A molecular phylogeny of the cotingas (Aves: Cotingidae)

The phylogenetic relationships of members of Cotingidae were investigated using >2100 bp of sequence data from two nuclear introns (myoglobin intron 2 and G3PDH intron 11) and one protein-coding mitochondrial gene (cytochrome b). Strong support was found for a monophyletic clade including 23 traditional cotingid genera, corresponding to the Cotingidae sensu [Remsen, J.V. Jr., Jaramillo, A., Nores, M., Pacheco, J.F., Robbins, M.B., Schulenberg, T.S., Stiles, F.G., da Silva, J.M.C., Stotz, D.F., Zimmer, K.J., 2005. Version 2005-11-15. A classification of the bird species of South America. American Ornithologists' Union. ]. Neither Oxyruncus nor any of the genera in Tityrinae sensu [Prum, R.O, Lanyon, W.E., 1989. Monophyly and phylogeny of the Schiffornis group (Tyrannoidea). Condor 91, 444-461.] are members of Cotingidae. Within Cotingidae a polytomy of four well-supported clades was recovered: (1) the fruiteaters Pipreola and Ampelioides; (2) the Ampelion group, including Phytotoma; (3) Rupicola and Phoenicircus; and (4) the 'core cotingas' consisting of the remainder of the Cotingas (e.g. fruitcrows, Cotinga, Procnias, Lipaugus, and Carpodectes), with Snowornis in a basal position. The separation of Snowornis from Lipaugus [Prum, R.O, Lanyon, W.E., 1989. Monophyly and phylogeny of the Schiffornis group (Tyrannoidea). Condor 91, 444-461.] was strongly supported, as were the close relationships between Gymnoderus and Conioptilon, and between Tijuca and Lipaugus. However, basal relationships among 'core cotinga' clades were not resolved.     

A molecular phylogeny of bullfinches Pyrrhula Brisson, 1760 (Aves: Fringillidae)

We present a molecular phylogeny of bullfinches (Pyrrhula Brisson, 1760) based on 2357bp DNA sequence information of mitochondrial genes (cyt-b, 16S rRNA) and nuclear introns (fib-7, GAPDH-11). The genus is clearly a monophyletic group. Within the limits of Pyrrhula, molecular methods support the subdivision of three main groups: (1) "Southeast-Asian bullfinches" (P. nipalensis and P. leucogenis), (2) "Himalayan bullfinches" (P. aurantiaca, P. erythaca, P. erythrocephala), and (3) "Eurasian bullfinches" (P. pyrrhula s.l.). Within the last group there are four different subgroups: (3a) P. (p.) murina, (3b) P. (p.) cineracea, (3c) P. (p.) griseiventris, and (3d) P. pyrrhula s.str. The centre of origin of the genus Pyrrhula was most probably Southeast Asia. Incomplete lineage sorting of both mitochondrial and nuclear genes is observed among two apparently good species (P. erythaca and P. erythrocephala) indicating a very recent speciation event within the Himalayan Mountain chain. According to our estimates, the Pyrrhula ancestors split from the Pinicola ancestors before the Pleistocene. Apart from the subsequent Pre-Pleistocene splits of the three ancestral main groups, most of the diversification of today's representatives probably took place during the past 600,000 years, possibly in interaction with Pleistocene refugia and successive colonization movements after the last glaciation. Thus our work confirms the traditional delimitation of the bullfinches towards the other members of the finch family Fringillidae and corroborates most of the classic intra-generic subdivisions.     

A new phylogeny of swiftlets (Aves: Apodidae) based on cytochrome-b DNA

Due to a lack of distinctive morphological characters, swift taxonomy and phylogeny has always been an area of disagreement. To shed more light on this subject, we reconstructed swift(let) phylogeny based on 1143 bp of mitochondrial cytochrome-b DNA sequence. Although this is not the first attempt to reconstruct swift phylogeny using molecular data, our results show higher support for many of the branches due to our much longer sequences. However, placement of Hydrochous is still unexpected. Implementation of more conservative genetic regions and sampling of more taxa could solve this problem. Most importantly, the Collocaliini resolve as a monophyletic group. The internal structure of the group shows that non-echolocating Collocalia and echolocating Aerodramus form two distinct clades. This is in congruence with earlier classifications based on morphological characters, but in contrast with more recent classifications.     

