122 Works

Data from: Genomic data reveals potential for hybridization, introgression, and incomplete lineage sorting to confound phylogenetic relationships in an adaptive radiation of narrow-mouth frogs

Alana Mary Alexander, Yong-Chao Su, Carl Hirang Oliveros, Karen Veronica Olson, Scott Louis Travers & Rafe M. Brown
The microhylid frog genus Kaloula is an adaptive radiation spanning the edge of the Asian mainland and multiple adjacent island archipelagos, with much of the clade's diversity associated with an endemic Philippine radiation. Relationships among clades from the Philippines, however, remain unresolved. With ultraconserved element (UCE) and mitogenomic data, we identified highly-supported differences in topology and areas of poor resolution, for each marker set. Using the UCE data, we then identified possible instances of contemporary...

Data from: The contrasting phylodynamics of human influenza B viruses

Dhanasekaran Vijaykrishna, Edward C. Holmes, Udayan Joseph, Mathieu Fourment, Yvonne C. F. Su, Rebecca Halpin, Raphael T. C. Lee, Yi-Mo Deng, Vithiagaran Gunalan, Xudong Lin, Tim Stockwell, Nadia B. Fedorova, Bin Zhou, Natalie Spirason, Denise K. Kühnert, Veronika Bošková, Tanja Stadler, Anna-Maria Costa, Dominic E. Dwyer, Q. Sue Huang, Lance C. Jennings, William Rawlinson, Sheena G. Sullivan, Aeron C. Hurt, Sebastian Maurer-Stroh … & Raphael TC Lee
A complex interplay of viral, host and ecological factors shape the spatio-temporal incidence and evolution of human influenza viruses. Although considerable attention has been paid to influenza A viruses, a lack of equivalent data means that an integrated evolutionary and epidemiological framework has until now not been available for influenza B viruses, despite their significant disease burden. Through the analysis of over 900 full genomes from an epidemiological collection of more than 26,000 strains from...

Data from: Profile of and risk factors for post-stroke cognitive impairment in diverse ethno-regional groups

Jessica W Lo, John D Crawford, David W Desmond, Olivier Godefroy, Hanna Jokinen, Simin Mahinrad, Hee-Joon Bae, Sebastian Köhler, Elles Douven, Julie Staals, Christopher Chen, Xin Xu, Eddie J Chong, Rufus O Akinyemi, Rajesh N Kalaria, Adesola Ogunniyi, Mélanie Barbay, Martine Roussel, Byung-Chul Lee, Velandai K Srikanth, Christopher Moran, Nagaendran Kandiah, Russell J Chander, Behnam Sabayan, J. Wouter Jukema … & Perminder S Sachdev
OBJECTIVE: To address the variability in prevalence estimates and inconsistencies in potential risk factors for post-stroke cognitive impairment (PSCI) using a standardised approach and individual participant data (IPD) from international cohorts in the STROKOG consortium. METHODS: We harmonised data from thirteen studies based in eight countries. Neuropsychological test scores 2 to 6 months after stroke or TIA and appropriate normative data were used to calculate standardised cognitive domain scores. Domain-specific impairment was based on percentile...

The yellow gene regulates behavioral plasticity by repressing male courtship in Bicyclus anynana butterflies

Yi Ting Ter, Heidi Connahs, Eunice Tan, Emilie Dion, Yuji Matsuoka, Ashley Bear & Antonia Monteiro
Seasonal plasticity in male courtship in Bicyclus anynana butterflies is due to variation in levels of the steroid hormone 20E (20-hydroxyecdysone) during pupation. Wet season (WS) males have high levels of 20E and become active courters. Dry season (DS) males, have lower levels of 20E and reduced courtship rates, although WS courtship rates can be achieved if DS male pupae are injected with 20E at 30% of pupation. Here we investigated the genes involved in...

