An annotated chromosome-scale reference genome for Eastern black-eared wheatear (Oenanthe melanoleuca).

Pervasive convergent evolution and in part high incidences of hybridization distinguish wheatears (songbirds of the genus Oenanthe) as a versatile system to address questions at the forefront of research on the molecular bases of phenotypic and species diversification. To prepare the genomic resources for this venture, we here generated and annotated a chromosome-scale assembly of the Eastern black-eared wheatear (Oenanthe melanoleuca). This species is part of the Oenanthe hispanica complex that is characterized by convergent evolution of plumage coloration and high rates of hybridization. The long-read-based male nuclear genome assembly comprises 1.04 Gb in 32 autosomes, the Z chromosome, and the mitogenome. The assembly is highly contiguous (contig N50, 12.6 Mb; scaffold N50, 70 Mb), with 96% of the genome assembled at the chromosome level and 95.5% benchmarking universal single-copy orthologs (BUSCO) completeness. The nuclear genome was annotated with 18,143 protein-coding genes and 31,333 mRNAs (annotation BUSCO completeness, 98.0%), and about 10% of the genome consists of repetitive DNA. The annotated chromosome-scale reference genome of Eastern black-eared wheatear provides a crucial resource for research into the genomics of adaptation and speciation in an intriguing group of passerines.

A Phylogenomic Assessment of Processes Underpinning Convergent Evolution in Open-Habitat Chats.

Insights into the processes underpinning convergent evolution advance our understanding of the contributions of ancestral, introgressed, and novel genetic variation to phenotypic evolution. Phylogenomic analyses characterizing genome-wide gene tree heterogeneity can provide first clues about the extent of ILS and of introgression and thereby into the potential of these processes or (in their absence) the need to invoke novel mutations to underpin convergent evolution. Here, we were interested in understanding the processes involved in convergent evolution in open-habitat chats (wheatears of the genus Oenanthe and their relatives). To this end, based on whole-genome resequencing data from 50 taxa of 44 species, we established the species tree, characterized gene tree heterogeneity, and investigated the footprints of ILS and introgression within the latter. The species tree corroborates the pattern of abundant convergent evolution, especially in wheatears. The high levels of gene tree heterogeneity in wheatears are explained by ILS alone only for 30% of internal branches. For multiple branches with high gene tree heterogeneity, D-statistics and phylogenetic networks identified footprints of introgression. Finally, long branches without extensive ILS between clades sporting similar phenotypes provide suggestive evidence for the role of novel mutations in the evolution of these phenotypes. Together, our results suggest that convergent evolution in open-habitat chats involved diverse processes and highlight that phenotypic diversification is often complex and best depicted as a network of interacting lineages.

Seasonal migration patterns and the maintenance of evolutionary diversity in a cryptic bird radiation.

Morphological differentiation associated with evolutionary diversification is often explained with adaptive benefits but the processes and mechanisms maintaining cryptic diversity are still poorly understood. Using genome-wide data, we show here that the pale sand martin Riparia diluta in Central and East Asia consists of three genetically deeply differentiated lineages which vary only gradually in morphology but broadly reflect traditional taxonomy. We detected no signs of gene flow along the eastern edge of the Qinghai-Tibetan plateau between lowland south-eastern Chinese R. d. fohkienensis and high-altitude R. d. tibetana. Largely different breeding and migration timing between these low and high altitude populations as indicated by phenology data suggests that allochrony might act as prezygotic isolation mechanism in the area where their ranges abut. Mongolian populations of R. d. tibetana, however, displayed signs of limited mixed ancestries with Central Asian R. d. diluta. Their ranges meet in the area of a well-known avian migratory divide, where western lineages take a western migration route around the Qinghai-Tibetan plateau to winter quarters in South Asia, and eastern lineages take an eastern route to Southeast Asia. This might also be the case between western R. d. diluta and eastern R. d. tibetana as indicated by differing wintering grounds. We hypothesize that hybrids might have nonoptimal intermediate migration routes and selection against them might restrict gene flow. Although further potential isolation mechanisms might exist in the pale sand martin, our study points towards contrasting migration behaviour as an important factor in maintaining evolutionary diversity under morphological stasis.

