cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.p3057
title: Data from: No evidence for larger leaf trait plasticity in ecological generalists compared to specialists

description: Aim: Phenotypic plasticity is hypothesized to contribute to a species’
 capacity to occupy broader ranges of conditions and to optimally exploit
 resource-rich environments. Although this is supported by case studies of
 individual species, we do not know whether larger plasticity in functional
 traits is generally associated with ecological characteristics of species
 such as their niche breadth or niche position. Here, we test whether there
 is such a relationship for plasticity in leaf functional traits. Location:
 Central Europe. Methods: We surveyed 110–132 grassland plant species for
 plasticity in five leaf traits [leaf thickness, leaf greenness, specific
 leaf area, leaf dry matter content (LDMC) and plant height] and for
 biomass changes in response to experimental fertilization, shading and
 waterlogging. Trait plasticity and changes in biomass were compared with
 species niche characteristics along three environmental axes (light,
 nutrient and soil moisture) derived from a vegetation-plot database.
 Results: Although response of several traits to experimental treatments
 correlated with niche position and breadth (change in leaf thickness,
 greenness and biomass in response to fertilization; change in LDMC due to
 shading; and change in plant height and biomass due to waterlogging), we
 did not find evidence that species with broader niches or species from
 resource-rich environments are more plastic. Ecological generalists even
 turned out to be less plastic in some traits, including leaf thickness
 after fertilization and waterlogging. Generalists also displayed smaller
 plastic response averaged across all five traits (‘composite plasticity’),
 though the relationship was not statistically significant. This composite
 plasticity was positively related to absolute change in biomass in all
 experimental treatments. Main conclusions: Our results suggest that larger
 species-level plasticity in leaf traits is not necessarily associated with
 a capacity to occupy a broader range of environments or with growth in
 resource-rich habitats; rather, it may indicate species’ sensitivity to
 environmental changes.
description: Plant species niche
 characteristics and trait data from the experimentNICHE.ZIP
DOI: 10.5061/dryad.r4b158n
title: Data from: A new Palaeocene crocodylian from southern Argentina sheds light on the early history of caimanines

description: Caimanines are crocodylians currently restricted to South and Central
 America and the oldest members are from lower Palaeocene localities of the
 Salamanca Formation (Chubut Province, Argentina). We report here a new
 caimanine from this same unit represented by a skull roof and partial
 braincase. Its phylogenetic relationships were explored in a cladistic
 analysis using standard characters and a morphogeometric two-dimensional
 configuration of the skull roof. The phylogenetic results were used for an
 event-based supermodel quantitative palaeobiogeographic analysis. The new
 species is recovered as the most basal member of the South American
 caimanines, and the Cretaceous North American lineage “Brachychampsa and
 related forms” as the most basal Caimaninae. The biogeographic results
 estimated north-central North America as the ancestral area of Caimaninae,
 showing that the Cretaceous and Palaeocene species of the group were more
 widespread than thought and became regionally extinct in North America
 around the Cretaceous–Palaeocene boundary. A dispersal event from
 north-central North America during the middle Late Cretaceous explains the
 arrival of the group to South America. The Palaeogene assemblage of
 Patagonian crocodylians is composed of three lineages of caimanines as a
 consequence of independent dispersal events that occurred between North
 and South America and within South America around the
 Cretaceous–Palaeogene boundary.
description: Bona et al Supplementary
 Information III character-taxon data matrixdata matrix of Eusuchia
 used in the cladistic analysisBona et al Supplementary
 Information III R2 (2).tnt
DOI: 10.5061/dryad.nr63f
title: Data from: Queen killing is linked to high worker-worker relatedness in a social wasp