Data from: Quaternary land bridges have not been universal conduits of gene flow

Emilie Cros, Balaji Chattopadhyay, Kritika M. Garg, Nathaniel Ng, Suzanne Tomassi, Suzan Benedick, David P. Edwards & Frank E. Rheindt
Quaternary climate oscillations are a well-known driver of animal diversification, but their effects are most well studied in areas where glaciations lead to habitat fragmentation. In large areas of the planet, however, glaciations have had the opposite effect, but here their impacts are much less well understood. This is especially true in Southeast Asia, where cyclical changes in land distribution have generated enormous land expansions during glacial periods. In this study, we selected a panel...

Illustrative inpatient blood glucose datasets for QcDM project

Ying Chen, Yilin Ning, Prem Thomas, Mark Salloway, Maudrene Luor Shyuan Tan, E-Shyong Tai, Shih Ling Kao & Chuen Seng Tan
Glucometrics is a set of measures designed to assess whether the blood glucose of patients with diabetes mellitus are effectively managed, and is useful in regular surveillance for adverse events such as hypoglycaemia and hyperglycaemia. To evaluate the quality of glycemic control using glucometrics, routinely collected blood glucose data needs to be consolidated, processed, and analysed in different units of analysis (i.e., patient-sample, patient-day, and patient-stay). Such procedure is challenging without dedicated manpower with specific...

Fear effects and group size interact to shape herbivory on coral reefs

Andrew Bauman, Andrew Hoey, Glenn Dunshea, Jenny Fong, Ian Chan & Peter Todd
1. Fear of predators (‘fear effects’) are an important determinant of foraging decisions by consumers across a range of ecosystems. Group size is one of the main behavioural mechanisms for mitigating fear effects but also provides foraging benefits to group members. Within coral reef ecosystems, fear effects have been shown to influence the feeding rates of herbivorous fishes (i.e. browsers), a key functional group that prevent macroalgal overgrowth. Yet, how fear effects and group size...

Phylogenomic analysis of ultraconserved elements resolves the evolutionary and biogeographic history of Segmented Trapdoor Spiders

Xin Xu, Yong-Chao Su, Simon Y. W. Ho, Matjaž Kuntner, Hirotsugu Ono, Fengxiang Liu, Chia-Chen Chang, Natapot Warrit, Varat Sivayyapram, Khin Pyae Pyae Aung, Dinh Sac Pham, Y. Norma-Rashid & Daiqin Li
The segmented trapdoor spiders (Liphistiidae) are the sole surviving family of the suborder Mesothelae, which forms the sister lineage to all other living spiders. Liphistiids have retained a number of plesiomorphic traits and their present-day distribution is limited to East and Southeast Asia. Studying this group has the potential to shed light on the deep evolutionary history of spiders, but the phylogeny and divergence times of the family have not been resolved with confidence. We...

Crop heterogeneity is positively associated with beneficial insect diversity in subtropical farmlands

Eben Goodale, Tharaka S. Priyadarshana, Myung-Bok Lee, John S. Ascher & Lu Qiu
Increasing crop configurational heterogeneity – smaller crop fields with more field margins – has been repeatedly found to support farmland biodiversity. But research on compositional crop heterogeneity – the number and evenness of crop types – has usually shown only weak effects. However, much of this research has been conducted in large-scale temperate agroecosystems. We examined smallholder subtropical agroecosystems in southern China to assess the effects of crop heterogeneity on beneficial insect biodiversity. In addition...

Discoid decorations function to shield juvenile Argiope spiders from avian predator attacks

Bingjun Wang, Long Yu, Nina Ma, Zengtao Zhang, Qian Liu, Wenrui Fan, Yu Rong, Shichang Zhang & Daiqin Li
Decorating behavior is common in various animal taxa and serves a variety of functions from camouflage to communication. One predominant function cited for decoration is to avoid predators. Conspicuous, disc-like (discoid) silk decorations spun by orb-web Argiope juvenile spiders are hypothesized, among others, to defend spiders against visual predators by concealing spider outlines on the web, deflecting attacks, shielding them from view or masquerading as bird-droppings. However, the direct evidence is limited for a specific...

