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The Long-billed Tailorbird ( Artisornis moreaui ), one of Africa’s rarest birds, has a strikingly disjunct distribution, the origin of which has long puzzled biogeographers. One small population (subspecies moreaui ) occurs in sub-montane forest in the East Usambara Mountains, a sky island near the coast of northern Tanzania, and another (subspecies sousae ) on Serra Jeci in northwestern Mozambique, 950 km away. The African Tailorbird, the putative sister-species of Long-billed Tailorbird, also occurs in the East Usambara Mountains and on Serra Jeci, but in addition occupies all the Eastern Arc Mountain forests between these disjunct sites. Stuart (1981) hypothesized that the two tailorbird distributions could be explained by strong ecological competition, with African Tailorbird populations having eliminated Long-billed Tailorbird populations via competitive exclusion in montane forests between the East Usambara and Serra Jeci. If such competitive exclusion explains these geographic distributions, the co-occurrence of the two species in the East Usambara and at Serra Jeci may be ephemeral, with the status of Long-billed Tailorbird especially in doubt. We sought to (1) determine whether the two species of African tailorbirds are indeed sister-species, and (2) test predictions from Stuart’s (1981) competitive exclusion hypothesis using genetic data. Phylogenetic analyses of our seven gene dataset (3 mtDNA, 4 introns; 4784 bp) indeed place these two species together in the genus Artisornis . Instead of finding shallow divergence among African Tailorbird populations and deep divergence between Long-billed Tailorbird populations as expected from Stuart’s hypothesis, we recover deep genetic divergence and geographic structure among populations of both tailorbird species. This result is consistent with long-term co-existence of the two species at East Usambara and Serra Jeci. Observational data from both the East Usambara and Serra Jeci suggest that the two species have diverged in use of forest canopy strata. From a conservation standpoint, our results suggest that extinction of the Long-billed Tailorbird as a function of competition with African Tailorbird is highly unlikely, and should not be viewed as imminent. Threats to its survival are instead anthropogenic, and conservation measures should take this into account. Finally, our empirical results suggest that mis-specification of the branch-length prior in Bayesian analyses of mitochondrial DNA data can have a profound effect on the overall tree-length (sum of branch-lengths), whereas the topology and support values tend to remain more stable. In contrast, mis-specification of the branch-length prior had a lesser impact on all aspects of the nuclear-only DNA analyses. This problem may be exacerbated when mitochondrial and nuclear DNA analyses are combined in a total evidence approach. [ABSTRACT FROM AUTHOR]

Abstract: Recent molecular studies on passerine birds have highlighted numerous discrepancies between traditional classification and the phylogenetic relationships recovered from sequence data. Among the traditional families that were shown to be highly polyphyletic are the Muscicapidae Old World flycatcher. This family formerly included all Old World passerines that forage on small insects by performing short sallies from a perch. Genera previously allocated to the Muscicapidae are now thought to belong to at least seven unrelated lineages. While the peculiarity of most of these lineages has been previously recognized by Linnean classification, usually at the rank of families, one, the so-called Stenostiridae, a clade comprising three Afrotropical and Indo-Malayan genera, has only recently been discovered. Here, we address in greater detail the phylogenetic relationships and biogeographic history of the Stenostiridae using a combination of mitochondrial and nuclear data. Our analyses revealed that one species, Rhipidura hypoxantha, previously attributed to the Rhipiduridae (fantails), is in fact a member of the Stenostiridae radiation and sister to the South African endemic genus Stenostira (Fairy Flycatcher). Our dating analyses, performed in a relative-time framework, suggest that the splits between Stenostira/R. hypoxantha and Culicicapa/Elminia occurred synchronously. Given that the Stenostiridae assemblage has been consistently recovered by independent studies, we clarify its taxonomic validity under the rules of the International Code of Zoological Nomenclature. [Copyright &y& Elsevier]

