The Time to Most Recent Common Ancestor Does Not (Usually) Approximate the Date of Divergence

• Published in: PloS one Vol. 10; no. 8; p. e0128407
• Main Author: Pettengill, James B.
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 14.08.2015; Public Library of Science (PLoS)
• Subjects: Analysis; Base Sequence; Bioinformatics; Computer applications; Computer simulation; Deoxyribonucleic acid; Divergence; DNA; Empirical analysis; Estimation; Evolution; Genetic Speciation; Genomes; Humans; Nucleotide sequence; Phylogenetics; Phylogeny; Population; Public health; Salmonella; Salmonella enterica; Simulation; Speciation; Staphylococcus aureus; Staphylococcus infections; Taxa; United States > US
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0128407

With the advent of more sophisticated models and increase in computational power, an ever-growing amount of information can be extracted from DNA sequence data. In particular, recent advances have allowed researchers to estimate the date of historical events for a group of interest including time to most recent common ancestor (TMRCA), dates of specific nodes in a phylogeny, and the date of divergence or speciation date. Here I use coalescent simulations and re-analyze an empirical dataset to illustrate the importance of taxon sampling, in particular, on correctly estimating such dates. I show that TMRCA of representatives of a single taxon is often not the same as divergence date due to issues such as incomplete lineage sorting. Of critical importance is when estimating divergence or speciation dates a representative from a different taxonomic lineage must be included in the analysis. Without considering these issues, studies may incorrectly estimate the times at which historical events occurred, which has profound impacts within both research and applied (e.g., those related to public health) settings.