57 Works

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...

Negative impacts of dominance on bee communities: Does the influence of invasive honey bees differ from native bees?

Lucas Alejandro Garibaldi, Lucas Garibaldi, Néstor Pérez-Méndez, Guaraci Cordeiro, Alice Hughes, Michael Orr, Isabel Alves Dos Santos, Breno Freitas, Favízia Freitas De Oliveira, Gretchen Lebuhn, Ignasi Bartomeus, Marcelo Aizen, Patricia Andrade, Betina Blochtein, Danilo Boscolo, Patricia Drumond, Maria Gaglianone, Barbara Gemmill-Herren, Rosana Halinski, Cristiane Krug, Marcia Maues, Lucia Piedade Kiill, Mardiore Pinheiro, Carmen Pires & Blandina Felipe Viana
Invasive species can reach high abundances and dominate native environments. One of the most impressive examples of ecological invasions is the spread of the African sub-species of the honey bee throughout the Americas, starting from its introduction in a single locality in Brazil. The invasive honey bee is expected to more negatively impact bee community abundance and diversity than native dominant species, but this has not been tested previously. We developed a comprehensive and systematic...

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: 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: 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: 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: 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...

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...

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: 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: Paternal epigenetic effects of population density on locust phase-related characteristics associated with heat-shock protein expression

Bing Chen, Shaoqin Li, Qiang Ren, Xiwen Tong, Xia Zhang & Le Kang
Many species exhibit transgenerational plasticity by which environmental cues experienced by either parent can be transmitted to their offspring, resulting in phenotypic variants in offspring to match ancestral environments. However, the manner by which paternal experiences affect offspring plasticity through epigenetic inheritance in animals generally remains unclear. In this study, we examined the transgenerational effects of population density on phase-related traits in the migratory locust Locusta migratoria. Using an experimental design that explicitly controls genetic...

Data from: Discriminative host sanction together with relatedness promote the cooperation in fig/fig wasp mutualism

Rui-Wu Wang, Bao-Fa Sun & Yan Yang
1. Sanctioning or punishing is regarded as one of the most important dynamics in the evolution of cooperation. However, it has not been empirically examined yet whether or not such enforcement selection by sanctioning or punishing and classical theories like kin or reciprocity selection are separate mechanisms contributing to the evolution of cooperation. In addition, it remains largely unclear what factors determine the intensity or effectiveness of sanction. 2. Here, we show that in the...

Supplementary material of the article “Elevation patterns and critical environmental drivers of the taxonomic, functional and phylogenetic diversity of small mammals in a karst mountain area”.

Jian Sun, Zhixin Wen, Anderson Feijó, Jilong Cheng, Yanqun Wang, Song Li, Deyan Ge, Lin Xia & Qisen Yang
Understanding how biodiversity components are related under different environmental factors is a fundamental challenge for ecology studies, yet there is little knowledge of this interplay among the biotas, especially small mammals, in karst mountain areas. Here, we examine the elevation patterns of the taxonomic diversity (TD), phylogenetic diversity (PD) and functional diversity (FD) of small mammals in a karst mountain area, the Wuling Mountains, Southwest China, and compare these patterns between taxa (Rodentia and Eulipotyphla)...

The impact of a native dominant plant, Euphorbia jolkinii, on plant-flower visitor networks and pollen deposition on stigmas of co-flowering species in sub-alpine meadows of Shangri-La, SW China

Yan-Hui Zhao, Jane Memmott, Ian Vaughan, Hai-Dong Li, Zong-Xin Ren, Amparo Lazaro, Wei Zhou, Xin Xu, Wei-Jia Wang, Huan Liang, De-Zhu Li & Hong Wang
1. Anthropogenic activity can modify the distribution of species abundance in a community leading to the appearance of new dominant species. While many studies report that an alien plant species which becomes increasingly dominant can change species composition, plant-pollinator network structure and the reproductive output of native plant species, much less is known about native plant species which become dominant in their communities. 2. Euphorbia jolkinii Boissier (Euphorbia, hereafter) has become a dominant native plant...

