Endogenous Gibbon Ape Leukemia Virus Identified in a Rodent (Melomys burtoni subsp.) from Wallacea (Indonesia).

UNLABELLED: Gibbon ape leukemia virus (GALV) and koala retrovirus (KoRV) most likely originated from a cross-species transmission of an ancestral retrovirus into koalas and gibbons via one or more intermediate as-yet-unknown hosts. A virus highly similar to GALV has been identified in an Australian native rodent (Melomys burtoni) after extensive screening of Australian wildlife. GALV-like viruses have also been discovered in several Southeast Asian species, although screening has not been extensive and viruses discovered to date are only distantly related to GALV. We therefore screened 26 Southeast Asian rodent species for KoRV- and GALV-like sequences, using hybridization capture and high-throughput sequencing, in the attempt to identify potential GALV and KoRV hosts. Only the individuals belonging to a newly discovered subspecies of Melomys burtoni from Indonesia were positive, yielding an endogenous provirus very closely related to a strain of GALV. The sequence of the critical receptor domain for GALV infection in the Indonesian M. burtoni subsp. was consistent with the susceptibility of the species to GALV infection. The second record of a GALV in M. burtoni provides further evidence that M. burtoni, and potentially other lineages within the widespread subfamily Murinae, may play a role in the spread of GALV-like viruses. The discovery of a GALV in the most western part of the Australo-Papuan distribution of M. burtoni, specifically in a transitional zone between Asia and Australia (Wallacea), may be relevant to the cross-species transmission to gibbons in Southeast Asia and broadens the known distribution of GALVs in wild rodents. IMPORTANCE: Gibbon ape leukemia virus (GALV) and the koala retrovirus (KoRV) are very closely related, yet their hosts neither are closely related nor overlap geographically. Direct cross-species infection between koalas and gibbons is unlikely. Therefore, GALV and KoRV may have arisen via a cross-species transfer from an intermediate host whose range overlaps those of both gibbons and koalas. Using hybridization capture and high-throughput sequencing, we have screened a wide range of rodent candidate hosts from Southeast Asia for KoRV- and GALV-like sequences. Only a Melomys burtoni subspecies from Wallacea (Indonesia) was positive for GALV. We report the genome sequence of this newly identified GALV, the critical domain for infection of its potential cellular receptor, and its phylogenetic relationships with the other previously characterized GALVs. We hypothesize that Melomys burtoni, and potentially related lineages with an Australo-Papuan distribution, may have played a key role in cross-species transmission to other taxa.

Risk factors for asphyxia neonatorum in public health centres of nosarara and pantoloan, Palu City.

OBJECTIVE: This study aims to determine the risk factors of asphyxia neonatorum in two PONED Public Health Centers of Nosarara and Pantoloan, in Palu City, Central Sulawesi. METHODS: This study used a case-control study design. Sampling was conducted by a simple random sampling technique. The sample size in this study was 60 samples. The data collected was secondary data from medical records at Nosarara and Patoloan Public Health Centers, Palu City. Multivariate analysis used to determine the main risk of the incidence of neonatal asphyxia. RESULTS: The results showed the Prolong Parturition OR=5.714 (95% CI 1.724-18.944); Prematurity OR=4.333 (95% CI 1.203-15.605); LBW OR=7.000 (95% CI 1.381-35.487). CONCLUSION: risk factors for neonatal asphyxia were prolonged labour, prematurity, and LBW. The main factors causing neonatal asphyxia were LBW.

Exploring the vertebrate fauna of the Bird's Head Peninsula (Indonesia, West Papua) through DNA barcodes.

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 vertebrate communities, 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.

Taxonomic evaluation of two similar bent-toed geckos Squamata: Gekkonidae: Cyrtodactylus Gray, 1827) from East Java, Indonesia.

The bent-toed geckos of the genus Cyrtodactylus are the most speciose land vertebrates of Southeast Asia (about 300 species so far) and new species continue to be recognized at a rapid rate. Within the last decade three new species were described from Java, Indonesia, C. semiadii, C. petani, and C. klakahensis. The latter two are very similar, except for differences in the precloacal depression in adult males. These two species have relatively close type localities, separated from each other by only about 50 km, and with similar habitat type and elevation. Our study aimed to evaluate the taxonomic status of C. klakahensis and C. petani using both morphological and genetic evidence. These two species are genetically similar, with a genetic divergence of only 1.5 to 1.6%. This divergence is well below the level of typically characterizes sister species of Cyrtodactylus (approximately 4% in the mitochondrial ND2 gene), and is more in line with population variation due to geographic distance. Further examination of specimens, from both type localities, showed no diagnostic morphological characters between the two species. Thus, we conclude that C. klakahensis and C. petani are conspecific, and following article 23 of the ICZN, C. klakahensis is herein considered a junior synonym of C. petani.

Biodiversity inventory of the grey mullets (Actinopterygii: Mugilidae) of the Indo-Australian Archipelago through the iterative use of DNA-based species delimitation and specimen assignment methods.

DNA barcoding opens new perspectives on the way we document biodiversity. Initially proposed to circumvent the limits of morphological characters to assign unknown individuals to known species, DNA barcoding has been used in a wide array of studies where collecting species identity constitutes a crucial step. The assignment of unknowns to knowns assumes that species are already well identified and delineated, making the assignment performed reliable. Here, we used DNA-based species delimitation and specimen assignment methods iteratively to tackle the inventory of the Indo-Australian Archipelago grey mullets, a notorious case of taxonomic complexity that requires DNA-based identification methods considering that traditional morphological identifications are usually not repeatable and sequence mislabeling is common in international sequence repositories. We first revisited a DNA barcode reference library available at the global scale for Mugilidae through different DNA-based species delimitation methods to produce a robust consensus scheme of species delineation. We then used this curated library to assign unknown specimens collected throughout the Indo-Australian Archipelago to known species. A second iteration of OTU delimitation and specimen assignment was then performed. We show the benefits of using species delimitation and specimen assignment methods iteratively to improve the accuracy of specimen identification and propose a workflow to do so.