Genetic Differentiation Among Populations of the Roseate Spoonbill (Platalea ajaja; Aves: Pelecaniformes) in Three Brazilian Wetlands

Effective population size, levels of genetic diversity, gene flow, and genetic structuring were assessed in 205 colonial Roseate spoonbills from 11 breeding colonies from north, central west, and south Brazil. Colonies and regions exhibited similar moderate levels of diversity at five microsatellite loci (mean expected heterozygosity range 0.50–0.62; allelic richness range 3.17–3.21). The central west region had the highest Ne (59). F _ST values revealed low but significant genetic structuring among colonies within the north and within the south regions. Significant global genetic structuring was found between the northern and central western populations as well as between the northern and southern populations. An individual-based Bayesian clustering method inferred three population clusters. Assignment tests correctly allocated up to 64% of individuals to their source regions. Collectively, results revealed complex demographic dynamics, with ongoing gene flow on a local scale, but genetic differentiation on a broader scale. Populations in the three regions may all be conserved, but special concern should be given to central western ones, which can significantly contribute to the species’ gene pool in Brazil.     

A multilocus molecular phylogeny of boxfishes (Aracanidae,Ostraciidae; Tetraodontiformes)

Boxfishes (superfamily Ostracioidea, order Tetraodontiformes) are comprised of 37 species within the families Aracanidae (13 sp.) and Ostracidae (24 sp.). These species are characterized by several dramatic reductive trends in their axial and appendicular skeleton, and by the presence of a carapace formed by enlarged and thickened scale plates. While strong support exists for the monophyly of both families, interspecific relationships remain unclear as no species-level molecular phylogeny currently exists for either of these two clades, and the only hypotheses of relationships are based on morphological studies that were mostly restricted to generic-level relationships. Here we present the results of a new phylogenetic study of a dataset composed of 9 loci for 26 species of boxfishes using both likelihood and Bayesian methods. Our topology strongly supports the monophyly of both groups, and additionally provides strongly supported resolution for the vast majority of species-level interrelationships. Based on this new phylogeny, we suggest changing the taxonomic status of the species Lactoria fornasini to Tetrasomus fornasini, and Rhynchostracion nasus to Ostracion nasus. Using a Bayesian approach to divergence time estimation we inferred a Paleocene origin of the Ostracioidea, with an estimated origin of the reef-associated ostraciids spanning the Eocene and Oligocene, and a Miocene/Pliocene origin of the aracanids.     

A phylogeny of the megapodes (Aves: Megapodiidae) based on nuclear and mitochondrial DNA sequences

DNA sequences from the first intron of the nuclear gene rhodopsin (RDP1) and from the mitochondrial gene ND2 were used to construct a phylogeny of the avian family Megapodiidae. RDP1 sequences evolved about six times more slowly than ND2 and showed less homoplasy, substitution bias, and rate heterogeneity across sites. Analysis of RDP1 produced a phylogeny that was well resolved at the genus level, but RDP1 did not evolve rapidly enough for intrageneric comparisons. The ND2 phylogeny resolved intrageneric relationships and was congruent with the RDP1 phylogeny except for a single node: this node was the only aspect of tree topology sensitive to weighting in parsimony analyses. Despite differences in sequence evolution, RDP1 and ND2 contained congruent phylogenetic signal and were combined to produce a phylogeny that reflects the resolving power of both genes. This phylogeny shows an early split within the megapodes, leading to two major clades: (1) Macrocephalon and the mound-building genera Talegalla, Leipoa, Aepypodius, and Alectura, and (2) Eulipoa and Megapodius. It differs significantly from previous hypotheses based on morphology but is consistent with affiliations suggested by a recent study of parasitic chewing lice.     