Target-capture phylogenomics provide insights on gene and species tree discordances in Old World Treefrogs (Anura: Rhacophoridae)

Kin Onn Chan, Carl Hutter, Perry Wood, Lee Grismer & Rafe Brown
Genome-scale data have greatly facilitated the resolution of recalcitrant nodes that Sanger-based datasets have been unable to resolve. However, phylogenomic studies continue to utilize traditional methods such as bootstrapping to estimate branch support; and high bootstrap values are still interpreted as providing strong support for the correct topology. Furthermore, relatively little attention is given to assessing discordances between gene and species trees, and the underlying processes that produce phylogenetic conflict. We generated novel genomic datasets...

Pupal brain transcriptome for Bicyclus anynana

Heidi Connahs, Eunice Tan, Yiting Ter, Emilie Dion, Ashely Bear, Yuji Matsuoka & Antonia Monteiro
Seasonal plasticity in male courtship in Bicyclus anynana butterflies is due to variation in levels of the steroid hormone 20E (20-hydroxyecdysone) during pupation. Wet season (WS) males have high levels of 20E and become active courters. Dry season (DS) males, have lower levels of 20E and reduced courtship rates, although WS courtship rates can be achieved if DS male pupae are injected with 20E at 30% of pupation. Here, we investigated the genes involved in...

Sexual selection on jumping spider colour pattern: investigation with a new quantitative approach

Wei Zhou, Long Yu, Bernetta Z.W. Kwek, Jin Ge, Hua Zeng & Daiqin Li
How animals assess information encoded in individual colour patches have been extensively studied, yet the role of both individual colour patches and gross colour pattern (i.e. the combination of colour patches) remains understudied. We tested the functioning of both individual colour patches and gross colour pattern in sexual selection using the jumping spider Siler semiglaucus as a study system. We first quantified sexual dimorphism in S. semiglaucus in both individual patches and gross colour pattern...

Transgenerational inheritance of learned preferences for novel host plant odors in Bicyclus anynana butterflies

V Gowri, Emilie Dion, Athmaja Viswanath, Florence Monteiro Piel & Antónia Monteiro
Many phytophagous insects have strong preferences for their host plants, which they recognize via odors, making it unclear how novel host preferences develop in the course of insect diversification. Insects may learn to prefer new host plants via exposure to their odors and pass this learned preference to their offspring. We tested this hypothesis by examining larval odor preferences before and after feeding them with leaves coated with control and novel odors and by examining...

Data from: Next-generation freshwater bioassessment: eDNA metabarcoding with a conserved metazoan primer reveals species-rich and reservoir-specific communities

Nicholas K. M. Lim, Ywee Chieh Tay, Amrita Srivathsan, Jonathan W. T. Tan, Jeffrey T. B. Kwik, Bilgenur Baloğlu, Rudolf Meier & Darren C. J. Yeo
Freshwater habitats are of high conservation value and provide a wide range of ecosystem services. Effective management requires regular monitoring. However, conventional methods based on direct observation or specimen collection are so invasive, expensive and labour-intensive that frequent monitoring is uncommon. Here, we test whether the evaluation of environmental DNA (eDNA) from water based on a simple protocol can be used for assessing biodiversity. We use universal metazoan primers for characterizing water eDNA across horizontal...

Data from: Degenerate adaptor sequences for detecting PCR duplicates in reduced representation sequencing data improve genotype calling accuracy

Mandy M. Y. Tin, Frank E. Rheindt, Emilie Cros & Alexander S. Mikheyev
RAD-tag is a powerful tool for high-throughput genotyping. It relies on PCR amplification of the starting material, following enzymatic digestion and sequencing adaptor ligation. Amplification introduces duplicate reads into the data, which arise from the same template molecule and are statistically nonindependent, potentially introducing errors into genotype calling. In shotgun sequencing, data duplicates are removed by filtering reads starting at the same position in the alignment. However, restriction enzymes target specific locations within the genome,...

