Is there a universal mtDNA clock for birds?

Garcı́a-Moreno, Jaime

doi:10.1111/j.0908-8857.2004.03316.x

Cited by 119 publications

(101 citation statements)

References 40 publications

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“…Though confidence intervals of all age estimates are relatively narrow, age dating based on phylogenetic trees is highly controversial and affected by a variety of parameters (review García-Moreno 2004;Lovette 2004;Päckert et al 2006Päckert et al , 2007. We furthermore stress that the calibration based on single gene trees as applied here does not take into account conflicting genealogical patterns as probably expected from a multi-locus approach nor that coalescence times inferred from population divergence might strikingly differ from those estimates inferred from gene divergence (Vinceck et al 1997;Edwards and Beerli 2000;Martínez-Cruz and Godoy 2007).…”

Section: Phylogeny and Systematicsmentioning

confidence: 88%

The Taiwan Firecrest (Regulus goodfellowi) belongs to the Goldcrest assemblage (Regulus regulus s. l.): evidence from mitochondrial DNA and the territorial song of the Regulidae

Päckert

Martens²,

Severinghaus

2008

J Ornithol

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We evaluated the phylogenetic relationships of the Taiwan Firecrest or Flamecrest, Regulus goodfellowi, on the basis of two mitochondrial markers (cytochrome b, 16S rRNA) and territorial song. Genetic samples from eighteen subspecies of all currently accepted crest and kinglet species were available for comparison. In all molecular tree reconstructions it was clearly apparent the Taiwan endemic species was the sister species of all the palearctic Goldcrests (Regulus regulus) from Bayesian inference of phylogeny, although with weak bootstrap support and conflicting position in the ML and NJ trees. Genetic distances based on cyt-b sequences between R. goodfellowi and subspecies of R. regulus ranged between 6.1 and 8.2%. Two separate divergence time estimates dated the colonization of Taiwan to the mid to late Pliocene from 5-2 Mya. The high-pitched territorial songs of R. goodfellowi strongly resemble those of Sino-Himalayan Goldcrests (ssp. himalayensis, sikkimensis, and yunnanensis), but the terminal flourish typical of Goldcrests is invariable and only rarely included in songs of R. goodfellowi. Discriminant analysis of spectral and temporal characteristics separated the songs of the Southeast Asian populations from those of two other large clusters, the Canarian and Northwest Palearctic. Songs of R. goodfellowi were 100% correctly assigned and well distinguishable from Sino-Himalayan songs. Cluster analysis of Regulus songs strongly corroborated the sister group relationship of R. goodfellowi and R. regulus as reconstructed from concatenated mitochondrial sequence data. All results from molecular and acoustic analysis justify the species rank of the Taiwan endemic species and suggest that it is only distantly related to the firecrest clade (R. ignicapillus, R. madeirensis).

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Section: Phylogeny and Systematicsmentioning

confidence: 88%

The Taiwan Firecrest (Regulus goodfellowi) belongs to the Goldcrest assemblage (Regulus regulus s. l.): evidence from mitochondrial DNA and the territorial song of the Regulidae

Päckert

Martens²,

Severinghaus

2008

J Ornithol

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“…As dating based on the molecular clock is uncertain (e.g. García-Moreno, 2004;Lovette, 2004;Penny, 2005; but see Weir and Schluter, 2008, whose average rate we have adopted), we emphasize the relative ages of different clades more than the actual ages inferred. Guillaumet et al (2005Guillaumet et al ( , 2006Guillaumet et al ( , 2008 discovered two primary clades within Galerida cristata, which had reached reciprocal monophyly in mtDNA and showed evidence of strong reproductive isolation in their narrow contact zone in Morocco.…”

Section: Taxonomic Implications At the Species Levelmentioning

confidence: 99%

Multilocus phylogeny of the avian family Alaudidae (larks) reveals complex morphological evolution, non-monophyletic genera and hidden species diversity

