Base compositional bias and phylogenetic analyses: A test of the ”flying DNA” hypothesis

Phylogenetic methods can produce biased estimates of phylogeny when base composition varies along dif-ferent lineages. Pettigrew (1994, Curr. Biol. 4:277–280) has suggested that base composition bias is respon-sible for the apparent support for the monophyly of bats (Chiroptera: megabats and microbats) from sev-eral different nuclear and mitochondrial genes. Petti-grew’s ‘‘flying DNA’ ’ hypothesis makes several predic-tions: (1) that metabolic constraints associated with flying result in elevated levels of adenine and thymine throughout the genome of both megabats and micro-bats, (2) that the resulting base compositional bias in bats is sufficient to mislead phylogenetic methods and account for the support for bat monophyly from sev-eral nuclear and mitochondrial genes, and (3) tha