New Guinea, the world's largest tropical island, supports the planet's richest insular avifauna. Large areas of New Guinea remain poorly surveyed, however, in part due to the island's challenging terrain. In hard-to-access areas, like many mountainous parts of New Guinea, automated surveying tools, like camera traps, may be especially helpful to address the survey deficit. Here we present the results of a camera-trap survey of the avifauna of the Cyclops Mountains, a range in New Guinea's western, Indonesian provinces (Indonesian Papua). To our knowledge, our results represent only the second published camera-trap survey of birds from Indonesian Papua. We deployed 73 camera traps along an elevation gradient (143-1963 m) of the Cyclops Mountains for 11,869 camera-trap nights, recording 22 bird species from 1696 independent detections. Our species list is, to our knowledge, the first to include observations from the upper northern slopes of the Cyclops Mountains. It documents the first record of Masked Bowerbird (Sericulus aureus) in the range and provides photographic rediscoveries of two 'lost' species: Mayr's Honeyeater (Ptiloprora mayri) and Mayr's Forest Rail (Rallicula mayri). We also report substantial elevation range extensions for several species, including numerous records of Northern Cassowary (Casuarius unappendiculatus) over 1000 m above its historically known elevation ceiling. These findings provide new insights into species distributions and ecological flexibility in New Guinea's montane systems, highlighting the potential for previously undocumented biodiversity in under-surveyed regions. Although camera traps detected fewer species than traditional ornithological methods, they were effective in documenting several elusive, ground-dwelling bird species, highlighting their value as a complementary tool for ornithological research in challenging terrain like New Guinea. Finally, we use our data to publish an updated bird species checklist for the Cyclops Mountains.

Papua is the second-largest island on earth and a major centre of biodiversity, but remainsunderexplored. The island’s montane fauna is particularly rich in endemic species, but most of itsexploration has historically focused on the main cordillera that stretches across the island from east towest. Exploration of a number of smaller, isolated outlying mountain ranges has recently produced asubstantial amount of new species discovery. We explored the avifauna of Gunung Q, an isolatedoutlying mountain in the province of Papua (Jayapura) rising to ~1800m, with no topographicconnection to any nearby mountain range. To the best of our knowledge, Gunung Q has never previouslybeen inventoried by biologists. Our fieldwork, which encompassed exploration of the mountain only upto ~1100m, produced various new regional records and suggests that Gunung Q has the potential forsubstantial undiscovered endemism at higher elevations.

Kalimantan comprises nearly three quarters of the island of Borneo and is the place where scientific study of Bornean birds began. We describe the history of bird research in Kalimantan from its beginning, highlighting the ornithologists who explored the region and how their interests and methods changed over time, from a concentration on specimen collection, to examinations of community ecology, to conservation in the face of habitat change and species depletion, to the latest investigations using satellite, genetic, and digital technology. We also highlight some future directions for research, especially the need for more work on basic ecology and biogeography. Following this historical review, we list in a gazetteer every site we could find where ornithologists and birdwatchers have conducted research or documented important records of bird occurrence. The gazetteer includes the latitude and longitude of each site and, in many cases, supplementary information on location, research history, specimen and vocal collections, and associated literature. It is followed by a bibliography of 693 references.

Alien species represent a global challenge to biodiversity and human society. In many parts of the world, however, they remain poorly documented. Here we review citizen science datasets and published avifaunal inventories to collate and document the scale and scope of alien bird species in Indonesia, an archipelago which, because of the well-documented pet bird trade, may reasonably be expected to have a high incidence of alien birds. We identify and map the non-native Indonesian ranges of 38 avian alien species, a number that has increased nearly three-fold since 1980, driven largely by an increase in the number of alien songbirds. These 38 species have native and non-native ranges that overlap with known trade and pet bird ownership hotspots in Indonesia, and have higher trade prevalence than would be expected by chance. We determine that Indonesia’s alien bird species have probably become established as a direct consequence of the bird trade. Likely means of establishment include from trade markets and households, post-confiscation releases by government authorities, merit releases and mercy releases. The consequences of so many avian alien species are unknown but unlikely to be positive; this represents an obvious avenue for future research.