Single nucleotide polymorphisms

Baocheng Guo, Yingnan Wang, Yu Wang, Yahui Zhao, Alexandra Kravchenko & Juha Merilä
Aim: Understanding the phylogeography of a species complex can provide important insights into its evolutionary history. However, phylogeographic inference often faces the dilemma of regionally inadequate sampling. Pungitius sticklebacks are a case in point: although the highest species diversity is found in Northeast Asia, their phylogeography in this region is still poorly understood. Location: Northeast Asia Methods: With the aid of whole genome resequencing data, we investigated the phylogeography of Northeast Asian Pungitius sticklebacks, with...

Challenging a host-pathogen paradigm: Susceptibility to chytridiomycosis is decoupled from genetic erosion

Donal Smith, David O'Brien, Jeanette Hall, Chris Sergeant, Lola Brookes, Xavier Harrison, Trenton Garner & Robert Jehle
The putatively positive association between host genetic diversity and the ability to defend against pathogens has long attracted the attention of evolutionary biologists. Chytridiomycosis, a disease caused by the chytrid fungus Batrachochytrium dendrobatidis (Bd), has emerged in recent decades as a cause of dramatic declines and extinctions across the amphibian clade. Bd susceptibility can vary widely across populations of the same species, but the relationship between standing genetic diversity and susceptibility has remained notably underexplored...

Cloning capacity helps seeds of Garcinia xanthochymus counter animal predation

Zhenyu Wang
Seed predators have the potential to act as agents of natural selection that influence seed traits and seed fates, which in turn affect the whole plant population dynamic. Accordingly, plants deploy a variety of mechanisms (e.g. resistance and tolerance strategies) to lessen the impact of predation on seed crop or on an individual seed. In this study, we described a novel mechanism, seed cloning strategy, in a tropical plant species in countering animal predation. By...

Data from: Is embryonic hypothermia tolerance common in birds?

Jin-Ming Zhao, Zhi-Ming Han & Yue-Hua Sun
Avian incubation temperatures oscillate within narrow limits to ensure proper embryonic development. However, field observations and experimental studies have found that some species can tolerate very low incubation temperatures, either regularly or occasionally. We artificially incubated eggs from five domestic species, which represent a range of egg sizes, to examine whether a diversity of avian species could exhibit an unusual hypothermia tolerance, as observed in the field. We found that eggs of the chicken (Gallus...

Data from: Turtle embryos move to optimal thermal environments within the egg

Bo Zhao, Teng Li, Richard Shine, Wei-Guo Du & W.-G. Du
A recent study demonstrated that the embryos of soft-shelled turtles can reposition themselves within their eggs to exploit locally warm conditions. In the current paper, we ask whether turtle embryos actively seek out optimal thermal environments for their development, as do post-hatching individuals. Specifically, (1) do reptile embryos move away from dangerously-high temperatures, as well as towards warm temperatures? and (2) is such embryonic movement due to active thermoregulation, or (more simply) to passive embryonic...

Data from: Population transcriptomes reveal synergistic responses of DNA polymorphism and RNA expression to extreme environments on the Qinghai–Tibetan Plateau in a predatory bird

Shengkai Pan, Tongzuo Zhang, Zhengqin Rong, Li Hu, Zhongru Gu, Qi Wu, Shanshan Dong, Qiong Liu, Zhenzhen Lin, Lucia Deutschova, Xin-Hai Li, Andrew Dixon, Michael W. Bruford, Xiangjiang Zhan & Xinhai Li
Low oxygen and temperature pose key physiological challenges for endotherms living on the Qinghai–Tibetan Plateau (QTP). Molecular adaptations to high-altitude living have been detected in the genomes of Tibetans, their domesticated animals and a few wild species, but the contribution of transcriptional variation to altitudinal adaptation remains to be determined. Here we studied a top QTP predator, the saker falcon, and analysed how the transcriptome has become modified to cope with the stresses of hypoxia...

