cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.387jh
title: Data from: Strong indirect herbicide effects on mycorrhizal associations through plant community shifts and secondary invasions

description: Million of acres of US wildlands are sprayed with herbicides to control
 invasive species, but relatively little is known about non-target effects
 of herbicide use. We combined greenhouse, field and laboratory experiments
 involving the invasive forb spotted knapweed (Centaurea stoebe) and native
 bunchgrasses to assess direct and indirect effects of the forb-specific
 herbicide picloram on arbuscular mycorrhizal fungi (AMF), which are
 beneficial soil fungi that colonize most plants. Picloram had no effect on
 bunchgrass viability and their associated AMF in the greenhouse, but
 killed spotted knapweed and reduced AM colonization of a subsequent host
 grown. Results were similar in the field where AMF abundance in
 bunchgrass-dominated plots was unaffected by herbicides one year after
 spraying based on 16:1ω5 phospholipid fatty acid (PLFA) and neutral lipid
 fatty acid (NLFA) concentrations. In spotted knapweed-dominated plots,
 however, picloram application shifted dominance from spotted knapweed, a
 good AMF host, to bulbous bluegrass (Poa bulbosa), a poor AMF host. This
 coincided with a 63% reduction in soil 16:1ω5 NLFA concentrations but no
 reduction of 16:1ω5 PLFA. Because 16:1ω5 NLFA quantifies AMF storage
 lipids and 16:1ω5 PLFA occurs in AMF membrane lipids, we speculate that
 the herbicide-mediated reduction in host quality reduced fungal carbon
 storage, but not necessarily fungal abundance after one year in the field.
 Overall, in greenhouse and field experiments, AMF were only affected when
 picloram altered host quantity and quality. This apparent lack of direct
 effect was supported by our in-vitro trial where picloram applied to AMF
 mycelia did not reduce fungal biomass and viability. We show that the
 herbicide picloram can have profound, indirect effects on AMF within a
 year. Depending on herbicide-mediated shifts in host quality, rapid
 interventions may be necessary post herbicide applications to prevent loss
 of AMF abundance. Future research should assess consequences of these
 potential shifts for the restoration of native plants that differ in
 mycorrhizal dependency.
description: Supplemental raw data
 filesField, greenhouse,
 in-vitro raw dataDRYAD
 submission.xlsx
DOI: 10.5061/dryad.c1m60s84
title: Data from: Measuring rates of phenotypic evolution and the inseparability of tempo and mode

description: Rates of phenotypic evolution are central to many issues in paleontology,
 but traditional rate metrics such as darwins or haldanes are seldom used
 because of their strong dependence on interval length. In this paper, I
 argue that rates are usefully thought of as model parameters that relate
 magnitudes of evolutionary divergence to elapsed time. Starting with
 models of directional evolution, random walks, and stasis, I derive for
 each a reasonable rate metric. These metrics can be linked to existing
 approaches in evolutionary biology, and simulations show that they can be
 estimated accurately at any temporal resolution via maximum likelihood,
 but only when that metric's underlying model is true. The estimation
 of generational rates of a random walk under realistic paleontological
 conditions is compared with simulations to that of a prominent alternative
 approach, Gingerich's LRI (log-rate, log-interval) method.
 Generational rates are estimated poorly by LRI; they often reflect
 sampling error more than the actual pace of change. Further simulations
 show that under some realistic conditions, it is simply not possible to
 infer generational rates from coarsely sampled populations. These modeling
 results indicate a complex dependence between evolutionary mode and the
 measurement of evolutionary rates, and that there is unlikely to be a rate
 metric that works well for all traits and time scales. Compilations of
 paleontological and phylogenetic data indicate that all of the three rate
 metrics derived here show some relationship with interval length. Although
 there is no perfect rate metric, at present the most practical choices
 derive from the parameters of the stasis and random walk models. The
 latter, called the step variance, is particularly promising as a rate
 metric in paleontology and comparative biology.
description: Supplementary Appendix 1
 - LRI simulationsR code used to test via
 simulation the performance of the LRI (log-rate, log-interval) method for
 inferring rates of evolution. The included code does the simulations and
 plots the results summarized in Figure 4 in the paper.Supplementary Table 1 -
 Fossil Rate EstimatesTable in XLSX format
 summarizing information and model parameter estimates for 251 time-series
 of traits measured in fossil lineages.Supplementary Table
 1.xlsxSupplementary Table 2 -
 Phylogenetic Rate EstimatesTable in XLSX format
 summarizing information and model parameter estimates for rate estimates
 generated from phylogenies of extant species. Original data are from
 Harmon et al (2010), Evolution 64(8):2385-2396.Supplementary Table
 2.xlsx
DOI: 10.5061/dryad.7jf10
title: Data from: Generality of toxins in defensive symbiosis: ribosome-inactivating proteins and defense against parasitic wasps in Drosophila