Abstract: We address the phylogenetic relationships of the drongos (Dicruridae) at the species-level using sequences from two nuclear (myoglobin intron-2 and c-mos) and two mitochondrial (ND2 and cytochrome b) loci. The resulting phylogenetic tree shows that the most basal species is D. aeneus, followed in the tree by a trichotomy including (1) the Asian D. remifer, (2) a clade of all African and Indian Ocean islands species as well as two Asian species (D. macrocercus and D. leucophaeus) and (3) a clade that includes all other Asian species as well as two Australasian species (D. megarhynchus and D. bracteatus). Our phylogenetic hypotheses are compared to [Mayr, E., Vaurie, C., 1948. Evolution of the family Dicruridae (Birds). Evolution 2, 238–265.] hypothetical family “tree” based on traditional phenotypic analysis and biogeography. We point out a general discrepancy between the so-called “primitive” or “unspecialized” species and their position in the phylogenetic tree, although our results for other species are congruent with previous hypotheses. We conduct dating analyses using a relaxed-clock method, and propose a chronology of clades formation. A particular attention is given to the drongo radiation in Indian Ocean islands and to the extinction–invasion processes involved. The first large diversification of the family took place both in Asia and Africa at 11.9 and 13.3Myr, respectively, followed by a dispersal event from Africa to Asia at ca 10.6Myr; dispersal over Wallace line occurred later at ca 6Myr. At 5Myr, Principe and Indian Ocean Islands have been colonized from an African ancestor; the most recent colonization event concerned Anjouan by an immigrating population from Madagascar. [Copyright &y& Elsevier]

Abstract: We investigated the phylogenetic relationships among the major lineages of the avian family Sturnidae and their placement within the Muscicapoidea clade using two nuclear (RAG-1 and myoglobin) and one mitochondrial gene (ND2). Among Muscicapoidea, we recovered three clades corresponding to the families Cinclidae, Muscicapidae and Sturnidae (sensu [Sibley, C.G., Monroe Jr., B.L., 1990. Distribution and Taxonomy of Birds of the World. Yale University Press, New Haven, CT]). Within the sturnoid lineage Mimini and Sturnini are sister groups, with Buphagus basal to them. We identified three major lineages of starlings: the Philippine endemic genus Rhabdornis, an Oriental-Australasian clade (genera Scissirostrum, Gracula, Mino, Ampeliceps, Sarcops, Aplonis), and an Afrotropical-Palaearctic clade (all African taxa, Sturnus and Acridotheres). We discuss the biogeographic implications of our findings and suggest an Asiatic origin for this family. The congruence between the age of major clades, estimated by NPRS, and palaeoclimatic data present evidence for the role of climatic changes in shaping present day distribution of the group. [Copyright &y& Elsevier]

The widespread Old World avian family Locustellidae (‘grassbirds and allies’) comprises 62 extant species in 11 genera. In the present study, we used one mitochondrial and, for most species, four nuclear loci to infer the phylogeny of this family. We analysed 59 species, including the five previously unsampled genera plus two genera that had not before been analysed in a densely sampled dataset. This study revealed extensive disagreement with current taxonomy; the genera Bradypterus , Locustella , Megalurus , Megalurulus and Schoenicola were all found to be non-monophyletic. Non-monophyly was particularly pronounced for Megalurus , which was widely scattered across the tree. Three of the five monotypic genera ( Amphilais , Buettikoferella and Malia ) were nested within other genera; one monotypic genus ( Chaetornis ) formed a clade with one of the two species of Schoenicola ; whereas the position of the fifth monotypic genus ( Elaphrornis ) was unresolved. Robsonius was confirmed as sister to the other genera. We propose a phylogenetically informed revision of genus-level taxonomy, including one new generic name. Finally, we highlight several non-monophyletic species complexes and deep intra-species divergences that point to conflict in taxonomy and suggest an underestimation of current species diversity in this group. [ABSTRACT FROM AUTHOR]