Molecular phylogeny of Palearctic-African Acrocephalus and Hippolais Warblers (Aves: Sylviidae)

Phylogenetic relationships of the reed warbler group (genera Acrocephalus, Hippolais, Chloropeta; Aves: Passeriformes) and their potential relatives were studied using nucleotide sequences (1 kb) of the mitochondrial cytochrome b gene. This species-rich but morphologically poorly differentiated group of insectivorous passerines is distributed in Eurasia, Africa, and Australasia. Intergeneric relationships were poorly resolved, but monophyly of the reed warbler group (including Chloropeta) versus other Sylviidae was strongly supported. A basal polytomy within the reed warbler group consists of seven branches and may indicate a rapid early radiation. In the genus Acrocephalus three major clades were identified, which corresponded to phenotypic groups characterized by body size and plumage patterns. However, current delimitation of some subgenera (Acrocephalus, Lusciniola, Bebrornis) is at variance with our phylogeny estimate, and appropriate revisions are proposed. The genus Hippolais, which may or may not be monophyletic, consisted of two well-supported clades of four species each. Some Acrocephalus taxa whose species status had been doubted (griseldis, tangorum, orientalis, australis) proved to be highly distinct genetically. Genetic distances between members of two pairs of allopatric Hippolais taxa (caligata/rama; opaca/elaeica) were as large or larger than between other closely related warbler species. Overall, cytochrome b sequences resolved phylogenetically young relationships quite well, whereas more ancient nodes remained poorly resolved.     

Evolution in Australasian mangrove forests: multilocus phylogenetic analysis of the Gerygone warblers (Aves: Acanthizidae)

The mangrove forests of Australasia have many endemic bird species but their evolution and radiation in those habitats has been little studied. One genus with several mangrove specialist species is Gerygone (Passeriformes: Acanthizidae). The phylogeny of the Acanthizidae is reasonably well understood but limited taxon sampling for Gerygone has constrained understanding of its evolution and historical biogeography in mangroves. Here we report on a phylogenetic analysis of Gerygone based on comprehensive taxon sampling and a multilocus dataset of thirteen loci spread across the avian genome (eleven nuclear and two mitochondrial loci). Since Gerygone includes three species restricted to Australia's coastal mangrove forests, we particularly sought to understand the biogeography of their evolution in that ecosystem. Analyses of individual loci, as well as of a concatenated dataset drawn from previous molecular studies indicates that the genus as currently defined is not monophyletic, and that the Grey Gerygone (G. cinerea) from New Guinea should be transferred to the genus Acanthiza. The multilocus approach has permitted the nuanced view of the group's evolution into mangrove ecosystems having occurred on multiple occasions, in three non-overlapping time frames, most likely first by the G. magnirostris lineage, and subsequently followed by those of G. tenebrosa and G. levigaster.     

A multilocus microsatellite phylogeny of the Drosophila virilis group

We used a set of 48 polymorphic microsatellites derived from Drosophila virilis to infer phylogenetic relationships in the D. virilis clade. Consistent with previous studies, D. virilis and D. lummei were the most basal species of the group. Within the D. montana phylad, the phylogenetic relationship could not be resolved. Special attention was given to the differentiation between D. americana texana, D. americana americana and D. novamexicana. Significant differences between these three groups were detected by F(ST) analyses. Similarly, a model-based clustering method for multilocus genotype data also provided strong support for the presence of three differentiated groups. This genome-wide differentiation between D. americana texana and D. americana americana contrasts with previous analyses based on DNA sequence data.     

A multi-gene phylogeny of aquiline eagles (Aves: Accipitriformes) reveals extensive paraphyly at the genus level

