Data from: Biotic and abiotic variables influencing plant litter breakdown in streams: a global studyLuz 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 rarityJessica 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...
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: Influences of climate and historical land connectivity on ant beta diversity in East AsiaPatricia 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...
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: Biodiversity-ecosystem functioning relationships in long-term time series and palaeoecological records: deep sea as a test bedMoriaki Yasuhara, Hideyuki Doi, Chih-Lin Wei, Roberto Danovaro & Sarah E. Myhre
The link between biodiversity and ecosystem functioning (BEF) over long temporal scales is poorly understood. Here, we investigate biological monitoring and palaeoecological records on decadal, centennial and millennial time scales from a BEF framework, by using deep-sea, soft-sediment environments as a test bed. Results generally show positive BEF relationships, in agreement with BEF studies based on present-day spatial analyses and short-term manipulative experiments. However, the deep-sea BEF relationship is much noisier across longer time scales...
Data from: Adjunctive use of modified Yunu-Jian in the non-surgical treatment of male smokers with chronic periodontitis: a randomized double-blind, placebo-controlled clinical trialKwan-Yat Zee, Pui Sze Chan, Johnson Chun Sing Ho, Stanley Man Lung Lai, Esmonde Francis Corbet & Wai Keung Leung
Background: Yunu-Jian (YJ) is a Chinese medicine (CM) heat purging formula, which is used to reduce wei huo (stomach-heat, SH) and enrich shen yin (kidney-yin, KY). This formula is also commonly used to manage diabetes mellitus and gum/oral inflammation. The activity of YJ can be modified or refined by the addition of other CM herbs and/or minor changes to one of its five key ingredients. The aim of this study was to evaluate the adjunctive...
Aim: Cenozoic dynamics of large-scale species diversity patterns remain poorly understood, especially for the Western Pacific, in part, because of the paucity of well-dated fossil records from the tropics. This article aims to reveal the spatiotemporal dynamics of species diversity in the Western Pacific through the Cenozoic, focusing on the tropical Indo-Australian Archipelago (IAA) biodiversity hotspot. Location: Tropical and north-western Pacific Ocean. Methods: We analysed well-preserved fossil ostracodes from the tropical Western Pacific and combined...
Data from: Assembling a species–area curve through colonization, speciation and human-mediated introductionEvan P. Economo, Milan Janda, Benoit Guénard & Eli Sarnat
Aim: The fundamental biogeographical processes of colonization, speciation and extinction shape island biotas in space–time. On oceanic islands, area and isolation affect these processes and resulting biodiversity patterns. In the Anthropocene, a new human-mediated colonization dynamic is altering insular ecosystems world-wide. Here, we test predictions about the roles of archipelago area and isolation in structuring ant diversity patterns through effects on both natural and anthropogenic biogeographical processes. Location: Tropical Pacific islands. Methods: We compiled a...
Data from: Response of subtropical submarine-cave ecosystem to Holocene cave development and Asian monsoon variabilityWing Tung Ruby Chiu, Moriaki Yasuhara, Hokuto Iwatani, Akihisa Kitamura & Kazuhiko Fujita
A submarine cave is a unique environment that is dark, food limited, semi-isolated from the outside, and sheltered from wave action. However, our knowledge of the long-term change in submarine-cave ecosystems remains limited. We document here the community-scale responses toward long-term change in a submarine cave, Daidokutsu in Okinawa in southern Japan. Using both metazoans (ostracods and bivalves) and protozoans (larger benthic foraminiferans) in two sediment cores obtained from the cave, we reconstruct the faunal...
Data from: ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated dataGuangchuang Yu, David K. Smith, Huachen Zhu, Yi Guan & Tommy Tsan-Yuk Lam
We present an r package, ggtree, which provides programmable visualization and annotation of phylogenetic trees. ggtree can read more tree file formats than other softwares, including newick, nexus, NHX, phylip and jplace formats, and support visualization of phylo, multiphylo, phylo4, phylo4d, obkdata and phyloseq tree objects defined in other r packages. It can also extract the tree/branch/node-specific and other data from the analysis outputs of beast, epa, hyphy, paml, phylodog, pplacer, r8s, raxml and revbayes...
Figs are keystone resources that sustain chimpanzees when preferred fruits are scarce. Many figs retain a green(ish) colour throughout development, a pattern that causes chimpanzees to evaluate edibility on the basis of achromatic accessory cues. Such behaviour is conspicuous because it entails a succession of discrete sensory assessments, including the deliberate palpation of individual figs, a task that requires advanced visuomotor control. These actions are strongly suggestive of domain-specific information processing and decision-making, and they...
University of Hong Kong12
University of Michigan-Ann Arbor2
Okinawa Institute of Science and Technology2
University of the Basque Country1
University of Washington1
University of California, Merced1
Swiss Federal Institute of Aquatic Science and Technology1