We reconstruct the phylogeny of imperial pigeons (genus Ducula ) using mitochondrial and nuclear sequence data. We evaluate the most likely biogeographic scenario for the evolution of this group that colonized many islands of the Pacific Ocean. The divergence time analysis suggests that the basal divergences within Ducula occurred more recently than in the fruit doves (genus Ptilinopus ), a group that is also well diversified in Oceania. The imperial pigeons colonized the Melanesian region several times independently, and the diversification within this region led to several species in sympatry, in particular in the Bismarck archipelago. Central Polynesia was also colonized several times, first by a lineage during the Miocene that led to the large D. latrans , sister to the New Caledonian endemic D. goliath , then more recently by the widespread D. pacifica , during the Pleistocene. The phylogenetic pattern obtained with the extant Ducula species showed that the Eastern Polynesian endemics do not form a monophyletic group, with the Pacific Imperial Pigeon D. pacifica sister species with good support to the Polynesian Imperial Pigeon D. aurorae . However, the impact of recent anthropic extinctions has been important for the imperial pigeons, more than for the smaller fruit doves, suggesting that several Ducula lineages might be missing today. [ABSTRACT FROM AUTHOR]

Highlights: [•] Ptilinopus forms a clade that includes Alectroenas and Drepanoptila. [•] Basal divergences dated to the Early Oligocene. [•] Fruit doves originated most probably from the proto New Guinea region. [•] Colonization of Oceania was not associated with a significant increase of diversification rate. [Copyright &y& Elsevier]

Abstract: The ever increasing number of analysed loci in phylogenetics has not only allowed resolution of some parts of the Tree of Life but has also highlighted parts of the tree where incongruent signals among loci were detected. Previous molecular studies suggested conflicting relationships for the New World genus Campephilus, being either associated to the Megapicini or Dendropocini. Yet, the limited number of analysed loci and the use of the concatenation approach to reconstruct the phylogeny prevented the disentanglement of lineage sorting and introgression as causal explanation of this topological conflict. We sequenced four mitochondrial, nine autosomal and three Z-linked loci and used a method that incorporates population level processes into the phylogenetic framework to understand which process (lineage sorting of genetic polymorphism or hybridization/introgression) best explains this conflict. Our analyses revealed that the autosomal FGB intron-7 and to a lesser extent the Z-linked loci have a different phylogenetic history from the mitochondrial loci and some other nuclear loci we analysed. We suggest that this conflicting pattern is the result of introgression consecutive to a hybridization event at the time when members of the Campephilus and melanerpine (Melanerpes and Sphyrapicus) lineages colonized the New World. The case of Campephilus highlights that the mitochondrial genome does not always carry the ‘wrong’ phylogenetic signal after a past hybridization event. Indeed, we here emphasise that the signature of such event can also be detected in the nuclear genome. With the ongoing increase in the number of loci analysed in phylogenetic studies, it is very likely that further cases will be discovered. Our current results indicate that (1) the genus Campephilus is related to the Asian genera Blythipicus, Chrysocolaptes and Reinwardtipicus, in accordance with morphological data and (2) that the nuclear genome of Campephilus is likely the mixture of two unrelated lineages. Yet, further work with a denser sampling of loci is necessary to evaluate the extant of the Sphyrapicus/Melanerpes lineage nuclear genome that introgressed into the Campephilus genome. [Copyright &y& Elsevier]

Abstract: Open-habitat chats (genera Myrmecocichla, Cercomela, Oenanthe and relative) are a morphologically and ecologically cohesive group of genera with unclear phylogenetic relationships. They are distributed mostly in open, arid and/or rocky habitats of Africa and Eurasia. Here, we present the most comprehensive molecular phylogenetic analysis of this group to date, with a complete taxon sampling at the species level. The analysis, based on a multilocus dataset including three mitochondrial and three nuclear loci, allows us to elucidate the phylogenetic relationships and test the traditional generic limits. All genera are non-monophyletic, suggesting extensive convergence on similar plumage patterns in unrelated species. While the colour pattern appear to be a poor predictor of the phylogenetic relationships, some of the ecological and behavioural traits agree relatively well with the major clades. Following our results, we also propose a revised generic classification for the whole group. [Copyright &y& Elsevier]

