Evolution of Modern Birds Revealed by Mitogenomics: Timing the Radiation and Origin of Major Orders

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.

Chromosomal Evolution in Psittaciformes. Revisited

“…Molecular genomic results seem to indicate an Eocene divergence of Psittaciformes in three basal lineages (Pacheco et al, 2011;Rheindt et al, 2014;Schweizer et al, 2010Schweizer et al, , 2011Tavares, Baker, Pereira, & Miyaki, 2006;Wright et al, 2008), which correspond to the most recent taxonomical classification of the order in three families; Strigopidae, Cacatuidae and Psittacidae (Winkler et al, 2015).…”

“…4; The question of when modern birds (Neornithes) first diversified has generated much debate among avian systematists. Fossil evidence generally supports a Cenozoic diversification; the Tertiary radiation hypothesis (Feduccia & Martin, 1976;Feduccia, 1995Feduccia, , 2003Olson, 1985), whereas the Gondwanaland origin hypothesis, or pre K-T radiation hypothesis, mainly supported by molecular data, favors an earlier diversification in the Cretaceous period (Brown & Toft, 1999;Cracraft, 1973Cracraft, , 2001Pacheco et al, 2011;Sibley & Ahlquist, 1990;Slack et al, 2006).…”

“…Early divergence of New Zealand Strigopidae parrots: kea (Nestor notabilis), kaka (Nestor meridionalis) (Tribe Nestorini) and kakapo (Strigops habroptilus) (Tribe Strigopini), has been (not unanimously) correlated to the Cretaceous separation of New Zealand from Gondwana 82-85 MYA (Pacheco et al, 2011;Rheindt et al, 2014;Schweizer et al, 2010Schweizer et al, , 2011Tavares et al, 2006;Wright et al, 2008), and it was cautiously assumed to be caused by vicariance (de Kloet & de Kloet, 2005;Wright et al, 2008), although alternative scenarios are contemplated (Pacheco et al, 2011;Rheindt et al, 2014;Schweizer et al, 2011;White et al, 2011).…”

“…Their basal diversification during the Oligocene, and ulterior radiation in early to middle Miocene has been well documented (Pacheco et al, 2011;Rheindt et al, 2014;Schweizer et al, 2011;White et al, 2011).…”

A falconid from the Late Miocene of northwestern China yields further evidence of transition in Late Neogene steppe communities

“…The 2 other well-preserved Miocene fossil Falconidae (Pediohierax and Thegornis) were scored from illustrations and descriptions in the literature (Becker 1987, Noriega et al 2011. Circus buffoni and Buteo lagopus (Accipitridae) were originally utilized as outgroup taxa in the analysis, on the basis of previous phylogenetic analyses of both molecular and morphological data (Pereira and Baker 2006, Livezey and Zusi 2007, Pacheco et al 2011. Other recent molecular analyses of relationships within Falconidae have also utilized accipitrid outgroups (Fuchs et al 2011(Fuchs et al , 2012.…”