cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.65bd3
title: Data from: Temporal sampling helps unravel the genetic structure of naturally occurring populations of a phytoparasitic nematode. 1. Insights from the estimation of effective population sizes

description: The sustainability of modern agriculture relies on strategies that can
 control the ability of pathogens to overcome chemicals or genetic
 resistances through natural selection. This evolutionary potential, which
 depends partly on effective population size (Ne), is greatly influenced by
 human activities. In this context, wild pathogen populations can provide
 valuable information for assessing the long-term risk associated with crop
 pests. In this study, we estimated the effective population size of the
 beet cyst nematode, Heterodera schachtii, by sampling 34 populations
 infecting the sea beet Beta vulgaris spp. maritima twice within a one-year
 period. Only 20 populations produced enough generations to analyze the
 variation in allele frequencies, with the remaining populations showing a
 high mortality rate of the host plant after only one year. The 20 analyzed
 populations showed surprisingly low effective population sizes, with most
 having Ne close to 85 individuals. We attribute these low values to the
 variation in population size through time, systematic inbreeding, and
 unbalanced sex-ratios. Our results suggest that H. schachtii has low
 evolutionary potential in natural environments. Pest control strategies in
 which populations on crops mimic wild populations may help prevent
 parasite adaptation to host resistance.
description: Data
 summaryThis table show, for
 each nematode population, the plant status in 2013, the effective size
 computed with Jorde & Ryman method, the effective size computed with
 Wang method, The number of cyst (corrected by the proportion of heterodera
 schachtii cysts) for samples of 2012 and 2013, and the FIS for samples of
 2012 and 2013Data_Dryad_Ne_HS.xlsGenetic DataThis zip contains our genetic data (8 microsatellites) for our nematode populations in a Fstat format. Each file correspond to one population (the name of the file),with the first lines ("1") corresponding to the sample of 2012 and the last ones ("2") corresponding to the sample of 2013.Genetic_Data.zip
DOI: 10.5061/dryad.761k6
title: Data from: Evolution to environmental contamination ablates the circadian clock of an aquatic sentinel species

description: Environmental contamination is a common cause of rapid evolution. Recent
 work has shown that Daphnia pulex, an important freshwater species, can
 rapidly evolve increased tolerance to a common contaminant, sodium
 chloride (NaCl) road salt. While such rapid evolution can benefit
 organisms, allowing them to adapt to new environmental conditions, it can
 also be associated with unforeseen tradeoffs. Given that exposure to
 environmental contaminants can cause circadian disruption, we investigated
 whether the circadian clock was affected by evolving a tolerance to high
 levels of road salt. By tracking the oscillations of a putative clock
 gene, period, we demonstrated that D. pulex express per mRNA with
 approximately 20-hour oscillations under control conditions. This putative
 circadian rhythm was ablated in response to high levels of salinity;
 populations adapted to high NaCl concentrations exhibited an ablation of
 period oscillation. Moreover, we showed that while gene expression is
 increased in several other genes, including clock, actin, and
 Na+/K+-ATPase, upon the adaptation to high levels of salinity, per
 expression is unique among the genes we tracked in that it is the only
 gene repressed in response to salt adaptation. These results suggest that
 rapid evolution of salt tolerance occurs with the tradeoff of suppressed
 circadian function. The resultant circadian disruption may have profound
 consequences to individuals, populations, and aquatic food webs by
 affecting species interactions. In addition, our research suggests that
 circadian clocks may also be disrupted by the adaptation to other
 environmental contaminants.
description: Coldsnow et
 al._Circadian_RawCT values from qPCR for
 the 24-hour and 48-hour experiment.Coldsnow et al_Circadian
 Daphnia_Raw data.xlsx
DOI: 10.5061/dryad.mk0n0h4
title: Data from: Gut bacterial and fungal communities in ground-dwelling beetles are associated with host food habit and habitat