description: Social insect colonies are pinnacles of evolved altruism, but also contain
 dramatic conflict among relatives [1, 2]. In many species, a colony’s
 workers compete with the queen and each other over the production of
 males. Interspecific comparisons demonstrate the importance of
 within-colony relatedness in determining the outcome of this conflict [3,
 4], but facultative responses to within-colony relatedness are rarely
 reported [5-7]. Here, I report facultative matricide (worker killing of a
 colony’s queen) in the social wasp, Dolichovespula arenaria. Matricide is
 strongly associated with high worker-worker relatedness, as predicted by
 theory, because closely-related workers value nephews more than brothers
 [8]. This pattern is the result of variation in both paternity frequency
 and the paternity skew of colonies with multiple patrilines, implicating
 worker-worker relatedness rather than a direct effect of multiple mating
 on queen survival. Furthermore, occasional inbreeding can explain why some
 multiple-patriline colonies exhibit high paternity skew associated with
 matricide. In general, these results support the hypothesis that workers
 can facultatively respond to intracolony relatedness determined by queen
 mating behavior, and demonstrate a novel benefit of polyandry in annual
 social insects. Facultative matricide shows dramatically how workers are
 evolutionary actors with interests that can diverge from the queen’s,
 rather than being ‘extrasomatic projections of her personal genome’ [9].
description: Genotype
 DataThis file contains the
 microsatellite genotypes for 421 workers at 4 loci, and the parentage
 assignments from Colony2.Genotype_Data.xlsx
DOI: 10.5061/dryad.vm36c
title: Data from: MR1-restricted mucosal-associated invariant T (MAIT) cells respond to mycobacterial vaccination and infection in nonhuman primates

description: Studies on mucosal-associated invariant T cells (MAITs) in nonhuman
 primates (NHP), a physiologically relevant model of human immunity, are
 handicapped due to a lack of macaque MAIT-specific reagents. Here we show
 that while MR1 ligand-contact residues are conserved between human and
 multiple NHP species, three T-cell receptor contact-residue mutations in
 NHP MR1 diminish binding of human MR1 tetramers to macaque MAITs.
 Construction of naturally loaded macaque MR1 tetramers facilitated
 identification and characterization of macaque MR1-binding ligands and
 MAITs, both of which mirrored their human counterparts. Using the macaque
 MR1 tetramer we show that NHP MAITs activated in vivo in response to both
 Bacillus Calmette-Guerin vaccination and Mycobacterium tuberculosis
 infection. These results demonstrate that NHP and human MR1 and MAITs
 function analogously, and establish a preclinical animal model to test
 MAIT-targeted vaccines and therapeutics for human infectious and
 autoimmune disease.
description: Rhesus Macaque TRAV and
 TRDV genesTRAV and TRDV genes
 extracted from the rhesus macaque genome. The gene features reported
 include L-PART1, V-INTRON, V-EXON, V-HEPTAMER, V-SPACER, and V-NONAMER.
 The FASTA header fields include the species name, rhesus macaque
 chromosome 7 accession number (NC_007864.1), start and end positions of
 the gene feature in the rhesus macaque chromosome 7, strand (-1 indicates
 that the reported sequences are the reverse complement), gene name, and
 gene feature.RhesusMacaque_TRAV_TRDV.fsaRhesus Macaque TRAJ genesTRAJ genes extracted from the rhesus macaque genome. The gene features reported include J-NONAMER, J-SPACER, and J-HEPTAMER. The FASTA header fields include the species name, rhesus macaque chromosome 7 accession number (NC_007864.1), start and end positions of the gene feature in the rhesus macaque chromosome 7, strand (-1 indicates that the reported sequences are the reverse complement), gene name, and gene feature.RhesusMacaque_TRAJ.fsa
DOI: 10.5061/dryad.2fc6677
title: Data from: Evolution of size-dependent intraspecific competition predicts body size scaling of metabolic rate

