cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.56ck582
title: Data from: Evidence for lower plasticity in CTMAX at warmer developmental temperatures

description: Understanding the capacity for different species to reduce their
 susceptibility to climate change via phenotypic plasticity is essential
 for accurately predicting species extinction risk. The climatic
 variability hypothesis suggests that spatial and temporal variation in
 climatic variables should select for more plastic phenotypes. However,
 empirical support for this hypothesis is limited. Here we examine the
 capacity for ten Drosophila species to increase their critical thermal
 maxima (CTMAX) through developmental acclimation and/or adult heat
 hardening. Using four fluctuating developmental temperature regimes,
 ranging from 13‐33 °C, we find that most species can increase their CTMAX
 via developmental acclimation and adult hardening, but found no
 relationship between climatic variables and absolute measures of
 plasticity. However, when plasticity was dissected across developmental
 temperatures, a positive association between plasticity and one measure of
 climatic variability(temperature seasonality) was found when development
 took place between 26‐28 °C, while a negative relationship was found when
 development took place between 20‐23 °C. In addition, a decline in CTMAX
 and egg‐to‐adult viability, a proxy for fitness, was observed in tropical
 species at the warmer developmental temperatures (26‐28 ̊C); this suggests
 that tropical species may be at even greater risk from climate change than
 currently predicted. The combined effects of developmental acclimation and
 adult hardening on CTMAX were small, contributing to a &lt;0.60 ̊C
 shift in CTMAX. Although small shifts in CTMAX may increase population
 persistence in the shorter‐term, the degree to which they can contribute
 to meaningful responses in the long term is unclear.
description: Raw data and
 environmental dataRaw data for
 developmental and hardening CTMAX and viability in ten Drosophila species.
 Means for estimates of plasticity and environment.Kellermann et al
 dryad.xlsx
DOI: 10.5061/dryad.63227hg
title: Data from: Native plant recovery following three years of common reed (Phragmites australis) control

description: Projects that aim to control invasive species often assume that a
 reduction of the target species will increase native species abundance.
 However, reports of the responses of native species following exotic
 species control are relatively rare. We assessed the recovery of the
 native community in five tidal wetland locations in which we attempted to
 eradicate the invasive common reed (Phragmites australis). We tested
 whether three years of treatment were able to eradicate Phragmites and
 promote recovery of the native plant community. After three years of
 treatment, Phragmites density declined sharply in all treated stands,
 though it was not eradicated in any of them. Native plant cover increased
 significantly in treated areas and community composition, particularly in
 smaller stands, converged toward that of uninvaded habitat. Thus, even
 within the relatively short time-scale of the treatments and monitoring,
 significant progress was made toward achieving the goals of controlling
 Phragmites infestations and promoting native biodiversity. There was a
 trend toward greater promise for success in smaller stands than larger
 stands, as has been observed in other studies. A greater emphasis on
 monitoring whole-community responses to exotic plant control, across a
 range of conditions, would enhance our ability to plan and design
 successful management strategies.
description: Plant Species Cover by
 Plot and YearMETADATA FOR RAMSHORN
 PHRAGMITIES TREATMENT - VEGETATION COVER DATA. Percent cover by species
 was estimated in 1 m2 randomly located plots within and surrounding five
 Phragmites stands. Each row is an individual species by plot and the
 columns include: year sampled, Phragmites stand #, plot number, plot type,
 species code, species full name, percent cover, and native/exotic. Plot
 type heading indicates if plot was in the interior of the stand or in the
 surrounding reference plant community. See Methods for details. For all
 years, sampling was in August before treatment in
 September.Vegetation_cover_2009_2013.csvPhragmites Live and Dead Stem CountMETADATA FOR RAMSHORN PHRAGMITIES TREATMENT - PHRAGMITIES STEM COUNT. Alive and dead Phragmites stems were counted in 1 m2 plots that were randomly located within five Phragmites stands. Each row is a plot and columns include: Phragmites stand #, year sampled, live stem, dead stem, stem height (m), and litter depth (cm). See Methods for details. For all years, sampling was in August before treatment in September.Phrag_stems.csvPhragmites Stand GIS FileArcGIS shapefile of five treated Phragmites stands in coordinate system NAD83 UTM Zone 18. Data collect with Trimble GPS unit.Phrag_Stands_Ramshorn_NY.zip
DOI: 10.5061/dryad.0488b
title: Data from: Spatiotemporal variation in local adaptation of a specialist insect herbivore to its long-lived host plant

