cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.h6q81d2
title: Data from: Biomass partitioning in a future dry and CO2 enriched climate: shading aggravates drought effects in Scots pine but not European black pine seedlings

description: 1. Climate change alters both water and CO2 availability for plants, but
 it is largely unknown how they interact with light to affect tree seedling
 establishment and early growth. Light availability is often regulated by
 forest management, thus understanding how these resources co-limit the
 regeneration success of tree species and populations with contrasting
 drought tolerances is essential for adaptive forest management and
 particularly for assisted migration. 2.We studied biomass partitioning of
 3-year-old Scots pine (Pinus sylvestris) and European black pine (Pinus
 nigra) seedlings in response to combined effects of light (22% and 40%
 shade), soil water availability (moist and dry conditions) and CO2
 (ambient and elevated), and examined the responses of seedlings from
 Central Alpine and Mediterranean origin. Seedlings of nine populations
 with varying drought tolerances were grown in a common garden in the
 European Central Alps. Shoot height, vertical root length, shoot and root
 biomass of the plants were assessed at the end of the third growing
 season. 3. Under 40% shade and dry conditions, P. sylvestris seedlings
 severely reduced shoot biomass, resulting in an increased specific shoot
 height (SSH) compared to seedlings under 22% shade and moist conditions.
 In contrast, P. nigra seedlings retained a constant shoot biomass under
 all treatment combinations. Seedlings from drier origin were generally
 larger, heavier, and had longer vertical roots than those from wetter
 locations. In order to keep up shoot height, seedlings from wetter origins
 disproportionately increased SSH under shaded conditions compared to
 populations from drier origin. 4. Synthesis and applications. Under high
 light availability, Scots pine (Pinus sylvestris) and European black pine
 (Pinus nigra) seedlings were well adapted to dry conditions. Moderate
 shading, however, substantially reduced Scots pine but not black pine
 growth, and potentially amplified the vulnerability of Scots pine
 seedlings to drought. Optimizing light conditions in forests, e.g. by
 thinning, may thus enhance early Scots pine regeneration in a drier future
 climate.27-Nov-2018
description: Bachofen-Shoot-and-Root-measurementsThis file contains all measurements: shoot and root biomass, shoot height, vertical root length. All other variables (root biomass fraction, specific shoot height, specific vertical root length) are derived from this data as described in the publication.
DOI: 10.5061/dryad.67136
title: Data from: Corticosterone: a costly mediator of signal honesty in sand lizards

description: The mechanisms underlying honest signal expression remain elusive and may
 involve the integration of social and physiological costs. Corticosterone
 is a socially modulated metabolic hormone that mediates energy investment
 and behavior and may therefore function to deter dishonest signal
 expression. We examined the relationship between corticosterone and green
 badge coloration in male sand lizards (Lacerta agilis), hypothesizing that
 physiological and behavioral costs resulting from elevated baseline
 glucocorticoids function in maintenance of honest signal expression. We
 found that large-badged males had higher corticosterone titer, with this
 relationship apparent at the end of the season and absent early in the
 season. Large-badged males also suffered higher ectoparasite load (number
 of tick nymphs), despite being in better condition than small-badged
 males. Ectoparasite load was positively related to corticosterone titer
 early in the season at the time of badge formation. High-condition
 individuals had lower corticosterone and lower numbers of ectoparasites
 than low-condition individuals, suggestive of conditional variation in
 ability to withstand costs of corticosterone. We found an opposing
 negative relationship between corticosterone titer and endoparasite load.
 Corticosterone titer was also negatively associated with male mobility, a
 fitness-determining behavior in this species. Because badge size is
 involved in mediating agonistic social interactions in this species, our
 results suggest that badge-dependent variation in corticosterone is likely
 reflective of variation in social conditions experienced over the course
 of the season. Our results implicate corticosterone in maintenance of
 signal honesty, both early in the season through enforcement of
 physiological costs (ectoparasite load) and during the season through
 behavioral costs (male mobility). We propose that socially modulated
 variation in corticosterone critically functions in mediation of signal
 honesty without requiring a direct role for corticosterone in trait
 expression.
description: Long-term observational
 dataObservational data on
 sand lizard badge size, body mass and snout vent length, and number of
 ectoparasites.LongDataSandlizardsEvoEco.xlsEarly-season badge sizeMeasurements of sand lizard badge size, body morphology, corticosterone, and ectoparasites taken early in the season near the time of badge formation.EarlyDataSandlizardEvoEco.xlsLate-season dataLate-season data used in analyses of end of season variation in ectoparasites, endoparasites, male mobility, badge size, and CORT.LateSandlizardCortPaperData.xls
DOI: 10.5061/dryad.kb110
title: Data from: Causes and consequences of individual variation in the extent of post-juvenile moult in the blue tit Cyanistes caeruleus (Passeriformes: Paridae)

