Introducing the Y-chromosomal Ancestral-like Reference Sequence—Improving the Capture of Human Evolutionary Information
Zehra Köksal, Annina Preussner, Jaakko Leinonen et al.
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Abstract
Summary of the research findings
The authors present Y-ARS, a Y-chromosomal ancestral-like reference sequence constructed by inferring ancestral alleles using a weighted maximum parsimony approach applied to diverse human and primate Y sequences. They benchmarked Y-ARS by aligning 40 short-read Y chromosome samples from major haplogroups to Y-ARS and to existing references (GRCh37, GRCh38, T2T-CHM13). Y-ARS produced the most consistent and highest number of SNPs per sample and called only evolutionarily derived alleles, whereas existing references yielded fewer variants and a substantial fraction of called SNPs that were ancestral relative to the species' MRCA. The paper also provides polaryzer, a tool to annotate variants as ancestral or derived in pre-aligned Y chromosome data, and makes the Y-ARS resource available for evolutionary analyses.
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