description: Local adaptation of interacting species to one another indicates
 geographically variable reciprocal selection. This process of adaptation
 is central in the organization and maintenance of genetic variation across
 populations. Given that the strength of selection and responses to it
 often vary in time and space, the strength of local adaptation should in
 theory vary between generations and among populations. However, such
 spatiotemporal variation has rarely been explicitly demonstrated in nature
 and local adaptation is commonly considered to be relatively static. We
 report persistent local adaptation of the short-lived herbivore Abrostola
 asclepiadis to its long-lived host plant Vincetoxicum hirundinaria over
 three successive generations in two studied populations and considerable
 temporal variation in local adaptation in six populations supporting the
 geographic mosaic theory. The observed variation in local adaptation among
 populations was best explained by geographic distance and population
 isolation, suggesting that gene flow reduces local adaptation. Changes in
 herbivore population size did not conclusively explain temporal variation
 in local adaptation. Our results also imply that short-term studies are
 likely to capture only a part of the existing variation in local
 adaptation.
description: Pupal mass of Abrostola
 aclepiadis 2011-2013Data on pupal mass of
 Abrostola asclepiadis (Noctuidae) from a multi-year experiment testing for
 local adaptation of this specialist herbivore to its host plant
 Vincetoxicum hirundinaria (Apocynaceae).PupalMass.csvPopulation data 2011-2013Data on strength of local adaptation of the herbivore Abrostola asclepiadis (Noctuidae) to its host plant Vincetoxicum hirundinaria (Apocynaceae) and estimates of leaf damage caused by the herbivores during 2011-2013.PopMetrics2011-13.csvPopulation dataData on average local adaptation of Abrostola asclepiadis (Noctuidae) to its host plant Vincetoxicum hirundinaria (Apocynaceae) and population isolation.PopMetricsAverage.csv
DOI: 10.5061/dryad.4605c
title: Data from: Mouth asymmetry in the textbook example of scale-eating cichlid fish is not a discrete dimorphism after all

description: Individuals of the scale-eating cichlid fish, Perissodus microlepis, from
 Lake Tanganyika tend to have remarkably asymmetric heads that are either
 left-bending or right-bending. The ‘left’ morph opens its mouth markedly
 towards the left and preferentially feeds on the scales from the right
 side of its victim fish and the ‘right’ morph bites scales from the
 victims’ left side. This striking dimorphism made these fish a textbook
 example of their astonishing degree of ecological specialization and as
 one of the few known incidences of negative frequency-dependent selection
 acting on an asymmetric morphological trait, where left and right forms
 are equally frequent within a species. We investigated the degree and the
 shape of the frequency distribution of head asymmetry in P. microlepis to
 test whether the variation conforms to a discrete dimorphism, as generally
 assumed. In both adult and juvenile fish, mouth asymmetry appeared to be
 continuously and unimodally distributed with no clear evidence for a
 discrete dimorphism. Mixture analyses did not reveal evidence of a
 discrete or even strong dimorphism. These results raise doubts about
 previous claims, as reported in textbooks, that head variation in P.
 microlepis represents a discrete dimorphism of left- and right-bending
 forms. Based on extensive field sampling that excluded ambiguous (i.e.
 symmetric or weakly asymmetric) individual adults, we found that left and
 right morphs occur in equal abundance in five populations. Moreover, mate
 pairing for 51 wild caught pairs was random with regard to head
 laterality, calling into question reports that this laterality is
 maintained through disassortative mating.
description: Wild-caught adult
 Perissodus microlepis fishMouth asymmetry (mouth
 bending angle) and body size (standard length) of 238 wild-caught adult
 Perissodus microlepis fishWild caught adult
 fish.xlsLab-reared 3 month old
 juvenile Perissodus microlepis fishMouth asymmetry (mouth
 bending angle) and PC-1 scores (geometric and morphometric analysis) of
 laboratory-reared 3 month old juvenile Perissodus microlepis
 fishLab-reared 3 month
 fish.xlsLab-reared 7 month old
 juvenile Perissodus microlepis fishMouth asymmetry (mouth
 bending angle), PC-1 scores (geometric and morphometric analysis) and body
 size (total length) of laboratory-reared 7 month old juvenile Perissodus
 microlepis fishLab-reared 7 month
 fish.xlsMorphometric_Lab-reared
 3 and 7 month fishTPS file for geometric
 and morphometric analysis on mouth asymmetry of laboratory-reared 3 and 7
 month old juvenile Perissodus microlepis fish
DOI: 10.5061/dryad.d4758
title: Data from: Molecular phylogeny of the deep-sea penaeid shrimp genus Parapenaeus (Crustacea: Decapoda: Dendrobranchiata)