description: 1. Growth in body size is accompanied by changes in foraging capacity and
 metabolic costs, which lead to changes in competitive ability during
 ontogeny. The resulting size-dependent competitive asymmetry influences
 population dynamics and community structure, but it is not clear whether
 natural selection leads to asymmetry in intraspecific competition. 2. We
 address this question by using a size-structured consumer-resource model,
 in which the strength and direction of competitive asymmetry between
 different consumer individuals depends on the scaling of maximum ingestion
 and maintenance metabolism with consumer body size. We use adaptive
 dynamics to study selection on the scaling exponents of these processes.
 3. Selection leads to an identical scaling of maximum ingestion and
 maintenance metabolism with consumer body size. Equal scaling exponents
 neutralise strong competitive differences within the consumer population,
 because all consumer individuals require the same amount of resources to
 cover maintenance requirements. Furthermore, the scaling exponents respond
 adaptively to changes in mortality such that biomass production through
 growth or reproduction increases in the life stage that is subject to
 increased mortality. Also, decreasing size at birth leads to increased
 investment in juvenile growth, while increasing maximum size leads to
 increased investment in post-maturation growth and reproduction. 4. These
 results provide an explanation for observed variation in the ontogenetic
 scaling of metabolic rate with body size. Data of teleost fish are
 presented that support these predictions. However, selection towards equal
 scaling exponents is contradicted by empirical findings, which suggests
 that additional ecological complexity beyond this basic consumer-resource
 interaction is required to understand the evolution of size-dependent
 asymmetry in intraspecific competition.
description: FE_Hin&DeRoos_Fig5_MetabolismLogSize_dataFE_Hin&DeRoos_Fig5_MetabolismLogSize_analysisR file for data analysis and plotting
DOI: 10.5061/dryad.835s6
title: Data from: Clearing muddied waters: capture of environmental DNA from turbid waters

description: Understanding the differences in efficiencies of various methods to
 concentrate, extract, and amplify environmental DNA (eDNA) is vital for
 best performance of eDNA detection. Aquatic systems vary in
 characteristics such as turbidity, eDNA concentration, and inhibitor load,
 thus affecting eDNA capture efficiency. Application of eDNA techniques to
 the detection of terrestrial invasive or endangered species may require
 sampling at intermittent water sources that are used for drinking and
 cooling; these water bodies may often be stagnant and turbid. We present
 our best practices technique for the detection of wild pig eDNA in water
 samples, a protocol that will have wide applicability to the detection of
 elusive vertebrate species. We determined the best practice for eDNA
 capture in a turbid water system was to concentrate DNA from a 15 mL water
 sample via centrifugation, purify DNA with the DNeasy mericon Food kit,
 and remove inhibitors with Zymo Inhibitor Removal Technology columns.
 Further, we compared the sensitivity of conventional PCR to quantitative
 PCR and found that quantitative PCR was more sensitive in detecting lower
 concentrations of eDNA. We show significant differences in efficiencies
 among methods in each step of eDNA capture, emphasizing the importance of
 optimizing best practices for the system of interest.
description: eDNA detection
 records_WilliamsDetection records for
 methods tested for eDNA capture, inhibitor removal, and amplification
 techniques.eDNA
 concentrations_WilliamsDNA concentration
 measurements for environmental water samples extracted and amplified with
 optimized method.
DOI: 10.5061/dryad.hn48m
title: Data from: Is behavioural plasticity consistent across different environmental gradients and through time?

description: Despite accumulating evidence for individual variation in behavioural
 plasticity, there is currently little understanding of the causes and
 consequences of this variation. An outstanding question is whether
 individual reaction norm (RN) slopes are consistent across different
 environmental variables – that is, whether an individual that is highly
 responsive to one environmental variable will be equally responsive to a
 second variable. Another important and related question is whether RNs are
 themselves consistently expressed through time or whether they are simply
 state dependent. Here, we quantified individual activity rates of
 zebrafish in response to independent manipulations of temperature and food
 availability that were repeated in discrete ‘bursts’ of sampling through
 time. Individuals that were thermally responsive were not also more
 responsive to food deprivation, but they were less predictable? did
 exhibit greater unexplained variation. Individual RN slopes were
 consistent (repeatable) over time for both temperature (Rslope = 0.92) and
 food deprivation responses (Rslope = 0.4), as were mean activity rates in
 the standard environment (Rintercept = 0.83). Despite the high potential
 lability of behaviour, we have demonstrated consistency of behavioural RN
 components and identified potential energetic constraints leading to high
 consistency of thermal RNs and low consistency of food deprivation RNs.
description: daniodatay = Activity rate, TEMP = -1 (24C) or 0 (28C), HUNG continuous between 0 and 30hrs (1), id of ifsh, MASS z-transformed, ARENA identity, BU = ID*Burst variable.
DOI: 10.5061/dryad.6pq7jg8p
title: Data from: Spatially explicit models of dynamic histories: examination of the genetic consequences of Pleistocene glaciation and recent climate change on the American Pika.

