Within the Indo-Pacific, understory birds have received the majority of phylogeographic investigation while canopy birds are comparatively under-studied. The White-bellied Cuckooshrike (Coracina papuensis), generally considered a canopy species, contains 13-15 described taxa but lacks a modern genomic dataset corroborating these distinctions. Therefore, we evaluated the phylogeography of C. papuensis using genome-wide single nucleotide polymorphisms for 49 individuals representing the taxa with available tissue samples (10 of the 13-15). We identified varying support for eight different lineages with limited diversification across the Australian continental shelf but surprisingly we found support for two lineages in eastern Papua New Guinea (Central and Oro Provinces) and evidence of long-distance dispersal.

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 Glade (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.

Malawimonadida is a deep-level (arguably "kingdom-scale") lineage of eukaryotes whose phylogenetic affinities are uncertain but of great evolutionary interest, as the group is suspected to branch close to the root of the tree of eukaryotes. Part of the difficulty in placing Malawimonadida phylogenetically is its tiny circumscription: at present, it comprises only two described and one cultured but undescribed species, all of them are freshwater suspension-feeding nanoflagellates. In this study, we cultivated and characterised Imasa heleensis gen. nov., sp. nov. (Imasidae fam. nov.), the first marine malawimonad to be described. Light and electron microscopy observations show that Imasa is largely similar to other malawimonads, but more frequently adheres to the substrate, often by means of a pliable posterior extension. Phylogenetic analyses based on two ribosomal RNA genes and four translated protein-coding genes using three different taxon sets place Imasa as sister to the three freshwater malawimonad strains with strong support. Imasa's mitochondrial genome is circular-mapping and shows a similar gene complement to other known malawimonads. We conclude that Imasa represents an important expansion of the range of taxa available for future evolutionary study.

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.

To meet local and global aspirations toward sustainable resource management, we must first understand what success looks like. At global levels, well-being can be narrowly defined, which may clash with local values and cause adverse impacts. Melanesia is home to a complex mosaic of resource management systems, and finding locally appropriate indicators of success poses particular challenges. We propose that biocultural approaches can assist in developing grounded and appropriate well-being indicators. Biocultural approaches frame issues from the perspectives of place-based communities and work with resource users to develop desired outcomes. In doing so, biocultural approaches recognize links between people and the environment and seek to understand feedbacks between social and ecological components. Biocultural approaches may help to improve the fit between local aspirations and national or international actions and can also cocreate knowledge that draws on local knowledge and practice as well as western science. Here, we report on one such approach in Western Province, Solomon Islands, where rural communities are weighing a variety of trade-offs around the use of natural resources. The work encompasses four locations and seeks to define local needs and priorities, develop appropriate local indicators of success, assess indicator baselines, and catalyze appropriate action. Implementation challenges have included scaffolding between local and national levels and the diversity of the four locations. These have, however, been offset by the engaged nature of indicator creation, which assists communities in planning toward action around local definitions of well-being.

As the terrestrial human footprint continues to expand, the amount of native forest that is free from significant damaging human activities is in precipitous decline. There is emerging evidence that the remaining intact forest supports an exceptional confluence of globally significant environmental values relative to degraded forests, including imperilled biodiversity, carbon sequestration and storage, water provision, indigenous culture and the maintenance of human health. Here we argue that maintaining and, where possible, restoring the integrity of dwindling intact forests is an urgent priority for current global efforts to halt the ongoing biodiversity crisis, slow rapid climate change and achieve sustainability goals. Retaining the integrity of intact forest ecosystems should be a central component of proactive global and national environmental strategies, alongside current efforts aimed at halting deforestation and promoting reforestation.

Monitoring and evaluation are central to ensuring that innovative, multi-scale, and interdisciplinary approaches to sustainability are effective. The development of relevant indicators for local sustainable management outcomes, and the ability to link these to broader national and international policy targets, are key challenges for resource managers, policymakers, and scientists. Sets of indicators that capture both ecological and social-cultural factors, and the feedbacks between them, can underpin cross-scale linkages that help bridge local and global scale initiatives to increase resilience of both humans and ecosystems. Here we argue that biocultural approaches, in combination with methods for synthesizing across evidence from multiple sources, are critical to developing metrics that facilitate linkages across scales and dimensions. Biocultural approaches explicitly start with and build on local cultural perspectives - encompassing values, knowledges, and needs - and recognize feedbacks between ecosystems and human well-being. Adoption of these approaches can encourage exchange between local and global actors, and facilitate identification of crucial problems and solutions that are missing from many regional and international framings of sustainability. Resource managers, scientists, and policymakers need to be thoughtful about not only what kinds of indicators are measured, but also how indicators are designed, implemented, measured, and ultimately combined to evaluate resource use and well-being. We conclude by providing suggestions for translating between local and global indicator efforts.