Data from: Construction of a species-level tree of life for the insects and utility in taxonomic profiling

Douglas Chesters
Although comprehensive phylogenies have proven an invaluable tool in ecology and evolution, their construction is made increasingly challenging both by the scale and structure of publically available sequences. The distinct partition between gene-rich (genomic) and species-rich (DNA barcode) data is a feature of data that has been largely overlooked, yet presents a key obstacle to scaling supermatrix analysis. I present a phyloinformatics framework for draft construction of a species-level phylogeny of insects (Class Insecta). Matrix-building...

Data from: Higher fungal diversity is correlated with lower CO2 emissions from dead wood in a natural forest

Chunyan Yang, Douglas A. Schaefer, Weijie Liu, Viorel D. Popescu, Chenxue Yang, Xiaoyang Wang, Chunying Wu & Douglas W. Yu
Wood decomposition releases almost as much CO2 to the atmosphere as does fossil-fuel combustion, so the factors regulating wood decomposition can affect global carbon cycling. We used metabarcoding to estimate the fungal species diversities of naturally colonized decomposing wood in subtropical China and, for the first time, compared them to concurrent measures of CO2 emissions. Wood hosting more diverse fungal communities emitted less CO2, with Shannon diversity explaining 26 to 44% of emissions variation. Community...

Data from: Population variation reveals independent selection towards small body size in Chinese Debao pony

Adiljan Kader, Yan Li, Kunzhe Dong, David M. Irwin, Qianjun Zhao, Xiaohong He, Jianfeng Liu, Yabin Pu, Neena Amatya Gorkhali, Xuexue Liu, Lin Jiang, Xiangchen Li, Weijun Guan, Yaping Zhang, Dong-Dong Wu & Yuehui Ma
Body size, one of the most important quantitative traits under evolutionary scrutiny, varies considerably among species and among populations within species. Revealing the genetic basis underlying this variation is very important, particularly in humans where there is a close relationship with diseases and in domestic animals as the selective patterns are associated with improvements in production traits. The Debao pony is a horse breed with small body size that is unique to China; however, it...

Data from: Wolbachia infection and dramatic intraspecific mitochondrial DNA divergence in a fig wasp

Jin-Hua Xiao, Ning-Xin Wang, Robert W. Murphy, James M. Cook, Ling-Yi Jia & Da-Wei Huang
Mitochondria and Wolbachia are maternally inherited genomes that exhibit strong linkage disequilibrium in many organisms. We surveyed Wolbachia infections in 187 specimens of the fig wasp species, Ceratosolen solmsi, and found an infection prevalence of 89.3%. DNA Sequencing of 20 individuals each from Wolbachia-infected and uninfected sub-populations revealed extreme mtDNA divergence (up to 9.2% and 15.3% in CO1 and cytochrome b, respectively) between infected and uninfected wasps. Further, mtDNA diversity was significantly reduced within the...

Data from: Comparing genetic diversity and demographic history in co-distributed wild South American camelids

Ciara S. Casey, Pablo Orozco-TerWengel, Katherine Yaya, Miranda Kadwell, Matilde Fernández, Juan Carlos Marin, Raul Rosadio, Lenin Maturrano, Domingo Hoces, Yibo Hu, Jane C. Wheeler & Michael W. Bruford
Vicuñas and guanacos are two species of wild South American camelids that are key ruminants in the ecosystems where they occur. Although closely related, these species feature differing ecologies and life history characters, which are expected to influence both their genetic diversity and population differentiation at different spatial scales. Here, using mitochondrial and microsatellite genetic markers, we show that vicuña display lower genetic diversity within populations than guanaco but exhibit more structure across their Peruvian...

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