description: The commercial deep-sea penaeid shrimp genus Parapenaeus contains 15
 species, three subspecies and two forms in the Indo-West Pacific and the
 Atlantic. Novel nucleotide sequence data from five different genes (COI,
 16S, 12S, NaK and PEPCK) were collected to estimate phylogenetic
 relationships and taxonomic status amongst all but one subspecies in this
 genus. The phylogenetic results only support two of the four species
 groups previously proposed for this genus and indicate an evolution
 direction of the genital organs from simple to complex. The present
 results suggest that Parapenaeus originated in the shallow waters of the
 West Pacific with subsequent migration to the deep sea and the Atlantic.
 The molecular data reveal that there was probably misidentification of
 females between Parapenaeus australiensis and Parapenaeus ruberoculatus,
 with females previously assigned as P. australiensis likely being the
 females of P. ruberoculatus, while material identified as P. australiensis
 forma nodosa being the true P. australiensis females. On the other hand,
 Parapenaeus longipes forma denticulata truly represents a variation of the
 same species, while the subspecies Parapenaeus fissuroides indicus
 warrants a specific rank.
description: Parapenaeus combined
 sequences from 5 genesThe raw data for Fig. 2
 in the maunscriptParaCOI sequences for all Parapenaeus speciesPara_coi
DOI: 10.5061/dryad.j3459
title: Data from: Selection in a fluctuating environment and the evolution of sexual dimorphism in the seed beetle Callosobruchus maculatus

description: Temperature changes in the environment, which realistically include
 environmental fluctuations, can create both plastic and evolutionary
 responses of traits. Sexes might differ in either or both of these
 responses for homologous traits, which in turn has consequences for sexual
 dimorphism and its evolution. Here we investigate both immediate changes
 in and the evolution of sexual dimorphism in response to a changing
 environment (with and without fluctuations) using the seed beetle
 Callosobruchus maculatus. We investigate sex differences in plasticity and
 also the genetic architecture of body mass and developmental time
 dimorphism to test two existing hypothesis on sex differences in
 plasticity (adaptive canalization hypothesis and condition dependence
 hypothesis). We found a decreased sexual size dimorphism in higher
 temperature and females responded more plastically than males, supporting
 the condition dependence hypothesis. However, selection in a fluctuating
 environment altered sex specific patterns of genetic and environmental
 variation, indicating support for the adaptive canalization hypothesis.
 Genetic correlations between sexes (r_MF) were affected by fluctuating
 selection, suggesting facilitated independent evolution of the sexes.
 Thus, the selective past of a population is highly important for the
 understanding of the evolutionary dynamics of sexual dimorphism.
description: JEB-2012-00106.R1_data_body mass at emergenceBody mass at emergence of C. maculatus collected in the laboratory. Presented are four selection treatments (C = Control, T = Trend, R = Red noise, W = White noise). split temp = two temperature environments the beetles were exposed to during the split brood experiment. replicate: replicate is nested within treatment(4 replicates per treatment). time point: time point of beetle collection during their emergence period (1 = early, 2 = intermediate, 3 = late hatching individuals). Fam = Family nested within replicate and treatment, per replicate 10 families were investigated. sex = sex of the individual measured. body mass = dry weight of beetle.JEB-2012-00106.R1_data_developmental_timeDevelopmental time of C. maculatus collected in the laboratory. Presented are four selection treatments (C = Control, T = Trend, R = Red noise, W = White noise). split temp = two temperature environments the beetles were exposed to during the split brood experiment. replicate: replicate is nested within treatment (4 replicates per treatment). Fam = Family nested within replicate and treatment, per replicate 10 families were investigated. sex = sex of the individual measured. emergence day = egg to adult developmental time, i.e. number of days after egg laying until emergence of adult beetle.
DOI: 10.5061/dryad.6bn34
title: Data from: The combined impacts of experimental defaunation and logging on seedling traits and diversity

