Unlocking the vault: next-generation museum population genomics.

Area of Science:

• Evolutionary Biology
• Genomics
• Conservation Biology

Background:

• Museum collections are vital for studying species' responses to climate change.
• Degraded DNA in historic samples limits genomic analysis of evolutionary consequences.
• Previous studies faced challenges with ancient DNA from museum specimens.

Purpose of the Study:

• To assess genomic diversity changes in alpine chipmunks (Tamias alpinus) linked to climate-driven range retraction.
• To demonstrate a method for analyzing degraded DNA from museum skins for population genomics.
• To explore the evolutionary impact of recent anthropogenic climate change on a high-elevation species.

Main Methods:

• Utilized custom, multiplexed exon capture to enrich and sequence DNA from early 20th-century museum skins.
• Developed bioinformatic pipelines to detect and filter DNA base misincorporations.
• Applied probabilistic methods for single-nucleotide polymorphism calling and allele frequency estimation with low-medium coverage data.

Main Results:

• Observed increased genetic subdivision in alpine chipmunks following their range retraction.
• Found no significant change in overall genetic diversity at nonsynonymous or synonymous sites.
• Successfully generated population genomic data from degraded DNA in museum skins.

Conclusions:

• Integrating advanced genomic and statistical tools enhances the utility of museum collections for evolutionary and conservation studies.
• This approach is valuable even without a pre-existing reference genome.
• Museum specimens offer a powerful resource for understanding species' adaptation and resilience to environmental change.