Sequences new to this study are indicated in Electronic Appendix part A along with their associated GenBank accession numbers. The equally weighted parsimony analysis of the RAG-1 and RAG-2 sequences in combination yielded 481 equally parsimonious trees, the consensus of which was well resolved, and which contained a large number of well-supported nodes ( and ). Bayesian analysis of the data yielded estimated nodal posterior probabilities that were completely consistent with the majority rule consensus of most-parsimonious trees (i.e. no node with greater then or equal to 0.95 estimated posterior probability conflicted with the parsimony consensus). The estimates presented are based on eight Metropolis-coupled Markov chain Monte Carlo (MC
3) runs of 400

000 generations, with the first 250

000 of each discarded as burn-in. With sampling of every 100th generation, this left 1500 trees per run, for a total of 12

000 sampled trees. The Bayesian analysis differed from the parsimony analysis only in significantly supporting four nodes that were not present in the parsimony consensus, but that were consistent with that consensus. Partitioned Bayesian analysis of RAG-1 and RAG-2 indicated that the two genes are similar, though distinguishable, in evolutionary dynamics (, see Electronic Appendix part B). The estimated nodal posterior probabilities from the partitioned analysis were indistinguishable from those derived from the eight unpartitioned analyses (not shown). A conservative approach was taken to the representation of the support values on the figure, with values over 75% (grey) and 90% (black) for maximum parsimony or over 0.95 estimated Bayesian posterior probability indicated. Estimated divergence dates are shown () along with minimum and maximum values for selected nodes numbered on the tree figure.
| Table 2Data characteristics and estimated evolutionary parameters from phylogenetic analyses. (The number and resolution of trees, tree length (MP); CI (ensemble consistency index), and RI (ensemble retention index) values are derived from equally weighted parsimony (more ...) |
| Table 3Inferred dates of oscine divergences. (Shown are the average, minimum, and maximum values from relaxed molecular clock analysis of 100 bootstrap replicates of the complete RAG-1 and RAG-2 matrix (see §2). Numbered nodes are labelled on (more ...) |
The relationships among higher taxa inferred here are largely congruent with those reported previously (
Barker et al. 2002,
2004), given the differences in taxon and character sampling. Namely, we recover
Acanthisitta as sister to all other passerines, and two major groups corresponding to the traditionally recognized suboscines and oscines. Further, within the oscine passerines, we recover a basal grade of Australasian groups, with
Menura sister to all other oscines (, see also Electronic Appendix part B), rendering
Sibley & Ahlquist's (1990) parvorder ‘Corvida’ a paraphyletic grade. Most corvoid lineages are comprised in a single, large, well supported group that has been termed the ‘core Corvoidea’ (
Barker et al. 2002,
2004). A large group roughly corresponding to Sibley & Ahlquist's parvorder Passerida finds strong support, as do three groups roughly corresponding to their superfamilies Muscicapoidea, Passeroidea and Sylvioidea (, see also Electronic Appendix part B). As previously, this ‘Passerida’ clade forms an effective trichotomy with two other lineages, the Australasian Petroicidae, and the African Picathartidae, with optimal trees favouring a sister group relationship between the Passerida and the Petroicidae.
In addition to this broad overview, we elaborate on the relationships of the focal enigmatic African taxa added in this study. Within the ‘core Corvoidea’ (),
L. torquatus received strong support as the sister to
Batis, but this lineage was not further resolved within a clade of corvidans that include Asian ioras and African bushshrikes. In the Passerida, the Herero chat (
N. herero) appears to be more closely related to the saxicolines than to the turdines, although the composition of each of those groups is in flux (compare
Cibois & Cracraft 2004;
Voelker & Spellman 2004). Nicators (
N. chloris) were not supported as bush shrikes (Malaconotidae) or bulbuls (Pycnonotidae), instead appearing in a basal grade with Alaudidae (larks) and many of
Sibley & Ahlquist's (1990) Sylvioidea, which name we use for this group for brevity's sake. Given the basal position of
Nicator, we suggest that the three species of nicators comprise a new family.
Three different clades with ‘African warblers’ are well resolved in this monophyletic assemblage of Sylvioidea. The first includes the crombecs and a disparate array of southern African endemics, including the Damara rockjumper (
A. pycnopygius), Cape grass-warbler (
S. afer) and Victorin's warbler (
Bradypterus/
Cryptillas victorini); this novel clade is relatively basal within the Sylvioidea, sister to more than 1000 species. This clade probably also includes the African endemic
Melocichla, which is grouped with
Sphenoeacus and
Sylvietta in
Sibley & Ahlquist's (1990, pp. 798,
866) DNA hybridization study, and which some traditional taxonomists allied with
Sphenoeacus (
Dickinson 2003). The second large group in the monophyletic assemblage of Sylvioidea includes the tailorbird (
O. sutorius, placed in acrocephaline warblers by
Sibley & Ahlquist (1990)) and the Kopje warbler (
E. subcinnamomea) in the Cisticolidae. The third clade includes the megalurine warblers, the broad-tailed warbler, and the endemic Malagasy radiation (
Cibois 1999).
Two additional clades are noteworthy in that they were not predicted by traditional classifications. The first includes
Promerops,
Arcanator and
Modulatrix, all endemic to sub-Saharan Africa; we propose that the latter two taxa either be included in Promeropidae or be recognized with their own family name. This new clade is sister to an unresolved group that includes other Old World nectarivores (Nectariniidae, Irenidae and Dicaeidae) and core passeridans. Surprisingly, the African endemic fairy flycatcher (
S. scita) is strongly supported as part of the previously recognized ‘sylvioid flycatcher’ clade, comprising the genera
Elminia and
Culicicapa. We suggest that these taxa, with
Stenostira (Viellot 1818) having seniority, be recognized as the family Stenostiridae. The possible affinity of the African endemic
Myioparus to
Stenostira, suggested by
Urban et al. (1997, p. 498), remains to be tested; other African or Asian species might conceivably fall into this novel clade. The taxonomic status of all these new higher-level groups will depend on further sampling within Passerida.