Higher phylogeny

Some 10,500 bird species are inhabiting the Earth today, but almost six hundred species have already gone extinct in historic times as a result of human activities, primarily due to deforestation and hunting (Sayol et al., 2020). 


The main radiations within Neognathae occurred around 65 mya, following the Chicxulub asteroid impact on the Yucatan peninsula in Mexico 66 mya, which sealed the demise of non-avian dinosaurs. 

 

Time-calibrated phylogenies, in which branch lengths are proportional to time, are usually referred to as chronograms or timetrees. The putative relationships among avian orders, which in birds are traditionally indicated by the suffix "iformes", are shown in the following timetree:

Order-level timetree of Aves according to Kuhl et al. (2021). Crown-group ages are indicated by blue lines. For orders that contain more than one family, crown group ages were derived from Kuhl et al. (2021, fig.3). Note that the clade name 'Passerea', which has been introduced by Jarvis et al. (2014), originally had a slightly different meaning and did not include Columbiformes, Mesitornithiformes, and Pterocliformes. 


References

Braun EL, and Kimball RT (2021), Data types and the phylogeny of Neoaves, Birds 2, 1-22. (pdf)

 

Burleigh JG, Kimball RT, and Braun EL (2015), Building the avian tree of life using a large-scale, sparse supermatrix, Mol. Phylogenet. Evol. 84, 53-63. (abstract)

 

Chen A, and Field DJ (2020)Phylogenetic definitions for Caprimulgimorphae (Yves) and major constituent clades under the International Code of  Phylogenetic Nomenclature, Vertebr. Zool. 70, 571-585. (pdf)

 

Claramunt S, and Cracraft J (2015), A new time tree reveals Earth history´s imprint on the evolution of modern birds, Sci. Adv. 2015, 1: e1501005. (pdf)

 

Cloutier A, Sackton TB, Grayson P, Clamp M, Baker WJ, and Edwards SV (2018) Whole-genome analyses resolve the phylogeny of flighless birds (Palaeognathae) in the presence of an empirical anomaly zone, BioRxiV(pdf)

 

Cracraft J. et al. (2015), Response to comment on „Whole-genome analyses resolve early branches in the tree of life of modern birds“, Science 349, 6255. (pdf)

 

Crouch NMA, Ramanauskas K, and Igic B (2019), Tip-dating and the origin of Telluraves, Mol. Phylogenet. Evol. 131, 55-63. (abstract)

 

de Quieroz K, Cantino PD, and Gauthier JA (Eds.) (2020), Phylonyms: a companion to the PhyloCode, CRC Press, Boca Raton, FL, USA

 

del HoyJ, Collar NJ, Christie DA, Elliott A, and Fishpool LDC (2014), Illustrated Checklist of the Birds of the World, volume I (Non-passerines), published by Lynx Edicions in association with BirdLife. (link)

 

Ericson PGP, Anderson CL, Britton T, Elzanowski A, Johansson US, Kallersjo M, Ohlson JI, Parsons TJ, Zuccon D, and Mayr G (2006), Diversification of Neoaves: integration of molecular sequence data and fossils, Biol. Lett. 2, 543-547. (pdf)

 

Field DJ, Berv JS, Hsiang AY, Lanfear R, Landis MJ, and Dornburg A (2019), Timing the extant avian radiation: the rise of modern birds, and the importance of modeling molecular rate variation, PeerJ Preprints. (pdf)

 

Field DJ, Benito J, Chen A, Jagt JWM, and Ksepka DT (2020), Late Cretaceous neornithine from Europe illuminates the origins of crown birds, Nature 579, 397-401. (abstract)

 

Gilbert PS, Wu J, Simon MW, Sinsheimer JS, and Alfaro ME (2019), Filtering nucleotide sites by phylogenetic signal to noise ratio increases confidence in the Neoaves phylogeny generated from ultraconserved elements, Mol. Phylogenet. Evol. 126, 116-128. (abstract)