description: A central goal of phylogeography is to identify and characterize the
 processes underlying divergence. One of the biggest impediments currently
 faced is how to capture the spatiotemporal dynamic under which a species
 evolved. Here we described an approach that couples species distribution
 models (SDMs), demographic and genetic models in a spatiotemporally
 explicit manner. Analyses of American Pika (Ochotona priniceps) from the
 sky islands of the central Rocky Mountains of North America are used to
 provide insights into key questions about integrative approaches in
 landscape genetics, population genetics and phylogeography. This includes
 (i) general issues surrounding the conversion of time-specific SDMs into
 simple continuous, dynamic landscapes from past to current, and (ii) the
 utility of SDMs to inform demographic models with deme-specific carrying
 capacities and migration potentials, as well as (iii) the contribution of
 the temporal dynamic of colonization history in shaping genetic patterns
 of contemporary populations. Our results support that the inclusion of a
 spatiotemporal dynamic is an important factor when studying the impact of
 distributional shifts on patterns of genetic data. Our results also
 demonstrate the utility of SDMs to generate species-specific predictions
 about patterns of genetic variation that account for varying degrees of
 habitat specialization and life-history characteristics of taxa.
 Nevertheless, the results highlight some key issues when converting SDMs
 for use in demographic models. Because the transformations have direct
 affects on the genetic consequence of population expansion by prescribing
 how habitat heterogeneity and spatiotemporal variation is related to the
 species-specific demographic model, it is important to consider
 alternative transformations when studying the genetic consequences of
 distributional shifts.
description: Brown_Knowles_Pika_Data
DOI: 10.5061/dryad.352q6
title: Data from: Changes in host-parasitoid food web structure with elevation

description: Gradients in elevation are increasingly used to investigate how species
 respond to changes in local climatic conditions. While many studies have
 shown elevational patterns in species richness and turnover, little is
 known about how food web structure is affected by elevation. Contrasting
 responses of predator and prey species to elevation may lead to changes in
 food web structure. We investigated how the quantitative structure of a
 herbivore-parasitoid food web changes with elevation in Australian
 subtropical rainforest. On four occasions, spread over one year, we
 hand-collected leaf miners at twelve sites, along three elevational
 gradients (between 493 m and 1159 m a.s.l). A total of 5030 insects,
 including 603 parasitoids were reared, and summary food webs were created
 for each site. We also carried out a replicated manipulative experiment by
 translocating an abundant leaf-mining weevil, Platynotocis sp., which
 largely escaped parasitism at high elevations (≥900m a.s.l.), to lower,
 warmer elevations, to test if it would experience higher parasitism
 pressure. We found strong evidence that the environmental change that
 occurs with increasing elevation affects food web structure. Quantitative
 measures of generality, vulnerability and interaction evenness decreased
 significantly with increasing elevation (and decreasing temperature),
 whilst elevation did not have a significant effect on connectance. Mined
 plant composition also had a significant effect on generality and
 vulnerability, but not on interaction evenness. Several relatively
 abundant species of leaf miner appeared to escape parasitism at higher
 elevations, but contrary to our prediction, Platynotocis sp. did not
 experience greater levels of parasitism when translocated to lower
 elevations. Our study indicates that leaf-mining herbivores and their
 parasitoids respond differently to environmental conditions imposed by
 elevation, thus producing structural changes in their food webs.
 Increasing temperatures and changes in vegetation communities that are
 likely to result from climate change may have a restructuring effect on
 host-parasitoid food webs. Our translocation experiment, however,
 indicated that leaf miners currently escaping parasitism at high
 elevations may not automatically experience higher parasitism under warmer
 conditions and future changes in food web structure may depend on the
 ability of parasitoids to adapt to novel hosts.
description: Food web and host plant
 dataFood web data of leaf
 miner hosts and their parasitoids from sites making up elevational
 transects at three locations in eastern Australian, subtropical rainforest
 and associated host plant data.SMaunsell_Foodweb_and_plant_data_Dryad.xlsx
DOI: 10.6084/m9.figshare.31153897
title: Additional file 6 of Molecular characterization of potential Plasmodium-Blocking Serratia spp. bacteria in field-caught malaria mosquito in Burkina Faso

