57 Works

Data from: Evaluating the reliability of microsatellite genotyping from low-quality DNA templates with a polynomial distribution model

Gang He, Kang Huang, SongTao Guo, WeiHong Ji, Yi Ren, XueLin Jin & BaoGuo Li
Molecular studies using trace DNA, such as from museum specimens, ancient or forensic samples and samples obtained noninvasively, often have a common problem of low quality of DNA templates. Amplification errors, such as allelic dropout and false allele, may arise during polymerase chain reaction (PCR) using such samples. A mathematical model which treats homozygotes and heterozygotes discriminately has been developed to measure sample quality and compute the confidence level of using multiple-tube approaches. We use...

Data from: Russian wheat aphids (Diuraphis noxia) in China: native range expansion or recent introduction?

Bo Zhang, Le Kang, Owain R. Edwards & Susan J. Fuller
In this study, we explore the population genetics of the Russian wheat aphid (RWA) (Diuraphis noxia), one of the world’s most invasive agricultural pests, in north-western China. We have analysed the data of 10 microsatellite loci and mitochondrial sequences from 27 populations sampled over 2 years in China. The results confirm that the RWAs are holocyclic in China with high genetic diversity indicating widespread sexual reproduction. Distinct differences in microsatellite genetic diversity and distribution revealed...

Data from: Significant genetic boundaries and spatial dynamics of giant pandas occupying fragmented habitat across southwest China

Lifeng Zhu, Shanning Zhang, Xiaodong Gu & Fuwen Wei
Understanding population history and genetic structure are key drivers of ecological research. Here we studied two highly fragmented and isolated populations (Xiaoxiangling and Daxiangling) of giant pandas (Ailuropoda melanoleuca) at the extreme southwestern edge of their distribution. This area also contains the Dadu River, national road 108 and various human infrastructure and development, providing an ideal region in which we can identify the effects of different barriers on animal movements. We used partial mitochondrial control...

Data from: Genetic structuring and recent demographic history of red pandas (Ailurus fulgens) inferred from microsatellite and mitochondrial DNA

Yibo Hu, Yu Guo, Dunwu Qi, Xiangjiang Zhan, Hua Wu, Michael W Bruford & Fuwen Wei
Clarification of the genetic structure and population history of a species can shed light on impacts of landscapes, historical climate change and contemporary human activities, and thus enables evidence-based conservation decisions for endangered organisms. The red panda (Ailurus fulgens) is an endangered species distributing at the edge of the Qinghai-Tibetan Plateau and is currently subject to habitat loss, fragmentation and population decline, thus representing a good model to test the influences of the above factors...

Data from: A phylogenomic perspective to diversity, hybridization and evolutionary affinities in the stickleback genus Pungitius

Guo Baocheng, Fang Bohao, Shikano Takahito, Momigliano Paolo, Wang Cui, Kravchenko Alexandra & Merilä Juha
Hybridization and convergent evolution are phenomena of broad interest in evolutionary biology, but their occurrence poses challenges for reconstructing evolutionary affinities among affected taxa. Sticklebacks in the genus Pungitius are a case in point: evolutionary relationships and taxonomic validity of different species and populations in this circumpolarly distributed species complex remain contentious due to convergent evolution of traits regarded as diagnostic in their taxonomy, and possibly also due to frequent hybridization among taxa. To clarify...

Family lineage and landscape quality data for wild bumblebee colonies across an agricultural landscape in Buckinghamshire, U.K.

C. Carvell, A.F.G. Bourke, S. Dreier, S.N. Freeman, S. Hulmes, W.C. Jordan, J.W. Redhead, J. Wang, S. Sumner & M.S. Heard
Family lineage relationships between spring queens, daughter workers and sister queens of three bumblebee species (Bombus terrestris, B. lapidarius and B. pascuorum) collected across the Hillesden Estate, Buckinghamshire, UK, between spring 2011 and spring 2012. A combination of land-use and habitat surveys, molecular genetics and spatial modelling was used to estimate the locations of wild colonies represented by greater than 1 worker and to calculate the proportions of cover represented by different habitat quality and...

Microsatellite genotype data for five species of bumblebee across an agricultural landscape in Buckinghamshire, UK

S. Dreier, J.W. Redhead, I. Warren, A.F.G. Bourke, M.S. Heard, W.C. Jordan, S. Sumner, J. Wang & C. Carvell
Microsatellite data for five species of common and declining bumblebee (Bombus terrestris, B. lapidarius, B. pascuorum, B. hortorum and B. ruderatus) collected across the Hillesden Estate, Buckinghamshire, UK, in summer 2011. Worker genotypes were determined from individuals sampled across an agricultural landscape and queen genotypes were reconstructed from sampled worker offspring. Data were collected as part of a project led by the Centre for Ecology & Hydrology, funded under the Insect Pollinators Initiative.

