cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.r92b0
title: Data from: How populations differentiate despite gene flow: sexual and natural selection drive phenotypic divergence within a land fish, the Pacific leaping blenny

description: Background: Divergence between populations in reproductively important
 features is often vital for speciation. Many studies attempt to identify
 the cause of population differentiation in phenotype through the study of
 a specific selection pressure. Holistic studies that consider the
 interaction of several contrasting forms of selection are more rare. Most
 studies also fail to consider the history of connectivity among
 populations and the potential for genetic drift or gene flow to facilitate
 or limit phenotypic divergence. We examined the interacting effects of
 natural selection, sexual selection and the history of connectivity on
 phenotypic differentiation among five populations of the Pacific leaping
 blenny (Alticus arnoldorum), a land fish endemic to the island of Guam.
 Results: We found key differences among populations in two male
 ornaments—the size of a prominent head crest and conspicuousness of a
 coloured dorsal fin—that reflected a trade-off between the intensity of
 sexual selection (male biased sex ratios) and natural selection (exposure
 to predators). This differentiation in ornamentation has occurred despite
 evidence suggesting extensive gene flow among populations, which implies
 that the change in ornament expression has been recent (and potentially
 plastic). Conclusions: Our study provides an early snapshot of divergence
 in reproductively important features that, regardless of whether it
 reflects genetic or plastic changes in phenotype, could ultimately form a
 reproductive barrier among populations.
description: MORGANS_CL-BMC-EVOL-BIOL-9452502551123027_dataAll data associated with Morgans et al. 2014
DOI: 10.5061/dryad.24ch1
title: Data from: Seabird species vary in behavioural response to drone census

description: Unmanned aerial vehicles (UAVs) provide an opportunity to rapidly census
 wildlife in remote areas while removing some of the hazards. However,
 wildlife may respond negatively to the UAVs, thereby skewing counts. We
 surveyed four species of Arctic cliff-nesting seabirds (glaucous gull
 Larus hyperboreus, Iceland gull Larus glaucoides, common murre Uria aalge
 and thick-billed murre Uria lomvia) using a UAV and compared censusing
 techniques to ground photography. An average of 8.5% of murres flew off in
 response to the UAV, but &gt;99% of those birds were non-breeders. We
 were unable to detect any impact of the UAV on breeding success of murres,
 except at a site where aerial predators were abundant and several birds
 lost their eggs to predators following UAV flights. Furthermore, we found
 little evidence for habituation by murres to the UAV. Most gulls flew off
 in response to the UAV, but returned to the nest within five minutes.
 Counts of gull nests and adults were similar between UAV and ground
 photography, however the UAV detected up to 52.4% more chicks because
 chicks were camouflaged and invisible to ground observers. UAVs provide a
 less hazardous and potentially more accurate method for surveying
 wildlife. We provide some simple recommendations for their use.
description: Counts and flushing of
 Thick-billed murresSheets 1: Thick-billed
 murres counts in various plots at Digges Island (with UAV and with ground
 camera). NA indicate days when we could not count murres in a plot due to
 various reasons. ///// Sheets 2: Thick-billed murre flushing pourcentage
 in a plot in reaction to an approaching drone at Coats Island. See the
 related article for details.
DOI: 10.5061/dryad.n36sn
title: Data from: Leaf meristems: an easily ignored component of the response to human disturbance in alpine grasslands

