cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.bs737
title: Data from: Influence of parameter settings in automated scoring of AFLPs on population genetic analysis

description: The use of procedures for the automated scoring of AFLP fragments has
 recently increased. Corresponding software does not only automatically
 score the presence or absence of AFLP fragments, but also allows an
 evaluation of how different settings of scoring parameters influence
 subsequent population genetic analyses. In this study, we used the
 automated scoring package RAWGENO to evaluate how five scoring parameters
 influence the number of polymorphic bins and estimates of pairwise genetic
 differentiation between populations (Fst). Steps were implemented in R to
 automatically run the scoring process in RAWGENO for a set of different
 parameter combinations. While we found the scoring parameters minimum bin
 width and minimum number of samples per bin to have only weak influence on
 pairwise Fst values, maximum bin width and bin reproducibility had much
 stronger effects. The minimum average bin fluorescence scoring parameter
 affected Fst values in an only moderate way. At a range of scoring
 parameters around the default settings of RAWGENO, the number of
 polymorphic bins as well as pairwise Fst values stayed rather constant.
 This study thus shows the particularities of AFLP scoring, be it either
 manual or automatical, can have profound effects on subsequent population
 genetic analysis.
description: BinaryAFLPdata0/1 AFLP matrix for 10 individuals of 24 Swiss locations of Chorthippus albomarginatus, scored using RAWGENO default settings
DOI: 10.5061/dryad.3vq00p7
title: Data from: Responses of a legume to inbreeding and the intensity of novel and familiar stresses

description: It is often assumed that the negative effects of inbreeding on fitness
 (inbreeding depression, ID) are particularly strong under stressful
 conditions. However, ID may be relatively mild under types of stress that
 plant populations have experienced for a long time, because
 environment-specific deleterious alleles may already have been purged. We
 examined the performance of open- and self-pollinated progeny of the
 short-lived calcareous grassland plant Anthyllis vulneraria under three
 intensities of each of five types of stress. Drought, nutrient deficiency
 and defoliation were chosen as stresses typical for the habitat of origin,
 while shade and waterlogging were expected to be novel, unfamiliar
 stresses for A. vulneraria. The stresses reduced plant biomass by up to
 91%, and the responses of the plants were mostly in line with the
 functional equilibrium hypothesis. There was significant ID in biomass (δ
 = 0.17), leaf chlorophyll content and the number of root nodules of the
 legume, but the magnitude of ID was independent of the stress treatments.
 In particular, there was no significant interaction between inbreeding and
 the intensity of any stress type, and ID was not higher under novel than
 under familiar stresses. In addition, phenotypic plasticity in biomass
 allocation, leaf functional traits and in root nodulation of the legume to
 the various stress treatments was not influenced by inbreeding. Our
 findings do not support the common hypothesis of stronger ID under
 stressful environments, not even if the stresses are novel to the plants.
description: Raw
 dataRaw data for the
 manuscript "Responses of a legume to inbreeding and the intensity of
 novel and familiar stresses" written by F. Rehling, D. Matthies &
 T. M. SandnerRehling et
 al_inbreeding_data.xlsx
DOI: 10.5061/dryad.b0846
title: Data from: The association of feeding behavior with the resistance and tolerance to parasites in recently diverged sticklebacks

description: Divergent natural selection regimes can contribute to adaptive population
 divergence, but can be sensitive to human-mediated environmental change.
 Nutrient loading of aquatic ecosystems, for example, might modify
 selection pressures by altering the abundance and distribution of
 resources and the prevalence and infectivity of parasites. Here, we used a
 mesocosm experiment to test for interactive effects of nutrient loading
 and parasitism on host condition and feeding ecology. Specifically, we
 investigated whether the common fish parasite Gyrodactylus sp.
 differentially affected recently diverged lake and stream ecotypes of
 three-spined stickleback (Gasterosteus aculeatus). We found that the
 stream ecotype had a higher resistance to Gyrodactylus sp. infections than
 the lake ecotype, and that both ecotypes experienced a cost of parasitism,
 indicated by negative relationships between parasite load and both stomach
 fullness and body condition. Overall, our results suggest that in the
 early stages of adaptive population divergence of hosts, parasites can
 affect host resistance, body condition, and diet.
description: Fish and Tank
 dataData including the raw
 values of the parasite load, prey items, condition indexes, and mortality
 data.Fish_and_TankData.xls
DOI: 10.5061/dryad.tt0d1
title: Data from: Behavioral plasticity and GxE of reproductive tactics in Nicrophorus vespilloides burying beetles