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

We report new observational and specimen data on the avifauna of Kolombangara, Western Province, Solomon Islands. These data, collected from 3-9 October 1974 and 13-21 May 2004, and supplemented with more recent observations, represent the first comprehensive survey of this globally significant island since 1927. All encounters of montane species are reported along with select species accounts for notable lower-elevation species. Numerous observations presented here suggest avifauna even more unique than previously reported. For example, we confirm a probable resident form of Peregrine Falcon (Falco peregrinus) and report the first observations and collected materials for a Blue-faced Parrotfinch (Erythrura trichroa) from Kolombangara. We observed all of the island's high-elevation endemics and found their relative abundances and patterns of occurrence to be consistent with those of an intact montane avifauna. Our findings suggest that despite large-scale modification of lowland habitat, montane forests on Kolombangara still maintain the full complement of endemic and other high elevation species described nearly 100 years ago, along with several additional taxa not previously recorded. However, incidental evidence suggests that forest change in the lowlands is impacting montane microclimates as indicated by extensive drying of epiphytic mosses at high elevations. Along with more recent collection of undescribed anurans, these findings confirm the global conservation significance of the montane forests and biodiversity on Kolombangara.

The diversity of microbial eukaryotes was surveyed by environmental sequencing from tropical lagoon sites of the South Pacific, collected through the American Museum of Natural History (AMNH)'s Explore21 expedition to the Solomon Islands in September 2013. The sampled lagoons presented low nutrient concentrations typical of oligotrophic waters, but contained levels of chlorophyll a, a proxy for phytoplankton biomass, characteristic of meso- to eutrophic waters. Two 18S rDNA hypervariable sites, the V4 and V8-V9 regions, were amplified from the total of eight lagoon samples and sequenced on the MiSeq system. After assembly, clustering at 97% similarity, and removal of singletons and chimeras, a total of 2741 (V4) and 2606 (V8-V9) operational taxonomic units (OTUs) were identified. Taxonomic annotation of these reads, including phylogeny, was based on a combination of automated pipeline and manual inspection. About 18.4% (V4) and 13.8% (V8-V9) of the OTUs could not be assigned to any of the known eukaryotic groups. Of these, we focused on OTUs that were not divergent and possessed multiple sources of evidence for their existence. Phylogenetic analyses of these sequences revealed more than ten branches that might represent new deeply-branching lineages of microbial eukaryotes, currently without any cultured representatives or morphological information.

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 the Monarcha castaneiventris flycatcher 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 melanic MC1R and ASIP allelic variants. Formal FST outlier tests corroborated the results of the GWAS and suggested that strong, directional selection drives the near fixation of the MC1R and ASIP variants 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.

Todiramphus chloris is the most widely distributed of the Pacific's 'great speciators'. Its 50 subspecies constitute a species complex that is distributed over 16 000 km from the Red Sea to Polynesia. We present, to our knowledge, the first comprehensive molecular phylogeny of this enigmatic radiation of kingfishers. Ten Pacific Todiramphus species are embedded within the T. chloris complex, rendering it paraphyletic. Among these is a radiation of five species from the remote islands of Eastern Polynesian, as well as the widespread migratory taxon, Todiramphus sanctus. Our results offer strong support that Pacific Todiramphus, including T. chloris, underwent an extensive range expansion and diversification less than 1 Ma. Multiple instances of secondary sympatry have accumulated in this group, despite its recent origin, including on Australia and oceanic islands in Palau, Vanuatu and the Solomon Islands. Significant ecomorphological and behavioural differences exist between secondarily sympatric lineages, which suggest that pre-mating isolating mechanisms were achieved rapidly during diversification. We found evidence for complex biogeographic patterns, including a novel phylogeographic break in the eastern Solomon Islands that separates a Northern Melanesian clade from Polynesian taxa. In light of our results, we discuss systematic relationships of Todiramphus and propose an updated taxonomy. This paper contributes to our understanding of avian diversification and assembly on islands, and to the systematics of a classically polytypic species complex.

