cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.8hb23
title: Data from: Mapping the fitness landscape of gene expression uncovers the cause of antagonism and sign epistasis between adaptive mutations

description: How do adapting populations navigate the tensions between the costs of
 gene expression and the benefits of gene products to optimize the levels
 of many genes at once? Here we combined independently-arising beneficial
 mutations that altered enzyme levels in the central metabolism of
 Methylobacterium extorquens to uncover the fitness landscape defined by
 gene expression levels. We found strong antagonism and sign epistasis
 between these beneficial mutations. Mutations with the largest individual
 benefit interacted the most antagonistically with other mutations, a trend
 we also uncovered through analyses of datasets from other model systems.
 However, these beneficial mutations interacted multiplicatively (i.e., no
 epistasis) at the level of enzyme expression. By generating a model that
 predicts fitness from enzyme levels we could explain the observed sign
 epistasis as a result of overshooting the optimum defined by a balance
 between enzyme catalysis benefits and fitness costs. Knowledge of the
 phenotypic landscape also illuminated that, although the fitness peak was
 phenotypically far from the ancestral state, it was not genetically
 distant. Single beneficial mutations jumped straight toward the global
 optimum rather than being constrained to change the expression phenotypes
 in the correlated fashion expected by the genetic architecture. Given that
 adaptation in nature often results from optimizing gene expression, these
 conclusions can be widely applicable to other organisms and selective
 conditions. Poor interactions between individually beneficial alleles
 affecting gene expression may thus compromise the benefit of sex during
 adaptation and promote genetic differentiation.
description: Collection of all
 filesChouetAlFiles.zip
DOI: 10.5061/dryad.5cv40
title: Data from: The influence of geographic heterogeneity in predation pressure on mating signal divergence in an Amazonian frog species complex

description: Sexual section plays an important role in mating signal divergence, but
 geographic variation in ecological factors can also contribute to
 divergent signal evolution. We tested the hypothesis that geographic
 heterogeneity in predation causes divergent selection on advertisement
 call complexity within the Engystomops petersi frog species complex. We
 conducted predator phonotaxis experiments at two sites where female choice
 is consistent with call trait divergence. Engystomops at one site produces
 complex calls, while the closely related species at the other site
 produces simple calls. Bats approached complex calls more than simple
 calls at both sites, suggesting selection against complex calls. Moreover,
 bat predation pressure was greater at the site with simple calls,
 suggesting stronger selection against complex calls and potentially
 precluding evolution of complex calls at this site. Our results show that
 geographic variation in predation may play an important role in the
 evolution and maintenance of mating signal divergence.
description: Bat visitations to
 complex and simple calls in E. petersi species complexIncludes field collected
 data showing nightly number of visits to complex versus simple calling
 speaker-model platforms in Yasuni Biological Field Station and La Selva
 Jungle Lodge, Ecuador.Trillo et
 al.xlsx
DOI: 10.5061/dryad.b7g24
title: Data from: Development, validation, and evaluation of an assay for the detection of wood frogs (Rana sylvatica) in environmental DNA

description: We developed and describe a qPCR assay for the detection of wood frogs
 (Rana sylvatica) using environmental DNA (eDNA) sampling. A single primer
 set was designed to amplify a 115-bp region of the wood frog cytochrome B
 gene and assessed for target specificity. There was no evidence of
 amplification in 11 non-target species. We evaluated the utility of the
 primer set in qPCR assay by conducting geo-referenced eDNA field surveys
 in Interior Alaska. Results indicate that the assay consistently detects
 wood frog DNA in the environment to 1.83 × 10−3 pg/μL. The assay provides
 a complement to traditional survey methods and can be readily applied in a
 wider conservation and management context.
description: Wood Frog eDNA Survey
 Results1 liter water samples
 collected around Fairbanks/North Pole for eDNA analysis. Filters were cut
 in half and DNA isolated via phenol-chloroform from one half. Other half
 is archived. qPCR (SYBR Green) conducted for detection of wood frog cytB
 (Rasy_00)..Spangler_eDNA2015.csv
DOI: 10.5061/dryad.gt86f
title: Data from: Continental-scale patterns of pathogen prevalence: a case study on the corncrake