description: Phenotypic plasticity is important in the evolution of traits and
 facilitates adaptation to rapid environmental changes. However, variation
 in plasticity at the individual level, and the heritable basis underlying
 this plasticity is rarely quantified for behavioral traits. Alternative
 behavioral reproductive tactics are key components of mating systems but
 are rarely considered within a phenotypic plasticity framework (i.e., as
 reaction norms). Here, using lines artificially selected for repeated
 mating rate, we test for genetic (GxE) sources of variation in
 reproductive behavior of male Nicrophorus vespilloides burying beetles
 (including signaling behavior), as well as the role of individual body
 size, in responsiveness to changes in social environment. The results show
 that body size influences the response of individuals’ signaling behavior
 to changes in the social environment. Moreover, there was GxE underlying
 the responses of males to variation in the quality of social environment
 experienced (relative size of focal male compared to his rival). This
 shows that individual variation in plasticity and social sensitivity of
 signaling behavior can evolve in response to selection on investment in
 mating behavior, with males selected for high mating investment having
 greater social sensitivity.
description: Carter_etal_data8_2014This is the data for the manuscript “Behavioral plasticity and GxE of reproductive tactics in Nicrophorus vespilloides burying beetles” by MJ Carter, ML Head, AJ Moore & NJ Royle. Data was collected by MJC. All methods are described in the associated manuscript. Column headings are described in the excel spreadsheet.
DOI: 10.5061/dryad.bm714
title: Data from: Allogeneic HY antibodies detected 3 months after female-to-male HCT predict chronic GVHD and nonrelapse mortality in humans

description: Allogeneic antibodies against minor histocompatibility antigens encoded on
 the Y chromosome (HY-Abs) develop after hematopoietic cell transplant
 (HCT) of male recipients with female donors (F→M). However, the temporal
 association between HY-Ab development and chronic graft-versus-host
 disease (cGVHD) has yet to be elucidated. We studied 136 adult F→M HCT
 patients, with plasma prospectively collected through 3 years
 posttransplant, and measured immunoglobulin G against 6 H-Y antigens.
 Multiple HY-Abs were frequently detected beginning at 3 months
 posttransplant: 78 (57%) of F→M patients were seropositive for at least 1
 of the 6 HY-Abs, and 3-month seropositivity for each HY-Ab was associated
 with a persistent seropositive response throughout the posttransplant
 follow-up period (P &lt; .001 in each). There were no associations
 between pretransplant features and 3-month overall HY-Ab development.
 Detection of multiple HY-Abs at 3 months (represented by HY score) was
 significantly associated with an increased risk of cGVHD (P &lt;
 .0001) and nonrelapse mortality (P &lt; .01). Compared to clinical
 factors alone, the addition of HY score to clinical factors improved the
 predictive potential of cGVHD (P &lt; .01). Monitoring HY-Ab
 development thus stratifies cGVHD risk in F→M HCT patients and may support
 preemptive prophylaxis therapy for cGVHD beginning at 3 months
 posttransplant.
description: MFI of HY-microarray 3m
 postHCT in FtoM ptsMFI of HY-microarray and
 clinical outcome of FtoM pts.xlsMFI of HY-microarray of
 healthy subjects
DOI: 10.5061/dryad.pk30p
title: Data from: Lack of genetic variation prevents adaptation at the geographic range margin in a damselfly

