The Phylogeny of Ratite Birds: Resolving Conflicts between Molecular and Morphological Data Sets

Lee, Krista; Feinstein, Julie; Cracraft, Joel

doi:10.1016/b978-012498315-1/50011-x

Cited by 80 publications

(112 citation statements)

References 27 publications

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“…At UP, a 1702 base pairs (bp) segment of the 16S rRNA gene was amplified using the primers L2313 and H4015 (Lee et al, 1997); an internal primer L2925 (Tieleman et al, 2003) was used for sequencing. For 16S the PCR protocol was identical to that for cytb, except for the modification of the primer annealing temperature (58°C, 30s).…”

Section: Dna Extraction and Sequencingmentioning

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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Section: Dna Extraction and Sequencingmentioning

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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“…Most recent studies have also strongly supported ratite monophyly (9)(10)(11)(12)14), suggesting a single loss of flight in their common ancestor. This puzzled biogeographers for more than a century, because ratites would be unable to achieve their current distribution on southern land masses if their common ancestor was flightless.…”

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confidence: 96%

“…DeBeer provided a developmental explanation for the similarities among ratites when he interpreted the paleognathous palate and other features of extant ratites as neotenic (7). Paleognath monophyly was questioned as late as the 1980s (8), but it has been confirmed by many recent morphological and molecular studies (9)(10)(11)(12)(13).…”

mentioning

confidence: 99%

Phylogenomic evidence for multiple losses of flight in ratite birds

Harshman

Braun

et al. 2008

Proc. Natl. Acad. Sci. U.S.A.

194

227

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Ratites (ostriches, emus, rheas, cassowaries, and kiwis) are large, flightless birds that have long fascinated biologists. Their current distribution on isolated southern land masses is believed to reflect the breakup of the paleocontinent of Gondwana. The prevailing view is that ratites are monophyletic, with the flighted tinamous as their sister group, suggesting a single loss of flight in the common ancestry of ratites. However, phylogenetic analyses of 20 unlinked nuclear genes reveal a genome-wide signal that unequivocally places tinamous within ratites, making ratites polyphyletic and suggesting multiple losses of flight. Phenomena that can mislead phylogenetic analyses, including long branch attraction, base compositional bias, discordance between gene trees and species trees, and sequence alignment errors, have been eliminated as explanations for this result. The most plausible hypothesis requires at least three losses of flight and explains the many morphological and behavioral similarities among ratites by parallel or convergent evolution. Finally, this phylogeny demands fundamental reconsideration of proposals that relate ratite evolution to continental drift.convergence ͉ flightlessness ͉ Paleognath ͉ homoplasy ͉ vicariance biogeography

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“…Ratites are a group of large flightless birds that lack a keel on their sternum, and include emu (Australia), cassowaries (Australia and New Guinea), rheas (South America), ostrich (Africa and formerly Asia), kiwis (New Zealand) and extinct moas (New Zealand) and elephant birds (Madagascar). Many studies using morphological and molecular data supported the monophyly of ratites and placed them sister to tinamous, although no consensus was achieved on relationships among ratites [1][2][3][4][5]. Their flightless condition and disjunct distribution on southern land masses led to a widely accepted biogeographic theory that their evolution and distribution was shaped by the break-up of Gondwana [1,3,5].…”

Section: Introductionmentioning

confidence: 99%

Multiple nuclear genes and retroposons support vicariance and dispersal of the palaeognaths, and an Early Cretaceous origin of modern birds

2012

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The origin and timing of the diversification of modern birds remains controversial, primarily because phylogenetic relationships are incompletely resolved and uncertainty persists in molecular estimates of lineage ages. Here, we present a species tree for the major palaeognath lineages using 27 nuclear genes and 27 archaic retroposon insertions. We show that rheas are sister to the kiwis, emu and cassowaries, and confirm ratite paraphyly because tinamous are sister to moas. Divergence dating using 10 genes with broader taxon sampling, including emu, cassowary, ostrich, five kiwis, two rheas, three tinamous, three extinct moas and 15 neognath lineages, suggests that three vicariant events and possibly two dispersals are required to explain their historical biogeography. The age of crown group birds was estimated at 131 Ma (95% highest posterior density 122-138 Ma), similar to previous molecular estimates. Problems associated with gene tree discordance and incomplete lineage sorting in birds will require much larger gene sets to increase species tree accuracy and improve error in divergence times. The relatively rapid branching within neoaves pre-dates the extinction of dinosaurs, suggesting that the genesis of the radiation within this diverse clade of birds was not in response to the Cretaceous-Paleogene extinction event.

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The Phylogeny of Ratite Birds: Resolving Conflicts between Molecular and Morphological Data Sets

Cited by 80 publications

References 27 publications

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

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

Phylogenomic evidence for multiple losses of flight in ratite birds

Multiple nuclear genes and retroposons support vicariance and dispersal of the palaeognaths, and an Early Cretaceous origin of modern birds

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