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The complex island archipelagoes of Wallacea and Melanesia have provided empirical data behind integral theories in evolutionary biology, including allopatric speciation and island biogeography. Yet, questions regarding the relative impact of the layered biogeographic barriers, such as deep-water trenches and isolated island systems, on faunal diversification remain underexplored. One such barrier is Wallace’s Line, a significant biogeographic boundary that largely separates Australian and Asian biodiversity. To assess the relative roles of biogeographic barriers—specifically isolated island systems and Wallace’s Line—we investigated the tempo and mode of diversification in a diverse avian radiation, Corvides (Crows and Jays, Birds-of-paradise, Vangas, and allies). We combined a genus-level data set of thousands of ultraconserved elements (UCEs) and a species-level, 12-gene Sanger sequence matrix to produce a well-resolved supermatrix tree that we leveraged to explore the group’s historical biogeography and the effects of the biogeographic barriers on their macroevolutionary dynamics. The tree is well resolved and differs substantially from what has been used extensively for past comparative analyses within this group. We confirmed that Corvides, and its major constituent clades, arose in Australia and that a burst of dispersals west across Wallace’s Line occurred after the uplift of Wallacea during the mid-Miocene. We found that dispersal across this biogeographic barrier was generally rare, though westward dispersals were two times more frequent than eastward dispersals. Wallacea’s central position between Sundaland and Sahul no doubt acted as a bridge for island-hopping dispersal out of Australia, across Wallace’s Line, to colonize the rest of Earth. In addition, we found that the complex island archipelagoes east of Wallace’s Line harbor the highest rates of net diversification and are a substantial source of colonists to continental systems on both sides of this biogeographic barrier. Our results support emerging evidence that island systems, particularly the geologically complex archipelagoes of the Indo-pacific, are drivers of species diversification. [Historical biogeography; island biogeography; Melanesia; molecular phylogenetics; state-dependent diversification and extinction.]

In this study, we infer genus-level relationships within shrikes (Laniidae), crows (Corvidae), and their allies using ultraconserved elements (UCEs). We confirm previous results of the Crested Shrikejay (Platylophus galericulatus) as comprising its own taxonomic family and find strong support for its sister relationship to laniid shrikes. We also find strong support that the African-endemic genus Eurocephalus, which comprises two allopatric species (E. ruppelli and E. anguitimens), are not “true-shrikes”. We propose elevating the white-crowned shrikes to their own family, Eurocephalidae.

Thoroughly sampled and well-supported phylogenetic trees are essential to taxonomy and to guide studies of evolution and ecology. Despite extensive prior inquiry, a comprehensive tree of heron relationships (Aves: Ardeidae) has not yet been published. As a result, the classification of this family remains unstable, and their evolutionary history remains poorly studied. Here, we sample genome-wide ultraconserved elements (UCEs) and mitochondrial DNA sequences (mtDNA) of >90% of extant species to estimate heron phylogeny using a combination of maximum likelihood, coalescent, and Bayesian inference methods. The UCE and mtDNA trees are mostly concordant with one another, providing a topology that resolves relationships among the 5 heron subfamilies and indicates that the genera Gorsachius, Botaurus, Ardea, and Ixobrychus are not monophyletic. We also present the first genetic data from the Forest Bittern Zonerodius heliosylus, an enigmatic species of New Guinea; our results suggest that it is a member of the genus Ardeola and not the Tigrisomatinae (tiger herons), as previously thought. Finally, we compare molecular rates between heron clades in the UCE tree with those in previously constructed mtDNA and DNA–DNA hybridization trees. We show that rate variation in the UCE tree corroborates rate patterns in the previously constructed trees—that bitterns (Ixobrychus and Botaurus) evolved comparatively faster, and some tiger herons (Tigrisoma) and the Boat-billed Heron (Cochlearius) more slowly, than other heron taxa.

Studies of natural hybrid zones can provide documentation of range shifts in response to climate change and identify loci important to reproductive isolation. Using a temporal (36-38 years) comparison of the black-capped (Poecile atricapillus) and Carolina (P. carolinensis) chickadee hybrid zone, we investigated movement of the western portion of the zone (western Missouri) and assessed whether loci and pathways underpinning reproductive isolation were similar to those in the eastern portion of the hybrid zone. Using 92 birds sampled along the hybrid zone transect in 2016 and 68 birds sampled between 1978 and 1980, we generated 11,669 SNPs via ddRADseq. These SNPs were used to assess movement of the hybrid zone through time and to evaluate variation in introgression among loci. We demonstrate that the interface has moved ~5 km to the northwest over the last 36-38 years, that is, at only one-fifth the rate at which the eastern portion (e.g., Pennsylvania, Ohio) of the hybrid zone has moved. Temperature trends over the last 38 years reveal that eastern areas have warmed 50% more than western areas in terms of annual mean temperature, possibly providing an explanation for the slower movement of the hybrid zone in Missouri. Our results suggest hybrid zone movement in broadly distributed species, such as chickadees, will vary between areas in response to local differences in the impacts of climate change.

