Search

Unlike most bird species, individual kingfisher species (Aves: Alcedinidae) are typically parasitized by only a single genus of louse (Alcedoffula,Alcedoecus, orEmersoniella). These louse genera are typically specific to a particular kingfisher subfamily. Specifically,AlcedoecusandEmersoniellaparasitize Halcyoninae, whereasAlcedoffulaparasitizes Alcedininae and Cerylinae. AlthoughEmersoniellais geographically restricted to the Indo-Pacific region,AlcedoecusandAlcedoffulaare geographically widespread. We used DNA sequences from two genes, the mitochondrial COI and nuclear EF-1αgenes, to infer phylogenies for the two geographically widespread genera of kingfisher lice,AlcedoffulaandAlcedoecus. These phylogenies included 47 kingfisher lice sampled from 11 of the 19 currently recognized genera of kingfishers. We compared louse phylogenies to host phylogenies to reconstruct their cophylogenetic history. Two distinct clades occur withinAlcedoffula, one that infests Alcedininae and a second that infests Cerylinae. All species ofAlcedoecuswere found only on host species of the subfamily Halcyoninae. Cophylogenetic analysis indicated thatAlcedoecus, as well as the clade ofAlcedoffulaoccurring on Alcedininae, do not show evidence of cospeciation. In contrast, the clade ofAlcedoffulaoccurring on Cerylinae showed strong evidence of cospeciation.

Evolutionary biologists have long used behavioral, ecological, and genetic data from contact zones between closely related species to study various phases of the speciation continuum. North America has several concentrations of avian contact zones, where multiple pairs of sister lineages meet, with or without hybridization. In a southern California contact zone, 2 species of woodpeckers, Nuttall’s Woodpecker (Dryobates nuttallii) and the Ladder-backed Woodpecker (D. scalaris), occasionally hybridize. We sampled these 2 species in a transect across this contact zone and included samples of their closest relative, the Downy Woodpecker (D. pubescens), to obtain large single nucleotide polymorphism panels using restriction-site associated DNA sequencing (RAD-seq). Furthermore, we used whole-genome resequencing data for 2 individuals per species to identify whether patterns of diversity inferred from RAD-seq were representative of whole-genome diversity. We found that these 3 woodpecker species are genomically distinct. Although low levels of gene flow occur between D. nuttallii and D. scalaris across the contact zone, there was no evidence for widespread genomic introgression between these 2 species. Overall patterns of genomic diversity from the RAD-seq and wholegenome datasets appear to be related to distributional range size and, by extension, are likely related to effective population sizes for each species.

Phylogeographic studies of Philippine vertebrates have demonstrated that genetic variation is broadly partitioned by Pleistocene island aggregation. Contemporary island discontinuity is expected to influence genetic differentiation, but remains relatively undocumented perhaps because the current episode of island isolation started relatively recently. We investigated inter- and intra-island population structure in a Philippine endemic bird genus (Sarcophanops) to determine if genetic differentiation has evolved during the recent period of isolation. We sequenced thousands of genome-wide RAD markers from throughout the Mindanao group to assess fine-scale genetic structure across islands. Specifically, we investigated patterns of gene flow and connectivity within and between taxonomic and geographic bounds. A previous assessment of mitochondrial DNA detected deep structure between Sarcophanops samarensis and sister species, S. steerii, but was insufficient to detect differentiation within either species. Analysis of RAD markers, however, revealed structure within S. samarensis between the islands of Samar/Leyte and Bohol. This genetic differentiation likely demonstrates an effect of recent geographic isolation (post-LGM) on the genetic structure of Philippine avifauna. We suggest that the general lack of evidence for differentiation between recently isolated islands is a failure to detect subtle population structure due to past genetic sampling constraints, rather than the absence of such structure.

Many species complexes have diversified rapidly and recently, resulting in morphologically diverse populations; however, the rapid pace of diversification often prevents identification of clear phylogeographic structure. Recently, the use of large genomic and reduced-representation genomic datasets has improved resolution of the evolutionary histories in such species and allowed identification of lineages on distinct evolutionary trajectories. The northern flicker (Colaptes auratus) and gilded flicker (Colaptes chrysoides) form a polytypic superspecies group with a complex taxonomic history. The superspecies group includes up to 13 described subspecies, which represent slight geographic variation among five main morphological groups: red-shafted flickers of western North America (cafer group), yellow-shafted flickers of eastern North America (auratus group), Cuban flickers of the Caribbean (chrysocaulosus group), gilded flickers of the U.S. south-west and Mexican north-west (chrysoides group), and Guatema...

Sky islands, or montane forest separated by different lowland habitats, are highly fragmented regions that potentially limit gene flow between isolated populations. In the sky islands of the Madrean Archipelago (Arizona, USA), various taxa display different phylogeographic patterns, from unrestricted gene flow among sky islands to complex patterns with multiple distinct lineages. Using genomic-level approaches allows the investigation of differential patterns of gene flow, selection, and genetic differentiation among chromosomes and specific genomic regions between sky island populations. Here, we used thousands of SNPs to investigate the putative contact zone of divergent Brown Creeper (Certhia americana) lineages in the Madrean Archipelago sky islands. We found the two lineages to be completely allopatric (during the breeding season) with a lack of hybridization and gene flow between lineages and no genetic structure among sky islands within lineages. Additionally, the two lineages inhabit different climatic and ecosystem conditions and have many local primary song dialects in the southern Arizona mountain ranges. We identified a positive relationship between genetic differentiation and chromosome size, but the sex chromosome (Z) was not found to be an outlier. Differential patterns of genetic differentiation per chromosome may be explained by genetic drift—possibly in conjunction with non-random mating and non-random gene flow—due to variance in recombination rates among chromosomes.

Despite a long history of biological exploration, there remains much to learn about the avifauna of the Solomon Islands. Here, we report new records of the Blue-faced Parrotfinch (Erythrura trichroa) on Malaita and Makira islands, thus expanding the known distribution of the species in the geographic Solomon Islands to include Bougainville, Kolombangara, Guadalcanal, Malaita, and Makira islands. Morphometric comparison of specimens from these populations showed no consistent differences in plumage or measurements, although sample sizes were small for all populations (n = 1–2 comparable specimens from 3 populations). Likewise, mitochondrial DNA sequence data showed little genetic differentiation among these populations. Our results suggest that the Blue-faced Parrotfinch exhibits some of the lowest interpopulation divergence of any montane bird species in the Solomon Islands and provides useful comparison to biogeographic patterns in other bird populations that share a similar distribution across multiple Pleistocene islands. Our discovery of 2 new populations of Blue-faced Parrotfinches highlights the need for continued biodiversity work in the region for both conservation and research.

