96 Works

Fossil microbodies are melanosomes: evaluating and rejecting the ‘fossilised decay-associated microbes’ hypothesis

Arindam Roy, Christopher Rogers, Thomas Clements, Michael Pittman, Olivier Habimana, Martin Peter & Jakob Vinther
Melanosomes are membrane-bound organelles of varying geometry, commonly found within a range of vertebrate tissues, that contain the pigment melanin. Melanosomes have been identified in the fossil record in many exceptionally preserved fossils allowing reconstructions of the coloration of many extinct animals. However, these microstructures have also been interpreted as “microbial cells” or melanin producing bacteria based on their geometric similarities to melanosomes. Here we test these two conflicting hypotheses experimentally. Our results demonstrate multiple...

Data from: Comparative genomics of Methicillin-resistant Staphylococcus aureus ST239: distinct geographical variants in Beijing and Hong Kong

Zheng Wang, Haokui Zhou, Hui Wang, Hongbin Chen, K. K. Leung, Stephen Tsui & Margaret Ip
Background: The ST239 lineage is a globally disseminated, multiply drug-resistant hospital-associated methicillin-resistant Staphylococcus aureus (HA-MRSA). We performed whole-genome sequencing of representative HA-MRSA isolates of the ST239 lineage from bacteremic patients in hospitals in Hong Kong (HK) and Beijing (BJ) and compared them with three published complete genomes of ST239, namely T0131, TW20 and JKD6008. Orthologous gene group (OGG) analyses of the Hong Kong and Beijing cluster strains were also undertaken. Results: Homology analysis, based on...

Data from: Sign epistasis limits evolutionary trade-offs at the confluence of single- and multi-carbon metabolism in Methylobacterium extorquens AM1

Sean Michael Carroll, Ming-Chun Lee & Christopher James Marx
Adaptation of one set of traits is often accompanied by attenuation of traits important in other selective environments, leading to fitness trade-offs. The mechanisms that either promote or prevent the emergence of trade-offs remain largely unknown, and are difficult to discern in most systems. Here, we investigate the basis of trade-offs that emerged during experimental evolution of Methylobacterium extorquens AM1 to distinct growth substrates. After 1500 generations of adaptation to a multi-carbon substrate, succinate (S),...

Data from: Economic costs and health-related quality of life for hand, foot and mouth disease (HFMD) patients in China

Yaming Zheng, Mark Jit, Joseph T. Wu, Juan Yang, Kathy Leung, Qiaohong Liao & Hongjie Yu
Background: Hand, foot and mouth disease (HFMD) is a common illness in China that mainly affects infants and children. The objective of this study is to assess the economic cost and health-related quality of life associated with HFMD in China. Method: A telephone survey of caregivers were conducted in 31 provinces across China. Caregivers of laboratory-confirmed HFMD patients who were registered in the national HFMD enhanced surveillance database during 2012-2013 were invited to participate in...

Data from: Biotic and abiotic variables influencing plant litter breakdown in streams: a global study

Luz Boyero, Richard Pearson, Cang Hui, Mark Gessner, Javier Perez, Markos Alexandrou, Manuel Graça, Bradley Cardinale, Ricardo Albariño, M. Arunachalam, Leon Barmuta, Andrew Boulton, Andreas Bruder, Marcos Callisto, Eric Chauvet, Russell Death, David Dudgeon, Andrea Encalada, Veronica Ferreira, Ricardo Figueroa, Alex Flecker, , Julie Helson, Tomoya Iwata, Tajang Jinggut … & Catherine Yule
Plant litter breakdown is a key ecological process in terrestrial and freshwater ecosystems. Streams and rivers, in particular, have high rates of carbon dioxide evasion and they contribute substantially to global carbon fluxes. However, there is little information available on the relative roles of different drivers of plant litter breakdown in fresh waters, particularly at large scales. We present a global-scale study of litter breakdown in streams to compare the roles of biotic, climatic and...

Data from: Assessing current genetic status of the Hainan gibbon using historical and demographic baselines: implications for conservation management of species of extreme rarity

Jessica V. Bryant, Dada Gottelli, Xinyuan Zeng, Xiaojiang Hong, Bosco P.L. Chan, John R. Fellowes, Ya-Ping Zhang, Jing Luo, Christopher Durrant, Thomas Geissmann, Helen J. Chatterjee & Samuel T. Turvey
Evidence-based conservation planning is crucial for informing management decisions for species of extreme rarity, but collection of robust data on genetic status or other parameters can be extremely challenging for such species. The Hainan gibbon, possibly the world's rarest mammal, consists of a single population of ~25 individuals restricted to one protected area on Hainan Island, China, and has persisted for over 30 years at exceptionally low population size. Analysis of genotypes at 11 microsatellite...