The phylogeny of the tribe Aquilini (eagles with fully feathered tarsi) was investigated using 4.2 kb of DNA sequence of one mitochondrial (cyt b) and three nuclear loci (RAG-1 coding region, LDH intron 3, and adenylate-kinase intron 5). Phylogenetic signal was highly congruent and complementary between mtDNA and nuclear genes. In addition to single-nucleotide variation, shared deletions in nuclear introns supported one basal and two peripheral clades within the Aquilini. Monophyly of the Aquilini relative to other birds of prey was confirmed. However, all polytypic genera within the tribe, Spizaetus, Aquila, Hieraaetus, turned out to be non-monophyletic. Old World Spizaetus and Stephanoaetus together appear to be the sister group of the rest of the Aquilini. Spizastur melanoleucus and Oroaetus isidori are nested among the New World Spizaetus species and should be merged with that genus. The Old World 'Spizaetus' species should be assigned to the genus Nisaetus (Hodgson, 1836). The sister species of the two spotted eagles (Aquila clanga and Aquila pomarina) is the African Long-crested Eagle (Lophaetus occipitalis). Hieraaetus fasciatus/spilogaster are closest to Aquila verreauxii and should be merged with that genus. Wahlberg's Eagle H. wahlbergi, formerly placed in Aquila, is part of a clade including three small Hieraaetus species (pennatus, ayresii, and morphnoides). The Martial Eagle (Polemaetus bellicosus) is the sister species of the Aquila/Hieraaetus/Lophaetus clade. Basal relationships within this clade remained unresolved. Parsimony reconstruction of the evolution of plumage pattern within Aquilini suggests that: (1) transverse barring of parts of the body plumage was lost in the Palearctic Aquila-Hieraaetus clade, (2) pale underparts in adult plumage evolved three times independently, and (3) dimorphic adult plumage is a derived character of the small-bodied Hieraaetus clade.     

A multilocus molecular phylogeny of the parrots (Psittaciformes): support for a Gondwanan origin during the cretaceous

The question of when modern birds (Neornithes) first diversified has generated much debate among avian systematists. Fossil evidence generally supports a Tertiary diversification, whereas estimates based on molecular dating favor an earlier diversification in the Cretaceous period. In this study, we used an alternate approach, the inference of historical biogeographic patterns, to test the hypothesis that the initial radiation of the Order Psittaciformes (the parrots and cockatoos) originated on the Gondwana supercontinent during the Cretaceous. We utilized broad taxonomic sampling (representatives of 69 of the 82 extant genera and 8 outgroup taxa) and multilocus molecular character sampling (3,941 bp from mitochondrial DNA (mtDNA) genes cytochrome oxidase I and NADH dehydrogenase 2 and nuclear introns of rhodopsin intron 1, tropomyosin alpha-subunit intron 5, and transforming growth factor ss-2) to generate phylogenetic hypotheses for the Psittaciformes. Analyses of the combined character partitions using maximum parsimony, maximum likelihood, and Bayesian criteria produced well-resolved and topologically similar trees in which the New Zealand taxa Strigops and Nestor (Psittacidae) were sister to all other psittaciforms and the cockatoo clade (Cacatuidae) was sister to a clade containing all remaining parrots (Psittacidae). Within this large clade of Psittacidae, some traditionally recognized tribes and subfamilies were monophyletic (e.g., Arini, Psittacini, and Loriinae), whereas several others were polyphyletic (e.g., Cyclopsittacini, Platycercini, Psittaculini, and Psittacinae). Ancestral area reconstructions using our Bayesian phylogenetic hypothesis and current distributions of genera supported the hypothesis of an Australasian origin for the Psittaciformes. Separate analyses of the timing of parrot diversification constructed with both Bayesian relaxed-clock and penalized likelihood approaches showed better agreement between geologic and diversification events in the chronograms based on a Cretaceous dating of the basal split within parrots than the chronograms based on a Tertiary dating of this split, although these data are more equivocal. Taken together, our results support a Cretaceous origin of Psittaciformes in Gondwana after the separation of Africa and the India/Madagascar block with subsequent diversification through both vicariance and dispersal. These well-resolved molecular phylogenies will be of value for comparative studies of behavior, ecology, and life history in parrots.     

A multilocus phylogeny of New World jay genera

We studied phylogenetic relationships of the New World Jays (NWJs) based on DNA sequences from three mitochondrial and two nuclear loci. Sampling included at least two individuals from each of the seven NWJ genera and four outgroups of closely related corvids, as well as six of the 16 Cyanocorax species (including two representatives of the previously recognized "Cissilopha"). Phylogenetic analyses were conducted using maximum parsimony, maximum likelihood, and Bayesian analyses for individual genes and a combined dataset. The combined phylogenetic analysis supports the basal position of Cyanolyca to all other NWJs, a (Cyanocorax (Calocitta, Psilorhinus)) clade, and a ((Cyanocitta, Aphelocoma) Gymnorhinus) clade that agrees with a novel morphological synapomorphy uniting Cyanocitta and Aphelocoma. Within Cyanocorax, C. yncas (former "Xanthoura") is basal to a split among former "Cyssilopha" species and the rest of the Cyanocorax species. To explore implications for the historical biogeography of the NJWs, we used Dispersal-Vicariance Analysis, which indicated that NWJs originated either in Mesoamerica or North America+Mesoamerica, with South American NWJs dispersing three times independently from Mesoamerica.     

