Evolution of modern birds revealed by mitogenomics: timing the radiation and origin of major orders - PubMed (original) (raw)

Evolution of modern birds revealed by mitogenomics: timing the radiation and origin of major orders

M Andreína Pacheco et al. Mol Biol Evol. 2011 Jun.

Abstract

Mitochondrial (mt) genes and genomes are among the major sources of data for evolutionary studies in birds. This places mitogenomic studies in birds at the core of intense debates in avian evolutionary biology. Indeed, complete mt genomes are actively been used to unveil the phylogenetic relationships among major orders, whereas single genes (e.g., cytochrome c oxidase I [COX1]) are considered standard for species identification and defining species boundaries (DNA barcoding). In this investigation, we study the time of origin and evolutionary relationships among Neoaves orders using complete mt genomes. First, we were able to solve polytomies previously observed at the deep nodes of the Neoaves phylogeny by analyzing 80 mt genomes, including 17 new sequences reported in this investigation. As an example, we found evidence indicating that columbiforms and charadriforms are sister groups. Overall, our analyses indicate that by improving the taxonomic sampling, complete mt genomes can solve the evolutionary relationships among major bird groups. Second, we used our phylogenetic hypotheses to estimate the time of origin of major avian orders as a way to test if their diversification took place prior to the Cretaceous/Tertiary (K/T) boundary. Such timetrees were estimated using several molecular dating approaches and conservative calibration points. Whereas we found time estimates slightly younger than those reported by others, most of the major orders originated prior to the K/T boundary. Finally, we used our timetrees to estimate the rate of evolution of each mt gene. We found great variation on the mutation rates among mt genes and within different bird groups. COX1 was the gene with less variation among Neoaves orders and the one with the least amount of rate heterogeneity across lineages. Such findings support the choice of COX 1 among mt genes as target for developing DNA barcoding approaches in birds.

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Figures

F<sc>IG</sc>. 1.

FIG. 1.

Phylogenetic hypotheses derived from MrBayes using a GTR + gamma + I using the 15 partitions analysis. Hypothesis A, unrooted tree estimated using 23 × 106 generations sampled every 100 steps. Posterior probabilities were calculated on 90,000 trees discarding 60% of the sampled phylogenies (140,000) as burn-in. Hypothesis B, rooted tree estimated by using 20 × 106 generations discarding 60% of the sampled phylogenies (120,000) as burn-in.

F<sc>IG</sc>. 1.

FIG. 1.

Phylogenetic hypotheses derived from MrBayes using a GTR + gamma + I using the 15 partitions analysis. Hypothesis A, unrooted tree estimated using 23 × 106 generations sampled every 100 steps. Posterior probabilities were calculated on 90,000 trees discarding 60% of the sampled phylogenies (140,000) as burn-in. Hypothesis B, rooted tree estimated by using 20 × 106 generations discarding 60% of the sampled phylogenies (120,000) as burn-in.

F<sc>IG</sc>. 2.

FIG. 2.

Timetrees estimated using phylogenetic hypothesis B. Timetree (A) was obtained using MDT; the calibration point within the outgroup (Galloanserae) could not be used in this method. Timetree (B) was obtained using BEAST; it includes the calibration point within the outgroup (Galloanserae). Both methods yield very similar time estimates.

F<sc>IG</sc>. 2.

FIG. 2.

Timetrees estimated using phylogenetic hypothesis B. Timetree (A) was obtained using MDT; the calibration point within the outgroup (Galloanserae) could not be used in this method. Timetree (B) was obtained using BEAST; it includes the calibration point within the outgroup (Galloanserae). Both methods yield very similar time estimates.

F<sc>IG</sc>. 3.

FIG. 3.

Rates distributions across branches (internal and external) for COX1 (the slower evolving gene) and ND2 (the fastest evolving gene).

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