Recent phylogenetic studies of gekkonid lizards have revealed unexpected, widespread paraphyly and polyphyly among genera, unclear generic boundaries, and a tendency towards the nesting of taxa exhibiting specialized, apomorphic morphologies within geographically widespread "generalist" clades. This is especially true in Australasia, where monophyly of Gekko proper has been questioned with respect to phenotypically ornate flap-legged geckos of the genus Luperosaurus, the Philippine false geckos of the genus Pseudogekko, and even the elaborately "derived" parachute geckos of the genus Ptychozoon. Here we employ sequence capture targeting 5060 ultraconserved elements (UCEs) to infer phylogenomic relationships among 42 representative ingroup gekkonine lizard taxa. We analyze multiple datasets of varying degrees of completeness (10, 50, 75, 95, and 100 percent complete with 4715, 4051, 3376, 2366, and 772 UCEs, respectively) using concatenated maximum likelihood and multispecies coalescent methods. Our sampling scheme addresses four persistent systematic questions in this group: (1) Are Luperosaurus and Ptychozoon monophyletic, and are any of these named species truly nested within Gekko? (2) Are prior phylogenetic estimates of Sulawesi's L. iskandari as the sister taxon to Melanesian G. vittatus supported by our genome-scale dataset? (3) Is the high-elevation L. gulat of Palawan Island correctly placed within Gekko? (4) And, finally, where do the enigmatic taxa P. rhacophorus and L. browni fall in a higher-level gekkonid phylogeny? We resolve these issues; confirm with strong support some previously inferred findings (placement of Ptychozoon taxa within Gekko; the sister taxon relationship between L. iskandari and G. vittatus); resolve the systematic position of unplaced taxa (L. gulat, and L. browni); and transfer L. iskandari, L. gulat, L. browni, and all members of the genus Ptychozoon to the genus Gekko. Our unexpected and novel systematic inference of the placement of Ptychozoon rhacophorus suggests that this species is not grouped with Ptychozoon or even Luperosaurus (as previously expected) but may, in fact, be most closely related to several Indochinese species of Gekko. With our resolved and strongly supported phylogeny, we present a new classification emphasizing the most inclusive, original generic name (Gekko) for these ~60 taxa, arranged into seven subgenera.

Significance Our understanding of the factors that affected the diversification of passerines, the most diverse and widespread bird order (Passeriformes), is limited. Here, we reconstruct passerine evolutionary history and produce the most comprehensive time-calibrated phylogenetic hypothesis of the group using extensive sampling of the genome, complete sampling of all passerine families, and a number of vetted fossil calibration points. Our phylogenetic results refine our knowledge of passerine diversity and yield divergence dates that are consistent with the fossil record, and our macroevolutionary analyses suggest that singular events in Earth history, such as increases in Cenozoic global temperature or the colonization of new continents, were not the primary forces driving passerine diversification., Avian diversification has been influenced by global climate change, plate tectonic movements, and mass extinction events. However, the impact of these factors on the diversification of the hyperdiverse perching birds (passerines) is unclear because family level relationships are unresolved and the timing of splitting events among lineages is uncertain. We analyzed DNA data from 4,060 nuclear loci and 137 passerine families using concatenation and coalescent approaches to infer a comprehensive phylogenetic hypothesis that clarifies relationships among all passerine families. Then, we calibrated this phylogeny using 13 fossils to examine the effects of different events in Earth history on the timing and rate of passerine diversification. Our analyses reconcile passerine diversification with the fossil and geological records; suggest that passerines originated on the Australian landmass ∼47 Ma; and show that subsequent dispersal and diversification of passerines was affected by a number of climatological and geological events, such as Oligocene glaciation and inundation of the New Zealand landmass. Although passerine diversification rates fluctuated throughout the Cenozoic, we find no link between the rate of passerine diversification and Cenozoic global temperature, and our analyses show that the increases in passerine diversification rate we observe are disconnected from the colonization of new continents. Taken together, these results suggest more complex mechanisms than temperature change or ecological opportunity have controlled macroscale patterns of passerine speciation.

Aim For terrestrial organisms, a faunal transition zone between the Indochinese and Sundaic regions is delimited north of the Isthmus of Kra on the Thai-Malay Peninsula. We used a mitochondrial marker to test the predicted location of intraspecific north–south divides for four species of bulbuls (Pycnonotus). Phylogenetic relationships among Thai-Malay populations and their closest relatives from the Greater Sundas were reconstructed from a multilocus data set including 35 Pycnonotus species. Location Indochina, Thai-Malay Peninsula, Greater Sundas. Methods We sampled target species along a north–south transect spanning the Isthmus of Kra and reconstructed phylogeographical patterns based on ND2 haplotype networks. Phylogenies were reconstructed using Maximum likelihood and Bayesian inference. Divergence time estimates were inferred from single-locus and multilocus data using *beast. Results We found mitochondrial north–south divides in all target species. Haplotypes of southern genetic clusters were distributed all across the Thai-Malay Peninsula and north into Central Thailand. Local overlap of genetic lineages was confirmed at one location in one species only. In three of the focal species, the southern limits of southern haplotype clusters were restricted to the Thai-Malay Peninsula and did not extend into the Greater Sundas. Peninsular north–south divides were dated to the late Pleistocene, whereas Indochinese-Sundaic lineage divergence was dated to the late Pliocene. Main conclusions Population boundaries did not coincide with the Isthmus of Kra, but instead were located north of the Thai-Malay Peninsula in Central Thailand. Only one of four divides represented an Indochinese-Sundaic transition. Different phylogeographical patterns among target species were presumably shaped by different ecological preferences in Pleistocene palaeohabitats. Pliocene Indochinese-Sundaic lineage divergence in bulbuls coincides with strong vegetational changes on the Peninsula that shaped two phytogeographical transitions. Distribution limits of bird species roughly coincide with these transition zones and therefore the avifaunal Thai-Malay transition represents a broad zone rather than a sharp boundary.

Combining ecological niche modeling with phylogeography has become a popular approach to understand how historical climate changes have created and maintained population structure. However, methodological choices in geographic extents and environmental layer sets employed in modeling may affect results and interpretations profoundly. Here, we infer range-wide phylogeographic structure and model ecological niches of Cyanoderma ruficeps, and compare results to previous studies that examined this species across mainland China and Taiwan only. Use of dense taxon sampling of closely related species as outgroups question C. ruficeps monophyly. Furthermore, previously unsampled C. ruficeps populations from central Vietnam were closely related to disjunct western populations (Nepal, Tibet, Myanmar, Yunnan), rather than to geographically proximate populations in northern Vietnam and eastern China. Phylogeographic structure is more complex than previously appreciated; niche model projections to Last Glacial Maximum climate scenarios identified larger areas of suitable conditions than previous studies, but potential distributional limits differed markedly between climate models employed and were dependent upon interpretation of non-analogous historical climate scenarios. Previously identified population expansion across central China may result from colonization from refugial distributions during the Last Interglacial, rather than the Last Glacial Maximum, as previously understood.

During the last 15–20 years, phylogenetic, phylogeographic, paleontological, geological, and habitat modeling studies have improved our knowledge of Sundaic biogeography dramatically. In light of these advances, we review (or postulate) where Sundaic rainforest birds came from, the causes of their endemism, and the influence of Pleistocene climatic perturbations on their diversification. We suggest that four scenarios make up a coherent, plausible explanation of patterns of extant diversity. First, relictual lineages, which represent hangovers from the warm, wet Eocene, survived the hard climatic times of the colder, drier Oligocene and Pliocene in the mountains and adjacent lowlands of eastern Borneo, where rainforest has existed continuously for the last 20–30 million years. Second, most modern SE Asian genera developed during the Miocene. Third, the rainforest of Sundaland and its avifauna were largely isolated from the rest of SE Asia during the late Miocene and Pliocene by seasonal habitats in southern Indochina and ocean boundaries elsewhere, increasing regional endemism. Finally, the advent of global glaciation in the Pleistocene introduced a different diversification dynamic to Sundaland. Early glacial events caused sufficient drying in central Sundaland to fragment rainforest and its avifauna into refugia in eastern and western Sundaland and to allow dry-habitat taxa to reach Java from Indochina. More recent glacial events resulted in sufficient perhumid habitat in central Sundaland to reconnect previously vicariated rainforest populations, creating the lowland and elevational parapatry we see today. This Pleistocene dynamic was probably not simply one period of separation and one period of connection, but rather a complex interplay of isolation and colonization, influenced by highly variable population sizes, changing levels of gene flow, and behavioral idiosyncrasies of the species involved. Throughout all of these events, Borneo played a seminal role in rainforest bird evolution by providing the habitat necessary for diversification and the long-term survival of taxa.

