudogenes (OR7D4, TAS2R42) in chemosensory receptor genes between western and eastern chimpanzees.

Conclusions:

• The developed analytical framework provides ecological insights into chimpanzee populations.
• The cost-effective exome-capture sequencing method is viable for studying non-human primates.
• This approach is potentially applicable to genome-scale evolutionary analysis in other endangered organisms.