This page is a resource for the phylogeny of living birds. It contains cladograms of some of the major schemes and comparions of the major competing hypothese. The page is used to develop cladograms that are added to main namespace articles.
The early diversification of the various neoavian groups occurred very rapidly around the Cretaceous–Paleogene extinction event.[14] As a result of the rapid radiation, attempts to resolve their relationships have produced conflicting results, some quite controversial, especially in the earlier studies.[15][16][7] Nevertheless, some recent large phylogenomic studies of Neoaves have led to much progress on defining orders and supraordinal groups within Neoaves. Still, the studies have failed to produce to a consensus on an overall high order topology of these groups.[2][3][5][7] A genomic study of 48 taxa by Jarvis et al. (2014) divided Neoaves into two main clades, Columbea and Passerea, but an analysis of 198 taxa by Prum et al. (2015) recovered different groupings for the earliest split in Neoaves.[2][3] A reanalysis with an extended dataset by Reddy et al. (2017) suggested this was due to the type of sequence data, with coding sequences favouring the Prum topology.[5] The disagreement on topology even with large phylogenomic studies led Suh (2016) to propose a hard polytomy of nine clades as the base of Neoaves.[4]
Current: An analysis by Houde et al. (2019) recovered Columbea and a reduced hard polytomy of six clades within Passerea.[6]Possible(down play reduced polytomy): ... although recovered some structure with a polytomy in Passerea. [6]
Despite other disagreements, these studies do agree on a number of supraorderal groups, which Reddy et al. (2017) dubbed the "magnificent seven", which together with three "orphaned orders" make up Neoaves.[5] Significantly, they both include a large waterbird clade (Aequornithes) and a large landbird clade (Telluraves). The groups defined by Reddy et al. (2017) are as follows:
Three more recent genome scale analyses have recovered some higher structure.[9][17][18] All three recover Columbaves. An explanation for the previous recovery of Columbea was provided by the finding of ... a 21 Mb outlier region of chromosome 4 with an abnormally strong signal for Columbea. OR a region of chromosome 4 with suppressed recombination that providing a misleading phylogenetic signal.Cite error: The <ref> tag has too many names (see the help page).Cite error: The <ref> tag has too many names (see the help page). Kuhl et al (2021) and Stiller et al (2024) found Mirandornithes as the earliest diverging Neoavian group, which is consistent with findings of Columbea once the affect of the chromosome 4 anomaly is accounted for. [how to say and source this]
Stiller et al (2024) recovered a clade combining the waterbirds with shorebirds and some landbird groups, which they named Elementaves [=Strisores+Gruimorphae+Opisthocomiformes+Phaethoquornithes]. A clade with the same composition had previously been recovered by Houde et al (2019). Wu el al (2024) found a similar clade, except it also included Mirandornithes. Kuhl et al (2021) also recovered a clade with Strisores and the orphan orders, but grouped with Columbaves rather than Phaethoquornithes. [again how to make these comparison with proper sourcing]
Comparison of different proposals for Neoavian radiation
Other: Hackett et al (2008), Yuri et al (2013), Suh et al (2016), Houde et al (2019)[4][6]
There is considerable disagreement on the arrangement of Neoaves, although the presence of two large clades representing water and land birds is a common feature.
Prum et al (2015) found no support for the the clades Columbea and Passerea found in the Jarvis et al (2014) analysis.
There is agreement that the supraordinal clades Strisores, Columbimorphae, and Otidimorphae have a relatively basal positions, although their arrangement differs.
The Mirandornithes are placed higher in the tree as sister to the shore birds of Charadriiformes in a large shore/waterbird clade.
A clade containing shorebirds, waterbirds and landbirds, along with the the hoatzin (Opisthocomiformes), is common to both studies, except for the presence or absence of the Mirandornithes. The arrangement differs substantially (see below).
HBW use an expanded Caprimulgiformes instead of Strisores, adding the three Apodiformes families rather than having four or five orders with a single family.
The latest TiF excel file (June 2018) elevates Strisores to the higher polytomy and places the Opisthocomiformes with the Gruiformes in Gruae (not clear why).
