333 Works

Data from: Genetic distance for a general non-stationary Markov substitution process

Benjamin D. Kaehler, Von Bing Yap, Rongli Zhang & Gavin A. Huttley
The genetic distance between biological sequences is a fundamental quantity in molecular evolution. It pertains to questions of rates of evolution, existence of a molecular clock, and phylogenetic inference. Under the class of continuous-time substitution models, the distance is commonly defined as the expected number of substitutions at any site in the sequence. We eschew the almost ubiquitous assumptions of evolution under stationarity and time-reversible conditions and extend the concept of the expected number of...

Data from: Microhabitats in the tropics buffer temperature in a globally coherent manner

Brett R. Scheffers, Theodore A. Evans, Stephen E. Williams & David P. Edwards
Vegetated habitats contain a variety of fine-scale features that can ameliorate temperate extremes. These buffered microhabitats may be used by species to evade extreme weather and novel climates in the future. Yet, the magnitude and extent of this buffering on a global scale remains unknown. Across all tropical continents and using 36 published studies, we assessed temperature buffering from within microhabitats across various habitat strata and structures (e.g. soil, logs, epiphytes and tree holes) and...

Data from: Comparing the effectiveness of metagenomics and metabarcoding for diet analysis of a leaf-feeding monkey (Pygathrix nemaeus)

Amrita Srivathsan, John C. M. Sha, Alfried P. Vogler & Rudolf Meier
Fecal samples are of great value as a non-invasive means to gather information on the genetics, distribution, demography, diet, and parasite infestation of endangered species. Direct shotgun sequencing of fecal DNA could give information on these simultaneously, but this approach is largely untested. Here we use two fecal samples to characterize the diet of two Red-Shanked Doucs Langurs (Pygathrix nemaeus) that were fed a known combination of foliage, fruits, vegetables and cereals. Illumina HiSeq sequencing...

Data from: Analysing small insect glands with UV-LDI MS: high-resolution spatial analysis reveals the chemical composition and use of the osmeterium secretion in Themira superba (Sepsidae: Diptera)

Diego P. Araujo, Mindy J. M. Tuan, Joanne Y. Yew & Rudolf Meier
For many insect species, pheromones are important communication tools, but chemical analysis and experimental study can be technically challenging because they require the detection and handling of complex chemicals in small quantities. One drawback of traditional mass spectrometry methods such as gas chromatography mass spectrometry is that whole-body extractions from one to several hundred individuals are required, with the consequence that intra- and interindividual differences cannot be detected. Here, we used the recently introduced UV-LDI...

Data from: An ancient origin for the enigmatic Flat-Headed Frogs (Bombinatoridae: Barbourula) from the islands of Southeast Asia

David C. Blackburn, David P. Bickford, Arvin C. Diesmos, Djoko T. Iskandar & Rafe M. Brown
Background: The complex history of Southeast Asian islands has long been of interest to biogeographers. Dispersal and vicariance events in the Pleistocene have received the most attention, though recent studies suggest a potentially more ancient history to components of the terrestrial fauna. Among this fauna is the enigmatic archaeobatrachian frog genus Barbourula, which only occurs on the islands of Borneo and Palawan. We utilize this lineage to gain unique insight into the temporal history of...

Data from: Coral settlement on a highly disturbed equatorial reef system

Andrew G. Bauman, James R. Guest, Glenn Dunshea, Jeffery Low, Peter A. Todd & Peter D. Steinberg
Processes occurring early in the life stages of corals can greatly influence the demography of coral populations, and successful settlement of coral larvae that leads to recruitment is a critical life history stage for coral reef ecosystems. Although corals in Singapore persist in one the world’s most anthropogenically impacted reef systems, our understanding of the role of coral settlement in the persistence of coral communities in Singapore remains limited. Spatial and temporal patterns of coral...

Inquiline predator increases nutrient-cycling efficiency of Nepenthes rafflesiana pitchers

Weng Ngai Lam, Ying Yi Chou, Felicia Leong & Hugh Tan
The modified-leaf pitchers of Nepenthes rafflesiana pitcher plants are aquatic, allochthonous ecosystems which are inhabited by specialist inquilines and sustained by the input of invertebrate prey. Detritivorous inquilines are known to increase the nutrient-cycling efficiency (NCE) of pitchers but it is unclear if predatory inquilines which prey on these detritivores decrease the NCE of pitchers by reducing detritivore populations or increase the NCE of pitchers by processing nutrients that may otherwise be locked up in...