Trophic niche shifts and phenotypic trait evolution are largely decoupled in Australasian parrots.

BACKGROUND: Trophic shifts from one dietary niche to another have played major roles in reshaping the evolutionary trajectories of a wide range of vertebrate groups, yet their consequences for morphological disparity and species diversity differ among groups. METHODS: Here, we use phylogenetic comparative methods to examine whether the evolution of nectarivory and other trophic shifts have driven predictable evolutionary pathways in Australasian psittaculid parrots in terms of ecological traits such as body size, beak shape, and dispersal capacity. RESULTS: We found no evidence for an 'early-burst' scenario of lineage or morphological diversification. The best-fitting models indicate that trait evolution in this group is characterized by abrupt phenotypic shifts (evolutionary jumps), with no sign of multiple phenotypic optima correlating with different trophic strategies. Thus, our results point to the existence of weak directional selection and suggest that lineages may be evolving randomly or slowly toward adaptive peaks they have not yet reached. CONCLUSIONS: This study adds to a growing body of evidence indicating that the relationship between avian morphology and feeding ecology may be more complex than usually assumed and highlights the importance of adding more flexible models to the macroevolutionary toolbox.

Linked-read sequencing enables haplotype-resolved resequencing at population scale.

The feasibility to sequence entire genomes of virtually any organism provides unprecedented insights into the evolutionary history of populations and species. Nevertheless, many population genomic inferences - including the quantification and dating of admixture, introgression and demographic events, and inference of selective sweeps - are still limited by the lack of high-quality haplotype information. The newest generation of sequencing technology now promises significant progress. To establish the feasibility of haplotype-resolved genome resequencing at population scale, we investigated properties of linked-read sequencing data of songbirds of the genus Oenanthe across a range of sequencing depths. Our results based on the comparison of downsampled (25×, 20×, 15×, 10×, 7×, and 5×) with high-coverage data (46-68×) of seven bird genomes mapped to a reference suggest that phasing contiguities and accuracies adequate for most population genomic analyses can be reached already with moderate sequencing effort. At 15× coverage, phased haplotypes span about 90% of the genome assembly, with 50% and 90% of phased sequences located in phase blocks longer than 1.25-4.6 Mb (N50) and 0.27-0.72 Mb (N90). Phasing accuracy reaches beyond 99% starting from 15× coverage. Higher coverages yielded higher contiguities (up to about 7 Mb/1 Mb [N50/N90] at 25× coverage), but only marginally improved phasing accuracy. Phase block contiguity improved with input DNA molecule length; thus, higher-quality DNA may help keeping sequencing costs at bay. In conclusion, even for organisms with gigabase-sized genomes like birds, linked-read sequencing at moderate depth opens an affordable avenue towards haplotype-resolved genome resequencing at population scale.

Genome-wide evidence supports mitochondrial relationships and pervasive parallel phenotypic evolution in open-habitat chats.

In wheatears and related species ('open-habitat chats'), molecular phylogenetics has led to a comprehensively revised understanding of species relationships and species diversity. Phylogenetic analyses have suggested that, in many cases, phenotypic similarities do not reflect species' relationships, revealing traditionally defined genera as non-monophyletic. This led to the suggestion of pervasive parallel evolution of open-habitat chats' plumage coloration and ecological phenotypes. However, to date, the molecular evidence for the phylogenetic relationships among open-habitat chats is mainly limited to mitochondrial DNA. Here, we assessed whether the mitochondrial relationships are supported by genome-wide data. To this end, we reconstructed the species tree among 14 open-habitat chat taxa using multi-species coalescent analyses based on ~1'300 SNPs. Our results confirm previous ones based chiefly on mitochondrial DNA; notably the paraphyly of the Oenanthe lugens complex and the clustering of individual species formerly placed in the genera Cercomela and Myrmecocichla within Oenanthe. Since several variable morphological and ecological characteristics occur in multiple places across the open-habitat chat phylogeny, our study consolidates the evidence for pervasive parallel evolution in the plumage coloration and ecology of open-habitat chats.

