Uncovering the magnitude of African pangolin poaching with extensive nanopore DNA genotyping of seized scales.

Trade in pangolins is illegal, and yet tons of their scales and products are seized at various ports. These large seizures are challenging to process and comprehensively genotype for upstream provenance tracing and species identification for prosecution. We implemented a scalable DNA barcoding pipeline in which rapid DNA extraction and MinION sequencing were used to genotype a substantial proportion of pangolin scales subsampled from 2 record shipments seized in Singapore in 2019 (37.5 t). We used reference sequences to match the scales to phylogeographical regions of origin. In total, we identified 2346 cytochrome b (cytb) barcodes of white-bellied (Phataginus tricuspis) (from 1091 scales), black-bellied (Phataginus tetradactyla) (227 scales), and giant (Smutsia gigantea) (1028 scales) pangolins. Haplotype diversity was higher for P. tricuspis scales (121 haplotypes, 66 novel) than that for P. tetradactyla (22 haplotypes, 15 novel) and S. gigantea (25 haplotypes, 21 novel) scales. Of the novel haplotypes, 74.2% were likely from western and west-central Africa, suggesting potential resurgence of poaching and newly exploited populations in these regions. Our results illustrate the utility of extensively subsampling large seizures and outline an efficient molecular approach for rapid genetic screening that should be accessible to most forensic laboratories and enforcement agencies.

Revelación de la magnitud de la caza furtiva del pangolín africano mediante el genotipo extenso de nanoporos de ADN de escamas incautadas Resumen Aunque el mercado de pangolines es ilegal, se incautan toneladas de sus escamas y productos derivados en varios puertos comerciales. Es un reto procesar estas magnas incautaciones y obtener el genotipo completo para usarlo en la trazabilidad logística ascendente e identificación de la especie y así imponer sanciones. Implementamos una canalización escalable del código de barras de ADN en el cual usamos la extracción rápida de ADN y la secuenciación MinION para obtener el genotipo de una proporción sustancial de las escamas de pangolín submuestreadas en dos cargamentos incautados en 2019 en Singapur (37.5 t). Usamos secuencias referenciales para emparejar las escamas con las regiones filogeográficas de origen. Identificamos en total 2,346 códigos de citocromo b (cytb) del pangolín de vientre blanco (Phataginus tricuspis) (de 1,091 escamas), de vientre negro (P. tetradactyla) (227 escamas) y del pangolín gigante (Smutsia gigantea) (1,028 escamas). La diversidad de haplotipos fue mayor en las escamas de P. tricuspis (121 haplotipos, 66 nuevos) que en las de P. tetradactyla (22 haplotipos, 15 nuevos) y S. gigantea (25 haplotipos, 21 nuevos). De los haplotipos nuevos, el 74.2% probablemente provenía del occidente y centro­occidente de África, lo que sugiere un resurgimiento potencial de la caza furtiva y poblaciones recién explotadas en estas regiones. Nuestros resultados demuestran la utilidad de submuestrear extensivamente las grandes incautaciones y esboza una estrategia molecular eficiente para un análisis genético rápido que debería ser accesible para la mayoría de los laboratorios forenses y las autoridades de aplicación.

Anthropogenic Transmission of SARS-CoV-2 from Humans to Lions, Singapore, 2021.

In Singapore, 10 captive lions tested positive for SARS-CoV-2 by real-time PCR. Genomic analyses of nanopore sequencing confirmed human-to-animal transmission of the SARS-CoV-2 Delta variant. Viral genomes from the lions and zookeeper shared a unique spike protein substitution, S:A1016V. Widespread SARS-CoV-2 transmission among humans can increase the likelihood of anthroponosis.

Detection of African Swine Fever Virus from Wild Boar, Singapore, 2023.

We detected African swine fever virus (ASFV) from a wild boar in Singapore. In <72 hours, we confirmed and reported ASFV p72 genotype II, CD2v serogroup 8, and IGR-II variant by using a combination of real-time PCR and whole-genome sequencing. Continued biosurveillance will be needed to monitor ASFV in Singapore.

The impact of gardening on mental resilience in times of stress: A case study during the COVID-19 pandemic in Singapore.

To curb the spread of Covid-19, Singapore, like other cities, had to impose movement restriction and social distancing measures that may affect the well-being of its residents. In this paper, we assessed the potential benefits of gardening on the mental well-being of Singapore residents, based on the concept of mental resilience. We hypothesized that gardening activities promote mental resilience. A survey was administered on 8,786 participants of a "Gardening with Edibles" programme, measuring their mental resilience status, engagement in gardening activities and socio-demographic information. The mental resilience scores of participants who engaged in weekly gardening were compared with the scores derived from another survey conducted during the pandemic on an online community comprising demographically representative respondents with an interest on Covid-19 related community care. The results showed that the mental resilience of those who gardened was statistically significantly higher than the online community. Within the gardening group, those with less than one hour of weekly gardening time had significantly lower scores in their total mental resilience, and five out of seven resilience factors, "emotional regulation", "relationship", "confidence", "positive thinking" and "spirituality", compared to those with more weekly gardening time, showing that the efficacy of the mediating effects may peak at a weekly gardening time of between one to four hours. Home gardening may be an effective way for people living in densely populated cities to interact with nature and build mental resilience during the pandemic.