A multi‐gene phylogeny disentangles the chat‐flycatcher complex (Aves: Muscicapidae)

Zuccon, D. & Ericson, P. G. P. (2010). A multi‐gene phylogeny disentangles the chat‐flycatcher complex (Aves: Muscicapidae).—Zoologica Scripta, 39, 213–224. We reconstructed the first well‐sampled phylogenetic hypothesis in the chat‐flycatcher complex combining nuclear and mitochondrial sequences. The dichotomy between chats‐terrestrial feeders and flycatchers‐aerial feeders does not reflect monophyletic groups. The flycatching behaviour and morphological adaptations to aerial feeding (short tarsi, broad bill, rictal bristles) evolved independently from chat ancestors in three different lineages. The genera Alethe, Brachypteryx, and Myiophonus are nested within the Muscicapidae radiation and their morphological and behavioural similarities with the true thrushes Turdidae are presumably the result of convergence. The postulated close relationships among Erithacus, Luscinia and Tarsiger cannot be confirmed. Erithacus is part of the African forest robin assemblage (Cichladusa, Cossypha, Pogonocichla, Pseudalethe, Sheppardia, Stiphrornis), while Luscinia and Tarsiger belong to a large, mainly Asian radiation. Enicurus belongs to the same Asian clade and it does not deserve the recognition as a distinct subfamily or tribe. We found good support also for an assemblage of chats adapted to arid habitats (Monticola, Oenanthe, Thamnolaea, Myrmecocichla, Pentholaea, Cercomela, Saxicola, Campicoloides, Pinarochroa) and a redstart clade (Phoenicurus, Chaimarrornis and Rhyacornis). Five genera (Muscicapa, Copsychus, Thamnolaea, Luscinia and Ficedula) are polyphyletic and in need of taxonomic revision.     

Speciational history of North American Haemorhous finches (Aves: Fringillidae) inferred from multilocus data

We investigated species relationships and timing of speciation in North American Haemorhous finches by using a mitochondrial phylogeographic approach combined with a multilocus species tree reconstruction. Haemorhous purpureus and H. cassinii were strongly supported as sister taxa, and H. mexicanus was sister to H. purpureus + H. cassinii. Our divergence times indicated that diversification within Haemorhous occurred progressively from the Late Miocene into the Pleistocene. Our inferred pattern of speciation demonstrates the complexity of the origins of North American birds, and provides additional evidence that a single cause for speciation in closely related North American birds, such as Late Pleistocene glacial–interglacial cycles, is unlikely.     

A molecular phylogeny of the African widowbirds and bishops, Euplectes spp. (Aves: Passeridae: Ploceinae)

The elaborate male displays and plumage ornaments in the African widowbirds and bishops (Euplectes spp.) have inspired classic studies on mating systems and sexual selection. In order to study the extreme divergence in ornament design and expression in this group, we present and discuss a well-supported molecular phylogeny of the genus and its placement within the Ploceinae subfamily. Parsimony and Bayesian analyses were performed on 2557bp of mitochondrial DNA (ATP6, Cyt b, ND2 and ND3) and a nuclear intron (G3PDH). All 17 Euplectes species, and 31 of 51 suggested subspecies, were included, as well as eight Ploceinae outgroups from four genera (Amblyospiza, Ploceus, Quelea and Foudia). Our results show monophyly of Euplectes, but not of the intrageneric groupings of bishops and widowbirds. Most notably, the Red-collared Widowbird E. ardens belongs to a subclade of bishops, and not to the sister subclade of 'true' widowbirds. Furthermore, the two bishops E. afer and E. aureus represent lineages that branched off before this basal split, which also refutes the proposed superspecies of E. afer and E. diadematus. Also somewhat surprisingly, and despite the striking plumage similarities among the red bishops, E. franciscanus is not closely related to either E. nigroventris or E. orix (of which it until recently was considered a subspecies). Finally, the Mountain Marsh Widowbird E. psammocromius is likely closest to the Long-tailed Widowbird E. progne, and not, as previously thought, to the Marsh Widowbird E. hartlaubi.     

