In-solution Y-chromosome capture-enrichment on ancient DNA libraries

Area of Science:

• Ancient DNA (aDNA) research
• Genomics and Bioinformatics
• Human Evolutionary Studies

Background:

• Ancient biological samples often contain limited endogenous DNA, necessitating enrichment of specific genomic regions before sequencing.
• In-solution capture-enrichment techniques are employed to isolate target sequences and minimize microbial DNA contamination.
• This study focuses on a novel Y-chromosome capture-enrichment (YCC) method applied to Caribbean archaeological remains.

Observation:

• Six ancient samples exhibited low to very low initial human endogenous DNA content (0.05%–1.54%).
• Capture enrichment strategies, including YCC alone and whole-genome capture followed by YCC (WGC+YCC), dramatically increased the recovery of targeted Y-chromosome sequences (12-9549-fold).
• On-target sequence read percentages improved significantly, reaching up to 23.5% with YCC compared to 0.00003% pre-capture.

Findings:

• YCC and WGC+YCC methods substantially increase Y-DNA sequence yield compared to non-enriched libraries.
• The effectiveness of WGC+YCC was reduced in samples with higher endogenous DNA due to loss of complexity in sequential captures.
• Phylogenetically informative Y-chromosome regions were successfully recovered, enabling the assignment of Y-chromosome haplogroups and insights into paternal lineages.

Implications:

• This YCC method represents a significant advancement for aDNA sequencing, enabling efficient identification of paternal lineages with reduced sequencing effort.
• Experimental design should consider the initial endogenous DNA content of samples.
• Avoiding consecutive capture rounds is recommended to mitigate increased clonality and maintain data integrity.