The avian genus Ficedula has been a model system for studying speciation, genomics, biogeography, and the evolution of migratory behavior. However, no multi-locus molecular phylogenetic hypothesis exists for the genus. We expanded taxon and character sampling over previous studies and produced a robust hypothesis of relationships for the genus. Many previous findings, such as the inclusion of Muscicapella and exclusion of Ficedula monileger from the genus, were verified, but many relationships differed compared to previous work. Some of the differences were due to increased sampling, but others were due to problematic sequence data produced from DNA extracted from historical museum specimens. The new phylogenetic hypothesis resulted in a simpler biogeographic scenario with fewer transitions between regions and fewer transitions between seasonally migratory and resident character states. Notably, all species endemic to the Philippines and Wallacea formed a clade, which included Ficedula dumetoria of the Sunda Shelf and Lesser Sundas. In addition, Ficedula hyperythra was not monophyletic; samples from Philippine populations formed a clade distantly related to a clade that comprised all other sampled populations.

Biodiversity patterns in Asia are poorly understood due to inferences drawn from incorrect taxonomy and limited survey effort. The Streak-breasted Scimitar Babblers (Pomatorhinus ruficollis complex) have a wide distribution across southern Asia and exhibit a high degree of plumage variability within and among populations. Continued use of traditional subspecies designations over revised species-limits based on plumage and DNA sequence data furthers confusion in this group and obscures complex biogeographic patterns. In this study, we combined previously published DNA sequences with newly sampled populations to produce a comprehensive dataset for the ruficollis complex. Phylogenetic analysis of these data confirms that traditional subspecies based on plumage alone are paraphyletic and therefore not good descriptors of evolutionary history. With increased sampling, our study supported previous delimitations of phylogenetic species as distinct units, refined the range limits of two taxa - P. reconditus (throughout central China) and P. nigrostellatus (Hainan, Guangxi, N Vietnam), showed two additional clades that may be distinct species, and uncovered a 'suture' zone where populations of multiple species occur in the same localities. Diversification within the ruficollis complex indicates a clade of Sino-Himalayan and SE Asian species sister to a clade distributed in central and southern China species. The 'suture' zone where different ruficollis species are in contact coincides with the meeting of these four major geographic areas in a highly geomorphologically complex region.

Topographically complex regions often contain the close juxtaposition of closely related species along elevational gradients. The evolutionary causes of these elevational replacements, and thus the origin and maintenance of a large portion of species diversity along elevational gradients, are usually unclear because ecological differentiation along a gradient or secondary contact following allopatric diversification can produce the same pattern. We used reduced representation genomic sequencing to assess genetic relationships and gene flow between three parapatric pairs of closely related songbird taxa (Arachnotheraspiderhunters,Chloropsisleafbirds, andEnicurusforktails) along an elevational gradient in Borneo. Each taxon pair presents a different elevational range distribution across the island, yet results were uniform: little or no gene flow was detected in any pairwise comparisons. These results are congruent with an allopatric “species-pump” model for generation of species diversity and elevational parapatry of congeners on Borneo, rather than in situ generation of species by “ecological speciation” along an elevational gradient.

Reduced representation genomic sequencing methods efficiently gather sequence data from thousands of loci throughout the genome. These data can be used to test previous phylogenetic hypotheses produced from limited numbers of mitochondrial and nuclear loci that often reveal intriguing, but conflicting, results. In this paper, we use phylogenomic data to revisit recent molecular phylogenetic work that clarified many taxonomic relationships within spiderhunters, but also questioned the monophyly of this distinctive genus of sunbirds (AVES: Nectariniidae; Arachnothera). DNA sequence data were produced by target-capture sequencing of ultraconserved elements (UCEs) to infer the evolutionary history of 11 species of Arachnothera and six outgroups, including the Purple-naped Sunbird (Hypogramma hypogrammicum), which previous work suggested might lie within Arachnothera. Although we recovered many different gene tree topologies, concatenated and coalescent methods of analysis converged on a species tree that strongly supports the monophyly of Arachnothera, with Hypogramma as its sister taxon.

The Rufous-tailed Tailorbird (Orthotomus sericeus)—a Sunda endemic—is divided into 3 morphologically based subspecies: one in western Sundaland (Malay Peninsula, Sumatra, and associated islands), one from the Natuna Islands in the South China Sea, and one on Borneo, Palawan, and smaller islands of the Sunda continental shelf east of Borneo. Previous study, however, suggested that these subspecies do not conform to molecular genetic subdivisions of the species. We reexamined the morphology and performed molecular phylogeographic and multi-locus coalescent analysis of two subspecies of Rufous-tailed Tailorbird comprising populations on the Malay Peninsula, Sumatra, Borneo, and Palawan. We found (1) little morphological difference among the two subspecies, (2) no substantial genetic differences between the Borneo and western Sunda populations, but (3) marked genetic divergence between the Palawan and other populations. We conclude that the Bornean and western Sunda populations interbred extensively ...

Avian diversification in oceanic archipelagos is largely attributed to isolation across marine barriers. During glacial maxima, lowered sea levels resulted in repeated land connections between islands joined by shallow seas. Consequently, such islands are not expected to show endemism. However, if climate fluctuations simultaneously caused shifts in suitable environmental conditions, limiting populations to refugia, then occurrence on and dispersal across periodic land bridges are not tenable. To assess the degree to which paleoclimate barriers, rather than marine barriers, drove avian diversification in the Philippine Archipelago, we produced ecological niche models for current-day, glacial maxima, and interglacial climate scenarios to infer potential Pleistocene distributions and paleoclimate barriers. We then tested marine and paleoclimate barriers for correspondence to geographic patterns of population divergence, inferred from DNA sequences from eight codistributed bird species. In all species, deep-water channels corresponded to zones of genetic differentiation, but six species exhibited deeper divergence associated with a periodic land bridge in the southern Philippines. Ecological niche models for these species identified a common paleoclimate barrier that coincided with deep genetic structure among populations. Although dry land connections joined southern Philippine islands during low sea level stands, unfavorable environmental conditions limited populations within landmasses, resulting in long-term isolation and genetic differentiation. These results highlight the complex nature of diversification in archipelagos: marine barriers, changes in connectivity due to sea level change, and climate-induced refugia acted in concert to produce great species diversity and endemism in the Philippines.

The birds of the Solomon Islands have received ample historical attention by explorers, collectors and researchers. Despite this, knowledge of the region's avifauna is categorised by BirdLife International as ‘poor’ and multiple new populations of birds have been found in recent years, highlighting our incomplete knowledge of the region's avifauna. Here, we present new information on the elevational occurrence, abundance and natural history for ten bird species we observed on Isabel Island. The data we present are based on three weeks of field work at three field sites that included the restricted montane forests above 1,000 m elevation on the Kubonitu-Sasari massif. In this poorly known montane area we observed multiple Island Leaf Warblers Phylloscopus maforensis for the first time since it was discovered on Isabel in 1927.

