Introducing the Y chromosome ancestral reference sequence - Improving the capture of human evolutionary information

Abstract

Reference sequences are essential for reproducible genetic analyses but are often chosen without regard to evolutionary relevance within the analyzed species. The human Y chromosome (chrY) is widely used in evolutionary studies, yet current references represent evolutionarily young sequences, which can lead to misleading variant calling. To address this issue, we constructed a Y-chromosomal ancestral-like reference sequence (Y-ARS) to improve the detection of evolutionarily informative variants on the Y chromosome. The Y-ARS was constructed by applying a weighted maximum parsimony approach to human and primate Y chromosome sequences. To benchmark the performance of the Y-ARS, 40 chrY short-read sequences from diverse haplogroups were aligned to Y-ARS and existing references (GRCh37, GRCh38, and T2T-CHM13). Overall, the Y-ARS yielded the highest and most consistent number of SNPs per sample (mean=1197; SD=105), while other references yielded on average fewer variants (mean=866-968) and showed greater variability across samples (SD=457-531) depending on their phylogenetic distance from the reference. Additionally, alignments to the Y-ARS resulted in calling solely SNPs with evolutionarily derived alleles, while alignments to other references resulted in calling on average 44% SNPs with ancestral alleles. This study demonstrates how the existing reference sequences fail to capture the full range of evolutionary information on the chrY. The Y-ARS improves capturing evolutionary information on the chrY, making it a valuable resource for various evolutionary applications, such as TMRCA estimations and phylogenetic analyses. Finally, alongside the Y-ARS, we provide a publicly available tool, polaryzer, to annotate variants as ancestral or derived in pre-aligned chrY data. Significance statementUsing current reference sequences results in calling genetic variants without information on whether the variant is ancestral or arose later in the species history, which is of interest for evolutionary studies. Here, we tackle this problem for the human Y chromosome by introducing the Y-chromosomal ancestral-like reference sequence, Y-ARS. The Y-ARS overcomes this issue by calling only evolutionarily derived variants on the Y chromosome in a reproducible way, which can directly be used for various downstream analyses in evolutionary genetics.