cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.46dt3
title: Data from: Evolution of tolerance in an invasive weed after reassociation with its specialist herbivore

description: The interaction between the European wild parsnip Pastinaca sativa and its
 coevolved florivore the parsnip webworm Depressaria pastinacella,
 established in North America for over 150 years, has resulted in evolution
 of local chemical phenotype matching. The recent invasion of New Zealand
 by webworms, exposing parsnips there to florivore selection for the first
 time, provided an opportunity to assess rates of adaptive response in a
 real-time experiment. We planted reciprocal common gardens in the USA and
 NZ with seeds from (1) US populations with a long history of webworm
 association; (2) NZ populations that had never been infested and (3) NZ
 populations infested for 3 years (since 2007) or 6 years (since 2004). We
 measured impacts of florivory on realized fitness, reproductive effort and
 pollination success and measured phenotypic changes in infested NZ
 populations relative to uninfested NZ populations to determine whether
 rapid adaptive evolution in response to florivory occurred. Irrespective
 of country of origin or location, webworms significantly reduced plant
 fitness. Webworms reduced pollination success in small plants but not in
 larger plants. Although defence chemistry remained unchanged, plants in
 infested populations were larger after 3–6 years of webworm florivory. As
 plant size is a strong predictor of realized fitness, evolution of large
 size as a component of florivore tolerance may occur more rapidly than
 evolution of enhanced chemical defence.
description: MAIN DATA
 FILEspreadsheet containing
 the main data1MAIN DATA
 FILE.csvR-code for
 analysesJogesh et al
 R-code.rtf
DOI: 10.5061/dryad.k5n8d
title: Data from: Evaluating interspecific niche overlaps in environmental and geographic spaces to assess the value of umbrella species

description: The concept of umbrella species assumes that concentrating resources on
 the protection of a single species contributes to the conservation of a
 suite of species and ecological processes belonging to the same ecosystem.
 The environmental requirements and geographical distribution of the
 umbrella species should thus overlap those of the group of targeted
 species. In western France, the conservation of several large grassland
 floodplains relies on agri-environmental schemes targeting one single bird
 species, the corncrake Crex crex. It is considered as an umbrella species
 but no real assessment of its effectiveness has been carried out so far.
 We used a two-step methodology to assess the potential of the corncrake to
 act as an umbrella species by estimating niche overlap in the
 environmental and geographic space between the main ground-nesting species
 of the bird community in these grasslands, including the corncrake and
 four passerines. The five species showed substantial differences in their
 ecological niches so that their distributions did not perfectly overlap.
 Overlaps in predicted distributions between pairs of species depended on
 the threshold used to convert suitability to binary maps. Moreover, the
 number of species that could be protected by a candidate umbrella species
 was affected by the overlap criterion of success. Although the corncrake
 may be used as an umbrella species, it would be outperformed by several
 passerine species. Our study highlights the potential of using niche
 overlap to select umbrella species. It also reveals the importance of
 analysing the sensitivity of outputs when changing thresholds and overlap
 criteria.
description: Species
 occurrencesSpecies occurrences
 coordinates; coordinate system: RGF93species_occurrences.csvEnvironmental variablesRaster files of environmental variables used for MaxEnt models and measures of ecological overlap: temperature, precipitation, percentage of meadow, density of hedgerows, TWI, winter NDVI, spring EVI; coordinate system: RGF93Environmental_variables.zipMaxent suitability outputsMaps of habitat suitability produced by MaxEnt for each species; coordinate system: RGF93Maxent_suitability.zip
DOI: 10.5061/dryad.d4f4s
title: Data from: Solute and sediment export from Amazon forest and soybean headwater streams

