132 Works

Foraging behaviour alters with social environment in a juvenile songbird

Victoria Franks, John Ewen, Mhairi McCready & Rose Thorogood
Early independence from parents is a critical period where social information acquired vertically may become outdated, or conflict with new information. However, across natural populations it is unclear if newly-independent young persist in using information from parents, or if group-level effects of conformity override previous behaviours. Here we test if wild juvenile hihi (Notiomystis cincta, a New Zealand passerine) retain a foraging behaviour from parents, or if they change in response to the behaviour of...

Data from: Automated DNA-based plant identification for large-scale biodiversity assessment

Anna Papadopoulou, Douglas Chesters, Indiana Coronado, Gissela De La Cadena, Anabela Cardoso, Jazmina C. Reyes, Jean-Michel Maes, Ricardo M. Rueda & Jesús Gómez-Zurita
Rapid degradation of tropical forests urges to improve our efficiency in large-scale biodiversity assessment. DNA-barcoding can assist greatly in this task, but commonly used phenetic approaches for DNA-based identifications rely on the existence of comprehensive reference databases, which are infeasible for hyperdiverse tropical ecosystems. Alternatively, phylogenetic methods are more robust to sparse taxon sampling but time-consuming, while multiple alignment of species-diagnostic, typically length-variable markers can be problematic across divergent taxa. We advocate the combination of...

Data from: Sexually selected dichromatism in the hihi Notiomystis cincta: multiple colours for multiple receivers

Leila K. Walker, John G. Ewen, Patricia Brekke & Rebecca M. Kilner
Why do some bird species show dramatic sexual dichromatism in their plumage? Sexual selection is the most common answer to this question. However, other competing explanations mean it is unwise to assume that all sexual dichromatism has evolved by this mechanism. Even if sexual selection is involved, further work is necessary to determine whether dichromatism results from competition amongst rival males, or by female choice for attractive traits, or both. Here we test whether sexually...

Data from: Weak olfaction increases seed scatter-hoarding by Siberian chipmunks: implication in shaping plant-animal interactions

Xianfeng Yi, Zhenyu Wang, Hongmao Zhang & Zhibin Zhang
Scatter-hoarding of seeds by animals plays an essential role in seed dispersal of plants and in shaping plant–animal interactions in forest ecosystems, but the function of scatter-hoarding behavior is still unclear. We hypothesize that weak olfactory cues between seeds and scatter-hoarding animals would increase scatter-hoarding. Using a rodent–plant system of Siberian chipmunks Tamias sibiricus and Korean pines Pinus koraiensis, we tested the effects on seed scatter-hoarding intensity by measuring and modifying the seed odor intensities...

Data from: Acoustic identification of Mexican bats based on taxonomic and ecological constraints on call design

Veronica Zamora-Gutierrez, Celia Lopez-Gonzalez, M. Cristina MacSwiney Gonzalez, Brock Fenton, Gareth Jones, Elisabeth K. V. Kalko, Sebastien J. Puechmaille, Vassilios Stathopoulos & Kate E. Jones
Monitoring global biodiversity is critical for understanding responses to anthropogenic change, but biodiversity monitoring is often biased away from tropical, megadiverse areas that are experiencing more rapid environmental change. Acoustic surveys are increasingly used to monitor biodiversity change, especially for bats as they are important indicator species and most use sound to detect, localise and classify objects. However, using bat acoustic surveys for monitoring poses several challenges, particularly in megadiverse regions. Many species lack reference...

Data from: No silver bullets in correlative ecological niche modeling: insights from testing among many potential algorithms for niche estimation

Huijie Qiao, Jorge Soberón & Andrew Townsend Peterson
The field of ecological niche modeling or species distribution modeling has seen enormous activity and attention in recent years, in light of exciting biological inferences that can be drawn from correlational models of species’ environmental requirements (i.e., ecological niches) and inferences of potential geographic distributions. Among the many methods used in the field, one or two are in practice assumed to be ‘best’ and are used commonly, often without explicit testing. We explore herein implications...

Data from: Using data from related species to overcome spatial sampling bias and associated limitations in ecological niche modeling

Huijie Qiao, Andrew Townsend Peterson, Liqiang Ji & Junhua Hu
1. Ecological niche modeling (ENM) is used widely to aid in conservation planning and management, often focusing on rare species characterized by the biased observations associated with restricted geographic ranges, habitat specialization, small population size, and limited natural history information. Generating reliable ENMs for such species is a challenge, however, owing to issues that arise from spatial sampling bias, such as model inaccuracy and overfitting. Here, using virtual scenarios, we assess the utility of integrating...

