Two centuries of biodiversity discovery and loss in Singapore.

There is an urgent need for reliable data on the impacts of deforestation on tropical biodiversity. The city-state of Singapore has one of the most detailed biodiversity records in the tropics, dating back to the turn of the 19th century. In 1819, Singapore was almost entirely covered in primary forest, but this has since been largely cleared. We compiled more than 200 y of records for 10 major taxonomic groups in Singapore (>50,000 individual records; >3,000 species), and we estimated extinction rates using recently developed and novel statistical models that account for "dark extinctions," i.e., extinctions of undiscovered species. The estimated overall extinction rate was 37% (95% CI [31 to 42%]). Extrapolating our Singapore observations to a future business-as-usual deforestation scenario for Southeast Asia suggests that 18% (95% CI [16 to 22%]) of species will be lost regionally by 2100. Our extinction estimates for Singapore and Southeast Asia are a factor of two lower than previous estimates that also attempted to account for dark extinctions. However, we caution that particular groups such as large mammals, forest-dependent birds, orchids, and butterflies are disproportionately vulnerable.

Singapore's herpetofauna: updated and annotated checklist, history, conservation, and distribution.

Given Singapore's location at the confluence of important maritime trading routes, and that it was established as a British East India Company trading post in 1819, it is unsurprising that Singapore has become one of the centres of natural history collecting and research in Southeast Asia. Despite its small size, Singapore is home to a diverse herpetofauna assemblage and boasts a rich herpetological history. The first systematic studies of Singapore's herpetofauna (within the Linnaean binomial framework) date back to Stamford Raffles and the naturalists hired by him who first came to the island in 1819. Specimens that were collected during and after this time were deposited in museums worldwide. Over time, 39 species from Singapore were described as new to science. Due to the entrepôt nature of Singapore with its associated purchasing and trading of specimens (both alive and dead), poor record-keeping, and human introductions, numerous extraneous species from outside of Singapore were reported to occur on the island. Such issues have left a complicated legacy of ambiguous records and taxonomic complications concerning the identity of Singapore's species-rich herpetofauna, many of which were only resolved in the past 30-40 years. By compiling a comprehensive collection of records and publications relating to the herpetofauna of Singapore, we construct an updated and more accurate listing of the herpetofauna of Singapore. Our investigation culminated in the evaluation of 309 species, in which we compiled a final species checklist recognising 166 species (149 native and 17 non-native established species). Among the 149 native species are two caecilians, 24 frogs, one crocodilian, 13 turtles (three visitors), 34 lizards, and 75 snakes. Of the 17 non-native species are five frogs, four turtles, six lizards, and two snakes. The remaining 143 species represent species to be excluded from Singapore's herpetofauna species checklist. For each of the 309 species examined, we provide species accounts and explanatory annotations. Furthermore, we discuss Singapore's herpetofauna from a historical and conservation perspective. Immediate deforestation and nationwide urbanisation following colonisation completely eliminated many species from throughout much of the country and restricted them to small, degraded forest patches. We hope this publication highlights the importance of publishing observations and serves as a valuable resource to future researchers, naturalists, biological consultants, and policy makers in initiating studies on species ecology, distribution, status, and promoting conservation efforts to safeguard Singapore's herpetofauna.

On the taxonomic status of Asthenodipsas vertebralis (Boulenger, 1900) (Squamata: Pareidae) in Borneo with the description of a new species.