description: While it has become increasingly clear that multicellular organisms often
 harbor microbial symbionts that protect their hosts against natural
 enemies, the mechanistic underpinnings underlying most defensive symbioses
 are largely unknown. Spiroplasma bacteria are widespread associates of
 terrestrial arthropods, and include strains that protect diverse
 Drosophila flies against parasitic wasps and nematodes. Recent work
 implicated a ribosome-inactivating protein (RIP) encoded by Spiroplasma,
 and related to Shiga-like toxins in enterohemorrhagic Escherichia coli, in
 defense against a virulent parasitic nematode in the woodland fly,
 Drosophila neotestacea. Here we test the generality of RIP-mediated
 protection by examining whether Spiroplasma RIPs also play a role in wasp
 protection, in D. melanogaster and D. neotestacea. We find strong evidence
 for a major role of RIPs, with ribosomal RNA (rRNA) from the larval
 endoparasitic wasps, Leptopilina heterotoma and Leptopilina boulardi,
 exhibiting the hallmarks of RIP activity. In Spiroplasma-containing hosts,
 parasitic wasp ribosomes show abundant site-specific depurination in the
 α-sarcin/ricin loop of the 28S rRNA, with depurination occurring soon
 after wasp eggs hatch inside fly larvae. Interestingly, we found that the
 pupal ectoparasitic wasp, Pachycrepoideus vindemmiae, escapes protection
 by Spiroplasma, and its ribosomes do not show high levels of depurination.
 We also show that fly ribosomes show little evidence of targeting by RIPs.
 Finally, we find that the genome of D. neotestacea’s defensive Spiroplasma
 encodes a diverse repertoire of RIP genes, which are differ in abundance.
 This work suggests that specificity of defensive symbionts against
 different natural enemies may be driven by the evolution of toxin
 repertoires, and that toxin diversity may play a role in shaping
 host-symbiont-enemy interactions.
description: RT-qPCR data and aligned
 RIP sequencesppathogens_2017_ballinger.zip
DOI: 10.5061/dryad.t4j7k
title: Data from: Understorey plant community composition reflects invasion history decades after invasive Rhododendron has been removed

