122 Works

Data from: Species-habitat relationships and ecological correlates of butterfly abundance in a transformed tropical landscape

Anuj Jain, Felix K. S. Lim & Edward L. Webb
Tropical butterfly conservation strategies often focus on total and/or common species richness to assess the conservation value of a patch or habitat. However, such a strategy overlooks the unique dynamics of rare species. We evaluated the species-habitat relationships of 209 common, intermediate, and rare butterfly species (including morphospecies) across four habitat types (mature, degraded, or fragmented forest, and urban parks) and two patch sizes (<400 ha, ≥400 ha) in Singapore. Common species richness was consistent...

Data from: The effect of repeated, lethal sampling on wild bee abundance and diversity

Zachariah J. Gezon, Eli S. Wyman, John S. Ascher, David W. Inouye & Rebecca E. Irwin
1. Bee pollinators provide a critical ecosystem service to wild and agricultural plants but are reported to be declining world-wide due to anthropogenic change. Long-term data on bee abundance and diversity are scarce, and the need for additional quantitative sampling using repeatable methods has been emphasized. Recently, monitoring programmes have begun using a standardized method that employs a combination of pan traps and sweep netting, resulting in lethal sampling of bees. This standardized method can...

Data from: Extant primitively segmented spiders have recently diversified from an ancient lineage

Xin Xu, Fengxiang Liu, Ren-Chung Cheng, Jian Chen, Xiang Xu, Zhisheng Zhang, Hirotsugu Ono, Dinh Sac Pham, Y. Norma-Rashid, Miquel A. Arnedo, Matjaž Kuntner, Daiqin Li & R.-C. Cheng
Living fossils are lineages that have retained plesiomorphic traits through long time periods. It is expected that such lineages have both originated and diversified long ago. Such expectations have recently been challenged in some textbook examples of living fossils, notably in extant cycads and coelacanths. Using a phylogenetic approach, we tested the patterns of the origin and diversification of liphistiid spiders, a clade of spiders considered to be living fossils due to their retention of...

Data from: Population-specific recombination sites within the human MHC region

Ee Chee Ren, Tze Hau Lam, Meixin Shen, Jer-Ming Chia & Soh Ha Chan
Genetic rearrangement by recombination is one of the major driving forces for genome evolution and recombination are known to occur in non-random, discreet recombination sites within the genome. Mapping of recombination sites have proved difficult particularly in the human MHC region that is complicated by both population variation and highly polymorphic HLA genes. To overcome these problems, HLA typed individuals from three representative populations: Asian, European and African were used to generate phased HLA haplotypes....

Data from: Deciphering the evolutionary history and developmental mechanisms of a complex sexual ornament: the abdominal appendages of Sepsidae (Diptera)

Julia H. Bowsher, Yuchen Ang, Tanner Ferderer & Rudolf Meier
Male abdomen appendages are a novel trait found within Sepsidae (Diptera). Here we demonstrate that they are likely to have evolved once, were lost three times, and then secondarily gained in one lineage. The developmental basis of these appendages was investigated by counting the number of histoblast cells in each abdominal segment in four species: two that represented the initial instance of appendage evolution, one that has secondarily gained appendages, and one species that did...

Indoor temperature - office work performance database

Jose Ali Porras-Salazar, Stefano Schiavon, Pawel Wargocki, Toby Cheung & Kwok Wai Tham
The objective of developing this database was to summarise all relevant published studies that have linked the thermal environment to office work performance within the most representative temperature range for office buildings (20 °C to 30 °C). We conducted a comprehensive literature review and collected the relevant published data into our database. A variety of combinations of keywords including temperature, thermal sensation, work, cognitive, and task performance, and office and commercial buildings, were used. In...

Land-use change erodes trophic redundancy in tropical forest streams: Evidence from amino acid stable isotope analysis

Kenny Chua, Jia Huan Liew, Clare Wilkinson, Amirrudin Ahmad, Heok Hui Tan & Darren Yeo
Studies have shown that food chain length is governed by interactions between species richness, ecosystem size, and resource availability. While redundant trophic links may buffer impacts of species loss on food chain length, higher extinction risks associated with predators may result in bottom-heavy food webs with shorter food chains. The lack of consensus in earlier empirical studies relating species richness and food chain length reflects the need to account robustly for the factors described above....

Phylogenomics of white-eyes, a ‘great speciator,’ reveals Indonesian archipelago as the center of lineage diversity

Chyi Yin Gwee, Kritika Garg, Balaji Chattopadhyay, Keren Sadanandan, Dewi Prawiradilaga, Martin Irestedt, Fu-Min Lei, Luke Bloch, Jessica Lee, Mohammad Irham, Tri Haryoko, Malcolm Soh, Kelvin Peh, Karen Rowe, Teuku Ferasyi, Shaoyuan Wu, Guinevere Wogan, Rauri Bowie & Frank Rheindt
Archipelagoes serve as important ‘natural laboratories’ which facilitate the study of island radiations and contribute to the understanding of evolutionary processes. The white-eye genus Zosterops is a classical example of a ‘great speciator’, comprising c. 100 species from across the Old World, most of them insular. We achieved an extensive geographic DNA sampling of Zosterops by using historical specimens and recently collected samples. Using over 700 genome-wide loci in conjunction with coalescent species tree methods...

Gene flow creates a mirage of cryptic species in a Southeast Asian spotted stream frog complex

Kin Onn Chan, Carl Hutter, Perry Lee Wood, Lee Grismer, Indraneil Das & Rafe Brown
Most new cryptic species are described using conventional tree- and distance-based species delimitation methods (SDMs), which rely on phylogenetic arrangements and measures of genetic divergence. However, although numerous factors such as population structure and gene flow are known to confound phylogenetic and species delimitation inferences, the influence of these processes on species estimation is not frequently evaluated. Using large amounts of exons, introns, and ultraconserved elements obtained using the FrogCap sequence-capture protocol, we compared conventional...