Data from: Deep-sea benthic ostracodes from multiple core and epibenthic sledge samples in Icelandic waters

Moriaki Yasuhara, Maria Grimm, Simone N. Brandão, Anna Jöst, Hisayo Okahashi, Hokuto Iwatani, Alexandra Ostmann & Pedro Martínez Arbizu
Deep-sea benthic Ostracoda (Crustacea) in Icelandic waters are poorly known. Here we report deep-sea ostracode assemblages from the multiple core (MUC) and the epibenthic sledge (EBS) samples collected from Icelandic waters by the first cruise of the IceAGE (Icelandic Marine Animals: Genetics and Ecology) project. Samples from shelf-edge and lower-bathyal working areas are examined. The results show (1) distinct MUC and EBS faunas due to the large difference in mesh size of MUC and EBS;...

Data from: Risky business: linking Toxoplasma gondii infection and entrepreneurship behaviours across individuals and countries

Stefanie K. Johnson, Fitza A. Markus, Daniel A. Lerher, Dana M. Calhoun, Marissa A. Beldon, Elsa T. Chan & Pieter T. J. Johnson
Disciplines such as business and economics often rely on the assumption of rationality when explaining complex human behaviours. However, growing evidence suggests that behaviour may concurrently be influenced by infec- tious microorganisms. The protozoan, Toxoplasma gondii, infects an estimated 2 billion people worldwide and has been linked to behavioural alterations in humans and other vertebrates. Here we integrate primary data from college students and business professionals with national-level information on cultural attitudes toward business to...

Respiratory virus shedding in exhaled breath and efficacy of face masks

Nancy H. L. Leung, Daniel K. W. Chu, Eunice Y. C. Shiu, Kwok-Hung Chan, James J. McDevitt, Benien J. P. Hau, Hui-Ling Yen, Yuguo Li, Dennis K. M. Ip, J. S. Malik Peiris, Wing-Hong Seto, Gabriel M. Leung, Donald K. Milton & Benjamin J. Cowling
We identified seasonal human coronaviruses, influenza viruses and rhinoviruses in the exhaled breath and coughs of children and adults with acute respiratory illness. Surgical face masks significantly reduced detection of influenza virus RNA in respiratory droplets and coronavirus RNA in aerosols, with a marginally significant reduction in coronavirus RNA in respiratory droplets. Our results indicate that surgical facemasks could prevent transmission of human coronaviruses and influenza viruses from symptomatic individuals.

Wood decomposition data from an experiment in Malaysian Borneo, 2015-2018

S.J. Law, L. Ashton, H. Griffiths, P. Eggleton & C. Parr
This dataset measures the decomposition of experimental wood blocks, Pinus radiata, over a period of one year in lowland, old growth, tropical rainforest. Wood blocks are placed on the ground or suspended above the ground in mesh bags that either allow or prevent entry of macro-invertebrates. The decomposition of ground placed wood blocks is measured during a period of drought and non-drought. Dry weight of wood blocks is measured at the start and end of...

Do heterogeneous seascapes of carbonate conditions across biogeographic breaks influence divergent phenotypic plasticity in natural populations?

Marco Lardies, Araceli Rodriguez-Romero, Tania Opitz, Juan Gaitan-Espitia & Lardies Lardies
Aim: Understanding how environmental variability influences stress tolerance, local adaptation, and phenotypic variation among populations is a key challenge for evolutionary ecology and climate change biology. Coastal biogeographic breaks are natural laboratories to explore this fundamental research question due to the contrasting environmental conditions experienced by natural populations across these regions. Location: In the South East Pacific (SEP) coast a major break (30º-32ºS) is characterized by extreme natural variability in seawater carbonate chemistry parameters related...

Data from: Phylogenomic analyses reveal convergent patterns of adaptive evolution in elephant and human ancestries

Morris Goodman, Kirstin N. Sterner, M. Munirul Islam, Monica Uddin, Chet C. Sherwood, Patrick R. Hof, Zhuo-Cheng Hou, Leonard Lipovich, Hui Jia, Lawrence I. Grossman, Derek E. Wildman, M. Islam & Z. C. Hou
Specific sets of brain-expressed genes, such as aerobic energy metabolism genes, evolved adaptively in the ancestry of humans and may have evolved adaptively in the ancestry of other large-brained mammals. The recent addition of genomes from two afrotherians (elephant and tenrec) to the expanding set of publically available sequenced mammalian genomes provided an opportunity to test this hypothesis. Elephants resemble humans by having large brains and long life spans; tenrecs, in contrast, have small brains...

