cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.fc0m627
title: Data from: The role of cuticular hydrocarbons in mate recognition in Drosophila suzukii

description: Cuticular hydrocarbons (CHCs) play a central role in the chemical
 communication of many insects. In Drosophila suzukii, an economically
 important pest insect, very little is known about chemical communication
 and the possible role of CHCs. In this study, we identified 60 CHCs of
 Drosophila suzukii and studied their changes in function of age
 (maturation), sex and interactions with the opposite sex. We demonstrate
 that age (maturation) is the key factor driving changes in the CHC
 profiles. We then test the effect on courtship behaviour and mating of six
 CHCs, five of which were positively associated with maturation and one
 negatively. The results of these experiments demonstrate that four of the
 major CHC peaks with a chain length of 23 carbons, namely 9-tricosene
 (9-C23:1), 7-tricosene (7-C23:1), 5-tricosene (5-C23:1) and tricosane
 (n-C23), negatively regulated courtship and mating, even though all these
 compounds were characteristic for sexually mature flies. We then go on to
 show that this effect on courtship and mating is likely due to the
 disruption of the natural ratios in which these hydrocarbons occur in
 Drosophila suzukii. Overall, these results provide key insights into the
 cuticular hydrocarbon signals that play a role in D. suzukii mate
 recognition.
description: Code for bioassay
 analysisCode written in R to
 analyze the bioassays to test the impact of CHCs on behavior of Drosophila
 suzukii.analysis
 bioassays.RCode to analyze CHC
 profilesCode written in R to
 analyze CHC profilesanalysis CHC
 profiles.RCHC_profiles_absolute
 quantities_ngAbsolute quantities in
 ng of all CHCs.data_fig4Data used to generate figure 4data_fig5Data used to generate figure 5.
DOI: 10.5061/dryad.cq983
title: Data from: The rules for symbiont community assembly change along a mutualism-parasitism continuum

description: Symbiont community assembly is driven by host-symbiont and
 symbiont-symbiont interactions.The effects that symbionts exert on their
 hosts are often context-dependent and existing theoretical frameworks of
 symbiont community assembly do not consider the implications of variable
 outcomes to assembly processes. We hypothesized that symbiont-symbiont
 interactions become increasingly important along a parasitism/mutualism
 continuum because; a) negative outcomes favor host resistance which in
 turn reduces symbiont colonization and subsequently reduce
 symbiont-symbiont interactions, whereas b) positive host outcomes favor
 tolerance and consequently higher symbiont colonization rates, leading to
 stronger interactions among symbionts. We found support for this
 hypothesis in the cleaning symbiosis between crayfish and ectosymbiotic
 branchiobdellidan worms. The symbiosis between crayfish and their worms
 can shift from parasitism/commensalism to mutualism as crayfish age. Here,
 field surveys identified changes in worm density, diversity, and
 composition that were concomitant to changing symbiosis outcomes. We
 conducted several laboratory experiments and behavioral assays to relate
 patterns from the field to their likely causal processes. Young crayfish
 typically hosted only two relatively small worm species. Older crayfish
 hosted two additional larger species. In laboratory experiments, young
 crayfish exhibited a directed grooming response to all worm species, but
 were unable to remove small species. Conversely, adult crayfish did not
 exhibit grooming responses to any worm species. Relaxed grooming allowed
 the colonization of large worm species and initiated symbiont-symbiont
 intraguild predation that reduced the abundance and altered the behavior
 of small worm species. Thus, the dominant processes of symbiont community
 assembly shifted from host resistance to symbiont-symbiont interactions
 through host ontogeny and a concomitant transition towards mutualism. This
 work shows that host resistance can have a prevailing influence over
 symbiont community assembly when symbiosis is disadvantageous to the host.
 However, when symbiosis is advantageous and resistance is relaxed,
 symbiont colonization rate and consequently abundance and diversity
 increases, and interactions among symbionts become increasingly important
 to symbiont community assembly.
description: Worm
 countsCounts of the number of
 each worm species remaining during the worm species interaction
 experiment.counts.csvCrayfish data for worm interaction experimentMetadata for all crayfish used in symbiont interaction experiment.crays.csvCrayfish surveyMetadata for crayfish collected during field survey.Crayfish.xlsxSURVEYWorms observed during field survey.behave_expBehaviors observed during behavior experiment.cray_expMetadata for crayfish used during behavior experiment.
DOI: 10.5061/dryad.8f0d4
title: Data from: Hybridization as a threat in climate relict Nuphar pumila (Nymphaeaceae)