description: Animals can have both positive (e.g. via seed dispersal) and negative
 (e.g. via herbivory) impacts on plants. The net effects of these
 interactions remain difficult to predict and may be affected by
 overhunting and habitat disturbance, two widespread threats to tropical
 forests. Recent studies have documented their separate effects on plant
 recruitment but our understanding of how defaunation and logging interact
 to influence tropical tree communities is limited. From 2013-2016, we
 followed the fate of marked tree seedlings (n = 1489) from 81 genera in
 and outside experimental plots. Our plots differentially excluded small,
 medium, and large-bodied mammal herbivores in logged and unlogged forest
 in Malaysian Borneo. We assessed the effects of experimental defaunation
 and logging on taxonomic diversity and plant trait (wood density, specific
 leaf area, fruit size) composition of seedling communities. Although
 seedling mortality was highest in the presence of all mammal herbivores
 (44%), defaunation alone did not alter taxonomic diversity nor plant trait
 composition. However, herbivores (across all body sizes) significantly
 reduced mean fruit size across the seedling community over time (95% CI:
 -0.09 to -0.01), particularly in logged forest (95% CI: -0.12 to -0.003).
 Our findings suggest that impacts of mammal herbivores on plant
 communities may be greater in forests with a history of disturbance and
 could subsequently affect plant functional traits and ecological processes
 associated with forest regeneration.
description: CWM plant trait
 dataCWM
 plant traits- Granados et al
 .xlsxSeedling mortality from
 exclosure treatmentsoverall seedling mortality-
 Granados et al.xlsx
DOI: 10.5061/dryad.3b8k6
title: Data from: Disentangling the influence of mutation and migration in clonal seagrasses using the Genetic Distance Spectrum for microsatellites

description: The recurrent lack of isolation by distance reported at regional scale in
 seagrass species was recently suggested to stem from stochastic events of
 large-scale dispersal. We explored the usefulness of phylogenetic
 information contained in microsatellite loci to test this hypothesis by
 using the Genetic Diversity Spectrum (GDS) on databases containing,
 respectively, 7 and 9 microsatellites genotypes for 1541 sampling units of
 Posidonia oceanica and 1647 of Cymodocea nodosa. The simultaneous increase
 of microsatellite and geographic distances that emerges reveals a coherent
 pattern of isolation by distance in contrast to the chaotic pattern
 previously described using allele frequencies, in particular, for the
 long-lived P. oceanica. These results suggest that the lack of isolation
 by distance, rather than the resulting from rare events of large-scale
 dispersal, reflects at least for some species a stronger influence of
 mutation over migration at the scale of the distribution range. The global
 distribution of genetic polymorphism may, therefore, result predominantly
 from ancient events of step-by-step (re)colonization followed by local
 recruitment and clonal growth, rather than contemporary gene flow. The
 analysis of GDS appears useful to unravel the evolutionary forces
 influencing the dynamics and evolution at distinct temporal and spatial
 scales by accounting for phylogenetic information borne by
 microsatellites, under an appropriate mutation model. This finding adds
 nuance to the generalization of the influence of large-scale dispersal on
 the dynamics of seagrasses.
description: GDSseagrassesExcel file containing Cymodocea nodosa (first sheet) and Posidonia oceanica (second sheet) datasets. First colums contain location identifiers (see Alberto et al., 2008 and Arnaud-Haond et al., 2007 for correspondencies), locus names are indicated in the first lines (see Albert et al., 2003 a&b) and genotypes matrix are filled without missing data and with 3digits per allele coprresponding to thei length on chromatograms. Full references are cited in the article
DOI: 10.5061/dryad.6s5pn
title: Data from: Investigating the genetics of Bti resistance using mRNA tag sequencing: application on laboratory strains and natural populations of the dengue vector Aedes aegypti