description: Grazing and fencing are two important factors that influence productivity
 and biomass allocation in alpine grasslands. The relationship between root
 (R) and shoot (S) biomass and the root:shoot ratio (R/S) are critical
 parameters for estimating the terrestrial carbon stocks and biomass
 allocation mechanism responses to human activities. Previous studies have
 often used the belowground:aboveground biomass ratio (Mb/Ma) to replace
 the R/S in alpine ecosystems. However, these studies may have neglected
 the leaf meristem biomass, which belongs to the shoot but occurs below the
 soil surface, leading to a significant overestimation of the R/S ratio. We
 conducted a comparative study to explore the differences between the R/S
 and Mb/Ma at both the species (Stipa purpurea, Carex moorcroftii, and
 Artemisia nanschanica) and community levels on a Tibetan alpine grassland
 with grazing and fencing management blocks. The results revealed that the
 use of the Mb/Ma to express the R/S appeared to overestimate the actual
 value of the R/S, both at species and community levels. For S. purpurea,
 the Mb/Ma was three times higher than the R/S. The Mb/Ma was approximately
 two times higher than the R/S for the species of C. moorcroftii and A.
 nanschanica and at the community level. The relationships between the R-S
 and Mb-Ma exhibited different slopes for the alpine plants across all the
 management practices. Compared to the fenced grasslands, the plants in the
 grazing blocks not only allocated more biomass to the roots but also to
 the leaf meristems. The present study highlights the contribution of leaf
 meristems to the accurate assessment of shoot and belowground biomasses.
 The R/S and Mb/Ma should be cautiously used in combination in the future
 research. The understanding of the distinction between the R-S and Mb-Ma
 may help to improve the biomass allocation mechanism response to human
 disturbances in an alpine area.
description: Biomass
 dataThe file contains all
 the biomass data in the experiment.
DOI: 10.5061/dryad.56cn1
title: Data from: Resistance to genetic insect control: modelling the effects of space

description: Genetic insect control, such as self-limiting RIDL2 (Release of Insects
 Carrying a Dominant Lethal) technology, is a development of the sterile
 insect technique which is proposed to suppress wild populations of a
 number of major agricultural and public health insect pests. This is
 achieved by mass rearing and releasing male insects that are homozygous
 for a repressible dominant lethal genetic construct, which causes death in
 progeny when inherited. The released genetically engineered
 ('GE') insects compete for mates with wild individuals,
 resulting in population suppression. A previous study modelled the
 evolution of a hypothetical resistance to the lethal construct using a
 frequency-dependent population genetic and population dynamic approach.
 This found that proliferation of resistance is possible but can be diluted
 by the introgression of susceptible alleles from the released
 homozygous-susceptible GE males. We develop this approach within a spatial
 context by modelling the spread of a lethal construct and resistance
 trait, and the effect on population control, in a two deme metapopulation,
 with GE release in one deme. Results show that spatial effects can drive
 an increased or decreased evolution of resistance in both the target and
 non-target demes, depending on the effectiveness and associated costs of
 the resistant trait, and on the rate of dispersal. A recurrent theme is
 the potential for the non-target deme to act as a source of resistant or
 susceptible alleles for the target deme through dispersal. This can in
 turn have a major impact on the effectiveness of insect population
 control.
description: Zip file of README text
 and R scriptsThis zip file contains R
 scripts containing code and functions for running simulations of the
 model. The README file describes what each file does.Watkinson-Powell_Alphey_JTB2017_code.zip
DOI: 10.5061/dryad.dk5gt88
title: Data from: Seasonally dependent relationship between insect herbivores and host plant density in Jatropha nana, a tropical perennial herb

description: The fact that plant spatial aggregation patterns shape insect herbivore
 communities in a variety of ways has resulted in a large body of
 literature on the subject. The landmark resource concentration hypothesis
 predicts that density of insect-herbivores per plant will increase as host
 plant density increases. I examined this prediction across temporal
 samplings using Jatropha nana and the associated specialist
 insect-herbivores as a system. Through 12 field samplings, I modelled the
 effect of host plant density on insect-herbivore loads. The initial
 samplings (2-3) provided evidence for the resource concentration
 hypothesis with insect loads increasing with increasing host plant
 density, whereas the later samplings (4-5, 7-11) showed the opposite- a
 resource dilution pattern with decline of insect loads with increasing
 host plant density. These patterns also depend on the biology of the
 herbivores and have important implications on J. nana population dynamics.
description: data for Dryad Nerlekar
 2018 RCH paperSheet 1 contains the
 predictor and response variables re-arranged and results for Poisson
 regression analysis. Sheet 2 contains raw data for ramet density, insect
 load and relative abundance of each species over
 samplings.
DOI: 10.5061/dryad.5bm68
title: Data from: Legacy effects of developmental stages determine the functional role of predators

