A phylogenetic hypothesis for passerine birds: taxonomic and biogeographic implications of an analysis of nuclear DNA sequence data

“I augmented the phylogenetic hypotheses of Sibley & Ahlqist (1990) with insights from new molecular phylogenetic analysis, which has particularly marked effects on the relationships of the passerines (Barker et al. 2002, 2004; Ericson et al. 2002, 2003).”

“Barker et al. (2002) inferred the Ptilonorhynchidae (Stonor, 1938; Cracraft, 1992a; Nunn & Cracraft, 1996; Cracraft & Feinstein, 2000; Johansson et al., 2001) to be the sister-group of the remaining passeriform taxa.”

“, nonsynonymous sites) are largely concordant with other published avian data sets [14–17], suggesting broad applicability of our locus-specific rates for population genetic and phylogenetic studies of avian taxa.”

“For birds, mesic ancestry was inferred from all phylogenies for passerines, particularly oscine passerines (Barker et al., 2002, 2004; Ericson et al., 2002, 2003; Chesser & ten Have, 2007) and for parrots among non-passerines (Wright et al., 2008; Schweizer et al., 2010).”

“Numerous apparently rapid divergence events within passerines have hindered reconstruction of their evolutionary interrelationships when sampling few loci (<10) (4, 9, 14, 15, 19) or few taxa (<70% of passerine families) (5, 17, 20).”

“…composite phylogeny used in the comparative analyses was based on Sibley and Ahlquist (1990), combined with information from other sources (Sheldon et al. 1992; Blondel et al. 1996; Badyaev 1997; Slikas et al. 1996; Helbig and Seibold 1999; Barker et al. 2001, 2004; Voelker and Spellman 2004) (Fig.”

“(6) have been supported by recent studies [41, 43-46].”

“Nucleotide sequence data from RAG1 have previously been analyzed in several vertebrate phylogenetic studies (e.g., Groth and Barrowclough, 1999; Barker et al., 2002; Baker et al., 2004; Gruber et al., 2007).”

“[47,48]), a linkage map of the Siberian jay may provide new insights into avian genome evolution, and thereby also to the extensive morphological, life historical and behavioural diversification within the order Passeriformes (see [47]).”

“We used the geological split between New Zealand and Antarctica as the calibration point, as this has been related to the basal separation of the Acanthisitta lineage from the other passerines (Barker et al. 2002, 2004; Ericson et al. 2002). Thus, we used a normally distributed tree prior with a mean of 78 mya and a s…”

“Psittaciformes, Bucerotiformes, and Passeroidea show very similar patterns in the palate and rostrum (Fig.”

“…from vireonidcorvid hosts appear to be in more basal positions within the Haemoproteus clade than are parasites recovered from nine-primaried oscines, paralleling the more basal position of vireonids and corvids within the passerif orm phylogeny (Sibley and Ahlquist, 1990; Barker et al., 2002).”

“…Spinks et al. (2004) CM1 (Cmos) 163 5 -GCCTGGTGCTCCATCGACTGGGA-3 Barker et al. (2002) CM2 (Cmos) 820 5 -GGGTGATGGCAAAGGAGTAGATGTC-3 Barker et al. (2002) Cmos1 (Cmos) 163 5 -GCCTGGTGCTCCATCGACTGGGATCA-3 This study Cmos3 (Cmos) 812 5 -GTAGATGTCTGCTTTGGGGGTGA-3 This study F2 (Rag2)…”

“Analyses using similar approaches suggest that both Passeriformes (Barker et al. 2002) and Columbiformes (Pereira et al. 2007) also originated in Gondwana during the Cretaceous.”

“…recognized by current taxonomy ( As immediate outgroups, we selected members of the family Fringillidae (the sister clade to the New World group; Barker et al. 2002; Ericson and Johansson 2003; Johansson et al. 2008), including the former tanager genera In addition, we included 2 members of the…”

“Now that molecular phylogenetic analyses have largely resolved such controversial relationships among higher taxa (Barker et al. 2002, 2004, 2013, Ericson and Johansson 2003), as well as revealing species-level relationships within most of the major emberizoid lineages (Lovette et al. 2010, Burns…”

“However, other oscine lineages—the core Corvoidea (crows and allies), comprising more than 700 species, and the Passerida (warblers, thrushes,finches, and other songbirds), comprisingmore than 3,500 species—originated in themid-Tertiary and dispersed all over the world (17, 18, 20).”

“Nearly the entire exon has been used to resolve ordinal phylogenetics among birds (Barker et al., 2002; Ericson et al., 2002; Groth and Barrowclough, 1999) and vertebrates (Frippiat et al.”

