Incomplete taxon sampling is not a problem for phylogenetic inference

A major issue in all data collection for molecular phylogenetics is taxon s ampling, which refers to the use of data from only a small representative s et of species for inferring higher-level evolutionary history. Insufficient taxon sampling is often cited as a significant source of error in phylogen etic 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, sp ecies sampling, and gene lengths-determined from data available in genomic databases. A comparison of the true tree with trees constructed by using ta xa 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 neighbor-joining, minimum evolution, maximum parsimony, and ma ximum likelihood methods. Furthermore, our results show that even though tr ees inferred by using progressively larger taxa subsamples of a real data s et become increasingly similar to trees inferred by using the full sample, all inferred trees are equidistant from the true tree in terms of phylogene tic error per internal branch. Our results suggest that longer sequences, r ather than extensive sampling, will better improve the accuracy of phylogen etic inference.