A multilocus phylogeny of Asian noodlefishes Salangidae (Teleostei: Osmeriformes) with a revised classification of the family

A group of small and transparent Asian noodlefishes (Osmeriformes: Salangidae) are commercially important fishery species, however, interrelationships among these fishes remain unresolved in previous studies using mitochondrial markers. We re-examine phylogenetic relationships of Salangidae by including complete taxon sampling, based on seven nuclear loci and one mitochondrial gene using a multilocus coalescence-based species-tree method. Our results show a well-resolved phylogeny of Salangidae that does not agree with previous hypotheses. The topology test suggests that our hypothesis represents the most likely phylogeny. Using the inferred species-tree as criterion, we recombine the rank of subfamilies and genera in the Salangidae, and erect a new genus Neosalangichthys. Our revised classification of Salangidae is well supported by reinterpreting previously proposed diagnostic characters. Finally, re-defined synapomorphic characters are used to erect a key to the genera of Salangidae.     

Multilocus perspectives on the monophyly and phylogeny of the order Charadriiformes (Aves)

Background  

The phylogeny of shorebirds (Aves: Charadriiformes) and their putative sister groups was reconstructed using approximately 5 kilobases of data from three nuclear loci and two mitochondrial genes, and compared to that based on two other nuclear loci.     

Molecular phylogeny of the genus Buteo (Aves: Accipitridae) based on mitochondrial marker sequences

DNA sequences of the mitochondrial nd6 gene and the non-repetitive part of the pseudo-control region (PsiCR) were isolated from 101 individuals to analyze the phylogenetic relationships among all buzzards of the genus Buteo and other buteonine genera. Comparisons of the two marker sequences indicate that the PsiCR evolved two times faster than the nd6 gene. The PsiCR proved to be an efficient, neutral genetic marker sequence for phylogenetic analyses at the intrageneric level, especially suitable for analyses based on old tissues, where only short fragments can be obtained. The molecular data set implies a neotropical origin of the genus Buteo. Monophyly of the genus Buteo as currently defined is contradicted due to the positions of Asturina nitida, Geranoaetus melanoleucus, Buteo magnirostris, and Buteo leucorrhous. These findings suggest several taxonomic consequences. A. nitida and G. melanoleucus should be included into the genus Buteo. Moreover, B. leucorrhous should be transferred into the genus Percnohierax (which clusters with Parabuteo), and B. magnirostris into the genus Rupornis. According to this classification of the genus Buteo, the basal lineage of the genus is formed by a clade containing Buteo polyosoma, Buteo poecilochrous, and Buteo melanoleucus. The "woodland buteos" form a paraphyletic assemblage with B. magnirostris as a clearly separated lineage basal to the genus Buteo.     

A molecular phylogeny of New Zealand's Petroica (Aves: Petroicidae) species based on mitochondrial DNA sequences

The New Zealand robin (Petroica australis), tomtit (P. macrocephala), and Chatham Island black robin (P. traversi) are members of the Petroicidae family of Australo-Papuan robins, found throughout Australasia and the western Pacific. In the nearly 200 years since the New Zealand members of Petroicidae were first described, the division of species, subspecies, and even genera has undergone many changes. In this study, we investigate whether molecular phylogenies based on mitochondrial DNA sequences support current taxonomic classifications based on morphology. Petroica traversi, P. australis, and P. macrocephala form distinct clades in phylogenetic trees constructed from Cytochrome b and control region sequences, however the position of the black robin is at odds with the morphological and behavioral data. The black robin does not appear to be a derivative of the New Zealand robin, instead it groups strongly with the tomtit, indicating that lineage sorting and/or introgressive hybridization may have occurred. There is some evidence to support the hypothesis that two invasions of Petroica from Australia have occurred, however additional data from Australian Petroica taxa are required to confirm this. Control region sequences confirm a deep split between the North and South Island P. australis lineages, but suggest a recent radiation of P. macrocephala.