Data from: Assessing the conservation value of secondary savanna for large mammals in the Brazilian Cerrado

Guilherme B. Ferreira, Jorge A. Ahumada, Marcelo J. R. Oliveira, Fernando F. De Pinho, Izabela M. Barata, Chris Carbone & Ben Collen
Debate about the conservation value of secondary habitats has tended to focus on tropical forests, increasingly recognizing the role of secondary forests for biodiversity conservation. However, there remains a lack of information about the conservation value of secondary savannas. Here, we conducted a camera trap survey to assess the effect of secondary vegetation on large mammals in a Brazilian Cerrado protected area, using a single-season occupancy framework to investigate the response of individual species (species-level...

Data from: Hot dogs: high ambient temperatures impact reproductive success in a tropical carnivore

Rosie Woodroffe, Rosemary Groom & J. Weldon McNutt
Climate change imposes an urgent need to recognise and conserve the species likely to be worst affected. However, while ecologists have mostly explored indirect effects of rising ambient temperatures on temperate and polar species, physiologists have predicted direct impacts on tropical species. The African wild dog (Lycaon pictus), a tropical species, exhibits few of the traits typically used to predict climate change vulnerability. Nevertheless, we predicted that wild dog populations might be sensitive to weather...

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: Estimating genotyping errors from genotype and reconstructed pedigree data

Jinliang Wang
1. Genotyping errors are rules rather than exceptions in reality, and are found in virtually all but very small datasets. These errors, even when occurring at an extremely low rate, can derail many genetic analyses such as parentage/sibship assignments and linkage/association studies. 2. Nonetheless, few robust and accurate methods are available for estimating the rate of occurrence of genotyping errors and for identifying individual erroneous genotypes at a locus. Methods based on duplicate genotyping are...

Data from: A novel approach to wildlife transcriptomics provides evidence of disease-mediated differential expression and changes to the microbiome of amphibian populations

Lewis J. Campbell, Stewart A. Hammond, Stephen J. Price, Manmohan D. Sharma, Trenton W.J. Garner, Inanc Birol, Caren C. Helbing, Lena Wilfert, Amber G.F. Griffiths & Trenton W. J. Garner
Ranaviruses are responsible for a lethal, emerging infectious disease in amphibians and threaten their populations throughout the world. Despite this, little is known about how amphibian populations respond to ranaviral infection. In the United Kingdom, ranaviruses impact the common frog (Rana temporaria). Extensive public engagement in the study of ranaviruses in the UK has led to the formation of a unique system of field sites containing frog populations of known ranaviral disease history. Within this...

Data from: Comparison of methods for molecular species delimitation across a range of speciation scenarios

Arong Luo, Cheng Ling, Simon Y.W. Ho, Chao-Dong Zhu & Simon Y W Ho
Species are fundamental units in biological research and can be defined on the basis of various operational criteria. There has been growing use of molecular approaches for species delimitation. Among the most widely used methods, the generalized mixed Yule-coalescent (GMYC) and Poisson tree processes (PTP) were designed for the analysis of single-locus data but are often applied to concatenations of multilocus data. In contrast, the Bayesian multispecies coalescent approach in the software BPP explicitly models...

Data from: Reef accessibility impairs the protection of sharks

Jean-Baptiste Juhel, Laurent Vigliola, David Mouillot, Michel Kulbicki, Tom B. Letessier, Jessica J. Meeuwig & Laurent Wantiez
1. Reef sharks are declining worldwide under ever increasing fishing pressure with potential consequences on ecosystem functioning. Marine protected areas (MPAs) are currently one of the management tools to counteract the pervasive impacts of fishing. However, MPAs in which reef sharks are abundant tend to be located in remote and underexploited areas preventing a fair assessment of management effectiveness beyond remoteness from human activities. 2. Here we determine the conditions under which MPAs can effectively...

Data from: Reconstructing the emergence of a lethal infectious disease of wildlife supports a key role for spread through translocations by humans

Stephen J. Price, Trenton W.J. Garner, Andrew A. Cunningham, Tom E.S. Langton & Richard A. Nichols
There have been few reconstructions of wildlife disease emergences, despite their extensive impact on biodiversity and human health. This is in large part attributable to the lack of structured and robust spatio-temporal datasets. We overcame logistical problems of obtaining suitable information by using data from a citizen science project and formulating spatio-temporal models of the spread of a wildlife pathogen (genus Ranavirus, infecting amphibians). We evaluated three main hypotheses for the rapid increase in disease...

Data from: Resource selection and landscape change reveal mechanisms suppressing population recovery for the world's most endangered antelope

Abdullahi H. Ali, Adam T. Ford, Jeffrey S. Evans, David P. Mallon, Matthew M. Hayes, Juliet King, Rajan Amin & Jacob R. Goheen
Understanding how bottom-up and top-down forces affect resource selection can inform restoration efforts. With a global population size of <500 individuals, the hirola Beatragus hunteri is the world's most endangered antelope, with a declining population since the 1970s. While the underlying mechanisms are unclear, some combination of habitat loss and predation are thought to be responsible for low abundances of contemporary populations. Efforts to conserve hirola are hindered by a lack of understanding as to...

