cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.qc603
title: Data from: Does the Platanthera dilatata (Orchidaceae) complex contain cryptic species or continuously variable populations?

description: Floral phenotypic traits are expected to reflect evolutionary changes and
 are used as a reliable basis for species delimitation. However, when
 traits overlap among populations of newly emerging species, this confounds
 identification of evolutionarily distinct lineages and reduces taxonomic
 stability. In this study, we quantified variation in ten floral traits and
 plastid DNA sequences across 26 populations of Platanthera dilatata
 (Orchidaceae) in North America to determine geographic structure among
 populations and to evaluate support for three varieties recognized in the
 current taxonomy. k-means clustering analysis, in the absence of a priori
 designation of groups, indicated two morphologically distinct groups. Spur
 length was the most distinctive character between groups. The group
 containing larger flowers with longer spurs corresponds to the var.
 leucostachys and most samples in this group are from western North
 America. The vars. albiflora and dilatata could not be distinguished
 within the second group, which exhibited flowers with short to
 intermediate spurs and include samples from eastern and western North
 America. Morphological variation in P. dilatata may reflect
 pollinator-mediated selection, particularly in spur length, which is known
 to vary in association with pollinators across Platanthera. Significant
 genetic divergence was observed between the two groups (F ST = 0.15; P ≤
 0.001), but we did not find corresponding phylogenetic structure, which
 may reflect recent divergence and retention of ancestral polymorphisms.
 Based on these results, we suggest preserving the current intraspecific
 taxonomy until further studies determine the origin of floral variation
 and the extent of gene flow between morphologically divergent populations.
description: P_dilatata plastid
 sequencesThis data file contains
 aligned sequences from 78 samples of Platanthera dilatata and 2 samples of
 Platanthera aquilonis for 6 plastid regions (rpl16_intron:1-648,
 ndhC_trnV:649-1301, accD_psaI:1302-2005, psbC_trnS:2006-2064,
 atpF_atpH:2065-2220, psbA_trnK:2221-2499) and gaps coded as simple
 characters (2500-2566).Dilatata_bayes.nex
DOI: 10.5061/dryad.rh094v7
title: Data from: Research on the mechanical behavior of shale based on multi-scale analysis

description: In view of the difficulty in obtaining the mechanical properties of shale,
 the multi-scale analysis of shale was performed on a shale outcrop from
 the Silurian Longmaxi Formation in the Changning area, Sichuan Basin,
 China. The nano/micro indentation test is an effective method for
 multi-scale mechanical analysis. In this paper, effective criteria for the
 shale indentation test were evaluated. The elastic modulus was evaluated
 at a multi-scale and the engineering validation of drilling cuttings was
 performed. The porosity tests showed that the pore distribution of shale
 from the nano-scale to macro-pore could be better displayed by the nuclear
 magnetic resonance test. The micro-scale elastic modulus and hardness
 increased nonlinearly with the increase in the clay packing density. It
 was observed that the size effect of the micro-hardness was based on
 porosity and composition. The partial spalling of shale at the micro-scale
 could lead to irregular bulges or steps in a load–displacement curve. The
 elastic modulus of pure clay minerals was 24.2 GPa on the parallel bedding
 plane, and 15.8 GPa on the vertical bedding plane. The contact hardness
 (pure clay minerals) was 0.51 GPa. The indentation results showed that the
 micro elastic modulus of shale obeyed the normal distribution, and the
 statistical average could predict the macro mechanical properties
 effectively. The present work provides a novel idea regarding the
 cognitive mechanics state of shale in the formation.
description: origin
 data
DOI: 10.5061/dryad.54k37
title: Data from: Patterns and biases in climate change research on amphibians and reptiles: a systematic review

description: Climate change probably has severe impacts on animal populations, but
 demonstrating a causal link can be difficult because of potential
 influences by additional factors. Assessing global impacts of climate
 change effects may also be hampered by narrow taxonomic and geographical
 research foci. We review studies on the effects of climate change on
 populations of amphibians and reptiles to assess climate change effects
 and potential biases associated with the body of work that has been
 conducted within the last decade. We use data from 104 studies regarding
 the effect of climate on 313 species, from 464 species–study combinations.
 Climate change effects were reported in 65% of studies. Climate change was
 identified as causing population declines or range restrictions in half of
 the cases. The probability of identifying an effect of climate change
 varied among regions, taxa and research methods. Climatic effects were
 equally prevalent in studies exclusively investigating climate factors
 (more than 50% of studies) and in studies including additional factors,
 thus bolstering confidence in the results of studies exclusively examining
 effects of climate change. Our analyses reveal biases with respect to
 geography, taxonomy and research question, making global conclusions
 impossible. Additional research should focus on under-represented regions,
 taxa and questions. Conservation and climate policy should consider the
 documented harm climate change causes reptiles and amphibians.
description: Variables included in
 studies on the effect of climate change on amphibians and
 reptilesEach row indicates the
 dependent and independent variables included in a specific study. Studies
 that investigated several species are represented by as many rows as
 species included.Amph_Reptile_5312015.csv
DOI: 10.5061/dryad.jk2m0
title: Data from: Genetic and environmental variation in condition, cutaneous immunity, and haematocrit in house wrens