Data from: Beyond the Coral Triangle: high genetic diversity and near panmixia in Singapore's populations of the broadcast spawning sea star Protoreaster nodosus

Ywee Chieh Tay, Michelle W.P. Chng, W. W. Genevieve Sew, Frank E. Rheindt, Karenne P.P. Tun, Rudolf Meier & M. W. P. Chng
The Coral Triangle is widely considered the most important centre of marine biodiversity in Asia while areas on its periphery such as the South China Sea, have received much less interest. Here, we demonstrate that a small population of the knobbly sea star Protoreaster nodosus in Singapore has similarly high levels of genetic diversity as comparable Indonesian populations from the Coral Triangle. The high genetic diversity of this population is remarkable because it is maintained...

Data from: Adaptation of brain functional and structural networks in aging

Annie Lee, Nagulan Ratnarajah, Ta Anh Tuan, Shen-Hsing Annabel Chen & Anqi Qiu
The human brain, especially the prefrontal cortex (PFC), is functionally and anatomically reorganized in order to adapt to neuronal challenges in aging. This study employed structural MRI, resting-state fMRI (rs-fMRI), and high angular resolution diffusion imaging (HARDI), and examined the functional and structural reorganization of the PFC in aging using a Chinese sample of 173 subjects aged from 21 years and above. We found age-related increases in the structural connectivity between the PFC and posterior...

Data from: Environmental gradients and the evolution of successional habitat specialization: a test case with 14 Neotropical forest sites

Susan G. Letcher, Jesse R. Lasky, Robin L. Chazdon, Natalia Norden, S. Joseph Wright, Jorge A. Meave, Eduardo A. Pérez-García, Rodrigo Muñoz, Eunice Romero-Pérez, Ana Andrade, José Luis Andrade, Patricia Balvanera, Justin M. Becknell, Tony V. Bentos, Radika Bhaskar, Frans Bongers, Vanessa Boukili, Pedro H. S. Brancalion, Ricardo G. César, Deborah A. Clark, David B. Clark, Dylan Craven, Alexander DeFrancesco, Juan M. Dupuy, Bryan Finegan … & G. Bruce Williamson
1. Successional gradients are ubiquitous in nature, yet few studies have systematically examined the evolutionary origins of taxa that specialize at different successional stages. Here we quantify successional habitat specialization in Neotropical forest trees and evaluate its evolutionary lability along a precipitation gradient. Theoretically, successional habitat specialization should be more evolutionarily conserved in wet forests than in dry forests due to more extreme microenvironmental differentiation between early and late successional stages in wet forest. 2....

Data from: Soil nutrients and dispersal limitation shape compositional variation in secondary tropical forests across multiple scales

Michiel Van Breugel, Dylan Craven, Hao Ran Lai, Mario Bailon, Benjamin L. Turner, Jefferson S. Hall & Mario Baillon
1. Soil resource partitioning and dispersal limitation have been shown to shape the tree community structure of mature tropical forests, but are poorly studied in the context of forest succession. We examined the relative contributions of both ecological processes to the variation in the species composition of young tropical secondary forests at different spatial scales, and if the relative importance of these two ecological processes changed during succession. At the species level, we examined if...

Data from: Plio-Pleistocene phylogeography of the Southeast Asian Blue Panchax killifish, Aplocheilus panchax

Samantha V. Beck, Gary R. Carvalho, Axel Barlow, Lukas Rüber, Heok Hui Tan, Estu Nugroho, Daisy Wowor, Siti Azizah Mohd Nor, Fabian Herder, Zainal A. Muchlisin & Mark De Bruyn
The complex climatic and geological history of Southeast Asia has shaped this region’s high biodiversity. In particular, sea level fluctuations associated with repeated glacial cycles during the Pleistocene both facilitated, and limited, connectivity between populations. In this study, we used data from two mitochondrial and three anonymous nuclear markers to determine whether a fresh/brackish water killifish, Aplocheilus panchax, Hamilton, 1822, could be used to further understand how climatic oscillations and associated sea level fluctuations have...

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, David C. Blackburn, Rafe M. Brown, David P. Bickford, Arvin C. Diesmos & Djoko T. Iskandar
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...

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Resource Types

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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