Abstract: The Malaconotidea (e.g., butcherbirds, bush-shrikes, batises, vangas) represent an Old World assemblage of corvoid passerines that encompass many different foraging techniques (e.g., typical flycatchers, flycatcher-shrikes, canopy creepers, undergrowth skulkers). At present, relationships among the primary Malaconotidea clades are poorly resolved, a result that could either be attributed to a rapid accumulation of lineages over a short period of time (hard polytomy) or to an insufficient amount of data having been brought to bear on the problem (soft polytomy). Our objective was to resolve the phylogenetic relationships and biogeographic history of the Malaconotidea using DNA sequences gathered from 10 loci with different evolutionary properties. Given the range of substitution rates of molecular markers we sequenced (mitochondrial, sex-linked, autosomal), we also sought to explore the effect of altering the branch-length prior in Bayesian tree estimation analyses. We found that changing the branch-length priors had no major effect on topology, but clearly improved mixing of the chains for some loci. Our phylogenetic analyses clarified the relationships of several genera (e.g., Pityriasis, Machaerirhynchus) and provide for the first time strong support for a sister-group relationship between core platysteirids and core vangids. Our biogeographic reconstruction somewhat unexpectedly suggests that the large African radiation of malaconotids originated after a single over-water dispersal from Australasia around 45–33.7mya, shedding new light on the origins of the Afrotropical avifauna. [Copyright &y& Elsevier]

Abstract: Relationships of the 133 species of the subfamily Carduelinae (Fringillidae) are poorly resolved. For a more robust phylogenetic resolution, we sequenced two mitochondrial protein-coding genes (ATPase 6 and ND3), two nuclear introns (myoglobin intron 2 and transforming growth factor-β2 intron 5) and one nuclear protein-coding gene (c-mos) from 50 cardueline taxa representing especially the large genera Serinus and Carduelis. A total of 2934bp obtained was subjected to maximum likelihood and Bayesian inference. Three of the five loci, as well as the combined dataset recovered the monophyly of the basal placement of Fringilla in the monophyletic Fringillidae, and the monophyly of the Carduelinae. While relationships within this group are moderately resolved by some individual gene trees (myoglobin and c-mos loci), high nodal support is provided in other individual gene trees and the combined tree. Among the well resolved terminal cardueline groups, Linurgus, Loxia and Pyrrhula are found to be monophyletic while genera Carpodacus, Carduelis and Serinus appear para- or polyphyletic. Within Serinus and Carduelis, the obtained phylogenetic structure corresponds well with the subdivisions suggested by H.E. Wolters, based on traditional methods. Thus, we support his generic subdivision (Ochrospiza, Dendrospiza and Crithagra for Serinus, and Chloris, Spinus, Sporagra, Pseudomitris, Acanthis and Linaria for Carduelis). Otherwise, we notice several cases of significant genetic divergence within traditional species suggesting incipient speciation in Linurgus olivaceus, Loxia curvirostra, Serinus mozambicus and Serinus burtoni. Some of these cases need a further phylogeographical study with a denser geographical sampling but for the case the most noteworthy, that of Serinus burtoni, we suggest a taxonomic change in this study. [Copyright &y& Elsevier]

Abstract: Laniarius is one of the larger genera within the avian bush-shrike radiation, the family Malaconotidae. Fairly homogenous by size and shape but highly variable by colours, these have been classified mainly on basis of plumage colours. In the present study, which is the first taxon-dense analysis of the genus Laniarius based on molecular sequence data (nuclear BRM15 intron-15, and mitochondrial ND2 and ATPase6 genes), we investigate interrelationships between 16 species and 34 subspecies of Laniarius. Altogether 2094bp were aligned and subjected to maximum likelihood and Bayesian inference analyses. Results strongly support the monophyly of Laniarius, and place it close to Chlorophoneus, but without outlining a precise sister-group. In a generally well-resolved phylogeny of Laniarius, L. leucorhynchus and L. atrococcineus constitute deep branches and the remaining species form five clades which are not concordant with previously defined superspecies. The black and white boubous belong to two different clades. L. aethiopicus appears polyphyletic and our results support the resurrection of Laniarius major, Laniarius erlangeri and Laniarius sublacteus. We also find that L. liberatus, described in 1991 based on the only known live individual, is identified as an unusual colour morph from L. erlangeri. The black boubous are not monophyletic; L. funebris and L. leucorhynchus appear as isolated species whereas L. poensis and L. fuelleborni are sister-taxa. We recovered the polyphyly of crimson boubous and new hypotheses on their relationships have been generated. Overall, the variation in pigments and patterns does not follow phylogenetic lineages. The plumage coloration could be thoroughly subject to modification and it could not reflect exactly colour plumages of the parents. From then on, the plumage coloration appears as an unreliable morphological character for defining species and species groups. [Copyright &y& Elsevier]