description: Beetles (Coleoptera) have the highest species diversity among all orders,
 and they have diverse food habits. Gut microbes may have contributed to
 this diversification of food habits. Here, we identified the pattern of
 the relationship between ground-dwelling beetles and their gut microbial
 communities (bacteria and fungi) in the field. We collected 46 beetle
 species of five families from secondary deciduous forests and grasslands
 in Japan and extracted microbial DNA from whole guts for amplicon
 sequencing. The gut bacterial and fungal communities differed among all
 habitats and all food habits of their hosts (carnivores, herbivores,
 omnivores, and scavengers) except for the fungal communities between
 carnivores and scavengers. Specifically, the abundant bacterial group
 varied among food habits: Xanthomonadaceae were abundant in scavengers,
 whereas Enterobacteriaceae were abundant in carnivores and herbivores.
 Phylogenetically closely related beetles had phylogenetically similar
 communities of Enterobacteriaceae, suggesting that the community structure
 of this family is related to the evolutionary change in beetle ecology.
 One of the fungal groups, Yarrowia species, which has been reported to
 have a symbiotic relationship with silphid beetles, was also detected from
 various carnivorous beetles. Our results suggest that the symbiotic
 relationships between ground-dwelling beetles and these microbes are
 widespread.
description: Beetle and yeast data
 used for analyses
DOI: 10.5061/dryad.5m5dr78
title: Data from: Evolution of increased intraspecific competitive ability following introduction: the importance of relatedness among genotypes.

description: 1.A long‐standing explanation for invasion success is that invasive plants
 could evolve to be more competitive following introduction. This evolution
 of increased competitive ability (EICA) hypothesis, however, has seldom
 been tested with regard to intraspecific competition. Given that plants
 can display different responses to related and unrelated conspecifics, the
 evolution of intraspecific competitive ability might be specific to
 genotypes of different relatedness. 2.Here, we grew five native (South
 American) and five introduced (North American) genotypes of the clonal
 herbaceous invasive plant Alternanthera philoxeroides alone, with
 aboveground competition from kin (the same genotype) or from one of two
 types of strangers (another genotype from the same range or another
 genotype from the other range). 3.When grown alone, introduced and native
 genotypes produced similar total biomass and storage‐root biomass.
 However, in response to intraspecific competition, introduced genotypes
 showed increases in total biomass and stem length, and a decrease in
 specific stem length, whereas native genotypes showed the opposite
 pattern. When grown with kin instead of strangers, introduced genotypes
 showed an increase in branch number, whereas native genotypes showed the
 opposite. 4.Synthesis. Our study provided evidence for evolution of
 increased intraspecific competitive responses in an invasive plant. We
 also found, for the first time, that the interactions among kin were
 likely to shift from competition towards facilitation following
 introduction.
description: data0data.xlsx
DOI: 10.5061/dryad.r531f
title: Data from: Populations at risk: conservation genetics of kangaroo mice (Microdipodops) of the Great Basin Desert

description: The Great Basin Desert of western North America has experienced frequent
 habitat alterations due to a complex biogeographic history and recent
 anthropogenic impacts, with the more recent alterations likely resulting
 in the decline of native fauna and flora. Dark (Microdipodops
 megacephalus) and pallid (M. pallidus) kangaroo mice are ecological
 specialists found within the Great Basin Desert and are potentially ideal
 organisms for assessing ecosystem health and inferring the biogeographic
 history of this vulnerable region. Herein, newly acquired nuclear-encoded
 microsatellite loci were utilized to assess patterns of variation within
 and among spatially discrete groups of kangaroo mice and to evaluate gene
 flow, demographic trends, and genetic integrity. Results confirm that
 there are at least three genetically distinct units within M. megacephalus
 and two such units within M. pallidus. The three units of M. megacephalus
 appear to have different demographic histories, with effectively no gene
 flow among them since their divergence. Similarly, the two units of M.
 pallidus also appear to have experienced different demographic histories,
 with effectively no gene exchange. Contemporary effective population sizes
 of all groups within Microdipodops appear to be low (&lt;500),
 suggesting that each genetic lineage may have difficulty coping with
 changing environmental pressures and hence may be at risk of extirpation.
 Results of this study indicate that each Microdipodops group should be
 recognized, and therefore managed, as a separate unit in an effort to
 conserve these highly specialized taxa that contribute to the diversity of
 the Great Basin Desert ecosystem.
description: MasterMSATmegacephalusOrderedLoci_11BMicrosatellite data for Microdipodops megacephlaus - 11 loci, 4 populationsMasterMSATpallidusOrderLoci_11BMicrodipodops pallidus raw microsatellite data - 10 loci, 2 populations.
DOI: 10.15468/dl.dvkrvs
title: Occurrence Download