Artisanal and small-scale gold mining (ASGM) is the largest anthropogenic source of mercury globally. Few studies have explored how this toxicant affects avian wildlife in Indonesia, an ASGM hotspot. Here, we use feather samples from museum specimens (n = 92) of Indonesian birds to examine changes through time in methylmercury (MeHg), diet, and foraging habitat (inferred from stable isotope ratios of nitrogen, δ15N, and carbon, δ13C, respectively). We ask how MeHg changes between time period (1860–1980 vs. 1980–2019) given increases in mercury emissions due to ASGM and describe how foraging guild and among-species variation in diet influence Indonesian bird feather MeHg concentrations. Time period was not a significant factor, with specimens associated with increased ASGM activity (collected post-1980) not significantly higher in MeHg concentrations compared to specimens collected pre-1980. Feather MeHg concentrations varied significantly among species, foraging guilds, and by habitat use. Carnivore and insectivore MeHg concentrations were above thresholds associated with sublethal effects. This is the first report of MeHg in Indonesian passerines, kingfishers, and woodpeckers. It provides critical information on mercury exposure in a region with high avian diversity that is severely impacted by mercury pollution.

Sulawesi is an important endemicity hotspot in Southeast Asia, with over 100 endemic species distributed on the island. Despite a long history of avian research on Sulawesi that has played a significant role in the development of evolutionary theory, many ornithological aspects remain unknown. The last few decades have seen novel discoveries, for example, in the form of new species range extensions and species discoveries in the face of ongoing habitat loss and conversion. We here report on a range extension and notes of morphological descriptions of the endemic Diabolical Nightjar and Indonesian Serin in Southeast Sulawesi, adding to our knowledge of the distribution of Sulawesi’s avifauna, especially in the southeastern part in which visits from ornithologists are less frequent. A review of recent museum collections adds another new locality for Diabolical Nightjar in South Sulawesi. Future taxonomic studies are needed to elucidate the status of both species, especially in the Indonesian Serin, as the subtle differences in the coloration of the forehead, rump, and upper tail covert may indicate more than one taxon exists in Sulawesi. In addition, we provide an annotated checklist of birds observed during the fieldwork encompassing areas around Kolaka and Makassar.

The Kangean islands are a biologically poorly known archipelago situated in the Java Sea, Indonesia, approximately 120 km directly north of Bali. These islands host an avifauna comprising at least 13 endemic subspecies, two of which have by some sources recently been considered species. We combine historical published literature with our own surveys of the archipelago in 2007–2008, 2010 and 2023 to produce a complete list of the islands’ birds (n=140 species) and their distribution across the islands. We evaluate in more detail the conservation status of all endemic taxa, as well as several others we consider to be of concern. Despite its listing as Vulnerable on the IUCN Red List, the endemic Kangean Tit-babbler Mixornis prillwitzi is highly tolerant of habitat degradation and is among the islands’ least threatened birds. However, because of trapping, the archipelago’s endemic taxon of Red-breasted Parakeet Psittacula alexandri kangeanensis, and its populations of Green Junglefowl Gallus varius and Common Hill Myna Gracula religiosa are likely at risk of extirpation. The endemic taxon of White-rumped Shama Copsychus malabaricus, sometimes afforded species rank as ‘Kangean Shama’ C. nigricauda, may already be (at least functionally) extinct in the main archipelago. We recommend longer and more detailed surveys of the islands’ birds, and that an effective protected area is established on main Kangean island, which hosts the largest area of remaining forest in the archipelago and most of its endemic taxa.

BACKGROUND:Empirical field studies allow us to view how ecological and environmental processes shape the biodiversity of our planet, but collecting samples in situ creates inherent challenges. The majority of empirical vertebrate gut microbiome research compares multiple host species against abiotic and biotic factors, increasing the potential for confounding environmental variables. To minimize these confounding factors, we focus on a single species of passerine bird found throughout the geologically complex island of Sulawesi, Indonesia. We assessed the effects of two environmental factors, geographic Areas of Endemism (AOEs) and elevation, as well as host sex on the gut microbiota assemblages of the Sulawesi Babbler, Pellorneum celebense, from three different mountains across the island. Using cloacal swabs, high-throughput-amplicon sequencing, and multiple statistical models, we identified the core microbiome and determined the signal of these three factors on microbial composition. RESULTS:The five most prevalent bacterial phyla within the gut microbiome of P. celebense were Proteobacteria (32.6%), Actinobacteria (25.2%), Firmicutes (22.1%), Bacteroidetes (8.7%), and Plantomycetes (2.6%). These results are similar to those identified in prior studies of passeriform microbiomes. Overall, microbiota diversity decreased as elevation increased, irrespective of sex or AOE. A single ASV of Clostridium was enriched in higher elevation samples, while lower elevation samples were enriched with the genera Perlucidibaca (Family Moraxellaceae), Lachnoclostridium (Family Lachnospiraceae), and an unidentified species in the Family Pseudonocardiaceae. CONCLUSIONS:While the core microbiota families recovered here are consistent with other passerine studies, the decreases in diversity as elevation increases has only been seen in non-avian hosts. Additionally, the increased abundance of Clostridium at high elevations suggests a potential microbial response to lower oxygen levels. This study emphasizes the importance of incorporating multiple statistical models and abiotic factors such as elevation in empirical microbiome research, and is the first to describe an avian gut microbiome from the island of Sulawesi.