“Furthermore, the monophyly of the Passeriformes is supported by several recent molecular studies that are based on nuclear DNA sequences (Barker et al. 2002).”

“Molecular data suggest that the oscine passerines had their early evolution in the Australo-Papuan region, from where several groups later dispersed (Barker et al., 2002, 2004; Ericson et al., 2002).”

“1) was derived from Sibley and Ahlquist (1990), with additional information from Friesen et al. (2002) and Barker et al. (2002).”

“For this we compiled a phylogeny for our species based on Hackett et al. (2008) and Barker et al. (2002, 2004).”

“When egg mass was corrected for body mass and clutch size, the residual variation was strongly correlated with nest predation across sites (Rp 5 20.64, df 5 66, P , 0.0001; see gray line in Fig.”

“In the parsimony analysis of Barker et al. (2002) the dipper grouped with the thrush-flycatcher clade, while it got a position basal to both this and the starling-mockingbird clade in the maximum-likelihood analysis.”

“, 2003; Ericson and Johansson, 2003; Barker et al., 2002, 2004; Cracraft and Barker, 2009; among others). Finally, to facilitate standardization of taxon names we generally follow Sibley et al. (1988) and Sibley and Monroe s (1990) suffixes for taxon names assigned to particular suprageneric ranks.”

“The suggested exclusion from both the suboscine and the oscine clade has recently been supported by DNA sequence data, which indicate that the New Zealand wrens are survivors of the earliest radiation of passerines (Barker et al. 2002, Ericson et al. 2002a) (Fig.”

“Besides the water birds, progress has been made with DNA sequence analyses in understanding relationships within other neoavian groups, including the Passeriformes (Johansson et al., 2001, 2002; Barker et al., 2002; Yuri and Mindell, 2002; Cracraft et al., 2004).”

“RAG-1 and RAG-2 genes were amplified and sequenced using multiple primer pairs (Groth and Barrowclough 1999; Barker et al. 2002, 2004).”

“proto-Australasia [45,46], whereas the Philesturnus/Cnemophilus/Toxorhampus/’core Corvoidea’ clade has been inferred to have originated in the proto-Papuan archipelago [43].”

“That the variation in syrinx morphology in passerines is generally consistent with molecular data is obvious when comparing the extensive morphological study by Ames (1971) with recent molecular findings (e.g. Barker et al. 2002, 2004; Ericson et al. 2002a; Irestedt et al. 2002).”

“, 2016; Fleming & Muchhala, 2008; Stiles, 1981), with a limited distribution overlap between these OW families (Barker et al., 2002).”

“Higher nodes for the nonpasserines were drawn from the DNA–DNA hybridization phylogeny of Sibley and Ahlquist (1990) and predominantly from Barker et al. (2001) for Passeriformes.”

“We did not use phylogeny of Barker et al. (2002) because it did not allow the resolution of branch lengths within families.”

“The early emergence of New Zealand wrens 28/8/08, page 5 of 28 within Passeriformes is consistent with a Gondwanan origin for the whole passerine group (Cracraft 2001; Barker et al. 2002; Edwards and Boles, 2002; Ericson et al. 2002a).”

“2005), based on evidence for an Australasian origin of songbirds (Barker et al. 2002) combined with the prevalence of female song among Australian species today.”

“We controlled for phylogeny with independent contrasts using the contrast.exe subroutine of PHYLIP (Felsenstein 1989) and the phylogenetic hypothesis presented by Barker et al. (2002) .”

“Both molecular clock analyses (van Tuinen & Hedges, 2001; M. van Tuinen, T. A. Stidham & E. A. Hadly, unpubl. data) and biogeographical interpretations (Cracraft, 2001; Barker et al., 2002) suggest a Cretaceous diversification for this large and diverse clade.”

“Outgroups were selected from sylvioid families known to be closely related to the Hirundinidae (Barker et al., 2001; Sheldon and Gill, 1996).”

“Significant events might have included the colonization of South America by several North American fringillid lineages (family Fringillidae, nine tribes), the escape of corvid lineages (family Corvidae, 16 tribes) from Australasia as the Australian plate approached Asia (Barker et al. 2002; Ericson et al. 2002), the c…”

“First, female song is prevalent in Australian birds (Robinson 1949), which are the ancestors of oscine passerines (Barker et al. 2002).”

“…analyses is the recognition of sister group relationship between the New Zealand Acanthisittidae and all other extant passeriform birds, the Eupasseres, which fall into two clades, the predominantly New World Suboscines and the Oscines (Barker et al. 2002, 2004; Ericson et al. 2002, 2003b).”

“Birds in the infraorder Corvida [1] (ravens, jays, bowerbirds) are renowned for their cognitive abilities [2–4], which include advanced problem solving with spatial inference [4–8], tool use and complex constructions [7–10], and bowerbird cognitive ability is associated with mating success [11].”

