Resolving the root of the avian mitogenomic tree by breaking up long branches

Abstract

Incomplete taxon sampling has been a major problem in resolving the early divergences in birds. Five new mitochondrial genomes are reported here (brush-turkey, lyrebird, suboscine flycatcher, turkey vulture, and a gull) and three break up long branches that tended to attract the distant reptilian outgroup. These long branches were to galliforms, and to oscine and suboscine passeriformes. Breaking these long branches leaves the root, as inferred by maximum likelihood and Bayesian phylogenetic analyses, between paleognaths and neognaths. This means that morphological, nuclear, and mitochondrial data are now in agreement on the position of the root of the avian tree and we can, move on to other questions. An overview is then given of the deepest divisions in the mitogenomic tree inferred from complete mitochondrial genomes. The strict monophyly of both the galloanseres and the passerines is strongly supported, leaving the deep six-way split within Neoaves as the next major question for which resolution is still lacking. Incomplete taxon sampling was also a problem for Neoaves, and although some resolution is now available there are still problems because current phylogenetic methods still fail to account for real features of DNA sequence evolution.

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).…”

“…Furthermore, tinamous have a much higher mtDNA evolutionary rate than other paleognaths (11), so long-branch attraction uniting tinamous with the long branch leading to the outgroup is likely (as described above). Thus, we do not consider mtDNA to be in strong conflict with ratite polyphyly; indeed, the ambivalent signal evident in recent analyses (22,23) suggests more sophisticated analyses of mtDNA may ultimately support polyphyly.…”

“…DNA-DNA hybridization (14) required extrapolation of distances far beyond the useful range of the method. Early studies using mtDNA strongly supported ratite monophyly (9-11), but recent analyses using more sophisticated methods revealed that support for a ratite clade is weak (22,23). Avian mtDNA evolves rapidly and exhibits high among-site rate variation (10,11), making analyses sensitive to the evolutionary model and taxon sample used (23).…”

“…In fact, one study based solely on cranial characters, where convergence may be less likely, suggested that ratites are not monophyletic (13). These morphological results are provocative in light of recent sophisticated analyses of mitochondrial DNA (mtDNA) that show equivocal support for ratite monophyly (22,23). Given the profound implications of this group for Gondwanan biogeography and the evolution of flightlessness, determining the true phylogeny of ratites is a key question in avian systematics.…”

Continuous Miocene, Pliocene and Pleistocene Influences on Mitochondrial Diversification of the Capybara (Hydrochoerus Hydrochoeris; Hydrochoeridae, Rodentia): Incapacity to Determine Exclusive Hypotheses on the Origins of the Amazon and Orinoco Diversity for This Species

“…These genes were selected because we are doing a mitogenomics project with different mammals. Many mitogenomic analyses have shown to be extremely useful in determining phylogenetic relationships and in estimating divergence times in many different groups of organisms, such as birds [34,35] and mammals [36][37][38][39][40][41][42][43][44][45]. Mitochondrial gene trees are more precise in reconstructing the divergence history among species than other molecular markers [46].…”