Comparative anatomy versus molecular phylogenetics. Birds break the tree of Darwin The similarities are not necessarily indicative of affinities . How many more examples to be found , so that everyone was convinced about this ? plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0054848 Evolutionary relationships among birds in Neoaves, the clade comprising the vast majority of avian diversity, have vexed systematists due to the ancient, rapid radiation of numerous lineages. We applied a new phylogenomic approach to resolve relationships in Neoaves using target enrichment (sequence capture) and high-throughput sequencing of ultraconserved elements (UCEs) in avian genomes. We collected sequence data from UCE loci for 32 members of Neoaves and one outgroup (chicken) and analyzed data sets that differed in their amount of missing data. An alignment of 1,541 loci that allowed missing data was 87% complete and resulted in a highly resolved phylogeny with broad agreement between the Bayesian and maximum-likelihood (ML) trees. Although results from the 100% complete matrix of 416 UCE loci were similar, the Bayesian and ML trees differed to a greater extent in this analysis, suggesting that increasing from 416 to 1,541 loci led to increased stability and resolution of the tree. ***************Novel results of our study include surprisingly close relationships between phenotypically divergent bird families, such as tropicbirds (Phaethontidae) and the sunbittern (Eurypygidae) as well as between bustards (Otididae) and turacos (Musophagidae). This phylogeny bolsters support for monophyletic waterbird and landbird clades and also strongly supports controversial results from previous studies, including the sister relationship between passerines and parrots and the non-monophyly of raptorial birds in the hawk and falcon families. Although significant challenges remain to fully resolving some of the deep relationships in Neoaves, especially among lineages outside the waterbirds and landbirds, this study suggests that increased data will yield an increasingly resolved avian phylogeny.*********************************** [.....] The Surprising Relationship between Tropicbirds and the Sunbittern This study adds to the overwhelming evidence for a sister relationship between the phenotypically divergent flamingo and grebe families . Our results also suggest another surprisingly close affinity between morphologically disparate groups – tropicbirds and the sunbittern. Three of four analyses lent strong support to this relationship, for which ML support increased sharply (43% to 96%) when genomic sampling increased from 416 to 1,541 loci (Fig. 2; Fig. S1 & S2). A close relationship between the sunbittern and tropicbirds is surprising because of dissimilarities in appearance, habitat, and geography. Tropicbirds are pelagic seabirds with mostly white plumage, elongated central tail feathers, and short legs that make walking difficult. Meanwhile, the sunbittern is a cryptic resident of lowland and foothill Neotropical forests that spends much of its time foraging on the ground in and near freshwater streams and rivers. The kagu, a highly terrestrial bird restricted to the island of New Caledonia (not sampled in our study), is the sister species of the sunbittern and may superficially bear some similarity to tropicbirds. These results should spark further research into shared morphological characteristics of tropicbirds, the sunbittern, and the kagu. A Sister Relationship between Bustards and Turacos? Another surprising sister relationship uncovered in our study is that between turacos and bustards (Fig. 2a). Turacos are largely fruit-eating arboreal birds of sub-Saharan Africa, whereas bustards are large, omnivorous, terrestrial birds widely distributed in the Old World. Despite some overlap in their biogeography, the two families have little in common and have, to our knowledge, never been hypothesized to be closely related based on phenotypic characteristics. Previous molecular studies have placed members of these two families near one another evolutionarily , but never as sister taxa. Our study did not include a member of the cuckoo family, which has often been considered a close relative of the turacos and thus might be its true sister taxon. An additional note of caution is that a turaco-bustard relationship was not supported outside the 1,541 locus tree, but neither was it contradicted. Thus, although confirming results are needed, our study provides some support for the idea that turacos and bustards are much more closely related than previously thought, if not actually sister families. Further Clarity for Waterbird Relationships We found consistent support across all analyses for relationships among the six sampled families within the waterbirds (Figs. 2 and 3). Prior to the availability of molecular data, the relationships within this clade were difficult to resolve due to the extreme morphological diversity of its members and the scarcity of apomorphic morphological characters. The topology we recovered within this portion of the tree is identical to that of Hackett et al. . For example, in both studies loons are the outgroup to all other waterbirds, and the morphologically divergent penguins are sister to tube-nosed seabirds in the family Procellariidae. Hoatzin: Still a Riddle Wrapped in a Mystery… Hoatzin (Opisthicomus hoazin), the only extant member of Opisthocomidae, is arguably the most enigmatic living bird species due to its unique morphology, folivorous diet, and confusion relative to its evolutionary affinities across numerous molecular