description: Moult, comprising the growth or replacement of feathers in birds, is an
 energetically demanding process. As a result, in many species, the extent
 of the post-juvenile moult can vary substantially. However, the reasons
 underlying this variation remain poorly understood, and the potential
 life-history consequences of variation in moult extent are even less
 clear. In the present study, we aimed to use individual-specific data to
 identify factors affecting the extent of the post-juvenile moult in a
 population of over 2500 blue tits Cyanistes caeruleus Linnaeus 1758, and
 to assess the consequences of individual variation in moult extent on
 reproduction in the first year of life. There was a substantial sex
 difference in post-juvenile moult extent, with males moulting more
 extensively than females. Putative immigrant birds had moulted on average
 less than those born locally. However, there was little evidence of
 carry-over effects of the natal environment on moult extent because we
 found no relationship between moult extent and fledging date or nestling
 mass. Evidence that moult extent, and hence feather brightness, affected
 subsequent reproductive success was limited. Moult extent had no effect on
 recruitment in males, although female recruits had moulted significantly
 less than nonbreeders. Because it was not influenced by features of the
 natal environment, moult extent may not be an honest signal of individual
 quality in C. caeruleus. As a result, the potential consequences of
 variation in moult extent for fitness are likely to be small.
description: Moult files for
 Dryad12 separate files in a
 zip folder: BREEDERF/M = comparing breeders v non-breeders for each sex.
 Clutchegg = analyses of clutch size and egg mass. DISP = dispersal
 distance analysis. FIVEF/M comparing age of partner in first year birds.
 hatched_in_wytham= natal effects data file. RES-IMM = comparison of
 residents v immigrants. SEX_DIFFERENCES = comparison of moult extent by
 sex. YRMALES/FEMALES = analysis of young ringed by moult extent for both
 sexes. All headings self-explanatory. PC1_F is our synthetic measure of
 moult extent.
DOI: 10.5061/dryad.pc5gc05
title: Data from: Disentangling the drivers of diversification in an imperiled group of freshwater fishes (Cyprinodontiformes: Goodeidae)

description: Background: One of the most perplexing questions in evolutionary biology
 is why some lineages diversify into many species, and others do not. In
 many cases, ecological opportunity has played an important role, leading
 to diversification along trophic or habitat-based axes. The Goodeidae
 (Teleostomi: Cyprinodontiformes) are a family of freshwater fishes with
 two subfamilies: Goodeinae (42 species, viviparous, heterogeneous
 habitats, Mesa Central of Mexico) and Empetrichthyinae (4 species,
 oviparous, homogeneous habitats, Great Basin of the United States). These
 discrepant sets of characteristics and their sister-group relationship
 make the goodeids amenable to a comparative study of diversification. We
 gathered lateral body images from more than 1,600 specimens of all extant
 species in the family. Geometric morphometric, and phylogenetic
 comparative analyses were used to address whether higher species diversity
 correlates with higher rates of morphological shape evolution and whether
 there are differences in functional/habitat modules between the two
 subfamilies. Results: This study recovered a higher rate of overall body
 shape evolution in the Goodeinae that is nearly double in magnitude
 compared to the Empetrichthyinae. A modularity test indicated that the
 Goodeinae displayed elevated rates of morphological evolution in
 comparison to the Empetrichthyinae when only trunk (locomotor) regions
 were compared between subfamilies. No significant differences in
 evolutionary shape rates were recovered when the trophic (head) regions
 were compared between subfamilies. Discussion: These results support the
 hypothesis that Mexican goodeids radiated via an ecological opportunity
 scenario into a wide-array of novel habitats in the island-like Mesa
 Central as evidenced by their high rate of shape evolution, relative to
 the Empetrichthyinae. This study quantitatively unraveled the drivers of
 evolution and eliminated trophic specialization as a driving force within
 the Goodeidae.
description: Body Shape
 MeansBody shapes (means) of
 all the Goodeidae, 2-dimensional landmark data.BSM_Goodeidae_Div.csvTable S2Museum catalog numbers for the landmark data.TableS1Genbank information for the taxa used in the chronogram.Head Shape MeansHead shape (means) for the 2-dimensional landmark data.HSM_allGoodeidae.csvGoodeidTree_BeastNexus file for Goodeidae tree used in comparative analyses.R Code for Anaylses_GoodeidaeCode for analyses used in R-package Geomorph. All coding was done in the program TinnR.Tail Shape Means_GoodeidaeCaudal region (means) for all 2-Dimensional landmark data in Goodeidae trunk analyses.Tail_SM.csv
DOI: 10.6084/m9.figshare.31062556.v1
title: Data_Ultra-low-dose ultra-high-resolution EUV ptychographic imaging

