Weighted Statistical Binning: Enabling Statistically Consistent Genome-Scale Phylogenetic Analyses
نویسندگان
چکیده
منابع مشابه
Weighted Statistical Binning: Enabling Statistically Consistent Genome-Scale Phylogenetic Analyses
Because biological processes can result in different loci having different evolutionary histories, species tree estimation requires multiple loci from across multiple genomes. While many processes can result in discord between gene trees and species trees, incomplete lineage sorting (ILS), modeled by the multi-species coalescent, is considered to be a dominant cause for gene tree heterogeneity....
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Frequencies of k-mers in sequences are sometimes used as a basis for inferring phylogenetic trees without first obtaining a multiple sequence alignment. We show that a standard approach of using the squared Euclidean distance between k-mer vectors to approximate a tree metric can be statistically inconsistent. To remedy this, we derive model-based distance corrections for orthologous sequences ...
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Paralogous genes from several families were found in four human chromosome regions (4p16, 5q33-35, 8p12-21, and 10q24-26), suggesting that their common ancestral region underwent several rounds of large-scale duplication. Searches in the EMBL databases, followed by phylogenetic analyses, showed that cognates (orthologs) of human duplicated genes can be found in other vertebrates, including bony...
متن کاملNaive binning improves phylogenomic analyses
MOTIVATION Species tree estimation in the presence of incomplete lineage sorting (ILS) is a major challenge for phylogenomic analysis. Although many methods have been developed for this problem, little is understood about the relative performance of these methods when estimated gene trees are poorly estimated, owing to inadequate phylogenetic signal. RESULTS We explored the performance of som...
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The heterogeneity of signals in the genomes of diverse organisms poses challenges for traditional phylogenetic analysis. Phylogenetic methods known as "species tree" methods have been proposed to directly address one important source of gene tree heterogeneity, namely the incomplete lineage sorting that occurs when evolving lineages radiate rapidly, resulting in a diversity of gene trees from a...
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ژورنال
عنوان ژورنال: PLOS ONE
سال: 2015
ISSN: 1932-6203
DOI: 10.1371/journal.pone.0129183