The Behavior of Admixed Populations in Neighbor-Joining Inference of Population Trees
The Behavior of Admixed Populations in Neighbor-Joining Inference of Population Trees
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种群树邻接推理中混合种群的行为
DOI：
10.1142/9789814447973_0027
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发表时间：
2012
影响因子：
--
通讯作者：
N. Rosenberg
中科院分区：
文献类型：
--
作者：
N. Kopelman;L. Stone;O. Gascuel;N. Rosenberg
邻居连接是构建进化树最常用的方法之一。这种来自系统发育学的方法经常被用在种群遗传学中，根据等位基因频率获得的距离矩阵被用来产生树形式的种群关系表示。在系统发育学中，邻居连接的效用部分源于这样一个结果：对于一类距离矩阵，包括那些相加的或类似树的距离矩阵，通过将连接树中分类群对的边上的权重相加来获得成对距离--应用邻居连接恰好恢复潜在的树。然而，对于一个物种内的种群，迁徙和混合可以产生比从多物种环境中典型的分叉树获得的距离矩阵更复杂的过程。混合种群--从最近分离的种群混合而来的种群--被观察到位于推断的邻接树的中心，短的外部分支出现在连接其源种群的路径上。在这里，我们使用一个简单的模型，从数学上探讨了邻居加入下的混合种群的行为。我们证明了在相加距离矩阵的情况下，两个源种群之间的混合种群必然位于两个源种群之间的路径上。放松可加性要求，我们研究了最小的非平凡情况-四个种群，其中一个混合在其他三个中的两个之间-表明在其中一个与混合种群合并之前，两个源种群永远不会彼此合并。此外，在构建的树上，混合种群和任一源种群之间的距离总是小于源种群之间的距离，并且混合种群的外部分支总是与连接两个源种群的路径关联。我们定义了三个性质，它们适用于四个分类群，并且我们的假设在更一般的条件下得到满足：聚集的先行性、距离的中间性和路径长度的中间性。我们的发现可以帮助解释邻接树与混合群体的关系，并为在人类种群中观察到的树的模式提供解释。
Neighbor-joining is one of the most widely used methods for constructing evolutionary trees. This approach from phylogenetics is often employed in population genetics, where distance matrices obtained from allele frequencies are used to produce a representation of population relationships in the form of a tree. In phylogenetics, the utility of neighbor-joining derives partly from a result that for a class of distance matrices including those that are additive or tree-like-generated by summing weights over the edges connecting pairs of taxa in a tree to obtain pairwise distances-application of neighbor-joining recovers exactly the underlying tree. For populations within a species, however, migration and admixture can produce distance matrices that reflect more complex processes than those obtained from the bifurcating trees typical in the multispecies context. Admixed populations-populations descended from recent mixture of groups that have long been separated-have been observed to be located centrally in inferred neighbor-joining trees, with short external branches incident to the path connecting their source populations. Here, using a simple model, we explore mathematically the behavior of an admixed population under neighbor-joining. We show that with an additive distance matrix, a population admixed among two source populations necessarily lies on the path between the sources. Relaxing the additivity requirement, we examine the smallest nontrivial case-four populations, one of which is admixed between two of the other three-showing that the two source populations never merge with each other before one of them merges with the admixed population. Furthermore, the distance on the constructed tree between the admixed population and either source population is always smaller than the distance between the source populations, and the external branch for the admixed population is always incident to the path connecting the sources. We define three properties that hold for four taxa and that we hypothesize are satisfied under more general conditions: antecedence of clustering, intermediacy of distances, and intermediacy of path lengths. Our findings can inform interpretations of neighbor-joining trees with admixed groups, and they provide an explanation for patterns observed in trees of human populations.
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DOI：
10.1073/pnas.88.3.839
发表时间：
1991-02-01
影响因子：
11.1
作者：
BOWCOCK, AM;KIDD, JR;CAVALLISFORZA, LL
通讯作者：
CAVALLISFORZA, LL
影响因子：
9.8
作者：
Atzmon, Gil;Hao, Li;Ostrer, Harry
通讯作者：
Ostrer, Harry
影响因子：
9.8
作者：
Mountain, JL;CavalliSforza, LL
通讯作者：
CavalliSforza, LL
对澳大利亚人、日本人和巴布亚新几内亚人测试的 79 种 DNA 多态性与其他五个人群的 DNA 多态性进行了比较。
DOI：
--
发表时间：
1994
期刊：
Gene geography : a computerized bulletin on human gene frequencies
影响因子：
--
作者：
Lin,AA;Hebert,JM;Mountain,JL;Cavalli-Sforza,LL
通讯作者：
Cavalli-Sforza,LL
现代人类的进化：核 DNA 多态性的证据。
DOI：
10.1098/rstb.1992.0093
发表时间：
1992
期刊：
Philosophical transactions of the Royal Society of London. Series B, Biological sciences
影响因子：
--
作者：
Mountain,JL;Lin,AA;Bowcock,AM;Cavalli-Sforza,LL
通讯作者：
Cavalli-Sforza,LL