Leveraging ancient DNA to uncover signals of natural selection in Europe lost due to admixture or drift.

Autor: Pandey D; Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA., Harris M; Department of Computational Medicine, University of California, Los Angeles, CA, USA., Garud NR; Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA. ngarud@ucla.edu.; Department of Human Genetics, University of California, Los Angeles, CA, USA. ngarud@ucla.edu., Narasimhan VM; Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA. vagheesh@utexas.edu.; Department of Statistics and Data Science, The University of Texas at Austin, Austin, TX, USA. vagheesh@utexas.edu.
Jazyk: angličtina
Zdroj: Nature communications [Nat Commun] 2024 Nov 12; Vol. 15 (1), pp. 9772. Date of Electronic Publication: 2024 Nov 12.
DOI: 10.1038/s41467-024-53852-8
Abstrakt: Large ancient DNA (aDNA) studies offer the chance to examine genomic changes over time, providing direct insights into human evolution. While recent studies have used time-stratified aDNA for selection scans, most focus on single-locus methods. We conducted a multi-locus genotype scan on 708 samples spanning 7000 years of European history. We show that the G12 statistic, originally designed for unphased diploid data, can effectively detect selection in aDNA processed to create 'pseudo-haplotypes'. In simulations and at known positive control loci (e.g., lactase persistence), G12 outperforms the allele frequency-based selection statistic, SweepFinder2, previously used on aDNA. Applying our approach, we identified 14 candidate regions of selection across four time periods, with half the signals detectable only in the earliest period. Our findings suggest that selective events in European prehistory, including from the onset of animal domestication, have been obscured by neutral processes like genetic drift and demographic shifts such as admixture.
Competing Interests: Competing interests The authors declare no competing interests.
(© 2024. The Author(s).)
Databáze: MEDLINE
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