生物
种内竞争
线粒体DNA
集合(抽象数据类型)
启发式
系统发育树
最小生成树
进化生物学
人口
最大节俭
溯祖理论
样品(材料)
系统发育学
系统发育网络
树(集合论)
算法
组合数学
成对比较
推论
遗传学
数学
计算机科学
人工智能
克莱德
基因
动物
社会学
人口学
化学
色谱法
程序设计语言
作者
Hans Jürgen Bandelt,Peter Forster,Arne Röhl
标识
DOI:10.1093/oxfordjournals.molbev.a026036
摘要
Reconstructing phylogenies from intraspecific data (such as human mitochondrial DNA variation) is often a challenging task because of large sample sizes and small genetic distances between individuals. The resulting multitude of plausible trees is best expressed by a network which displays alternative potential evolutionary paths in the form of cycles. We present a method ("median joining" [MJ]) for constructing networks from recombination-free population data that combines features of Kruskal's algorithm for finding minimum spanning trees by favoring short connections, and Farris's maximum-parsimony (MP) heuristic algorithm, which sequentially adds new vertices called "median vectors", except that our MJ method does not resolve ties. The MJ method is hence closely related to the earlier approach of Foulds, Hendy, and Penny for estimating MP trees but can be adjusted to the level of homoplasy by setting a parameter epsilon. Unlike our earlier reduced median (RM) network method, MJ is applicable to multistate characters (e.g., amino acid sequences). An additional feature is the speed of the implemented algorithm: a sample of 800 worldwide mtDNA hypervariable segment I sequences requires less than 3 h on a Pentium 120 PC. The MJ method is demonstrated on a Tibetan mitochondrial DNA RFLP data set.
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