description: Additional File 6: Text S1. Result of sequence alignments using the Muscle program in MEGA 12.0 software
DOI: 10.6084/m9.figshare.31153897.v1
title: Additional file 6 of Molecular characterization of potential Plasmodium-Blocking Serratia spp. bacteria in field-caught malaria mosquito in Burkina Faso

description: Additional File 6: Text S1. Result of sequence alignments using the Muscle program in MEGA 12.0 software
DOI: 10.5061/dryad.2g7mr
title: Data from: Size evolution in microorganisms masks trade-offs predicted by the growth rate hypothesis

description: Adaptation to local resource availability depends on responses in growth
 rate and nutrient acquisition. The growth rate hypothesis (GRH) suggests
 that growing fast should impair competitive abilities for phosphorus and
 nitrogen due to high demand for biosynthesis. However, in microorganisms,
 size influences both growth and uptake rates, which may mask trade-offs
 and instead generate a positive relationship between these traits (size
 hypothesis, SH). Here, we evolved a gradient of maximum growth rate (μmax)
 from a single bacterium ancestor to test the relationship among μmax,
 competitive ability for nutrients and cell size, while controlling for
 evolutionary history. We found a strong positive correlation between μmax
 and competitive ability for phosphorus, associated with a trade-off
 between μmax and cell size: strains selected for high μmax were smaller
 and better competitors for phosphorus. Our results strongly support the
 SH, while the trade-offs expected under GRH were not apparent. Beyond
 plasticity, unicellular populations can respond rapidly to selection
 pressure through joint evolution of their size and maximum growth rate.
 Our study stresses that physiological links between these traits tightly
 shape the evolution of competitive strategies.
description: Experimental
 dataThe file contains 3 data
 tables of the traits measured at the end of the experiment on ancestral
 and evolved bacterial strains: one for demographic traits (maximum per
 capita growth rate and maximal optical density) extracted from growth
 curves performed on Low-N and low-P media (with R software); one for
 cytometry (relative cell size data); and one for X-ray data (cell content
 of nitrogen and phosphorus). Data were compiled in a xls
 file.Experimental_data_Gounand-et-al_ProcB_2016.xlsx
DOI: 10.15468/dl.jrf8r3
title: Occurrence Download

description: A dataset containing 57 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Nierembergia calycina",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 57 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000959-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.mp2p2
title: Data from: Sexual selection is influenced by both developmental and adult environments

description: Sexual selection is often assumed to be strong and consistent, yet
 increasing research shows it can fluctuate over space and time. Few
 experimental studies have examined changes in sexual selection in response
 to natural environmental variation. Here, we use a difference in resource
 quality to test for the influence of past environmental conditions and
 current environmental conditions on male and female mate choice and
 resulting selection gradients for leaf-footed cactus bugs, Narnia
 femorata. We raised juveniles on natural high and low quality diets,
 cactus pads with and without ripe cactus fruits. New adults were again
 assigned a cactus pad with or without fruit, paired with a potential mate,
 and observed for mating behaviors. We found developmental and adult
 encounter environments affected mating decisions and the resulting
 patterns of sexual selection for both males and females. Males were not
 choosy in the low quality encounter environment, cactus without fruit, but
 they avoided mating with small females in the high quality encounter
 environment. Females were choosy in both encounter environments, avoiding
 mating with small males. However, they were the choosiest when they were
 in the low quality encounter environment. Female mate choice was also
 context-dependent by male developmental environment. Females were more
 likely to mate with males that had developed on cactus with fruit when
 they were currently in the cactus with fruit environment. This pattern
 disappeared when females were in the cactus without fruit environment.
 Altogether, these results experimentally demonstrate context-dependent
 mate choice by both males and females. Furthermore, we demonstrate that
 simple, seasonal changes in resources can lead to fluctuations in sexual
 selection.
description: Sexual selection is
 influenced by both developmental and adult environments -
 dataData used in generalized
 linear models and selection analysesDRYAD file
 2014_submission.xlsx