Whole mitochondrial genome sequences have been used in studies of animal phylogeny for two decades, and current technologies make them ever more available, but methods for their analysis are lagging and best practices have not been established. Most studies ignore variation in base composition and evolutionary rate within the mitogenome that can bias phylogenetic inference, or attempt to avoid it by excluding parts of the mitogenome from analysis. In contrast, partitioned analyses accommodate heterogeneity, without discarding data, by applying separate evolutionary models to differing portions of the mitogenome. To facilitate use of complete mitogenomic sequences in phylogenetics, we (1) suggest a set of categories for dividing mitogenomic datasets into subsets, (2) explore differences in evolutionary dynamics among those subsets, and (3) apply a method for combining data subsets with similar properties to produce effective and efficient partitioning schemes. We demonstrate these procedures with a case study, using the mitogenomes of species in the grackles and allies clade of New World blackbirds (Icteridae). We found that the most useful categories for partitioning were codon position, RNA secondary structure pairing, and the coding/noncoding distinction, and that a scheme with nine data groups outperformed all of the more complex alternatives (up to 44 data groups) that we tested. As hoped, we found that analyses using whole mitogenomic sequences yielded much better-resolved and more strongly-supported hypotheses of the phylogenetic history of that locus than did a conventional 2-kilobase sample (i.e. sequences of the cytochrome b and ND2 genes). Mitogenomes have much untapped potential for phylogenetics, especially of birds, a taxon for which they have been little exploited except in investigations of ordinal-level relationships.
Bibliographical noteFunding Information:
We thank J.C. Avise and D. Walker for purified mitochondrial samples of Agelaius and Molothrus, and the following institutions for maintaining and making available the other specimens that made this study possible: Academy of Natural Sciences of Drexel University, American Museum of Natural History, Field Museum of Natural History, Louisiana State University Museum of Natural Science, and the Marjorie Barrick Museum of Natural History. We thank S.A. Jansa and F.J. Cuthbert for comments on the manuscript. This study was supported in part by NSF DEB-0316092 to FKB and SML and by the University of Minnesota.
- Avian RNA structure
- Dataset partitioning
- Mitochondrial genome
- Phylogenetic analysis