description: Intensive cropland agriculture commonly increases streamwater solute
 concentrations and export from small watersheds. In recent decades, the
 lowland tropics have become the world's largest and most important
 region of cropland expansion. Although the effects of intensive cropland
 agriculture on streamwater chemistry and watershed export have been widely
 studied in temperate regions, their effects in tropical regions are poorly
 understood. We sampled seven headwater streams draining watersheds in
 forest (n=3) or soybeans (n=4) to examine the effects of soybean cropping
 on stream solute concentrations and watershed export in a region of rapid
 soybean expansion in the Brazilian state of Mato Grosso. We measured
 stream flows and concentrations of NO3-, PO43-, SO42-, Cl-, NH4+, Ca2+,
 Mg2+, Na+, K+, Al3+, Fe3+ and dissolved organic carbon (DOC) biweekly to
 monthly to determine solute export. We also measured stormflows and
 stormflow solute concentrations in a subset of watersheds (2 forest, 2
 soybean) during 2 to 3 storms, and solutes and δ18O in groundwater,
 rainwater and throughfall to characterize watershed flowpaths.
 Concentrations of all solutes except K+ varied seasonally in streamwater,
 but only Fe3+ concentrations differed between land uses. The highest
 streamwater and rainwater solute concentrations occurred during the peak
 season of wildfires in Mato Grosso, suggesting that regional changes in
 atmospheric composition and deposition influence seasonal stream solute
 concentrations. Despite no concentration differences between forest and
 soybean land uses, annual export of NH4+, PO43-, Ca2+, Fe3+, Na+, SO42-,
 DOC and TSS were significantly higher from soybean than forest watersheds
 (5.6-fold mean increase). This increase largely reflected a 4.3-fold
 increase in water export from soybean watersheds. Despite this increase,
 total solute export per unit watershed area (i.e. yield) remained low for
 all watersheds (&lt;1 kg NO3- N/ha/yr, &lt;2.1 kg NH4+-N/ha/yr,
 &lt;0.2 kg PO43--P/ha/yr, &lt;1.5 kg Ca2+/ha/yr). Responses of
 both streamflows and solute concentrations to crop agriculture appear to
 be controlled by high soil hydraulic conductivity, groundwater-dominated
 hydrologic flowpaths on deep soils, and the absence of nitrogen
 fertilization. To date, these factors have buffered streams from the large
 increases in solute concentrations that often accompany intensive
 croplands in other locations.
description: Solute concentration
 DataThis file includes all
 solute concentration data in stream baseflow, stormflow, rain, groundwater
 and throughfall.Riskin et al. Chemistry
 Data.xlsxStream Discharge
 DataFile includes annual
 time series of hourly discharge data for all streams in the
 study.Riskin et al. Discharge
 Data.zip
DOI: 10.5061/dryad.23cg1
title: Data from: Ancient mitochondrial DNA provides high-resolution time scale of the peopling of the Americas

description: The exact timing, route, and process of the initial peopling of the
 Americas remains uncertain despite much research. Archaeological evidence
 indicates the presence of humans as far as southern Chile by 14.6 thousand
 years ago (ka), shortly after the Pleistocene ice sheets blocking access
 from eastern Beringia began to retreat. Genetic estimates of the timing
 and route of entry have been constrained by the lack of suitable
 calibration points and low genetic diversity of Native Americans. We
 sequenced 92 whole mitochondrial genomes from pre-Columbian South American
 skeletons dating from 8.6 to 0.5 ka, allowing a detailed, temporally
 calibrated reconstruction of the peopling of the Americas in a Bayesian
 coalescent analysis. The data suggest that a small population entered the
 Americas via a coastal route around 16.0 ka, following previous isolation
 in eastern Beringia for ~2.4 to 9 thousand years after separation from
 eastern Siberian populations. Following a rapid movement throughout the
 Americas, limited gene flow in South America resulted in a marked
 phylogeographic structure of populations, which persisted through time.
 All of the ancient mitochondrial lineages detected in this study were
 absent from modern data sets, suggesting a high extinction rate. To
 investigate this further, we applied a novel principal components multiple
 logistic regression test to Bayesian serial coalescent simulations. The
 analysis supported a scenario in which European colonization caused a
 substantial loss of pre-Columbian lineages.
description: xml files for
 BEAST1.8.0A total of 370 whole
 mitochondrial genomes (WMGs) corresponding to Native Central and South
 American populations were collected from published studies. Of note, the
 large dataset of 215 Mexican WMGs from Kumar et al. 2011 was not used to
 prevent an over-representation of Mexican samples. We randomly selected
 three replicate datasets of 87 sequences, all of which contained
 exclusively the five Native American haplogroups A2, B2, C1, D1, and D4h3a
 (table S3). We added 20 East Siberian individuals from sister lineages
 within haplogroups A, B, C and D in order to estimate the time of the
 split between Siberian and American lineages. We also added the 92 ancient
 WMGs from the study, as well as the Anzick-1 mitogenome, to obtain three
 replicate datasets of 200 sequences. The Anzick-1 WMG was included as it
 added a deep time calibration at 12.6 kya, was the only ancient D4h3a
 sequence available, and because the Anzick-1 individual can reasonably be
 considered a descendant of the first wave of
 colonizers.xml_files_for_BEAST1.8.0.zip
DOI: 10.5061/dryad.fj604
title: Data from: Covariation in levels of nucleotide diversity in homologous regions of the avian genome long after completion of lineage sorting