The radiation of so-called “great speciators” represents a paradox among the myriad of avian radiations endemic to the southwest Pacific. In such radiations, lineages otherwise capable of dispersing across vast distances of open ocean differentiate rapidly and frequently across relatively short geographic barriers. Here, we evaluate the phylogeography of the Rufous Fantail (Rhipidura rufifrons). Although a presumed “great-speciator”, no formal investigations across its range have been performed. Moreover, delimitation of lineages within R. rufifrons, and the biogeographic implications of those relationships, remain unresolved. To investigate whether R. rufifrons represents a great speciator we identified thousands of single nucleotide polymorphisms for 89 individuals, representing 19 described taxa. Analyses recovered 7 divergent lineages and evidence of gene flow between geographically isolated populations. We also found plumage differences to be a poor proxy for evolutionary relationships. Given the relatively recent divergence dates for the clade (1.35–2.31 mya), rapid phenotypic differentiation, and evidence for multiple independent lineages within the species complex, we determine that R. rufifrons possesses the characteristics of a great speciator.

Phylogeographical 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 in relatively recent times. We investigated inter- and intra-island population structure in a Philippine endemic bird genus (Sarcophanops) to determine whether genetic differentiation has evolved during the recent period of isolation. We sequenced thousands of genome-wide restriction site associated DNA (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 geographical bounds. A previous assessment of mitochondrial DNA detected deep structure between Sarcophanops samarensis and a sister species, Sarcophanops 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 probably demonstrates an effect of recent geographical isolation (after the Last Glacial Maximum) on the genetic structure of Philippine avifauna. We suggest that the general lack of evidence for differentiation between recently isolated populations is a failure to detect subtle population structure owing to past genetic sampling constraints, rather than the absence of such structure.

As a dispersive lineage expands its distribution across a heterogeneous landscape, it leaves behind allopatric populations with varying degrees of geographic isolation that often differentiate rapidly. In the case of oceanic islands, even narrowly separated populations often differentiate, which seems contrary to the highly dispersive nature of the founding lineage. This pattern of highly dispersive lineages differentiating across narrow sea barriers has perplexed biologists for more than a century. We used two reduced-representation genomic datasets to examine the diversification of a recent, rapid geographic radiation, the white-eyes (Aves: Zosterops) of the Solomon Islands. We incorporated methods that targeted phylogenetic structure, population structure, and explicit tests for gene flow. Both datasets showed evidence of gene flow among species, but not involving the closely spaced islands in the New Georgia Group. Instead, gene flow has occurred among the larger islands in the archipelago, including those recently connected by land bridges as well as those isolated by large expanses of deep ocean. Populations separated by shallow seas, and connected by land bridges during glacial cycles, ranged from no differentiation to both phenotypic and genomic differentiation. These complex patterns of gene flow and divergence support a model of rapid geographic radiation in which lineages differentially evolve dispersal disparity and phenotypic differences.

Aim: Variation in species diversity among different geographical areas may result from differences in speciation and extinction rates, immigration and time for diversification. An area with high species diversity may be the result of a high net diversification rate, multiple immigration events from adjacent regions, and a long time available for the accumulation of species (known as the 'time-for-speciation effect'). Here, we examine the relative importance of the three aforementioned processes in shaping the geographical diversity patterns of a large radiation of passerine birds.Location: Global.Taxon: Babblers (Aves: Passeriformes).Methods: Using a comprehensive phylogeny of extant species (similar to 90% sampled) and distributions of the world's babblers, we reconstructed their biogeographical history and analysed the diversification dynamics. We examined how species richness correlates with the timing of regional colonization, the number of immigration events and the rate of speciation within all 13 geographical distribution regions.Results: We found that babblers likely originated in the Sino-Himalayan Mountains (SHM) in the early Miocene, suggesting a long time for diversification and species accumulation within the SHM. Regression analyses showed the regional diversity of babblers can be well explained by the timing of the first colonization within of these areas, while differences in rates of speciation or immigration have far weaker effects. Nonetheless, the rapid speciation of Zosterops during the Pleistocene has accounted for the increased diversification and accumulation of species in the oceanic islands.Main Conclusions: Our results suggest that the global diversity patterns of babblers have predominantly been shaped by the time-for-speciation effect. Our findings also support an origin centred in tropical and subtropical parts of the SHM, with a cradle of recent diversification in the oceanic islands of the Indo-Pacific and Indian Ocean regions, which provides new insights into the generation of global biodiversity hotspots.