Data from: The ‘Oxycythereis’ problem: taxonomy and palaeobiogeography of deep-sea ostracod genera Pennyella and Rugocythereis

Moriaki Yasuhara, Gene Hunt, Hisayo Okahashi & Simone N. Brandão
Systematic revision of the globally distributed deep-sea ostracod genera Pennyella Neale, 1974 and Rugocythereis Dingle, Lord and Boomer, 1990, which have been considered to correspond, at least partially, to nomen nudum but widely used genus name ‘Oxycythereis,’ was conducted to reduce taxonomic uncertainty of these important components of the Modern and fossil deep-sea ostracod community. Approximately 100 specimens from 18 species were examined, ranging in age from the Cretaceous to the present day. Nine new...

Data from: Influences of climate and historical land connectivity on ant beta diversity in East Asia

Patricia H. Wepfer, Benoit Guénard & Evan P. Economo
Aim Biodiversity patterns reflect both ecological and evolutionary processes interacting with geographical variation in climate and the current and historical connectivity between land areas. We sought to disentangle these effects in explaining the organization of ant diversity across geographical areas and islands in East Asia. Location The Japanese Archipelago including the Ryukyu and Ogasawara Islands, Taiwan and coastal continental regions of Korea, China and Russia. Methods We aggregated species occurrence records from published literature, specimen...

Data from: Multichannel feeding by spider functional groups is driven by feeding strategies and resource availability

Matthew J. Perkins, Richard Inger, Stuart Bearhop & Dirk Sanders
Multichannel feeding, whereby consumers feed across resource channels such as upon herbivore and detritivore resources, acts to link discrete compartments of a food web with implications for ecosystem functioning and stability. Currently however, we have little understanding which feeding strategies of consumers underlie multichannel feeding. We therefore link spider functional group and resource density-dependent or density-independent feeding strategies to multichannel feeding by quantifying not only consumer diet, but also the relative availability of resources. Here...

Data from: Ecophysiological variation across a forest-ecotone gradient produces divergent climate change vulnerability within species

Félix Landry Yuan, Adam H. Freedman, Laurent Chirio, Matthew LeBreton & Timothy C. Bonebrake
Climate change related risks and impacts on ectotherms will be mediated by habitats and their influence on local thermal environments. While many studies have documented morphological and genetic aspects of niche divergence across habitats, few have examined thermal performance across such gradients and directly linked this variation to contemporary climate change impacts. In this study, we quantified variation in thermal performance across a gradient from forest to gallery forest-savanna mosaic in Cameroon for a skink...

Data from: Individual correlates of infectivity of influenza A virus infections in households

Tim Tsang, Vicky Fang, Kwok-Hung Chan, Dennis Ip, Gabriel Leung, J. S. Peiris, Benjamin Cowling, Simon Cauchemez, Tim K. Tsang, Vicky J. Fang, Dennis K. M. Ip, Gabriel M. Leung, J. S. Malik Peiris & Benjamin J. Cowling
Background: Identifying individual correlates of infectivity of influenza virus is important for disease control and prevention. Viral shedding is used as a proxy measure of infectivity in many studies. However, the evidence for this is limited. Methods: In a detailed study of influenza virus transmission within households in 2008–12, we recruited index cases with confirmed influenza infection from outpatient clinics, and followed up their household contacts for 7–10 days to identify secondary infections. We used...

Data from: The global antigenic diversity of swine influenza A viruses

Nicola S. Lewis, Colin A. Russell, Tavis K. Anderson, Kathryn Berger, David F. Burke, Judith M. Fonville, Ronald A.M. Fouchier, Paul Kellam, Bjorn F. Koel, Tung Nguyen, Bundit Nuansrichy, J. S. Malik Peiris, Takehiko Saito, Gaelle Simon, Eugene Skepner, Nobuhiro Takemae, ESNIP3 Consortium, Richard J. Webby, Kristien Van Reeth, Sharon M. Brookes, Lars Larsen, Ian H. Brown, Amy L. Vincent, Pinky Langat, Filip Bielejec … & JS Malik Peiris
Swine influenza presents a substantial disease burden for pig populations worldwide and poses a potential pandemic threat to humans. There is considerable diversity in both H1 and H3 influenza viruses circulating in swine due to the frequent introductions of viruses from humans and birds coupled with geographic segregation of global swine populations. Much of this diversity is characterized genetically but the antigenic diversity of these viruses is poorly understood. Critically, the antigenic diversity shapes the...

