Sequence capture of ultraconserved elements from bird museum specimens

Area of Science:

• Genomics
• Molecular Evolution
• Bioinformatics

Background:

• Museum specimens offer a vast, untapped resource for genomic research.
• Degraded DNA in older specimens poses challenges for next-generation sequencing (NGS).
• Understanding NGS efficacy on historical samples is crucial for expanding genomic studies.

Purpose of the Study:

• To evaluate the effectiveness of sequence capture of ultraconserved elements (UCEs) for genomic data recovery from old museum bird specimens.
• To assess the impact of specimen age and sequencing depth on data quality and quantity.
• To compare phylogenetic accuracy using concatenated UCE loci versus single nucleotide polymorphisms (SNPs) derived from UCEs.

Main Methods:

• Applied UCE sequence capture to 27 museum specimens of western scrub-jays (Aphelocoma californica) up to 120 years old.
• Sequenced samples and analyzed data to recover UCE loci and single nucleotide polymorphisms (SNPs).
• Constructed phylogenetic trees using both concatenated UCE loci and SNP data, while assessing sample contamination.

Main Results:

• Thousands of UCE loci and SNPs were recovered from specimens up to 120 years old.
• Older specimens yielded fewer and shorter loci, but increased sequencing depth improved locus recovery.
• Contamination was detected, particularly in older, less-sequenced samples, impacting concatenated UCE phylogenies but not SNP-based species trees.

Conclusions:

• Sequence capture of UCEs is a viable method for extracting genomic data from ancient museum specimens.
• SNP analysis from UCE data provides a robust method for phylogenetic reconstruction, mitigating contamination effects.
• Millions of historical natural history specimens can now be considered valuable genomic resources for evolutionary studies.