Data from: Opportunities for biodiversity gains under the world’s largest reforestation programme

Fangyuan Hua, Xiaoyang Wang, Xinlei Zheng, Robert Dorazio, Brendan Fisher, Lin Wang, Jianguo Zhu, Ya Tang, Douglas W. Yu & David S. Wilcove
Reforestation is a critical means of addressing the environmental and social problems of deforestation. China’s Grain-for-Green Program (GFGP) is the world’s largest reforestation scheme. Here we provide the first nationwide assessment of the tree composition of GFGP forests and the first combined ecological and economic study aimed at understanding GFGP’s biodiversity implications. Across China, GFGP forests are overwhelmingly monocultures or compositionally simple mixed forests. Focusing on birds and bees in Sichuan Province, we find that...

Data from: Metabarcoding of freshwater invertebrates to detect the effects of a pesticide spill

Carmelo Andujar, Paula Arribas, Clare Gray, Katherine Bruce, Guy Woodward, Douglas W. Yu & Alfried P. Vogler
Biomonitoring underpins the environmental assessment of freshwater ecosystems and guides management and conservation. Current methodology for surveys of (macro)invertebrates uses coarse taxonomic identification where species-level resolution is difficult to obtain. Next-generation sequencing of entire assemblages (metabarcoding) provides a new approach for species detection, but requires further validation. We used metabarcoding of invertebrate assemblages with two fragments of the cox1 "barcode" and partial nuclear ribosomal (SSU) genes, to assess the effects of a pesticide spill in...

Data from: Inferring the origin of populations introduced from a genetically structured native range by approximate Bayesian computation: case study of the invasive ladybird Harmonia axyridis

Eric Lombaert, Thomas Guillemaud, Cathleen E. Thomas, Lori J. Lawson Handley, Jiahui Li, Su Wang, Hong Pang, Irina Goryacheva, Ilya A. Zakharov, Emmanuelle Jousselin, Remy L. Poland, Alain Migeon, Joop Van Lenteren, Patrick De Clercq, Nick Berkvens, Walker Jones & Arnaud Estoup
Correct identification of the source population of an invasive species is a prerequisite for testing hypotheses concerning the factors responsible for biological invasions. The native area of invasive species may be large, poorly known and/or genetically structured. Because the actual source population may not have been sampled, studies based on molecular markers may generate incorrect conclusions about the origin of introduced populations. In this study, we characterized the genetic structure of the invasive ladybird Harmonia...

Data from: Impacts of species richness on productivity in a large-scale subtropical forest experiment

Yuanyuan Huang, Yuxin Chen, Nadia Castro-Izaguirre, Martin Baruffol, Matteo Brezzi, Anne Lang, Ying Li, Werner Härdtle, Werner Von Oheimb, Xuefeu Yang, Xiaojuan Liu, Kequan Pei, Sabine Both, Bo Yang, David Eichenberg, Thorsten Assmann, Jürgen Bauhus, Thorsten Behrens, François Buscot, Xiao-Yong Chen, Douglas Chester, Bing-Yang Ding, Walter Durka, Alexandra Erfmeier, Jingyun Fang … & Bernhard Schmid
Biodiversity experiments have shown that species loss reduces ecosystem functioning in grassland. To test whether this result can be extrapolated to forests, the main contributors to terrestrial primary productivity, requires large-scale experiments. We manipulated tree species richness by planting more than 150,000 trees in plots with 1 to 16 species. Simulating multiple extinction scenarios, we found that richness strongly increased stand-level productivity. After 8 years, 16-species mixtures had accumulated over twice the amount of carbon...

Data from: Effects of hypoxia on the thermal physiology of a high-elevation lizard: Implications for upslope-shifting species

Zhong Wen Jiang, Liang Ma, Chun Rong Mi & Wei Guo Du
Montane reptiles are predicted to move to higher elevations in response to climate warming. However, whether upwards-shifting reptiles will be physiologically constrained by hypoxia at higher elevations remains unknown. We investigated the effects of hypoxic conditions on preferred body temperatures (Tpref) and thermal tolerance capacity of a montane lizard (Phrynocephalus vlangalii) from two populations on the Qinghai-Tibet Plateau. Lizards from 2600 m asl were exposed to O2 levels mimicking those at 2600 m (control) and...

