122 Works

Data from: Analysis of protein phosphorylation in nerve terminal reveals extensive changes in active zone proteins upon exocytosis

Mahdokht Kohansal-Nodehi, John J. E. Chua, Henning Urlaub, Reinhard Jahn, Dominika Czernik & John JE Chua
Neurotransmitter release is mediated by the fast, calcium-triggered fusion of synaptic vesicles with the presynaptic plasma membrane, followed by endocytosis and recycling of the membrane of synaptic vesicles. While many of the proteins governing these processes are known, their regulation is only beginning to be understood. Here we have applied quantitative phosphoproteomics to identify changes in phosphorylation status of presynaptic proteins in resting and stimulated nerve terminals isolated from the brains of Wistar rats. Using...

Data from: Conserving evolutionary history does not result in greater diversity over geological timescales

Juan Cantalapiedra, Tracy Aze, Marc Cadotte, Giulio Valentino Dalla Riva, Danwei Huang, Florent Mazel, Matthew Pennell, María Ríos & Arne Mooers
Alternative prioritization strategies have been proposed to safeguard biodiversity over macro-evolutionary timescales. The first prioritizes the most distantly related species (maximizing phylogenetic diversity) in the hopes of capturing at least some lineages that will successfully diversify into the future. The second prioritizes lineages that are currently speciating, in the hopes that successful lineages will continue to generate species into the future. These contrasting schemes also map onto contrasting predictions about the role of slow diversifiers...

Data from: Distal-less activates butterfly eyespots consistent with a reaction diffusion process

Heidi Connahs, Sham Tlili, Jelle Van Creij, Tricia Y. J. Loo, Tirtha Das Banerjee, Timothy E Saunders & Antonia Monteiro
Eyespots on the wings of nymphalid butterflies represent colorful examples of pattern formation, yet the developmental origins and mechanisms underlying eyespot center differentiation are still poorly understood. Using CRISPR-Cas9 we re-examine the function of Distal-less (Dll) as an activator or repressor of eyespots, a topic that remains controversial. We show that the phenotypic outcome of CRISPR mutations depends upon which specific exon is targeted. In Bicyclus anynana, exon 2 mutations are associated with both missing...

Genetic structures across a biogeographical barrier reflect dispersal potential of four Southeast Asian mangrove plant species

Alison Wee, Annika Noreen, Junya Ono, Koji Takayama, Prakash Kumar, Hugh Tan, Mohd Saleh, Tadashi Kajita, Edward Webb, Alison K. S. Wee, Annika M. E. Noreen, Prakash P. Kumar, Hugh T. W. Tan, Mohd N. Saleh & Edward L. Webb
Aim Biogeographic barriers restrict the movement of individuals, resulting in population divergence, genetic differentiation, endemism and speciation. Yet, some barriers demonstrate unequal effect across species depending on species dispersal, which manifests in varying genetic structure. We test the hypotheses that the genetic structure of four coastal mangrove species would reflect differences in dispersal potential across the Malay Peninsula, a major biogeographic barrier in the Indo-West Pacific region. Location Twelve sites from the east and west...

Data from: Dung beetle-megafauna trophic networks in Singapore’s fragmented forests

Xin Rui Ong, Eleanor M. Slade & Matthew L. M. Lim
We investigated trophic networks between dung beetles and megafauna species in five forest fragments in Singapore varying in size and isolation. We found that Singapore’s dung beetle communities were attracted to extant and extinct dung types from different dietary groups. All forest fragment networks were similar, and displayed high generalism and high nestedness.

The different fates of two Asian horseshoe crab species with different dispersal abilities

Qian Tang, Prashant Shingate, Yusli Wardiatno, Akbar John, Boon Hui Tay, Ywee Chieh Tay, Laura-Marie Yap, Jasmin Lim, Hor Yee Tong, Karenne Tun, Byrappa Venkatesh & Frank E. Rheindt
Impending anthropogenic climate change will severely impact coastal organisms at unprecedented speed. Knowledge on organisms’ evolutionary responses to past sea level fluctuations and estimation of their evolutionary potential is therefore indispensable in efforts to mitigate the effects of future climate change. We sampled tens of thousands of genomic markers of ~300 individuals in two of the four extant horseshoe crab species across the complex archipelagic Singapore Straits. Carcinoscorpius rotundicauda Latreille, a less mobile mangrove species,...