description: Mosquito control is often the main method used to reduce
 mosquito-transmitted diseases. In order to investigate the genetic basis
 of resistance to the bio-insecticide Bacillus thuringiensis subsp.
 israelensis (Bti), we used information on polymorphism obtained from cDNA
 tag sequences from pooled larvae of laboratory Bti-resistant and
 susceptible Aedes aegypti mosquito strains to identify and analyse 1520
 single nucleotide polymorphisms (SNPs). Of the 372 SNPs tested, 99.2% were
 validated using DNA Illumina GoldenGate® array, with a strong correlation
 between the allelic frequencies inferred from the pooled and individual
 data (r = 0.85). A total of 11 genomic regions and five candidate genes
 were detected using a genome scan approach. One of these candidate genes
 showed significant departures from neutrality in the resistant strain at
 sequence level. Six natural populations from Martinique Island were
 sequenced for the 372 tested SNPs with a high transferability (87%), and
 association mapping analyses detected 14 loci associated with Bti
 resistance, including one located in a putative receptor for Cry11 toxins.
 Three of these loci were also significantly differentiated between the
 laboratory strains, suggesting that most of the genes associated with
 resistance might differ between the two environments. It also suggests
 that common selected regions might harbour key genes for Bti resistance.
description: AAEL004226
 sequencesFasta file of the
 sequences for the gene AAEL004226. AE samples corespond to the susceptible
 Aedes aegypti Bora-Bora strain. LiTOX samples corespond to the Bti
 resistant strain.AAEL004226.fasAAEL004738 sequencesFasta file of the sequences for the gene AAEL004738. AE samples corespond to the susceptible Aedes aegypti Bora-Bora strain. LiTOX samples corespond to the Bti resistant strain.AAEL004738.fasAAEL007488 sequencesFasta file of the sequences for the gene AAEL007488. AE samples corespond to the susceptible Aedes aegypti Bora-Bora strain. LiTOX samples corespond to the Bti resistant strain.AAEL007488.fasAAEL007892 sequencesFasta file of the sequences for the gene AAEL007892. AE samples corespond to the susceptible Aedes aegypti Bora-Bora strain. LiTOX samples corespond to the Bti resistant strain.AAEL007892.fasAAEL008155 sequencesFasta file of the sequences for the gene AAEL008155. AE samples corespond to the susceptible Aedes aegypti Bora-Bora strain. LiTOX samples corespond to the Bti resistant strain.AAEL008155.fasAAEL009077 sequencesFasta file of the sequences for the gene AAEL009077. AE samples corespond to the susceptible Aedes aegypti Bora-Bora strain. LiTOX samples corespond to the Bti resistant strain.AAEL009077.fasAAEL012778 sequencesFasta file of the sequences for the gene AAEL012778. AE samples corespond to the susceptible Aedes aegypti Bora-Bora strain. LiTOX samples corespond to the Bti resistant strain.AAEL012778.fas
DOI: 10.5061/dryad.50h1r7j
title: Data from: Validation of grain yield QTL from soft winter wheat using a CIMMYT spring wheat panel

description: Validation of quantitative trait loci (QTLs) is an essential step in
 marker-assisted breeding. The objectives of this study were to validate
 grain yield (GY) QTLs previously identified in soft red winter wheat
 (Triticum aestivum L.) through biparental and association mapping using
 the spring wheat association mapping initiative (WAMI) panel from CIMMYT,
 Mexico, and to identify allele combinations of the validated QTLs that
 resulted to the highest GY. Linked single-nucleotide polymorphisms for
 IWA3560 (3A), IWA1818 (4B), and IWA755 (6B) were significantly associated
 (P &lt; 0.001) with GY, grain number, and thousand-grain weight in the
 WAMI. Lines possessing the favorable allele for the QTL at the 3A, 4B, and
 6B loci (ACG allele combination) validated on the WAMI had the highest
 mean GY at 4.55 t ha−1, but three other haplotypes (ACA, GCA, and GCG)
 differing by one or two alleles in the validated QTL regions were not
 significantly different. These results validate GY QTLs across winter and
 spring wheat through genome-wide association analysis and further
 demonstrate the potential for pyramiding favorable alleles for the genetic
 improvement of wheat breeding populations.
description: Supplementary Figure
 1PCA
 biplots of the environments across each measured trait for the WAMI spring
 wheat panel from CIMMYT, Mexico. Environments with H2&lt; 0.50 were
 excluded from the analyses. Dendogram (lower right) showing the
 relationship among environments for grain yield using the Ward
 method.Supplementary Table
 1Heritability of the
 measured traits on each environment.Supplementary Table
 2Description of the
 different phenotypic datasets used for QTL validation through genomewide
 association mapping.