Although theoretical studies have suggested that base-compositional heterogeneity can adversely affect phylogenetic reconstruction, only a few empirical examples of this phenomenon, mostly among ancient lineages (with divergence dates >100 Mya), have been reported. In the course of our phylogenetic research on the New World marsupial family Didelphidae, we sequenced 2790 bp of the RAG1 exon from exemplar species of most extant genera. Phylogenetic analysis of these sequences recovered an anomalous node consisting of two clades previously shown to be distantly related based on analyses of other molecular data. These two clades show significantly increased GC content at RAG1 third codon positions, and the resulting convergence in base composition is strong enough to overwhelm phylogenetic signal from other genes (and morphology) in most analyses of concatenated datasets. This base-compositional convergence occurred relatively recently (over tens rather than hundreds of millions of years), and the affected gene region is still in a state of evolutionary disequilibrium. Both mutation rate and substitution rate are higher in GC-rich didelphid taxa, observations consistent with RAG1 sequences having experienced a higher rate of recombination in the convergent lineages.
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ACKNOWLEDGMENTS We particularly thank Keith Barker and George Barrowclough for helpful discussions and comments. As ever, we are grateful to the curators and collections support personnel of the many museums that provided tissue samples for this work. In particular, we thank Phil Myers and Steve Hinshaw (UMMZ), Bruce Patterson and Bill Stanley (FMNH), Mark Engstrom and Burton Lim (ROM), Jim Patton (MVZ), and Robert Baker (TTU). Andrew Simons, Robert Zink, Mark Hafner, Rod eric Page, Peter Foster, and two anonymous reviewers provided helpful comments on an earlier draft. The University of Minnesota Supercomputing Institute provided valuable computing time and resources. This study was supported by funds from the National Science Foundation (DEB-0211952) and the University of Minnesota.
- Biased gene conversion
- Nucleotide composition