cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.55044
title: Data from: Sex-linked genomic variation and its relationship to avian plumage dichromatism and sexual selection

description: Background: Sexual dichromatism is the tendency for sexes to differ in
 color pattern and represents a striking form of within-species
 morphological variation. Conspicuous intersexual differences in avian
 plumage are generally thought to result from Darwinian sexual selection,
 to the extent that dichromatism is often treated as a surrogate for the
 intensity of sexual selection in phylogenetic comparative studies. Intense
 sexual selection is predicted to leave a footprint on genetic evolution by
 reducing the relative genetic diversity on sex chromosome to that on the
 autosomes. Results: In this study, we test the association between plumage
 dichromatism and sex-linked genetic diversity using eight species pairs
 with contrasting levels of dichromatism. We estimated Z-linked and
 autosomal genetic diversity for these non-model avian species using
 restriction-site associated (RAD) loci that covered ~3 % of the genome. We
 find that monochromatic birds consistently have reduced sex-linked genomic
 variation relative to phylogenetically-paired dichromatic species and this
 pattern is robust to mutational biases. Conclusions: Our results are
 consistent with several interpretations. If present-day sexual selection
 is stronger in dichromatic birds, our results suggest that its impact on
 sex-linked genomic variation is offset by other processes that lead to
 proportionately lower Z-linked variation in monochromatic species. We
 discuss possible factors that may contribute to this discrepancy between
 phenotypes and genomic variation. Conversely, it is possible that
 present-day sexual selection -- as measured by the variance in male
 reproductive success -- is stronger in the set of monochromatic taxa we
 have examined, potentially reflecting the importance of song, behavior and
 other non-plumage associated traits as targets of sexual selection. This
 counterintuitive finding suggests that the relationship between genomic
 variation and sexual selection is complex and highlights the need for a
 more comprehensive survey of genomic variation in avian taxa that vary
 markedly in social and genetic mating systems.
description: Readme, scripts and
 summary statsArchive.zipsp111.tarsp112.tarsp121.tarsp122.tarsp123.tarsp211.tarsp212.tarsp221.tarsp222.tarsp311.tarsp312.tarsp313.tarsp321.tarsp323.tarsp411.tarsp412.tarsp421.tarsp422.tarsp423.tarsp511.tarsp512.tarsp521.tarsp522.tarsp811.tarsp812.tarsp813.tarsp821.tarsp822.tarsp823.tarsp911.tarsp912.tarsp913.tarsp921.tarsp922.tarsp923.tarsp1012.tarsp1013.tarsp1021.tarsp1022.tarsp1023.tarsp1024.tar
DOI: 10.5061/dryad.3qn2r
title: Data from: Plant neighbours rather than soil biota determine impact of an alien plant invader

description: 1. Various factors have been shown contributing to the ecosystem impact of
 invasive alien plants, but their relative importance remains unclear. We
 focused on the effects of neighbouring plant community and soil biota as
 these biotic factors have been repeatedly put forward to explain invasion
 success (e.g. as components of the novel weapons and of the biotic release
 hypothesis). 2. To assess their relative importance in explaining the high
 impact of Centaurea stoebe during the invasion of new sites in the
 introduced range, we conducted a greenhouse experiment with both European
 (EU) and North American (NA) tetraploid C. stoebe competing with/without
 EU vs. NA neighbouring community and with the two neighbouring communities
 growing without C. stoebe. Plants were grown in sterilized commercial soil
 inoculated with naïve soil (from rhizosphere of plants other than C.
 stoebe) originating either from the home EU or the introduced NA range and
 half of which was sterilized to remove soil biota. 3. In the competition
 pots, relative competitive ability (difference between the relative growth
 rates of C. stoebe and neighbouring community) and impact level (biomass
 of the neighbouring community relative to that in non-competition pots) of
 C. stoebe was significantly higher when grown with the NA than with the EU
 neighbouring community, although growth rates of EU and NA neighbouring
 communities did not differ in the non-competition pots. Both soil origin
 and C. stoebe origin had no effect on these processes. Soil sterilization
 increased growth of both C. stoebe and neighbouring communities, but had
 only a moderate effect on impact level and type, and no effect on the
 relative competitive ability of C. stoebe. 4. These results suggest that
 during the colonization of new sites in North American grasslands, the
 impact of C. stoebe is strongly driven by reduced competitive ability of
 NA neighbours compared with EU neighbours, while altered biotic soil
 conditions in the introduced range and post-introduction evolutionary
 changes in the invader are of less importance. This differential impact
 appears to be due to inherently different mechanisms underlying the
 competitive interactions between EU and NA neighbouring communities when
 grown with C. stoebe.
description: competitionbiomass data in the presence of competitionreduction in biomassReduction in biomass of Centaurea stoebe and neighbouring communityreduction.csvREI
DOI: 10.5061/dryad.635md
title: Data from: Daily energy expenditure during lactation is strongly selected in a free-living mammal

