Data Requirement for Phylogenetic Inference from Multiple Loci: A New Distance Method

Gautam Dasarathy, Robert Nowak, Sebastien Roch

Research output: Contribution to journalArticle

22 Scopus citations

Abstract

We consider the problem of estimating the evolutionary history of a set of species (phylogeny or species tree) from several genes. It is known that the evolutionary history of individual genes (gene trees) might be topologically distinct from each other and from the underlying species tree, possibly confounding phylogenetic analysis. A further complication in practice is that one has to estimate gene trees from molecular sequences of finite length. We provide the first full data-requirement analysis of a species tree reconstruction method that takes into account estimation errors at the gene level. Under that criterion, we also devise a novel reconstruction algorithm that provably improves over all previous methods in a regime of interest.

Original languageEnglish (US)
Article number6917051
Pages (from-to)422-432
Number of pages11
JournalIEEE/ACM Transactions on Computational Biology and Bioinformatics
Volume12
Issue number2
DOIs
StatePublished - Mar 1 2015
Externally publishedYes

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Keywords

  • distance methods
  • incomplete lineage sorting
  • molecular clock
  • multispecies coalescent
  • phylogenetic inference
  • sample complexity

ASJC Scopus subject areas

  • Biotechnology
  • Genetics
  • Applied Mathematics

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