Data from: Transcriptome profiling of maternal stress-induced wing dimorphism in pea aphids

Lin Hu, Wanying Gui, Bing Chen & Li Chen
Wing dimorphism, i.e., wingless and winged forms, can be induced by maternal stress signals and is an adaptive response of aphids to environmental changes. Here, we investigated the ecological and molecular effects of three kinds of stress, namely, crowding, predation, and aphid alarm pheromone, on wing dimorphism. These three stressors induced high proportion of up to 60% of winged morphs in offspring. Transcriptome analysis of stress-treated female aphids revealed different changes in maternal gene expression...

The role of evolutionary time, diversification rates and dispersal in determining the global diversity of a large radiation of passerine birds

Tianlong Cai, Shimiao Shao, Jonathan Kennedy, Per Alström, Robert Moyle, Yanhua Qu, Fumin Lei & Jon Fjeldså
Aim: Variation in species diversity among different geographic areas may result from differences in speciation and extinction rates, immigration and time for diversification. An area with high species diversity may be the result of a high net diversification rate, multiple immigration events from adjacent regions,anda long time available for the accumulation of species (know as the “time-for-speciation effect”). Here, we examine the relative importance of the three aforementionedprocesses in shaping the geographic diversity patterns of...

Variation in butterfly diapause duration in relation to voltinism suggests adaptation to autumn warmth, not winter cold

Olle Lindestad, Loke Von Schmalensee, Philipp Lehmann & Karl Gotthard
1. The life cycles of animals vary in relation to local climate, as a result of both direct environmental effects and population-level variation in plastic responses. Insects often respond to the approach of winter by entering diapause, a hormonally programmed resting state where development is suspended and metabolism suppressed. Populations often differ in the duration of diapause, but the adaptive reasons for this are unclear. 2. We performed a common-garden overwintering experiment with respirometric measurements...

Geographic distances between pairs of wild bumblebee colonies across an agricultural landscape in Buckinghamshire, UK

S. Dreier, J.W. Redhead, I. Warren, A.F.G. Bourke, M.S. Heard, W.C. Jordan, S. Sumner, J. Wang & C. Carvell
Geographic distances between pairs of wild bumblebee colonies across an agricultural landscape centred on the Hillesden Estate, Buckinghamshire, UK. Colony locations were estimated using the foraging locations of workers sampled in summer 2011, genotyped and grouped into full-sib families. The spatial structure of five Bombus species (Bombus terrestris, B. lapidarius, B. pascuorum, B. hortorum and B. ruderatus) was determined, with inter-colony distances varying from 7 to 5264 metres. Data were collected as part of a...

Data from: Kinship underlies costly cooperation in Mosuo villages

Matthew Gwynfryn Thomas, Ting Ji, JiaJia Wu, Qiao-Qiao He, Yi Tao, Ruth Mace & QiaoQiao He
The relative importance of social evolution theories such as kin selection, direct reciprocity and needs-based transfers in explaining real-world cooperation is the source of much debate. Previous field studies of cooperation in human communities have revealed variability in the extent to which each of these theories drive human sociality in different contexts. We conducted multivariate social network analyses predicting costly cooperation—labouring on another household’s farm—in 128,082 dyads of Mosuo farming households in southwest China. Through...

Data from: Discovery of a relict lineage and monotypic family of passerine birds

Per Alström, Daniel M. Hooper, Yang Liu, Urban Olsson, Dhananjai Mohan, Magnus Gelang, Hung Le Manh, Jian Zhao, Fumin Lei, Trevor D. Price & P. Alstrom
Analysis of one of the most comprehensive datasets to date of the largest passerine bird clade, Passerida, identified 10 primary well-supported lineages corresponding to Sylvioidea, Muscicapoidea, Certhioidea, Passeroidea, the ‘bombycillids’ (here proposed to be recognized as Bombycilloidea), Paridae/Remizidae (proposed to be recognized as Paroidea), Stenostiridae, Hyliotidae, Regulidae (proposed to be recognized as Reguloidea) and spotted wren-babbler Spelaeornis formosus. The latter was found on a single branch in a strongly supported clade with Muscicapoidea, Certhioidea and...

Data from: Measuring population differentiation using GST or D? A simulation study with microsatellite DNA markers under a finite island model and nonequilibrium conditions

Liang Leng & De-Xing Zhang
Genetic differentiation of populations is a key question in population genetic investigations. Wright’s FST (and its relatives such as GST) has been a standard measure of differentiation. However, the deficiencies of these indexes and their significance have been increasing realized in recent years, leading to some new measures being proposed, such as Jost’s (2008) D. This has also stimulated some considerable debate which, in certain sense, makes empirical biologists even more confused, for example, on...