description: 1. Energy expenditure is a trait of central importance in ecological and
 evolutionary theory. We examined the correlates of, the strength of
 selection on, and the heritability of, daily energy expenditure (DEE;
 kJ/day) during lactation in free-ranging North American red squirrels
 (Tamiasciurus hudsonicus). 2. Over seven years, lactating squirrels with
 greater DEE had higher annual reproductive success (ARS; standardized
 selection gradient: β’ = 0.47; top 12% of published estimates).
 Surprisingly, positive fecundity selection on lactation DEE for increased
 ARS did not result because lactation DEE was correlated with typical
 measures of reproductive performance and/or investment. 3. We found no
 evidence of costs of elevated lactation DEE acting through female
 survival, subsequent year lactation DEE, or subsequent year reproduction.
 4. Lactation DEE was not significantly repeatable and heritability was not
 significantly different from zero. 5. Elevated lactation DEE enhances ARS
 through a link between DEE and an unidentified measure of maternal or
 environmental quality, but there is limited evolutionary potential for
 lactation DEE to respond to our documented selection.
description: Lactating squirrel daily
 energy expenditure dataFile containing daily
 energy expenditure data of lactating female squirrels and other variables
 associated with these values.DryadLactatingSquirrelDailyEnergyExpenditureData.csvRed squirrel pruned pedigreePedigree of all the individuals exposed to the doubly labelled water technique and all its known ancestors. Individuals that were not related to the squirrel exposed to the doubly labelled water technique have been removed from this pedigree (i.e. these individuals have been pruned from the pedigree).DryadRedSquirrelPrunedPedigree.csv
DOI: 10.5061/dryad.08m6t
title: Data from: A new analytical approach to landscape genetic modeling: least-cost transect analysis and linear mixed models

description: Landscape genetics aims to assess the effect of the landscape on
 intraspecific genetic structure. To quantify interdeme landscape
 structure, landscape genetics mostly uses landscape resistance surfaces
 and least-cost paths or straight-line transects. However, both approaches
 have drawbacks. Parameterization of resistance surfaces is a subjective
 process, and least-cost paths represent a single migration route. A
 transect-based approach might oversimplify migration patterns by assuming
 rectilinear migration. To overcome these limitations, we combined these
 two methods in a new landscape genetic approach: least-cost transect
 analysis (LCTA). Habitat-matrix resistance surfaces were used to create
 least-cost paths, which were subsequently buffered to form transects in
 which the abundance of several landscape elements was quantified. To
 maintain objectivity, this analysis was repeated so that each landscape
 element was in turn regarded as migration habitat. The relationship
 between landscape predictor variables and genetic distances was then
 assessed following a mixed modeling approach to account for the
 non-independence of values in distance matrices. Subsequently, predictor
 variables were selected making use of the R_β^2 statistic. We applied LCTA
 and the mixed model approach to an empirical genetic dataset on the
 endangered damselfly, Coenagrion mercuriale. We compared the results to
 those obtained from traditional least-cost, effective and resistance
 distance analysis and showed that LCTA not only outperforms existing
 methods in a statistical way, but also provides more information about the
 migration ecology of the focal species. Although we believe the
 statistical approach to be an improvement for the analysis of distance
 matrices in landscape genetics, more stringent testing is needed.
description: CoordinatesPairwise_FstLCTA_v1-2Individual_genotypesExplanatory_variables_mh_Agriculture_sf_15
DOI: 10.5061/dryad.t5557
title: Data from: Phylogenetic diversity and coevolutionary signals among trophic levels change across a habitat edge

