Systematics and biogeography of Indo-Pacific ground-doves

Ground-doves represent an insular bird radiation distributed across the Indo-Pacific. The radiation comprises sixteen extant species, two species believed to be extinct and six species known to be extinct. In the present study, we present a molecular phylogeny for all sixteen extant species, based on two mitochondrial markers. We demonstrate that the Gallicolumba as currently circumscribed is not monophyletic and recommend reinstalling the name Alopecoenas for a monophyletic radiation comprising ten extant species, distributed in New Guinea, the Lesser Sundas and Oceania. Gallicolumba remains the name for six species confined to New Guinea the Philippines and Sulawesi. Although our phylogenetic analyses fail to support a single origin for the remaining Gallicolumba species, we suspect that the addition of nuclear sequence data may alter this result. Because a number of ground-dove taxa have gone extinct, it is difficult to assess biogeographical patterns. However, the Alopecoenas clade has clearly colonized many remote oceanic islands rather recently, with several significant water crossings. The Gallicolumba radiation(s), on the other hand, is significantly older and it is possible that diversification within that group may in part have been shaped by plate tectonics and corresponding re-arrangements of land masses within the Philippine and Sulawesi region.     

Specialization in plant-hummingbird networks is associated with species richness, contemporary precipitation and quaternary climate-change velocity

Large-scale geographical patterns of biotic specialization and the underlying drivers are poorly understood, but it is widely believed that climate plays an important role in determining specialization. As climate-driven range dynamics should diminish local adaptations and favor generalization, one hypothesis is that contemporary biotic specialization is determined by the degree of past climatic instability, primarily Quaternary climate-change velocity. Other prominent hypotheses predict that either contemporary climate or species richness affect biotic specialization. To gain insight into geographical patterns of contemporary biotic specialization and its drivers, we use network analysis to determine the degree of specialization in plant-hummingbird mutualistic networks sampled at 31 localities, spanning a wide range of climate regimes across the Americas. We found greater biotic specialization at lower latitudes, with latitude explaining 20-22% of the spatial variation in plant-hummingbird specialization. Potential drivers of specialization--contemporary climate, Quaternary climate-change velocity, and species richness--had superior explanatory power, together explaining 53-64% of the variation in specialization. Notably, our data provides empirical evidence for the hypothesized roles of species richness, contemporary precipitation and Quaternary climate-change velocity as key predictors of biotic specialization, whereas contemporary temperature and seasonality seem unimportant in determining specialization. These results suggest that both ecological and evolutionary processes at Quaternary time scales can be important in driving large-scale geographical patterns of contemporary biotic specialization, at least for co-evolved systems such as plant-hummingbird networks.     

A new genus of rodent from Wallacea (Rodentia: Muridae: Murinae: Rattini), and its implication for biogeography and Indo‐Pacific Rattini systematics

We describe Halmaheramys bokimekot Fabre, Pagès, Musser, Fitriana, Semiadi & Helgen gen. et sp. nov. , a new genus and species of murine rodent from the North Moluccas, and study its phylogenetic placement using both molecular and morphological data. We generated a densely sampled mitochondrial and nuclear DNA data set that included most genera of Indo‐Pacific Murinae, and used probabilistic methodologies to infer their phylogenetic relationships. To reconstruct their biogeographical history, we first dated the topology and then used a Lagrange analysis to infer ancestral geographic areas. Finally, we combined the ancestral area reconstructions with temporal information to compare patterns of murine colonization among Indo‐Pacific archipelagos. We provide a new and comprehensive molecular phylogenetic reconstruction for Indo‐Pacific Murinae, with a focus on the Rattus division. Using previous results and those presented in this study, we define a new Indo‐Pacific group within the Rattus division, composed of Bullimus, Bunomys, Paruromys, Halmaheramys, Sundamys, and Taeromys. Our phylogenetic reconstructions revealed a relatively recent diversification from the Middle Miocene to Plio‐Pleistocene associated with several major dispersal events. We identified two independent Indo‐Pacific dispersal events from both western and eastern Indo‐Pacific archipelagos to the isolated island of Halmahera, which led to the speciations of H. bokimekot gen. et sp. nov. and Rattus morotaiensis Kellogg, 1945. We propose that a Middle Miocene collision between the Halmahera and Sangihe arcs may have been responsible for the arrival of the ancestor of Halmaheramys to eastern Wallacea. Halmaheramys bokimekot gen. et sp. nov. is described in detail, and its systematics and biogeography are documented and illustrated. © 2013 The Linnean Society of London     