To help resolve phylogenetic and phylogeographic relationships of Southeast Asian birds, we have collected specimens in Borneo, Sumatra, and Java for phylogenetic and morphological study. Here, we compare mitochondrial ND2 gene sequences from some of these new specimens to sequences obtained in previous studies to shed light on genealogical relationships in nine passerine clades: Erythropitta venusta/granatina/ussheri (pittas); Dicrurus hottentottus (drongos); Alophoixus bulbuls; Napothera, Turdinus and Pellorneum babblers; Anthipes flycatchers; Brachypteryx shortwings; and Myophonus whistling thrushes. These comparisons resolve or shed substantial light on taxonomic problems in pittas, Alophoixus, Napothera, Dicrurus, Brachypteryx, and Myophonus, and they confirm assumed (but previously unquantified) genetic relationships within Turdinus and Anthipes. The resulting trees also allow us to (1) suggest improved taxonomic arrangements in several groups, (2) confirm the rediscovery of a “lost” species within Napothera, and (3) provide the basis for the description of a new subspecies of Alophoixus.

Complex speciation, involving rapid divergence and multiple bouts of post-divergence gene flow, can obfuscate phylogenetic relationships and species limits. In North America, cases of complex speciation are common, due at least in part to the cyclical Pleistocene glacial history of the continent. Scrub-Jays in the genus Aphelocoma provide a useful case study in complex speciation because their range throughout North America is structured by phylogeographic barriers with multiple cases of secondary contact between divergent lineages. Here, we show that a comprehensive approach to genomic reconstruction of evolutionary history, i.e., synthesizing results from species delimitation, species tree reconstruction, demographic model testing, and tests for gene flow, is capable of clarifying evolutionary history despite complex speciation. We find concordant evidence across all statistical approaches for the distinctiveness of an endemic southern Mexico lineage (A. w. sumichrasti), culminating in support for the species status of this lineage under any commonly applied species concept. We also find novel genomic evidence for the species status of a Texas endemic lineage A. w. texana, for which equivocal species delimitation results were clarified by demographic modeling and spatially explicit models of gene flow. Finally, we find that complex signatures of both ancient and modern gene flow between the non-sister California Scrub-Jay (Aphelocoma californica) and Woodhouse’s Scrub-Jay (Aphelocoma woodhouseii) result in discordant gene trees throughout the species’ genomes despite clear support for their overall isolation and species status. In sum, we find that a multi-faceted approach to genomic analysis can increase our understanding of complex speciation histories, even in well-studied groups. Given the emerging recognition that complex speciation is relatively commonplace, the comprehensive framework that we demonstrate for interrogation of species limits and evolutionary history using genomic data can provide a necessary roadmap for disentangling the impacts of gene flow and incomplete lineage sorting (ILS) to better understand the systematics of other groups with similarly complex evolutionary histories. [Gene flow; genomics; introgression; phylogenomics; population genetics; species delimitation; species trees; systematics.]

Little is known of the natural history of the Solomons Nightjar (Eurostopodus nigripennis) due to its restricted range and reclusive nature. Here we describe the breeding biology of E. nigripennis based on nests found in the Western Province, Solomon Islands, between June and October 2019. Four nests were discovered on 3 small islands: Tetepare, Hehevai, and Nanakatopa; the latter 2 are first island records for this species. We observed all stages of the species' nesting cycle, from egg to post-fledging care of juveniles by adults, each with a single nestling (n = 4). We describe the eggs, nestlings, and juvenile plumage of the species with additional detail on nesting habitat and document new breeding locations in the Western Province.

Recently described vocal variation within the monotypic Yellow-spotted Barbet Buccanodon duchaillui has been used to suggest the presence of two allopatric species separated by the Dahomey Gap in western Africa. Using mitochondrial and nuclear DNA sequences from two genes, we investigated molecular patterns of divergence across the species' range, in light of the published vocal variation. We found support for a genetic break at the Dahomey Gap, but also identified much deeper divergence among other populations in the eastern part of the species' range. Deep genetic divergence, and geographic variation in the species' vocalisations, suggest a greater degree of diversity in this species than currently recognised.

