Properties of 2-locus genealogies and linkage disequilibrium in temporally structured samples.
Properties of 2-locus genealogies and linkage disequilibrium in temporally structured samples.
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DOI：
10.1093/genetics/iyac038
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发表时间：
2022-05-05
期刊：
影响因子：
3.3
通讯作者：
Novembre, John
中科院分区：
文献类型：
--
作者：
Biddanda, Arjun;Steinrucken, Matthias;Novembre, John
考古遗传学是革命性的，揭示了对人口历史和最近积极选择的见解。然而，迄今为止的大多数研究都忽略了不同位点遗传变异的非随机关联（即连锁不平衡）。这可能部分是因为不同时期样品中连锁不平衡的基本特性仍然没有得到很好的理解。在这里，我们得出了在时间分层采样模型下单倍型变异汇总统计的几个结果：（1）在具有和不具有严格群体连续性的模型中，时间交错样本（）之间观察到的成对差异数量之间的相关性； （2）古代和现代样本之间连锁不平衡系数D的乘积，它是现代和古代样本之间单倍型相似性的度量； (3) Li 和 Stephens 单倍型复制模型中的预期转换率。后者对古代样本与现代参考面板的基因型估算和定相具有影响。总体而言，这些结果提供了单倍型模式如何受样本年龄、重组率和群体规模影响的特征。我们期望这些结果将有助于指导对古代和现代样本的单倍型数据的解释和分析。
Archeogenetics has been revolutionary, revealing insights into demographic history and recent positive selection. However, most studies to date have ignored the nonrandom association of genetic variants at different loci (i.e. linkage disequilibrium). This may be in part because basic properties of linkage disequilibrium in samples from different times are still not well understood. Here, we derive several results for summary statistics of haplotypic variation under a model with time-stratified sampling: (1) The correlation between the number of pairwise differences observed between time-staggered samples () in models with and without strict population continuity; (2) The product of the linkage disequilibrium coefficient, D, between ancient and modern samples, which is a measure of haplotypic similarity between modern and ancient samples; and (3) The expected switch rate in the Li and Stephens haplotype copying model. The latter has implications for genotype imputation and phasing in ancient samples with modern reference panels. Overall, these results provide a characterization of how haplotype patterns are affected by sample age, recombination rates, and population sizes. We expect these results will help guide the interpretation and analysis of haplotype data from ancient and modern samples.
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影响因子：
4.3
作者：
Kelleher J;Etheridge AM;McVean G
通讯作者：
McVean G
影响因子：
9.8
作者：
Browning, Sharon R.;Browning, Brian L.
通讯作者：
Browning, Brian L.
影响因子：
5.4
作者：
HILL W G;ROBERTSON A
通讯作者：
ROBERTSON A
DOI：
10.1007/978-0-387-78168-6_1
发表时间：
2008-01-01
期刊：
PROBABILITY MODELS FOR DNA SEQUENCE EVOLUTION, SECOND EDITION
影响因子：
--
作者：
Durrett, Richard
通讯作者：
Durrett, Richard
影响因子：
2.8
作者：
Fenner, JN
通讯作者：
Fenner, JN