Incomplete taxon sampling is not a problem for phylogenetic inference

Michael S. Rosenberg, Sudhir Kumar

Research output: Contribution to journalArticle

225 Scopus citations

Abstract

A major issue in all data collection for molecular phylogenetics is taxon sampling, which refers to the use of data from only a small representative set of species for inferring higher-level evolutionary history. Insufficient taxon sampling is often cited as a significant source of error in phylogenetic studies, and consequently, acquisition of large data sets is advocated. To test this assertion, we have conducted computer simulation studies by using natural collections of evolutionary parameters - rates of evolution, species sampling, and gene lengths - determined from data available in genomic databases. A comparison of the true tree with trees constructed by using taxa subsamples and trees constructed by using all taxa shows that the amount of phylogenetic error per internal branch is similar; a result that holds true for the neighborjoining, minimum evolution, maximum parsimony, and maximum likelihood methods. Furthermore, our results show that even though trees inferred by using progressively larger taxa subsamples of a real data set become increasingly similar to trees inferred by using the full sample, all inferred trees are equidistant from the true tree in terms of phylogenetic error per internal branch. Our results suggest that longer sequences, rather than extensive sampling, will better improve the accuracy of phylogenetic inference.

Original languageEnglish (US)
Pages (from-to)10751-10756
Number of pages6
JournalProceedings of the National Academy of Sciences of the United States of America
Volume98
Issue number19
DOIs
StatePublished - Sep 11 2001

ASJC Scopus subject areas

  • General

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