description: Pathogen infections can represent a substantial threat to wild
 populations, especially those already limited in size. To determine how
 much variation in the pathogens observed among fragmented populations is
 caused by ecological factors, one needs to examine systems where host
 genetic diversity is consistent among the populations, thus controlling
 for any potentially confounding genetic effects. Here, we report
 geographic variation in haemosporidian infection among European
 populations of corncrake. This species now occurs in fragmented
 populations, but there is little genetic structure and equally high levels
 of genetic diversity among these populations. We observed a longitudinal
 gradient of prevalence from western to Eastern Europe negatively
 correlated with national agricultural yield, but positively correlated
 with corncrake census population sizes when only the most widespread
 lineage is considered. This likely reveals a possible impact of local
 agriculture intensity, which reduced host population densities in Western
 Europe and, potentially, insect vector abundance, thus reducing the
 transmission of pathogens. We conclude that in the corncrake system, where
 metapopulation dynamics resulted in variations in local census population
 sizes, but not in the genetic impoverishment of these populations,
 anthropogenic activity has led to a reduction in host populations and
 pathogen prevalence.
description: Infection status of
 corncrake samplesInfection status and
 haemosporidian lineages detected in 354 corncrake (Crex crex) samples
 collected in 9 populations across Europe.Dryad_infection_status.xlsx
DOI: 10.5061/dryad.sg2bn08
title: Data from: Experimental evaluation of the robustness of the growth-stress tolerance trade-off within the perennial grass Dactylis glomerata

description: 1. A core tenet of functional ecology is that the vast phenotypic
 diversity observed in the plant kingdom could be partly generated by a
 trade- off between the ability of plants to grow quickly and acquire
 resources in rich environments vs. the ability to conserve resources and
 avoid mortality under stress. However, experimental demonstrations remain
 scarce and potentially blurred by phylogenetic constraints in
 cross-species analyses. Here we experimentally decoupled growth potential
 and stress survival by applying an off-season stress on contrasting
 populations of the perennial grass Dactylis glomerata exhibiting a range
 of seasonal dormancy. 2. Seventeen populations of D. glomerata,
 originating from a latitudinal gradient from Norway to Morocco, were
 subjected to three types of dehydration stress: winter frost in Norway,
 summer drought, and early spring (off-season) drought stress in the south
 of France. Growth rate, and two leaf traits (leaf width and leaf dry
 matter content) suspected to be involved in the adaptation to dehydration
 stress, were monitored under optimal conditions. We quantified plant
 dehydration survival as the amount of plant recovery after a severe
 stress. 3. Nordic populations were found to be winter dormant. Winter and
 summer dormant populations better survived frost and summer drought,
 respectively. However, no trade-off between growth potential and
 dehydration survival was detected in non-dormant plants in early spring
 when dehydration occurred unseasonably for all populations. Furthermore,
 Mediterranean populations better survived an early spring drought. 4. Our
 results highlight the importance of assessing plant growth potential as a
 response to seasonal environmental cues. They suggest that growth
 potential and stress survival trade-off when plants exhibit seasonal
 dormancy but can be functionally independent at other seasons.
 Consequently, the growth-stress survival relationship could be better
 described as a dynamic linkage rather than a constant and general
 trade-off. Moreover, leaf trait values, such as thinner and more lignified
 leaves reflecting drought adaptation, may have contributed to the improved
 drought-stress survival without resulting in a cost to growth. 5. Further
 exploration of the growth-stress survival relationship should permit
 deciphering the suite of plant traits and trait covariations involved in
 plants’ responses to increasing stress.
description: Bristiel-data_Dryad-FE
DOI: 10.15468/dl.gpc5bc
title: Occurrence Download