description: Field studies and conceptual work on hybridization-mediated extinction
 risk in climate relicts are extremely rare. Nuphar pumila (Nymphaeaceae)
 is one of the most emblematic climate relicts in Europe with few isolated
 populations in the Alpine arc. The extent of introgression with related
 lowland and generalist species Nuphar lutea has never been studied using
 molecular methods. All biogeographical regions where N. pumila naturally
 occurs in the neighbourhood of the Alpine arc were sampled and studied
 using nuclear microsatellite markers. Furthermore, we used forward-in-time
 simulations and Approximate Bayesian Computation to check whether an
 introgression scenario fits with the observed admixture patterns and
 estimated the demographic parameters associated with this process. Our
 study confirms ongoing hybridization between N. pumila and N. lutea and
 validates it by the use of population models. More than 40 % of
 investigated N. pumila individuals were admixed and hybrids were found in
 over 60 % of studied populations. The introgression is bidirectional and
 is most likely a result of very recent gene flow. Our work provides strong
 evidence for rapid extinction risk and demographic swamping between
 specialized climatic relicts and closely related generalists. The
 remaining pure populations of N. pumila are rare in the Alpine arc and
 deserve high conservation priority.
description: Nuphar_ABC_Arrigo2016This folder contains: - SSR/ = empirical SSR dataset - data/ = ini files, hard coded - Qoutputs/ = quantinemo outputs - Qparams/ = quantinemo parameter files - Qstats/ = final summary stats - scripts/ = all needed scripts, look at README.jpg to get an idea how how the pipeline works - quantinemo = QuantiNemo V 1.6.0 (unreleased), can be downloaded at http://www.unil.ch/popgen/softwares/quantinemo/blaser_et_al_evolution.zip otherwise, contact Samuel Neuenschwander for getting a copy. Note that the pipeline must be started from scripts/ using the following command: perl ABC_loader.pl ncores nmax -ncore = number of parallel instances of quantiNemo you want to run -nmax = launch jobs until reaching nmax CPU load Dependencies: ## Linux OS, Ubuntu 10.04 ## Perl v5.10.1 threads; threads::shared; File::Basename; List::Util qw(shuffle); ## R &gt;= 3.0.0 e1071 ## QuantiNemo: V 1.6.0
DOI: 10.5061/dryad.p0s3g
title: Data from: Vitally important – does early innate immunity predict recruitment and adult innate immunity?

description: The immune system is one of the most important adaptations that has
 evolved to protect animals from a wide range of pathogens they encounter
 from early life onwards. During the early developmental period this is
 particularly true for the innate immunity, as other components of the
 immune system are, as yet, poorly developed. But innate immunity may not
 only be crucial for early life survival, but may also have long-lasting
 effects, for example if early life immunity reflects the functioning of
 the immune system as a whole. For this reason, we investigated the
 importance of four constitutive innate immune parameters (natural
 antibodies, complement activity, concentrations of haptoglobin, and
 concentrations of nitric oxide) for recruitment in free-living great tits.
 We compared nestling immunity of recruits with nestling immunity of their
 nonrecruited siblings. We also investigated within individual consistency
 of these innate immune parameters for those individuals that recruited,
 which may be taken as a measure of immune capacity. In accordance with
 previous studies, we found a clear effect of tarsus length and a trend for
 body mass on the likelihood to recruit. Nevertheless, we found no evidence
 that higher levels of constitutive innate immunity as a nestling
 facilitated local recruitment. Furthermore, individual innate immunity was
 not consistent across life stages, that is to say, nestling immune
 parameters did not determine, or respectively, reflect adult innate immune
 parameters. This plasticity in innate immune components may explain why we
 did not find long-lasting survival benefits.
description: Vermeulen_et_al_DryadDataData on recruitment and immunity of great tits sampled in the field are presented. There are four sheets available, one for each main analysis as explained in the manuscript. Sheet names give a more clear view of the data in the Excel file. The first sheet "All" contains data for all recruited birds, their non-recruited siblings and randomly analysed samples from nests containing no recruits. The second sheet "recruits night + breeding seas." contains data of all recruits, that is birds that established a territory either in winter or during the breeding season, and their non-recruited siblings. The third sheet "recruits only breeders" contains data of only birds that eventually bred and their non-recruited siblings. Finally, the last sheet "consistency" contains data of recruited nestlings and the same individuals as adults. Relevant abbreviations are explained in the Excel file.
DOI: 10.5061/dryad.fh174
title: Data from: Individual versus pseudo-repeatability in behaviour: lessons from translocation experiments in a wild insect