Jarvis-2014 TENT (total evidence nuclotide tree) - Columbea and Passerea (based on 42 Mbp of data extracted from 48 complete avian genomes) [character rich; 46% intron, 32% exon, 22% non-coding UCEs]
Prum et al. (2015) - no Columbea+Passerea split, extended waterbird clade (based on 0.4 Mbp of data from 259 loci obtained by sequence capture (anchored hybrid enrichment) and sampled for 198 bird species) [taxon rich; 82.5% exonic]
Suh-2016 hard polytomy (Fig 1, left) - nine-way hard polytomy
Reddy-2017 consensus (Fig 8) - groups clades VII and VII (Columbea) with Passerea in a seven-way polytomy
Reddy-2017 early bird II tree (non-coding, extended sampling) - basal split into Columbea (VII+VI) and Passerea (I-V + 3 orphaned orders) follows Jarvis-2014 TENT, but Passera split into two large clades (sequential listing):
There is also general agreement on the arrangement of core land birds in Telluraves. The main difference is that Prum et al (2015) find the hawks and vultures basal within core landbirds, rather than within Afroaves (making Afroaves paraphyletic).
Boyd's Taxonomy in Flux follows Jarvis et al (2014) and Prum et al (2015), except for the position of Coliiformes (which follows Suh et al, 2015). Yuri et al (2013) has them as sister to Strigiformes
^ abcdefPrum, Richard O.; Berv, Jacob S.; Dornburg, Alex; Field, Daniel J.; Townsend, Jeffrey P.; Lemmon, Emily Moriarty; Lemmon, Alan R. (2015). "A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing". Nature. 526 (7574): 569–573. doi:10.1038/nature15697. ISSN0028-0836. PMID26444237. S2CID205246158. Cite error: The named reference "Prum-2015" was defined multiple times with different content (see the help page).
^ abcdeBraun, Edward L.; Cracraft, Joel; Houde, Peter (2019). "Resolving the Avian Tree of Life from Top to Bottom: The Promise and Potential Boundaries of the Phylogenomic Era". Avian Genomics in Ecology and Evolution. pp. 151–210. doi:10.1007/978-3-030-16477-5_6. ISBN978-3-030-16476-8. S2CID198399272. Cite error: The named reference "BraunCracraft2019" was defined multiple times with different content (see the help page).
^Oliveros, Carl H.; Field, Daniel J.; Ksepka, Daniel T.; Barker, F. Keith; Aleixo, Alexandre; Andersen, Michael J.; Alström, Per; Benz, Brett W.; Braun, Edward L.; Braun, Michael J.; Bravo, Gustavo A.; Brumfield, Robb T.; Chesser, R. Terry; Claramunt, Santiago; Cracraft, Joel; Cuervo, Andrés M.; Derryberry, Elizabeth P.; Glenn, Travis C.; Harvey, Michael G.; Hosner, Peter A.; Joseph, Leo; Kimball, Rebecca T.; Mack, Andrew L.; Miskelly, Colin M.; Peterson, A. Townsend; Robbins, Mark B.; Sheldon, Frederick H.; Silveira, Luís Fábio; Smith, Brian Tilston; White, Noor D.; Moyle, Robert G.; Faircloth, Brant C. (2019). "Earth history and the passerine superradiation". Proceedings of the National Academy of Sciences. 116 (16): 7916–7925. doi:10.1073/pnas.1813206116. ISSN0027-8424.
^ abDickinson, EC; Remsen, JV Jr (2013). The Howard and Moore complete checklist of the birds of the world. Vol. 1. Passerines. (4th ed.). Aves Press, Eastbourne.
^ abDickinson, EC; Christidis, L (2014). The Howard and Moore complete checklist of the birds of the world. Vol. 2. Passerines (4th ed.). Aves Press, Eastbourne.
^Cracraft, J. (2014). "Avian Higher-level Relationships and Classification: Passeriforms". In Dickinson, E.C. &; Christidis, L. (eds.). The Howard and Moore Complete Checklist of the Birds of the World. Vol. 2 (4th ed.). Eastbourne, U.K.: Aves Press. pp. xvii–xlv.
^Mitchell, K. J.; Llamas, B.; Soubrier, J.; Rawlence, N. J.; Worthy, T. H.; Wood, J.; Lee, M. S. Y.; Cooper, A. (2014-05-23). "Ancient DNA reveals elephant birds and kiwi are sister taxa and clarifies ratite bird evolution". Science. 344 (6186): 898–900. doi:10.1126/science.1251981. PMID24855267. S2CID206555952.
^Stiller, J.; Feng, S.; Chowdhury, A-A.; et al. (2024). "Complexity of avian evolution revealed by family-level genomes". Nature: in press. doi:10.1038/s41586-024-07323-1.
^Kimball, R.T. et al. (2013) Identifying localized biases in large datasets: A case study using the Avian Tree of Life. Mol Phylogenet Evol. doi:10.1016/j.ympev.2013.05.029
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