description: 1. Incorporating the evolutionary history of species into community
 ecology enhances understanding of community composition, ecosystem
 functioning and responses to environmental changes. 2. Phylogenetic
 history might partly explain the impact of fragmentation and land-use
 change on assemblages of interacting organisms, and even determine
 potential cascading effects across trophic levels. However, it remains
 unclear whether phylogenetic diversity of basal resources is reflected at
 higher trophic levels in the food web. In particular, phylogenetic
 determinants of community structure have never been incorporated into
 habitat edge studies, even though edges are recognised as key factors
 affecting communities in fragmented landscapes. 3. Here we test whether
 phylogenetic diversity at different trophic levels (plants, herbivores,
 parasitoids) and signals of coevolution (i.e. phylogenetic congruence)
 among interacting trophic levels change across an edge gradient between
 native and plantation forests. To ascertain whether there is a signal of
 coevolution across trophic levels, we test whether related consumer
 species generally feed on related resource species. 4. We found
 differences across trophic levels in how their phylogenetic diversity
 responded to the habitat edge gradient. Plant and native parasitoid
 phylogenetic diversity changed markedly across habitats, while
 phylogenetic variability of herbivores (which were predominantly native)
 did not change across habitats, though phylogenetic evenness declined in
 plantation interiors. Related herbivore species did not appear to feed
 disproportionately on related plant species (i.e. there was no signal of
 coevolution) even when considering only native species, potentially due to
 the high trophic generality of herbivores. However, related native
 parasitoid species tended to feed on related herbivore species, suggesting
 the presence of a coevolutionary signal at higher trophic levels.
 Moreover, this signal was stronger in plantation forests, indicating that
 this habitat may impose stresses on parasitoids that constrain them to
 attack only host species for which they are best adapted. 5. Overall,
 changes in land use across native to plantation forest edges
 differentially affected phylogenetic diversity across trophic levels, and
 may also exert a strong selective pressure for particular coevolved
 herbivore-parasitoid interactions.
description: PHYLOGENETIC JAE
 DATAThe file contains the
 plant-herbivore interaction metaweb, the herbivore-parasitoid interaction
 metaweb, parasitoid species abundance by sampling plot, plant species
 biomass by sampling plot, herbivore species abundance by sampling plot,
 and the native herbivore-parasitoid interactions present on the different
 sampling plots.
DOI: 10.5061/dryad.3mp67
title: Data from: Evolution of increased adult longevity in Drosophila melanogaster populations selected for adaptation to larval crowding

description: In holometabolous animals such as Drosophila melanogaster, larval crowding
 can affect a wide range of larval and adult traits. Adults emerging from
 high larval density cultures have smaller body size and increased mean
 life span compared to flies emerging from low larval density cultures.
 Therefore, adaptation to larval crowding could potentially affect adult
 longevity as a correlated response. We addressed this issue by studying a
 set of large, outbred populations of D. melanogaster, experimentally
 evolved for adaptation to larval crowding for 83 generations. We assayed
 longevity of adult flies from both selected (MCUs) and control populations
 (MBs) after growing them at different larval densities. We found that MCUs
 have evolved increased mean longevity compared to MBs at all larval
 densities. The interaction between selection regime and larval density was
 not significant, indicating that the density dependence of mean longevity
 had not evolved in the MCU populations. The increase in longevity in MCUs
 can be partially attributed to their lower rates of aging. It is also
 noteworthy that reaction norm of dry body weight, a trait probably under
 direct selection in our populations, has indeed evolved in MCU
 populations. To the best of our knowledge, this is the first report of the
 evolution of adult longevity as a correlated response of adaptation to
 larval crowding.
description: Evolution of increased
 adult longevity in Drosophila melanogaster populations selected for
 adaptation to larval crowding.File type: Microsoft
 excel (.xlsx)Shenoi_et_al_2015_JEB.xlsx
DOI: 10.15468/dl.379dqt
title: Occurrence Download

description: A dataset containing 3180 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Hydrangea febrifuga",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 3180 records from 48 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001054-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.1tc43
title: Data from: The value of biodiversity for the functioning of tropical forests: insurance effects during the first decade of the Sabah biodiversity experiment

description: One of the main environmental threats in the tropics is selective logging,
 which has degraded large areas of forest. In southeast Asia, enrichment
 planting with seedlings of the dominant group of dipterocarp tree species
 aims to accelerate restoration of forest structure and functioning. The
 role of tree diversity in forest restoration is still unclear, but the
 ‘insurance hypothesis’ predicts that in temporally and spatially varying
 environments planting mixtures may stabilize functioning owing to
 differences in species traits and ecologies. To test for potential
 insurance effects, we analyse the patterns of seedling mortality and
 growth in monoculture and mixture plots over the first decade of the Sabah
 biodiversity experiment. Our results reveal the species differences
 required for potential insurance effects including a trade-off in which
 species with denser wood have lower growth rates but higher survival. This
 trade-off was consistent over time during the first decade, but growth and
 mortality varied spatially across our 500 ha experiment with species
 responding to changing conditions in different ways. Overall, average
 survival rates were extreme in monocultures than mixtures consistent with
 a potential insurance effect in which monocultures of poorly surviving
 species risk recruitment failure, whereas monocultures of species with
 high survival have rates of self-thinning that are potentially wasteful
 when seedling stocks are limited. Longer-term monitoring as species
 interactions strengthen will be needed to more comprehensively test to
 what degree mixtures of species spread risk and use limited seedling
 stocks more efficiently to increase diversity and restore ecosystem
 structure and functioning.
description: SBE First Decade
 Survival and GrowthThis ZIP file contains
 three data sets needed to reproduce the models and figures presented in
 the associated research paper. One data set for tree survival, one for
 tree growth and a third for species traits. The data sets provided here
 have already been prepared, meaning they are in the same form as they were
 analysed for the paper. The R code needed to reproduce the research
 results can be found as supplementary material for the paper. For
 descriptions of columns in each data set, see the
 ReadMe.sbeDryad.zip
DOI: 10.5061/dryad.t0j7s
title: Data from: Evolutionary hotspots in the Mojave Desert