The evolution of pantropically distributed clades has puzzled palaeo- and neontologists for decades regarding the different hypotheses about where they originated. In this study, we explored how a pantropical distribution arose in a diverse clade with a rich fossil history: the avian order Coraciiformes. This group has played a central role in the debate of the biogeographical history of Neoaves. However, the order lacked a coherent species tree to inform study of its evolutionary dynamics. Here, we present the first complete species tree of Coraciiformes, produced with 4858 ultraconserved elements, which supports two clades: (1) Old World-restricted bee-eaters, rollers and ground-rollers; and (2) New World todies and motmots, and cosmopolitan kingfishers. Our results indicated two pulses of diversification: (1) major lineages of Coraciiformes arose in Laurasia approximately 57 Ma, followed by independent dispersals into equatorial regions, possibly due to tracking tropical habitat into the lower latitudes—the Coracii (Coraciidae + Brachypteraciidae) into the Afrotropics, bee-eaters throughout the Old World tropics, and kingfishers into the Australasian tropics; and (2) diversification of genera in the tropics during the Miocene and Pliocene. Our study supports the important role of Laurasia as the geographical origin of a major pantropical lineage and provides a new framework for comparative analyses in this charismatic bird radiation.

Cream-vented Bulbul Pycnonotus simplex of Borneo was previously considered to be polymorphic in iris colour, having either red or white (creamy-yellow) irides. Mitochondrial DNA sequence comparisons, however, indicate that white- and red-eyed Bornean individuals are not closely related to one another. Instead, white-eyed birds are sister to Ashy-fronted Bulbul P. cinereifrons of Palawan Island, in the south-west Philippines, and red-eyed birds are sister to white-eyed P. simplex of the Thai-Malay Peninsula. Consequently, we elect to treat the white-eyed Bornean population as a distinct, previously overlooked species. In respect to plumage, white- and red-eyed individuals are almost identical, varying only slightly in the amount of yellow coloration in their feathers. The two taxa are sympatric at some localities, but white-eyed individuals are rarer and more consistently associated with mature forest than red-eyed birds.

The Mountain Black-eye (Chlorocharis emiliae) is an endemic white-eye (Zosteropidae) of Borneo with a unique ‘‘sky island’’ distribution. We compared mitochondrial ND2, ND3, Cytb, and control region DNA sequences (2,194 nucleotides) to study the phylogeographic relationships of five populations of this species that span its range: Mounts Kinabalu, Trus Madi, Murud, Mulu, and Pueh. These comparisons showed that black-eyes are divided into two main clades that correspond generally to subspecific morphological groups: one in Sabah, Malaysia (Kinabalu and Trus Madi), and one in Sarawak, Malaysia (Murud, Mulu, and Pueh). The genetic and morphologic subdivision of black-eyes disputes the expected merging of populations during the Last Glacial Maximum (LGM), when montane forest presumably expanded and provided the opportunity for currently isolated populations to intermingle. Instead the genetic aging of black-eye populations indicates they diversified long before the LGM, and either did not expand sufficiently in range during the LGM to reach one another, or were reproductively isolated by the time of the LGM and thus prevented from interbreeding. Moreover, the subdivision between black-eyes in Sabah and Sarawak means that this species (and probably several other montane species) has a phylogeographic structure remarkably similar to Borneo’s lowland bird populations, which are presumed to have evolved under different paleo-geographic conditions. The similar phylogeographic pattern found in both montane and lowland species requires that we rethink the causes of bird population diversification on the island of Borneo.

Long celebrated for its spectacular landscapes and strikingly high levels of endemic biodiversity, the Philippines has been studied intensively by biogeographers for two centuries. Concentration of so many endemic land vertebrates into a small area and shared patterns of distribution in many unrelated forms has inspired a search for common mechanisms of production, partitioning, and maintenance of life in the archipelago. In this review, we (a) characterize an ongoing renaissance of species discovery, (b) discuss the changing way biogeographers conceive of the archipelago, (c) review the role molecular phylogenetic studies play in understanding the evolutionary history of Philippine vertebrates, and (d) describe how a 25-year Pleistocene island connectivity paradigm continues to provide some explanatory power, but has been augmented by increased understanding of the archipelago's geological history and ecological gradients. Finally, we (e) review new insights provided by studies of adaptive versus nonadaptive radiation and phylogenetic perspectives on community ecology.

With more than 70 described subspecies distributed from Java to Fiji, the Golden Whistler species complex (Aves: Pachycephala pectoralis/melanura) is the world's most geographically variable bird species. We sequenced ten genes totalling 5743 bp from 202 individuals and 32 nominal subspecies, mostly from the Australasian and Polynesian lineages. We used concatenated maximum likelihood and Bayesian inference, as well as coalescent species tree analysis, to reconstruct a phylogeny. The resulting phylogeny is the most densely sampled and robust estimate of this group's evolutionary history to date and many novel relationships are revealed. The ingroup comprised three well-supported clades. An Australasian clade inclusive of Vanuatu was sister to a clade including the Bismarck Archipelago, the Solomon Islands, and the Polynesian taxa minus Vanuatu, and sister to these two clades was Pachycephala citreogaster collaris of the Louisiade Archipelago. Some species-level taxa endemic to the Pacific were found to be embedded in the ingroup (e.g. Pachycephala feminina, Pachycephala flavifrons, and Pachycephala jacquinoti), whereas others were found to be outside of the species complex (e.g. Pachycephala implicata). Generally, most nodes in the tree had strong support with the exception of several Polynesian lineages whose relationships remain equivocal. Relationships within each clade are discussed in detail, and current taxonomic treatments are critiqued in light of our results. © 2013 The Linnean Society of London

The Robsonius ground-warblers are forest birds endemic to the Luzon Island complex in the Philippine archipelago. Their systematic relationships have long remained ambiguous; until recently they were included in the timaliid genus Napothera. Two Robsonius species are currently recognized on the basis of plumage differences: R. rabori from northern Luzon in the Cordillera Central and the northern Sierra Madre, and R. sorsogonensis from southern Luzon and Catanduanes Island. Recent specimen collections, including the first adult specimen from the Cordillera Central, establish plumage differences between populations of R. rabori in the Cordillera Central and Sierra Madre and reveal a third diagnosable population within Luzon. These differences have gone unnoticed because R. rabori (sensu stricto) had been known only from the juvenile holotype. Molecular phylogenetic data further support the hypothesis that three highly divergent taxa occur across the Luzon Island complex: Robsonius rabori is known ...

Phylogenetic analyses of nuclear and mitochondrial DNA sequences were used to test a recent phylogenetic hypothesis for the avian genus Gallicolumba that relied heavily on preserved museum study skins for DNA samples. Our comparisons show that several published gene sequences represent pseudogenes or chimeras of multiple taxa, and these sequences had an adverse influence on phylogeny estimation. A new phylogenetic hypothesis strongly supports the monophyly of Philippine bleeding-hearts, the monophyly of Gallicolumba sensu stricto, and places Leucosarcia as part of an Australasian radiation rather than sister to Alopecoenas. These findings clarify Gallicolumba biogeography and also highlight the need for greater caution in the use of suboptimal source material in molecular systematic studies.