 

Hackett SJ, Kimball RT, Reddy S, Bowie RCK, Braun EL, Braun MJ, Chojnowski JL, Cox WA, Han KL, Harshman J, Huddleston CJ, Marks BD, Miglia KJ, Moore WS, Sheldon FH, Steadman DW, Witt CC, and Yuri T (2008), A phylogenetic study of birds reveals their evolutionary history, Science 320, 1763-67. (abstract)

 

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Houde P, Braun EL, Narula N, Minjares U, and Mirarab S (2019), Phylogenetic signal of indels and the Neoavian radiation, Diversity 11, 108. (pdf)

 

Jarvis ED et al. (2014), Whole-genome analysis resolve early branches in the tree of life of modern birds, Science 346, 1320-31. (pdf)

 

Kimball RT, Oliveros CH, Wang N, White ND, Barker FK, Field DJ, Ksepka DT, Chesser RT, Moyle RG, Braun MJ, Brumfield RT, Faircloth BC, Smith BT, and Braun EL (2019), A phylogenomic supertree of birds, Diversity 11, 109. (pdf)

 

Ksepka DT, Stidham TA, and Williamson TE (2017), Early Paleocene landbird supports rapid phylogenetic and morphological diversification of crown birds after the K-Pg mass extinction, PNAS 114, 8047-52. (pdf)

 

Kuhl H, Frankl-Vilches C, Bakker A, Mayr G, Nikolaus G, Boerno ST, Klages S, Timmermann B, and Gahr M (2021), An unbiased molecular approach using  3'UTRs resolves the avian family-level tree of life, Mol. Biol. Evol. 38, 108-127. (pdf)

 

Mitchell KJ, Cooper A, and Phillips MJ (2015), Comment on "Whole-genome analyses resolve early branches in the tree of life of modern birds", Science 351. (pdf)

 

Prum RO, Berv JS, Dornburg A, Field DJ, Townsend JP, Lemmon EM, and Lemmon AR (2015), A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing, Nature 526, 569-57. (abstract)

 

Reddy S et al. (2017), Why do phylogenomic data sets yield conflicting trees? Data type influences the avian tree of life more than taxon sampling, Syst. Biol. 66, 857-879. (pdf)

 

Sayol F, Steinbauer MJ, Blackburn TM, Antonelli A, and Faurby S (2020), Anthropogenic extinctions conceal widespread flightlessness in birds. Sci. Adv. 6: eabb6095. (pdf)

 

Suh A, Smeds L, and Ellegren H (2015), The dynamics of incomplete lineage sorting across the ancient adaptive radiation of neoavian birds, PLoS Biology 13: e1002224. (pdf)

 

Suh A (2016), The phylogenetic forest of bird trees contains a hard polytomy at the root of Neoaves, Zool. Scr. 45, 50-62. (pdf)

 

Tamashiro RA, White ND, Braun MJ, Faircloth BC, Braun EL, and Kimball RT (2019), What are the roles of taxon sampling and model fit in tests of cyto-nuclear discordance using avian mitogenomic data?, Mol. Phylogenet. Evol. 130, 132-142. (abstract)

 

Vellekoop J, Sluijs A, Smit J, Schouten S, Weijers JWH, Sinninghe Dámste JS, and Brinkhuis H (2014), Rapid short-term cooling following the Chicxulub impact at the Cretaceous-Paleogene boundary, PNAS 111, 7537-41. (pdf)

 

Yuri T, Kimball RT, Harshman J, Bowie RCK, Braun MJ, Chojnowski JL, Han KL, Hackett SJ, Huddleston CJ, Moore WS, Reddy S, Sheldon FH, Steadman DW, Witt CC, and Braun EL (2013), Parsimony and model-based analyses of indels in avian nuclear genes reveal congruent and incongruent phylogenetic signals, Biology 2, 419-444. (pdf)