description: A dataset containing 26 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Solanum dimorphandrum",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 26 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001004-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.sn577
title: Data from: A second-generation diagnostic single nucleotide polymorphism (SNP)-based assay, optimized to distinguish among eight poplar (Populus L.) species and their early hybrids

description: Rapid identification of Populus L. species and hybrids can be achieved
 with relatively little effort through the use of primer extension-based
 single nucleotide polymorphism (SNP) genotyping assays. We present an
 optimized set of 36 SNP markers from 28 gene regions that diagnose eight
 poplar species (Populus angustifolia James, Populus balsamifera L.,
 Populus deltoides Bartram, Populus fremontii Watson, Populus laurifolia
 Ledeb., Populus maximowiczii Henry, Populus nigra L., and Populus
 trichocarpa Torr. & Gray). A total of 700 DNA sequences from six
 Populus species (1–15 individuals per species) were used to construct the
 array. A set of flanking and probe oligonucleotides was developed and
 tested. The accuracy of the SNP assay was validated by genotyping 448
 putatively “pure” individuals from 14 species of Populus. Overall, the SNP
 assay had a high success rate (97.6 %) and will prove useful for the
 identification of all Aigeiros Duby and Tacamahaca Spach. species and
 their early-generation hybrids within natural populations and breeding
 programs. Null alleles and intraspecific polymorphisms were detected for a
 few locus/species combinations in the Aigeiros and Tacamahaca sections.
 When we attempted to genotype aspens of the section Populus (Populus alba
 L., Populus grandidentata Michx., Populus tremula L., and Populus
 tremuloides Michx.), the success rate of the SNP array decreased by 13 %,
 demonstrating moderate cross-sectional transferability.
description: SUPPLEMENTARY_FileS1_(genotypes)SUPPLEMENTARY_FileS2_(hybrids)
DOI: 10.5061/dryad.j9m92
title: Data from: Are macroalgal blooms necessarily bad? Nutrient impacts on seagrass in upwelling-influenced estuaries

description: Knowledge of nutrient pathways and their resulting ecological interactions
 can alleviate numerous environmental problems associated with nutrient
 increases in both natural and managed systems. Although not unique,
 coastal systems are particularly prone to complex ecological interactions
 resulting from nutrient inputs from both the land and sea. Nutrient inputs
 to coastal systems often spur ulvoid macroalgal blooms, with negative
 consequences for seagrasses, primarily through shading, as well as through
 changes in local biogeochemistry. We conducted complementary field and
 mesocosm experiments in an upwelling-influenced estuary, where
 marine-derived nutrients dominate, to understand the direct and indirect
 effects of nutrients on the macroalgal–eelgrass (Zostera marina L.)
 interaction. In the field experiment, we found weak evidence that
 nutrients and/or macroalgal treatments had a negative effect on eelgrass.
 However, in the mesocosm experiment, we found that a combination of
 nutrient and macroalgal treatments led to strongly negative eelgrass
 responses, primarily via indirect effects associated with macroalgal
 additions. Together, increased total light attenuation and decreased
 sediment oxygen levels were associated with larger effects on eelgrass
 than shading alone, which was evaluated using mimic algae treatments that
 did not alter sediment redox potential. Nutrient addition in the mesocosms
 directly affected seagrass density, biomass, and morphology, but not as
 strongly as macroalgae. We hypothesize that the contrary results from
 these parallel experiments are a consequence of differences in the
 hydrodynamics between field and mesocosm settings. We suggest that the
 high rates of water movement and tidal submersion of our intertidal field
 experiments alleviated the light reduction and negative biogeochemical
 changes in the sediment associated with macroalgal canopies, as well as
 the nutrient effects observed in the mesocosm experiments. Furthermore,
 adaptation of ulvoids and eelgrass to high, but variable, background
 nutrient concentrations in upwelling-influenced estuaries may partly
 explain the venue-specific results reported here. In order to manage
 critical seagrass habitats, nutrient criteria and macroalgal indicators
 must consider variability in marine-based nutrient delivery and local
 physical conditions among estuaries.
description: Field and Mesocosm
 Experimental DataData files on seagrass
 and covariate responses to macroalgal and nutrient additions in mesocosms
 and field experiments.
DOI: 10.5061/dryad.hh76j
title: Data from: Taxonomic and functional diversity in Mediterranean pastures: Insights on the biodiversity-productivity trade-off