description: Data_Ultra-low-dose ultra-high-resolution EUV ptychographic imaging
DOI: 10.5061/dryad.fn0f4
title: Data from: Costs of immunity and their role in the range expansion of the house sparrow in Kenya

description: There are at least two reasons to study traits that mediate successful
 range expansions. First, dispersers will found new populations and thus
 impact the distribution and evolution of species. Second, organisms moving
 into new areas will influence the fate of resident communities, directly
 competing with or indirectly affecting residents by spreading non-native
 or spilling-back native parasites. The success of invaders in new areas is
 likely mediated by a counterbalancing of costly traits. In new areas where
 threats are comparatively rare, individuals that grow rapidly and breed
 prolifically should be at an advantage. High investment in defenses should
 thus be disfavored. In the present study, we compared the energetic,
 nutritional and collateral damage costs of an inflammatory response among
 Kenyan house sparrow (Passer domesticus) populations of different ages,
 asking whether costs were related to traits of individuals from three
 different capture sites. Kenya is among the world's most recent range
 expansions for this species, and we recently found that the expression of
 Toll-like receptors (TLRs), leukocyte receptors that instigate
 inflammatory responses when bound to microbial elements, was related to
 the range expansion across the country. Here, we found (contrary to our
 expectations) that energetic and nutritional costs of inflammation were
 higher, but damage costs were lower, in range-edge compared with core
 birds. Moreover, at the individual level, TLR-4 expression was negatively
 related to commodity costs (energy and a critical amino acid) of
 inflammation. Our data thus suggest that costs of inflammation, perhaps
 mediated by TLR expression, might mitigate successful range expansions.
description: costs of inflammatory
 responses in Kenyan house sparrowsThese data are for a
 study of the energetic, oxidative damage, and nutritional costs of an
 inflammatory response in house sparrows from Kenyafor Martin et al., JEB 2017,
 Kenya.zip
DOI: 10.5061/dryad.p0c10
title: Data from: The importance of microhabitat for biodiversity sampling