description: Background: Life-history studies of wild bird populations often focus on
 the relationship between an individual’s condition and its capacity to
 mount an immune response, as measured by a commonly-employed assay of
 cutaneous immunity, the PHA skin test. In addition, haematocrit, the
 packed cell volume in relation to total blood volume, is often measured as
 an indicator of physiological performance. A multi-year study of a wild
 population of house wrens has recently revealed that those exhibiting the
 highest condition and strongest PHA responses as nestlings are most likely
 to be recruited to the breeding population and to breed through two years
 of age; in contrast, intermediate haematocrit values result in the highest
 recruitment to the population. Selection theory would predict, therefore,
 that most of the underlying genetic variation in these traits should be
 exhausted resulting in low heritability, although such traits may also
 exhibit low heritability because of increased residual variance. Here, we
 examine the genetic and environmental variation in condition, cutaneous
 immunity, and haematocrit using an animal model based on a pedigree of
 approximately 2,800 house wrens. Results: Environmental effects played a
 paramount role in shaping the expression of the fitness related traits
 measured in this wild population, but two of them, condition and
 haematocrit, retained significant heritable variation. Condition was also
 positively correlated with both the PHA response and haematocrit, but in
 the absence of any significant genetic correlations, it appears that this
 covariance arises through parallel effects of the environment acting on
 this suite of traits. Conclusions: The maintenance of genetic variation in
 different measures of condition appears to be a pervasive feature of wild
 bird populations, in contradiction of conventional selection theory. A
 major challenge in future studies will be to explain how such variation
 persists in the face of the directional selection acting on condition in
 house wrens and other species.
description: Sakaluk et al house wren
 pedigree and trait valuesThis file contains the
 pedigree on which the animal model was based (tab labeled
 'Pedigree') and the trait values of nestlings that were analyzed
 (tab labeled 'Nestling trait values'.Sakaluk house wren pedigree and
 trait values.xlsx
DOI: 10.5061/dryad.n4b4c
title: Data from: Comparison of reproductive investment in native and non-native populations of common wall lizards reveals sex differences in adaptive potential.

description: Non-native animals can encounter very different environments than those
 they are adapted to. Functional changes in morphology, physiology and
 life-history following introduction show that organisms can adapt both
 fast and efficiently. It remains unclear, however, if female reproductive
 characters and male sexually selected behaviour show the same adaptive
 potential. Furthermore, the invasion success and evolutionary trajectory
 of non-native species might often depend on the ability of the sexes to
 coordinate shifts in characters associated with reproductive strategy. The
 common wall lizard, Podarcis muralis, has been repeatedly introduced from
 Southern Europe to England over the past 80 years. Lizards in England
 experience a cool, seasonal climate that effectively restricts recruitment
 to the first clutch of the season, whereas in their native range up to
 three clutches per season recruit. As a consequence, both females and
 males in non-native populations should benefit from reducing or even
 eliminating their reproductive investment in second clutches. Using a
 combination of field data and experiments, we show that non-native females
 produce relatively larger and heavier first seasonal clutches and smaller
 and lighter second seasonal clutches compared to native females. In
 contrast, non-native and native males do not differ in their territorial
 and sexual behaviour later in the season. An adaptive shift in male
 seasonal reproductive investment may be constrained because males use
 breeding females as cues for sexual behaviour. If this is so, we expect a
 general pattern across climatic regimes whereby female reproductive
 investment evolves first, with responses in males lagging behind.
description: MacGregoretal2017Oikos_Datasetmorphology, clutch investment, genotypes, and experimental males.
DOI: 10.5061/dryad.64dh070
title: Data from: Interplay between age-based competitive asymmetries within the brood and direct competition between inbred and outbred offspring in a burying beetle