description: What limits a species' distribution in the absence of physical
 barriers? Genetic load due to asymmetric gene flow and the absence of
 genetic variation due to lack of gene flow are hypothesized to constrain
 adaptation to novel environments in marginal populations, preventing range
 expansion. Here, we examined the genetic structure and geographic
 variation in morphological traits in two damselflies (Ischnura asiatica
 and I. senegalensis) along a latitudinal gradient in Japan, which is the
 distribution centre of I. asiatica and the northern limit of I.
 senegalensis. Genomewide genetic analyses found a loss of genetic
 diversity at the edge of distribution in I. senegalensis but consistently
 high diversity in I. asiatica. Gene flow was asymmetric in a south–north
 direction in both species. Although body size and wing loading showed
 decreasing latitudinal clines (smaller in north) in I. asiatica in Japan,
 increasing latitudinal clines (larger in north) in these phenotypic
 markers were observed in I. senegalensis, particularly near the northern
 boundary, which coincided well with the location where genetic diversity
 began a sharp decline. In ectothermic animals, increasing latitudinal
 cline in these traits was suggested to be established when they failed to
 adapt to thermal gradient. Therefore, our findings support the possibility
 that a lack of genetic variation rather than geneflow swamping is
 responsible for the constraint of adaptation at the margin of geographic
 distribution.
description: Data on morphology and
 SNPsSNP data files (labeled
 by gene_pop) of Ischnura asiatica and I. senegalensis. Data used for
 BaysAss is labeled by "BaysAss". Morphology data include both
 abdomen length of wing length.dataME.zip
DOI: 10.5061/dryad.dr559
title: Data from: Do respiratory limitations affect metabolism of insect larvae before moulting: an empirical test at the individual level

description: Recent data suggest that oxygen limitation may induce moulting in larval
 insects. This oxygen dependent induction of moulting (ODIM) hypothesis
 stems from the fact that the tracheal respiratory system of insects grows
 primarily at moults, whereas tissue mass increases massively between
 moults. This may result in a mismatch between oxygen supply and demand at
 the end of each larval instar because oxygen demand of growing tissues
 exceeds the relatively fixed supply capacity of the respiratory system.
 The ODIM hypothesis predicts that, within larval instars, respiration and
 metabolic rates of an individual larva first increase with increasing body
 mass but eventually level off once the supply capacity of the tracheal
 system starts to constrain metabolism. Here, we provide the first
 individual-level test of this key prediction of the ODIM hypothesis. We
 use a novel methodology where we repeatedly measure respiration and
 metabolic rates throughout the penultimate- and final-instar larvae in the
 butterfly Pieris napi. In the penultimate instar, respiration and
 metabolic rates gradually decelerated along with growth, supporting the
 ODIM hypothesis. However, respiration and metabolic rates increased
 linearly during growth in the final instar, contradicting the prediction.
 Moreover, our data suggest considerable variation among individuals in the
 association between respiration rate and mass in the final instar.
 Overall, the results provide partial support for the ODIM hypothesis and
 suggest that oxygen limitation may emerge gradually within a larval
 instar. The results also suggest that there may be different moult
 induction mechanisms in larva-to-larva moults compared to the final
 metamorphic moult.
description: Kivelä et al._MR
 data
DOI: 10.5061/dryad.bq21j
title: Data from: In a warmer Arctic, mosquitoes avoid increased mortality from predators by growing faster

description: Climate change is altering environmental temperature, a factor that
 influences ectothermic organisms by controlling rates of physiological
 processes. Demographic effects of warming, however, are determined by the
 expression of these physiological effects through predator–prey and other
 species interactions. Using field observations and controlled experiments,
 we measured how increasing temperatures in the Arctic affected development
 rates and mortality rates (from predation) of immature Arctic mosquitoes
 in western Greenland. We then developed and parametrized a demographic
 model to evaluate how temperature affects survival of mosquitoes from the
 immature to the adult stage. Our studies showed that warming increased
 development rate of immature mosquitoes (Q10 = 2.8) but also increased
 daily mortality from increased predation rates by a dytiscid beetle (Q10 =
 1.2–1.5). Despite increased daily mortality, the model indicated that
 faster development and fewer days exposed to predators resulted in an
 increased probability of mosquito survival to the adult stage. Warming
 also advanced mosquito phenology, bringing mosquitoes into phenological
 synchrony with caribou. Increases in biting pests will have negative
 consequences for caribou and their role as a subsistence resource for
 local communities. Generalizable frameworks that account for multiple
 effects of temperature are needed to understand how climate change impacts
 coupled human–natural systems.
description: Arctic mosquito and pond
 environmental dataThe datafile contains
 multiple sheets of data from a study of Arctic mosquitoes in southwest
 Greenland. Included are pond temperatures, mosquito development times at
 different temperatures, mosquito masses, and predation rates on mosquitoes
 by dytiscids at multiple temperatures.Data.xlsx
DOI: 10.5061/dryad.q2d3v
title: Data from: Hierarchical analysis of genetic structure in the habitat-specialist Eastern Sand Darter (Ammocrypta pellucida)