description: 1) A growing awareness of the destructive effects of non-native invasive
 species has led to a massive increase in removal programmes around the
 world. Little is typically known about what happens to sites following the
 removal of the invasives, however, and the implicit assumption that the
 native community will return, unaided, to pre-invasion conditions is often
 left untested. 2) We assessed recovery of the native understorey plant
 community following removal of the non-native invasive Rhododendron
 ponticum L. from Scottish Atlantic oak woodland. We recorded understorey
 community composition in sites covering a gradient of increasing R.
 ponticum density, and across a separate series of sites covering a
 chronosequence of time since R. ponticum removal. We then compared both of
 these series to the target community found in uninvaded sites. We also
 analysed differences in soil chemistry between the sites to test for
 chemical legacy effects of invasion in the soil. 3) Native understorey
 cover declined as R. ponticum density increased, with bryophytes dropping
 to less than a third of the cover present in uninvaded sites and forbs and
 grasses being completely extirpated under dense stands. 4) Cleared sites
 showed no evidence of returning to the target community even after 30
 years of recovery, and instead formed a bryophyte-dominated ‘novel
 community’, containing few of the typical oak woodland vascular plants. 5)
 Contrary to expectation, soil pH, C:N ratio, and nutrient concentrations
 (N, P, K, Ca and Mg) were not affected by the invasion of R. ponticum, and
 chemical legacy effects in the soil were not responsible for the failure
 of the native community to revert to pre-invasion conditions. Instead, we
 hypothesise that the rapid formation of a bryophyte mat, coupled with the
 often-substantial distances to potential seed sources, hindered vascular
 plant recolonisation. 6) Synthesis and applications. Clear evidence of
 invasion history can be detected in the understorey plant community even
 decades after the successful removal of invasive R. ponticum. This finding
 demonstrates that native communities may be unable to recover effectively
 of their own accord following invasive species removal and will require
 further management interventions in order to achieve restoration
 goals.30-Jun-2017
description: maclean_rhodo_understorey_plotPlot level data on average percent cover and species richness in plots spanning a range of 1) R. ponticum density and 2) time since R. ponticum clearance. Also included are data on soil nutrient status in a subset of the plots.maclean_rhodo_comcompCommunity composition data from plots spanning 1) a gradient of increasing R. ponticum density and 2) a gradient of increasing time since R. ponticum clearance.
DOI: 10.15468/dl.qr843c
title: Occurrence Download

description: A dataset containing 406 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Country is Mexico",
 "TaxonKey is Thamnophis proximus",
 "Year 1960-2026"
 ]
}

 The dataset includes 406 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000728-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.12c56
title: Data from: The response of the alpine dwarf shrub Salix herbacea to altered snowmelt timing: lessons from a multi-site transplant experiment

description: Climate change is altering spring snowmelt patterns in alpine and arctic
 ecosystems, and these changes may alter plant phenology, growth and
 reproduction. To predict how alpine plants respond to shifts in snowmelt
 timing, we need to understand trait plasticity, its effects on growth and
 reproduction, and the degree to which plants experience a home-site
 advantage. We tested how the common, long-lived dwarf shrub Salix herbacea
 responded to changing spring snowmelt time by reciprocally transplanting
 turfs of S. herbacea between early-exposure ridge and late-exposure
 snowbed microhabitats. After the transplant, we monitored phenological,
 morphological and fitness traits, as well as leaf damage, during two
 growing seasons. Salix herbacea leafed out earlier, but had a longer
 development time and produced smaller leaves on ridges relative to
 snowbeds. Longer phenological development times and smaller leaves were
 associated with reduced sexual reproduction on ridges. On snowbeds, larger
 leaves and intermediate development times were associated with increased
 clonal reproduction. Clonal and sexual reproduction showed no response to
 altered snowmelt time. We found no home-site advantage in terms of sexual
 and clonal reproduction. Leaf damage probability depended on snowmelt and
 thus exposure period, but had no short-term effect on fitness traits. We
 conclude that the studied populations of S. herbacea can respond to shifts
 in snowmelt by plastic changes in phenology and leaf size, while
 maintaining levels of clonal and sexual reproduction. The lack of a
 home-site advantage suggests that S. herbacea may not be adapted to
 different microhabitats. The studied populations are thus unlikely to
 react to climate change by rapid adaptation, but their responses will also
 not be constrained by small-scale local adaptation. In the short term,
 snowbed plants may persist due to high stem densities. However, in the
 long term, reduction in leaf size and flowering, a longer phenological
 development time and increased exposure to damage may decrease overall
 performance of S. herbacea under earlier snowmelt.
description: Raw data of Sedlacek et
 al. 2015 in PLOS ONEThis is the data set
 used for the analyses presented in Sedlacek et al. 2015 (PLOS ONE). The
 data come from a reciprocal transplant experiment of Salix herbacea plants
 between snowbed and ridge microhabitats in the Swiss Alps. On the
 transplanted plants, we determined phenology (leaf expansion, flowering,
 fruiting), damage by herbivores and pathogens, leaf size, and fitness
 proxies (flowering and change in stem number).Sedlacek_etal_TransplantData.csv
DOI: 10.5061/dryad.9k358
title: Data from: Intrinsic honesty and the prevalence of rule violations across societies