Parallel plumage colour evolution and introgressive hybridization in wheatears.

Genetic and phenotypic mosaics, in which various phenotypes and different genomic regions show discordant patterns of species or population divergence, offer unique opportunities to study the role of ancestral and introgressed genetic variation in phenotypic evolution. Here, we investigated the evolution of discordant phenotypic and genetic divergence in a monophyletic clade of four songbird taxa-pied wheatear (O. pleschanka), Cyprus wheatear (Oenanthe cypriaca), and western and eastern subspecies of black-eared wheatear (O. h. hispanica and O. h. melanoleuca). Phenotypically, black back and neck sides distinguish pied and Cyprus wheatears from the white-backed/necked black-eared wheatears. Meanwhile, mitochondrial variation only distinguishes western black-eared wheatear. In the absence of nuclear genetic data, and given frequent hybridization among eastern black-eared and pied wheatear, it remains unclear whether introgression is responsible for discordance between mitochondrial divergence patterns and phenotypic similarities, or whether plumage coloration evolved in parallel. Multispecies coalescent analyses of about 20,000 SNPs obtained from RAD data mapped to a draft genome assembly resolve the species tree, provide evidence for the parallel evolution of colour phenotypes and establish western and eastern black-eared wheatears as independent taxa that should be recognized as full species. The presence of the entire admixture spectrum in the Iranian hybrid zone and the detection of footprints of introgression from pied into eastern black-eared wheatear beyond the hybrid zone despite strong geographic structure of ancestry proportions furthermore suggest a potential role for introgression in parallel plumage colour evolution. Our results support the importance of standing heterospecific and/or ancestral variation in phenotypic evolution.

Contrasting patterns of diversification in two sister species of martins (Aves: Hirundinidae): The Sand Martin Riparia riparia and the Pale Martin R. diluta.

Species not only responded idiosyncratically to past climate changes, there were also regionally contrasting effects on spatio-temporal diversification patterns. Studies of closely related species appear to be a particularly promising comparative approach to disentangle such regionally differential impacts. In this study, we undertook a comprehensive geographic sampling to investigate the evolutionary history of the Holarctic Sand Martin Riparia riparia and the chiefly Central and East Asian Pale Martin R. diluta. Previous phylogenetic studies using only a limited geographic sampling, particularly for the latter, revealed the two to be genetically distinct, with the former showing only a shallow genetic structure in mitochondrial DNA. Based on one mitochondrial, one autosomal and one Z-linked nuclear marker, we confirmed the shallow genetic structure in R. riparia even when including the morphologically relatively distinct subspecies R. r. shelleyi from the Nile Valley in Egypt and probably the Middle East. On the other hand the different subspecies of R. diluta, i.e. R. d. diluta from Central Asia, R. d. indica from the northwestern Indian Subcontinent, R. d. tibetana from the Tibetan Plateau and R. d. fohkienensis from southeastern China, were found to be genetically distinct. Their diversification started before the Early to Middle Pleistocene Transition, which was followed by a pronounced succession of glacial and interglacial periods. These rather old divergence events contrast with the lack of any strong phylogeographic structure in R. riparia. Strongly structured populations and regional diversification have been reported in different forest passerine families of South-East Asia. Here we demonstrate, however, that species characteristic of open-country habitats such as R. diluta might display a similar pattern. Morphometric analyses of 120 individuals revealed no clear differences between the different subspecies of R. diluta. Given their similarity also in plumage features, we refrain from proposing any splits despite their marked genetic differentiation, pending further studies and particularly the discovery of potential secondary contact zones.

Morphology captures diet and locomotor types in rodents.

