# 编者信息 熊荣川 明湖实验室 xiongrongchuan@126.com http://blog.sciencenet.cn/u/Bearjazz Multifurcations A fact related to the persistence of ancestral haplotypes in the population is that a single ancestral haplotype will often give rise to multiple descendant haplotypes, yielding a haplotype tree with true multifurcations. Indeed, population genetics theory predicts that the older the haplotype, the more descendant haplotypes will be associated with it (Box 2). 多分叉 与种群中祖先单倍型的持续性相关的一个事实是，一个单一的祖先单倍型通常会产生多个后代单倍型，从而产生一个具有多岐分叉的单倍型树。事实上，群体遗传学理论预测，单倍型越老，其后代的单倍型越多（框注 2 ）。 Posada D , Crandall K A . Intraspecific gene genealogies: trees grafting into networks . Trends in Ecology and Evolution, 2001, 16(1):0-45.
# 编者信息 熊荣川 明湖实验室 xiongrongchuan@126.com http://blog.sciencenet.cn/u/Bearjazz Extant ancestral nodes In natural populations, most haplotypes in the gene pool exist as sets of multiple, identical copies that originated by DNA replication. When one of these copies mutates to a new haplotype, it is extremely unlikely that other copies of the ancestral haplotype also mutate or that all copies of the ancestral haplotype rapidly become extinct. Thus, the ancestral haplotypes are expected to persist in the population and to be sampled together with their descendants. Traditional phylogenetic methods, based on a bifurcating TREE, can detect and artificially represent persistent ancestral haplotypes as occupying a branch of zero length at the basal node of a cluster. However, this approach relies on modifying (e.g. by estimation of branch lengths) an inappropriate model – a bifurcating tree with all haplotypes occupying tips or terminal branches. 现存的祖先节点 在自然种群中，基因库中的大多数单倍型以多组拷贝形式存在，这些拷贝由 DNA 复制而来。当这些拷贝中的一个突变为一个新的单倍型时，祖先单倍型的其他拷贝极不可能也跟着突变，或者祖先单倍型的所有拷贝都很快灭绝。因此，祖先的单倍型将在种群中持续存在，并与后代一起被取样。传统的系统发育方法基于一个分叉树，可以检测并人工表示持续的祖先单倍型，即在一个簇的基部节点上占据一个零长度的分支。然而，这种方法依赖于设置（例如，通过估计分支长度）一个不合适的模型，在这一分叉树模型中，所有单倍型都占据末梢或末端分支。 Posada D , Crandall K A . Intraspecific gene genealogies: trees grafting into networks . Trends in Ecology and Evolution, 2001, 16(1):0-45.
# 编者信息 熊荣川 明湖实验室 xiongrongchuan@126.com http://blog.sciencenet.cn/u/Bearjazz The interest of ancestral segregating haplotypes is multiple: Regional association mapping studies can be performed in order to detect causative variants related to quantitative animal traits of interest , thus providing greater power than simple SNP-based genome-wide association analyses when LD is extensive . Furthermore, the study of the frequency distribution of ancestral segregating haplotypes provides information about population dynamics such as bottlenecks and adaptation . Ancestral haplotype frequencies are expected to vary due to perturbations in the population, leading to a potential deficit of some haplotypes after moderate bottlenecks and/or to unusual high frequency of specific haplotypes in certain sub-populations due to genetic drift and/or selection. Selective sweeps resulting from recent intensive selection lead to extended LD patterns and long highly frequent haplotypes , whereas old selection is expected to lead to shorter haplotypes as a consequence of recombination breaking the original blocks over the generations. Moreover, additional genomic characteristics such as recombination hotspots can also be detected , as these genomic regions show a higher haplotype variation than expected under neutral theory. 分离祖先单倍型的好处是多方面的：可以进行区域关联映射研究，以检测与特定动物量化特征相关的变异 ，从而在 LD （连锁不平衡）广泛存在时比简单的基于单核苷酸多态性的全基因组关联分析提供更大的力量 。此外，研究祖先分离单倍型的频率分布提供了有关种群动态的信息，如瓶颈和适应 。由于种群的扰动，祖先的单倍型频率预计会发生变化，导致中度瓶颈后某些单倍型的潜在缺失 和 / 或由于遗传漂变和 / 或选择导致某些亚种群中特定单倍型的异常高频率。由于最近的密集选择所导致的选择清除作用导致较长的连锁不平衡以及长且高频的单倍型 ，而时间较远的选择作用由于重组破坏了最初的基因块，预计将导致较短的单倍型。此外，还可以检测到其他的基因组特征，如重组热点 ，因为这些基因组区域显示出比中性理论预期的更高的单倍型变异。 Sanchez-Molano E , Tsiokos D , Chatziplis D , et al. A practical approach to detect ancestral haplotypes in livestock populations . BMC Genetics, 2016, 17(1):91.
# 编者信息 熊荣川 明湖实验室 xiongrongchuan@126.com http://blog.sciencenet.cn/u/Bearjazz In a haplotype network, how to determine which one is the root or where is the origin of the spp. and where does it invaded from. Coalescent theory predicts that ancestral haplotypes will be the haplotypes most frequently sampled. They are usually more broadly distributed geographically, and more likely to have a larger number of connections or descendant nodes/haplotypes. If I recall correctly, TCS calculates the haplotype that has the highest outgroup probability (potentially the most ancestral haplotype) and displays it as a square, whereas other haplotypes are displayed as ovals. Regarding from where the species invaded: Additional geographic, molecular dating, and natural history data would be helpful in determining the answer to that question. You might consider the geographic locality/region of the haplotype with the highest outgroup probability. if that haplotype is concentrated in a certain geographic area, it may indicate a glacial refugium or point of invasion. This would depend on the scale of your sampling, mobility of organism, etc. 在一个单倍型网络中，如何确定哪一个单倍型是根，或者物种的起源在哪里，以及它从哪里入侵。 根据溯祖理论预测，祖先的单倍型将是最常被抽样到的单倍型。它们通常在地理上分布更广，并具具有更多的连接或后代节点 / 单倍型。如果我记得正确的话， TCS 计算出具有最高外群（连接）概率的单倍型（可能是最原始的单倍型），并将其显示为一个正方形，而其他单倍型则显示为椭圆形。 关于物种入侵的来源： 额外的地理、分子年代测定和自然历史数据将有助于确定这个问题的答案。您可以考虑具有最高的外群概率单倍型的地理位置 / 区域。如果这种单倍型集中在某个地理区域，可能表明是冰川避难所或入侵点。这将取决于你的取样规模、生物体的流动性等。 https://www.researchgate.net/post/How_do_I_explain_the_haplotype_network_in_population_genetics
标签: 祖先单倍型