Abstract: Previous studies have suggested that the woodpecker genus Picus (Aves: Picidae) may not be monophyletic. In order to evaluate this hypothesis, we analyzed DNA sequences from all but two species of Picus, as well as from representatives of all genera in the tribe Malarpicini, within which Picus is nested. We sequenced seven loci (four autosomal, one Z-linked and two mitochondrial) with different evolutionary dynamics. The species currently placed in Picus fall into two subclades that may not form a monophyletic assemblage. Consequently, we propose to place miniaceus Pennant 1769, flavinucha Gould 1834 and mentalis Temminck 1825 in the genus Chrysophlegma Gould, 1850, while the remaining species are retained in Picus. The inclusion in our study of representatives of all genera included in the tribe Malarpicini, a group of woodpeckers which has proven difficult to resolve in several previous molecular studies, also allowed us to determine the earliest divergences within this clade. The results suggest that the low level of basal resolution in Malarpicini is attributable to multiple cladogenetic events in a short period of time rather than insufficient character sampling. This conclusion is supported by the observation of nucleotide insertion–deletions that support mutually exclusive phylogenetic hypotheses in different gene trees. We attribute this pattern of incongruent indels, together with short internodes in the tree, to incomplete lineage sorting. [Copyright &y& Elsevier]

Abstract: The systematic relationships among avian families within Crown Corvida have been poorly studied so far and as such been of limited use for biogeographic interpretations. The group has its origin in Australia and is thought to have colonized Africa and the New World via Asia beginning some 35Mya when terranes of Australian origin approached Asian landmasses. Recent detailed tectonic mapping of the origin of land masses in the region around Wallace’s line have revealed a particularly complex movement of terranes over the last 20–30Myr. Thus the biogeographic dispersal pattern of Crown Corvida is a particularly exciting case for linking vicariance and dispersal events with Earth history. Here we examine phylogenetic affinities among 72 taxa covering a broad range of genera in the basal radiations within Crown Corvida with an emphasis on Campephagidae and Pachycephalidae. Bayesian analyses of nuclear DNA sequence data identified the family Campephagidae as monophyletic but the large genus Coracina is not. Within the family Pachycephalidae the genera Pachycephala and Colluricincla are paraphyletic with respect to each other. The resulting phylogeny suggests that patterns of dispersal across Wallace’s line are complex and began at least 25Mya. We find evidence of explosive radiations and multi-directional dispersal within the last 10Myr, and three independent long distance ocean dispersal events between Wallacea and Africa at 10–15Mya. Furthermore, the study reveals that in the Campephagidae a complex series of dispersal events rather than vicariance is the most likely explanation for the current biogeographic pattern in the region. [Copyright &y& Elsevier]

Abstract: The Campephagidae (minivets, cuckoo-shrikes and trillers, seven genera and 81 species) represents an Old World corvid clade of tropical birds with a mixed diet that forage in different manners, i.e., flycatching, foliage-gleaning or shriking. This family has never been the focus of any phylogenetic survey, so their phylogenetic relationships and biogeographic history remain largely unknown. To address these questions, we sequenced four loci (ND2, myoglobin intron-2, GAPDH intron-11 and c-mos) for 27 species of Campephagidae. Our analyses suggest that Coracina consists of five unrelated lineages and that Lalage is paraphyletic. Our dating analyses, using a Bayesian relaxed-clock method, indicate that the split between the Indo-Malayan genus Pericrocotus and the remaining Campephagidae occurred synchronously with other splits involving Indo-Malayan corvid lineages, suggesting that several lineages of Indo-Malayan birds were isolated at the same time from their closest relatives. The African stock of cuckoo-shrikes is likely the result of three independent trans-oceanic dispersals from Australasia. [Copyright &y& Elsevier]