Remote oceanic islands have high potential to harbor unique fauna and flora, but opportunities to conduct in-depth biotic surveys are often limited. Furthermore, underrepresentation of existing biodiversity in the literature has the potential to detract from conservation planning and action. Between 18 and 29 October 2018, we surveyed the terrestrial vertebrates of East Rennell, a UNESCO World Heritage Site in Solomon Islands. We documented 56 species, including 15 squamates, 13 mammals, and 38 birds, and present four new vertebrate records for the island: Stephan's emerald dove (Chalcophaps stephani), Maluku myotis (Myotis moluccarum), littoral skink (Emoia atrocostata) and brahminy blindsnake (Indotyphlops braminus). East Rennell was designated a World Heritage site for its significant on-going ecological and biological processes, and importance for the study of island biogeography. The new records presented here provide evidence that continued field studies combined with DNA analysis will continue to uncover even greater endemic biodiversity. Rennell is currently experiencing major habitat destruction in parts of the island that are not under World Heritage protection, and we anticipate collateral damage will likely extend into protected areas. Our survey also underscores the incredible vertebrate biodiversity that stands to be lost unless conservation actions and local community needs are intertwined to promote beneficial outcomes on both fronts.

We report the characteristics of the mitochondrial genomes of 22 individuals in the bird genus Piranga, including all currently recognized species in the genus (n = 11). Elements follow the standar...

The honeyeaters are the most species-rich clade of birds east of Wallace’s Line. They occupy a wide range of habitats, from desert to rainforest, and occur throughout Australia, New Guinea,...

Disjunct, pantropical distributions are a common pattern among avian lineages, but disentangling multiple scenarios that can produce them requires accurate estimates of historical relationships and timescales. Here, we clarify the biogeographical history of the pantropical avian family of trogons (Trogonidae) by re‐examining their phylogenetic relationships and divergence times with genome‐scale data. We estimated trogon phylogeny by analysing thousands of ultraconserved element (UCE) loci from all extant trogon genera with concatenation and coalescent approaches. We then estimated a time frame for trogon diversification using MCMCTree and fossil calibrations, after which we performed ancestral area estimation using BioGeoBEARS. We recovered the first well‐resolved hypothesis of relationships among trogon genera. Trogons comprise three clades, each confined to one of three biogeographical regions: Africa, Asia and the Neotropics, with the African clade sister to the others. These clades diverged rapidly during the Oligocene‐Miocene transition. Our biogeographical analyses identify a Eurasian origin for stem trogons and a crown clade arising from ancestors broadly distributed across Laurasia and Africa. The pantropical ranges of trogons are relicts of a broader Afro‐Laurasian distribution that was fragmented across Africa, Asia and the New World in near coincident fashion during the Oligocene‐Miocene transition by global cooling and changing habitats along the Beringian land bridge and North Africa.

The utility of islands as natural laboratories of evolution is exemplified in the patterns of differentiation in widespread, phenotypically variable lineages. The whistlers (Aves: Pachycephalidae) are one of the most complex avian radiations, with a combination of widespread and locally endemic taxa spanning the vast archipelagos of the Indo-Pacific, making them an ideal group to study patterns and processes of diversification on islands. Here, we present a robust, species-level phylogeny of all five genera and 85% of species within Pachycephalidae, based on thousands of ultraconserved elements (UCEs) generated with a target-capture approach and high-throughput sequencing. We clarify phylogenetic relationships within Pachycephala and report on divergence timing and ancestral range estimation. We explored multiple biogeographic coding schemes that incorporated geological uncertainty in this complex region. The biogeographic origin of this group was difficult to discern, likely owing to aspects of dynamic Earth history in the Indo-Pacific. The Australo-Papuan region was the likely origin of crown-group whistlers, but the specific ancestral area could not be identified more precisely than Australia or New Guinea, and Wallacea may have played a larger role than previously realized in the evolutionary history of whistlers. Multiple independent colonizations of island archipelagos across Melanesia, Wallacea, and the Philippines contributed to the relatively high species richness of extant whistlers. This work refines our understanding of one of the regions' most celebrated bird lineages and adds to our growing knowledge about the patterns and processes of diversification in the Indo-Pacific.

