General Information
Phylogeny and Classification of the Birds: A Study in Molecular Evolution (Hardcover)
by Charles G. Sibley, Jon E. Ahlquist

Phylogenetic relationships of birds (review)
Cracraft, J. et al. 2004.
Phylogenetic relationships among modern birds (Neornithes).
In Assembling the tree of life. Cracraft, J., Donoghue, M., (Eds). Oxford University Press, Oxford.

Ericson PGP, Irestedt M, Johansson US.
Evolution, biogeography, and patterns of diversification in passerine birds.

Diversification analysis
Jetz W, Thomas GH, Joy JB, Hartmann K, & Mooers AO (2012)
The global diversity of birds in space and time. Nature 491(7424):444-448.
=> All extent 9,9993 bird species were assigned to 158 clades identified using a backbone phylogeny (Hackett et al. 2008).

Phylogenetics analysis and divergence time estimation of birds
Prum RO, et al. (2015)
A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing. Nature.

Jarvis ED (2014)
Whole-genome analyses resolve early branches in the tree of life of modern birds. Science.

Haddrath O & Baker AJ (2012)
Multiple nuclear genes and retroposons support vicariance and dispersal of the palaeognaths, and an Early Cretaceous origin of modern birds. P Roy Soc B-Biol Sci 279(1747):4617-4625.

Brown, JW, JS Rest, J Garcia-Moreno, MD Sorenson, DP Mindell. 2008.
Strong mitochondrial DNA support for a Cretaceous origin of modern avian lineages. Bmc Biology 6:-.

Allan J. Baker, SeLrgio L. Pereira and Tara A. Paton
Phylogenetic relationshipsand divergence times of Charadriiformes genera:multigene evidence forthe Cretaceous origin ofat least 14 cladesof shorebirds
Biol. Lett. (2007) 3, 205-209

Ericson, P. G. P., C. L. Anderson, T. Britton, A. Elzanowski, U. S. Johansson, M. Kallersjo, J. I. Ohlson, T. J. Parsons, D. Zuccon, and G. Mayr. 2006. Diversification of Neoaves: integration of molecular sequence data and fossils. Biology Letters 2: 543-U541.

Brown, J. W., R. B. Payne, and D. P. Mindell. 2007. Nuclear DNA does not reconcile 'rocks' and 'clocks' in Neoaves: a comment on Ericson et al. Biology Letters 3: 257-259.

Turner, AH; Pol, D; Clarke, JA, et al. 2007.
A basal Dromaeosaurid and size evolution preceding avian flight
SCIENCE: 317, 1378-1381

Pereira SL, Baker AJ. 2006.
A mitogenomic timescale for birds detects variable phylogenetic rates of molecular evolution and refutes the standard molecular clock

Paton T, Haddrath O, Baker AJ. 2002.
Complete mitochondrial DNA genome sequences show that modern birds are not descended from transitional shorebirds.
Proc Biol Sci. 22: 839-846. [PubMed]

Phylogenetic relationships of birds
Pratt, R. C. et al., 2009.
Toward Resolving Deep Neoaves Phylogeny: Data, Signal Enhancement, and Priors. Mol. Biol. Evol 26: 313-326.

Hackett, S. J., et al. 2008.
A phylogenomic study of birds reveals their evolutionary history.
Science 320: 1763-1768.

Harrison GL, McLenachan PA, Phillips MJ, Slack KE, Cooper A, Penny D. 2004.
Four new avian mitochondrial genomes help get to basic evolutionary questions in the late cretaceous.
Mol Biol Evol. 2004 Jun;21(6):974-983. [PubMed]

Harlid A, Janke A, Arnason U. 1998.
The complete mitochondrial genome of Rhea americana and early avian divergences.
J Mol Evol. 46: 669-79. [PubMed]

Haddrath O, Baker AJ. 2001.
Complete mitochondrial DNA genome sequences of extinct birds: ratite phylogenetics and the vicariance biogeography hypothesis.
Proc Biol Sci. 268: 939-45.

Cooper A, Lalueza-Fox C, Anderson S, Rambaut A, Austin J, Ward R. 2001.
Complete mitochondrial genome sequences of two extinct moas clarify ratite evolution.
Nature. 409: 704-7.

Nishibori M, Tsudzuki M, Hayashi T, Yamamoto Y, Yasue H. 2002.
Complete nucleotide sequence of the Coturnix chinensis (blue-breasted quail) mitochondrial genome and a phylogenetic analysis with related species.
J Hered. 93: 439-44. [PubMed]

Divergence time estimation of galliforms
Pereira SL, Baker AJ
A molecular timescale for galliform birds accounting for uncertainty in time estimates and heterogeneity of rates of DNA substitutions across lineages and sites.

Divergence time estimation of Columbiformes
Pereira, S., K. Johnson, D. Clayton, and A. Baker. 2007. Mitochondrial and Nuclear DNA Sequences Support a Cretaceous Origin of Columbiformes and a Dispersal-Driven Radiation in the Paleogene. Syst. Biol. 56: 656|672.

Phylogenetic relationships and divergence times of penguins
Baker AJ, Pereira SL, Haddrath OP, et al.
Multiple gene evidence for expansion of extant penguins out of Antarctica due to global cooling.

Phylogenetic relationships and divergence times of parrots
Tavares ES, Baker AJ, Pereira SL, et al.
Phylogenetic relationships and historical biogeography of Neotropical parrots (Psittaciformes : Psittacidae : Arini) inferred from mitochondrial and nuclear DNA sequences
SYSTEMATIC BIOLOGY 55 (3): 454-470 JUN 2006

Phylogenetic relationships of Charadriiformes
Paton TA, Baker AJ, Groth JG, Barrowclough GF.
Related Articles, Links RAG-1 sequences resolve phylogenetic relationships within Charadriiform birds.
Mol Phylogenet Evol. 2003 Nov;29(2):268-78.