New large-scale analysis of modern bird phylogeny, incorporating more taxa (but fewer characters) than Jarvis et al. (2014):

Prum RO, Berv JS, Dornburg A, Field DJ, Townsend JP, Moriarty Lemmon E, Lemmon AR 2015 A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing. Nature doi:10.1038/nature15697
http://www.nature.com/nature/journal/vaop/ncurrent/full/nature15697.html

Although reconstruction of the phylogeny of living birds has progressed tremendously in the last decade, the evolutionary history of Neoaves—a clade that encompasses nearly all living bird species—remains the greatest unresolved challenge in dinosaur systematics. Here we investigate avian phylogeny with an unprecedented scale of data: >390,000 bases of genomic sequence data from each of 198 species of living birds, representing all major avian lineages, and two crocodilian outgroups. Sequence data were collected using anchored hybrid enrichment, yielding 259 nuclear loci with an average length of 1,523 bases for a total data set of over 7.8 × 10^7 bases. Bayesian and maximum likelihood analyses yielded highly supported and nearly identical phylogenetic trees for all major avian lineages. Five major clades form successive sister groups to the rest of Neoaves: (1) a clade including nightjars, other caprimulgiforms, swifts, and hummingbirds; (2) a clade uniting cuckoos, bustards, and turacos with pigeons, mesites, and sandgrouse; (3) cranes and their relatives; (4) a comprehensive waterbird clade, including all diving, wading, and shorebirds; and (5) a comprehensive landbird clade with the enigmatic hoatzin (Opisthocomus hoazin) as the sister group to the rest. Neither of the two main, recently proposed Neoavian clades—Columbea and Passerea1—were supported as monophyletic. The results of our divergence time analyses are congruent with the palaeontological record, supporting a major radiation of crown birds in the wake of the Cretaceous–Palaeogene (K–Pg) mass extinction.

Commentary:

Thomas GH 2015 An avian explosion. Nature doi:10.1038/nature15638
http://www.nature.com/nature/journal/vaop/ncurrent/full/nature15638.html

h/t: David Storch


Thoughts:

The topological conflicts with the results of Jarvis et al. (2014) are limited to a rearrangement of the same broader groups that are estimated to diverge from one another very close to (and probably immediately after) the K–Pg boundary. These groups usually include several traditional "orders", with the exception of the hoatzin, whose notorious phylogenetic instability probably stems from the fact that it represents a lineage which is both extremely old and extremely species-poor.

Although Prum et al. choose to discuss their results in terms of the supposed superiority of dense taxon sampling over whole-genome datasets that are larger but less taxonomically inclusive, very little can be said to be novel about their results, and even less suggests that they represent an improvement on earlier findings. Their tree conflicts with Jarvis et al.'s preferred phylogeny (ExaML TENT; Jarvis et al. 2014: Figure 1) only in those places where the latter didn't receive bootstrap support values of 100% or where it conflicted with the results obtained from other analyses of the same dataset (e.g., the MP-EST* TENT species tree or the WGT tree).

There is one exception to this, though, and it's very unlikely to be correct: Prum et al. break up the grouping of "Australasian ratites" (recently named Novaeratitae), which is supposed to unite the kiwis of New Zealand with the Australian casuariids (the emu and cassowaries). Instead, they find the South American tinamous to be the sister group of casuariids. This goes against all previous phylogenomic results (e.g., Hackett et al. 2008) and mtDNA data (e.g., Phillips et al. 2010), let alone biogeographical intuition. The monophyly of Novaeratitae even represents one of the few cases where morphology came to support what had originally been a molecular hypothesis (Bledsoe 1988).

I'm actually more surprised that the Prum et al. tree retains some of the supraordinal groups recovered by Jarvis et al. that weren't recovered even by the first couple of phylogenomic analyses (Ericson et al. 2006; Hackett et al. 2008): for example, the sister group relationship between Aequornithes (the "core water bird" assemblage) and a group including tropicbirds, the kagu, and the sunbittern; or a cuckoo-turaco-bustard clade (Otidimorphae).

Overall, the new analysis ties in very neatly with the conclusions of Suh et al.'s (2015), who had attacked the findings of Jarvis et al. (2014) from a different -- and, IMO, much more interesting -- point of view. While Prum et al. (2015) simply believe that Jarvis et al.'s tree is wrong and theirs is right, Suh et al. (2015) argue that there's no single "right" tree accounting for the whole history of Neoaves. They suggest that the radiation at the base of the clade was so rapid that the relationships among its constituent lineages can be represented only by a network. If that's correct, then the conflicting phylogenies of Jarvis et al. (2015) and Prum et al. (2015) simply highlight different, partially overlapping parts of that network, but neither of them provides the complete picture about the complex speciation that produced it. Unfortunately, the Prum et al. paper was completed before Suh et al. published their analysis, and therefore doesn't discuss or incorporate their results.