description: Quantifying spatial genetic structure can reveal the relative influences
 of contemporary and historic factors underlying localized and regional
 patterns of genetic diversity and gene flow – important considerations for
 the development of effective conservation efforts. Using 10 polymorphic
 microsatellite loci, we characterize genetic variation among populations
 across the range of the Eastern Sand Darter (Ammocrypta pellucida), a
 small riverine percid that is highly dependent on sandy substrate
 microhabitats. We tested for fine scale, regional, and historic patterns
 of genetic structure. As expected, significant differentiation was
 detected among rivers within drainages and among drainages. At finer
 scales, an unexpected lack of within-river genetic structure among
 fragmented sandy microhabitats suggests that stratified dispersal
 resulting from unstable sand bar habitat degradation (natural and
 anthropogenic) may preclude substantial genetic differentiation within
 rivers. Among-drainage genetic structure indicates that postglacial (14
 kya) drainage connectivity continues to influence contemporary genetic
 structure among Eastern Sand Darter populations in southern Ontario. These
 results provide an unexpected contrast to other benthic riverine fish in
 the Great Lakes drainage and suggest that habitat-specific fishes, such as
 the Eastern Sand Darter, can evolve dispersal strategies that overcome
 fragmented and temporally unstable habitats.
description: 10 microsatellite loci
 from Ginson et al. doi: 10.1002/ece3.1392Allele fragment sizes,
 in 3 digit Genepop format, for 10 microsatellite loci used in Ginson et
 al. (doi: 10.1002/ece3.1392).Ginson_et_al_ESD_usats.txt
DOI: 10.5061/dryad.nn493
title: Data from: Colour polymorphism torn apart by opposing positive frequency-dependent selection, yet maintained in space

description: 1. Polymorphic warning signals in aposematic species are enigmatic because
 predator learning and discrimination should select for the most common
 coloration, resulting in positive frequency-dependent survival selection.
 2. Here, we investigated whether differential mating success could create
 sufficiently strong negative frequency-dependent selection for rare morphs
 to explain polymorphic (white and yellow) warning coloration in male wood
 tiger moths (Parasemia plantaginis). 3. We conducted an experiment in
 semi-natural conditions where we estimated mating success for both white
 and yellow male moths under three different morph frequencies. 4. Contrary
 to expectations, mating success was positively frequency-dependent: white
 morph males had high relative fitness when common, likewise yellow morph
 males had high relative fitness when instead they were common. We hence
 built a model parameterized with our data to examine whether polymorphism
 can be maintained despite two sources of positive frequency dependence.
 The model includes known spatial variation in the survival advantage
 enjoyed by the yellow morph and assumes that relative mating success
 follows our experimentally derived values. It predicts that polymorphism
 is possible under migration for up to approximately 20% exchange of
 individuals between subpopulations in each generation. 5. Our results
 suggest that differential mating success combined with spatial variation
 in predator communities may operate as a selection mosaic that prevents
 complete fixation of either morph.
description: Enclosure Updated Data
 SheetData for Gordon et al.
 JAE-2015-00035.R1 Colour polymorphism, torn apart by opposing positive
 frequency-dependent selection, yet maintained in space. Gordon, Swanne;
 Kokko, Hanna; Rojas, Bibiana; Nokelainen, Ossi; Mappes,
 Johanna
DOI: 10.5061/dryad.ks131
title: Data from: Field performance of Bt eggplants (Solanum melongena L.) in the Philippines: Cry1Ac expression and control of the eggplant fruit and shoot borer (Leucinodes orbonalis Guenée)

