New 2013 Family list with annotations

I have just completed this fourth and most credible family order on my website. Of course, in a sense, such task is never finished, as new analyses will compel modifications although I think the papers by Hacket et al. 2008 and Yuri et al. 2013 make it unlikely that there will be major changes at this level. I am placing this document to show how the Science 2008 paper by Hackett at al., and also several papers by Jønsson and Fjeldså, notably their (2006) paper, on the higher-order taxonomy of the passeriformes, and anumber of other contributions, revolutionise the Family List.

An important contribution to the study of the Non-Passerine portion of this family list is the following study: S. J. Hacket, R. T. Kimball, S. Reddy, R. C. K. Bowie, E. L. Braun, M. J. Braun, J. L. Chojnowski, W. A. Cox, Kin-Han Lan, J. Harshman, C. J. Huddlestone, B. D. Marks, K .J. Miglia, W. S. Moore, F. H. Sheldon, D. W. Steadman, C. J. Witt and T.Yuri (2008) A phylogenetic study of birds reveals their evolutionary history. Science 320, 1763.
This study examined ~32 kilobases of aligned nuclear DNA sequences from 19 independent nuclear loci located on 15 different chromosomes in the chicken genome with introns (74%), coding exons(23%) and untranslated regions(3%).This represented 169 species, representing all major extant groups. The study recovered a robust phylogeny supported by multiple methods.

Many of the features of this analysis have survived in all subsequent analyses. The largest clade in Neoaves was a well supported land bird clade that contained all the Passeriformes, plus several morphologically diverse orders: Piciformes (woodpeckers and Allies), Falconiformes (hawks and falcons), Strigiformes (owls), Coraciiformes (kingfishers, hornbills, rollers and allies), Psittaciformes (parrots), Coliiformes (mousebirds), and Trogoniformes (trogons). Surprisingly, all studies confirmed that the closest order to the Passeriformes was the Psittaciformes, with Falconidae (falcons) sister to this clade. Sister to the land birds mentioned so far are the Charadriiformes (shorebirds, gulls and alcids).

Quite separate is a water bird clade, including members of the Pelecaniformes (totipalmate birds), Ciconiiformes (storks and allies), Procellariiformes (tube-nosed birds), Sphenisciformes (penguins), and Gaviiformes (loons). Basal to the water birds are two clades of terrestrial and arboreal taxa: Musophagiformes (turacos), and a clade including core Gruiformes (rails, cranes and allies), Cuculiformes (cuckoos) and Otitidae (bustards). Apodiformes (swifts and hummingbirds) form part of a Caprimulgiformes (nightjars and clade); and Piciformes (woodpeckers, barbets and Honeyguides) form part of a Coraciiformes clade.

This study contradicted that claim in Sibley & Monroe (1990) that the Cathartidae (New World vultures) formed part of the Ciconiidae. Instead, the Cathartidae were consistently placed within the land birds, usually with the Accipitridae. Turnix (buttonquails) belongs within the Charadriiformes; and Podicipediformes (grebes) and Phoenicopteriformes (flamingoes) are sister taxa. A sister relationship was recovered between Rhynchetos (kagu) and Eurypyga (sunbittern).

The broad structure of the study suggested diversification along general ecological divisions, such as water birds, shorebirds and land birds. But adaptations to these environments clearly arose several times, because many aquatic birds were not part of the water bird clade (e.g. tropicbirds, flamingoes and grebes) and terrestrial birds were found outside the land bird clade (e.g. turacos, doves, sandgrouse and cuckoos). The study also revealed that several distinctive niches, such as nocturnal (owls, nightjars and allies), raptorial (falcons, hawks, eagles, New World vultures, seriema and owls) or pelagic (tube-nosed birds, frigatebirds and tropicbirds) lifetyles have evolved multiple times. The results of the study also reveal surprising evolutions of various adaptations (e.g. the diurnal Apodiformes evolved from the nocturnal/crepuscular Caprimulgiformes; and the flighted Tinamidae arose within the flightless Struthioniformes.

Significant changes to the analysis proposed by Hacket et al. (2008) have been made in the following paper: Yuri, T., Kimball, R. T., Harshman, J., Bowie, R.C.K., Brown, M. J., Chojnowski, J. L., Han. K-L., Hackett, S. J., Huddleston, C.J., Moore, W. S., Reddy, S., Sheldon, F. H., Steadman, D. W., Witt, C.C. and Braun, E.L. (2013) Parsimony and model-based analysis of Indels in Avian Nuclear Genes reveal Congruent and Incongruent Phylogenetic Signals. Biology, 2: 419-444. They stated: Here, we report analyses of 12,030 gap characters from an alignment of avian nuclear genes In this family list. I basically follow the higher categories and family list for non-passerines put forward in this document.

I have also used a paper dealing with the higher level analysis of the passeriformes, namely, K. A. Jønsson and J. Fjeldså (2006) A phylogenetic supertree of oscine passerine birds (Aves Passeri). Zoologica Scripta 35,no.2,pp.149-186. This recognises that the oscine passeriformes are made up of four parvorders or superfamilies: Corvida; Passeroidea; Muscicapoidea and Sylvioidea. This paper is very important because if its clades are accurate, they will require reanalysis of many families and many genera.

Several important papers since then have added significant modifications: the superfamily Bombycilloidea has been added; Fuchs J, Irestedt M, Fjeldså J, Couloux A, Pasquet E & Bowie RCK (2012) Molecular phylogeny of African bush-shrikes and allies: tracing the biogeographic history of an explosive radiation of corvoid birds. Molecular Phylogenetics and Evolution 64: 93-105; and Zuccon D, Prys-Jones R, Rasmussen PC & Ericson PCP (2011) The phylogenetic relationships and generic limits of finches (Fringillidae). Molecular Phylogenetics and Evolution. 62:581-596. More recently still, several papers have clarified the issue of families within the Sylvoidea: notably Fregin, S, Haase, M, Olsson, U & Alström, P. (2012) New insights into family relationships within the avian superfamily Sylvioidea (Passeriformes) based on seven molecular markers. BMC Evolutionary Biology, 12, 157. (doi:10.1186/1471-2148-12-157).

I have also drawn on a paper by Ohlson, J., Fjeldså, J. & Ericson, P.G.P. (2008) Tyrant Flycatchers coming out into the open: phylogeny and ecological radiation of Tyrnnidae (Aves Passeriiformes). Zoologica Scripta 37, no.3: 315-335. This both analysed the Tyrnnidae in terms of five subfamilies: Pipromorphinae,Elaeniinae, Myarchinae, Tyranninae and Fluvicolinae, but also proposed a new sequence for Tyrannid genera.
Tello, J.G., Moyle,R.G., Marchese, D.J. & Cracraft, J. (2009) Phylogeny and phylogenetic classification of the tyrant flycatchers, cotingas, manakins and their allies. Cladistics 29:429-467 also proposed the recognition of an additional family:Hirundineinae, which corresponds to clade G in Figure 2 of the paper by Olson et al. (2008)

However, I have decided to modify the higher level structure of the Passerines on the basis of a paper Christidis & Norman (2010) Evolution of the Australasian songbird fauna Emu 110: 21-31.