description: Deception is common in nature and humans are no exception. Modern
 societies have created institutions to control cheating, but many
 situations remain where only intrinsic honesty keeps people from cheating
 and violating rules. Psychological, sociological and economic theories
 suggest causal pathways to explain how the prevalence of rule violations
 in people’s social environment, such as corruption, tax evasion or
 political fraud, can compromise individual intrinsic honesty. Here we
 present cross-societal experiments from 23 countries around the world that
 demonstrate a robust link between the prevalence of rule violations and
 intrinsic honesty. We developed an index of the ‘prevalence of rule
 violations’ (PRV) based on country-level data from the year 2003 of
 corruption, tax evasion and fraudulent politics. We measured intrinsic
 honesty in an anonymous die-rolling experiment. We conducted the
 experiments with 2,568 young participants (students) who, due to their
 young age in 2003, could not have influenced PRV in 2003. We find
 individual intrinsic honesty is stronger in the subject pools of low PRV
 countries than those of high PRV countries. The details of lying patterns
 support psychological theories of honesty. The results are consistent with
 theories of the cultural co-evolution of institutions and values, and show
 that weak institutions and cultural legacies that generate rule violations
 not only have direct adverse economic consequences, but might also impair
 individual intrinsic honesty that is crucial for the smooth functioning of
 society.
description: GaechterSchulzDATA&CODEContains all experimental and auxiliary data (institutional and demographic variables) reported in the article and the supplementary information (in both csv and STATA format). A list of variables and their labels is in the ReadMe file.Also contains the STATA codes (do-files) of the analyses reported in the article and the Supplementary Information.
DOI: 10.5061/dryad.8b3d1
title: Data from: Positive relationship between genetic- and species diversity on limestone outcrops in the Carpathian Mountains

description: We asked if the genetic diversity of Saponaria bellidifolia (a habitat
 specialist plant) and the species diversity of its habitat are driven by
 parallel landscape-level processes in an island-like system of limestone
 outcrops in the Carpathian Mountains. We tested the relationship of these
 two diversity levels at local and regional geographic scales. Local
 genetic and species diversity showed parallel patterns influenced by the
 number of plant communities. Likewise, at regional level there was strong
 evidence for parallel equilibrial dynamics of genotypes and species.
 However, a superimposed matrix effect enhanced the regional species
 diversity only. Genetic diversity of habitat specialist organisms and
 species diversity of these limestone outcrop islands on mainland are
 modulated by parallel landscape-level processes at different geographic
 scales, and mechanisms may be identified at very high spatial resolutions.
description: VegetationPlots_Saponaria bellidifoliaHabitat_Apuseni MtsVegetation data sampled within Saponaria bellidifolia habitat in the Apuseni Mountains (Carpathian Mountains, Romania).RAPD_Saponaria bellidifolia_Apuseni MtsRAPD analysis of 10 plants/population for 7 Saponaria bellidifolia populations within Apuseni Mountains.
DOI: 10.5061/dryad.3274n
title: Data from: AFLP diversity and spatial structure of Calycophyllum candidissimum (Rubiaceae), a dominant tree species of Nicaragua’s critically endangered seasonally dry forest