description: 1. Repeatability represents a key parameter in ecological and evolutionary
 research. Repeatability is underpinned by developmental plasticity and
 genetic variation but may become biased upwards by repeatable differences
 in environments to which individuals respond plastically. The extent of
 upward bias caused by the latter mechanism (causing
 “pseudo-repeatability”) is important yet rarely investigated in ecological
 research. 2. We repeatedly assayed a key behaviour (flight initiation
 distance) affecting longevity in a wild cricket population (Gryllus
 campestris). We used naturally moving, translocated, and forced-stationary
 individuals to study bias in repeatability caused by spatial variability
 in environmental conditions. 3. Our experiments acknowledged that
 translocations might themselves bias repeatability estimates if animals
 respond to handling procedures (a necessary component of translocations).
 Individuals were therefore either (i) repeatedly translocated and assayed,
 or (ii) assayed at multiple burrows as part of natural movements. This
 enabled estimation of behavioural variance attributable to individual,
 burrow, and residual components within each treatment; comparison across
 treatments addressed whether translocations caused bias. We also
 calculated repeatability for individuals that forced to be stationary to
 investigate whether this led to upward biases of repeatability. 4. For
 adult crickets, individual explained 17.8% versus 17.2%, and burrow 8.7%
 versus 10.3%, of the behavioural variance in translocated versus
 natural-movement treatments. Repeatability for forced-stationary adults
 was 31.1%, thereby demonstrating experimentally that certain study designs
 bias repeatability upwards. For translocated juveniles, individual
 explained 10.0% and burrow 6.0% of the variance while in the
 natural-movement treatment those components could not be separated as
 juveniles do not switch burrows. Translocations did not lead to detectable
 biases in behavioural mean or variance. 5. Repeatability was not biased
 for adults subjected to the natural-movement treatment because individuals
 were assayed under many different environments, facilitating the
 separation of individual from burrow effects. Upward bias would have
 occurred with less optimal sampling schemes: if individuals had been
 assayed repeatedly at the same burrow. We therefore recommend that
 translocation experiments are more commonly applied, particularly in
 stationary species, to ensure the unbiased estimation of repeatability.
description: Niemela and
 Dingemanse_Journal of Animal Ecology 2017
DOI: 10.5061/dryad.mn324
title: Data from: Distinct neural and neuromuscular strategies underlie independent evolution of simplified advertisement calls

description: Independent or convergent evolution can underlie phenotypic similarity of
 derived behavioural characters. Determining the underlying neural and
 neuromuscular mechanisms sheds light on how these characters arose. One
 example of evolutionarily derived characters is a temporally simple
 advertisement call of male African clawed frogs (Xenopus) that arose at
 least twice independently from a more complex ancestral pattern. How did
 simplification occur in the vocal circuit? To distinguish shared from
 divergent mechanisms, we examined activity from the calling brain and
 vocal organ (larynx) in two species that independently evolved simplified
 calls. We find that each species uses distinct neural and neuromuscular
 strategies to produce the simplified calls. Isolated Xenopus borealis
 brains produce fictive vocal patterns that match temporal patterns of
 actual male calls; the larynx converts nerve activity faithfully into
 muscle contractions and single clicks. In contrast, fictive patterns from
 isolated Xenopus boumbaensis brains are short bursts of nerve activity;
 the isolated larynx requires stimulus bursts to produce a single click of
 sound. Thus, unlike X. borealis, the output of the X. boumbaensis
 hindbrain vocal pattern generator is an ancestral burst-type pattern,
 transformed by the larynx into single clicks. Temporally simple
 advertisement calls in genetically distant species of Xenopus have thus
 arisen independently via reconfigurations of central and peripheral vocal
 neuroeffectors.
description: Leininger_KelleyInter-click and inter-CAP intervals from bouts of vocal activity from calling animals (measured using Signal Sound Analysis software) and fictive activity from isolated brains (measured using Clampfit). Click heights from isolated X. boumbaensis larynx (measured using Clampfit).
DOI: 10.15468/dl.tap8zg
title: Occurrence Download