The taxonomic status of Asthenodipsas vertebralis in Borneo has been plagued with uncertainty over the last eighty years. An examination of museum collections resulted in the discovery of a voucher specimen of A. vertebralis from Sarawak, East Malaysia that confirms the presence of the species in Borneo and a previously unrecognised species, Asthenodipsas ingeri sp. nov. from Mount Kinabalu, Sabah. Asthenodipsas ingeri sp. nov. can be differentiated from its congeners by the combination of an absence of preoculars and suboculars, 1st and 3rd pair of infralabials in contact, two pairs of posterior inframaxillaries, supralabials 3-5 (sometimes 3 4) in contact with orbit, 15/15/15 rows of dorsal scales, presence of sharp vertebral keel, and divided subcaudals. This study highlights the importance of careful re-examination of museum collections that could potentially harbour new species hiding in plain sight. These discoveries also add to the growing number of reptile and amphibian species being described from Borneo that shows no signs of abating but are already potentially threatened by the continued deforestation and developments on the island.

Seeing through sedimented waters: environmental DNA reduces the phantom diversity of sharks and rays in turbid marine habitats.

BACKGROUND: Sharks and rays are some of the most threatened marine taxa due to the high levels of bycatch and significant demand for meat and fin-related products in many Asian communities. At least 25% of shark and ray species are considered to be threatened with extinction. In particular, the density of reef sharks in the Pacific has declined to 3-10% of pre-human levels. Elasmobranchs are thought to be sparse in highly urbanised and turbid environments. Low visibility coupled with the highly elusive behaviour of sharks and rays pose a challenge to diversity estimation and biomonitoring efforts as sightings are limited to chance encounters or from carcasses ensnared in nets. Here we utilised an eDNA metabarcoding approach to enhance the precision of elasmobranch diversity estimates in urbanised marine environments. RESULTS: We applied eDNA metabarcoding on seawater samples to detect elasmobranch species in the hyper-urbanised waters off Singapore. Two genes-vertebrate 12S and elasmobranch COI-were targeted and amplicons subjected to Illumina high-throughput sequencing. With a total of 84 water samples collected from nine localities, we found 47 shark and ray molecular operational taxonomic units, of which 16 had species-level identities. When data were compared against historical collections and contemporary sightings, eDNA detected 14 locally known species as well as two potential new records. CONCLUSIONS: Local elasmobranch richness uncovered by eDNA is greater than the seven species sighted over the last two decades, thereby reducing phantom diversity. Our findings demonstrate that eDNA metabarcoding is effective in detecting shark and ray species despite the challenges posed by the physical environment, granting a more consistent approach to monitor these highly elusive and threatened species.

Vertebrate Scavengers Control Abundance of Diarrhea-causing Bacteria in Tropical Plantations.

Scavenging is a common phenomenon, particularly amongst carnivorous vertebrates. By consuming carrion, vertebrate scavengers reduce resource availability for both pathogenic bacteria and their insect vectors. We investigated the ability of wild vertebrate scavengers to control agents of human diarrheal diseases (specifically Salmonella spp. and Shiga toxin-producing Escherichia coli [STEC]) in oil palm plantations in Sabah (East Malaysia), and the existence of spillover effect whereby additional vertebrate scavengers from adjacent forest patches result in greater disease control in plantation sections near these forest edges. Experimental carcasses were removed by common scavengers (Varanus salvator, Canis lupus familiaris, and Viverra tangalunga) at different time points, and this determined the length of time that the carcasses persisted in the environment. The amount of pathogenic bacteria on the surfaces of filth flies collected above the experimental carcasses was positively correlated to the duration of carcass persistence, and reduction in pathogenic bacterial abundances was largely due to carcass consumption by these vertebrate scavengers. Instead of a predicted positive spillover effect (greater scavenger activity near forest edges, hence reduced pathogen abundance), we detected a weak inverse spillover effect in which STEC counts were marginally higher in plantation sections near forest patches, and human hunting along the forest-plantation boundaries could explain this. We propose that making oil palm plantations scavenger-friendly could yield great human health benefits for the millions of workers employed in this rapidly-expanding industry, without drastically changing current management practices.

A taxonomic revision of Asthenodipsas malaccana Peters, 1864 (Squamata: Pareidae) with a description of a new species from Borneo.

