Four New Avian Mitochondrial Genomes Help Get to Basic Evolutionary Questions in the Late Cretaceous

Abstract

Good phylogenetic trees are required to test hypotheses about evolutionary processes. We report four new avian mitochondrial genomes, which together with an improved method of phylogenetic analysis for vertebrate mt genomes give results for three questions in avian evolution. The new mt genomes are: magpie goose (Anseranas semipalmata), an owl (morepork, Ninox novaeseelandiae); a basal passerine (rifleman, or New Zealand wren, Acanthisitta chloris); and a parrot (kakapo or owl-parrot, Strigops habroptilus). The magpie goose provides an important new calibration point for avian evolution because the well-studied Presbyornis fossils are on the lineage to ducks and geese, after the separation of the magpie goose. We find, as with other animal mitochondrial genomes, that RY-coding is helpful in adjusting for biases between pyrimidines and between purines. When RY-coding is used at third positions of the codon, the root occurs between paleognath and neognath birds (as expected from morphological and nuclear data). In addition, passerines form a relatively old group in Neoaves, and many modern avian lineages diverged during the Cretaceous. Although many aspects of the avian tree are stable, additional taxon sampling is required.

Phylogenomic evidence for multiple losses of flight in ratite birds

“…Although the traditional view is that the root lies between paleognath and neognath clades (12,27,46), early analyses of mtDNA placed the root either between passerines and all other birds (47) or within passerines (48,49), contradicting neognath monophyly. More sophisticated analyses (e.g., RY-coding) of mtDNA data strongly support the traditional rooting (22,23,50,51), unlike the early analyses. Some morphological studies also suggest nonmonophyly of paleognaths (8,45).…”

Mitochondrial genomes suggest that hexapods and crustaceans are mutually paraphyletic

“…Recent work on mammalian and avian mitochondrial genomes has shown that recoding of the third positions of codons from ACGT to purines (R) and pyrimidines (Y) can recover some signal from saturated or biased third position data Harrison et al 2004). Delsuc et al (2003) specifically advocate this approach for arthropod mitochondrial sequences.…”

“…Our analysis uses the complete set of mitochondrial protein-encoding genes. Similar approaches have been used successfully to address relationships among arthropods, mammals and birds (García-Machado et al 1999;Arnason et al 2002;Nardi et al 2003a;Harrison et al 2004;Negrisolo et al 2004). …”

Obtaining mtDNA genomes from next-generation transcriptome sequencing: A case study on the basal Passerida (Aves: Passeriformes) phylogeny

“…We constructed trees from the full nucleotide data and from a dataset where third-codon positions were coded as RY (purines coded as R and pyrimidines as Y). RY coding of the third codon position limits the influence of base composition heterogeneity among species and among-site rate variation on phylogenetic reconstruction (e.g., Delsuc et al, 2003), and has proven valuable for more accurate phylogenetic inference in previous studies of avian mtDNA genomes (Harrison et al, 2004;Gibb et al, 2007). For the Bayesian analyses we used the MRBAYES software (version 3.1, Ronquist and Huelsenbeck, 2003) applying the substitution model selected by JMODELTEST with a partition of the dataset according to the genes or to the codons positions.…”