Alström

Barnes

Olsson

et al. 2013

Molecular Phylogenetics and Evolution

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The Alaudidae (larks) is a large family of songbirds in the superfamily Sylvioidea. Larks are cosmopolitan, although species-level diversity is by far largest in Africa, followed by Eurasia, whereas Australasia and the New World have only one species each. The present study is the first comprehensive phylogeny of the Alaudidae. It includes 83.5% of all species and representatives from all recognised genera, and was based on two mitochondrial and three nuclear loci (in total 6.4 kbp, although not all loci were available for all species). In addition, a larger sample, comprising several subspecies of some polytypic species was analysed for one of the mitochondrial loci. There was generally good agreement in trees inferred from different loci, although some strongly supported incongruences were noted. The tree based on the concatenated multilocus data was overall well resolved and well supported by the data.We stress the importance of performing single gene as well as combined data analyses, as the latter may obscure significant incongruence behind strong nodal support values. The multilocus tree revealed many unpredicted relationships, including some non-monophyletic genera (Calandrella, Mirafra, Melanocorypha, Spizocorys). The tree based on the extended mitochondrial data set revealed several unexpected deep divergences between taxa presently treated as conspecific (e.g. within Ammomanes cinctura, Ammomanes deserti, Calandrella brachydactyla, Eremophila alpestris), as well as some shallow splits between currently recognised species (e.g. Certhilauda brevirostris-C. semitorquata-C. curvirostris; Calendulauda barlowi-C. erythrochlamys; Mirafra cantillans-M. javanica). Based on our results, we propose a revised generic classification, and comment on some species limits. We also comment on the extraordinary morphological adaptability in larks, which has resulted in numerous examples of parallel evolution (e.g.

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“…Below, we provide a comprehensive review of recent phylogeographic data presented for several lineages of Amazonian birds and evaluate to what extent they fit the landscape evolution scenario proposed by Rossetti et al (2005). When not stated otherwise, the translation of genetic distances into divergence times assumed a mtDNA substitution rate of 2% per million years (Klicka and Zink 1997;references below), which was the most frequently used calibration among the studies reviewed (see Garcia-Moreno (2004) and Lovette (2004a) for discussions on the problems associated with the 2% per million years' calibration).…”

Section: Amazonian Geology Revisited: Implications For Avian Historicmentioning

confidence: 99%

Avian gene trees, landscape evolution, and geology: towards a modern synthesis of Amazonian historical biogeography?

Aleixo

Rossetti

2007

J Ornithol

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ABSTRACT. As the number of phylogeographic studies on Amazonian birds increases, spatially and temporally different scenarios are gradually replacing previous interpretations of Amazonian historical biogeography. At the same time, recent studies have improved significantly our understanding of Amazonian geological history during the late Tertiary and Quaternary, two periods regarded as critical for the recent diversification of the Amazonian avifauna. The notion that geologically older and more stable areas of Amazonia (such as the Brazilian and Guianan shields) functioned as "species-pumps", whereas geologically more dynamic areas (such as the western Amazonian lowlands) mostly "captured" part of the diversity generated nearby, was supported by a recent phylogeographic study focusing on a species complex of the genus Xiphorhynchus (Dendrocolaptidae). Here, I review 14 recent additional molecular datasets to assess whether this historical scenario can be extended to other lineages of Amazonian birds as well. The reviewed datasets indicated, among other things, a clear dichotomy in the diversification histories of species associated with seasonally flooded versus upland forests, and those with high versus low dispersal capabilities. Many "core" lineages of upland species found nowadays in western Amazonia are clearly associated with more basal lineages from the Brazilian shield, Guianan shield, and the Andes, indicating a more recent history in this geologically dynamic region. On the other hand, lineages associated with seasonally flooded forests seem to have an ancient history in western Amazonia, apparently expanding over the geologically more stable areas only recently. Most sister taxa of the reviewed lineages exhibited levels of pairwise sequence divergence consistent with splitting events dating back to a time frame stretching from the late Miocene to the early Pleistocene (late Tertiary and early Quaternary periods), a period when significant physiographic and landscape changes took place in Amazonia. When interpreted together, all reviewed studies provide evidence that geology and landscape evolution are tightly linked with the timing and mode of differentiation of Amazonian birds.

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Is there a universal mtDNA clock for birds?

Cited by 119 publications

References 40 publications

The Taiwan Firecrest (Regulus goodfellowi) belongs to the Goldcrest assemblage (Regulus regulus s. l.): evidence from mitochondrial DNA and the territorial song of the Regulidae

The Taiwan Firecrest (Regulus goodfellowi) belongs to the Goldcrest assemblage (Regulus regulus s. l.): evidence from mitochondrial DNA and the territorial song of the Regulidae

Multilocus phylogeny of the avian family Alaudidae (larks) reveals complex morphological evolution, non-monophyletic genera and hidden species diversity

Avian gene trees, landscape evolution, and geology: towards a modern synthesis of Amazonian historical biogeography?

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