description: Theory suggests that intraspecific competition associated with direct
 competition between inbred and outbred individuals should be an important
 determinant of the severity of inbreeding depression. The reason is that,
 if outbred individuals are stronger competitors than inbred ones, direct
 competition should have a disproportionate effect on the fitness of inbred
 individuals. However, an individual’s competitive ability is not only
 determined by its inbreeding status but also by competitive asymmetries
 that are independent of an individual’s inbreeding status. When this is
 the case, such competitive asymmetries may shape the outcome of direct
 competition between inbred and outbred individuals. Here we investigate
 the interface between age-based competitive asymmetries within broods and
 direct competition between inbred and outbred offspring in the burying
 beetle Nicrophorus vespilloides. We found that inbred offspring had lower
 survival than outbred ones confirming that there was inbreeding
 depression. Furthermore, seniors (older larvae) grew to a larger size and
 had higher survival than juniors (younger larvae), confirming that there
 were age-based competitive asymmetries. Nevertheless, there was no
 evidence that direct competition between inbred and outbred larvae
 exacerbated inbreeding depression, no evidence that inbreeding depression
 was more severe in juniors, and no evidence that inbred juniors suffered
 disproportionately due to competition from outbred seniors. Our results
 suggest that direct competition between inbred and outbred individuals
 does not necessarily exacerbate inbreeding depression and that inbred
 individuals are not always more sensitive to poor and stressful conditions
 than outbred ones.
description: Miller, Ratz, Richardson
 & Smiseth JEB2018Data from: Interplay
 between age-based competitive asymmetries within the brood and direct
 competition between inbred and outbred offspring in a burying beetle.
 Miller et al. JEB.
DOI: 10.5061/dryad.n8379
title: Data from: Environmental factors influence both abundance and genetic diversity in a widespread bird species

description: Genetic diversity is one of the key evolutionary variables that correlate
 with population size, being of critical importance for population
 viability and the persistence of species. Genetic diversity can also have
 important ecological consequences within populations, and in turn,
 ecological factors may drive patterns of genetic diversity. However, the
 relationship between the genetic diversity of a population and how this
 interacts with ecological processes has so far only been investigated in a
 few studies. Here, we investigate the link between ecological factors,
 local population size, and allelic diversity, using a field study of a
 common bird species, the house sparrow (Passer domesticus). We studied
 sparrows outside the breeding season in a confined small valley dominated
 by dispersed farms and small-scale agriculture in southern France.
 Population surveys at 36 locations revealed that sparrows were more
 abundant in locations with high food availability. We then captured and
 genotyped 891 house sparrows at 10 microsatellite loci from a subset of
 these locations (N = 12). Population genetic analyses revealed weak
 genetic structure, where each locality represented a distinct substructure
 within the study area. We found that food availability was the main factor
 among others tested to influence the genetic structure between locations.
 These results suggest that ecological factors can have strong impacts on
 both population size per se and intrapopulation genetic variation even at
 a small scale. On a more general level, our data indicate that a patchy
 environment and low dispersal rate can result in fine-scale patterns of
 genetic diversity. Given the importance of genetic diversity for
 population viability, combining ecological and genetic data can help to
 identify factors limiting population size and determine the conservation
 potential of populations.
description: Microsatellites
 genotypesMicrosatellites
 genotypes of 891 individual house sparrows (Passer domesticus) at 10 loci.
 Details of genotype matrix see ReadMe file.Passer domesticus genotype in
 Liu_et_al-2013EcolEvol.xlsx
DOI: 10.5061/dryad.q1b6v
title: Data from: Different clades and traits yield similar grassland functional responses

description: Plant functional traits are viewed as key to predicting important
 ecosystem and community properties across resource gradients within and
 among biogeographic regions. Vegetation dynamics and ecosystem processes,
 such as aboveground net primary productivity (ANPP), are increasingly
 being modeled as a function of the quantitative traits of species, which
 are used as proxies for photosynthetic rates, and nutrient and water-use
 efficiency. These approaches rely on an assumption that a certain trait
 value consistently confers a specific function or response under given
 environmental conditions. Here, we provide a critical test of this idea
 and evaluate whether the functional traits that drive the well-known
 relationship between precipitation and aboveground net primary
 productivity (ANPP) differ between systems with distinct biogeographic
 histories and species assemblages. Specifically, we compared grasslands
 spanning a broad precipitation gradient (~200-1000 mm/year) in North
 America and South Africa that differ in the relative representation and
 abundance of grass phylogenetic lineages. We found no significant
 difference between the regions in the positive relationship between annual
 precipitation and ANPP, yet the trait values underlying this relationship
 differed dramatically. Our results challenge the trait-based approach to
 predicting ecosystem function by demonstrating that different combinations
 of functional traits can act to maximize ANPP in a given environmental
 setting. Further, we show the importance of incorporating biogeographic
 and phylogenetic history in predicting community and ecosystem properties
 using traits.
description: Genbank
 AccessionsTaxa included in the
 phylogenetic analyses along with corresponding Genbank accession
 numbers.GenbankAccessions.docxCommunity _Trait_DataCommunity composition, environmental, production and trait data for North American and South African sites and species.PhylogeniesPhylogenies of dominant grass species sampled in North America and South Africa.R_scriptsR scripts written to conduct all analyses.
DOI: 10.5061/dryad.8jj28
title: Data from: Fruit flies diversify their offspring in response to parasite infection

