% pubman genre = article
@article{item_3630025,
title = {{Resolving the source of branch length variation in the Y chromosome phylogeny}},
author = {Swiel, Yaniv and Kelso, Janet and Peyr{\'e}gne, St{\'e}phane},
language = {eng},
issn = {1474-760X},
doi = {10.1186/s13059-024-03468-4},
year = {2025},
abstract = {{Abstract{\textless}br{\textgreater}Background: Genetic variation in the non-recombining part of the human Y chromo-{\textless}br{\textgreater}some has provided important insight into the paternal history of human populations.{\textless}br{\textgreater}However, a significant and yet unexplained branch length variation of Y chromo-{\textless}br{\textgreater}some lineages has been observed, notably amongst those that are highly diverged{\textless}br{\textgreater}from the human reference Y chromosome. Understanding the origin of this variation,{\textless}br{\textgreater}which has previously been attributed to changes in generation time, mutation rate,{\textless}br{\textgreater}or efficacy of selection, is important for accurately reconstructing human evolutionary{\textless}br{\textgreater}and demographic history.{\textless}br{\textgreater}Results: Here, we analyze Y chromosomes from present-day and ancient mod-{\textless}br{\textgreater}ern humans, as well as Neandertals, and show that branch length variation{\textless}br{\textgreater}amongst human Y chromosomes cannot solely be explained by differences in demo-{\textless}br{\textgreater}graphic or biological processes. Instead, reference bias results in mutations being{\textless}br{\textgreater}missed on Y chromosomes that are highly diverged from the reference used for align-{\textless}br{\textgreater}ment. We show that masking fast-evolving, highly divergent regions of the human Y{\textless}br{\textgreater}chromosome mitigates the effect of this bias and enables more accurate determina-{\textless}br{\textgreater}tion of branch lengths in the Y chromosome phylogeny.{\textless}br{\textgreater}Conclusion: We show that our approach allows us to estimate the age of ancient{\textless}br{\textgreater}samples from Y chromosome sequence data and provide updated estimates{\textless}br{\textgreater}for the time to the most recent common ancestor using the portion of the Y chromo-{\textless}br{\textgreater}some where the effect of reference bias is minimized.}},
journal = {{Genome Biology}},
volume = {26},
number = {1},
eid = {4},
}