description: Agricultural intensification is one of the main causes of biodiversity
 loss world-wide. The inclusion of semi-natural features in agricultural
 landscapes is suggested as a means of enhancing farm biodiversity, but
 this practice may have potential negative effects on yield production.
 Moreover, little evidence exists for effects of semi-natural features on
 other components of biodiversity, such as functional diversity. Yet this
 could provide a more comprehensive understanding of
 biodiversity–productivity trade-offs. Here, we report the effects of
 semi-natural woody vegetation on taxonomic and functional diversity, and
 biomass production of herbaceous species at the field and farm scales by
 sampling 50 fields, ranging from 0 to 90% woody vegetation cover, on nine
 similarly managed farms in central-western Spain. We found significant
 differences in herbaceous species richness among farms. Both taxonomic and
 functional β-diversity exhibited significant negative relationships with
 herbage production, highlighting the trade-off between biodiversity and
 productivity in these agroecosystems. Woody vegetation cover had a
 significant negative relationship with biomass production and a unimodal
 relationship with species richness at the field scale. At high values of
 woody vegetation cover, species richness and functional diversity indices
 were decoupled, suggesting that at this extreme of the woody vegetation
 gradient, only herbaceous species with contrasting trait values were
 present. Our results showed both convergent and divergent patterns of
 trait values, suggesting that different assembly processes are acting
 concurrently along the gradient of woody vegetation. Synthesis and
 applications. Our result indicates that management of woody vegetation may
 indeed increase both taxonomic and functional diversity, but this may come
 at the expense of key ecosystem services or other management goals, namely
 herbage production. Optimization of the trade-off between herbage
 diversity and productivity can be reached with a woody vegetation cover of
 c. 30% at the field scale.
description: Rolo et al
 DataThis data set includes
 herbaceous species abundances and yield production recorded in 50 fields
 within nine farms of central-western Spain. Farms were located along a
 gradient of semi-natural features cover.
DOI: 10.5061/dryad.c1483
title: Data from: Colony pace: a life-history trait affecting social insect epidemiology

description: Among colonies of social insects, the worker turnover rate (colony ‘pace’)
 typically shows considerable variation. This has epidemiological
 consequences for parasites, because in ‘fast-paced’ colonies, with
 short-lived workers, the time of parasite residence in a given host will
 be reduced, and further transmission may thus get less likely. Here, we
 test this idea and ask whether pace is a life-history strategy against
 infectious parasites. We infected bumblebees (Bombus terrestris) with the
 infectious gut parasite Crithidia bombi, and experimentally manipulated
 birth and death rates to mimic slow and fast pace. We found that fewer
 workers and, importantly, fewer last-generation workers that are
 responsible for rearing sexuals were infected in colonies with faster
 pace. This translates into increased fitness in fast-paced colonies, as
 daughter queens exposed to fewer infected workers in the nest are less
 likely to become infected themselves, and have a higher chance of founding
 their own colonies in the next year. High worker turnover rate can thus
 act as a strategy of defence against a spreading infection in social
 insect colonies.
description: Buechel &
 Schmid-Hempel 2015data for Proceedings B:
 Buechel & Schmid-Hempel 2015
DOI: 10.5061/dryad.7k5c3r8
title: Data from: A seascape genetic analysis of a stress-tolerant coral species along the Western Australian coast