Gene tree discordance is expected in phylogenomic trees and biological processes are often invoked to explain it. However, heterogeneous levels of phylogenetic signal among individuals within data sets may cause artifactual sources of topological discordance. We examined how the information content in tips and subclades impacts topological discordance in the parrots (Order: Psittaciformes), a diverse and highly threatened clade of nearly 400 species. Using ultraconserved elements from 96% of the clade’s species-level diversity, we estimated concatenated and species trees for 382 ingroup taxa. We found that discordance among tree topologies was most common at nodes dating between the late Miocene and Pliocene, and often at the taxonomic level of the genus. Accordingly, we used two metrics to characterize information content in tips and assess the degree to which conflict between trees was being driven by lower-quality samples. Most instances of topological conflict and nonmonophyletic genera in the species tree could be objectively identified using these metrics. For subclades still discordant after tip-based filtering, we used a machine learning approach to determine whether phylogenetic signal or noise was the more important predictor of metrics supporting the alternative topologies. We found that when signal favored one of the topologies, the noise was the most important variable in poorly performing models that favored the alternative topology. In sum, we show that artifactual sources of gene tree discordance, which are likely a common phenomenon in many data sets, can be distinguished from biological sources by quantifying the information content in each tip and modeling which factors support each topology. [Historical DNA; machine learning; museomics; Psittaciformes; species tree.]

White-eyes are an iconic radiation of passerine birds that have been the subject of studies in evolutionary biology, biogeography, and speciation theory. Zosterops white-eyes in particular are thought to have radiated rapidly across continental and insular regions of the Afro- and Indo-Pacific tropics, yet their phylogenetic history remains equivocal. Here, we sampled 77% of the genera and 47% of known white-eye species and sequenced thousands of ultraconserved elements to infer the phylogeny of the avian family Zosteropidae. We used concatenated maximum likelihood and species tree methods and found strong support for seven clades of white-eyes and three clades within the species-rich Zosterops radiation.

We report the characteristics of the mitochondrial genomes of 22 individuals in the bird genus Piranga, including all currently recognized species in the genus (n = 11). Elements follow the standard avian mitogenome series, including two ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, 13 protein coding genes, and the mitochondrial control region. Excluding tRNA sequences, sequence divergence rate was lowest in rRNA genes and highest in genes encoding NADH (specifically ND1, ND2, ND3) and the control region. Gene trees assembled from 16 elements (non-tRNAs) varied greatly in topological concordance compared to the recognized species tree (based on thousands of nuclear loci), with no one gene tree precisely recovering all relationships in the genus. We also investigated patterns of concordance between the mitogenome tree and the nuclear species tree and found some discrepancies. Across non-tRNA gene trees (n = 16), the species tree topology was recovered by as few as three elements at a particular node and complete concordance (i.e. 16/16 gene trees matched the species tree topology) was recovered at only one node. We found mitochondrial gene regions that are often used in vertebrate systematics (e.g. CytB, ND2) recovered nearly the exact same topology as the nuclear species tree topology.

Two species of Erythrura parrotfinches, differing mainly in bill size, are described from the New Guinea highlands: Blue-faced Parrotfinch E. trichroa and Papuan Parrotfinch E. papuana. Morphological measurements from museum specimens support two non-overlapping groups, but mitochondrial DNA sequence data show negligible differences between the two species. These observations suggest that E. trichroa and E. papuana may form a single species in the highlands of New Guinea that exhibits a resource-based bill size polymorphism.

Phylogeographical 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 in relatively recent times. We investigated inter- and intra-island population structure in a Philippine endemic bird genus (Sarcophanops) to determine whether genetic differentiation has evolved during the recent period of isolation. We sequenced thousands of genome-wide restriction site associated DNA (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 geographical bounds. A previous assessment of mitochondrial DNA detected deep structure between Sarcophanops samarensis and a sister species, Sarcophanops 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 probably demonstrates an effect of recent geographical isolation (after the Last Glacial Maximum) on the genetic structure of Philippine avifauna. We suggest that the general lack of evidence for differentiation between recently isolated populations is a failure to detect subtle population structure owing to past genetic sampling constraints, rather than the absence of such structure.

Islands are separated by natural barriers that prevent gene flow between terrestrial populations and promote allopatric diversification. Birds in the South Pacific are an excellent model to explore the interplay between isolation and gene flow due to the region’s numerous archipelagos and well-characterized avian communities. The wattled honeyeater complex (Foulehaio spp.) comprises three allopatric species that are widespread and common across Fiji, Tonga, Samoa, and Wallis and Futuna. Here, we explored patterns of diversification within and among these lineages using genomic and morphometric data. We found support for three clades of Foulehaio corresponding to three recognized species. Within F. carunculatus, population genetic analyses identified nine major lineages, most of which were composed of sub-lineages that aligned nearly perfectly to individual island populations. Despite genetic structure and great geographic distance between populations, we found low levels of gene flow between populations in adjacent archipelagos. Additionally, body size of F. carunculatus varied randomly with respect to evolutionary history (as Ernst Mayr predicted), but correlated negatively with island size, consistent with the island rule. Our findings support a hypothesis that widespread taxa can show population structure between immediately adjacent islands, and likely represent many independent lineages loosely connected by gene flow.

