43 Works

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: 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: 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: 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...

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: 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: 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: 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: 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: 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...

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: 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...

Data from: Biodiversity soup: metabarcoding of arthropods for rapid biodiversity assessment and biomonitoring

Douglas W. Yu, Yinqiu Ji, Brent C. Emerson, Xiaoyang Wang, Chengxi Ye, Chunyan Yang & Zhaoli Ding
1) Traditional biodiversity assessment is costly in time, money, and taxonomic expertise. Moreover, data are frequently collected in ways (e.g. visual bird lists) that are unsuitable for auditing by neutral parties, which is necessary for dispute resolution. 2) We present protocols for the extraction of ecological, taxonomic and phylogenetic information from bulk samples of arthropods. The protocols combine mass trapping of arthropods, mass-PCR amplification of the COI barcode gene, pyrosequencing, and bioinformatic analysis, which together...

Data from: Population size and time since island isolation determine genetic diversity loss in insular frog populations

Supen Wang, Wei Zhu, Xu Gao, Xianping Li, Yan Shaofei, Xuan Liu, Ji Yang, Zengxiang Gao, Yiming Li & Shaofei Yan
Understanding the factors that contribute to loss of genetic diversity in fragmented populations is crucial for conservation measurements. Land-bridge archipelagoes offer ideal model systems for identifying the long-term effects of these factors on genetic variations in wild populations. In this study, we used 9 microsatellite markers to quantify genetic diversity and differentiation of 810 pond frogs (Pelophylax nigromaculataus) from 24 islands of the Zhoushan Archipelago and 3 sites on nearby mainland China and estimated the...

Data from: Recent northward range expansion promotes song evolution in a passerine bird, the Light-vented Bulbul

Xiaoying Xing, Per Alström, Xiaojing Yang, Fumin Lei, F. M. Lei & X. J. Yang
In common with human speech, song is culturally inherited in oscine passerine birds (‘songbirds’). Intraspecific divergence in birdsong, such as development of local dialects, might be an important early step in the speciation process. It is therefore vital to understand how songs diverge, especially in founding populations. The northward expansion of the Light-vented Bulbul Pycnonotus sinensis (J. F. Gmelin, 1789) into north China in the last 30 years provides an excellent opportunity to study birdsong...

Data from: Heat shock protein expression enhances heat tolerance of reptile and bird embryos

Jing Gao, Wen Zhang, Wei Dang, Yi Mou, Yuan Gao, Bao-Jun Sun, Wei-Guo Du, W.-G. Du & B.-J. Sun
The role of heat shock proteins (HSPs) in heat tolerance has been demonstrated in cultured cells and animal tissues, but rarely in whole organisms because of methodological difficulties associated with gene manipulation. By comparing HSP70 expression patterns among representative species of reptiles and birds, and by determining the effect of HSP70 overexpression on embryonic development and hatchling traits, we have identified the role of HSP70 in the heat tolerance of amniote embryos. Consistent with their...

Data from: The evolutionary road from wild moth to domestic silkworm

Hui Xiang, Xiaojing Liu, Muwang Li, Ya'nan Zhu, Lizhi Wang, Yong Cui, Liyuan Liu, Gangqi Fang, Heying Qian, Anying Xu, Wen Wang & Shuai Zhan
The Silk Road, which derives its name from the trade of silk produced by the domestic silkworm Bombyx mori, was an important episode in the development and interaction of human civilizations. However, the detailed history behind silkworm domestication remains ambiguous, and little is known about the underlying genetics with respect to important aspects of its domestication. Here, we reconstruct the domestication processes and identify selective sweeps by sequencing 137 representative silkworm strains. The results present...

Data from: Walking in a heterogeneous landscape: dispersal, gene-flow and conservation implications for the giant panda in the Qinling Mountains

Tianxiao Ma, Yibo Hu, Isa-Rita Russo, Yonggang Nie, Tianyou Yang, Lijuan Xiong, Shuai Ma, Tao Meng, Han Han, Ximing Zhang, Mike W. Bruford, Fuwen Wei, Isa-Rita M. Russo & Michael W. Bruford
Understanding the interaction between life history, demography and population genetics in threatened species is critical for the conservations of viable populations. In the context of habitat loss and fragmentation, identifying the factors that underpin the structuring of genetic variation within populations can allow conservationists to evaluate habitat quality and connectivity and help to design dispersal corridors effectively. In this study, we carried out a detailed, fine-scale landscape genetic investigation of a giant panda population for...

Data from: Within- and between-group dynamics in an obligate cooperative breeder

Rosie Woodroffe, Helen O'Neill & Daniella Rabaiotti
1. Cooperative behaviour can have profound effects on demography. In many cooperative species, components of fitness (e.g. survival, reproductive success) are diminished in smaller social groups. These effects (termed group-level component Allee effects) may lead smaller groups to grow relatively slowly or fail to persist (termed group-level demographic Allee effects). 2. If these group-level effects were to propagate to the population level, small populations would grow slowly or decline to extinction (termed population-level demographic Allee...

Location data of worker bumblebees across an agricultural landscape in Buckinghamshire, UK

C. Carvell, A.F.G. Bourke, S. Dreier, M.S. Heard, W.C. Jordan, S. Sumner, J. Wang & J.W. Redhead
This dataset contains locations of worker bumblebees of five species (Bombus terrestris, B. lapidarius, B. pascuorum, B. hortorum, B. ruderatus) across an agricultural landscape centred on the Hillesden Estate, Buckinghamshire, UK. Locations were recorded in the field using a handheld GPS unit. Workers were non-lethally DNA sampled between June and August 2011, and genetic analysis used to confirm species and assign individuals to full-sib groups (colonies). Data were collected as part of a project led...

Scaling the extinction vortex: Body size as a predictor of population dynamics close to extinction events

Nathan Williams, Louise McRae, Robin Freeman, Pol Capdevila & Christopher Clements
Mutual reinforcement between abiotic and biotic factors can drive small populations into a catastrophic downward spiral to extinction – a process known as the ‘extinction vortex.’ However, empirical studies investigating extinction dynamics in relation to species’ traits have been lacking. We assembled a database of 35 vertebrate populations monitored to extirpation over a period of at least ten years, represented by 32 different species, including 25 birds, five mammals and two reptiles. We supplemented these...

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...

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...

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...

Registration Year

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  • 2012

Resource Types

  • Dataset


  • Institute of Zoology
  • Zoological Society of London
  • Chinese Academy of Sciences
  • Cardiff University
  • University of Chinese Academy of Sciences
  • University of East Anglia
  • Kunming Institute of Zoology
  • University of Bristol
  • University of Reading
  • University of Kansas