Natural history museums are vital repositories of specimens, samples and data that inform about the natural world; this Formal Comment revisits a Perspective that advocated for the adoption of compassionate collection practices, querying whether it will ever be possible to completely do away with whole animal specimen collection.

We describe a new species ofZosteropswhite‐eye, which is restricted to Wangi‐wangi, a single island of roughly 155 km2in the Wakatobi Archipelago, Indonesia. Informally known as the Wangi‐wangi White‐eye, the new species is highly distinct both morphologically and genetically. It is considerably larger in body and bill size compared with other regionalZosteropsspecies. The Wangi‐wangi White‐eye remains locally common but its habitat is dwindling. Given its minute area of occupancy and the threat from the bird trade, we recommend the IUCN status Endangered.

The biodiversity loss in Southeast Asia indicates an urgent need for long-term monitoring, which is lacking. Much attention is being directed toward bird diversity monitoring using remote sensing, based on relation to forest structure. However, few studies have utilized space-borne active microwave remote sensing, which has considerable advantages in terms of repetitive observations over tropical areas. Here, we evaluate threatened bird occurrence from L-band satellite data explaining forest structure in Sumatra, Indonesia. First, we identified L-band parameters with strong correlations with the forest layer structure, defined as forest floor, understory, and canopy layers. Then, we analyzed the correlation between threatened bird occurrence and L-band parameters identified as explaining forest structure. The results reveal that several parameters can represent the layers of forest floor, understory, and canopy. Subsequent statistical analysis elucidated that forest-dependent and threatened bird species exhibit significant positive correlations with the selected L-band parameters explaining forest floor and understory. Our results highlight the potential of applying microwave satellite remote sensing to evaluate bird diversity through forest structure estimation, although a more comprehensive study is needed to strengthen our findings.

Helmeted hornbills (Rhinoplax vigil, J.R. Forster, 1781) are ‘Critically Endangered’ due to illegal hunting for their casques which are carved and traded for ornamental purposes. DNA species identification techniques can aid enforcement efforts, and validated wildlife forensic techniques for the species identification of R. vigil are needed. Here we tested multiple methods for sampling and extracting DNA from R. vigil casques and a validated a previously published assay using cytochrome B (cytB) primers to identity species and origin of traded casques. Phenol-chloroform: isoamyl alcohol extractions resulted in samples with higher quantity and quality of DNA than those extracted using the commercial Qiagen DNeasy Blood and Tissue kit. Samples collected from the caudal side of the casque yielded higher DNA quantity and quality than rostral and lateral sides, regardless of sampling method. We then assessed the repeatability, reproducibility, robustness, sensitivity, specificity, and phylogenetic resolution of a previously published species identification assay. We confirm the ability of this method to phylogenetically distinguish between R. vigil and closely related hornbills with high bootstrap support (99%). We also report the first genetic evidence of illegally traded R. vigil in Hong Kong using confiscated casques and provide more reference samples of R. vigil for future work. Overall, we provide multiple protocols for sampling and extracting DNA, and a validated species identification assay for amplifying DNA from R. vigil casques with potential to aid law enforcement in illegal wildlife crimes.

We describe two new bird species from the Meratus Mountains of southeastern Borneo, Indonesia: a jungle-flycatcher (genus Cyornis) and a white-eye (genus Zosterops). Our descriptions are based on comparisons of plumage, mitochondrial ND2 DNA sequences, and vocalizations of the new species and their congeners. The new Meratus jungle-flycatcher is most closely related to Cyornis montanus but morphologically distinguished by lighter blue on the upperparts and more whitish and less reddish on the underparts. The new Meratus white-eye is most closely related to Zosterops chloris but distinguished by olive upperparts and darker underparts. Vocalizations and genetic divergence values also corroborate species status for both new taxa. Both new species are probably confined to the Meratus Mountains, which are currently surrounded by degraded lower elevation secondary woodland or converted agricultural landscape. They appear to have diverged from their sister species through geographic isolation in this remote mountain range compounded by altered population dynamics in a depauperate montane bird community. Although both species are relatively common in the restricted area of the Meratus Mountains, continued habitat alteration and the imminent threat of poaching may be in the process of endangering them. Therefore, we recommend the IUCN Red List status of " Vulnerable" for the new species based on criteria B1 and B2.