I studied the ability and willingness of European Starlings (Stumus vulgaris) and Budgerigars (Melopsittacus undulatus) to fly under different lighting conditions in a wind tunnel. My observations indicate that these birds can fly under conditions that supply no visual reference points, but their flight ability is more proficient when some light is available. The addition of a single horizon line to dark conditions improved the birds' flight ability and willingness, as indicated by an increase in the number of birds that took flight after landing. When small flocks were flown in the wind tunnel there was contact between birds in all lighting conditions. The collisions did not cause major disruptions of flight, but the birds seemed to be limited by the small space of the flight chamber. I conclude that (a) mechanisms in addition to sight may influence flock structure and (b) lack of visual cues may affect the primary orientation of birds enough to cause behavioral effects.

The babblers are a diverse group of passerine birds comprising 452 species. The group was long regarded as a “scrap basket” in taxonomic classification schemes. Although several studies have assessed the phylogenetic relationships for subsets of babblers during the past two decades, a comprehensive phylogeny of this group has been lacking. In this study, we used five mitochondrial and seven nuclear loci to generate a dated phylogeny for babblers. This phylogeny includes 402 species (ca. 89% of the overall clade) from 75 genera (97%) and all five currently recognized families, providing a robust basis for taxonomic revision. Our phylogeny supports seven major clades and reveals several non-monophyletic genera. Divergence time estimates indicate that the seven major clades diverged around the same time (18–20 million years ago, Ma) in the early Miocene. We use the phylogeny in a consistent way to propose a new taxonomy, with seven families and 64 genera of babblers, and a new linear sequence of names.

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

The Philippine archipelago is recognized as a biodiversity hotspot because of its high levels of endemism and numerous threatened species. Avian lineages in the Philippines feature morphologically distinct allopatric taxa, which have been variably treated either as species or subspecies depending on species concepts and recognition criteria. To understand how alternative species limits would alter diversity metrics and patterns of endemism in the Philippines, we selected 19 focal lineages of birds, each containing multiple described taxa within the Mindanao Island Group. We delimited species in an integrative, lineage-based framework using three operational criteria: species must (1) form well-supported, geographically circumscribed clades, (2) be monophyletic with significant genetic differentiation identified by a coalescent model, and (3) feature fixed differences in phenotypic characters. Our criteria identified 40 species from the original 19 focal lineages, a 50–74% increase over recent comprehensive taxonomic treatments. Genetic criteria in isolation identified an additional 10 populations that could be cryptic species in need of further study. We identified fine-scale endemism within the Mindanao Island Group, with multiple unrecognized avian endemics restricted to Samar/Leyte, Bohol Island, and the Zamboanga Peninsula. Genetic and phenotypic information support the hypothesis that polytypic bird species in the Philippines tend to be composed of evolutionarily distinct, range-restricted, allopatric replacements rather than widespread and variable “superspecies”. We conclude that lack of species recognition has resulted in underestimates of species diversity and overlooked fine-scale endemism in the Philippines. Recognizing this diversity would alter conservation priorities, shifting efforts to protect microendemics on smaller islands and finer scale endemic areas within larger islands.

The small and conserved genomes of birds are likely a result of flight-related metabolic constraints. Recombination-driven deletions and minimal transposable element (TE) expansions have led to continually shrinking genomes during evolution of many lineages of volant birds. Despite constraints of genome size in birds, we identified multiple waves of amplification of TEs in Piciformes (woodpeckers, honeyguides, toucans, and barbets). Relative to other bird species’ genomic TE abundance (

Chalcophaps is a morphologically conserved genus of ground-walking doves distributed from India to mainland China, south to Australia, and across the western Pacific to Vanuatu. Here, we reconstruct the evolutionary history of this genus using DNA sequence data from two nuclear genes and one mitochondrial gene, sampled from throughout the geographic range of Chalcophaps. We find support for three major evolutionary lineages in our phylogenetic reconstruction, each corresponding to the three currently recognized Chalcophaps species. Despite this general concordance, we identify discordant mitochondrial and nuclear ancestries in the subspecies C. longirostris timorensis, raising further questions about the evolutionary history of this Timor endemic population. Within each of the three species, we find evidence for isolation by distance or hierarchical population structure, indicating an important role for geography in the diversification of this genus. Despite being distributed broadly across a highly fragmented geographic region known as a hotspot for avian diversification, the Chalcophaps doves show modest levels of phenotypic and genetic diversity, a pattern potentially explained by strong population connectivity owing to high overwater dispersal capability.