description: Genetic diversity within species provides the raw material for adaptation
 and evolution. Just as regions of high species diversity are conservation
 targets, identifying regions containing high genetic diversity and
 divergence within and among populations may be important to protect future
 evolutionary potential. When multiple co-distributed species show spatial
 overlap in high genetic diversity and divergence, these regions can be
 considered evolutionary hotspots. We mapped spatial population genetic
 structure for 17 animal species across the Mojave Desert, USA. We analyzed
 these in concurrence and located 10 regions of high genetic diversity,
 divergence or both among species. These were mainly concentrated along the
 western and southern boundaries where ecotones between mountain, grassland
 and desert habitat are prevalent, and along the Colorado River. We
 evaluated the extent to which these hotspots overlapped protected lands
 and utility-scale renewable energy development projects of the Bureau of
 Land Management. While 30–40% of the total hotspot area was categorized as
 protected, between 3–7% overlapped with proposed renewable energy project
 footprints, and up to 17% overlapped with project footprints combined with
 transmission corridors. Overlap of evolutionary hotspots with renewable
 energy development mainly occurred in 6 of the 10 identified hotspots.
 Resulting GIS-based maps can be incorporated into ongoing landscape
 planning efforts and highlight specific regions where further
 investigation of impacts to population persistence and genetic
 connectivity may be warranted.
description: Chionactis occipitalis
 microsatellite dataTable of microsatellite
 genotypes and collection location information for C/ occipitalis
 individuals from throughout the Mojave Desert. In CSV
 format.Chio_msats.csv
DOI: 10.5061/dryad.814g3
title: Data from: Quantity over quality: light intensity, but not red/far-red ratio, affects extrafloral nectar production in Senna mexicana var. chapmanii

description: Extrafloral nectar (EFN) mediates food-for-protection mutualisms between
 plants and insects and provides plants with a form of indirect defense
 against herbivory. Understanding sources of variation in EFN production is
 important because such variations affect the number and identity of insect
 visitors and the effectiveness of plant defense. Light represents a
 potentially crucial tool for regulating resource allocation to defense, as
 it not only contributes energy but may help plants to anticipate future
 conditions. Low red/far-red (R/FR) light ratios can act as a signal of the
 proximity of competing plants. Exposure to such light ratios has been
 shown to promote competitive behaviors that coincide with reduced resource
 allocation to direct chemical defenses. Little is known, however, about
 how such informational light signals might affect indirect defenses such
 as EFN, and the interactions that they mediate. Through controlled
 glasshouse experiments, we investigated the effects of light intensity,
 and R/FR light ratios, on EFN production in Senna mexicana var. chapmanii.
 Plants in light-limited conditions produced significantly less EFN, and
 leaf damage elicited increased EFN production regardless of light
 conditions. Ratios of R/FR light, however, did not appear to affect EFN
 production in either damaged or undamaged plants. Understanding the
 effects of light on indirect defenses is of particular importance for
 plants in the threatened pine rockland habitats of south Florida, where
 light conditions are changing in predictable ways following extensive
 fragmentation and subsequent mismanagement. Around 27% of species in these
 habitats produce EFN and may rely on insect communities for defense.
description: Light filter
 experimentThe data file attached
 describes extrafloral nectar collected from Senna mexicana var. chapmanii
 plants in a greenhouse experiment conducted at Florida International
 University. The data set is made up of 12 columns described below. A.
 Plant number. Each plant used in the study has a designated number. B.
 Light treatment: C=clear film; S=shade film; R=shade film with increased
 far red/ red light ratio. C. Damage treatments: D=damage; C=no damage. D.
 Factorial treatment numbers: eg: 1= clear film + damage. E.F.G. Quantity
 of extrafloral nectar collected (E=µl; F=any additional portion of a µl
 tube filled with nectar; G=total nectar volume collected). H. Nectar
 concentration measured using a hand held refractometer. I. Sugar
 production calculated using volume and concentration data. J. Sugar mass
 (g)/µl K. Sugar mass(mg)/µl L. Total mass of sugar produced by each plant
 at each time of measurement
DOI: 10.5061/dryad.68s67
title: Data from: Madagascar's ephemeral palaeo-grazer guild: who ate the ancient C4 grasses?

description: [No abstract entered]
description: Supplementary isotope
 and radiocarbon data on subfossil hippos and tortoises of
 MadagascarRaw and corrected d13C
 data and 14C and calibrated radiocarbon ages before present, and data
 sources for now-extinct Hippopotamus and Aldabrachelys on
 MadagascarSupplementary Table_for
 submission.xls