Most recent phylogenetic studies have agreed that modern birds fall into three clades:
- Palaeognathae, containing the ratites and tinamous
- Galloanserae divided into
- Neoaves containing everything else.
Since the discovery of Vegavis iaai Clark et al. 2005, a bird belonging to the Anseriformes from the Cretaceous, it is clear that this division in four lineages represents radiations from before the K/T boundary. The identification of Austinornis lentus from the Cretaceous Austin Chalk as a member of the Pangalliformes attested for the presence of the other branch of the Galloanserae before the K/T-boundary.
Within the Neoaves, however, relationships have long been almost completely unresolved. Most references still use the classification established by Wetmore for the sake of convenience, but it has long been suspected that many of the classical orders (such as Ciconiiformes or Gruiformes) are polyphyletic and represent ecological rather than phylogenetic assemblages.
How much - if any - of the diversity within this clade stems from before the K/T boundary is still a matter of - at times hot - debate. Genetic results do seem to indicate an extremely rapid radiation producing a large number of lineages in relatively short period of time. This actually makes it difficult to establish the degree to which lineages are related. The early years of the Paleocene, just after the species diversity of the planet had been seriously diminished are an obvious candidate for a period in which such rapid radiation could have happened.
An earlier study in the 1990's based on DNA hybridization caused much (justified) skepticism about the validity of its conclusions, e.g. a vast extension of the Ciconiiformes to include amongst others the New World vultures. After the turn of the millennium vastly improved methods of DNA-based comparisons and of statistical processing methods for this type of data made it possible to shed new light on the relations within the Neoaves clade.
In 2004, Fain and Houde published a phylogenetic analysis using the β-fibrinogen gene with a rather radical result - the Neoaves fell into two major clades, with the smaller of the two clades, the Metaves, composed of an assemblage of birds of which most members had never previously been suspected as relatives, and had indeed been assigned to orders whose other members fell within the Coronaves. As pointed out by the authors, about the only feature shared by all the members of Metaves was that they had all been regarded as phylogenetically uncertain. Despite the heterodoxy of the results, they were well-supported by both bootstrapping and indel distribution. A later, independent analysis by Ericson et al. (2006) using a larger assortment of genes also recovered the same result. It also supported a division of the Coronaves into three major clades – the Charadriiformes, a clade roughly corresponding to the "higher land birds" and a clade composed mostly of waterbirds (this division had been found by Fain and Houde, but not well-suppported). The tree below is based on the results of Ericson et al. – time will tell whether they continue to be supported. A later rather extensive study by Hackett et al. (2008) did confirm the overall tree with a few changes. The clade Metaves e.g. is not very well supported as its support relies heavily on one signal only. The divisions within the group are very deep. A study on mitochondrial DNA by Morgan-Richards et al. (2008) refutes that Metaves is a valid clade. The sister relationship between grebes (Podicipedidae) and flamingos (Phoenicopteriformes) is more generally accepted. Additional information was derived from similarities of their parasites (lice; Johnson, Kevin P 2006). Initially this information was taken to indicate a relationship with the Anseriformes, but later it became clear that ducks had received some of their parasites from the grebes, rather than the other way around. The name Mirandornithes was proposed for the clade unififying the two groups.