Longer is not always better: optimizing barcode length for large-scale species discovery and identification

Darren Yeo, Rudolf Meier & Amrita Srivathsan
New techniques for the species-level sorting of millions of specimens are needed in order to accelerate species discovery, determine how many species live on earth, and develop efficient biomonitoring techniques. These sorting methods should be reliable, scalable and cost-effective, as well as being largely insensitive to low-quality genomic DNA, given that this is usually all that can be obtained from museum specimens. Mini-barcodes seem to satisfy these criteria, but it is unclear how well they...

What’s in a band? The function of the colour and banding pattern of the Banded Swallowtail

Eunice Tan, Bodo Wilts, Brent Tan & Antonia Monteiro
Butterflies have evolved a diversity of colour patterns, but the ecological functions for most of these patterns are still poorly understood. The Banded Swallowtail butterfly, Papilio demolion demolion, is a mostly black butterfly with a greenish-blue band that traverses the wings. The function of this wing pattern remains unknown. Here, we examined the morphology of black and green-blue coloured scales, and how the colour and banding pattern affects predation risk in the wild. The protective...

Genome-wide markers redeem the lost identity of a heavily managed gamebird

Qian Tang, Giovanni Forcina, Qian Tang, Emilie Cros, Monica Guerrini, Frank Rheindt & Filippo Barbanera
Heavily managed wildlife may suffer from genetic homogenisation and reshuffling of locally adapted genotypes with non-native ones. This phenomenon often affects natural populations by reducing their evolutionary potential and speeding up the ongoing biodiversity crisis. For decades, the red-legged partridge (Alectoris rufa), an intensively managed gamebird of conservation concern and considerable socio-economic importance, has been subjected to extensive releases of farm-reared hybrids with the chukar partridge (A. chukar) and translocations irrespective of subspecific affinity. These...

Detritus decorations as the extended phenotype deflect avian predator attack increasing fitness in an orb‐web spider

Nina Ma, Long Yu, Deyong Gong, Zeyuan Hua, Hua Zeng, Luyao Chen, Aijia Mao, Zhizhao Chen, Ruxing Cai, Yubing Ma, Zengtao Zhang, DQ Li, Jing Luo & Shichang Zhang
A number of strategies that divert attacks of visually guided predators, such as birds, have evolved multiple times in animals. Detritus web decorations built by certain orb-web spider species are thought to deflect avian predator attacks away from spiders and towards their web decorations. Still, empirical evidence for this function and its adaptive significance is lacking. The orb-web spider, Cyclosa monticola, adorns its web using a linear detritus decoration consisting of moults, egg sacs, prey...

Data from: Evolution and biogeography of Memecylon

Prabha Amarasinghe, Sneha Joshi, Navendu Page, Lahiru S. Wijedasa, Mary Merello, Hashendra Kathriarachchi, Robert Douglas Stone, Walter Judd, Ullasa Kodandaramaiah & Nico Cellinese
Premise The woody plant group Memecylon (Melastomataceae) is a large clade occupying diverse forest habitats in the Old World tropics and exhibiting high regional endemism. Its phylogenetic relationships have been previously studied using ribosomal DNA with extensive sampling from Africa and Madagascar. However, divergence times, biogeography, and character evolution of Memecylon remain uninvestigated. We present a phylogenomic analysis of Memecylon to provide a broad evolutionary perspective of this clade. Methods One hundred supercontigs of 67...

Data from: Impacts of habitat on butterfly dispersal in tropical forests, parks and grassland patches embedded in an urban landscape

Anuj Jain, Simon Kee Mun Chan, Petr Vlasanek & Edward Layman Webb
Dispersal distances of 17 species of butterflies in tropical Singapore were significantly greater in forest than in urban habitat. Butterflies in urban plots frequently moved within suitable habitat (park/grassland) patches but rarely crossed non-habitat patches suggesting potential isolation and a need for urban corridors.

Data from: Tolerability and efficacy of long-term medical therapy in primary aldosteronism

Fengjie Tang, Lih M Loh, Roger S Foo, Wann J Loh, Dawn ST Lim, Meifen Zhang, Pei T Tan, Lynette Lee, Du S Swee, Joan Khoo, Donovan Tay, Eberta Tan, Shui B Soh, Ling Zhu, Sarah Y Tan, Peng C Kek & Troy Hai Puar
Introduction: Patients with primary aldosteronism (PA) have increased cardiovascular risk and studies have found that medical therapy fails to ameliorate this. This may be due to side effects and limited efficacy of medications at tolerable doses. Methods: We conducted a retrospective study on 201 patients with PA treated with medical therapy (spironolactone, eplerenone or amiloride) for PA from 2000-2020 at two tertiary centres. Patients were assessed for efficacy to achieve clinical and biochemical control, and...