To understand the functional meaning of morphological features, we need to relate what we know about morphology and ecology in a meaningful, quantitative framework. Closely related species usually share more phenotypic features than distant ones, but close relatives do not necessarily have the same ecologies. Rodents are the most diverse group of living mammals, with impressive ecomorphological diversification. We used museum collections and ecological literature to gather data on morphology, diet and locomotion for 208 species of rodents from different bioregions to investigate how morphological similarity and phylogenetic relatedness are associated with ecology. After considering differences in body size and shared evolutionary history, we find that unrelated species with similar ecologies can be characterized by a well-defined suite of morphological features. Our results validate the hypothesized ecological relevance of the chosen traits. These cranial, dental and external (e.g. ears) characters predicted diet and locomotion and showed consistent differences among species with different feeding and substrate use strategies. We conclude that when ecological characters do not show strong phylogenetic patterns, we cannot simply assume that close relatives are ecologically similar. Museum specimens are valuable records of species' phenotypes and with the characters proposed here, morphology can reflect functional similarity, an important component of community ecology and macroevolution.

Inference of Evolutionary Jumps in Large Phylogenies using Lévy Processes.

Although it is now widely accepted that the rate of phenotypic evolution may not necessarily be constant across large phylogenies, the frequency and phylogenetic position of periods of rapid evolution remain unclear. In his highly influential view of evolution, G. G. Simpson supposed that such evolutionary jumps occur when organisms transition into so-called new adaptive zones, for instance after dispersal into a new geographic area, after rapid climatic changes, or following the appearance of an evolutionary novelty. Only recently, large, accurate and well calibrated phylogenies have become available that allow testing this hypothesis directly, yet inferring evolutionary jumps remains computationally very challenging. Here, we develop a computationally highly efficient algorithm to accurately infer the rate and strength of evolutionary jumps as well as their phylogenetic location. Following previous work we model evolutionary jumps as a compound process, but introduce a novel approach to sample jump configurations that does not require matrix inversions and thus naturally scales to large trees. We then make use of this development to infer evolutionary jumps in Anolis lizards and Loriinii parrots where we find strong signal for such jumps at the basis of clades that transitioned into new adaptive zones, just as postulated by Simpson's hypothesis. [evolutionary jump; Lévy process; phenotypic evolution; punctuated equilibrium; quantitative traits.

Reprising the taxonomy of Cyprus Scops Owl Otus (scops) cyprius, a neglected island endemic.

The endemic Cyprus Scops Owl Otus (scops) cyprius has been treated as a subspecies of the widespread Eurasian Scops Owl O. scops since at least the 1940s. However, its song is distinct from that of all other subspecies of O. scops in being double-noted, rather than single-noted. Its plumage also differs, most obviously in being consistently darker than other subspecies and in lacking a rufous morph. However, it shows no biometric differences from O. s. cycladum and southern populations of O. s. scops. It is also unusual among scops (s. l.) populations in being at least partially resident, although two specimens showing characters of this taxon were collected in Israel in early spring, and the numbers of birds that are resident on Cyprus appear to vary, with few recent winter records. It differs from O. s. scops by one synapomorphic nucleotide exchange in the analysed mitochondrial marker, indicating a recent separation. Given that large numbers of O. s. scops and O. s. cycladum pass through Cyprus on spring migration, and that the latter breeds in adjacent countries, it seems probable that cycladum would colonize the island, but for the presence of cyprius. That it does not do so, and that cyprius retains its distinctive song and plumage, suggests that isolating mechanisms exist. We recommend that cyprius be considered specifically distinct, as are other distinctively voiced insular Otus populations.

Molecular phylogenetics suggests a New Guinean origin and frequent episodes of founder-event speciation in the nectarivorous lories and lorikeets (Aves: Psittaciformes).