<==Neoaves (see below for synonymy) | i. s.: Pelagornithidae WH02 | Protopelicanus Reichenbach 1852 M05, M02 | `--*P. cuvieri Reichenbach 1852 M02 |--Metaves HK08 | |--+--Caprimulgiformes HK08 | | `--Eurypygae L98 | | |--Eurypyga Illiger 1811 HK08, L98 [Eurypygidae, Eurypygides] | | | `--E. helias HK08 | | `--Rhynochetoidea [Rhynochetides] L98 | | |--Rhynochetos Verreaux & des Murs 1860 HK08, L98 [Rhynocheti, Rhynochetidae] | | | |--R. jubatus HK08 | | | `--R. orarius L98 | | `--Aptornis Mantell 1848 [=Apterornis Owen 1848; Aptornithidae] WH02 | | |--A. defossor Owen 1871 WH02 [=A. otidiformis defossor GM91] | | `--A. otidiformis (Owen 1844) [=Dinornis otidiformis] WH02 | `--+--+--Juncitarsus Olson & Feduccia 1980 M05, M02 [Juncitarsinae] | | | |--*J. gracillimus Olson & Feduccia 1980 M02 | | | `--J. merkeli Peters 1987 M02 | | `--+--Phoenicopteriformes HK08 | | `--Podicipedidae HK08 | `--+--Phaethontes HK08 | `--Columbiformes HK08 | |--Pteroclidae HK08 | `--+--Columbidae HK08 | `--Mesitornithidae [Mesitidae, Mesitornithes, Mesoenatidae, Mesoenatides] HK08 | |--Monias Oustalet & Grandidier 1903 HK08, L98 [Moniidae] | | `--M. benschi HK08 | `--Mesitornis Bonaparte 1855 HK08, L98 (see below for synonymy) | |--M. unicolor (Des Murs 1845) ME04 [=Mesoenas unicolor A61] | `--M. variegata ME04 `--Coronaves (see below for synonymy) HK08 |--+--Charadriiformes HK08 | `--Anomalogonatae HK08 `--+--Opisthocomidae [Opisthocomi, Opisthocomiformes] HK08 | |--Hoazinoides magdalenae FP64 | `--Opisthocomus Illiger 1811 HK08, B94 | `--O. hoazin (Müller 1776) ME04 `--+--+--Otididae HK08 | `--+--Cuculidae HK08 | `--Grues HK08 `--+--Musophagidae HK08 `--Natatores LZ07 |--Gaviiformes HK08 `--+--Procellariimorphae LZ07 | |--Procellariiformes HK08 | `--+--Phocavis maritimus M04 | `--+--Impennes A94 | | |--Spheniscidae HK08 | | `--Cladornis Ameghino 1895 A94, S46 (see below for synonymy) | | `--*C. pachypus Ameghino 1895 S46 | `--Plotopteridae M04 | |--Tonsala hildegardae M04 | `--Copepteryx hexeris M04 `--Steganograllatores [Herodiones, Pelecanides, Steganopodes] LZ07 |--Ciconiidae HK08 `--+--+--Suloidea HK08 | `--Fregata Lacépède 1799 HK08, B94 (see below for synonymy) | |--F. andrewsi VP89 | |--F. aquila FP64 | |--F. ariel (Gray 1845) R85 | |--F. magnificens HK08 | `--F. minor (Gmelin 1789) R85 [=Pelecanus minor FST81] | |--F. m. minor Mo03 | `--F. m. palmerstoni Mo03 `--+--+--Pelecanidae HK08 | `--+--Balaeniceps Gould 1850 HK08, B94 (see below for synonymy) | | `--B. rex HK08 | `--Scopus Brisson 1760 HK08, B94 [Scopi, Scopidae] | |--S. umbretta HK08 | `--S. xenopus Olson 1984 B93 `--+--Threskiornithidae HK08 `--Ardeiformes LZ07 |--Ardeidae HK08 `--Cochlearius Brisson 1760 LZ07, B94 (see below for synonymy) `--*C. cochlearius FS5 |--C. c. cochlearius FS55 `--C. c. zeledoni FS55
Nomen nudum: Aptornis bulleri Owen in Buller 1888 WH02
Inorganic: Opisthocomidus opisthocomidus minilorientalus Okamura 1987 O87
Balaeniceps Gould 1850 HK08, B94 [Balaenicipites, Balaenicipitidae, Balaenicipitiformes]
Cladornis Ameghino 1895 A94, S46 [Cladornidae, Cladornithes, Cladornithidae]
Cochlearius Brisson 1760 LZ07, B94 [incl. Cancroma Linné 1766 B94; Cancromini, Cochleariidae, Cochleariini]
Coronaves [Anomalogonates, Coccyges, Cuculiformes, Cuculimorphae, Gaviae, Longipennes, Oxypterae, Pelecani, Ralliformes]
Fregata Lacépède 1799 HK08, B94 [incl. Atagen Kaup 1829 B94, Attagen Möhring 1752 (pre-Linnean) B94, Tachypetes Vieillot 1816 B94; Atagenidae, Attagenidae, Fregatae, Fregatidae, Fregatides, Fregatoidea, Tachypetidae]
Mesitornis Bonaparte 1855 HK08, L98 [incl. Mesites Geoffroy-St. Hilaire 1838 non Schönherr 1838 B94, Mesoenas Reichenbach 1862 B94]
Neoaves [Charadriimorphae, Ciconiae, Ciconiiformes, Ciconiimorphae, Ciconioidea, Dendrornithes, Eurypygoidea, Gavii, Gaviomorphae, Grallae, Gruiformes, Incessores, Paludicolae, Pelecaniformes, Pelecanimorphae, Phaethontiformes, Plethornithes, Psittacimorphae, Pygopodes, Pygopodotubinares, Simplicirostres, Strisores, Terrestrornithes, Turniciformes]
* Type species of generic name indicated
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[FS55] Felten, H., & J. Steinbacher. 1955. Zur Vogelfauna von El Salvador. Senckenbergiana Biologica 36: 9-19.
[FP64] Fisher, J., & R. T. Peterson. 1964. The World of Birds: A comprehensive guide to general ornithology. Macdonald: London.
[GM91] Gill, B., & P. Martinson. 1991. New Zealand’s Extinct Birds. Random Century: Auckland (New Zealand).
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[LZ07] Livezey, B. C., & R. L. Zusi. 2007. Higher-order phylogeny of modern birds (Theropoda, Aves: Neornithes) based on comparative anatomy. II. Analysis and discussion. Zoological Journal of the Linnean Society 149 (1): 1-95.
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[VP89] Viney, C., & K. Phillipps. 1989. Birds of Hong Kong 5th ed. Government Printer: Hong Kong.
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