description: Predators are instrumental in structuring natural communities and
 ecosystem processes. The strong effects of predators are often attributed
 to their high trophic position in the food web. However, most predators
 have to grow and move up the food chain before reaching their final
 trophic position and during this developmental process, their traits,
 interactions, and abundances change. Here we show that this process of
 “moving up” the food chain during development strongly determines the
 ecological role of a predator. By experimentally manipulating the
 succession of developmental stages of a predatory salamander in seasonal
 aquatic ecosystem, we found that effects of this apex predator on the
 ecosystem typically declined with age and size. Furthermore, younger,
 smaller predator stages had long-lasting effects on community structure
 and ecosystem function that determined effects of subsequent older, larger
 stages. Consequently, legacy effects of early stages largely shaped the
 impact of the predator on the ecosystem, which could not simply be
 inferred from its final trophic position. Our results highlight that
 accounting for all life stages when managing natural populations is
 crucial to preserve functioning of natural ecosystems, especially given
 that early life stages of species are often particularly vulnerable to
 natural and anthropogenic disturbances.
description: Cohort experiment
 dataThis file contains data
 for primary producers, decomposition rates, net primary productivity and
 respiration rates, community structure, and biomass of functional groups,
 either as repeated samples or final measurements at the end of the
 experiment. Details on individual data sheet are given in readme
 file.Cohort_data_all.zip
DOI: 10.5061/dryad.b0jt8h3
title: Data from: Female ornamentation and the fecundity trade-off in a sex-role reversed pipefish

description: Sexual ornaments found only in females are a rare occurrence in nature.
 One explanation for this is that female ornaments are costly to produce
 and maintain and, therefore, females must trade-off resources related to
 reproduction to promote ornament expression. Here, we investigate whether
 a trade-off exists between female ornamentation and fecundity in the
 sex-role reversed, wide-bodied pipefish, Stigmatopora nigra. We measured
 two components of the disk-shaped, ventral-striped female ornament, body
 width and stripe thickness. After controlling for the influence of body
 size, we found no evidence of a cost of belly width or stripe thickness on
 female fecundity. Rather, females that have larger ornaments have higher
 fecundity and thus accurately advertise their reproductive value to males
 without incurring a cost to fecundity. We also investigated the
 relationship between female body size and egg size and found that larger
 females suffered a slight decrease in egg size and fecundity, although
 this decrease was independent of female ornamentation. More broadly,
 considered in light of similar findings in other taxa, lack of an apparent
 fecundity cost of ornamentation in female pipefish underscores the need to
 revisit theoretical assumptions concerning the evolution of female
 ornamentation.
description: Data for male and female
 Stigmatopora nigraData from Museum
 Victoria Stigmatopora nigra collections used in the study of female
 ornamentation. Collection information, body size (total length, snout-vent
 length), damage to fish, numbers of eggs in the male brood pouch, numbers
 of eggs in ovaries, egg size, and ornament (belly width, stripe thickness)
 details are given.Mobley et al Stigmatopora nigra
 data.xlsx
DOI: 10.5061/dryad.58q4d
title: Data from: Sexually selected dichromatism in the hihi Notiomystis cincta: multiple colours for multiple receivers

