%0 Journal Article %A Swiel, Yaniv %A Kelso, Janet %A Peyrégne, Stéphane %+ Computational Ancient Genomics, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Max Planck Society Computational Ancient Genomics, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Max Planck Society Computational Ancient Genomics, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Max Planck Society %T Resolving the source of branch length variation in the Y chromosome phylogeny : %G eng %U https://hdl.handle.net/21.11116/0000-0010-6F95-A %R 10.1186/s13059-024-03468-4 %7 2025-01-06 %D 2025 %8 06.01.2025 %* Review method: peer-reviewed %X Abstract
Background: Genetic variation in the non-recombining part of the human Y chromo-
some has provided important insight into the paternal history of human populations.
However, a significant and yet unexplained branch length variation of Y chromo-
some lineages has been observed, notably amongst those that are highly diverged
from the human reference Y chromosome. Understanding the origin of this variation,
which has previously been attributed to changes in generation time, mutation rate,
or efficacy of selection, is important for accurately reconstructing human evolutionary
and demographic history.
Results: Here, we analyze Y chromosomes from present-day and ancient mod-
ern humans, as well as Neandertals, and show that branch length variation
amongst human Y chromosomes cannot solely be explained by differences in demo-
graphic or biological processes. Instead, reference bias results in mutations being
missed on Y chromosomes that are highly diverged from the reference used for align-
ment. We show that masking fast-evolving, highly divergent regions of the human Y
chromosome mitigates the effect of this bias and enables more accurate determina-
tion of branch lengths in the Y chromosome phylogeny.
Conclusion: We show that our approach allows us to estimate the age of ancient
samples from Y chromosome sequence data and provide updated estimates
for the time to the most recent common ancestor using the portion of the Y chromo-
some where the effect of reference bias is minimized. %K Reference bias, Ancient DNA, Y chromosome, Sequence alignment, Molecular dating, Mutation rate, Generation time %J Genome Biology %V 26 %N 1 %] 4 %@ 1474-760X