description: A dataset containing 44 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Nicotiana attenuata",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 44 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000953-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.jr81f
title: Data from: Rewetting of drained boreal spruce swamp forests results in rapid recovery of Sphagnum production

description: 1. Peatland rewetting aims to restore biomass accumulation from
 peat-forming plants for climate change mitigation, biotope conservation
 and water purification purposes. Boreal spruce swamp forests in Europe
 have suffered heavily from drainage for forestry and are now a focus of
 restoration efforts. 2. We measured Sphagnum height and biomass increment
 by allowing Sphagnum to grow through mesh nets located in nine undrained,
 nine drained and 18 rewetted boreal spruce swamp forests. 3. At the moss
 patch level, rewetting led to a recovery of Sphagnum growth: height
 increment and biomass increment at the rewetted sites (5·9 ± 0·7 cm year−1
 and 147 ± 15 g m−2 year−1, mean ± SE) were similar to increment at the
 undrained sites (4·9 ± 0·5 cm year−1 and 128 ± 12 g m−2 year−1), while
 remnant patches of Sphagnum at the drained sites showed smaller increment
 (2·8 ± 0·8 cm year−1 and 76 ± 19 g m−2 year−1). Sphagnum in the ditches at
 the drained sites showed similar increment as the moss at the undrained
 and rewetted sites, while ditches at the rewetted sites had the greatest
 increment (8·7 ± 0·7 cm year−1 and 183 ± 16 g m−2 year−1). A higher
 water-table increased Sphagnum growth, and Sphagnum riparium grew more
 rapidly than the other species. 4. At the ecosystem level, where
 information on moss cover was utilized, rewetting had increased Sphagnum
 production to values close to the undrained sites. At the drained sites,
 biomass production was 8 ± 17 g (mean ± SE) m−2 year−1, at the rewetted
 sites 42 ± 15 g m−2 year−1 and at the undrained sites 66 ± 12 g m−2
 year−1. Sphagnum cover was the most important variable that determined
 Sphagnum production in the ecosystem. 5. Synthesis and applications.
 Drained spruce swamp forests appear to be a suitable target for
 restoration as they respond readily to rather inexpensive rewetting. The
 result points out that even in boreal conditions, restoration results can
 be achieved in a time-scale of years rather than decades. At the ecosystem
 level, rewetting had resulted in a biomass gain of 34 g m−2 year−1 when
 compared to drained sites.
description: Sphagnum height and
 biomass increment in undrained, drained and rewetted boreal spruce swamp
 forestsMeasured using
 grow-through mesh nets located in nine undrained, nine drained and 18
 rewetted sites in 2011-2012.sphagnumgrowth_Maanaviljaetal.csvSphagnum cover in undrained, drained and rewetted boreal spruce swamp forestsSphagnum cover results from a vegetation survey conducted in 2009 (sphagcover_veg). Estimated Sphagnum cover of the growth measurement patches in 2011-2012 (sphagcover_patch). Vegetation survey results first published in: Maanavilja, L., Aapala, K., Haapalehto, T., Kotiaho, J.S. & Tuittila, E. (2014) Impact of drainage and hydrological restoration on vegetation structure in boreal spruce swamp forests. Forest Ecology and Management, 330, 115-125.sphagnumcover_Maanaviljaetal.csv
DOI: 10.5061/dryad.6408r
title: Data from: Pathogen burden, co-infection and major histocompatibility complex variability in the European badger (Meles meles)