description: 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
 dichromatic hihi (Notiomystis cincta) plumage is currently under sexual
 selection, with detailed behavioural and genetic analyses of a free-living
 island population. Bateman gradients measured for males and females reveal
 the potential for sexual selection, whilst selection gradients, relating
 reproductive success to specific colourful traits, show there is
 stabilizing selection on white ear tuft length in males. By correlating
 colourful male plumage with different components of reproductive success,
 we show that properties of yellow plumage are most likely a product of
 male-male competition, whilst properties of the black and white plumage
 are an outcome of both male-male competition and female choice. Male
 plumage therefore potentially signals to multiple receivers (rival males
 and potential mates) and this may explain the multi-coloured appearance of
 one of the most strikingly dichromatic species in New Zealand.
description: island colour
 variationYellow colour variables
 for male hihi from three different islandsplumage
 traitsMale plumage colour
 variables and measures of reproductive success, used to calculate
 selection gradientsreproductive
 successMeasures of male and
 female mating and reproductive success, used to calculate Bateman
 gradientsunknown
 fertilizationsFather id (and plumage
 traits) of each offspring, used to test whether unknown fertilizations may
 bias results
DOI: 10.5061/dryad.19m2k
title: Data from: Chimeric viruses blur the borders between the major groups of eukaryotic single-stranded DNA viruses

description: Metagenomic studies have uncovered an astonishing diversity of ssDNA
 viruses encoding replication proteins (Reps) related to those of
 eukaryotic Circoviridae, Geminiviridae or Nanoviridae; however, exact
 evolutionary relationships among these viruses remain obscure. Recently, a
 unique chimeric virus (CHIV) genome, which has apparently emerged via
 recombination between ssRNA and ssDNA viruses, has been discovered. Here
 we report on the assembly of 13 new CHIV genomes recovered from various
 environments. Our results indicate a single event of capsid protein (CP)
 gene capture from an RNA virus in the history of this virus group. The
 domestication of the CP gene was followed by an unprecedented recurrent
 replacement of the Rep genes in CHIVs with distant counterparts from
 diverse ssDNA viruses. We suggest that parasitic and symbiotic
 interactions between unicellular eukaryotes were central for the emergence
 of CHIVs and that such turbulent evolution was primarily dictated by
 incongruence between the CP and Rep proteins.
description: Assembled_chimeric_viruses_Gb-filesThis zip package contains the annotated genbank file for each chimeric virus genome described and analyzed in the manuscript.
DOI: 10.5061/dryad.6b578
title: Data from: Selection on an extreme weapon in the frog legged leaf beetle (Sagra femorata)

description: Biologists have been fascinated with the extreme products of sexual
 selection for decades. However, relatively few studies have characterized
 patterns of selection acting on ornaments and weapons in the wild. Here,
 we measure selection on a wild population of weapon-bearing beetles (frog
 legged leaf beetles: Sagra femorata) for two consecutive breeding seasons.
 We consider variation in both weapon size (hindleg length), and in
 relative weapon size (deviations from the population average scaling
 relationship between hindleg length and body size), and provide evidence
 for directional selection on weapon size per se and stabilizing selection
 on a particular scaling relationship in this population. We suggest that
 whenever growth in body size is sensitive to external circumstance such as
 nutrition, then considering deviations from population-level scaling
 relationships will better reflect patterns of selection relevant to
 evolution of the ornament or weapon than will variation in trait size per
 se. This is because trait-size versus body-size scaling relationships
 approximate underlying developmental reaction norms relating trait growth
 with body condition in these species. Heightened condition-sensitive
 expression is a hallmark of the exaggerated ornaments and weapons favored
 by sexual selection, yet this plasticity is rarely reflected in the way we
 think about – and measure – selection acting on these structures in the
 wild.
description: Allometry
 2015Allometry data from 2015
 seasonallometry_2015.csvMating Success 2015Mating success data from 2015 seasonmating_success_2015.csvMating Success and Allometry 2014Data for allometry and mating success for 2014 season.mating_success_allometry_2014.csv
DOI: 10.5061/dryad.q84p862
title: Data from: A method that accounts for differential detectability in mixed samples of long-term infections with applications to the case of Chronic Wasting Disease in cervids