description: Genetic diversity and connectivity are key factors in determining a
 population’s resilience to future disturbance. This is especially relevant
 to corals, which are in global decline due to increasing frequency and
 strength of thermal anomalies and severe tropical cyclones. While many
 studies have investigated genetic diversity and population structure in
 corals, they focused on species being removed at the greatest rate from
 coral reefs, Acroporids and Pocilloporids, and it is unclear whether the
 patterns observed in these species reflects those found in more resilient
 species. Here, we use microsatellite markers and two lagrangian models
 with differing resolutions, to investigate population structure in a
 stress-tolerant coral survivor Cyphastrea microphthalma, Family
 Merulinidae, along the north-western Australian coastline. We found
 evidence of four genetic clusters with some level of admixture among them.
 However, while there was evidence of population structure within the
 intensively sampled Pilbara region, the patterns of connectivity differed
 to those reported previously. WA populations of C. microphthalma were also
 characterised by lower levels of genetic diversity at higher latitudes.
 High- and moderate-resolution lagrangian models did not significantly
 predict regional-scale genetic connectivity across the Pilbara and
 Ningaloo (500 km). Although the high-resolution model explained an order
 of magnitude more genetic variation, suggesting model resolution and
 resolving coastal processes are important. Over broad spatial scales
 (nearly 2000 km), all moderate-resolution model particle release durations
 significantly predicted the genetic differentiation, although over water
 distance best predicted genetic distance across this spatial scale. This
 study improves the understanding of connectivity in this region by
 focusing on a stress tolerant species incorporating a spatially more
 intensive sampling effort than previous coral studies. It also shows that
 further development of lagrangian models is required, such as inclusion of
 multi-generational stepwise models and larval behaviour, to improve
 predictions of connectivity for this coral species in this region.
description: Data from: A seascape
 genetic analysis of a stress-tolerant coral species along the Western
 Australian coastMicrosatellite data for
 Cyphastrea microphthalmaC_microphthalma_for_Dryad.csv
DOI: 10.5061/dryad.dr71n
title: Data from: Genetic rescue, the greater prairie chicken and the problem of conservation reliance in the Anthropocene

description: A central question in conservation is how best to manage biodiversity,
 despite human domination of global processes (= Anthropocene). Common
 responses (i.e. translocations, genetic rescue) forestall potential
 extirpations, yet have an uncertain duration. A textbook example is the
 greater prairie chicken (GRPC: Tympanuchus cupido pinnatus), where
 translocations (1992–1998) seemingly rescued genetically depauperate
 Illinois populations. We re-evaluated this situation after two decades by
 genotyping 21 microsatellite loci from 1831 shed feathers across six leks
 in two counties over 4 years (2010–2013). Low migration rates (less than
 1%) established each county as demographically independent, but with
 declining-population estimates (4 year average N = 79). Leks were
 genetically similar and significantly bottlenecked, with low effective
 population sizes (average Ne = 13.1; 4 year Ne/N = 0.166). Genetic
 structure was defined by 12 significantly different family groups, with
 relatedness r = 0.31 &gt; half-sib r = 0.25. Average heterozygosity,
 indicating short-term survival, did not differ among contemporary, pre-
 and post-translocated populations, whereas allelic diversity did. Our
 results, the natural history of GRPC (i.e. few leks, male dominance
 hierarchies) and its controlled immigration suggest demographic expansion
 rather than genetic rescue. Legal protection under the endangered species
 act (ESA) may enhance recovery, but could exacerbate political–economic
 concerns on how best to manage ‘conservation-reliant’ species, for which
 GRPC is now an exemplar.
description: Microsatellite Genotype
 DataThis file includes raw
 genotype scores for 21 microsatellite loci across 82 Greater Prairie
 Chicken sampled from Jasper and Marion Counties in Illinois from
 2010-2012.GRPC_Msat_Data.xlsx