The authors also give names to the novel groupings appearing on their tree: "Columbaves", "Aequorlitornithes", "Inopinaves", "Eutelluraves". For the reasons above, I don't think that's a good idea -- in fact, I'd say we'll probably never hear of these ever again.

Finally, there is one important point of agreement between Jarvis et al. (2014) and Prum et al. (2015): in contrast to earlier molecular dating analysis, but in agreement with the known fossil record, the great neoavian radiation occured mostly, and perhaps entirely, in the Paleogene. However, the methodology that allowed Prum et al. to reach this conclusion might be a bit problematic. I like the fact that they used Waimanu (the oldest known penguin, 61 Ma) as the hard lower bound for the age of Neornithes (modern or crown-clade birds) instead of Vegavis (a latest-Cretaceous bird that seems to be very closely related to living ducks). Mayr (2013) argued that the position of Vegavis as a deeply nested neornithine is actually a lot less robust than most people think it is -- it's mostly based on a single (albeit complex) character that is known to be homoplastic within crown-clade birds. It's nice to see someone taking this into account. That said, I think that Prum et al.'s usage of the 86.5 Ma time horizon (based on the age of the Niobrara Formation) as a soft upper bound for the age of Neornithes (only 2.5% of the total probability mass was assigned to dates older than that) might be too restrictive. After all, there's a possible stem-galliform (Austinornis) at 85 Ma, although its position is nowhere near robust.


Refs:

Bledsoe AH 1988 A phylogenetic analysis of postcranial skeletal characters of the ratite birds. Ann Carnegie Mus 57: 73–90

Ericson PGP, Anderson CL, Britton T, Elżanowski A, Johansson US, Källersjö M, Ohlson JI, Parsons TJ, Zuccon D, Mayr G 2006 Diversification of Neoaves: Integration of molecular sequence data and fossils. Biol Lett 2(4): 543–7

Hackett SJ, Kimball RT, Reddy S, Bowie RC, Braun EL, Braun MJ, Chojnowski JL, Cox WA, Han K, Harshman J, Huddleston CJ, Marks BD, Miglia KJ, Moore WS, Sheldon FH, Steadman DW, Witt CC, Yuri T 2008 A phylogenomic study of birds reveals their evolutionary history. Science 320(5884): 1763–8

Jarvis ED, Mirarab S, Aberer AJ, Li B, Houde P, Li C, Ho SYW, Faircloth BC, Nabholz B, Howard JT, Suh A, Weber CC, Fonseca RRd, Li J, Zhang F, Li H, Zhou L, Narula N, Liu L, Ganapathy G, Boussau B, Bayzid MdS, Zavidovych V, Subramanian S, Gabaldón T, Capella-Gutiérrez S, Huerta-Cepas J, Rekepalli B, Munch K, Schierup M, Lindow B, Warren WC, Ray D, Green RE, Bruford M, Zhan X, Dixon A, Li S, Li N, Huang Y, Derryberry EP, Bertelsen MF, Sheldon FH, Brumfield RT, Mello CV, Lovell PV, Wirthlin M, Schneider MPC, Prosdocimi F, Samaniego JA, Velazquez AMV, Alfaro-Núñez A, Campos PF, Petersen B, Sicheritz-Ponten T, Pas A, Bailey T, Scofield P, Bunce M, Lambert DM, Zhou Q, Perelman R, Driskell AC, Shapiro B, Xiong Z, Zeng Y, Liu S, Li Z, Liu B, Wu K, Xiao J, Yinqi X, Zheng Q, Zhang Y, Yang H, Wang J, Smeds L, Rheindt FE, Braun M, Fjeldså J, Orlando L, Barker K, Jønsson KA, Johnson W, Koepfli KP, OBrien S, Haussler D, Ryder OA, Rahbek C, Willerslev E, Graves GR, Glenn TC, McCormack J, Burt D, Ellegren H, Alström P, Edwards SW, Stamatakis A, Mindell DP, Cracraft J, Braun EL, Warnow T, Jun W, Gilbert MTP, Zhang G 2014 Whole genome analyses resolve the early branches in the tree of life of modern birds. Science 346(6215): 1320–31

Mayr G 2013 The age of the crown group of passerine birds and its evolutionary significance – molecular calibrations versus the fossil record. Syst Biodivers 11(1): 7–13

Phillips MJ, Gibb GC, Crimp EA, Penny D 2010 Tinamous and moa flock together: mitochondrial genome sequence analysis reveals independent losses of flight among ratites. Syst Biol 59(1): 90–107

Suh A, Smeds L, Ellegren H 2015 The dynamics of incomplete lineage sorting across the ancient adaptive radiation of neoavian birds. PLoS Biol 13(8): e1002224
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