description: 1. Surveillance of wildlife diseases is logistically difficult, and
 imperfect detection is a recurrent challenge for disease estimation. Using
 citizen science can increase sample sizes, but it is associated with a
 cost in terms of the anatomical type and quality of the sample.
 Additionally, biological tissue samples from remote areas lose quality due
 to autolysis. These challenges are faced in the case of emerging Chronic
 Wasting Disease (CWD) in cervids. 2. Here, we develop a stochastic
 scenario tree model of diagnostic sensitivity, allowing for a mixture of
 tissue sample types (lymph nodes and brain) and qualities while accounting
 for different detection probabilities during the CWD infection, lasting
 2-3 years. We apply the diagnostic sensitivity in a Bayesian framework,
 enabling estimation of age-class-specific true prevalence, including the
 prevalence in latent, recently infected stages. We provide a simulation
 framework to estimate the sensitivity of the surveillance system (i.e.,
 the probability of detecting the infection in a given population), when
 detectability varies among individuals due to different disease
 progression. 3. We demonstrate the utility of our framework by applying it
 to the recent emergence of CWD in a European population of reindeer. We
 estimated apparent CWD prevalence at 1.2 % of adults in the infected
 population of wild reindeer, while the true prevalence was 1.6 %. The
 sensitivity estimation of the CWD surveillance was performed in an
 adjacent small (~500) and a large (~10,000) reindeer population,
 demonstrating low certainty of CWD absence. 4. Our method has immediate
 application to the mandatory testing for CWD in EU countries commencing in
 2018. Similar approaches that account for latent stages and a serial
 disease progression in various tissues with a temporal pattern of
 diagnostic sensitivity may enhance the estimation of the prevalence of
 wildlife diseases more generally.
description: datViljugrein_etal2018Data on tested reindeer for Nordfjella and Hardangervidda used in application 1 and/or 2Application2_PrDetectingDiseasescript for Application 2Functions_modelling_dSeFunctions for modelling diagnostic sensitivityModelling_dSeThe modelling of diagnostic sensitivity (dSE)NordfjellaPrevalenceModelApplication 1, Set up the bug-models used in Run_dhyper_CWDprevalence.RRun_dhyper_CWDprevalenceApplication 1, Estimating prevalence
DOI: 10.5061/dryad.k8776
title: Data from: Climate effects on growth, body condition and survival depend on the genetic characteristics of the population

description: Climatic change is expected to affect individual life-histories and
 population dynamics, potentially increasing vulnerability to extinction.
 The importance of genetic diversity has been highlighted for adaptation
 and population persistence. However, whether responses of life-history
 traits to a given environmental condition depend on the genetic
 characteristics of a population remains elusive. Here we tested this
 hypothesis in the lizard Zootoca vivipara, by simultaneously manipulating
 habitat humidity, a major climatic predictor of Zootoca's
 distribution, and adult male colour morph frequency, a trait with
 genome-wide linkage. Interactive effects of humidity and morph frequency
 had immediate effects on growth and body condition of juveniles and
 yearlings, and on adult survival, and delayed effects on offspring size.
 In yearlings, higher humidity led to larger female body size, and lower
 humidity led to higher male compared to female survival. In juveniles and
 yearlings, some treatment effects were compensated over time. The results
 show that individual responses to environmental conditions depend on the
 population's colour morph frequency, age class and sex, and that
 these affect intra- and inter-age class competition. Moreover, humidity
 affected the competitive environment, rather than imposing trait-based
 selection on specific colour morphs. This indicates that species'
 responses to changing environments, e.g. to climate change, are highly
 complex, and difficult to accurately reconstruct and predict without
 information on the genetic characteristics and demographic structure of
 populations.
description: Data Romero-Diaz et al
 2017Data on juvenile,
 yearling and adult growth rate, body condition and survival, clutch size
 and offspring traits (snout-vent-length, tail length and body condition at
 hatching)