A Phylogenomic Study of Birds Reveals Their Evolutionary History

@article{Hackett2008APS,
  title={A Phylogenomic Study of Birds Reveals Their Evolutionary History},
  author={Shannon J. Hackett and Rebecca T. Kimball and Sushma Reddy and Rauri C. K. Bowie and Edward L. Braun and Michael J. Braun and Jena L. Chojnowski and W. Andrew Cox and Kin‐Lan Han and John S. Harshman and Christopher J. Huddleston and Ben D. Marks and Kathleen J. Miglia and William S. Moore and Frederick H. Sheldon and David W. Steadman and Christopher C. Witt and Tamaki Yuri},
  journal={Science},
  year={2008},
  volume={320},
  pages={1763 - 1768}
}
Deep avian evolutionary relationships have been difficult to resolve as a result of a putative explosive radiation. Our 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. We documented well-supported, previously unrecognized interordinal relationships (such as a sister relationship between passerines and… 
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1,739 Citations

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References

SHOWING 1-10 OF 55 REFERENCES
PARALLEL RADIATIONS IN THE PRIMARY CLADES OF BIRDS
TLDR
Examination of intron 7 of the β-fibrinogen gene in the most taxonomically inclusive survey of DNA sequences of nonpasserine bird families and orders to date suggests that Neoaves consist of two sister clades with ecological parallelisms comparable to those found between marsupial and placental mammals.
More taxa, more characters: the hoatzin problem is still unresolved.
TLDR
The potential of a moderately sized mtDNA data set, supplemented with data from a nuclear intron, to resolve relationships among avian orders is explored and a basal split between Galloanserae and Neoaves within Neognathae and monophyly of both Galliformes and Anseriformes is supported.
Interordinal relationships of birds and other reptiles based on whole mitochondrial genomes.
TLDR
Support is found for a sister relationship between turtles and a bird/crocodilian clade, and for rejecting both the Haemothermia hypothesis and the placement of turtles as basal within the phylogenetic tree for amniote animals.
BIRDS IN A BUSH: FIVE GENES INDICATE EXPLOSIVE EVOLUTION OF AVIAN ORDERS
  • S. Poe, A. Chubb
  • Biology
    Evolution; international journal of organic evolution
  • 2004
TLDR
The evidence of extremely short branches for interordinal relationships across independent gene trees and topological incongruence among gene trees suggests that the bird tree includes essentially simultaneous radiation of multiple lineages, explaining why a robust phylogeny of birds has not been produced despite much effort on the part of avian systematists.
Strong mitochondrial DNA support for a Cretaceous origin of modern avian lineages
TLDR
This work fails to reconcile molecular genetic divergence time estimates with dates taken from the fossil record, but finds strong support for an ancient origin of modern bird lineages, with many extant orders and families arising in the mid-Cretaceous, consistent with previous molecular estimates.
Mammalian phylogenomics comes of age.
Examining Basal avian divergences with mitochondrial sequences: model complexity, taxon sampling, and sequence length.
TLDR
The conclusions of several recent studies using complete mitochondrial genome sequences from birds have suggested that the passeriforms are one of the most ancient groups of extant birds and that the paleognaths are derived.
Phylogenomics and the reconstruction of the tree of life
TLDR
This work has demonstrated the power of the phylogenomics approach, which has the potential to provide answers to several fundamental evolutionary questions, but challenges for the future have also been revealed.
Explosive Evolution in Tertiary Birds and Mammals
The traditional view of avian evolution over the past century is that of sluggish gradualism, in which many living orders of birds are thought to have originated from the mid-Cretaceous or so (1),…
Higher-order phylogeny of modern birds (Theropoda, Aves: Neornithes) based on comparative anatomy. II. Analysis and discussion
TLDR
A phylogenetic (cladistic) analysis of 150 taxa of Neornithes, including exemplars from all non-passeriform families, and subordinal representatives of Passeriformes, confirmed the topology among outgroup Theropoda and achieved robust resolution at virtually all levels of the NeornIthes.
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