Monarch flycatchers are a major component of Australo-Pacific and Wallacean avifaunas. To date, the family has received incomplete attention by molecular systematists who focused on subclades with minimal character and/or taxon sampling. As a result, Monarchidae taxonomy is still out-of-date, and biogeographic reconstructions have been based on poorly-resolved phylogenies, limiting their interpretation. Here, we produced a comprehensive, molecular phylogeny of the Monarchidae inferred from mitochondrial and nuclear loci using both concatenated and multilocus coalescent frameworks. We sampled 92% of the 99 recognized monarchid biological species and included deeper sampling within several phylogenetic species complexes, including Monarcha castaneiventris, Symposiachrus barbatus, and Terpsiphone rufiventer. Melampitta is identified as sister to the monarch flycatchers, which themselves comprise four major lineages. The first lineage comprises Terpsiphone and allies, the second lineage is Grallina, the third is Arses and Myiagra, and the fourth lineage comprises a diverse assemblage of genera including the "core monarchs" and the most geographically isolated groups like Chasiempis (Hawaii) and Pomarea (eastern Polynesia). Gene tree discordance was evident in Myiagra, which has implications for basal lineages in the genus (e.g., M. azureocapilla, M. hebetior, and M. alecto). Numerous genera within the core monarchs are paraphyletic, including Mayrornis and Pomarea, whereas the validity of others such as Metabolus are questionable. We recognize polytypic taxa as multiple species, including Lamprolia victoriae and Myiagra azureocapilla. In general, the topology of species complexes included short internodes that were not well resolved, owing to their rapid diversification across island archipelagos. Terpsiphone rufiventer comprises multiple lineages, including a heretofore-unappreciated West African lineage, but relationships within these rapid radiations will require extensive genomic sampling for further resolution. This study establishes a new benchmark for Monarchidae systematics and it provides an excellent framework for future work on biogeography and character evolution in a diverse Australo-Papuan radiation.

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 5743bp 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.(c) 2013 The Linnean Society of London

Guided by deeply held cultural values, First Nations in Canada are rapidly regaining legal authority to manage natural resources. We present a research collaboration among academics, tribal government, provincial and federal government, resource managers, conservation practitioners, and community leaders supporting First Nation resource authority and stewardship. First, we present results from a molecular genetics study of grizzly bears inhabiting an important conservation area within the territory of the Heiltsuk First Nation in coastal British Columbia. Noninvasive hair sampling occurred between 2006 and 2009 in the Koeye watershed, a stronghold for grizzly bears, salmon, and Heiltsuk people. Molecular demographic analyses revealed a regionally significant population of bears, which congregate at the Koeye each salmon- spawning season. There was a minimum of 57 individual bears detected during the study period. Results also pointed to a larger than expected source geography for salmon- feeding bears in the study area (> 1000 km), as well as early evidence of a declining trend in the bear population potentially explained by declining salmon numbers. Second, we demonstrate and discuss the power of integrating scientific research with a culturally appropriate research agenda developed by indigenous people. Guided explicitly by principles from Gvi'ilas or customary law, this research methodology is coupled with Heiltsuk culture, enabling results of applied conservation science to involve and resonate with tribal leadership in ways that have eluded previous scientific endeavors. In this context, we discuss the effectiveness of research partnerships that, from the outset, create both scientific programs and integrated communities of action that can implement change. We argue that indigenous resource management requires collaborative approaches like ours, in which science- based management is embedded within a socially and culturally appropriate context. We emerge not only with a set of guiding principles for resource management by the Heiltsuk, but a broadly applicable strategy that fosters intimacy with traditional lands and resources and provides a powerful engine for conservation.

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 in other bird species, such as the close relationship of taxa on Bougainville, Choiseul, and Isabel. By contrast, the sister relationship between populations on Guadalcanal and the New Georgia Group is novel. We discuss species limits and make taxonomic recommendations to treat all 15 subspecies of C. lepidus as species. Received 31 May 2012, accepted 5 November 2012.

We reconstruct the phylogeny of fruit doves (genus Ptilinopus) and allies with a dense sampling that includes almost all species, based on mitochondrial and nuclear sequence data. We evaluate the most likely biogeographic scenario for the evolution of this group that colonized many islands of the Pacific Ocean. We also investigate the evolution of one of the main plumage character of fruit doves (the color of the crown), and we propose several revisions of the group's systematics. All Ptilinopus taxa formed a monophyletic group that includes two morphologically distinct genera, Alectroenas and Drepanoptila, confirming a previous result found with less species and genes. The divergence time analysis suggests that the basal divergences within Ptilinopus dated to the Early Oligocene, and the biogeographic analysis indicates that fruit doves originated most probably from the proto New Guinea region. The earliest dispersals from the New Guinea region to Oceania occurred with the colonization of New Caledonia and Fiji. A large group of Polynesian species (Central and Eastern), as well as the three taxa found in Micronesia and four species from the Guinean-Moluccan region, form the "purpuratus" clade, the largest diversification of fruit doves within Oceania, which also has a New Guinean origin. However, the eastbound colonization of fruit doves was not associated with a significant increase of their diversification rate. Overall, the Melanesian region did not act as a cradle for fruit doves, in contrast to the New Guinea region which is found as the ancestral area for several nodes within the phylogeny.