description: A dataset containing 10669 records in GBIF matching the query:
SELECT
 '409' AS fish_cell,
 GBIF_MGRSCode(1000, decimalLatitude, decimalLongitude, 0) AS cell, -- NO randomization
 COUNT(DISTINCT speciesKey) AS species_richness
 FROM occurrence
 WHERE hasCoordinate = TRUE
 AND speciesKey IS NOT NULL
 AND NOT ARRAY_CONTAINS(issue, 'ZERO_COORDINATE')
 AND NOT ARRAY_CONTAINS(issue, 'COORDINATE_OUT_OF_RANGE')
 AND NOT ARRAY_CONTAINS(issue, 'COORDINATE_INVALID')
 AND NOT ARRAY_CONTAINS(issue, 'COUNTRY_COORDINATE_MISMATCH')
 AND decimalLatitude &gt;= 37.42857426825602
 AND decimalLatitude &lt;= 41.89415215079384
 AND decimalLongitude &gt;= 34.5384730764328
 AND decimalLongitude &lt;= 41.95852326653772
 AND "year" &gt;= 2015
 AND "year" &lt;= 2026
 AND (coordinateUncertaintyInMeters &lt;= 100 OR coordinateUncertaintyInMeters IS NULL)
 GROUP BY fish_cell, cell

 The dataset's 10669 records were derived from 134 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001321-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.84mf4
title: Data from: Using social parasitism to test reproductive skew models in a primitively eusocial wasp

description: Remarkable variation exists in the distribution of reproduction (skew)
 among members of cooperatively breeding groups, both within and between
 species. Reproductive skew theory has provided an important framework for
 understanding this variation. In the primitively eusocial Hymenoptera, two
 models have been routinely tested: concessions models, which assume
 complete control of reproduction by a dominant individual, and tug-of-war
 models, which assume on-going competition among group members over
 reproduction. Current data provide little support for either model, but
 uncertainty about the ability of individuals to detect genetic relatedness
 and difficulties in identifying traits conferring competitive ability mean
 that the relative importance of concessions versus tug-of-war remains
 unresolved. Here, we suggest that the use of social parasitism to generate
 meaningful variation in key social variables represents a valuable
 opportunity to explore the mechanisms underpinning reproductive skew
 within the social Hymenoptera. We present a direct test of concessions and
 tug-of-war models in the paper wasp Polistes dominulus by exploiting
 pronounced changes in relatedness and power structures that occur
 following replacement of the dominant by a congeneric social parasite.
 Comparisons of skew in parasitized and unparasitized colonies are
 consistent with a tug-of-war over reproduction within P. dominulus groups,
 but provide no evidence for reproductive concessions.
description: Reproductive skew data
 for parasitised and unparasitised nestsNest attributes (group
 size, nest size, presence of workers, site) come from field records.
 Numbers of eggs produced by dominants and subordinates were obtained
 through microsatellite genotyping of parents and offspring. Relatedness
 estimates were calculated based on microsatellite genotypes of nest-mates.
 Body size data and data on egg size and number were obtained through
 morphological measurements.
DOI: 10.5061/dryad.1t1f5
title: Data from: RADseq dataset with 90% missing data fully resolves recent radiation of Petalidium (Acanthaceae) in the ultra-arid deserts of Namibia

description: Deserts, even those at tropical latitudes, often have strikingly low
 levels of plant diversity, particularly within genera. One remarkable
 exception to this pattern is the genus Petalidium (Acanthaceae), in which
 37 of 40 named species occupy one of the driest environments on Earth, the
 Namib Desert of Namibia and neighboring Angola. To contribute to
 understanding this enigmatic diversity, we generated RADseq data for 47
 accessions of Petalidium representing 22 species. We explored the impacts
 of 18 different combinations of assembly parameters in de novo assembly of
 the data across nine levels of missing data plus a best practice assembly
 using a reference Acanthaceae genome for a total of 171 sequence datasets
 assembled. RADseq data assembled at several thresholds of missing data,
 including 90% missing data, yielded phylogenetic hypotheses of Petalidium
 that were confidently and nearly fully resolved, which is notable given
 that divergence time analyses suggest a crown age for African species of
 3.6–1.4 Ma. De novo assembly of our data yielded the most strongly
 supported and well-resolved topologies; in contrast, reference-based
 assembly performed poorly, perhaps due in part to moderate phylogenetic
 divergence between the reference genome, Ruellia speciosa, and the
 ingroup. Overall, we found that Petalidium, despite the harshness of the
 environment in which species occur, shows a net diversification rate
 (0.8–2.1 species per my) on par with those of diverse genera in tropical,
 Mediterranean, and alpine environments.
description: 7_Supp_Script_from_rawseq_to_treesThis zip file contains an example workflow for processing raw RADseq data to the output and summary of phylogenetic trees. See the README.txt within the zip file for more details.
DOI: 10.5061/dryad.45t51
title: Data from: Effects of habitat fragmentation on parental correlations in the seed rain of a bird-dispersed species