The lories and lorikeets (Aves: Loriinae: Loriini) are a readily recognizable, discrete group of nectarivorous parrots confined to the Indo-Pacific region between Wallace's Line and the Pitcairn Island group in the central-east Pacific Ocean. We present the first phylogenetic analysis of all currently recognized genera in the group using two mitochondrial and five nuclear loci. Our analyses suggest a New Guinean origin for the group at about 10million years ago (95% HPD 4.8-14.8) but this origin must be interpreted within the context of that island's complicated, recent geological history. That is, the origin and early diversification of the group may have taken place as New Guinea's Central Cordillera arose and the final constituent terranes that form present-day New Guinea were accreted. The latter activity may have promoted dispersal as a key element in the group's history. We have detected several instances of dispersal out of New Guinea that we argue constitute instances of founder-event speciation. Some phenotypically cohesive genera are affirmed as monophyletic but other genera are clearly in need of taxonomic dismantlement and reclassification. We recognize Parvipsitta Mathews, 1916 for two species usually placed in Glossopsitta and we advocate transfer of Chalcopsitta cardinalis into Pseudeos Peters, 1935. Other non-monophyletic genera such as Charmosyna, Psitteuteles and, probably, Trichoglossus, require improved taxon sampling and further phylogenetic analysis before their systematics can be resolved. Cursory examination of trait mapping across the group suggests that many traits are ancestral and of little use in determining genus-level systematics.

Multiple lines of evidence confirm that Hume's Owl Strix butleri (A. O. Hume, 1878) is two species, with description of an unnamed species (Aves: Non-Passeriformes: Strigidae).

Genetic and morphological analyses revealed that the type specimen of Hume's Owl Strix butleri, the geographical provenance of which is open to doubt, differs significantly from all other specimens previously ascribed to this species. Despite the absence of vocal data definitively linked to the same population as the type specimen, we consider that two species-level taxa are involved, principally because the degree of molecular differentiation is close to that seen in other taxa of Strix traditionally recognised as species. Partially complicating this otherwise straightforward issue is the recent description of "Omani Owl S. omanensis" from northern Oman based solely on photographs and sound-recordings. We consider that there is clear evidence of at least some morphological congruence between the butleri type and the phenotype described as "omanensis". As a result, we review the relative likelihood of three potential hypotheses: that "omanensis" is a synonym of butleri; that "omanensis" is a subspecies of butleri; or that "omanensis" and butleri both represent species taxa. Until such time as specimen material of "omanensis" becomes available for genetic and comparative morphological analyses, we recommend that this name be considered as a synonym of butleri, especially bearing in mind the possibility (not previously considered in detail) that the type of butleri could have originated in Arabia, specifically from Oman. We describe other populations heretofore ascribed to S. butleri as a new species. 

Conservation action based on threatened species capture taxonomic and phylogenetic richness in breeding and wintering populations of Central Asian birds.

Although phylogenetic diversity has been suggested to be relevant from a conservation point of view, its role is still limited in applied nature conservation. Recently, the practice of investing conservation resources based on threatened species was identified as a reason for the slow integration of phylogenetic diversity in nature conservation planning. One of the main arguments is based on the observation that threatened species are not evenly distributed over the phylogenetic tree. However this argument seems to dismiss the fact that conservation action is a spatially explicit process, and even if threatened species are not evenly distributed over the phylogenetic tree, the occurrence of threatened species could still indicate areas with above average phylogenetic diversity and consequently could protect phylogenetic diversity. Here we aim to study the selection of important bird areas in Central Asia, which were nominated largely based on the presence of threatened bird species. We show that although threatened species occurring in Central Asia do not capture phylogenetically more distinct species than expected by chance, the current spatially explicit conservation approach of selecting important bird areas covers above average taxonomic and phylogenetic diversity of breeding and wintering birds. We conclude that the spatially explicit processes of conservation actions need to be considered in the current discussion of whether new prioritization methods are needed to complement conservation action based on threatened species.

Parallel adaptations to nectarivory in parrots, key innovations and the diversification of the Loriinae.

Specialization to nectarivory is associated with radiations within different bird groups, including parrots. One of them, the Australasian lories, were shown to be unexpectedly species rich. Their shift to nectarivory may have created an ecological opportunity promoting species proliferation. Several morphological specializations of the feeding tract to nectarivory have been described for parrots. However, they have never been assessed in a quantitative framework considering phylogenetic nonindependence. Using a phylogenetic comparative approach with broad taxon sampling and 15 continuous characters of the digestive tract, we demonstrate that nectarivorous parrots differ in several traits from the remaining parrots. These trait-changes indicate phenotype-environment correlations and parallel evolution, and may reflect adaptations to feed effectively on nectar. Moreover, the diet shift was associated with significant trait shifts at the base of the radiation of the lories, as shown by an alternative statistical approach. Their diet shift might be considered as an evolutionary key innovation which promoted significant non-adaptive lineage diversification through allopatric partitioning of the same new niche. The lack of increased rates of cladogenesis in other nectarivorous parrots indicates that evolutionary innovations need not be associated one-to-one with diversification events.