description: The evolution of sexual reproduction is often explained by Red Queen
 dynamics: Organisms must continually evolve to maintain fitness relative
 to interacting organisms, such as parasites. Recombination accompanies
 sexual reproduction and helps diversify an organism’s offspring, so that
 parasites cannot exploit static host genotypes. Here we show that
 Drosophila melanogaster plastically increases the production of
 recombinant offspring after infection. The response is consistent across
 genetic backgrounds, developmental stages, and parasite types but is not
 induced after sterile wounding. Furthermore, the response appears to be
 driven by transmission distortion rather than increased recombination. Our
 study extends the Red Queen model to include the increased production of
 recombinant offspring and uncovers a remarkable ability of hosts to
 actively distort their recombination fraction in rapid response to
 environmental cues.
description: InfectionRecombinationRawDataThis excel spreadsheet contains all of the raw data for all of the experiments reported in the main text of the associated manuscript.InfectionRecombinationForDyrad.xls
DOI: 10.5061/dryad.2q9d0
title: Data from: Interaction between digestive strategy and niche specialization predicts speciation rates across herbivorous mammals

description: Biotic and abiotic factors often are treated as mutually exclusive drivers
 of diversification processes. In this framework, ecological specialists
 are expected to have higher speciation rates than generalists if abiotic
 factors are the primary controls on species diversity but lower rates if
 biotic interactions are more important. Speciation rate is therefore
 predicted to positively correlate with ecological specialization in the
 purely abiotic model but negatively correlate in the biotic model. In this
 study, I show that the positive relationship between ecological
 specialization and speciation expected from the purely abiotic model is
 recovered only when a species-specific trait, digestive strategy, is
 modeled in the terrestrial, herbivorous mammals (Mammalia). This result
 suggests a more nuanced model in which the response of specialized
 lineages to abiotic factors is dependent on a biological trait. I also
 demonstrate that the effect of digestive strategy on the ecological
 specialization–speciation rate relationship is not due to a difference in
 either the degree of ecological specialization or the speciation rate
 between foregut- and hindgut-fermenting mammals. Together, these findings
 suggest that a biological trait, alongside historical abiotic events,
 played an important role in shaping mammal speciation at long temporal and
 large geographic scales.
description: Supplementary
 informationThis data file is a Word
 document that contains legends for Tables S1-S3 (found in the accompanying
 Excel spreadsheet), Figure S1, and references for the enclosed
 supplementary materials.Tran_AmNat_supplementary_information.docSupplementary TablesThis data file is an Excel spreadsheet that contains Tables S1-S3 on individual worksheets.Tran_AmNat_TablesS1_S2_S3.xls
DOI: 10.5061/dryad.0p401
title: Data from: Neglected patterns of variation in phenotypic plasticity: age- and sex-specific antipredator plasticity in a cichlid fish

description: The ability of organisms to plastically respond to changing environments
 is well studied. However, variation in phenotypic plasticity during
 ontogeny is less well understood despite its relevance of being an
 important source of phenotypic variation in nature. Here, we
 comprehensively study ontogenetic variation in morphological antipredator
 plasticity across multiple traits in Pelvicachromis taeniatus, a Western
 African cichlid fish with sexually dimorphic ornamentation. In a
 split-clutch design, fish were raised under different levels of perceived
 predation risk (conspecific alarm cues or distilled water). Morphological
 plasticity varied substantially across ontogeny: it was first observable
 at an early juvenile stage where alarm cue-exposed fish grew faster.
 Subsequently, significant plasticity was absent until the onset of sexual
 maturity. Here, alarm-cue-exposed males were bigger than control males,
 which led to deeper bodies, longer dorsal spines, bigger caudal peduncles
 and increased eye diameters. Sexual ornamentation emerged delayed in alarm
 cue-exposed males. In later adulthood, the plastic responses receded.
 Despite small effect sizes, these responses represent putative adaptive
 plasticity as they are likely to reduce predation risk. In females, we did
 not observe any plasticity. In accordance with theory, these results
 suggest fine-tuned expression of plasticity that potentially increases
 defenses during vulnerable developmental stages and reproductive output.
description: Morphological
 measurements of alarm cue-exposed and control Pelvicachromis
 taeniatusThis data originates
 from a laboratory study on Pelvicachromis taeniatus. In a split-clutch
 design, fish were raised under different levels of perceived predation
 risk (conspecific alarm cues or distilled water) and the morphological
 data contained in this document was obtained across developmental stages
 for two years. Column headings contain both the variable name (before the
 dot) and the unit (after the dot) where applicable. d=day. Detailed
 information on how this data was obtained is contained in the
 corresponding manuscript.Dataset_AmNat_final.xlsx