description: Pathogen-mediated selection is thought to maintain the extreme diversity
 in the major histocompatibility complex (MHC) genes, operating through the
 heterozygote advantage, rare-allele advantage and fluctuating selection
 mechanisms. Heterozygote advantage (i.e., recognizing and binding a wider
 range of antigens than homozygotes) is expected to be more detectable when
 multiple pathogens are considered simultaneously. Here, we test if MHC
 diversity in a wild population of European badgers (Meles meles) is driven
 by pathogen-mediated selection. We examined individual prevalence
 (infected or not), infection intensity and co-infection of 13 pathogens
 from a range of taxa, and examined their relationships with MHC class I
 and class II variability. This population has a variable, but relatively
 low, number of MHC alleles and is infected by a variety of
 naturally-occurring pathogens, making it very suitable for the
 investigation of MHC-pathogen relationships. We found associations between
 pathogen infections and specific MHC haplotypes and alleles. Co-infection
 status was not correlated with MHC heterozygosity, but there was evidence
 of heterozygote advantage against individual pathogen infections. This
 suggests that rare-allele advantages and/or fluctuating selection, as well
 as heterozygote advantage are likely to be the selective forces shaping
 MHC diversity in this species. We show stronger evidence for
 MHC-associations with infection intensity than for prevalence, and
 conclude that examining both pathogen prevalence and infection intensity
 is important. Moreover, examination of a large number and diversity of
 pathogens, and both MHC class I and II genes (which have different
 functions), provide an improved understanding of the mechanisms driving
 MHC diversity.
description: MHC, microsatellite and
 pathogen dataco-infection
 data
DOI: 10.5061/dryad.d8p5g
title: Data from: The socio-genetics of a complex society: female gelada relatedness patterns mirror association patterns in a multi-level society.

description: Multilevel societies with fission–fusion dynamics—arguably the most
 complex animal societies—are defined by two or more nested levels of
 organization. The core of these societies are modular social units that
 regularly fission and fuse with one another. Despite convergent evolution
 in disparate taxa, we know strikingly little about how such societies form
 and how fitness benefits operate. Understanding the kinship structure of
 complex societies could inform us about the origins of the social
 structure as well as about the potential for individuals in these
 societies to accrue indirect fitness benefits. Here, we combined genetic
 and behavioural data on geladas (Theropithecus gelada), an Old World
 Monkey, to complete the most comprehensive socio-genetic analysis of a
 multilevel society to date. In geladas, individuals in the core social
 ‘units’, associate at different frequencies to form ‘teams’, ‘bands’ and,
 the largest aggregations, ‘communities’. Units were composed of closely
 related females, and females remained with their close kin during
 permanent fissions of units. Interestingly, female–female relatedness also
 significantly predicted between-unit, between-team and between-band
 association patterns, while male–male relatedness did not. Thus, it is
 likely that the socio-genetic structure of gelada society results from
 females maintaining associations with their female relatives during
 successive unit fissions—possibly in an attempt to balance the direct and
 indirect fitness benefits of group living. Overall, the persistence of
 associations among related females across generations appears to drive the
 formation of higher levels of gelada society, suggesting that females seek
 kin for inclusive fitness benefits at multiple levels of gelada society
description: Genetic and demographic
 dataExcel spreadsheet with
 genotypes, demographic data, and association indices for all study animals
 and units.data for
 dryad.xlsx
DOI: 10.5061/dryad.26256
title: Data from: Conservation versus livelihoods: spatial management of non-timber forest product harvests in a two-dimensional model

description: Areas of high biodiversity often coincide with communities living in
 extreme poverty. As a livelihood support, these communities often harvest
 wild products from the environment. But harvest activities can have
 negative impacts on fragile and globally important ecosystems. This paper
 examines trade-offs in ecological protection and community welfare from
 the harvest of wild products. With a novel model and empirical evidence, I
 show that management of harvest activity does not always resolve these
 trade-offs. In a model of continuous harvests in a two-dimensional
 landscape, managed harvest activity improves welfare, but is uniformly bad
 for other ecosystem services that are sensitive to the presence (as
 opposed to the intensity) of human activity. Empirical results from a
 unique dataset of mushroom harvesters in Yunnan, China suggest more
 experienced, poorer, and more vulnerable individuals tend to rely on more
 distant harvests. Thus, policies that limit the extent of forest travel,
 such as protected areas, may protect fragile ecosystems but can have a
 disproportionately negative effect on those most vulnerable.
description: Robinson_2016_spatialforest_datasetField collected data, July-August 2009. See README text file for metadata and variable descriptions.spatialforest_data.csv