Aim Kingfishers are the most species-rich family in the avian order, Coraciiformes. Their modern distribution is largely pantropical; however, global species diversity is unevenly distributed. For example, 19 of the 114 kingfisher species occur in New Guinea, whereas only six species occur in the entire New World. This disparity in diversity suggests regions with high species richness could represent the ancestral range of the family. Furthermore, some clades of kingfishers (Ceyx, Todiramphus) are thought to be the product of rapid insular radiations. Here, we investigated the biogeographical history and speciation dynamics of the Alcedinidae using a fully sampled molecular phylogeny. Location Global. Taxon Kingfishers (Aves: Coraciiformes: Alcedinidae). Methods We inferred a time-calibrated, species-level phylogeny of kingfishers from DNA sequences. Our data set comprised up to five Sanger-sequenced gene regions for all species (one mitochondrial, one nuclear exon and three nuclear introns), plus genus-level sampling of thousands of ultraconserved elements. We estimated ancestral ranges of kingfishers and explored macroevolutionary rate shifts and diversification rates across the phylogeny. Results We recovered a well-supported phylogeny of kingfishers that includes 34 species whose phylogenetic relationships were not previously known. The pygmy-kingfishers (subfamily Alcedininae) sit on a long branch, sister to all other kingfishers: subfamilies Cerylinae and Halcyoninae. Crown-group kingfishers originated in the Indomalayan region approximately 27 Ma with subsequent colonizations into Africa (six times), the New World (twice) and Australasia (representing several major radiations). Main conclusions Oceanic islands of Wallacea, the Philippines and Oceania promoted multiple, independent radiations in three species-rich genera: Ceyx, Actenoides and Todiramphus. In particular, Todiramphus showed patterns consistent with explosive and recent diversification relative to the background speciation rate of non-Todiramphus kingfishers, which we attribute to recent colonization of the vast archipelagos of Wallacea and the Pacific.

Aim: Our understanding of population diversification in the lowlands of Sundaland has improved substantially over the last 20 years through phylogeographical study, but we know almost nothing about population diversification in the mountains of the region. Here, we apply genomic analysis and habitat modelling to the phylogeography of Chlorocharis emiliae, the Mountain Black-eye, an endemic montane bird of Borneo with a sky-island distribution, to investigate the structure and interconnectivity of its populations. In the process, we consider factors driving population diversification in the mountains versus lowlands on the island, and how population structure of C. emiliae compares with structure of previously studied lowland species. Location: Borneo. Methods: Using RAD-seq, we produced thousands of SNPs in 25 individuals from five sky-island populations of C. emiliae. These populations represent the species entire range across Borneo. Genetic structure and species tree analyses were applied to measure population relationships and connectivity. Ecological niche modelling was used to estimate habitat distributions during current and LGM time periods. Results: We identified slight to moderate genetic distinctiveness among all populations. Based on demographic models, isolation with migration was the main pattern of divergence, and the most admixture occurred among three populations in north-eastern Borneo: Kinabalu, Trus Madi and Murud. The most divergent population, Pueh, in north-western Borneo, has low genetic diversity and a small effective population size, is geographically isolated and has diverged in isolation without notable gene flow. These results, based on a large genomic dataset, contradict the evolutionary relationships identified in an earlier mitochondrial DNA study. Main conclusions: Genomic phylogeographical comparisons indicate that diversification among sky-island populations of C. emiliae was driven largely by distance and historical habitat distribution, resulting in isolation but also some inter-population gene flow. During Pleistocene glacial events, cooler temperatures would have caused montane forest to descend and spread, thereby increasing connectivity among sky-island populations. However, despite increased montane habitat, the north-western population of Pueh remained isolated. This montane pattern contrasts with phylogeographical patterns in the Bornean lowlands, where populations often display evidence of vicariance followed by secondary contact. © 2017 John Wiley & Sons Ltd.

