A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing

@article{Prum2015ACP,
  title={A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing},
  author={Richard O. Prum and Jacob S. Berv and Alex Dornburg and Daniel J. Field and Jeffrey P. Townsend and Emily Moriarty Lemmon and Alan R Lemmon},
  journal={Nature},
  year={2015},
  volume={526},
  pages={569-573}
}
Although reconstruction of the phylogeny of living birds has progressed tremendously in the last decade, the evolutionary history of Neoaves—a clade that encompasses nearly all living bird species—remains the greatest unresolved challenge in dinosaur systematics. Here we investigate avian phylogeny with an unprecedented scale of data: >390,000 bases of genomic sequence data from each of 198 species of living birds, representing all major avian lineages, and two crocodilian outgroups. Sequence… Expand
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References

SHOWING 1-10 OF 175 REFERENCES
A Phylogeny of Birds Based on Over 1,500 Loci Collected by Target Enrichment and High-Throughput Sequencing
TLDR
This phylogeny bolsters support for monophyletic waterbird and landbird clades and also strongly supports controversial results from previous studies, including the sister relationship between passerines and parrots and the non-monophyly of raptorial birds in the hawk and falcon families. Expand
Phylogeny and diversification of the largest avian radiation.
TLDR
The historical framework suggests multiple waves of passerine dispersal from Australasia into Eurasia, Africa, and the New World, commencing as early as the Eocene, essentially reversing the classical scenario of oscine biogeography. Expand
A mitogenomic timescale for birds detects variable phylogenetic rates of molecular evolution and refutes the standard molecular clock.
TLDR
The first comprehensive analysis of mitogenomic data of 48 vertebrates, including 35 birds, is performed to derive a Bayesian timescale for avian evolution and to estimate rates of DNA evolution, finding no support for the hypothesis that the molecular clock in birds "ticks" according to a constant rate of substitution per unit of mass-specific metabolic energy rather than per unitOf time, as recently suggested. Expand
THE FOSSIL RECORD AND EVOLUTION OF MOUSEBIRDS (AVES: COLIIFORMES)
TLDR
A review of all known fossil mousebirds and a new phylogenetic analysis suggest that the Lower Eocene Eocolius is the most basal member of clade Coliiformes, while the Lower–Middle Eocene Sandcoleidae form a basal clade with respect to all other known coliiforms. Expand
Whole-genome analyses resolve early branches in the tree of life of modern birds
TLDR
A genome-scale phylogenetic analysis of 48 species representing all orders of Neoaves recovered a highly resolved tree that confirms previously controversial sister or close relationships and identifies the first divergence in Neoaves, two groups the authors named Passerea and Columbea. Expand
Molecular Phylogenetics and the Diversification of Hummingbirds
TLDR
This work estimates the age of the crown-group hummingbird assemblage, investigates the timing and patterns of lineage accumulation for hummingbirds overall and regionally, and evaluates the role of Andean uplift in hummingbird speciation. Expand
A Phylogenomic Study of Birds Reveals Their Evolutionary History
TLDR
This study examined ∼32 kilobases of aligned nuclear DNA sequences from 19 independent loci for 169 species, representing all major extant groups, and recovered a robust phylogeny from a genome-wide signal supported by multiple analytical methods. Expand
Phylogeny, diversity, and classification of the Accipitridae based on DNA sequences of the RAG-1 exon
TLDR
DNA sequences from the large nuclear RAG-1 exon are used to investigate the phylogenetic relationships of the avian family Accipitridae and found strong support for a monophyletic clade comprising the secretarybird Sagittarius serpentarius, the osprey Pandion haliaetus, and the traditional accipitrids. Expand
Evolution of terrestrial birds in three continents: biogeography and parallel radiations
TLDR
The analysis showed that three reciprocally monophyletic groups of terrestrial birds have diversified in the Gondwanan land areas of Australia, South America and Africa, respectively. Expand
The phylogeny of the living and fossil Sphenisciformes (penguins)
TLDR
The results do not support an expansion of the Spheniscidae from a cooling Continental Antarctica, but instead suggest those species that currently breed in that area are the descendants of colonizers from the Subantarctic. Expand
...
1
2
3
4
5
...