Micro-stepping Extended Focus reduces photobleaching and preserves structured illumination super-resolution features

Xian Hu, Salma Jalal, Michael Sheetz, Oddmund Bakke & Felix Margadant
Despite progress made in confocal microscopy, even fast systems still have insufficient temporal resolution for detailed live cell volume imaging, such as tracking rapid movement of membrane vesicles in three-dimensional space. Depending on the shortfall, this may result in undersampling and/or motion artifacts that ultimately limit the quality of the imaging data. By sacrificing the detailed information in the Z-direction, we propose a new imaging modality that involves capturing fast “projections” from the field of...

The interplay of color and bioacoustic traits in the differentiation of a Southeast Asian songbird complex

Chyi Yin Gwee, Qiao Le Lee, Simon Mahood, Le Manh Hung, Robert Tizard, Krairat Eiamampai, Philip Round & Frank Rheindt
Morphological traits have served generations of biologists as a taxonomic indicator, and have been the main basis for defining and classifying species diversity for centuries. A quantitative integration of behavioural characters, such as vocalizations, in studies on biotic differentiation has arisen more recently, and the relative importance of these different traits in the diversification process remains poorly understood. To provide a framework within which to interpret the evolutionary interplay between morphological and behavioral traits, we...

Development of a multi-excitation fluorescence (MEF) imaging method to improve the information content of benthic coral reef surveys

Elena Bollati
Benthic surveys are a key component of monitoring and conservation efforts for coral reefs worldwide. While traditional image-based surveys rely on manual annotation of photographs to characterise benthic composition, automatic image annotation based on computer vision is becoming increasingly common. However, accurate classification of some benthic groups from reflectance images presents a challenge to local ecologists and computers alike. Most coral reef organisms produce one or a combination of fluorescent pigments, such as Green Fluorescent...

Data from: Occurrence-habitat mismatching and niche truncation when modelling distributions affected by anthropogenic range contractions

Sean E. H. Pang
Aims: Human-induced pressures such as deforestation cause anthropogenic range contractions (ARCs). Such contractions present dynamic distributions that may engender data misrepresentations within species distribution models. The temporal bias of occurrence data—where occurrences represent distributions before (past bias) or after (recent bias) ARCs—underpins these data misrepresentations. Occurrence-habitat mismatching results when occurrences sampled before contractions are modelled with contemporary anthropogenic variables; niche truncation results when occurrences sampled after contractions are modelled without anthropogenic variables. Our understanding of...

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: 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...

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...

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...

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

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...

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...

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...

A novel catapult mechanism for male spiders to avoid sexual cannibalism

Shichang Zhang, Yangjié Liu, Yubing Ma, Hao Wang, Yao Zhao, Matjaž Kuntner & Daiqin Li
The animal world provides numerous examples of mechanisms that allow for extremely fast actions or reactions via slowly storing energy, typically into elastic structures, that is then nearly instantly released 1-4, similar to the operation of a catapult. While these mechanisms are usually employed for prey capture1, 2 or for predator avoidance3,4, such superfast actions have not been reported as a mechanism to dodge sexual cannibalism. Here, we unveil a novel mechanism in a communal...

A community and functional comparison of coral and reef fish assemblages between four decades of coastal urbanisation and thermal stress.

Katie Cook, Hirotaka Yamagiwa, Maria Beger, Giovanni Masucci, Stuart Ross, Hui Yian Lee, Rick Stuart-Smith & James Reimer
Urbanised coral reefs experience anthropogenic disturbances caused by coastal development, pollution and nutrient runoff, resulting in turbid, marginal conditions in which only certain species can persist. Mortality effects are exacerbated by increasingly regular thermal stress events, leading to shifts towards novel communities dominated by habitat generalists and species with low structural complexity. There is limited data on the turnover processes that occur due to this convergence of anthropogenic stressors, and how novel urban ecosystems are...

The Cenozoic history of palms: Global diversification, biogeography, and the decline of megathermal forests

Jun Ying Lim, Huasheng Huang, Alexander Farnsworth, Daniel Lunt, William Baker, Robert Morley, W. Daniel Kissling & Carina Hoorn
Aim: Megathermal rainforests and mangroves are much smaller in extent today than in the early Cenozoic, primarily due to global cooling and drying trends since the Eocene--Oligocene Transition (~ 34 Ma). The general reduction of these biomes is hypothesized to shape the diversity and biogeographic history of tropical plant clades. However, this has rarely been examined due to a paucity of good fossil records of tropical taxa and the difficulty in assigning them to modern...

Semi‐quantitative metabarcoding reveals how climate shapes arthropod community assembly along elevation gradients on Hawaii Island

Jun Ying Lim, Jairo Patiño, Suzuki Noriyuki, Henrik Krehenwinkel, Luis Simmari, Rosemary Gillespie, Luis Cayetano & Rosemary G. Gillespie
Spatial variation in climatic conditions along elevation gradients provides an important backdrop by which communities assemble and diversify. Lowland habitats tend to be connected through time, whereas highlands can be continuously or periodically isolated, conditions that have been hypothesized to promote high levels of species endemism. This tendency is expected to be accentuated among taxa that show niche conservatism within a given climatic envelope. While species distribution modeling approaches have allowed extensive exploration of niche...

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Affiliations

  • National University of Singapore
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