Accumulated Coalescence Rank and Excess Gene Count for Species Tree Inference
نویسندگان
چکیده
Proof: Maximum R′ G(x, y) includes λG(r) of the root r in G. Further, it should include the coalescence ranks of the internal nodes lying at the lowest levels of the either side of the root. For a height balanced complete binary gene tree, coalescence rank of each of the lowest level internal nodes is N (dlgNe 1) = N + 1 dlgNe. So, maximum R′ G(x, y) will twice include the values from (N + 1 dlgNe) to (N 1), and also include N , thus equaling 2× { N−1 ∑
منابع مشابه
From gene trees to species trees II: Species tree inference in the deep coalescence model
When gene copies are sampled from various species, the resulting gene tree might disagree with the containing species tree. The primary causes of gene tree and species tree discord include lineage sorting, horizontal gene transfer, and gene duplication and loss. Each of these events yields a different parsimony criterion for inferring the (containing) species tree from gene trees. With lineage ...
متن کاملMean deep coalescence cost under exchangeable probability distributions
We derive formulas for mean deep coalescence cost, for either a fixed species tree or a fixed gene tree, under probability distributions that satisfy the exchangeability property. We then apply the formulas to study mean deep coalescence cost under two commonly used exchangeable models—the uniform and Yule models. We find that mean deep coalescence cost, for either a fixed species tree or a fix...
متن کاملNon-hereditary Minimum Deep Coalescence trees
— One of the goals of phylogenetic research is to find the species tree describing the evolutionary history of a set of species. But the trees derived from geneti data with the help of tree inference methods are gene trees that need not coincide with the species tree. This can for example happen when so-called deep coalescence events take place. It is also known that species trees can differ fr...
متن کاملThe accuracy of species tree estimation under simulation: a comparison of methods.
Numerous simulation studies have investigated the accuracy of phylogenetic inference of gene trees under maximum parsimony, maximum likelihood, and Bayesian techniques. The relative accuracy of species tree inference methods under simulation has received less study. The number of analytical techniques available for inferring species trees is increasing rapidly, and in this paper, we compare the...
متن کاملRobustness to divergence time underestimation when inferring species trees from estimated gene trees.
To infer species trees from gene trees estimated from phylogenomic data sets, tractable methods are needed that can handle dozens to hundreds of loci. We examine several computationally efficient approaches-MP-EST, STAR, STEAC, STELLS, and STEM-for inferring species trees from gene trees estimated using maximum likelihood (ML) and Bayesian approaches. Among the methods examined, we found that t...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
عنوان ژورنال:
دوره شماره
صفحات -
تاریخ انتشار 2016