Molecular phylogenetic analysis of all members of the genus Elminia confirms their presence within the Stenostiridae clade

The genus Elminia has had a jumbled taxonomic history, being placed among ‘old world flycatchers’ or ‘monarch flycatchers’, where it was for a long time lumped with Trochocercus. It was recently suggested that it might represent a deep clade in the large sylvioid radiation. Using one mitochondrial protein‐coding gene (ND2, 1041 bp) and one nuclear intron (myoglobin intron 2, 700 bp) DNA sequences, we obtained robust evidence for the phylogenetic placement of Elminia in the new family Stenostiridae, which is strongly supported by a synapomorphic insertion of one base in the nuclear myoglobin intron 2 sequence. Our analyses confirm the monophyly of Elminia and resolve relationships within this genus, but cannot confidently identify its sister‐taxon within the stenostirid clade. Two clades were strongly supported within the genus Elminia: one with the two fairy blue flycatchers and another with the three white‐tailed crested‐flycatchers. Within the first clade, Elminia longicauda appears non‐monophyletic but remains strongly related to E. albicauda. In the second clade, E. albiventris is sister to E. albonotata while the Dusky Crested Flycatcher (E. nigromitrata) appears in a basal position within this clade. According to our molecular dating, several geological events in western Africa and the Albertine Rift area seem to be related to the historical distribution of Elminia. Thus, the differentiation between E. albonotata and E. albiventris could be directly related to the tectonic history of these two regions. According to our molecular dating, at least one intercontinental dispersal event involving Culicicapa took place within the Stenostiridae clade at a time when the Middle East was forested.     

Breeding system evolution influenced the geographic expansion and diversification of the core Corvoidea (Aves: Passeriformes)

Birds vary greatly in their life‐history strategies, including their breeding systems, which range from brood parasitism to a system with multiple nonbreeding helpers at the nest. By far the most common arrangement, however, is where both parents participate in raising the young. The traits associated with parental care have been suggested to affect dispersal propensity and lineage diversification, but to date tests of this potential relationship at broad temporal and spatial scales have been limited. Here, using data from a globally distributed group of corvoid birds in concordance with state‐dependent speciation and extinction models, we suggest that pair breeding is associated with elevated speciation rates. Estimates of transition between breeding systems imply that cooperative lineages frequently evolve biparental care, whereas pair breeders rarely become cooperative. We further highlight that these groups have differences in their spatial distributions, with pair breeders overrepresented on islands, and cooperative breeders mainly found on continents. Finally, we find that speciation rates appear to be significantly higher on islands compared to continents. These results imply that the transition from cooperative breeding to pair breeding was likely a significant contributing factor facilitating dispersal across tropical archipelagos, and subsequent world‐wide phylogenetic expansion among the core Corvoidea.     