Aim Colonization and subsequent isolation across deep-water barriers is thought to be the primary driver of diversification in insular birds. Shallow-water barriers and intra-island isolation are less well-documented drivers of avian diversification. We examined the relative roles of different geographical barriers in the diversification of Aethopyga sunbirds, a widespread Southeast Asian genus that has its greatest diversity in the Philippine Archipelago. Location Philippines, Southeast Asia, Wallacea. Methods We reconstructed the phylogenetic relationships among Aethopyga sunbirds with mitochondrial and nuclear DNA sequences. Phylogeny was inferred using concatenated and coalescent frameworks, implemented in maximum likelihood and Bayesian analyses. We used maximum likelihood ancestral state reconstructions to examine the ancestral distribution and colonization history of Aethopyga. To determine whether the diversification at each node occurred within a continent, across a shallow-water barrier, across a deep-water barrier or within an island, we used a series of statements based on the phylogeny, current distribution of species and bathymetric reconstructions. Results Ancestral state reconstructions inferred that the core Aethopyga ancestor was continental, and that the diversity of Aethopyga on oceanic islands is the result of three or four independent colonization events. Dispersal and subsequent isolation across deep-water barriers was the most common mode of diversification in insular Aethopyga, although intra-island isolation contributed to diversity, producing a small montane radiation within Mindanao. Analyses inferred only a single unequivocal event of diversification across a shallow-water barrier. Deep molecular divergences between phenotypically distinct subspecies suggested that the taxonomy of Aethopyga is overly conservative and obscures biogeographical patterns. We recommend elevating five subspecies, all of which are endemic to the Philippines, to full species. Main conclusions In addition to corroborating the importance of isolation across deep-water barriers, these data also underscore a potential role for additional isolating mechanisms in the generation of biodiversity on oceanic islands. A clade of four montane Aethopyga taxa evolved in situ within the Mindanao sky-island system, an exception to the paradigm that birds do not diversify within the geographical confines of oceanic islands.

We reconstructed the phylogeographic relationships of the Variable Dwarf-Kingfisher (Ceyx lepidus) using DNA sequence data. Maximum likelihood and Bayesian analysis methods were used to reconstruct trees from a multilocus data set of all 15 named subspecies of the Ceyx lepidus species complex. The concatenated data-set length was 2,471 base pairs and included two mitochondrial genes and two noncoding nuclear introns. Support for the monophyly of C. lepidus was equivocal. We instead found support for a clade including all C. lepidus subspecies plus two endemic Philippine taxa: C. argentatus and C. cyanopectus. Relationships among subspecific taxa were not well resolved, and many nodes were collapsed into polytomies suggesting a rapid and widespread colonization. In situ diversification likely played a role in generating current diversity within four archipelagos: the Philippines, Malukus, Bismarcks, and Solomons. Some biogeographic patterns recovered for the Solomon Islands taxa match those seen ...

Songbirds (oscine passerines) are the most species-rich and cosmopolitan bird group, comprising almost half of global avian diversity. Songbirds originated in Australia, but the evolutionary trajectory from a single species in an isolated continent to worldwide proliferation is poorly understood. Here, we combine the first comprehensive genome-scale DNA sequence data set for songbirds, fossil-based time calibrations, and geologically informed biogeographic reconstructions to provide a well-supported evolutionary hypothesis for the group. We show that songbird diversification began in the Oligocene, but accelerated in the early Miocene, at approximately half the age of most previous estimates. This burst of diversification occurred coincident with extensive island formation in Wallacea, which provided the first dispersal corridor out of Australia, and resulted in independent waves of songbird expansion through Asia to the rest of the globe. Our results reconcile songbird evolution with Earth history and link a major radiation of terrestrial biodiversity to early diversification within an isolated Australian continent., Songbirds originated in Australia and have now diversified into approximately 5,000 species found across the world. Here, Moyle et al. combine phylogenomic and biogeographic analyses to show that songbird diversification was associated with the formation of islands providing a route out of Australia.

The independent evolution of similar traits across multiple taxa provides some of the most compelling evidence of natural selection. Little is known, however, about the genetic basis of these convergent or parallel traits: are they mediated by identical or different mutations in the same genes, or unique mutations in different genes? Using a combination of candidate gene and reduced representation genomic sequencing approaches, we explore the genetic basis of and the evolutionary processes that mediate similar plumage colour shared by isolated populations of theMonarcha castaneiventrisflycatcher of the Solomon Islands. A genome-wide association study (GWAS) that explicitly controlled for population structure revealed that mutations in known pigmentation genes are the best predictors of parallel plumage colour. That is, entirely black or melanic birds from one small island share an amino acid substitution in the melanocortin-1 receptor (MC1R), whereas similarly melanic birds from another small island over 100 km away share an amino acid substitution in a predicted binding site of agouti signalling protein (ASIP). A third larger island, which separates the two melanic populations, is inhabited by birds with chestnut bellies that lack the melanicMC1RandASIPallelic variants. FormalFSToutlier tests corroborated the results of the GWAS and suggested that strong, directional selection drives the near fixation of theMC1RandASIPvariants across islands. Our results, therefore, suggest that selection acting on different mutations with large phenotypic effects can drive the evolution of parallel melanism, despite the relatively small population size on islands.

We present the first molecular phylogenetic hypothesis for Knipolegus (black-tyrants), a widespread genus of South American tyrant-flycatchers, based on nuclear and mitochondrial DNA sequences. Bayesian and maximum-likelihood analyses support three clades within Knipolegus, one confined to northern South America, one confined to southeast Brazil, and one confined to the Southern Cone and southern Andes. Within each clade, two or more species are broadly sympatric or parapatric, overlapping in general distribution but differing in habitat specialization. Maximum-likelihood ancestral state reconstructions using an equal-rate stochastic model support a single origin of austral migration in the southern group. Contrasting with these strong geographic patterns, ancestral state reconstructions of plumage and display evolution were more complex, with multiple inferred character-state changes. Ancestral state reconstructions suggest a sexually dimorphic ancestor of Knipolegus, and sexually similar pluma...

The phylogeny of spiderhunters (Nectariniidae: Arachnothera) was reconstructed by comparing mitochondrial and nuclear DNA sequences of all currently recognized species and with broad geographic sampling of two particularly variable species complexes, the Little Spiderhunter (Arachnothera longirostra) and the streaky spiderhunters (A. modesta and A. affinis). It appears to be a relatively old group, whose diversification was not caused by recent sea-level changes. However, the modern, highly sympatric distribution of the large species in the Sunda lowlands was probably a result of dispersal via recent land bridges. Within the highly variable A. longirostra group, there are substantially diverged taxa in the Philippines that should be considered different species. Within the A. affinis—modesta complex, there are three distinct species and a closely related fourth, which describe a clear allopatric distribution: A. affinis in Java, A. modesta in the rest of the Sunda lowlands (except Sabah), A. mag...