Gene flow increases phylogenetic structure and inflates cryptic species estimations: a case study on widespread Philippine puddle frogs (Occidozyga laevis)

Kin Onn Chan
In cryptic amphibian complexes, there is a growing trend to equate high levels of genetic structure with hidden cryptic species diversity. Typically, phylogenetic structure and distance-based approaches are used to demonstrate the distinctness of clades and justify the recognition of new cryptic species. However, this approach does not account for gene flow, spatial, and environmental processes that can obfuscate phylogenetic inference and bias species delimitation. As a case study, we sequenced genome-wide exons and introns...

Data from: Leaf litter decomposition in tropical freshwater swamp forests is slower in swamp than non-swamp conditions

Weng Ngai Lam, Jun Jie Lian, Pin Jia Chan, Ying Ying Ting, Rie Chong, Nur Estya Rahman, Lorraine Tan, Qian Yi Ho, Sorain Ramchunder, Kelvin Peh, Yixiong Cai & Kwek Yan Chong
Decomposition is a key ecosystem function, and the rate of decomposition in forests affects their carbon storage potentials. Processes and factors determining leaf litter decomposition rates in dry-land and temperate forests are well understood, but these are generally poorly studied in tropical wetland forests, especially freshwater swamp forests (FSF). The home-field advantage (HFA) hypothesis predicts that soil microbes specialize in decomposing leaf litter produced by the tree species in their immediate vicinity. However, empirical support...

Untangling the molecular basis of coral response to sedimentation

Elena Bollati
Urbanized coral reefs are often chronically affected by sedimentation and reduced light levels, yet many species of corals appear to be able to thrive under these highly disturbed conditions. Recently, these marginal ecosystems have gained attention as potential climate change refugia due to the shading effect of suspended sediment, as well as potential reservoirs for stress-tolerant species. However, little research exists on the impact of sedimentation on coral physiology, particularly at the molecular level. Here,...

Post‐agriculture rain forest succession on a tropical Pacific island

Edward L. Webb, Avele Iofi Lalogafu’afu’a, Martin Van De Bult, Wei Kit Lee, Siaifoi Fa'aumu, Muhammad Izuddin, Mark A. MacDonald, Roger Meyer, Rachel Rui Ying Oh, Alden P. Tagarino, Rachel C. Webb, Adam C. Miles & Martin Bult
We surveyed the tree and seedling community in 34 vegetation plots in mature and >50 y old secondary lowland rain forest on the Polynesian island of Tutuila, American Samoa. The main data set includes original data from the tree surveys as well as all repeat surveys of seedling plots. We also include all R code and data sets used in analyses, including soil and environmental data, species by plot matrices for NMDS, and processed data...

Data from: Episodic radiations in the fly tree of life

Brian M. Wiegmann, Michelle D. Trautwein, Isaac S. Winkler, Norman B. Barr, Jung-Wook Kim, Christine Lambkin, Matthew A. Bertone, Brian K. Cassel, Keith M. Bayless, Alysha M. Heimberg, Benjamin M. Wheeler, Kevin J. Peterson, Thomas Pape, Bradley J. Sinclair, Jeffrey H. Skevington, Vladimir Blagoderov, Jason Caravas, Sujatha Narayanan Kutty, Urs Schmidt-Ott, Gail E. Kampmeier, F. Christian Thompson, David A. Grimaldi, Andrew T. Beckenbach, Gregory W. Courtney, Markus Friedrich … & J.-W. Kim
Flies are one of four superradiations of insects (along with beetles, wasps, and moths) that account for the majority of animal life on Earth. Diptera includes species known for their ubiquity (Musca domestica house fly), their role as pests (Anopheles gambiae malaria mosquito), and their value as model organisms across the biological sciences (Drosophila melanogaster). A resolved phylogeny for flies provides a framework for genomic, developmental, and evolutionary studies by facilitating comparisons across model organisms,...

