Interordinal relationships of birds and other reptiles based on whole mitochondrial genomes

Several different groups of birds have been proposed as being the oldest or earliest diverging extant lineage within the avian phylogenetic tree, part icularly ratites (Struthioniformes), waterfowl (Anseriformes), and shorebir ds (Charadriiformes). Difficulty in resolving this issue stems from several factors, including the relatively rapid radiation of primary (ordinal) bir d lineages and the lack of characters from an extant outgroup for birds tha t is closely related to them by measure of time. To help resolve this quest ion, we have sequenced entire mitochondrial genomes for five birds (a rhea, a duck a falcon, and two perching birds), one crocodilian, and one turtle. Maximum parsimony and maximum likelihood analyses of these new sequences t ogether with published sequences (18 taxa total) yield the same optimal tre e topology. in which a perching bird (Passeriformes) is sister to all the o ther bird taxa. A basal position for waterfowl among the bird, study taxa i s rejected by maximum likelihood analyses However, neither the conventional view in which ratites (including rhea) are basal to other birds, nor tree topologies with falcon or chicken basal among birds could be rejected in th e same manner. In likelihood analyses of a subset of when birds, alligator, ;and turtle (9 taxa total), we find that increasing the number of parameter s in the model shifts the optimal topology from one with a perching bird ba sal among birds to the conventional view with ratites diverging basally; mo reover, likelihood scores for the two trees are not significantly different . Thus, although our largest set of taxa and characters supports a tree wit h perching birds diverging basally among birds, the position of this earlie st divergence among birds appears unstable. Our analyses indicate a sister relationship between a waterflow/chicken clade and ratites, relative to per ching birds and falcon We find support for a sister relationship between tu rtles and a bird/crocodilian dade, and for rejecting both the Haemothermia hypothesis (birds and mammals as sister taxa) and the placement of turtles as basal within the phylogenetic tree for amniote animals.