phylogenies. One phylogenetic study found no support for a sister relationship between hoatzin and the Galloanserae, nor with turacos, cuckoos, falcons, trogons, or mousebirds in Neoaves; the study found some, albeit weak, support for a sister relationship between hoatzin and doves . The 416 locus Bayesian tree placed the hoatzin sister to a shorebird (Fig. 2b) with high support, but we did not observe this relationship in either the ML tree or the species tree. Furthermore, support for any definitive placement of the hoatzin eroded in the 1,541 locus tree (Fig. 2a). A close relationship of hoatzin to shorebirds would be extremely surprising and in stark contrast to any prior hypotheses [68]. Our results raise the question of whether or not more data will eventually lead to a definitive conclusion on the phylogenetic position of the hoatzin. Given the phylogenetic distinctiveness of the hoatzin, better taxonomic sampling may be as beneficial as further genomic sampling in the search for shared, derived characters deep in the tree. Thus, we present a link between the hoatzin and shorebirds, a large family whose members are found in diverse terrestrial and aquatic habitats, as an intriguing phylogenetic hypothesis. An Early Divergence for Pigeons and Doves? Another place where our 416 locus trees showed support for a relationship not found in the 1,541 locus trees was in the placement of the pigeon and dove family (Columbidae). Most prior studies either placed pigeons and doves in an unresolved position or sister to sandgrouse (Pteroclididae) within Metaves . However, amino acid sequences of feather beta-keratins have suggested a basal position of Columbidae within Neoaves . We found complete support in the 416-locus Bayesian tree for a sister relationship between Columbidae and the rest of Neoaves (Fig. 2b). We also recovered this relationship in the 416-locus ML tree and species tree, although with weak support (Fig. S2). However, the 1,541 locus trees disagreed by placing pigeons and doves in a more conventional position sister to sandgrouse and instead placing trumpeters sister to the rest of Neoaves (Fig. 2a). Support for Controversial Relationships within the Landbirds One of the biggest challenges to conventional thought on bird phylogeny contained in Hackett et al. was in the relationships among landbirds. Their finding that parrots were the sister family to passerines is still viewed as controversial (bootstrap support for parrots+passerines from Hackett et al. was 77%), despite corroborating evidence from rare genomic changes encoded in retroposons and expanded data sets. Our results across all analyses strongly support the sister relationship between passerines (in this study represented by a suboscine Pitta and an oscine Vidua) and parrots (perfect support in all Bayesian and ML trees; 85% support in the species tree). Our results also support another controversial finding from Hackett et al.: the absence of a sister relationship between raptorial birds in the hawk (Accipitridae) and falcon (Falconidae) families. Both ML and Bayesian trees from the 1,541 locus analysis provided perfect support for falcons sister to the parrot+passerine clade, whereas the representative of the hawk family was sister to the vultures with high support, improving upon the weak support for hawks+vultures from Hackett et al. Finally, the larger 1,541 analysis helped resolve deeper relationships within the landbirds among four main clades: (i) passerines+parrots+falcons, (ii) hawks+vultures, (iii) the group sometimes called the “near passerines” (e.g., barbet, woodpecker, woodhoopoe, motmot, and trogon, also known as the CPBT clade in because it includes the families Coraciiformes, Piciformes, Bucerotiformes, and Trogoniformes), and (iv) owls (Fig. 2a). The Bayesian tree placed owls sister to the “near passerines” and then hawks+vultures sister to owls+“near passerines”, a topology that also appeared in the ML tree with weak support. Meanwhile, the evolutionary affinities of mousebirds, whose position in prior studies has been uncertain , remain equivocal. The 416 locus trees positioned mousebirds sister to the “near passerines”, but the 1,541 locus trees placed mousebirds sister to passerines. Wang et al.also found mousebirds moving between these two clades depending on the analysis. Other relationships within the “near passerines” were consistent with previous results except that the positions of trogons and motmots switched between the 416 and 1,541 locus trees. A Scarcity of Indels on Short Internal Branches Our finding that informative indels were generally scarce (found only on four of the longest internal branches in the phylogeny; Fig. 4) corroborates previous work on rare genomic changes in retroposons, which also found little evidence for shared events deep in the bird phylogeny . The low prevalence of informative indels may be exacerbated by the lack of major structural changes in and around UCE loci, although this has not been well studied. Previous work on nuclear introns has identified a handful of indels supporting major subdivisions deep in avian phylogeny, However, lessons from coalescence theory caution that, when drawing phylogenetic inferences from rare genomic changes, numerous loci supporting particular subdivisions are required to account for the expected high variance in gene histories . The study of bird phylogeny awaits a genome-scale analysis of many hundreds of rare genomic events including indels, retroposons, and microRNAs.
Posted on: Sun, 16 Mar 2014 06:32:31 +0000
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