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解析Y染色体系统发育中分支长度变异的来源。

Resolving the source of branch length variation in the Y chromosome phylogeny.

作者信息

Swiel Yaniv, Kelso Janet, Peyrégne Stéphane

机构信息

Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.

出版信息

Genome Biol. 2025 Jan 6;26(1):4. doi: 10.1186/s13059-024-03468-4.

DOI:10.1186/s13059-024-03468-4
PMID:39762943
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11702058/
Abstract

BACKGROUND

Genetic variation in the non-recombining part of the human Y chromosome has provided important insight into the paternal history of human populations. However, a significant and yet unexplained branch length variation of Y chromosome 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 modern humans, as well as Neandertals, and show that branch length variation amongst human Y chromosomes cannot solely be explained by differences in demographic or biological processes. Instead, reference bias results in mutations being missed on Y chromosomes that are highly diverged from the reference used for alignment. We show that masking fast-evolving, highly divergent regions of the human Y chromosome mitigates the effect of this bias and enables more accurate determination 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 chromosome where the effect of reference bias is minimized.

摘要

背景

人类Y染色体非重组部分的基因变异为了解人类群体的父系历史提供了重要线索。然而，人们观察到Y染色体谱系存在显著且尚未得到解释的分支长度变异，特别是在那些与人类参考Y染色体高度分化的谱系中。了解这种变异的起源（此前曾归因于世代时间、突变率或选择效力的变化）对于准确重建人类进化和人口历史至关重要。

结果

在这里，我们分析了来自现代和古代现代人以及尼安德特人的Y染色体，并表明人类Y染色体之间的分支长度变异不能仅由人口统计学或生物学过程的差异来解释。相反，参考偏差导致在与用于比对的参考序列高度分化的Y染色体上遗漏突变。我们表明，掩盖人类Y染色体快速进化、高度分化的区域可减轻这种偏差的影响，并能更准确地确定Y染色体系统发育中的分支长度。

结论

我们表明，我们的方法使我们能够根据Y染色体序列数据估计古代样本的年龄，并使用参考偏差影响最小化的Y染色体部分，为最近共同祖先的时间提供更新的估计。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6b57/11702058/44ee97e3b57f/13059_2024_3468_Fig7_HTML.jpg
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https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6b57/11702058/44ee97e3b57f/13059_2024_3468_Fig7_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6b57/11702058/ac09150bbe0a/13059_2024_3468_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6b57/11702058/7c59ef7f090f/13059_2024_3468_Fig2_HTML.jpg
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https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6b57/11702058/2bf7de0b95d2/13059_2024_3468_Fig6_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6b57/11702058/44ee97e3b57f/13059_2024_3468_Fig7_HTML.jpg

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