The partitioning of Africa: statistically defined biogeographical regions in sub‐Saharan Africa

Aim To test whether it is possible to establish a common biogeographical regionalization for plants and vertebrates in sub‐Saharan Africa (the Afrotropical Region), using objective multivariate methods. Location Sub‐Saharan Africa (Afrotropical Region). Methods We used 1° grid cell resolution databases for birds, mammals, amphibians and snakes (4142 vertebrate species) and c. 13% of the plants (5881 species) from the Afrotropical Region. These databases were analysed using cluster analysis techniques to define biogeographical regions. A β(sim) dissimilarity matrix was subjected to a hierarchical classification using the unweighted pair‐group method with arithmetic averages (UPGMA). The five group‐specific biogeographical regionalizations were compared against a regionalization developed from a combined database, and a regionalization that is maximally congruent with the five group‐specific datasets was determined using a consensus classification. The regionalizations were interpreted against measures of spatial turnover in richness and composition for the five datasets as well as the combined dataset. Results We demonstrate the existence of seven well‐defined and consistent biogeographical regions in sub‐Saharan Africa. These regionalizations are statistically defined and robust between groups, with minor taxon‐specific biogeographical variation. The proposed biogeographical regions are: Congolian, Zambezian, Southern African, Sudanian, Somalian, Ethiopian and Saharan. East Africa, the West African coast, and the transitions between the Congolian, Sudanian and Zambezian regions are unassigned. The Cape area in South Africa, Afromontane areas and the coastal region of East Africa do not emerge as distinct regions but are characterized by high neighbourhood heterogeneity, rapid turnover of species and high levels of narrow endemism. Main conclusions Species distribution data and modern cluster analysis techniques can be used to define biogeographical regions in Africa that reflect the patterns found in both vertebrates and plants. The consensus of the regionalizations between different taxonomic groups is high. These regions are broadly similar to those proposed using expert opinion approaches. Some previously proposed transitional zones are not recognized in this classification.     

Phylogeny of Laniarius: molecular data reveal L. liberatus synonymous with L. erlangeri and "plumage coloration" as unreliable morphological characters for defining species and species groups

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 2094 bp 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.     

Phylogenetic relationships within Passerida (Aves: Passeriformes): a review and a new molecular phylogeny based on three nuclear intron markers

The avian clade Passerida was first identified based on DNA-DNA hybridization data [C.G. Sibley, J.E. Ahlquist, Phylogeny and Classification of Birds, 1990, Yale University Press, New Haven, CT]. Monophyly of the Passerida, with the exception of a few taxa, has later been corroborated in several studies; however, the basal phylogenetic relationships have remained poorly understood. In this paper, we review the current knowledge of the phylogenetic relationships within Passerida and present a new phylogeny based on three nuclear introns (myoglobin intron 2, ornithine decarboxylase introns 6 and 7, as well as beta-fibrinogen intron 5). Our findings corroborate recent molecular hypotheses, but also identify several hitherto unrecognized relationships.     

Explosive avian radiations and multi-directional dispersal across Wallacea: evidence from the Campephagidae and other Crown Corvida (Aves)

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 35 Mya 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 20-30 Myr. 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 25 Mya. We find evidence of explosive radiations and multi-directional dispersal within the last 10 Myr, and three independent long distance ocean dispersal events between Wallacea and Africa at 10-15 Mya. 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.     

Molecular phylogenetics and diversification within one of the most geographically variable bird species complexes Pachycephala pectoralis/melanura

The golden‐mangrove whistler complex Pachycephala pectoralis/melanura is, with 66 named populations, described as the most complex avian example of geographic variation in the World. It represents a well‐known example of niche differentiation where one species P. pectoralis is found on faunistically rich larger islands (and mainland) and the other P. melanura is confined to adjacent, faunistically poor islets. Except for a comparison of some Solomon Island populations, the relationships among these taxa have not been tested using molecular data. Here we combine a dense taxon sampling (22 populations of 12 named taxa distributed east of New Guinea and in Australia), with molecular data (two nuclear and two mitochondrial markers) to unravel more of the evolutionary history behind the golden whistler complex. In particular we examine relationships between Pachycephala melanura, and the very similar‐looking P. citreogaster (Bismarcks Islands) and P. pectoralis (Australia). We demonstrate that a well‐supported group of golden whistlers inhabit the Bismarck Islands and that several small islets in the immediate vicinity are inhabited by another monophyletic group consisting of P. melanura, mangrove golden whistler.