description: Closely related species may show similar levels of genetic diversity in
 homologous regions of the genome owing to shared ancestral variation still
 segregating in the extant species. However, after completion of lineage
 sorting, such covariation is not necessarily expected. On the other hand,
 if the processes that govern genetic diversity are conserved, diversity
 may potentially covary even among distantly related species. We mapped
 regions of conserved synteny between the genomes of two divergent bird
 species—collared flycatcher and hooded crow—and identified more than 600
 Mb of homologous regions (66% of the genome). From analyses of
 whole-genome resequencing data in large population samples of both species
 we found nucleotide diversity in 200 kb windows to be well correlated
 (Spearman's ρ = 0.407). The correlation remained highly similar after
 excluding coding sequences. To explain this covariation, we suggest that a
 stable avian karyotype and a conserved landscape of recombination rate
 variation render the diversity-reducing effects of linked selection
 similar in divergent bird lineages. Principal component regression
 analysis of several potential explanatory variables driving heterogeneity
 in flycatcher diversity levels revealed the strongest effects from
 recombination rate variation and density of coding sequence targets for
 selection, consistent with linked selection. It is also possible that a
 stable karyotype is associated with a conserved genomic mutation
 environment contributing to covariation in diversity levels between
 lineages. Our observations imply that genetic diversity is to some extent
 predictable.
description: DutoitetalDataTableThis table windows_based values needed to replicate all the analyses described in the paper.
DOI: 10.5061/dryad.bd21p
title: Data from: Specificity in the symbiotic association between fungus-growing ants and protective Pseudonocardia bacteria

description: Fungus-growing ants (tribe Attini) engage in a mutualism with a fungus
 that serves as the ants' primary food source, but successful fungus
 cultivation is threatened by microfungal parasites (genus Escovopsis).
 Actinobacteria (genus Pseudonocardia) associate with most of the
 phylogenetic diversity of fungus-growing ants; are typically maintained on
 the cuticle of workers; and infection experiments, bioassay challenges and
 chemical analyses support a role of Pseudonocardia in defence against
 Escovopsis through antibiotic production. Here we generate a two-gene
 phylogeny for Pseudonocardia associated with 124 fungus-growing ant
 colonies, evaluate patterns of ant–Pseudonocardia specificity and test
 Pseudonocardia antibiotic activity towards Escovopsis. We show that
 Pseudonocardia associated with fungus-growing ants are not monophyletic:
 the ants have acquired free-living strains over the evolutionary history
 of the association. Nevertheless, our analysis reveals a significant
 pattern of specificity between clades of Pseudonocardia and groups of
 related fungus-growing ants. Furthermore, antibiotic assays suggest that
 despite Escovopsis being generally susceptible to inhibition by diverse
 Actinobacteria, the ant-derived Pseudonocardia inhibit Escovopsis more
 strongly than they inhibit other fungi, and are better at inhibiting this
 pathogen than most environmental Pseudonocardia strains tested. Our
 findings support a model that many fungus-growing ants maintain
 specialized Pseudonocardia symbionts that help with garden defence.
description: Combined alignment for
 phylogenetic analysesCombined Dataset of 16s
 rRNA and EF Tu aligned reads used for Bayesian and Likelihood Phylogenetic
 Analyses (Nexus format)actinocombine_novolcan.nex16s only alignment for permutation testAligned partial 16s rRNA reads used for permutation test (Nexus format)16s.nexEf Tu Alignment for Permutation TestAligned partial Ef Tu reads used for permutation test (Nexus format)ef1a.nex
DOI: 10.5061/dryad.sf804
title: Data from: Predator-mediated natural selection on the wings of the damselfly Calopteryx splendens: differences in selection among trait types

