TY - JOUR
T1 - Incomplete taxon sampling is not a problem for phylogenetic inference
AU - Rosenberg, Michael S.
AU - Kumar, Sudhir
PY - 2001/9/11
Y1 - 2001/9/11
N2 - 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.
AB - 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.
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U2 - 10.1073/pnas.191248498
DO - 10.1073/pnas.191248498
M3 - Article
C2 - 11526218
AN - SCOPUS:0035845536
SN - 0027-8424
VL - 98
SP - 10751
EP - 10756
JO - Proceedings of the National Academy of Sciences of the United States of America
JF - Proceedings of the National Academy of Sciences of the United States of America
IS - 19
ER -