A reappraisal of the taxonomic status of the Dark-necked Slug Snake (Asthenodipsas malaccana Peters, 1864) across its range revealed that populations from Borneo are not conspecific with true A. malaccana from the Thai-Malay Peninsula and Sumatra, and is therefore described herein as new. Asthenodipsas borneensis sp. nov. can be distinguished from A. malaccana and other congeners by the absence of a preocular and suboculars, seven or eight supralabials with 3rd and 4th in contact with orbit, 4-7 infralabials with 2nd or 3rd pair in contact, two pairs of posterior inframaxillaries, 15/15/15 rows of dorsal scales, presence of sharp vertebral keel, divided subcaudals, maximum recorded SVL=441 mm, 166-179 ventrals, 35-48 subcaudals, head white to greyish brown and dorsum beige to orange-brown with a conspicuous dark-brown or black patch on the neck followed by multiple, narrow, vertical, dark bands along the rest of the body and tail. This discovery adds to a growing number of new slug snake species recently described from Southeast Asia and highlights the underestimated diversity in this family, especially in Borneo. Taxonomic revisions of the reptiles and amphibians of Borneo are still needed before the true diversity of the island and the relationships of the various taxa can be fully understood.

A taxonomic reappraisal of the Smooth Slug Snake Asthenodipsas laevis (Boie, 1827) (Squamata: Pareidae) in Borneo with the description of two new species.

A review of the taxonomic status of the Smooth Slug Snake (Asthenodipsas laevis) in Borneo resulted in the discovery of two previously unrecognised species from the highlands of Sabah, East Malaysia. Asthenodipsas jamilinaisi sp. nov. and A. stuebingi sp. nov. are presumed to be closely related to A. laevis based on similarities in pholidosis and patterning but can be separated from A. laevis by their dorsal scale rows of 15/15/15 vs 15/15/13 and the presence of a sharp vertebral keel. Asthenodipsas jamilinaisi sp. nov. can be further differentiated from A. stuebingi sp. nov. by the greatly enlarged size of the vertebral scales, higher number of ventrals in males (173-175 vs 165), higher number of subcaudals (53 vs 35-47) and colour pattern (dark overall with indistinct bands vs lighter head and body with clear, distinct bands and a dark neck patch). The discovery highlights the need for more careful examination of much of the herpetofauna of Borneo that still remains underestimated and understudied. There is an urgent need for continued surveys into its diversity and the collection of genetic material for integrated taxonomic revisions.

Taxonomical and morphological notes on two species of mudskippers, Periophthalmus walailakae and Periophthalmodon schlosseri (Teleostei: Gobiidae) from Singapore.

The mudskipper Periophthalmus walailakae is recorded from Singapore, where it was previously misidentified as Periophthalmodon schlosseri, with which it is syntopic. Periophthalmus walailakae is distinguished from its congeners by the following combination of characters: pelvic fins completely united and shaped like a disk, and first dorsal fin dark brown or black, with a rounded posterior edge and a white distal margin. This species most closely resembles Pn. schlosseri but has one row of teeth on the upper jaw, scales on the isthmus, and a different upper lip and jaw morphology. Contrary to an earlier report, scales are present on the snout, interorbital, and isthmus of Ps. walailakae. The two species can also be distinguished by size, external morphology, and body color patterns.

Mitochondrial DNA sequence analyses in Bornean sucker fishes (Balitoridae: Teleostei: Gastromyzontinae).

Phylogenetic relationships among Bornean sucker fishes (Teleostei: Balitoridae: Gastromyzontinae) were investigated by comparing cytochrome b gene sequences from eight species. The results were in general agreement with previous morphology-based studies. It was found that the genera Gastromyzon and Neogastromyzon are both monophyletic and that the Chinese homalopterid Crossostoma lacustre (Homalopterinae) is not related to the Bornean species. This molecular-level study of cytochrome b gene variation in Bornean gastromyzontins will undoubtedly help to shed light on the molecular systematics of this unique freshwater fish.