Phylogenetic bias in the likelihood method caused by missing data

• Activity Number: 521
• Type: Topic Contributed
• Date/Time: Wednesday, August 7, 2013 : 10:30 AM to 12:20 PM
• Sponsor: Biometrics Section
• Author(s): Xuhua Xia*+
• Companies: University of Ottawa
• Keywords: comparative genomics ; molecular phylogenetics ; molecular evolution ; genetics ; stochastic process ; likelihood ratio test

Abstract

Phylogenetic researchers often concatenate gene sequences to produce supermatrices in the hope that larger data sets will lead to better phylogenetic resolution. Almost all of these supermatrices contain a high proportion of missing data which could cause phylogenetic bias that has been little studied and little understood. Here I illustrate two types of such biases by using the likelihood method which features a statistically reasonable approach to handle missing data. The first type can be traced to the imperfect implementation of the likelihood method (e.g., DNAML in the PHYLIP package and BASEML in the PAML package). The second is due to missing data associated with differential evolution rates among different genes. Both types of bias tend to lead species sharing missing data to be grouped together. If the sequence concatenation leads to closely related species sharing the missing data, then these closely related species will tend to be grouped together to produce "robust" trees. However, such "robust" trees are purchased with illegal phylogenetic currency.