Data from: Transcriptome-wide differential gene expression in Bicyclus anynana butterflies: female vision-related genes are more plastic

Aide Macias-Muñoz, Gilbert Smith, Antónia Monteiro & Adriana D. Briscoe
cave-adapted species down-regulate the expression of vision genes or even lose their eyes and associated eye genes entirely. Alternatively, organisms that live in fluctuating environments, with different requirements for vision at different times, may evolve phenotypic plasticity for expression of vision genes. Here we use a global transcriptomic and candidate gene approach to compare gene expression in the heads of a polyphenic butterfly. Bicyclus anynana have two seasonal forms that display sexual dimorphism and plasticity...

Data from: Accurate predictions of coexistence in natural systems require the inclusion of facilitative interactions and environmental dependency

Malyon D. Bimler, Daniel B. Stouffer, Hao Ran Lai & Margaret M. Mayfield
1. Coexistence between plant species is well known to depend on the outcomes of species interactions within an environmental context. The incorporation of environmental variation into empirical studies of coexistence are rare, however, due to the complex experiments needed to do so and the lack of feasible modelling approaches for determining how environmental factors alter specific coexistence mechanisms. 2. In this paper, we present a simple modelling framework for assessing how variation in species interactions...

Data from: The N-end Rule Pathway and Ubr1 enforce protein compartmentalization via P2-encoded cellular location signals

Anthony Tran
The Arg/N-end Rule Pathway and Ubr1, an E3 ligase conserved from yeast to humans, is involved in the degradation of misfolded proteins in the cytosol. However, the root physiological purpose of this activity is not completely understood. Through a systematic examination of single residue P2-position mutants of misfolded proteins, and global and targeted bioinformatic analyses of the yeast proteome, we determined that Ubr1 preferentially targets mistranslocated secretory and mitochondrial proteins in the cytosol. Degradation by...

Data from: Social structure of the harem-forming promiscuous fruit bat, Cynopterus sphinx, is the harem truly important?

Kritika M. Garg, Balaji Chattopadhyay & Uma Ramakrishnan
Bats are social animals and display a diverse variety of mating and social systems, with most species exhibiting some form of polygyny. Their social organization is fluid and individuals frequently switch partners and roosting sites. While harem-like social organization is observed in multiple tropical species, its importance is contested in many of them. In this study, we investigated the role of harems in the social organization of the old world fruit bat Cynopterus sphinx. Based...

Data from: Dipteran larvae and microbes facilitate nutrient sequestration in the Nepenthes gracilis pitcher plant host

Weng Ngai Lam, Kwek Yan Chong, Ganesh S. Anand & Hugh Tiang Wah Tan
The fluid-containing traps of Nepenthes carnivorous pitcher plants (Nepenthaceae) are often inhabited by organisms known as inquilines. Dipteran larvae are key components of such communities and are thought to facilitate pitcher nitrogen sequestration by converting prey protein into inorganic nitrogen, although this has never been demonstrated in Nepenthes. Pitcher fluids are also inhabited by microbes, although the relationship(s) between these and the plant is still unclear. In this study, we examined the hypothesis of digestive...

Data from: Evolution of the assassin’s arms: insights from a phylogeny of combined transcriptomic and ribosomal DNA data (Heteroptera: Reduvioidea)

Junxia Zhang, Eric R. L. Gordon, Michael Forthman, Wei Song Hwang, Kim Walden, Daniel R. Swanson, Kevin P. Johnson, Rudolf Meier & Christiane Weirauch
Assassin bugs (Reduvioidea) are one of the most diverse (>7,000 spp.) lineages of predatory animals and have evolved an astounding diversity of raptorial leg modifications for handling prey. The evolution of these modifications is not well understood due to the lack of a robust phylogeny, especially at deeper nodes. We here utilize refined data from transcriptomes (370 loci) to stabilize the backbone phylogeny of Reduvioidea, revealing the position of major clades (e.g., the Chagas disease...

Data from: Climate warming and the potential extinction of fig wasps, the obligate pollinators of figs

Alexander G. R. Goh, Richard T. Corlett & Nanthinee Jevanandam
Figs (Ficus) have a reciprocally obligate mutualism with tiny, short-lived (1–2 days) fig wasps (Agaonidae). The small size and short life of these pollinators is expected to make them more vulnerable to climate change than their larger and longer-lived hosts. We experimentally tested the thermal tolerances of four species of adult female fig wasps from equatorial Singapore. The results suggest that an increase of ≥ 3oC above the current temperatures experienced across much of the...

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