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: Evolutionarily distinct “living fossils” require both lower speciation and lower extinction rates

Dominic J. Bennett, Mark D. Sutton & Samuel T. Turvey
As a label for a distinct category of life, ‘living fossil’ is controversial. The term has multiple definitions and it is unclear whether the label can be genuinely used to delimit biodiversity. Even taking a purely phylogenetic perspective where a proxy for the living fossil is evolutionary distinctness (ED), an inconsistency arises: does it refer to “dead-end” lineages doomed to extinction or “panchronic” lineages that survive through multiple epochs? Recent tree-growth model studies indicate that...

Data from: Thyroid hormone modulates offspring sex ratio in a turtle with temperature-dependent sex determination

Bao-Jun Sun, Teng Li, Yi Mu, Jessica K. McGlashan, Arthur Georges, Richard Shine & Wei-Guo Du
The adaptive significance of temperature-dependent sex determination (TSD) has attracted a great deal of research, but the underlying mechanisms by which temperature determines the sex of a developing embryo remain poorly understood. Here, we manipulated the level of a thyroid hormone (TH), triiodothyronine (T3), during embryonic development (by adding excess T3 to the eggs of the red-eared slider turtle Trachemys scripta, a reptile with TSD), to test two competing hypotheses on the proximate basis for...

Data from: A multi-genome analysis approach enables tracking of the invasion of a single Russian wheat aphid (Diuraphis noxia) clone throughout the New World

Le Kang, Bo Zhang, Susan Fuller & Owain Edwards
This study investigated the population genetics, demographic history and pathway of invasion of the Russian wheat aphid (RWA) from its native range in Central Asia, the Middle East and Europe to South Africa and the Americas. We screened microsatellite markers, mitochondrial DNA, and endosymbiont genes in 504 RWA clones from nineteen populations worldwide. Following pathway analyses of microsatellite and endosymbiont data, we postulate that Turkey and Syria were the most likely sources of invasion to...

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: Predator size and prey size-gut capacity ratios determine kill frequency and carcass production in terrestrial carnivorous mammals

Annelies De Cuyper, Marcus Clauss, Chris Carbone, Daryl Codron, An Cools, Myriam Hesta & Geert P. J. Janssens
Carnivore kill frequency is a fundamental part of predator-prey interactions, which are important shapers of ecosystems. Current field kill frequency data are rare and existing models are insufficiently adapted to carnivore functional groups. We developed a kill frequency model accounting for carnivore mass, prey mass, pack size, partial consumption of prey and carnivore gut capacity. Two main carnivore functional groups, small prey-feeders vs large prey-feeders, were established based on the relationship between stomach capacity (C)...

Data from: Resolving ambiguity of concatenation in multi-locus sequence data for the construction of phylogenetic supermatrices

Alfried P. Vogler & Douglas Chesters
The construction of supermatrices from mining of DNA metadata is problematic due to incomplete species identification and incongruence of gene trees that hamper sequence concatenation based on Linnaean binomials. We applied methods from graph theory to minimize ambiguity of concatenation globally over a large data set. An initial step establishes sequence clusters for each locus that broadly correspond to Linnaean species. These clusters frequently are not consistent with binomials and specimen identifiers, which greatly complicates...

Data from: Does catch and release affect the mating system and individual reproductive success of wild Atlantic salmon (Salmo salar L.)?

Antoine Richard, Mélanie Dionne, Jinliang Wang & Louis Bernatchez
In this study, we documented the breeding system of a wild population of Atlantic salmon (Salmo salar L.) by genetically sampling every returning adult and assessed the determinants of individual fitness. We then quantified the impacts of catch and release (C&R) on mating and reproductive success. Both sexes showed high variance in individual reproductive success, and the estimated standardized variance was higher for males (2.86) than for females (0.73). We found a weak positive relationship...

Data from: Isolation and no-entry marine reserves mitigate anthropogenic impacts on grey reef shark behavior

Jean-Baptiste Juhel, Laurent Vigliola, Laurent Wantiez, Tom B. Letessier, Jessica J. Meeuwig & David Mouillot
Reef sharks are vulnerable predators experiencing severe population declines mainly due to overexploitation. However, beyond direct exploitation, human activities can produce indirect or sub-lethal effects such as behavioral alterations. Such alterations are well known for terrestrial fauna but poorly documented for marine species. Using an extensive sampling of 367 stereo baited underwater videos systems, we show modifications in grey reef shark (Carcharhinus amblyrhynchos) occurrence and feeding behavior along a marked gradient of isolation from humans...

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