Data from: Fear effects associated with predator presence and habitat structure interact to alter herbivory on coral reefs

Andrew Bauman, Jovena Seah, Fraser Januchowski-Hartley, Andrew Hoey, Jenny Fong & Peter Todd
Non-consumptive fear effects are an important determinant of foraging decisions by consumers across a range of ecosystems. However, how fear effects associated with the presence of predators interact with those associated with habitat structure remains unclear. Here, we used predator fish models (Plectropomus leopardus) and experimental patches of the macroalga Sargassum ilicifolium of varying densities to investigate how predator- and habitat-associated fear effects influence herbivory on coral reefs. We found the removal of macroalgal biomass...

Data from: Barcoding snakeheads (Teleostei, Channidae) revisited: discovering greater species diversity and resolving perpetuated taxonomic confusions

Cecilia Conte-Grand, Ralf Britz, Neelesh Dahanukar, Rajeev Raghavan, Rohan Pethiyagoda, Hoek Hui Tan, Renny Kurnia Hadiaty, Norsham S. Yaakob, Lukas Rüber & Heok Hui Tan
Snakehead fishes of the family Channidae are predatory freshwater teleosts from Africa and Asia comprising 38 valid species. Snakeheads are important food fishes (aquaculture, live food trade) and have been introduced widely with several species becoming highly invasive. A channid barcode library was recently assembled by Serrao and co-workers to better detect and identify potential and established invasive snakehead species outside their native range. Comparing our own recent phylogenetic results of this taxonomically confusing group...

Data from: Pythons, parasites and pests: anthropogenic impacts on Sarcocystis (Sarcocystidae) transmission in a multi-host system

Anne Devan-Song, Sonja Luz, Abraham Mathew, Mary-Ruth Low & David P. Bickford
Parasites are essential components of ecosystems and can be instrumental in maintaining host diversity and populations; however, their role in trophic interactions has often been overlooked. Three apicomplexan parasite species of Sarcocystis (S. singaporensis, S. zamani, and S. villivillosi) use the reticulated python as their definitive hosts and several species within the Rattus genus as intermediate hosts, and they form a system useful for studying interactions between host–parasite and predator–prey relationships, as well as anthropogenic...

Development of an automatic integrated gene detection system for novel severe acute respiratory syndrome-related coronavirus (SARS-CoV2)

Yuchang Li, Jing Li, Ying Zhang, Lizhong Dai, Lin Li, Juan Liu, Sen Zhang, Xiaoyan Wu, Yi Hu, Chengfeng Qin, Tao Jiang & Xiaoping Kang
In December 2019, Wuhan, China suffered a serious outbreak of a novel coronavirus infectious disease (COVID) caused by novel severe acute respiratory syndrome-related coronavirus (SARS-CoV 2). To quickly identify the pathogen, we designed and screened primer sets, and established a sensitive and specific qRT-PCR assay for SARS-CoV 2; the lower limit of detection (LOD) was 15 (95% CI: 9.8–21) copies per reaction. We combined this qRT-PCR assay with an automatic integration system for nucleic acid...

Data from: Aggressive spiders make the wrong decision in a difficult task

Chia-Chen Chang, Zhi Yun Lim, Danielle A. Klomp, Yusoff Norma-Rashid & Daiqin Li
Accurate and timely decisions are critical for foraging, predator avoidance, and reproductive success. However, there is often a trade-off between speed and accuracy in decision-making, where individuals that make decisions more quickly make more mistakes. An individual’s personality may influence its decision-making style (i.e. whether it errs more in the speed or accuracy of a decision) and this relationship may change depending on contexts. Despite growing research on invertebrate personality, how personality correlates with decision-making...

Factors influencing nature interactions vary between cities and types of nature interactions

Rui Ying Rachel Oh, Kelly Fielding, Thi Phuong Le Nghiem, Chia-Chen Chang, Danielle Shanahan, Kevin Gaston, Román Carrasco & Richard Fuller
1. There is mounting concern that people living more urbanised, modern lifestyles have fewer and lower quality interactions with nature, and therefore have limited access to the associated health and wellbeing benefits. Yet, variation in the different types of nature interactions and the factors that influence these interactions across populations are poorly understood. 2. We compared four types of nature interactions by administering surveys across two cities that differ markedly in urbanisation pattern and population...

Defining the Syrian hamster as a highly susceptible preclinical model for SARS-CoV-2 infection

Kyle Rosenke, Kimberly Meade-White, Michael Letko, Chad Clancy, Frederick Hansen, Yanan Liu, Atsushi Okumura, Tsing-Lee Tang-Huau, Rong Li, Greg Saturday, Friederike Feldmann, Dana Scott, Zhongde Wang, Vincent Munster, Michael A. Jarvis & Heinz Feldmann
Following emergence in late 2019, SARS-CoV-2 rapidly became pandemic and is presently responsible for millions of infections and hundreds of thousands of deaths worldwide. There is currently no approved vaccine to halt the spread of SARS-CoV-2 and only very few treatment options are available to manage COVID-19 patients. For development of preclinical countermeasures, reliable and well-characterized small animal disease models will be of paramount importance. Here we show that intranasal inoculation of SARS-CoV-2 into Syrian...