description: Traits that increase mating success in males may come at a cost, such as
 an increased risk of predation. However, predator-mediated selection is
 challenging to document in natural populations, hampering our
 understanding of the trade-offs between sexual selection and predation.
 Here we report on a study of predator-mediated natural selection on wing
 traits in the damselfly Calopteryx splendens, the males of which possess
 conspicuous wing patches. Wagtails (genus Motacilla) are important avian
 predators of C. splendens, capturing them in flight and removing the wings
 prior to consumption. Using geometric morphometric techniques, we
 quantified the strength and mode of selection on wing traits by comparing
 wings from depredated individuals with the standing variation present in
 the population. Our results reveal that predator-mediated selection is
 stronger on secondary sexual characters than on size and shape, suggesting
 that traits related to flight performance are closer to their adaptive
 peaks. This could be a consequence of the long-term evolutionary
 association with avian predators, whereas stronger selection on
 conspicuous secondary sexual traits may reflect trade-offs between sexual
 and natural selection. Finally, even though C. splendens possesses nearly
 identical fore- and hindwings, we found evidence for divergent selection
 between them.
description: 2008 Klingavälsån Sweden
 GMM dataThis data file includes
 the relative warps (principal component axes) and linear measures used for
 the selection analyses in Kuchta and Svensson 2014 American Naturalist.
 There are separate variables as well for wing (front vs. hind) and fitness
 (live, or found dead at a feeding station).2008 Klinga GMM data
 Dryad.txt
DOI: 10.5061/dryad.q2c86hb2
title: Data from: Exploitation of a turbot (Scophthalmus maximus L.) immune-related expressed sequence tag (EST) database for microsatellite screening and validation

description: In this study, we identified and characterized 160 microsatellite loci
 from an expressed sequence tag (EST) database generated from
 immune-related organs of turbot (Scophthalmus maximus). A final set of 83
 new polymorphic microsatellites were validated after the analysis of 40
 individuals from Atlantic origin including both wild and farmed
 individuals. The allele number and the expected heterozygosity ranged from
 2 to 18 and from 0.021 to 0.951, respectively. Evidences of null alleles
 at moderate-high frequencies were detected at six loci using population
 data. None of the analyzed loci showed deviations from Mendelian
 segregation after analysis of five full-sib families including ~92
 individuals/family. The markers are used to consolidate the turbot genetic
 map and, since they are mostly EST-derived, they will be very useful for
 comparative genomic studies within flatfishes and with model fish species.
 Using an in silico approach, we detected significant homologies of
 microsatellite sequences with the EST databases of the flatfish species
 with highest genomic resources (Senegalese sole, Atlantic halibut, bastard
 halibut) at 31% of these turbot markers. The conservation of these
 microsatellites within Pleuronectiformes will pave the way for anchoring
 genetic maps of different species and identifying genomic regions related
 to productive traits.
description: Table_1Summary of the the technical characteristics of the 83 polymorphic microsatellite loci validated from the turbot (Scophthalmus maximus) EST database.Table_S1Comparative analysis of turbot microsatellites with Senegalese sole (Solea senegalensis), bastard halibut (Paralichthys olivaceus) and Atlantic halibut (Hippoglossus hippoglossus).
DOI: 10.5061/dryad.hf2746d
title: Data from: Increase in light interception cost and metabolic mass component of leaves are coupled for efficient resource use in the high altitude vegetation