description: Seed dispersal plays a crucial role in natural forest regeneration.
 Changes in the seed rain due to anthropogenic habitat alteration can
 influence seedling recruitment patterns and affect the evolutionary
 dynamics of populations. Using a combined endocarp-embryo microsatellite
 assay of naturally dispersed seeds, we concomitantly quantify the
 contribution of contemporary pollen and seed dispersal to the genetic
 structure of the seed rain of the shrub species Pistacia lentiscus L. The
 study was conducted in two consecutive seasons at four forest fragments
 embedded in contrasting (connected vs. isolated) landscapes. Interseasonal
 variation in the parental genetic structure of the seed rain was assessed
 through analysis of molecular variance, and paternal and maternal
 correlations and effective parental numbers were computed for different
 fragments and microhabitats (within fragments) using genetic kinship
 analysis. Temporal variation in the genetic structure of the dispersed
 seeds was higher for maternal gametes, reflecting a more temporally
 variable contribution of individual mother plants to the seed rain, as a
 potential consequence of masting and/or natural heterogeneity. Higher
 effective numbers of fathers than mothers were consistently observed in
 all studied forest fragments and microhabitats, the difference being more
 pronounced for connected than for isolated fragments. The effective number
 of mothers, directly influenced by disperser birds’ behavior, was
 apparently insensitive to fragmentation. Despite potentially high mobility
 of pollen by wind and seeds by birds, habitat fragmentation could
 influence the parental structure of dispersed seeds, with potential
 consequences for the genetic structure of the adult generation.
description: Microsatellite
 data
DOI: 10.15468/dl.2b6xpz
title: Occurrence Download

description: A dataset containing 87 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Leucothoe griffithiana",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 87 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001339-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.gr756
title: Data from: Direct and plant trait-mediated effects of the local environmental context on butterfly oviposition patterns

description: Variation in the intensity of plant-animal interactions over different
 spatial scales is widespread and might strongly influence fitness and
 trait selection in plants. Differences in traits among plant individuals
 have been shown to influence variation in interaction intensities within
 populations, while differences in environmental factors and community
 composition are shown to be important for variation over larger scales.
 However, little is still known about the relative importance of the local
 environmental context vs. plant traits for the outcome of interactions
 within plant populations. We investigated how oviposition by the
 seed-predator butterfly Phengaris alcon on its host plant Gentiana
 pneumonanthe was related to host plant traits and to local environmental
 variation, as well as how oviposition patterns translated into effects on
 host plant fruit set. We considered the local environmental context in
 terms of height of the surrounding vegetation and abundance of the
 butterfly’s second host, Myrmica ants. The probability of oviposition was
 higher in plants that were surrounded by lower vegetation, and both the
 probability of oviposition and the number of eggs increased in
 early-flowering and tall plants with many flowers in the three study
 populations. Flowering phenology, shoot height and flower production were,
 in turn, related to higher surrounding vegetation. Myrmica abundance was
 correlated with vegetation height, but had no effect on oviposition
 patterns. Oviposition and subsequent seed predation by the caterpillars
 strongly reduced host plant fruit set. Our results show that plant-animal
 interactions are context-dependent not only because the context influences
 the abundance or the behavior of the animal interactor, but also because
 it influences the expression of plant traits that affect the outcome of
 the interaction. The results also demonstrate that heterogeneity in
 environmental conditions at a very local scale can be important for the
 outcomes of interactions.
description: Data on plant traits and
 fruit set of Gentiana pneumonanthe, local environmental context and
 intensity of seed predation by the butterfly Phengaris
 alcondatafile_Oikos.txt
DOI: 10.5061/dryad.kd873
title: Data from: Population variation in the life history of a land fish, Alticus arnoldorum, and the effects of predation and density