“In any event, the increased taxonomic and genetic sampling of Barker et al. (2004) implied several waves of dispersal out of Australasia, from 45–47 Myr for Picathartidae to 26–29 Myr for crown Corvoidea.”

“2) indicated that the New Zealand wren A. chloris, member of a group sometimes considered suboscine, was sister to all other passerines, consistent with previous studies using sequence data (Barker et al., 2002; Ericson et al., 2002).”

“Barker et al., 2002, 2004; Ericson et al., 2002) strongly supported a basal topology for Passeriformes in which the oscine passerines are sister to all suboscines.”

“We now believe that the Corvida as originally recognized includes the Passerida, which branched from the old Australian stock only after several major taxa had emerged and radiated in Australia ( Barker et al. 2002; Ericson et al. 2002).”

“To calibrate the tree we used the geological split between New Zealand and Antarctica, as it has been associated with the basal separation of the Acanthisitta-lineage from all other passerines [ 45 ,46].”

“For the analyses, we used a composite phylogenetic hypothesis, reported in electronic Appendix B and mainly based on Sibley & Ahlquist (1990) and Barker et al. (2002).”

“We would like to stimulate the discussion further by postulating that, given the probable Australasian origin of oscine passerines [ 9 ] and the prevalence of female song in Australian birds [10], song in both sexes could be the ancestral condition.”

“Molecular analyses of the oscine passerines give strong support to an east Gondwanan origin of the group (Sibley and Ahlquist 1990, Barker et al. 2002, Ericson et al. 2002b, 2003).”

“(1990). Although this phylogeny has been criticized (see for example Barker et al. 2002 ) it has been validated by several independent data sets (Sibley 1994) and is the most widely used working hypothesis of the true phylogeny of birds.”

“Mitochondrial and nuclear sequence data (Barker et al., 2002; Cracraft and Feinstein, 2000; Ericson et al., 2002a,b) confirm close affinities between the Meliphagidae , Pardalotidae–Acanthizidae, and Maluridae.”

“Barker et al. (2002) and Sorenson et al. (2003) used ambiguity codes and specified their treatment as polymorphisms, an approach that would have particular power using transversion-parsimony and in ML analyses.”

“We used a composite phylogeny based on information in Sibley and Ahlquist (1990) and Barker et al. (2001) for families and orders, combined with information in Badyaev (1997), Blondel et al. (1996), Cibois and Pasquet (1999), Leisler et al. (1997), Martin and Clobert (1996), Møller et al. (2001),…”

“Over 60% of all terrestrial birds globally are passerines and Australia was the major early centre of their radiation 5,6 .”

“Besides the water birds, progress has been made with DNA sequence analyses in understanding relationships within other neoavian groups, including the Passeriformes [Johansson et al., 2001, 2002; Barker et al., 2002; Yuri and Mindell, 2002; Cracraft et al., 2004].”

“The composite phylogenies used in the comparative analyses were based on Sibley and Ahlquist (1990), combined with information from other sources (Sheldon et al. 1992; Blondel et al. 1996; Slikas et al. 1996; Badyaev 1997; Helbig and Seibold 1999; Barker et al. 2001, 2004; Voelker and Spellman 2004) (Supplementary Fig…”

“While the phylogeny of Sibley & Ahlquist (1990) is controversial (Lanyon, 1992), phylogenetic analysis of mitochondrial cytochrome b sequences (Johnson, 2001) and nuclear gene sequences (Barker et al., 2002) for a large number of avian taxa produces similar relationships and identifies similar major groupings of birds.”

“We used species of two ‘‘warbler’’ radiations for our analysis: Old World Sylviid warblers, which are not a monophyletic assemblage (Sibley and Ahlquist 1990; Barker et al. 2001) and North American parulids.”

“It marks a geographical separation between divergent assemblages of birds, mammals, reptiles, insects and fishes, whose phylogenetic distinctness is confirmed by recent molecular phylogenetic studies (DeBoer & Duffels 1996; Keogh 1998; Barker et al. 2002 ).”

“…have previously been proven useful in resolving the earliest divergences in the avian phylogeny (Groth and Barrowclough 1999; Johansson et al. 2001; Barker et al. 2002; Ericson et al. 2002a; Irestedt et al. 2002), and the genes show low levels of homoplasy at this phylogenetic level (Groth and…”

“More recently, molecular phylogenies revealed the paraphyletic status of Corvida with the monophyletic Passerida nested within (Barker et al., 2004; 2002; Ericson et al., 2002). This new proposal switched the synchronous diversification scenario of Passerida in the Northern hemisphere and Corvida in the Southern hemis…”