Monophyly of the scimitar babblers (Pomatorhinus, Xiphirhynchus: Timaliidae), traditionally defined by the characteristic of having long, curved bills, has been questioned by recent molecular phylogenetic results. We examined representatives of all scimitar babbler species complexes, including all distinct lineages of four complexes as well as several potential relatives, and corroborate that Xiphirhynchus and some species of Stachyris group within Pomatorhinus. Pomatorhinus species comprise three separate clades: larger scimitar babblers (Pomatorhinus hypoleucos, Pomatorhinus erythrogenys complexes); orange- and coral-billed scimitar babblers (Pomatorhinus ochraceiceps, Pomatorhinus ferruginosus complexes); and small scimitar babblers (Pomatorhinus schisticeps, Pomatorhinus ruficollis, Pomatorhinus horsfieldii, Pomatorhinus montanus complexes). Additionally, at least two of the traditional species complexes are not monophyletic. Lineages of the ruficollis and schisticeps groups are intertwined, and P. montanus and P. horsfieldi group within the schisticeps complex. Upon revision of four traditional species complexes, P. hypoluecos, P. ferruginosus, P. schisticeps, and P. ruficollis (with 41 subspecies described in total), 27 distinct, independent lineages or phylogenetic species were distinguished. Two contrasting biogeographical patterns are evident in these groups: Sino-Himalayan areas are either sister to south-east Asian areas or are embedded within a clade of other Asian areas. The present study demonstrates the need for unraveling the confusion in traditional taxonomy to allow the study of complex biodiversity patterns in tropical Asia. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 102, 846–869.

Sundaland, a biogeographic region of Southeast Asia, is a major biodiversity hotspot. However, little is known about the relative importance of Pleistocene habitat barriers and rivers in structuring populations and promoting diversification here. We sampled 16 lowland rainforest bird species primarily from peninsular Malaysia and Borneo to test the long-standing hypothesis that animals on different Sundaic landmasses intermixed extensively when lower sea-levels during the Last Glacial Maximum (LGM) exposed land-bridges. This hypothesis was rejected in all but five species through coalescent simulations. Furthermore, we detected a range of phylogeographic patterns; Bornean populations are often genetically distinct from each other, despite their current habitat connectivity. Environmental niche modeling showed that the presence of unsuitable habitats between western and eastern Sundaland during the LGM coincided with deeper interpopulation genetic divergences. The location of this habitat barrier had been hypothesized previously based on other evidence. Paleo-riverine barriers are unlikely to have produced such a pattern, but we cannot rule out that they acted with habitat changes to impede population exchanges across the Sunda shelf. The distinctiveness of northeastern Borneo populations may be underlied by a combination of factors such as rivers, LGM expansion of montane forests and other aspects of regional physiography.

We describe the nest and eggs of two Philippine endemic passerines, the Rusty-faced Babbler (Robsonius rabori) and the Blue-breasted Blue Flycatcher (Cyornis herioti). We also describe a novel type of nest and nest placement for the Short-crested Monarch (Hypothymis helenae), and provide the first description of the eggs of this species. We discuss similarities among eggs and nests of these species with their relatives, and the need for more information regarding natural history and breeding habits for the Philippine avifauna.

Aim Nearly 150 years ago, T. H. Huxley modified Wallace’s Line, including the island of Palawan as a component of the Asian biogeographic realm and separating it from the oceanic Philippines. Although Huxley recognized some characteristics of a transition between the regions, Palawan has since been regarded primarily as a peripheral component of the Sunda Shelf. However, several recent phylogenetic studies of Southeast Asian lineages document populations on Palawan to be closely related to taxa from the oceanic Philippines, apparently contradicting the biogeographic association of Palawan with the Sunda Shelf. In the light of recent evidence, we evaluate taxonomic and phylogenetic data in an attempt to identify the origin(s) of Palawan’s terrestrial vertebrate fauna. Location The Sunda Shelf and the Philippines. Methods We review distributional and phylogenetic data for populations of terrestrial vertebrates from Palawan. Using taxonomic data, we compare the number of Palawan taxa (species and genera) shared with the Sunda Shelf and oceanic Philippines. Among widespread lineages, we use phylogenetic data to identify the number of Palawan taxa with sister relationships to populations or species from the Sunda Shelf or oceanic Philippines. Results Although many terrestrial vertebrate taxa are shared between Palawan and the Sunda Shelf, an increasing number of species and populations are now recognized as close relatives of lineages from the oceanic Philippines. Among the 39 putative lineages included in molecular phylogenetic studies with sampling from the Sunda Shelf, Palawan and the oceanic Philippines, 17 of them reveal sister relationships between lineages from Palawan and the oceanic Philippines. Main conclusions Rather than a simple nested subset of Sunda Shelf populations, Palawan is best viewed as having played multiple biogeographic roles, including a young and old extension of the Sunda Shelf, a springboard to diversification in the oceanic Philippines, and a biogeographic component of the Philippine archipelago. Palawan has a long, complex geological history, which may explain this variation in pattern. Huxley originally noted transitional elements in Palawan’s fauna; we therefore suggest that his modification of Wallace’s Line should be recognized as a filter zone, reflecting both his original intent and available taxonomic and molecular evidence.

Mistakenly classifying morphologically cryptic endemic species as populations of widespread species potentially interferes with the conservation of biodiversity because undetected endemics that are imperilled may lack appropriate protection. It also impedes the reconstruction of the evolutionary history of a taxon by obscuring the number and distributional limits of species. Here, we present genetic and phylogenetic evidence corroborated by morphology that Philippine populations of seven widespread, non-migratory passerine birds might represent unrecognized, distinct species. An extrapolation based on this finding suggests that the proportion of endemic bird species in the Philippines could be much higher than currently estimated. This high degree of cryptic diversity in a well-studied, volant taxon implies that large numbers of unrecognized species can be expected in less thoroughly studied groups. We predict that genetic investigations of insular populations of widespread species will frequently reveal unrecognized island endemics, and because of the vulnerability of island habitats and their biota, these taxa may be particularly susceptible to extinction.

H. C. Lim (hlim1@tigers.lsu.edu) and F. H. Sheldon, Mus. of Nat. Sci. and Dept. of Biol. Sci., Louisiana State Univ., Baton Rouge,LA 70803, USA. R. G. Moyle, Dept. of Ecol. and Evol. Biol. and Biodiv. Res. Centre, Univ. of Kansas, Lawrence, KS 66045, USA.Extensive plumage color polymorphism in the oriental dwarf kingfisher Ceyx erithaca has long intrigued ornithologists ofthe Indo Malayan region. A large proportion of birds in Sumatra, Peninsular Malaysia and Borneo have plumagesintermediate between the northerly black form and the southerly rufous form. We used molecular genetic techniques toinvestigate whether the pattern is likely caused by selection, contemporary hybridization or past introgression of genes.These data consist of DNA sequences of a mitochondrial gene (ND2) and five nuclear intronic loci. Phylogenetic analysesindicated that birds from continental southeast Asia (excluding the Thai Malay Peninsula) are well differentiated fromthose from insular southeast Asia. This genetic distinction correlates well with a fixed difference in mantle coloration.Northern birds have black mantles and are consistently dark; southern birds, though highly variable in parts of theplumage, consistently possess a rusty brown mantle. Multivariate analyses of morphometric data also support clusteringbirds in the two groups defined by mantle coloration. Coalescent analyses suggest that gene flow occurred after initialpopulation splitting. We hypothesized that the dynamic geography of the Indo Malayan Archipelago, as driven byeustatic sea-level changes related to glacial cycles, is responsible for extensive secondary contact, and gene flow, betweenthe two color forms. Such periodic contacts, after initial separation of the populations, may be equally common in othergeographically dynamic regions of the world.