description: Life history variation can often reflect differences in age-specific
 mortality within populations, with the general expectation that
 reproduction should be shifted away from ages experiencing increased
 mortality. Investigators of life history in vertebrates frequently focus
 on the impact of predation, but there is increasing evidence that
 predation may have unexpected impacts on population density that in turn
 prompt unexpected changes in life history. There are also other reasons
 why density might impact life history independently of predation or
 mortality more generally. We investigated the consequences of predation
 and density on life history variation among populations of the Pacific
 leaping blenny, Alticus arnoldorum. This fish from the island of Guam
 spends its adult life out of the water on rocks in the splash zone, where
 it is vulnerable to predation and can be expected to be sensitive to
 changes in population density that impact resource availability. We found
 populations invested more in reproduction as predation decreased, while
 growth rate varied primarily in response to population density. These
 differences in life history among populations are likely plastic given the
 extensive gene flow among populations revealed by a previous study. The
 influence of predation and density on life history was unlikely to have
 operated independently of each other, with predation rate tending to be
 associated with reduced population densities. Taken together, our results
 suggest predation and density can have complex influences on life history,
 and that plastic life history traits could allow populations to persist in
 new or rapidly changing environments.
description: PLATT-PLOSONE-2015-PONE-D-15-17561R2_populationlevel_datadata on the estimated predation rate, density, female growth rate and ovarian weight of fish from five populations of Alticus arnoldorum from GuamPLATT-PLOSONE-2015-PONE-D-15-17561R2_growth_datadata on the estimated age and size of female fish from five populations of Alticus arnoldorum from GuamPLATT-PLOSONE-2015-PONE-D-15-17561R2_ovaryweight_datadata on the size, weight of ovaries and reproductive state of female fish from five populations of Alticus arnoldorum from Guam
DOI: 10.5061/dryad.13250
title: Data from: Adherence to trained standards after a faculty development workshop on “Teaching With Simulated Patients”

description: Background: Nowadays, faculty development programs to improve teaching
 quality are considered to be very important by medical educators from all
 over the world. However, the assessment of the impact of such programs
 rarely exceeds tests of participants’ knowledge gain or self-assessments
 of their teaching behavior. It remains unclear what exactly is expected of
 the attending faculty and how the transfer to practice may be measured
 more comprehensively and accurately. Method: This study evaluates how
 specific teaching standards were applied after a workshop (10 teaching
 units) focusing on teaching communication skills with simulated patients.
 Trained observers used a validated checklist to observe 60 teaching
 sessions (held by 60 different teachers) of a communication skills course
 integrating simulated patients. Additionally, we assessed the amount of
 time that had passed since their participation in the workshop and asked
 them to rate the importance of communication and social skills in medical
 education. Results: The observations showed that more than two thirds of
 teaching standards were met by at least 75% of teachers. Fulfillment of
 standards was significantly connected to teachers’ rating of the
 importance of communication and social skills (tb=-.21, p=.03). In
 addition, the results suggest a slight decrease in the amount of fulfilled
 standards over time (r=-.14, p=.15). Conclusions: Teachers' adherence
 to basic teaching standards was already satisfying after a one-day
 workshop. More complex issues need to be re-addressed in further faculty
 development courses with a special focus on teachers’ attitude towards
 teaching. In future, continuing evaluations of the transfer of knowledge
 and skills from faculty development courses into practice, preferably
 including pre-tests or control groups, are needed.
description: data_teacher_adherence