Abstract: Based on some general similarities in feeding adaptations, a large number of Old World passerine birds were in the past lumped in one broad family, the Sylviidae. Recent molecular studies, starting with the DNA–DNA hybridization work by Sibley et al. [Sibley, C.G., Ahlquist, J.E., 1990. Phylogeny and Classification of Birds: A Study in Molecular Evolution, Yale University Press, New Haven, CT], have revealed that this group is in fact a paraphyletic assemblage, mainly in the superfamily Sylvioidea, and within this assemblage a distinct group (the Cisticolidae) can be identified around the genus Cisticola. In this study we try to define natural lineages within it, based on DNA sequence data from 35 ingroup taxa representing 12 putative genera. Both nuclear myoglobin intron II (630bp in our study) and mitochondrial ND2 (1041bp) genes were sequenced, and 1671bp were aligned and subjected to parsimony, maximum likelihood and Bayesian analyses. The results strongly support the monophyly of a cisticolid clade, with the Malagasy warblers Neomixis constituting the deepest branch within the clade. Three major clades receive statistical support, but not all relationships between and within these are well resolved. All species of the genus Bathmocercus belong to the Cisticolidae but in two different clades. The tailorbirds appear also polyphyletic with most species of the genus Orthotomus (but O. cucullatus falling in the outgroup) and the African metopias being in two different clades. Also the genus Apalis is polyphyletic, but all other included genera seem to be confirmed as natural units. Based on these findings we resurrect the genera Scepomycter and Artisornis. Calamonastes is confirmed to be in the Cisticolidae and grouped with Camaroptera. Main basic nest types do not follow the phylogenetic branching, and notably the peculiar “tailorbird” technique of stitching leaves together around the nest is found in different parts of the phylogeny. The basic types of nests seem to be found in particular environments, and the sewing may therefore have evolved in some ancestor of the Cisticolidae and was later lost or modified in some genera or species following the spread of drier habitats from the mid-Miocene. [Copyright &y& Elsevier]

Abstract: The African genus Hyliota includes three or four species of warbler-like birds of uncertain phylogenetic affinities, as it has historically been placed in different avian families that are now known to represent unrelated lineages: Malaconotidae (bush-shrikes), Platysteiridae (batises and wattle-eyes), Muscicapidae (Old World flycatchers) and Sylviidae (Old-World Warblers). To assess the affinities of Hyliota we sequenced a mitochondrial protein-coding gene (ND2, 1018bp) and a nuclear intron (myoglobin intron-2, 685bp). Our analyses suggest that all previous hypotheses concerning the affinities of Hyliota are erroneous. Instead, Hyliota represents a basal branch in the Passerida radiation with no close relatives. Our results, which also include analyses of relationships among other of other atypical songbird genera, lend support to an African origin of the Passerida songbird radiation. [Copyright &y& Elsevier]

The African bush-shrikes and helmet-shrikes (Malaconotidae sensu [A Complete Checklist of the Birds of the World, third ed., Helm Editions, London, 2003]) include 10 genera and 52 species of predatory passerine birds for which monophyly, sister-group, and inter-generic relationships are disputed. To resolve their relationships, we analyzed 2313bp of sequence data obtained from two nuclear introns (myoglobin intron-2, β-fibrinogen intron-5) and a mitochondrial protein-coding gene (ND2) using parsimony, maximum likelihood, and Bayesian inference. A strongly supported clade that included representatives of the Malaconotidae, Platysteiridae, and Vangidae was found in all analyses. Three main groups emerged within this clade but relationships between these three groups were always poorly supported. The first group included the helmet-shrikes (Prionops), flycatcher-shrikes (Bias and Megabyas), and vangas (Cyanolanius and Pseudobias), currently placed in the families Malaconotidae, Platysteiridae, and Vangidae, respectively. The second group consisted of four Platysteiridae genera (Lanioturdus, Batis, Platysteira, and Dyaphorophyia), with the remaining Malaconotidae genera (‘core malaconotids’) forming the last group. Two main clades emerged within the ‘core malaconotids,’ with the position of the genus Nilaus being variable. The first clade included Malaconotus, Dryoscopus, Bocagia, and Tchagra and the second Chlorophoneus, Laniarius, Rhodophoneus, and Telophorus. Monophyly of the genus Chlorophoneus was never recovered, a result that is consistent with morphological data. [Copyright &y& Elsevier]