Forsberg Roald, Drummond Alexei J, Hein Jotun
Bioinformatics Research Center, Department of Genetics and Ecology, University of Aarhus, Arhus, Denmark.
BMC Genet. 2005 Jun 16;6:35. doi: 10.1186/1471-2156-6-35.
Time-structured genetic samples are a valuable source of information in population genetics because they provide several correlated observations of the underlying evolutionary processes. In this paper we study basic properties of the genetic variation in time-structured samples as reflected in the genealogies relating individuals and the number of segregating sites observed. Our emphasis is on "measurably evolving populations" i.e. populations from which it is possible to obtain time-structured samples that span a significant interval of evolutionary time.
We use results from the coalescent process to derive properties of time-structured samples. In the first section we extend existing results to attain measures on coalescent trees relating time-structured samples. These include the expected time to a most recent common ancestor, the expected total branch length and the expected length of branches subtending only ancient individuals. The effect of different sampling schemes on the latter measure is studied. In the second section we study the special case where the full sample consists of a group of contemporary extant samples and a group of contemporary ancient samples. As regards this case, we present results and applications concerning the probability distribution of the number of segregating sites where a mutation is unique to the ancient individuals and the number of segregating sites where a mutation is shared between ancient and extant individuals.
The methodology and results presented here is of use to the design and interpretation of ancient DNA experiments. Furthermore, the results may be useful in further development of statistical tests of e.g. population dynamics and selection, which include temporal information.
时间结构化的基因样本是群体遗传学中宝贵的信息来源，因为它们提供了关于潜在进化过程的多个相关观察结果。在本文中，我们研究时间结构化样本中基因变异的基本特性，这些特性反映在个体之间的谱系关系以及观察到的分离位点数量上。我们重点关注“可测量进化的群体”，即能够获得跨越显著进化时间间隔的时间结构化样本的群体。
我们利用溯祖过程的结果来推导时间结构化样本的特性。在第一部分，我们扩展现有结果以获得关于与时间结构化样本相关的溯祖树的度量。这些度量包括到最近共同祖先的期望时间、期望总分支长度以及仅包含古代个体的分支的期望长度。研究了不同抽样方案对后一种度量的影响。在第二部分，我们研究全样本由一组当代现存样本和一组当代古代样本组成的特殊情况。针对这种情况，我们给出了关于古代个体特有的突变的分离位点数量以及古代个体和现存个体共有的突变的分离位点数量的概率分布的结果和应用。
本文提出的方法和结果可用于古代DNA实验的设计和解释。此外，这些结果可能有助于进一步发展例如包含时间信息的群体动态和选择的统计检验。