Predictor complexity and feature selection affect Maxent model transferability: evidence from global freshwater invasive species

Bi Wei Low, Yiwen Zeng, Heok Hui Tan & Darren C. J. Yeo
This dataset contains the following: Occurrence datasets of five global freshwater invasive species (African sharptooth catfish Clarias gariepinus, Mozambique tilapia Oreochromis mossambicus, American bullfrog Lithobates catesbeianus, red swamp crayfish Procambarus clarkii, and Australian redclaw crayfish Cherax quadricarinatus) Background points for presence-only ecological niche modelling (e.g., Maxent) Example R script (with annotations inline) to conduct model tuning and transferability assessments using Maxent

Data from: Effects of sampling effort on biodiversity patterns estimated from environmental DNA metabarcoding surveys

Erin K. Grey, Louis Bernatchez, Phillip Cassey, Kristy Deiner, Marty Deveney, Kimberley L. Howland, Anaïs Lacoursière-Roussel, Sandric Chee Yew Leong, Yiyuan Li, Brett Olds, Michael E. Pfrender, Thomas A. A. Prowse, Mark A. Renshaw & David M. Lodge
Environmental DNA (eDNA) metabarcoding can greatly enhance our understanding of global biodiversity and our ability to detect rare or cryptic species. However, sampling effort must be considered when interpreting results from these surveys. We explored how sampling effort influenced biodiversity patterns and nonindigenous species (NIS) detection in an eDNA metabarcoding survey of four commercial ports. Overall, we captured sequences from 18 metazoan phyla with minimal differences in taxonomic coverage between 18 S and COI primer...

Empirical food webs of 12 tropical reservoirs in Singapore

Clare Wilkinson, Rayson B. H. Lim, Jia Huan Liew, Jeffrey T. B. Kwik, Darren C. J. Yeo, Claudia L. Y. Tan & Heok Hui Tan
We present 12 food webs from tropical reservoir communities in Singapore, and summarise the topology of each with widely used network indices (e.g., connectance, link density). Each reservoir was surveyed over 4–6 sampling occasions, during which, representative animal groups (i.e., fish species, and taxonomic/functional groups of zooplankton and benthic macroinvertebrates) and all likely sources of primary production (i.e., macrophytes, periphyton, phytoplankton, and riparian terrestrial plants) were collected. We determined and measured gut content in fishes...

Toxoplasma gondii infection in white spoonbills (Platalea leucorodia) from Henan Province, China

Yurong Yang, Nan Jiang, Shilin Xin & Longxian Zhang
Toxoplasma gondii oocysts in the environment are a threat to humans and animals. This study is aimed to evaluate the prevalence of T. gondii in white spoonbills and isolate viable T. gondii from white spoonbills. In 28.6% (2/7) of white spoonbills, T. gondii antibodies were found in heart juice by the modified agglutination test (cut-off: 1:4). T. gondii DNA was detected in tissues of 42.9% (3/7) white spoonbills. One viable T. gondii strain, named TgSpoonbillCHn1,...

Genomic evidence supporting the clonal expansion of extensively drug-resistant tuberculosis bacteria belonging to a rare proto-Beijing genotype

Prapaporn Srilohasin, Therdsak Prammananan, Kiatichai Faksri, Jody E. Phelan, Prapat Suriyaphol, Phalin Kamolwat, Saijai Smithtikarn, Areeya Disratthakit, Sanjib Mani Regmi, Manoon Leechawengwongs, Rick Twee-Hee Ong, Yik Ying Teo, Sissades Tongsima, Taane G. Clark & Angkana Chaiprasert
Tuberculosis disease (TB), caused by Mycobacterium tuberculosis, is a major public health issue in Thailand. The high prevalence of modern Beijing (Lineage 2.2.1) strains has been associated with multi- and extensively drug-resistant infections (MDR-, XDR-TB), complicating disease control. The impact of rarer proto-Beijing (L2.1) strains is less clear. In our study of thirty-seven L2.1 clinical isolates spanning thirteen years, we found a high prevalence of XDR-TB cases (32.4%). With ≤ 12 pairwise SNP distances, 43.2%...

Wolbachia infection in wild mosquitoes (Diptera: Culicidae): Implications for transmission modes and host-endosymbiont associations in Singapore

Huicong Ding, Huiqing Yeo & Nalini Puniamoorthy
Background: Wolbachia are intracellular bacterial endosymbionts found in most insect lineages. In mosquitoes, the influence of these endosymbionts on host reproduction and arboviral transmission has spurred numerous studies aimed at using Wolbachia infection as a vector control technique. However, there are several knowledge gaps in the literature and little is known about natural Wolbachia infection across species, their transmission modes, or associations between various Wolbachia lineages and their hosts. This study aims to address these...