description: Plants expressing Cry proteins from the bacterium, Bacillus thuringiensis
 (Bt), have become a major tactic for controlling insect pests in maize and
 cotton globally. However, there are few Bt vegetable crops. Eggplant
 (Solanum melongena) is a popular vegetable grown throughout Asia that is
 heavily treated with insecticides to control the eggplant fruit and shoot
 borer, Leucinodes orbonalis (EFSB). Herein we provide the first publicly
 available data on field performance in Asia of eggplant engineered to
 produce the Cry1Ac protein. Replicated field trials with five Bt eggplant
 open-pollinated (OP) lines from transformation event EE-1 and their non-Bt
 comparators were conducted over three cropping seasons in the Philippines
 from 2010–2012. Field trials documented levels of Cry1Ac protein expressed
 in plants and evaluated their efficacy against the primary target pest,
 EFSB. Cry1Ac concentrations ranged from 0.75–24.7 ppm dry weight with the
 highest in the terminal leaves (or shoots) and the lowest in the roots.
 Cry1Ac levels significantly increased from the vegetative to the
 reproductive stage. Bt eggplant lines demonstrated excellent control of
 EFSB. Pairwise analysis of means detected highly significant differences
 between Bt eggplant lines and their non-Bt comparators for all field
 efficacy parameters tested. Bt eggplant lines demonstrated high levels of
 control of EFSB shoot damage (98.6–100%) and fruit damage (98.1–99.7%) and
 reduced EFSB larval infestation (95.8–99.3%) under the most severe pest
 pressure during trial 2. Moths that emerged from larvae collected from Bt
 plants in the field and reared in their Bt eggplant hosts did not produce
 viable eggs or offspring. These results demonstrate that Bt eggplant lines
 containing Cry1Ac event EE-1 provide outstanding control of EFSB and can
 dramatically reduce the need for conventional insecticides.
description: Bt eggplant in the
 Philippines Raw DataThe raw data was
 obtained from confined field trials of Bt and non-Bt eggplants in
 Pangasinan, Philippines from 2010 - 2012. The raw data is in MS Excel file
 with four sheets, namely: (1) Cry1Ac protein expression levels (parts per
 million dry weight, ppm DW) of different Bt eggplants plant parts for two
 trials; (2) Cry1Ac protein expression levels (ppm DW) in terminal leaves
 of Bt eggplants at different growth stages for two trials; (3) percent
 shoot damage of Bt and non-Bt eggplants for three trials; and, (4) percent
 fruit damage and larval count of Bt and non-Bt eggplants for three
 trials.Bt_eggplant_in_the
 Philippines_RawData.xlsx
DOI: 10.5061/dryad.r8ph6
title: Data from: Reproductive plasticity and landscape heterogeneity benefit a ground-nesting bird in a fire-prone ecosystem

description: Disturbance is critical for the conservation of rangeland ecosystems
 worldwide and many of these systems are fire dependent. Although it is
 well established that restoring fire as an ecological process can lead to
 increased biodiversity in grasslands and shrublands, the underlying
 mechanisms driving community patterns are poorly understood for fauna in
 fire-prone landscapes. Much of this uncertainty stems from the paucity of
 studies that examine the effects of fire at scales relevant to organism
 life histories. We assessed the response of a non-migratory
 ground-dwelling bird to disturbance (i.e., prescribed fire) and
 environmental stochasticity over the course of a 4 year period, which
 spanned years of historic drought and record rainfall. Specifically, we
 investigated the nesting ecology of northern bobwhite (Colinus
 virginianus; hereafter bobwhite) to illuminate possible avenues by which
 individuals respond to dynamic landscape patterns during a critical
 reproductive stage (i.e., nesting) in a mixed-grass shrubland in western
 Oklahoma, USA. We found that bobwhites exhibited extreme plasticity in
 nest substrate use among time since fire categories (TSF) and subsequently
 maintained high nest survival (e.g., 57 – 70%). Bobwhites were
 opportunistic in nest substrate use among TSF categories (i.e., 72% of
 nest sites in shrubs in 0-12 months post fire compared to 71% in
 herbaceous vegetation in &gt;36 months post fire), yet nesting
 decisions were first filtered by similar structural components (i.e.,
 vertical and horizontal cover) within the vicinity of nest sites
 regardless of TSF category. Despite being a non-migratory and
 comparatively less mobile ground-nesting bird species, bobwhites adjusted
 to dynamic vegetation mosaics on a fire-prone landscape under stochastic
 climatic conditions which culminated in stable and high nest survival.
 Broadly, our findings provide a unique depiction of organism response
 strategies to fire at scales relevant to a critical life-stage, a topic
 that has been previously understudied and poorly understood. We also
 demonstrate how doing so can better inform conservation practices aimed at
 restoring fire regimes on grassland and shrubland landscapes.
description: Nest_DataThis file includes nesting data for the 2012 - 2015 northern bobwhite breeding seasons at the Packsaddle Wildlife Management Area, western Oklahoma, USA. The file includes 16 management, life history, weather and temporal covariates for each nest that was monitored.Weather_DataThis file includes weather data for the relevant northern bobwhite breeding seasons from 2012-2015 at the Packsaddle Wildlife Management Area, western Oklahoma, USA.