Anthropogenic habitat changes and the introduction of pigs, dogs, cats and rats have caused acatastrophic decline in the terrestrial biodiversity of Pacific archipelagos. At present, economicglobalization and an increased demand for timber are promoting industrial logging and plantationexpansion. Commercial logging can be sustainable but in practice it more often leads to landdegradation, especially on small flat islands. On large and mountainous islands, however, moremodest impacts can be expected as the narrowly endemic species tend to inhabit montane forestswhere logging is difficult. In this study we use ornithological data collected at different elevationsto assess the extent to which the avifauna of Makira, a large mountainous island in Melanesia, willbe affected by deforestation of the lowlands, most of which are under timber concessions. Our datasuggest that a majority of the endemic bird species use lowland forest to some extent and that thismay even apply to species hitherto associated with montane forest. If current commercial forestryprogrammes are continued, the forest habitat may be disturbed or lost over large parts of Makira,potentially undermining the natural resource base for the local subsistence economy, exacerbatingclimate change and threatening the integrity of one of the most important areas for biodiversityconservation on earth. Our study highlights the importance of understanding the habitat require-ments of endemic species and the urgency of establishing and effectively managing community-based protected areas in suitable lowland forests of the Pacific.Keywords: biodiversity, forestry, Galathea 3 expedition, montane fauna, Pacific Islands, SolomonIslands

Aim We use molecular-based phylogenetic methods and ancestral area reconstructions to examine the systematic relationships and biogeographical history of the Indo-Pacific passerine bird family Pachycephalidae (whistlers). Analysed within an explicit spatiotemporal framework, we elucidate distinct patterns of diversification across the Melanesian and Indonesian archipelagos and explore whether these results may be explained by regional palaeogeological events. We further assess the significance of upstream colonization and its role in species accumulation within the region. Location The Indo-Pacific region, with an emphasis on the archipelagos on either side of the Australo-Papuan continent. Methods We used three nuclear and two mitochondrial markers to construct a molecular phylogenetic hypothesis of the Pachycephalidae by analysing 35 of the 49 species known to belong to the family. The programs diva and MrBayes were used to reconstruct ancestral area relationships and to examine biogeographical relationships across the family, and beast was implemented to assess the timing of dispersal events. Results We constructed a molecular phylogenetic hypothesis for the Pachycephalidae and estimated divergence times and ancestral area relationships. Different colonization patterns are apparent for the Pachycephalidae in the Indonesian and the Melanesian archipelagos. The Indonesian archipelago was colonized numerous times, whereas one or two colonizations of the Melanesian archipelagos account for the entire diversity of that region. After initial colonization of the Melanesian archipelagos some whistler species recolonized Australia and may have commenced a second round of colonization into Melanesia. Main conclusions The contrasting dispersal patterns of whistlers in archipelagos on either side of the Australo-Papuan continent are congruent with the arrangement and history of islands in each of the regions and demonstrate that knowledge of palaeogeography is important for an understanding of evolutionary patterns in archipelagos. We also highlight that recolonization of continents from islands may be more common than has previously been assumed.

Nyari, A ´ . S., Benz, B. W., Jonsson, K. A., Fjeldsa u, J. & Moyle, R. G. (2009). Phylogenetic relationships of fantails (Aves: Rhipiduridae). — Zoologica Scripta, 38, 553-561. We explore the phylogenetic relationships of fantails (Aves: Rhipiduridae) using molecular characters derived from two nuclear introns and two mitochondrial genes. Our results indicate that Rhipidura hypoxantha is not a true fantail, but rather a member of the Stenos- tiridae clade that is morphologically and behaviourally convergent with fantails. Within the true Rhipiduridae, we identified six distinct clades; however, phylogenetic relationships among these groups were unresolved. The only well-supported sister relationship was between members of the grey and the rufous fantail complexes. Clades recovered through our model-based phylogenetic analyses generally correspond to previously proposed fantail complexes based on morphological characters. The phylogenetic position of R. atra and R. diluta remain unclear, as sister relationships varied between analyses for the prior whereas the latter was placed as sister to the New Guinea thicket fantails, R. leucothorax and R. threnothorax; yet significant node support was not recovered for either taxa. Biogeographi- cally, fantails appear to have radiated rapidly and the six clades are not geographically

Phylogenetic relationships among the Tyrannides were assessed using over 4000 base pairs of nuclear recombination activating 1 (RAG-1) and 2 (RAG-2) DNA sequence data from about 93% of all described genera, which represents the most complete assessment of relationships for this diverse New World radiation to date. With this sampling we propose a significantly expanded interpretation of higher-level relationships within the group. The Tyrannides are shown to be comprised of six major lineages, all of which represent traditional family-level taxa (sensuFitzpatrick, 2004a and Snow, 2004a,b; del Hoyo et al., 2004): (i) manakins (Pipridae); (ii) cotingas (Cotingidae); (iii) the sharpbill (Oxyruncus) + onychorhynchine flycatchers (Onychorhynchini); (iv) tityrines (Tityridae); (v) rhynchocycline flycatchers (Rhynchocyclidae); and (vi) the tyrant flycatchers (Tyrannidae). In addition, the RAG data recovered isolated lineages with uncertain relationships, including Neopipo, Platyrinchus, Piprites, and Tachuris. The Pipridae are the sister-group to all the other Tyrannides. Within the latter, the clade ((Oxyruncidae + Tityridae) + Cotingidae) is the sister-group of the Tyrannoidea. Within the Tyrannoidea, the Rhynchocyclidae and their allies are sisters to Neopipo + Tyrannidae. Using our phylogenetic hypothesis, we propose the first comprehensive phylogenetic classification that attempts to achieve isometry between the tree and a classification scheme using subordination and phyletic sequencing. This study thus provides a phylogenetic framework for understanding the evolution of this diverse New World assemblage, and identifies many avenues for further systematic study. © The Willi Hennig Society 2009.

The infraorder Furnariides is a diverse group of suboscine passerine birds comprising a substantial component of the Neotropical avifauna. The included species encompass a broad array of morphologies and behaviours, making them appealing for evolutionary studies, but the size of the group (ca. 600 species) has limited well-sampled higher-level phylogenetic studies. Using DNA sequence data from the nuclear RAG-1 and RAG-2 exons, we undertook a phylogenetic analysis of the Furnariides sampling 124 (more than 88%) of the genera. Basal relationships among family-level taxa differed depending on phylogenetic method, but all topologies had little nodal support, mirroring the results from earlier studies in which discerning relationships at the base of the radiation was also difficult. In contrast, branch support for family-rank taxa and for many relationships within those clades was generally high. Our results support the Melanopareidae and Grallariidae as distinct from the Rhinocryptidae and Formicariidae, respectively. Within the Furnariides our data contradict some recent phylogenetic hypotheses and suggest that further study is needed to resolve these discrepancies. Of the few genera represented by multiple species, several were not monophyletic, indicating that additional systematic work remains within furnariine families and must include dense taxon sampling. We use this study as a basis for proposing a new phylogenetic classification for the group and in the process erect new family-group names for clades having high branch support across methods.