description: Responses to microhabitat are often neglected when ecologists sample
 animal indicator groups. Microhabitats may be particularly influential in
 non-passive biodiversity sampling methods, such as baited traps or light
 traps, and for certain taxonomic groups which respond to fine scale
 environmental variation, such as insects. Here we test the effects of
 microhabitat on measures of species diversity, guild structure and biomass
 of dung beetles, a widely used ecological indicator taxon. We demonstrate
 that choice of trap placement influences dung beetle functional guild
 structure and species diversity. We found that locally measured
 environmental variables were unable to fully explain trap-based
 differences in species diversity metrics or microhabitat specialism of
 functional guilds. To compare the effects of habitat degradation on
 biodiversity across multiple sites, sampling protocols must be
 standardized and scale-relevant. Our work highlights the importance of
 considering microhabitat scale responses of indicator taxa and designing
 robust sampling protocols which account for variation in microhabitats
 during trap placement. We suggest that this can be achieved either through
 standardization of microhabitat or through better efforts to record
 relevant environmental variables that can be incorporated into analyses to
 account for microhabitat effects. This is especially important when
 rapidly assessing the consequences of human activity on biodiversity loss
 and associated ecosystem function and services.
description: Mehrabi et al. The
 importance of microhabitat for biodiversity sampling
 datasetData set for the
 publication associated with this Dryad data package, on the effects of
 microhabitat on biodiversity metrics, using dung beetles as a focal taxon.
 This data set contains a species by site matrix, trap based environmental
 variables, and species dry biomass estimates. The data set xls. file was
 created using Microsoft Excel 2011. See README for more details and
 metadata.Mehrabietal_importanceofmicrohabitat_data.xls
DOI: 10.5061/dryad.75pp8f32
title: Data from: Nondestructive sampling of insect DNA from defensive secretion

description: Nondestructive techniques to obtain DNA from organisms can further genetic
 analyses such as estimating genetic diversity, dispersal, and lifetime
 fitness, without permanently removing individuals from the population.
 Possible DNA sources for insects include wing and leg clippings or frass
 samples. However, these are not feasible approaches for organisms that
 cannot be removed from their natural environment for long periods or when
 adverse effects of tissue removal must be avoided. This study evaluated
 the impacts and efficacy of extracting hemolymph from a defensive
 secretion to obtain DNA for amplification of microsatellites. A secretion
 containing hemolymph was obtained from Bolitotherus cornutus (the forked
 fungus beetle) by perturbation of the defensive gland with a capillary
 tube. A laboratory experiment demonstrated that the sampling methodology
 had no impact on mortality, reproductive success, or gland expression. To
 evaluate the quality of DNA obtained in natural samples, hemolymph was
 collected from 187 individuals in the field and successfully genotyped at
 18 microsatellite loci for 95.7% of samples. These results indicate that
 hemolymph-rich defensive secretions contain DNA and can be sampled without
 negative impacts on the health or fitness of individual insects.
description: Egg
 DataQubit
 AnalysisSurvivorship and gland
 health
DOI: 10.5061/dryad.s6n57
title: Data from: Genetic variation in invasive species response to direct and indirect species interactions

description: Biotic resistance to invasion arises from strong species interactions that
 decrease the fitness and population growth rates of potential invaders.
 Strong, direct interactions such as predation and competition are
 typically thought to drive biotic resistance, but in diverse communities,
 indirect interactions among species may also affect biotic resistance.
 Further, genetic variation in traits of the invading species that affect
 species interactions may allow some genotypes to overcome biotic
 resistance. We investigated the direct and indirect effects of a native
 legume (Acmispon wrangelianus) and insect herbivores on the fitness of
 different genotypes of an invasive legume (Medicago polymorpha) in a
 California grassland. Insect herbivores decreased Medicago fitness, but
 only in the presence of Acmispon, suggesting that indirect interactions
 mediated through insects and Acmispon are important for deterring Medicago
 invasion. Some Medicago genotypes were less affected by interactions with
 other species, however. This genetic variance suggests that while biotic
 resistance reduced the reproductive success of most genotypes, a few
 genotypes were able to overcome these complex interactions. However,
 Medicago invasion was unsuccessful in all treatments at several of our
 sites, suggesting that factors beyond those manipulated here also play a
 key role at many sites. At sites where biotic resistance is important,
 spatial and temporal variation in community composition and the genetic
 composition of the invasion pool may explain the invasion success of
 Medicago into this community.
description: Medicago
 FecundityFecundity values for
 each plantfor
 Dryad.xls
DOI: 10.5061/dryad.n3m2qh2
title: Data from: Diet and provisioning rate differ predictably between dispersing and philopatric pied flycatchers