Data from: Omnivorous ants are less carnivorous and more protein-limited in exotic plantations

Toby Pak Nok Tsang, Benoit Guénard & Timothy Carlton Bonebrake
1. Diets of species are crucial in determining how they influence food webs and community structures, and how their populations are regulated by different bottom-up processes. Omnivores are able to adjust their diet flexibly according to environmental conditions, such that their impacts on food webs and communities, and the macronutrients constraining their population, can be plastic. In particular, omnivore diets are known to be influenced by prey availability, which exhibit high spatial and temporal variation....

Activity niches outperform thermal physiological limits in predicting global ant distributions

Fengyi Guo, Benoit Guénard, Evan Economo, Curtis Deutsch & Timothy Bonebrake
Aim: Thermal physiology is commonly used in mechanistic models to predict species distributions and project distribution change. Such thermal constraints for ants are often measured under laboratory conditions as critical thermal limits (CTmax and CTmin), but have also been observed in the field as foraging thermal limits (FTmin and FTmax). Here we compared distribution projections based on ant physiological and behavioural thermal limits with their realized distributions to assess the validity of using ecophysiological models...

Data from: Alien species richness is currently unbounded in all but the most urbanized bird communities

Toby P. Tsang, Ellie E. Dyer & Tim C. Bonebrake
Urban areas suffer high pressure of introductions of alien species compared to other habitats due to intensive human activities. As trading globally continues to rise, more species will likely be introduced into urban areas. To determine whether this increase in introduction pressure will lead to increased alien species richness in urban areas, or whether other processes would act to impose an upper limit on species richness, we examined how the shape of the relationship between...

Predator presence and recent climatic warming raise body temperatures of island lizards

Felix Landry Yuan
In ectothermic predator-prey relationships, evasion of predation by prey depends on physiological and behavioural responses relating to the thermal biology of both predator and prey. On Japan’s Izu Islands, we investigated a prey lizard’s physiological and thermal responses to the presence of a snake predator over geologic time in addition to recent climatic warming. Foraging lizard body temperatures increased by 1.0°C from 1981 to 2019 overall, yet were 2.9°C warmer on snake islands relative to...

Fluorescence‐based detection of field targets using an autonomous unmanned aerial vehicle system

Thomas G Kaye & Michael Pittman
This dataset comprises of the IDL code referenced in the 'Open Research' section of the Kaye and Pittman (2020) study 'Fluorescence‐based detection of field targets using an autonomous unmanned aerial vehicle system' published in Methods in Ecology and Evolution (https://doi.org/10.1111/2041-210X.13402). This study describes a proof‐of‐concept autonomous unmanned aerial vehicle (UAV) system that utilizes the fluorescence characteristics unique to different materials to scan and acquire targets in the field e.g. fossils, rocks and minerals, organisms and...

Exchange Rates and Individual Good’s Price Misalignment: Some Preliminary Evidence of Long-Horizon Predictability

Wei Dong & Deokwoo Nam
When prices are sticky, movements in the nominal exchange rate have a direct impact on international relative prices. A relative price misalignment would trigger an adjustment in consumption and employment, and may help to predict future movements in the exchange rate. Although purchasing-power-parity fundamentals, in general, have only weak predictability, currency misalignment may be indicated by price differentials for some goods, which could then have predictive power for subsequent re-evaluation of the nominal exchange rate....

Termite abundance and ecosystem processes in Maliau Basin, 2015-2016

L.A. Ashton, H.M. Griffiths, C.L. Parr, T.A. Evans & P. Eggleton
This dataset consists of invertebrate abundance data and associated ecosystem measurements (Including leaf litter depth and mass, seedlings, soil moisture and nutrients, and rainfall) measured within an area of lowland, old growth dipterocarp rainforest in the Maliau Basin Conservation Area, Sabah, Malaysia between 2015 and 2016. Data were collected during a collaborative project which was included in the NERC Human-modified tropical forest (HMTF) programme.

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  • University of Hong Kong
  • Harvard University
  • Smithsonian Institution
  • University of Washington
  • Stanford University
  • Chinese Academy of Sciences
  • National Taiwan University
  • University of Michigan-Ann Arbor
  • University of Florida
  • United States Geological Survey