Data from: Inbreeding and inbreeding avoidance in wild giant pandas

Yibo Hu, Yonggang Nie, Fuwen Wei, Tianxiao Ma, Russell Van Horn, Xiaoguang Zheng, Ronald Swaisgood, Zhixin Zhou, Wenliang Zhou, Li Yan & Zejun Zhang
Inbreeding can have negative consequences on population and individual fitness, which could be counteracted by inbreeding avoidance mechanisms. However, the inbreeding risk and inbreeding avoidance mechanisms in endangered species are less studied. The giant panda, a solitary and threatened species, lives in many small populations and suffers from habitat fragmentation, which may aggravate the risk of inbreeding. Here, we performed long-term observations of reproductive behaviour, sampling of mother-cub pairs and large-scale genetic analyses on wild...

Data from: Non-random latitudinal gradients in range size and niche breadth predicted by spatial patterns of climate

Erin E. Saupe, Corinne E. Myers, A. Townsend Peterson, Jorge Soberón, Joy Singarayer, Paul Valdes & Huijie Qiao
Aim. Tropical species are thought to experience and be adapted to narrow ranges of abiotic conditions. This idea has been invoked to explain a broad array of biological phenomena, including the latitudinal diversity gradient and differential rates of speciation and extinction. However, debate continues regarding the broad-scale applicability of this pattern and potential processes responsible. Here, we use a simulation approach to test two propositions: (1) strong geographic patterns of variation in realized niche breadth...

Ancient volcanos as species pumps: A case study of freshwater amphipods in Northeast Asia

Yueyao Hu, Shuqiang Li, Hongguang Liu, Seung-Tae Kim, Dmitry K. Kurenshchikov & Zhonge Hou
Volcano-tectonic processes have been viewed as primary divers in the formation of present-day diversity. Volcanos associated with mountain uplifts drives allopatric speciation through vicariance and may impact the surrounding areas like species pump or species attractor. However, the application of these hypotheses to aquatic fauna has rarely been tested explicitly. We conducted this research in the Changbai Mountains (Mts), which are one of the most typical, active volcanic ranges in Northeast (NE) Asia with a...

Data from: A multilocus molecular phylogeny for the avian genus Liocichla (Passeriformes: Leiothrichidae: Liocichla)

Herman L. Mays, Bailey D. McKay, Dieter Thomas Tietze, Cheng-Te Yao, Lindsey N. Miller, Kathleen N. Moreland & Fumin Lei
Background: Historically the babblers have been assigned to the family Timaliidae but several recent studies have attempted to rest the taxonomy of this diverse passerine assemblage on a more firm evolutionary footing. The result has been a major rearrangement of the group. A well-supported and comprehensive phylogeny for this widespread avian group is an important part of testing evolutionary and biogeographic hypotheses, especially in Asia where the babblers are a key component of many forest...

Data from: High-throughput monitoring of wild bee diversity and abundance via mitogenomics

Min Tang, Chloe J. Hardman, Yinqiu Ji, Guanliang Meng, Shanlin Liu, Meihua Tang, Shenzhou Yang, Ellen D. Moss, Jiaxin Wang, Chenxue Yang, Catharine Bruce, Tim Nevard, Simon G. Potts, Xin Zhou, Douglas W. Yu & Meihua Tan
1. Bee populations and other pollinators face multiple, synergistically acting threats, which have led to population declines, loss of local species richness and pollination services, and extinctions. However, our understanding of the degree, distribution and causes of declines is patchy, in part due to inadequate monitoring systems, with the challenge of taxonomic identification posing a major logistical barrier. Pollinator conservation would benefit from a high-throughput identification pipeline. 2. We show that the metagenomic mining and...

Data from: Willing or unwilling to share primary biodiversity data: results and implications of an international survey

Xiaolei Huang, Bradford A. Hawkins, Fumin Lei, Gary L. Miller, Colin Favret, Ruiling Zhang & Gexia Qiao
Biodiversity science and conservation increasingly depend on the sharing and integration of large amounts of data, but many researchers resist sharing their primary biodiversity data. We recently conducted an international survey to ascertain the attitudes, experiences, and expectations regarding biodiversity data sharing and archiving of researchers. The results show that whereas most respondents are willing to share paper-related biodiversity data, more than sixty percent of respondents are unwilling to share primary data before publishing. Results...

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