Effective conservation relies on accurate taxonomy, because we cannot protect what we do not know. Species limits among phenotypically differentiated and allopatrically distributed populations on Southwest Pacific islands are poorly understood. This likely has led to an underestimate of species richness in the Southwest Pacific, and, consequently, a biased application of conservation effort. The silktail Lamprolia victoriae is a bird species endemic to Fiji. Two subspecies are known from Vanua Levu and Taveuni Islands, but uncertainty remains whether they should be considered one or two species. If the latter, increased conservation effort is warranted to protect forest habitat where isolated populations occur only on the Natewa Peninsula. Here, we address this question by examining 8859 single nucleotide polymorphisms produced by restriction-site associated DNA sequencing. We find that the silktail is best considered two species, due to high genetic differentiation and low gene flow between the two subspecies. These differences match known phenotypic differences (size and plumage), as well as allopatric island distributions. We suggest that the silktail be used as an icon for conservation efforts of the heavily degraded forest habitats on the Natewa Peninsula. Finally, we reassess the divergence age estimates of Lamprolia and its relatives, Chaetorhynchus and Rhipidura, in light of new phylogenomic evidence from oscine passerines.

The typical owl family (Strigidae) comprises 194 species in 28 genera, 14 of which are monotypic. Relationships within and among genera in the typical owls have been challenging to discern because mitochondrial data have produced equivocal results and because many monotypic genera have been omitted from previous molecular analyses. Here, we collected and analyzed DNA sequences of ultraconserved elements (UCEs) from 43 species of typical owls to produce concatenated and multispecies coalescent-based phylogenetic hypotheses for all but one genus in the typical owl family. Our results reveal extensive paraphyly of taxonomic groups across phylogenies inferred using different analytical approaches and suggest the genera Athene, Otus, Asio, Megascops, Bubo, and Strix are paraphyletic, whereas Ninox and Glaucidium are polyphyletic. Secondary analyses of protein-coding mitochondrial genes harvested from off-target sequencing reads and mitochondrial genomes downloaded from GenBank generally support the extent of paraphyly we observe, although some disagreements exist at higher taxonomic levels between our nuclear and mitochondrial phylogenetic hypotheses. Overall, our results demonstrate the importance of taxon sampling for understanding and describing evolutionary relationships in this group, as well as the need for additional sampling, study, and taxonomic revision of typical owl species. Additionally, our findings highlight how both divergence and convergence in morphological characters have obscured our understanding of the evolutionary history of typical owls, particularly those with insular distributions.

Islands were key to the development of allopatric speciation theory because they are a natural laboratory of repeated barriers to gene flow caused by open water gaps. Despite their proclivity for promoting divergence, little empirical work has quantified the extent of gene flow among island populations. Following classic island biogeographic theory, two metrics of interest are relative island size and distance. Fiji presents an ideal system for studying these dynamics, with four main islands that form two large-small pairs. We sequenced thousands of ultraconserved elements (UCEs) of the Fiji bush-warbler Horornis ruficapilla, a passerine distributed on these four Fijian islands, and performed a demographic analysis to test hypotheses of the effects of island size and distance on rates of gene flow. Our demographic analysis inferred low levels of gene flow from each large island to its small counterpart and little or none in the opposite direction. The difference in the distance between these two island pairs manifested itself in lower levels of gene flow between more distant islands. Both findings are generally concordant with classic island biogeography. The amount of reduction in gene flow based on distance was consistent with predictions from island biogeographic equations, while the reduction from small to large islands was possibly greater than expected. These findings offer a hypothesis and framework to guide future study of interisland gene flow in archipelagos as the study of island biogeography progresses into the genomic era.

Understanding how biotic and abiotic interactions influence community assembly and composition is a fundamental goal in community ecology. Addressing this issue is particularly tractable along elevational gradients in tropical mountains that feature substantial abiotic gradients and rates of species turnover. We examined elevational patterns of avian community structure on 2 mountains in Malaysian Borneo to assess changes in the relative strength of biotic interactions and abiotic constraints. In particular, we used metrics based on (1) phylogenetic relatedness and (2) functional traits associated with both resource acquisition and tolerance of abiotic challenges to identify patterns and causes of elevational differences in community structure. High elevation communities were composed of more phylogenetically and functionally similar species than would be expected by chance. Resource acquisition traits, in particular, were clustered at high elevations, suggesting low resource and habitat diversity were important drivers of those communities. Traits typically associated with tolerance of cold temperatures and low atmospheric pressure showed no elevational patterns. All traits were neutral or overdispersed at low elevations suggesting an absence of strong abiotic filters or an increased influence of interspecific competition. However, relative bill size, which is important for thermoregulation, was larger in low elevation communities, suggesting abiotic factors were also influential there. Regardless of metric, clustered and neutral communities were more frequent than overdispersed communities overall, implying that interspecific competition among close relatives may not be a pervasive driver of elevational distribution and community structure of tropical birds. Overall, our analyses reveal that a diverse set of predominantly biotic factors underlie elevational variation in community structure on tropical mountains.

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.

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...

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.

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.

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.