description: The Central American seasonally dry tropical (SDT) forest biome is one of
 the worlds’ most endangered ecosystems, yet little is known about the
 genetic consequences of its recent fragmentation. A prominent constituent
 of this biome is Calycophyllum candidissimum, an insect-pollinated and
 wind-dispersed canopy tree of high socio-economic importance, particularly
 in Nicaragua. Here, we surveyed amplified fragment length polymorphisms
 across 13 populations of this species in Nicaragua to elucidate the
 relative roles of contemporary vs historical factors in shaping its
 genetic variation. Genetic diversity was low in all investigated
 populations (mean HE=0.125), and negatively correlated with latitude.
 Overall population differentiation was moderate (ΦST=0.109,
 P&lt;0.001), and Bayesian analysis of population structure revealed
 two major latitudinal clusters (I: ‘Pacific North’+’Central Highland’; II:
 ‘Pacific South’), along with a genetic cline between I and II.
 Population-based cluster analyses indicated a strong pattern of ‘isolation
 by distance’ as confirmed by Mantel’s test. Our results suggest that (1)
 the low genetic diversity of these populations reflects
 biogeographic/population history (colonisation from South America,
 Pleistocene range contractions) rather than recent human impact; whereas
 (2) the underlying process of their isolation by distance pattern, which
 is best explained by ‘isolation by dispersal limitation’, implies
 contemporary gene flow between neighbouring populations as likely
 facilitated by the species’ efficient seed dispersal capacity. Overall,
 these results underscore that even tree species from highly decimated
 forest regions may be genetically resilient to habitat fragmentation due
 to species-typical dispersal characteristics, the necessity of broad-scale
 measures for their conservation notwithstanding.
description: Calycophyllum
 candidissimum_Nicaragua_AFLP matrixThis is a
 presence/absence matrix generated based on AFLP fingerprinting for 220
 individuals from thirteen populations spread around the Seasonal Tropical
 Dry Forest of Nicaragua. As result of three AFLP primer combination, it
 was successfully scored 226 unambiguous fragments ranging from 87 to 411
 base pairs (bp), of which 147 markers were polymorphic.
DOI: 10.5061/dryad.6nh3j
title: Data from: Differential survival between visual environments supports a role of divergent sensory drive in cichlid fish speciation

description: Identifying the selective forces that initiate ecological speciation is a
 major challenge in evolutionary biology. Sensory drive has been implicated
 in speciation in various taxa, largely based on phenotype-environment
 correlations and signatures of selection in sensory genes. Here, we
 present a reciprocal transplant experiment revealing species differences
 in performance in alternative visual environments, consistent with
 speciation by divergent sensory drive. The closely related cichlids
 Pundamilia pundamilia and P. nyererei inhabit different visual
 environments in Lake Victoria and show associated differences in visual
 system properties. Mimicking the two light environments in the laboratory,
 we find a substantial reduction in survival of both species when reared in
 the other species' visual environment. This implies that the observed
 differences in Pundamilia colour vision are indeed adaptive, and
 substantiates the implicit assumption in sensory drive speciation models
 that divergent environmental selection is strong enough to drive
 divergence in sensory properties.
description: Maanetal2016_AmNatExcel file containing 1) 6-month and 12-month survival data; 2) spectrometry data from field and lab.
DOI: 10.5061/dryad.qh376
title: Data from: Muscle shortening velocity depends on tissue inertia and level of activation during submaximal contractions

description: In order to perform external work, muscles must do additional internal
 work to deform their tissue, and in particular, to overcome the inertia
 due to their internal mass. However, the contribution of the internal mass
 within a muscle to the mechanical output of that muscle has only rarely
 been studied. Here, we use a dynamic, multi-element Hill-type muscle model
 to examine the effects of the inertial mass within muscle on its
 contractile performance. We find that the maximum strain-rate of muscle is
 slower for lower activations and larger muscle sizes. As muscle size
 increases, the ability of the muscle to overcome its inertial load will
 decrease, as muscle tension is proportional to cross-sectional area and
 inertial load is proportional to mass. Thus, muscles that are larger in
 size will have a higher inertial cost to contraction. Similarly, when
 muscle size and inertial load are held constant, decreasing muscle
 activation will increase inertial cost to contraction by reducing muscle
 tension. These results show that inertial loads within muscle contribute
 to a slowing of muscle contractile velocities (strain-rates), particularly
 at the submaximal activations that are typical during animal locomotion.
description: Simulation results for
 16 point masses, and muscle contracting from an initial normalized length
 of 1 with no additional external loadSimulated electronically
 in Wolfram Mathematica (Wolfram Research, Inc., Mathematica, Version 10.0,
 Champaign, IL, 2014).manuscript_data.txt
DOI: 10.15468/dl.wf8xzy
title: Occurrence Download

description: A dataset containing 2724 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Lao People’s Democratic Republic",
 "OccurrenceStatus is Present",
 "TaxonKey is one of (Lycopodiopsida, Polypodiopsida)"
 ]
}

 The dataset includes 2724 records from 35 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000729-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.