Description of the tadpoles of three rare species of megophryid frogs (Amphibia: Anura: Megophryidae) from Gunung Mulu, Sarawak, Malaysia.

The megophryid frogs Leptobrachella brevicrus, Leptolalax dringi and Megophrys dringi are species exclusively known  from highly localised areas in isolated mountain ranges on Borneo. The tadpoles and adults in this study were collected at the shared type locality for the three species in Gunung Mulu National Park, Sarawak, Malaysia (Borneo). The species identities of larvae were determined via comparison to syntopic adults using DNA barcoding techniques based on partial 16S rRNA mitochondrial gene sequences. The genetic data supported the status of the three taxa as valid species. Descriptions of colouration in life and after preservation, external morphological features, morphometric measurements and ecological notes in comparison to congeneric species are supplied. The tadpoles of L. brevicrus and L. dringi show similar adaptations to a fossorial lifestyle. These include an elongated, vermiform body, a relatively long tail and small eyes. Both were found in the gravel beds of a small mountain stream. In contrast, the larvae of M. dringi are adapted to occupying and feeding at the surface of pools within the stream. 

Saxicola syenitica Heuglin, 1869 (Aves: Passeriformes: Muscicapidae), an overlooked taxon of Oenanthe?

The North African population of the Black Wheatear has been treated as Oenanthe leucura syenitica for over 100 years. The type of syenitica was collected by Heuglin in June 1852 near the southern Egypt/northern Sudan border, well outside the range of the sedentary Black Wheatear. Morphometric inference and genetic analyses of partial sequences of the mitochondrial gene COI demonstrate that the type specimen of syenitica is not conspecific with O. leucura, but instead is closely related to O. lugens of the Middle East and North Africa, being most similar in plumage to O. lugens warriae of the basalt deserts of north-east Jordan and southern Syria. While syenitica was not separable in the analysed part of its mitochondrial DNA from O. l. lugens and O. l. warriae, it differs in morphometrics and plumage features from the latter. The type specimen is a first-summer bird with abraded plumage as expected for June, and may thus have been collected in its breeding range. Its morphological distinctiveness implies that syenitica might be taxonomically distinct from warriae. However, as it is known only from the type and its few associated data, we propose to treat it as a subspecies inquirenda of O. lugens. As a consequence of this, and the fact that we found no genetic or morphological differences between North African populations of O. leucura and riggenbachi Hartert, 1909, the name originally applied to the population in Western Sahara, the North African population takes the oldest available name to become O. leucura riggenbachi.

Phylogeny of the Oenanthe lugens complex (Aves, Muscicapidae: Saxicolinae): paraphyly of a morphologically cohesive group within a recent radiation of open-habitat chats.