Attenuation of porcine deltacoronavirus disease severity by porcine reproductive and respiratory syndrome virus coinfection in a weaning pig model

Xinrong Zhou, Xinna Ge, Yongning Zhang, Jun Han, Xin Guo, Yanhong Chen, Lei Zhou & Hanchun Yang
Porcine deltacoronavirus (PDCoV) is a potentially emerging zoonotic pathogen that causes severe diarrhea in young pigs, with a risk of fatal dehydration. Its pathogenicity on neonatal piglet has been previously reported, however, it is less known if the coinfection with immunosuppressive pathogens can influence PDCoV disease manifestation. Here, a coinfection model of PDCoV and porcine reproductive and respiratory syndrome virus (PRRSV), a global-spread immunosuppressive virus, was set to study their interaction. Weaning pigs in the...

Data from: Equivalent effect of UV coloration and vibratory signal on mating success in a jumping spider

Hua Zeng, Samantha S.E. Wee, Christina J. Painting, Shichang Zhang, Daiqin Li & Samantha S E Wee
Ultraviolet (UV; wavelengths: 280–400 nm) colouration has been shown to be an important visual signal but has not been studied in conjunction with other signals such as vibratory signals previously. Here we investigated multimodal signal function in the visual and substrate-borne vibratory modalities of the UV-ornamented jumping spider Cosmophasis umbratica, in which the importance of UV colouration in courtship displays has been demonstrated. We first described vibratory signals produced by courting males. We found that...

Data from: Patterns of nitrogen-fixing tree abundance in forests across Asia and America

Duncan N. L. Menge, Ryan A. Chisholm, Stuart J. Davies, Kamariah Abu Salim, David Allen, Mauricio Alvarez, Norm Bourg, Warren Y. Brockelman, Sarayudh Bunyavejchewin, Nathalie Butt, Min Cao, Wirong Chanthorn, Wei-Chun Chao, Keith Clay, Richard Condit, Susan Cordell, João Batista Da Silva, H. S. Dattaraja, Ana Cristina Segalin De Andrade, Alexandre A. Oliveira, Jan Den Ouden, Michael Drescher, Christine Fletcher, Christian P. Giardina, C. V. Savitri Gunatilleke … & Tak Fung
Symbiotic nitrogen (N)‐fixing trees can provide large quantities of new N to ecosystems, but only if they are sufficiently abundant. The overall abundance and latitudinal abundance distributions of N‐fixing trees are well characterised in the Americas, but less well outside the Americas. Here, we characterised the abundance of N‐fixing trees in a network of forest plots spanning five continents, ~5,000 tree species and ~4 million trees. The majority of the plots (86%) were in America...

Morphology and mini-barcodes: The inclusion of larval sampling and NGS-based barcoding improves robustness of ecological analyses of mosquito communities

Huiqing Yeo, Tze Xuan Yeoh, Huicong Ding, Theodore Lee & Nalini Puniamoorthy
A significant proportion of vector-borne diseases are transmitted by blood-sucking dipterans, including mosquitoes. Understanding transmission risks requires accurate identification of species across heterogenous habitats, but many cryptic and polymorphic species are overlooked when using morphological identification. Estimates of mosquito diversity are typically based on adult female trapping methods which tend to target host-seeking species and may represent a biased snapshot of community structure. Unfortunately, diversity estimates based on larval data are rarely included in mosquito...

Data from: Barriers and corridors of gene flow in an urbanised tropical reef system

Lutfi Afiq-Rosli
Information about the distribution of alleles among marine populations is critical for determining patterns of genetic connectivity that are essential in modern conservation planning. To estimate population connectivity in Singapore’s urbanised equatorial reef system, we analysed single nucleotide polymorphisms (SNPs) from two species of reef-building corals with distinct life histories. For Porites sp., a broadcast-spawning coral, we found cryptic lineages which were differentially distributed at inshore and central-offshore sites that could be attributed to contemporary...

Registration Year

  • 2023
  • 2022
  • 2021
  • 2020
  • 2019
  • 2018
  • 2017
  • 2016
  • 2015
  • 2014

Resource Types

  • Dataset


  • National University of Singapore
  • Chinese Academy of Sciences
  • Capital Medical University
  • Fudan University
  • Chinese Academy of Medical Sciences & Peking Union Medical College
  • Zhejiang University
  • West China Hospital of Sichuan University
  • Wenzhou Medical University
  • Shanghai Jiao Tong University
  • Sichuan University