Aim The oriental magpie-robin (Copsychus saularis) of South and Southeast Asia is a phenotypically variable species that appears to be closely related to two endemic species of the western Indian Ocean: the Madagascar magpie-robin (Copsychus albospecularis) and the Seychelles magpie-robin (Copsychus sechellarum). This unusual distribution led us to examine evolutionary relationships in magpie-robins, and also the taxonomic significance of their plumage variation, via a molecular phylogenetic and population genetic analysis of C. saularis and C. albospecularis. Location Southern Asia from Nepal across Indochina to southern China, and the Indian Ocean from Madagascar to the Greater Sunda and Philippine islands. Methods We sequenced 1695 nucleotides of mitochondrial DNA comprising the complete second subunit of the nicotinamide adenine dinucleotide dehydrogenase (ND2) gene and 654 bases of the cytochrome c oxidase subunit I (COI) region in 51 individuals of eight C. saularis subspecies, 10 individuals of C. albospecularis (one subspecies) and single individuals of two other Copsychus species as outgroups. The data were analysed phylogenetically, with maximum likelihood, Bayesian, relaxed clock and parsimony methods, and geographically for patterns of genetic diversity. Results Phylogenetic analysis indicated that C. albospecularis lies within the nominal C. saularis, making C. saularis polyphyletic. Malagasy and non-Philippine Asian populations form a monophyletic group that is sister to a clade of Philippine populations. Within non-Philippine Asian populations, two groups are evident: black-bellied birds in the eastern Greater Sunda islands and white-bellied birds in the western Sundas and on mainland Asia. Main conclusions The phylogeny of magpie-robins suggests a novel pattern of dispersal and differentiation in the Old World. Ancestral magpie-robins appear to have spread widely among islands of the Indian Ocean in the Pliocene, probably aided by their affinity for coastal habitats. Populations subsequently became isolated in island groups, notably the Philippines, Madagascar and the Greater Sundas, leading to speciation in all three areas. Isolation in the Philippines may have been aided by competitive exclusion of C. saularis from Palawan by a congener, the white-vented shama (Copsychus niger). In the Greater Sundas, white-bellied populations appear to have invaded Borneo and Java recently, where they hybridize with resident black-bellied birds.

Factors that influence speciation rates among groups of organisms are integral to deciphering macroevolutionary processes; however, they remain poorly understood. Here, we use molecular phylogenetic data and divergence time estimates to reconstruct the pattern and tempo of speciation within a widespread and homogeneous bird family (white-eyes, Zosteropidae) that contains an archetypal “great speciator.” Our analyses show that the majority of this species-rich family constitutes a clade that arose within the last 2 million years, yielding a per-lineage diversification rate among the highest reported for vertebrates (1.95–2.63 species per million years). However, unlike most rapid radiations reported to date, this burst of diversification was not limited in geographic scope, but instead spanned the entire Old World tropics, parts of temperate Asia, and numerous Atlantic, Pacific, and Indian Ocean archipelagos. The tempo and geographic breadth of this rapid radiation defy any single diversification paradigm, but implicate a prominent role for lineage-specific life-history traits (such as rapid evolutionary shifts in dispersal ability) that enabled white-eyes to respond rapidly and persistently to the geographic drivers of diversification.

Changes in mating signals among populations contribute to species formation. Often these signals involve a suite of display traits of different sensory modalities ("multimodal signals"); however, few studies have tested the consequences of multimodal signal divergence with most focusing on only a single divergent signal or suite of signals of the same sensory modality. Populations of the chestnut-bellied flycatcher Monarcha castaneiventris vary in song and plumage color across the Solomon Islands. Using taxidermic mount presentation and song playback experiments, we tested for the relative roles of divergent song and color in homotypic ("same type") recognition between one pair of recently diverged sister taxa (the nominate chestnut-bellied M. c. castaneiventris and the white-capped M. c. richardsii forms). We found that both plumage and song type influenced the intensity of aggressive response by territory-owners, with plumage color playing a stronger role. These results indicate that differences in plumage and song are used in homotypic recognition, suggesting the importance of multimodal signal divergence in the evolution of premating reproductive isolation.

The classification of New World martins (Progne) has a convoluted history because taxonomists have relied on plumage traits that vary continuously across populations. We estimated the phylogeny of Progne by analyzing mitochondrial cytochrome b DNA sequences of 27 individuals of eight of the nine species (10 subspecies) and nuclear β-fibrinogen intron 7 sequences of 20 individuals of six species (8 subspecies). The Brown-chested Martin (P. tapera) is sister to other Progne species. The Middle American taxa—Sinaloa Martin (P. sinaloae), Cuban Martin (P. cryptoleuca), Caribbean Martin (P. dominicensis), and Central American populations of Gray-breasted Martin (P. chalybea)—form a well supported clade. This group is distinct from Purple Martin (P. subis), which has no particularly close relatives. All four Middle American taxa appear to be good species, although Cuban and Caribbean martins could be merged in view of their similar plumage and low genetic divergence (1.2%). Two of the South American ta...

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.

Restriction-site associated DNA sequencing (RAD-seq) and target capture of specific genomic regions, such as ultraconserved elements (UCEs), are emerging as two of the most popular methods for phylogenomics using reduced-representation genomic data sets. These two methods were designed to target different evolutionary timescales: RAD-seq was designed for population-genomic level questions and UCEs for deeper phylogenetics. The utility of both data sets to infer phylogenies across a variety of taxonomic levels has not been adequately compared within the same taxonomic system. Additionally, the effects of uninformative gene trees on species tree analyses (for target capture data) have not been explored. Here, we utilize RAD-seq and UCE data to infer a phylogeny of the bird genus Piranga. The group has a range of divergence dates (0.5–6 myr), contains 11 recognized species, and lacks a resolved phylogeny. We compared two species tree methods for the RAD-seq data and six species tree methods for the UCE data. Additionally, in the UCE data, we analyzed a complete matrix as well as data sets with only highly informative loci. A complete matrix of 189 UCE loci with 10 or more parsimony informative (PI) sites, and an approximately 80% complete matrix of 1128 PI single-nucleotide polymorphisms (SNPs) (from RAD-seq) yield the same fully resolved phylogeny of Piranga. We inferred non-monophyletic relationships of Pirangalutea individuals, with all other a priori species identified as monophyletic. Finally, we found that species tree analyses that included predominantly uninformative gene trees provided strong support for different topologies, with consistent phylogenetic results when limiting species tree analyses to highly informative loci or only using less informative loci with concatenation or methods meant for SNPs alone.

The bee-eaters (family Meropidae) comprise a group of brightly colored, but morphologically homogeneous, birds with a wide variety of life history characteristics. A phylogeny of bee-eaters was reconstructed using nuclear and mitochondrial DNA sequence data from 23 of the 25 named bee-eater species. Analysis of the combined data set provided a well-supported phylogenetic hypothesis for the family. Nyctiornis is the sister taxon to all other bee-eaters. Within the genus Merops, we recovered two well-supported clades that can be broadly separated into two groups along geographic and ecological lines, one clade with mostly African resident species and the other clade containing a mixture of African and Asian taxa that are mostly migratory species. The clade containing resident African species can be further split into two groups along ecological lines by habitat preference into lowland forest specialists and montane forest and forest edge species. Intraspecific sampling in several of the taxa revealed moderate to high (3.7–6.5%, ND2) levels of divergence in the resident taxa, whereas the lone migratory taxon showed negligible levels of intraspecific divergence. This robust molecular phylogeny provides the phylogenetic framework for future comparative tests of hypotheses about the evolution of plumage patterns, sociality, migration, and delayed breeding strategies. 2007 Elsevier Inc. All rights reserved.