The morphologically inferred Oenanthe lugens complex comprises nine taxa of open-habitat chats which occur in rocky and/or mountainous areas adjacent to the Saharo-Sindian desert belt. It has traditionally been divided into the lugubris group of north-east Africa, the lugentoides group of the southern part of the Arabian Peninsula and the lugens group of North Africa and the Middle East. Previous molecular phylogenetic studies have shown that the O. lugens complex might not be monophyletic. However, it remained unclear how this result might have been affected by incomplete taxon sampling, as the lugentoides group and two out of three taxa of the lugubris group have not been analyzed so far. In this study, we present a phylogenetic hypothesis of the O. lugens complex based on two mitochondrial genes and one nuclear intron using, for the first time, a complete taxon sampling. The application of a multispecies coalescent approach allowed us to simultaneously estimate the sequence and timing of speciation events. The O. lugens complex was consistently revealed as a polyphyletic assemblage and the traditionally recognized groups should be treated as at least three different species: O. lugens, Oenanthelugubris, and Oenanthelugentoides. While O. lugubris and O. lugentoides were revealed to be sister groups, O. lugens was found to be closely related to the species pair Oenanthechrysopygia/Oenanthexanthoprymna. The latter differ quite strongly in morphology and have traditionally not been associated with members of the lugens complex. We thus corroborate the results of previous studies, which demonstrated that morphology seems to be a poor predictor of phylogenetic relationships in Oenanthe. In contrast to the mtDNA markers analyzed, it was revealed that differences among taxa were not fixed in the nuclear intron. In the case of the taxa persica of the lugens group, an influence of introgression in autosomal markers cannot be excluded and deserves further study. The three species O. lugens, O. lugubris, and O. lugentoides and their associated taxa comprise a comparatively young radiation, which started to diversify in the Pliocene with major diversification events during the Pleistocene. The different taxa seem to have evolved during periods of increased aridity in isolation in rocky mountainous areas adjacent to hyper arid regions.

Diversification in a biodiversity hotspot--the evolution of Southeast Asian rhacophorid tree frogs on Borneo (Amphibia: Anura: Rhacophoridae).

The tree-frog family Rhacophoridae is a major group contributing to the high pecies richness and reproductive diversity among vertebrates of Sundaland. Nonetheless, rhacophorid evolution, specially on Borneo, has not been studied within a phylogenetic context. In this study, we examine the phylogenetic relationships of 38 (out of 41) Bornean species of Rhacophoridae, in combination with data from previous phylogenetic studies. In the final super matrix of 91 species, we analyse sequence data from two mitochondrial and three nuclear genes. The resulting trees show the genus Rhacophorus as a paraphyletic assemblage. As a consequence, we transfer Rhacophorus appendiculatus and R. kajau to two other genera and propose the new phylogeny-based combinations--Kurixalus appendiculatus and Feihyla kajau, respectively. Furthermore, we use our phylogenetic hypotheses to reconstruct the evolution of reproductive modes in rhacophorid tree frogs. Direct development to the exclusion of a free larval stage evolved twice independently, once in an ancestor of the Pseudophilautus+Raorchestes clade in India and Sri Lanka, and once within Philautus in Southeast Asia. The deposition of egg clutches covered by a layer of jelly in Feihyla is also present in F. kajau and thus confirms our generic reassignment. The remarkably high diversity of rhacophorid tree frogs on Borneo is the outcome of a complex pattern of repeated vicariance and dispersal events caused by past changes in the climatic and geological history of the Sunda shelf. We identified geographic clades of closely related endemic species within Rhacophorus and Philautus, which result from local island radiations on Borneo.

The evolutionary diversification of parrots supports a taxon pulse model with multiple trans-oceanic dispersal events and local radiations.

Vicariance is thought to have played a major role in the evolution of modern parrots. However, as the relationships especially of the African taxa remained mostly unresolved, it has been difficult to draw firm conclusions about the roles of dispersal and vicariance. Our analyses using the broadest taxon sampling of old world parrots ever based on 3219bp of three nuclear genes revealed well-resolved and congruent phylogenetic hypotheses. Agapornis of Africa and Madagascar was found to be the sister group to Loriculus of Australasia and Indo-Malayasia and together they clustered with the Australasian Loriinae, Cyclopsittacini and Melopsittacus. Poicephalus and Psittacus from mainland Africa formed the sister group of the Neotropical Arini and Coracopsis from Madagascar and adjacent islands may be the closest relative of Psittrichas from New Guinea. These biogeographic relationships are best explained by independent colonization of the African continent via trans-oceanic dispersal from Australasia and Antarctica in the Paleogene following what may have been vicariance events in the late Cretaceous and/or early Paleogene. Our data support a taxon pulse model for the diversification of parrots whereby trans-oceanic dispersal played a more important role than previously thought and was the prerequisite for range expansion into new continents.