description: Dispersal is an essential process for most animal populations to persist
 in changing environments. Dispersers are often a non-random sample of the
 population, and differ consistently from non-dispersers in a suite of
 correlated phenotypic traits (‘dispersal syndromes’). This phenotypic
 integration is thought to be adaptive. Here, we investigate whether
 dispersal tendency of individual pied flycatchers (Ficedula hypoleuca)
 covaries with a set of repeatable behaviors that should confer advantages
 for surviving and reproducing in novel environments. We specifically focus
 on the link between dispersal, foraging behavior and aggressiveness
 because selection on foraging tactics or social behaviors likely differs
 between individuals staying in familiar or dispersing to novel
 environments. Using repeated measures of nestling provisioning data of
 pied flycatcher parents in one year, we tested if immigrants and
 philopatric individuals (local recruits and experienced breeders) differed
 in diet specialization, provisioning rates, levels of aggression and
 reproductive success. Results show that individuals differed consistently
 in their foraging behavior, with immigrants having a more generalist diet
 and higher feeding rates than philopatric birds, but not in
 aggressiveness. More generalist males fledged more young. Our findings
 suggest that prior local knowledge facilitates diet specialization, and
 that more generalist diets could be adaptive for immigrants breeding in
 unknown environments. Aggressiveness was not part of the dispersal
 syndrome in our population, perhaps because high aggression levels are too
 costly to maintain in high density populations. Understanding the
 proximate causes and ultimate consequences of variation in dispersal
 syndromes requires now experimental manipulations of individual dispersal
 decisions.
description: data1: multivariate
 mixed models dataThis table contains the
 data used for producing Table 1 (bivariate mixed model: diet and
 provisioning rate) and Table S2 (multivariate mixed model: prey
 types)data1.xlsxdata2: data of univariate mixed models of diet and provisioning ratedata set used to produce Table 2 (univariate mixed models of diet and provisioning rate) and Table S3A and S3B (Covariation between foraging behavior and the main preys found in the diet)data2.xlsxdata3: fitness data and parent's provisioning behaviourData set used to produce Table 3 (Best general linear models explaining variation in components of annual fitness)data3.xlsx
DOI: 10.5061/dryad.3k0m625
title: Data from: Bioturbation by mammals and fire interact to alter ecosystem-level nutrient dynamics in longleaf pine forests

description: Activities of ecosystem engineers can interact with other disturbances to
 modulate rates of key processes such as productivity and nutrient cycling.
 Bioturbation, movement of soil by organisms, is a widespread form of
 ecosystem engineering in terrestrial ecosystems. We propose that
 bioturbation by southeastern pocket gophers (Geomys pinetis), an abundant
 but declining ecosystem engineer in longleaf pine (Pinus palustris Mill.)
 forests, accelerates nutrient dynamics of the forest floor by burying
 litter and then reduces litter consumption and nitrogen (N) volatilization
 losses in the presence of fire. We evaluated our hypothesis by measuring
 how litter burial alters decomposition and N and phosphorus (P) turnover
 of longleaf pine and turkey oak (Quercus laevis Walt.) litter over four
 years, and then simulated interactive ecosystem-level effects of litter
 burial and low-intensity fires on N and P dynamics of the litter layer. In
 the field, mass loss was over two times greater and N and P were released
 much more rapidly from litter buried beneath mounds than on the surface of
 the forest floor. At a measured rate of mound formation covering 2.3 ±
 0.6% of the forest floor per year, litter mass and N and P content of the
 forest floor simulated over an eight-year period were approximately 11%
 less than amounts in areas without pocket gopher mounds. In contrast to
 unburied litter, litter beneath mounds is protected from consumption
 during fires, and as fire interval increased, consumption rates decreased
 because mounds cover more years of accumulated litter. Our research
 indicates that bioturbation and burial of litter by pocket gophers
 accelerates turnover of N and P on the forest floor, and in the presence
 of fire, conserves N in this ecosystem where productivity is known to be
 nutrient limited.
description: Pocket Gopher Mound
 Surveys Clark et al PLOS ONEPocket Gopher Mound
 Surveys for Clark et al PLOS ONEMass Nitrogen and
 Phosphorus in Litterfall Clark et al PLOS ONEMass, Nitrogen and
 Phosphorus in Litterfall for Clark et al PLOS ONEMass Nitrogen and
 Phosphorus in Litterbags Clark et al PLOS ONEPercent Mass, Nitrogen
 and Phosphorus Remaining in Litterbags Clark et al PLOS
 ONE