Disentangling the taxonomy of the subfamily Rasborinae (Cypriniformes, Danionidae) in Sundaland using DNA barcodes.

Sundaland constitutes one of the largest and most threatened biodiversity hotspots; however, our understanding of its biodiversity is afflicted by knowledge gaps in taxonomy and distribution patterns. The subfamily Rasborinae is the most diversified group of freshwater fishes in Sundaland. Uncertainties in their taxonomy and systematics have constrained its use as a model in evolutionary studies. Here, we established a DNA barcode reference library of the Rasborinae in Sundaland to examine species boundaries and range distributions through DNA-based species delimitation methods. A checklist of the Rasborinae of Sundaland was compiled based on online catalogs and used to estimate the taxonomic coverage of the present study. We generated a total of 991 DNA barcodes from 189 sampling sites in Sundaland. Together with 106 previously published sequences, we subsequently assembled a reference library of 1097 sequences that covers 65 taxa, including 61 of the 79 known Rasborinae species of Sundaland. Our library indicates that Rasborinae species are defined by distinct molecular lineages that are captured by species delimitation methods. A large overlap between intraspecific and interspecific genetic distance is observed that can be explained by the large amounts of cryptic diversity as evidenced by the 166 Operational Taxonomic Units detected. Implications for the evolutionary dynamics of species diversification are discussed.

Hiding in plain sight on Gunung Muria: A new species and first record of rock gecko (Cnemaspis Strauch, 1887; Squamata, Gekkonidae) from Java, Indonesia.

We describe a new species of rock gecko of the genus Cnemaspis from Java, Indonesia, representing the first record of the genus for this Island. The new species was collected from the southern slopes of Gunung Muria, a dormant volcano in Central Java. The new species is easily distinguished from all congeners by having a maximum SVL of 58.1 mm in males and 56.9 mm in females; a pair of sharp conical tubercle clusters on the occiput; a warty bridge on the nuchal loop, extending from the upper tympanum and curving to the nape; dorsal tubercles not linearly arranged; 18-20 paravertebral tubercles; postmentals separated by one scale; gular, pectoral and abdominal scales, ventral scales of fore- and hindlimbs, and subcaudal scales keeled; no tubercles on lower flank; precloacal and femoral pores absent; enlarged submetacarpal scales present on the first digit of the manus; 38-40 ventral scales; 31-35 lamellae under fourth toe; two postcloacal tubercles on each side; enlarged median subcaudal scales row present; caudal tubercles encircling tail; and a sexually dimorphic ventral color pattern, with males having a yellow belly and females white and the ventral surface of the tail in males yellow proximally changing to white at mid-length, whereas in females, alternating black and white rings completely encircle the tail, which is black distally.

Daytime behavior of Pteropus vampyrus in a natural habitat: the driver of viral transmission.

Flying foxes, the genus Pteropus, are considered viral reservoirs. Their colonial nature and long flight capability enhance their ability to spread viruses quickly. To understand how the viral transmission occurs between flying foxes and other animals, we investigated daytime behavior of the large flying fox (Pteropus vampyrus) in the Leuweung Sancang conservation area, Indonesia, by using instantaneous scan sampling and all-occurrence focal sampling. The data were obtained from 0700 to 1700 hr, during May 11-25, 2016. Almost half of the flying foxes (46.9 ± 10.6% of all recorded bats) were awake and showed various levels of activity during daytime. The potential behaviors driving disease transmission, such as self-grooming, mating/courtship and aggression, peaked in the early morning. Males were more active and spent more time on sexual activities than females. There was no significant difference in time spent for negative social behaviors between sexes. Positive social behaviors, especially maternal cares, were performed only by females. Sexual activities and negative/positive social behaviors enable fluid exchange between bats and thus facilitate intraspecies transmission. Conflicts for living space between the flying foxes and the ebony leaf monkey (Trachypithecus auratus) were observed, and this caused daily roosting shifts of flying foxes. The ecological interactions between bats and other wildlife increase the risk of interspecies infection. This study provides the details of the flying fox's behavior and its interaction with other wildlife in South-East Asia that may help explain how pathogen spillover occurs in the wild.

Syphacia (Syphacia) maxomyos sp. n. (Nematoda: Oxyuridae) from Maxomys spp. (Rodentia: Muridae) from Sulawesi and Sumatra, Indonesia.

The present report describes Syphacia (Syphacia) maxomyos sp. n. (Nematoda: Oxyuridae) from two species of spiny rats, Maxomys musschenbroekii from Sulawesi and M. whiteheadi from Sumatra. It is characterized by a cephalic plate extending laterally with dorsoventral constriction and stumpy eggs with an operculum rim reaching pole. It is readily distinguishable by the former feature from all of hitherto known representatives of this genus in Indonesia, but it resembles parasites in Murini and Hydromyni rodents in continental Asia and Sahul. This is the first Syphacia species distributed in both the Sunda Shelf and Sulawesi with the exception of Syphacia muris, a cosmopolitan pinworm found in rodents of the of genus Rattus. It is surmised that S. maxomyos is specific to Maxomys and that it was introduced to Sulawesi by dispersal of some Maxomys from the Sunda Shelf.