122 Works

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...

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: 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: 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...

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...

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...

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: 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: 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...

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: 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: 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...

Data from: Genomic analysis reveals hidden biodiversity within colugos, the sister group to primates

Victor C. Mason, Gang Li, Patrick Minx, Jurgen Schmitz, Gennady Churakov, Liliya Doronina, Amanda D. Melin, Nathaniel J. Dominy, Norman T-L. Lim, Mark S. Springer, Richard K. Wilson, Wesley C. Warren, Kristofer M. Helgen & William J. Murphy
Colugos are one of the most poorly studied mammals despite their centrality to resolving supraordinal primate relationships. Two described species of these gliding mammals are the sole living members of the order Dermoptera, distributed throughout Southeast Asia. We generated a draft genome sequence for a Sunda colugo and a Philippine colugo reference alignment, and used these to identify colugo-specific genetic changes that were enriched in sensory and musculo-skeletal related genes that likely underlie their nocturnal...

Data from: Bee communities along a prairie restoration chronosequence: similar abundance and diversity, distinct composition

Rebecca K. Tonietto, John S. Ascher & Daniel J. Larkin
Recognition of the importance of bee conservation has grown in response to declines of managed honey bees and some wild bee species. Habitat loss has been implicated as a leading cause of declines, suggesting that ecological restoration is likely to play an increasing role in bee conservation efforts. In the Midwestern USA, restoration of tallgrass prairie has traditionally targeted plant community objectives without explicit consideration for bees. However, restoration of prairie vegetation is likely to...

Data from: Eyespots deflect predator attack increasing fitness and promoting the evolution of phenotypic plasticity

Kathleen L. Prudic, Andrew M. Stoehr, Bethany R. Wasik & Antónia Monteiro
Some eyespots are thought to deflect attack away from the vulnerable body, yet there is limited empirical evidence for this function and its adaptive advantage. Here, we demonstrate the conspicuous ventral hindwing eyespots found on Bicyclus anynana butterflies protect against invertebrate predators, specifically praying mantids. Wet season (WS) butterflies with larger, brighter eyespots were easier for mantids to detect, but more difficult to capture compared to dry season (DS) butterflies with small, dull eyespots. Mantids...

Data from: Nymphalid eyespot serial homologs originate as a few individualized modules

Jeffrey C. Oliver, Jeremy M. Beaulieu, Lawrence F. Gall, William H. Piel & Antónia Monteiro
Serial homologues are repeated traits that share similar development but occur in different parts of the body. Variation in number of repeats accounts for substantial diversity in animal form and considerable work has focused on identifying the factors accounting for this variation. Little is known, however, about how serial homologues originally become repeated, or about the relative timing of repeat individuation relative to repeat origin. Here, we show that the serially repeated eyespots on nymphalid...

Data from: “Direct PCR” optimization yields a rapid, cost-effective, non-destructive, and efficient method for obtaining DNA barcodes without DNA extraction

Wing Hing Wong, Ywee Chieh Tay, Jayanthi Puniamoorthy, Michael Balke, Peter S. Cranston & Rudolf Meier
Macroinvertebrates that are collected in large numbers pose major problems in basic and applied biodiversity research: identification to species via morphology is often difficult, slow, and/or expensive. DNA barcodes are an attractive alternative or complementary source of information. Unfortunately obtaining DNA barcodes from specimens requires many steps and thus time and money. Here, we promote a short-cut to DNA barcoding; i.e., a non-destructive PCR method that skips DNA extraction (“direct PCR”) and that can be...

Data from: Effects of macrophytes on lake‐water quality across latitudes: a meta‐analysis

Yiluan Song, Jia Huan Liew, Darren Zong Han Sim, Maxine Allayne Darlene Mowe, Simon Mark Mitrovic, Hugh Tiang Wah Tan & Darren Chong Jinn Yeo
Macrophytes are widely recognized for improving water quality and stabilizing the desirable clear‐water state in lakes. The positive effects of macrophytes on water quality have been noted to be weaker in the (sub)tropics compared to those of temperate regions. We conducted a global meta‐analysis using 47 studies that met our set criteria to assess the overall effects of macrophytes on water quality (measured by phytoplankton chlorophyll a concentration, total nitrogen concentration, total phosphorus concentration, Secchi...

Data from: Use of ancient sedimentary DNA as a novel conservation tool for high-altitude tropical biodiversity

Sanne Boessenkool, Gayle McGlynn, Laura S. Epp, David Taylor, Manuel Pimentel, Abel Gizaw, Sileshi Nemomissa, Christian Brochmann & Magnus Popp
Conservation of biodiversity may in the future increasingly depend upon the availability of scientific information to set suitable restoration targets. In traditional paleoecology, sediment-based pollen provides a means to define preanthropogenic impact conditions, but problems in establishing the exact provenance and ecologically meaningful levels of taxonomic resolution of the evidence are limiting. We explored the extent to which the use of sedimentary ancient DNA (sedaDNA) may complement pollen data in reconstructing past alpine environments in...

