Rxivist logo

Rxivist combines preprints from bioRxiv with data from Twitter to help you find the papers being discussed in your field. Currently indexing 65,428 bioRxiv papers from 289,803 authors.

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

By Diana I Cruz Dávalos, María A Nieves-Colón, Alexandra Sockell, G. David Poznik, Hannes Schroeder, Anne C. Stone, Carlos D Bustamante, Anna-Sapfo Malaspinas, María C Ávila-Arcos

Posted 22 Nov 2017
bioRxiv DOI: 10.1101/223214 (published DOI: 10.1186/s12864-018-4945-x)

Background: As most ancient biological samples have low levels of endogenous DNA, it is advantageous to enrich for specific genomic regions prior to sequencing. One approach - in-solution capture-enrichment - retrieves sequences of interest and reduces the fraction of microbial DNA. In this work, we implement a capture-enrichment approach targeting informative regions of the Y chromosome in six human archaeological remains excavated in the Caribbean and dated between 200 and 3,000 years BP. We compare the recovery rate of Y-chromosome capture (YCC) alone, whole-genome capture followed by YCC (WGC+Y) versus non-enriched (pre-capture) libraries. Results: We recovered 17-4,152 times more targeted unique Y-chromosome sequences after capture, where 0.01-6.2% (WGC+Y) and 0.01-23.5% (YCC) of the sequence reads were on-target, compared to 0.0002-0.004% pre-capture. In samples with endogenous DNA content greater than 0.1%, we found that WGC followed by YCC (WGC+Y) yields lower enrichment due to the loss of complexity in consecutive capture experiments, whereas in samples with lower endogenous content, WGC+Y yielded greater enrichment than YCC alone. Finally, increasing recovery of informative sites enabled us to assign Y-chromosome haplogroups to some of the archeological remains and gain insights about their paternal lineages and origins. Conclusions: We present to our knowledge the first in-solution capture-enrichment method targeting the human Y-chromosome in aDNA sequencing libraries. YCC and WGC+Y enrichments lead to an increase in the amount of Y-DNA sequences, as compared to libraries not enriched for the Y-chromosome. Our probe design effectively recovers regions of the Y-chromosome bearing phylogenetically informative sites, allowing us to identify paternal lineages with less sequencing than needed for pre-capture libraries. Finally, we recommend considering the endogenous content in the experimental design and avoiding consecutive rounds of capture for low-complexity libraries, as clonality increases considerably with each round.

Download data

  • Downloaded 499 times
  • Download rankings, all-time:
    • Site-wide: 20,377 out of 65,428
    • In genomics: 2,347 out of 4,463
  • Year to date:
    • Site-wide: 53,549 out of 65,428
  • Since beginning of last month:
    • Site-wide: 60,611 out of 65,428

Altmetric data

Downloads over time

Distribution of downloads per paper, site-wide

Sign up for the Rxivist weekly newsletter! (Click here for more details.)