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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.

We here describe a new species of Myzomela honeyeater from the Lesser Sunda island of Alor (southeast Indonesia). The new species is phylogenetically most closely related to Myzomela kuehni from the adjacent island of Wetar and most closely resembles that species in plumage. However, it differs in important morphological, bioacoustic and ecological characteristics. The discovery of a new bird species on Alor is of great biogeographic importance and elevates this island to the status of an Endemic Bird Area. The new Alor Myzomela is restricted to montane eucalypt woodland mostly above 900 m elevation and is currently known from few sites across the island. Based on its occurrence records and human population trends in the highlands of Alor Island, we recommend classification under the IUCN threat status endangered.

Biodiversity knowledge is widely heterogeneous across the Earth's biomes. Some areas, due to their remoteness and difficult access, present large taxonomic knowledge gaps. Mostly located in the tropics, these areas have frequently experienced a fast development of anthropogenic activities during the last decades and are therefore of high conservation concerns. The biodiversity hotspots of Southeast Asia exemplify the stakes faced by tropical countries. While the hotspots of Sundaland (Java, Sumatra, Borneo) and Wallacea (Sulawesi, Moluccas) have long attracted the attention of biologists and conservationists alike, extensive parts of the Sahul area, in particular the island of New Guinea, have been much less explored biologically. Here, we describe the results of a DNA-based inventory of aquatic and terrestrial vertebratecommunities, which was the objective of a multidisciplinary expedition to the Bird's Head Peninsula (West Papua, Indonesia) conducted between 17 October and 20 November 2014. This expedition resulted in the assembly of 1005 vertebrate DNA barcodes. Based on the use of multiple species-delimitation methods (GMYC, PTP, RESL, ABGD), 264 molecular operational taxonomic units (MOTUs) were delineated, among which 75 were unidentified and an additional 48 were considered cryptic. This study suggests that the diversity of vertebrates of the Bird's Head is severely underestimated and considerations on the evolutionary origin and taxonomic knowledge of these biotas are discussed., Fieldwork and laboratory activities were supported by the Lengguru 2014 Project (www.lengguru.org), conducted by the French National Research Institute for Sustainable Development (IRD), the Indonesian Institute of Sciences (LIPI) with the Research Centre for Biology (RCB), and the Politeknik KP Sorong, with the help of the Institut Français in Indonesia (IFI) and the French embassy in Jakarta, with corporate sponsorship from COLAS SA Company (Environment Department), Total Foundation, ABS, Wasco, Veolia Eau, SDV-Bolloré

Archipelagoes serve as important ‘natural laboratories’ which facilitate the study of island radiations and contribute to the understanding of evolutionary processes. The white-eye genus Zosterops is a classical example of a ‘great speciator’, comprising c. 100 species from across the Old World, most of them insular. We achieved an extensive geographic DNA sampling of Zosterops by using historical specimens and recently collected samples. Using over 700 genome-wide loci in conjunction with coalescent species tree methods and gene flow detection approaches, we untangled the reticulated evolutionary history of Zosterops, which comprises three main clades centered in Indo-Africa, Asia, and Australasia, respectively. Genetic introgression between species permeates the Zosterops phylogeny, regardless of how distantly related species are. Crucially, we identified the Indonesian archipelago, and specifically Borneo, as the major center of diversity and the only area where all three main clades overlap, attesting to the evolutionary importance of this region.

White-eyes (Zosterops spp.) are a group of small passerines distributed across the Eastern Hemisphere that have become a textbook example of rapid speciation. However, traditional taxonomy has relied heavily on conservative plumage features to delimit white-eye species boundaries, resulting in several recent demonstrations of misclassification. Resolution of confused taxonomy is important in order to correctly delimit species and identify taxa which may require conservation, particularly in Asia where the songbird trade is decimating wild populations. In this study, we aim to untangle multiple instances of confused taxonomic treatment in three large, widespread Asian wastebasket species complexes of white-eye (Oriental White-eye Zosterops palpebrosus, Japanese White-eye Zosterops japonicus and Mountain White-eye Zosterops montanus) renowned for their conservative morphology. Using mitochondrial DNA from 173 individuals spanning 42 taxa, we uncovered extensive polyphyly in Z. palpebrosus and Z. japonicus and propose some radically revised species limits under which former members of Z. palpebrosus and Z. japonicus would be reassigned into four and two different species, respectively. The revised taxonomy results in a net loss of two previously recognized species and a net gain of two newly recognized species, leading to significant taxonomic change but a lack of additional species-level diversity. One of the newly elevated species, Zosterops melanurus from Java and Bali, is also the world’s most heavily traded songbird and requires urgent conservation attention.

Peat swamp forest is an important refuge for biodiversity in Southeast Asia and is now becoming a target of exploitation. The scarcity of information on avifauna and ecology of birds in peat swamp forests prevents understanding of the effects of land use change on avifauna. In this study, we describe the bird assemblages in habitats with different land uses by comparing species richness, community composition, and feeding guild patterns in Bukit Batu, Indonesia. Bird assemblages in natural peat swamp forests (NPF), high-maintenance industrial acacia plantations (planted acacia forest, PAF), low-maintenance rubber plantations (jungle rubber forest, JRF), and village areas (VIL) were studied using a fixed-radius point-count method. Of the 95 species observed, 45, 20, 35, and 48 species were observed in NPF, PAF, JRF, and VIL, respectively. Estimated species richness was the highest in NPF, followed by VIL, JRF, and PAF. NPF had the highest species diversity and β-diversity, more endangered species, and a distinctive species composition characterized by fly-catching insectivores. The relative conservation value of PAF was notably low, particularly compared with JRF. The avifauna in VIL was characterized by more generalists that favor open spaces and therefore is not considered an important habitat for forest-dependent birds that are of conservation concern. Our results indicate that NPF has irreplaceable value for bird diversity conservation, but low-maintenance rubber plantations were home to several forest-dependent species and partially supported bird diversity, particularly compared with high-maintenance acacia plantations.