A natural hybrid of Sindora (Fabaceae, Detarioideae) from Singapore.

Sindora×changiensis L.M.Choo, Loo, W.F.Ang & K.Er is a new hybrid from the subfamily Detarioideae in Fabaceae. This is the first reported instance of natural hybridisation in Sindora. Based on population genetics analyses using ddRAD and morphological observations, this taxon represents a fertile hybrid between Sindoracoriacea and Sindoraechinocalyx. This new hybrid is so far only known to occur naturally from Changi at the north-eastern coast of Singapore. It has pods that are sparsely spiny. This is intermediate between the smooth, non-spiny pods of S.coriacea, and the densely spiny pods of S.echinocalyx. The calyx is smooth and unarmed, resembling S.coriacea. Last but not least, the ovary is entirely pubescent, different from S.coriacea and S.echinocalyx. The ovary of S.coriacea has a glabrous patch in the middle, while that of S.echinocalyx has minute spines protruding from the dense pubescence. A taxonomic description and an updated key to the Sindora of Singapore and Peninsular Malaysia are also provided.

The influence of the COVID-19 pandemic on the demand for different shades of green.

COVID-19 has heightened the dependence of urban dwellers on cultural ecosystem services provided by urban green spaces (UGS), specifically in regard to the provision of recreational opportunities, and psychological and physical health benefits arising from their use.As different types and levels of cultural ecosystem services are provided by different types of UGS, people may seek out different UGS to satisfy personal needs over various phases of COVID-19 mobility restrictions imposed by cities. We report on a study that took advantage of the different phases of COVID-19 mobility restrictions to assess the demand for and perception of different types of UGS in Singapore.The study utilised four datasets to compare demand for and visitorship patterns of UGS before the pandemic (Pre-Circuit Breaker), the duration of the strictest mobility restrictions (Circuit Breaker), and after the measures were relaxed (Post-Circuit Breaker). We used Google Search trends as a proxy for UGS demand, Google mobility data for an overview of population visitorship trends, visitor counts for granular insights on actual visitorship trends, and qualitative data on perception of parks by park visitors after restrictions eased. Parks were categorised as manicured and less manicured UGS for analysis.Search interest for UGS overall fell by more than 50% from during Circuit Breaker but the post-Circuit Breaker levels exceeded pre-Circuit Breaker, with a 70.9% increase for less manicured UGS compared to 20.8% for manicured UGS. This corroborated with Google mobility and visitor counts, which showed a steep decrease in park use followed by a rapid increase in the same periods, and with increased visitorship in the less manicured UGS. The perception study also showed that more than 50% of respondents reported visiting parks that they have never visited before, and there was a greater appreciation and use of UGS after the pandemic and preference for less manicured and more naturalistic landscapes.The pandemic has heightened the demand for cultural ecosystem services provided by UGS. Our study showed that this demand is not uniform across different types of UGS, with an increase visitorship and preference for less manicured green spaces. Read the free Plain Language Summary for this article on the Journal blog.

Shorebirds wintering in Southeast Asia demonstrate trans-Himalayan flights.

Many birds wintering in the Indian subcontinent fly across the Himalayas during migration, including Bar-headed Geese (Anser indicus), Demoiselle Cranes (Anthropoides virgo) and Ruddy Shelducks (Tadorna ferruginea). However, little is known about whether shorebirds migrate across the Himalayas from wintering grounds beyond the Indian subcontinent. Using geolocators and satellite tracking devices, we demonstrate for the first time that Common Redshanks (Tringa totanus) and Whimbrels (Numenius phaeopus) wintering in Singapore can directly fly over the Himalayas to reach breeding grounds in the Qinghai-Tibet Plateau and north-central Russia respectively. The results also show that migratory shorebirds wintering in Southeast Asia can use both the Central Asian Flyway and the East Asian-Australasian Flyway. For Redshanks, westerly-breeding birds crossed the Himalayas while more easterly breeders on the Plateau migrated east of the Himalayas. For Whimbrels, an individual that crossed the Himalayas was probably from a breeding population that was different from the others that migrated along the coast up the East Asian-Australasian Flyway. The minimum required altitude of routes of trans-Himalayan Redshanks were no higher on average than those of eastern migrants, but geolocator temperature data indicate that birds departing Singapore flew at high elevations even when not required to by topography, suggesting that the Himalayan mountain range may be less of a barrier than assumed.