Intraspecific polymorphism in birds, especially plumage colour polymorphism, and the mechanisms that control it are an area of active research in evolutionary biology. The black-headed bulbul (Brachypodius atriceps) is a polymorphic species with two distinct morphs, yellow and grey. This species inhabits the mainland and virtually all continental islands of Southeast Asia where yellow morphs predominate, but on two islands in the Sunda region, Bawean and Maratua, grey morphs are common or exclusive. Here, we generated a high-quality reference genome of a yellow individual and resequenced genomes of multiple individuals of both yellow and grey morphs to study the genetic basis of coloration and population history of the species. Using PCA and STRUCTURE analysis, we found the Maratua Island population (which is exclusively grey) to be distinct from all other B. atriceps populations, having been isolated c. 1.9 million years ago (Ma). In contrast, Bawean grey individuals (a subset of yellow and grey individuals on that island) are embedded within an almost panmictic Sundaic clade of yellow birds. Using FST and dxy to compare variable genomic segments between Maratua and yellow individuals, we located peaks of divergence and identified candidate loci involved in the colour polymorphism. Tests of selection among coding-proteins in high FST regions, however, did not indicate selection on the candidate genes. Overall, we report on some loci that are potentially responsible for the grey/yellow polymorphism in a species that otherwise shows little genetic diversification across most of its range.

The Tanimbar Islands located in the Wallacea region have particularly important ornithological values due to high level of endemism.Avian researchers have carried out expeditions to Tanimbar since long time ago starting with Forbes in 1882.An iconic bird of the Tanimbar Islands is the endemic Tanimbar corella (Cacatua goffiniana).This species is considered near threatened by the IUCN, listed in CITES Appendix I, and is protected under Indonesian law.The objectives of the study were to assess bird diversity, habitat use, and association between C. goffiniana and other bird species on the Tanimbar Islands.Data were collected between 2015 and 2019 on Yamdena, Larat, Selaru, and Vaimar Island of Kepulauan Tanimbar Regency, Maluku Province.Direct observation and mist-netting technique were conducted to assess the bird diversity.The habitat use was mapped using ArcGIS 10.5.Descriptive analysis was used to reveal associations between Tanimbar corella and other species.The diversity assessment recorded 142 species in which there were 13 new records for this location.The Tanimbar Islands offer several types of habitats, namely forests, open land, swamps, mangroves, and coastal areas.Associations between C. goffiniana and other birds were recorded with regards to competition and sharing of food resources and nesting sites.C. goffiniana competes with Eclectus roratus for nesting opportunities, and they have an overlapping diet.In addition, C. goffiniana often shares nesting sites with Eos reticulata or Aplonis crassa by using the same trees, and sometimes even the same hollows for nesting.During the observation in August-November 2015, several species were found entering breeding period, namely C. goffiniana, E. roratus, E. reticulata, A. crassa, Philemon mollucensis, Chalcophaps indica, Rhipidura rufifrons, and Lonchura quinticolor.Deforestation resulting in loss of nest and foraging trees pose the major threat to the wild bird population, especially C. goffiniana.By promoting C. goffiniana as an umbrella species we expect to conserve the biodiversity in the region.

To reveal the diversity of Indonesian bent-toed geckos, we pay attention to Kalimantan (Borneo)an island which has received less attention than other Indonesian islands such as Sumatra, Java, Sulawesi, the Moluccas, and the Lesser Sunda archipelagos. About 30 years after Hikida (1990) described three new Cyrtodactylus from Borneo, four more species were described, namely C. limajalur and C. muluensis in 2019, and C. hantu and C. miriensis in 2021, all by Davis et al. Through examination of the collection at MZB and three addition specimens collected from Tawau, we found several undescribed species, one of which we describe here. This new species is easily differentiated from all other congeners by the combination of the following characters: maximum SVL of at least 65.8 mm; no tubercles on dorsal surface of upper arm; tubercles present in the ventrolateral body folds; 2830 paravertebral tubercles; 1720 longitudinal dorsal tubercle rows; 3946 ventral scale rows at midbody; 1719 subdigital lamellae on fourth toe; precloacal pit with 57 pores in males arranged in a wide -shape but absent in females; no enlarged transverse median subcaudals; paired dark brown semilunar-shaped markings on the upper nape. Further study is needed to reveal its molecular phylogenetic position and biogeographical history.

