Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA.
Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA.
Genetics. 2022 May 5;221(1). doi: 10.1093/genetics/iyac038.
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 (πΔt) 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.
古遗传学具有革命性意义，揭示了人口历史和近期正选择的深入见解。然而，迄今为止的大多数研究都忽略了不同基因座（即连锁不平衡）的遗传变异之间的非随机关联。这可能部分是因为不同时期样本中连锁不平衡的基本性质仍未得到很好的理解。在这里，我们根据具有时间分层抽样的模型推导出了几种关于单倍型变异的摘要统计量的结果：（1）在具有和不具有严格人口连续性的模型中，时间交错样本之间观察到的成对差异（πΔt）的相关性；（2）古代和现代样本之间的连锁不平衡系数 D 的乘积，这是衡量现代和古代样本之间单倍型相似性的指标；（3）Li 和 Stephens 单倍型复制模型中的预期转换率。后者对具有现代参考面板的古代样本中的基因型推断和相位具有影响。总体而言，这些结果提供了对单倍型模式如何受样本年龄、重组率和种群大小影响的描述。我们希望这些结果将有助于指导对古代和现代样本中单倍型数据的解释和分析。