description: Global syntheses of leaf trait scaling relationships report an increase in
 light interception costs or ‘diminishing returns’ with increase in leaf
 area. However, variation in light interception costs across ecological
 gradients and plant strategies to cope up with these costs are not
 adequately understood. We analyzed leaf area (A) - leaf dry mass (M), leaf
 water mass (W) - M and W - A scaling relationships in plants occurring in
 a high altitude region of western Himalaya across environmental gradients
 to understand changes in light interception cost and metabolic mass
 component. M represents light interception cost, whereas, W is considered
 as a proxy of metabolic mass component for liquid phase being the ultimate
 source of metabolic activity. Trait values were measured from 9278 leaves
 belonging to 136 dominant species occurring at different sites, slope
 aspects, elevations and habitat types. Overall, light interception cost
 increased with increasing A (scaling exponent (α) &lt;1 in A-M
 relationship) and metabolic mass component increased disproportionately
 high with increasing M and A. We found significant differences in scaling
 exponents of leaf trait relationship between sites, elevations, slope
 aspects and habitat types, indicating that increase in light interception
 cost was more evident at higher elevations, southern slopes and open
 habitats. Further, with increase in light interception cost, metabolic
 mass component also increased (α&gt;1 in W-M and W-A relationships).
 The changes in scaling exponents of various leaf trait relationships
 across ecological gradients indicated that vegetation of different regions
 have differences in light interception cost and metabolic mass component.
 Moreover, increasing light interception cost (increase in mechanical and
 hydraulic tissues) with increasing A and increasing metabolic mass (leaf
 thickness) with increasing A and M are favored in high altitude
 vegetation. This could be a key strategy of high altitude plants for
 efficient resource capture and use in harsh environments.
description: Functional trait
 data_high altitude HimalayaData file containing
 leaf traits measured ifrom the high altitude vegetation of Western
 HimalayaData file_high altitude
 Himalaya.csv
DOI: 10.5061/dryad.5003g
title: Data from: Patterns of MHC-dependent mate selection in humans and non-human primates: a meta-analysis

description: Genes of the major histocompatibility complex (MHC) in vertebrates are
 integral for effective adaptive immune response and are associated with
 sexual selection. Evidence from a range of vertebrates supports MHC-based
 preference for diverse and dissimilar mating partners, but evidence from
 human mate choice studies has been disparate and controversial.
 Methodologies and sampling peculiarities specific to human studies make it
 difficult to know whether wide discrepancies in results among human
 populations are real or artefact. To better understand what processes may
 affect MHC-mediated mate choice across humans and nonhuman primates, we
 performed phylogenetically controlled meta-analyses using 58 effect sizes
 from 30 studies across seven primate species. Primates showed a general
 trend favouring more MHC-diverse mates, which was statistically
 significant for humans. In contrast, there was no tendency for
 MHC-dissimilar mate choice, and for humans, we observed effect sizes
 indicating selection of both MHC-dissimilar and MHC-similar mates.
 Focusing on MHC-similar effect sizes only, we found evidence that
 preference for MHC similarity was an artefact of population ethnic
 heterogeneity in observational studies but not among experimental studies
 with more control over sociocultural biases. This suggests that human
 assortative mating biases may be responsible for some patterns of
 MHC-based mate choice. Additionally, the overall effect sizes of primate
 MHC-based mating preferences are relatively weak (Fisher's Z
 correlation coefficient for dissimilarity Zr = 0.044, diversity Zr =
 0.153), calling for careful sampling design in future studies. Overall,
 our results indicate that preference for more MHC-diverse mates is
 significant for humans and likely conserved across primates.
description: Primate
 treeFull phylogenetic tree
 from primate 10KTree used for analyses.primate_tree.nexR code for analysisThis R file contains the examples necessary to reproduce our analyses using the accompanying data set. This code has been written by Jamie Winternitz, who can be contacted at jcwinternitz-at-gmail-dot-com. The file consists of the nine following sections: # 1. Loading and visualizing data # 2. DIC-based model selection for random effects # 3. Heterogeneity estimation # 4. Univariate estimates of moderators and contrasts # 5. Forest plots # 6. Tests for publication bias # 7. Testing if negative MHC effect sizes (indicating similarity) differ from zero # 8. Bivariate models for MHC~Neutral marker correlations # 9. Power analysis for random-effects meta-analysis # 10. Plotting the phylogenetic signal of MHC-associated mate choiceWinternitz_et_al_Rcode_MHCDissimilarity.RHuman and non-human primate datasetFull dataset used for analyses.human.primate.matechoice.csv