ABSTRACT These studies aim to identify the lineages and genetic structures of white-rumped shama from captivity in Jambi. Mitochondrial ND2 analysis was performed from 20 individuals of the white-rumped shama and sequences from Gen Bank i.e. K.m.tricolor (Malay Peninsula), K.m. interposita (Indochina), K.m.suavis (Borneo), K.m.stricklandii (Borneo), K.luzoniensis (Philippines), K. nigra (Philippines), and Acridothers javanicus as the outgroup. The phylogeny tree was reconstructed by neighbor-joining (NJ) and maximum likelihood (ML). Meanwhile, the genetic structures were determined by haplotype, haplotype diversity, and Tajima-D. AMOVA and FST were used to see population differentiation. The phylogenetic tree showed that the white-rumped shama from captivity in Jambi was divided into two lineages, namely K. m. tricolor and K. m. interposita with intersubspecies genetic distance between 0.3% - 0.5%. The haplotypes of white-rumped shama from Jambi were 13 with haplotype diversity of 0.95. The AMOVA of K. malabarica showed a significant value of FST at 80.54. Nonetheless, the FST between Jambi - Indochina, and Jambi - Malay Peninsula are significantly low at 0.147 and 0.271, respectively. This study indicated that the breeders used various broodstock, including the lineage of K. m. tricolor and K. m. interposita . Keywords: white-rumped shama, subspecies, lineage, phylogenetic, genetic structure. ABSTRAK Penelitian ini bertujuan untuk mengidentifikasi garis keturunan dan struktur genetika kucica hutan hasil penangkaran dari Jambi. Analisis mitokondria ND2 dilakukan dari 20 individu kucica hutan dan sekuen dari GenBank, yang meliputi K. m. tricolor (Semenanjung Malaysia), K. m. interposita (Indochina), K. m. suavis (Borneo), K. m. stricklandii (Borneo), K. luzoniensis (Filipina), K. nigra (Filipina), dan Acridothers javanicus sebagai outgroup. Pohon filogeni direkonstruksi dengan neighbour-joining (NJ) dan maximum likelihood (ML). Struktur genetik dianalisis untuk mengetahui jumlah haplotipe, diversitas haplotipe, dan Tajima-D. AMOVA dan FST digunakan untuk melihat diferensiasi populasi. Hasil analisis filogeni menunjukkan bahwa kucica hutan asal penangkaran Jambi terbagi menjadi dua garis keturunan, yaitu K. m. tricolor dan K. m. interposita dengan jarak genetik intersubspesies antara 0.3% - 0.5%. Haplotipe kucica hutan dari Jambi berjumlah 13 dengan diversitas haplotipe bernilai 0.95. K. malabarica menunjukkan nilai populasi divergensi yang tinggi dan signifikan, yaitu FST 80.54. Nilai FST paling rendah ditunjukkan antara populasi Jambi-Indochina dan Jambi – Semenanjung Malaysia, yaitu 0.147 dan 0.271. Hasil dari analisis filogeni dan struktur genetika mengindikasikan bahwa para penangkar mengembangbiakan kucica hutan dari berbagai sumber indukan yang meliputi garis keturunan K. m. tricolor dan K. m. interposita . Kata kunci: kucica hutan, subspesies, garis keturunan, filogeni, struktur genetik

Birds keeping, especially songbirds, has been considered as one of the major drivers that lead to species extinction in Indonesia. The demand for songbirds either for songbird’s competition or to be enjoyed at home is considerably high, especially in Java. As the native Javan population has been depleted due to habitat conversion and excessive trapping, the supply of songbirds is provided by other islands in Indonesia such as Sumatera and Kalimantan. We conducted long term monitoring of songbird’s trade on Jambi. Data on bird’s trade was obtained by examining the transaction records from wholesalers from the period of 2016 – 2020. The results showed that there were shifting in species target especially after 2018 due to implementation of new regulation on protected species. However, the total number remains high. The trade comparison for the same period between trade records in 2016 and 2020 demonstrated the reduction in the number of species from around 32 species to 25 species, however, the total volume of traded birds is higher in 2020 which is 20.600 compare to 7.198 during the first sixth months. Considering the pandemic situation, the songbirds trade activities is seemingly not affected especially for the distribution chain from hunter to wholesalers.

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.