Data from: Association between the dopamine D4 receptor gene exon III variable number of tandem repeats and political attitudes in female Han Chinese

Richard P. Ebstein, Mikhail V. Monakhov, Yunfeng Lu, Yushi Jiang, Poh San Lai & Soo Hong Chew
Twin and family studies suggest that political attitudes are partially determined by an individual's genotype. The dopamine D4 receptor gene (DRD4) exon III repeat region that has been extensively studied in connection with human behaviour, is a plausible candidate to contribute to individual differences in political attitudes. A first United States study provisionally identified this gene with political attitude along a liberal–conservative axis albeit contingent upon number of friends. In a large sample of 1771...

Data from: Persistence of long-distance, insect-mediated pollen movement for a tropical canopy tree species in remnant forest patches in an urban landscape

Annika M.E. Noreen, Matti A. Niissalo, Shawn K.Y. Lum & Edward L. Webb
As deforestation and urbanization continue at rapid rates in tropical regions, urban forest patches are essential repositories of biodiversity. However, almost nothing is known about gene flow of forest-dependent tree species in urban landscapes. In this study, we investigated gene flow in the insect-pollinated, wind-dispersed tropical tree Koompassia malaccensis in and among three remnant forest patches in the urbanized landscape of Singapore. We genotyped the vast majority of adults (N=179) and a large number of...

Data from: Multiple habitat use by declining migratory birds necessitates joined-up conservation

Micha V Jackson, L R Carrasco, Chi-Yeung Choi, Jing Li, Zhijun Ma, David S Melville, Tong Mu, He-Bo Peng, Bradley K Woodworth, Ziyou Yang, Lin Zhang & Richard A Fuller
Many species depend on multiple habitats at different points in space and time. Their effective conservation requires an understanding of how and when each habitat is used, coupled with adequate protection. Migratory shorebirds use intertidal and supratidal wetlands, both of which are affected by coastal landscape change. Yet the extent to which shorebirds use artificial supratidal habitats, particularly at highly developed stopover sites, remains poorly understood leading to potential deficiencies in habitat management. We surveyed...

Data from: Sorting specimen-rich invertebrate samples with cost-effective NGS barcodes: validating a reverse workflow for specimen processing

Wendy Y. Wang, Amrita Srivathsan, Maosheng Foo, Seiki K. Yamane & Rudolf Meier
Biologists frequently sort specimen-rich samples to species. This process is daunting when based on morphology, and disadvantageous if performed using molecular methods that destroy vouchers (e.g., metabarcoding). An alternative is barcoding every specimen in a bulk sample and then presorting the specimens using DNA barcodes, thus mitigating downstream morphological work on presorted units. Such a “reverse workflow” is too expensive using Sanger sequencing, but we here demonstrate that is feasible with an NGS barcoding pipeline...

Data from: Prevalence of preoperative anemia, abnormal mean corpuscular volume and red cell distribution width among surgical patients in Singapore, and their influence on one year mortality

Yilin Eileen Sim, Hide Wee, Ai Leen Ang, Niresh Ranjakunalan, Biauw Chi Ong & Hairil Rizal Abdullah
Introduction Preoperative anemia and high red cell distribution width (RDW) are associated with higher perioperative mortality. Conditions with high RDW levels can be categorized by mean corpuscular volume (MCV). The relationship between RDW, anemia and MCV may explain causality between high RDW levels and outcomes. We aim to establish the prevalence of preoperative anemia and distribution of RDW and MCV among pre-surgical patients in Singapore. In addition, we aim to investigate the association between preoperative...

Data from: Aggressive jumping spiders make quicker decisions for preferred prey but not at the cost of accuracy

Chia-Chen Chang, Pangilinan Ng & Daiqin Li
There has been an increasing interest in consistent interindividual differences in behavior (i.e., personality) in recent years. However, consistent interindividual differences in cognitive styles remain largely unexplored. Individual differences in cognitive styles are hypothesized to be functionally related to differences in personality types. It is assumed that proactive individuals make faster decisions at the expense of accuracy (i.e., the speed–accuracy trade-offs hypothesis). Here, we investigated the relationship between personality and speed–accuracy trade-off using Portia labiata,...

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  • National University of Singapore
  • Nanyang Technological University
  • Hubei University
  • University of Kansas
  • Yale-NUS College
  • University of Queensland
  • James Cook University
  • National Museum
  • University of Malaya
  • University of Minnesota