cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.187k0
title: Data from: Reliability of macrofossils in woodrat (Neotoma) middens for detecting low-density tree populations

description: Macrofossils from woodrat (Neotoma) middens serve as an important proxy
 for reconstructing past vegetation in arid and semiarid regions of North
 America. The presence/absence of plant macrofossils in middens can provide
 valuable information on temporal and spatial patterns of plant migration
 and range boundaries. The primary aim of this study was to determine how
 local plant abundance, distance of plant populations from midden sites,
 and species population density on the landscape affect the probability of
 occurrence of macrofossils in middens. The study was designed with the
 primary intent of determining the reliability of middens in detecting
 scattered populations of Pinus ponderosa. We analyzed macrofossil
 assemblages from 42 modern woodrat middens from West Carrizo Canyon in
 southeastern Colorado, near the current eastern range margin of Pinus
 ponderosa. We compared midden contents with composition of the surrounding
 vegetation, measuring distance from the midden to the nearest individual
 of selected plant species, and the percent cover of each species within 30
 m of the midden. We used this information to model the probability of
 species presence in a midden across a range of population densities on the
 landscape. Macrofossils of Juniperus spp., Quercus gambelii, and Opuntia
 spp. were consistently found in middens regardless of their local
 abundance in vegetation, although populations occurred within 30 m of all
 middens. Pinus edulis and P. ponderosa occurred in nearly all middens
 within 20-30 m of individual trees. P. ponderosa was rare in middens
 &gt;20-30 m away from individual trees. Results of a simple simulation
 model suggest that middens become absolutely reliable indicators of P.
 ponderosa presence on the landscape only when average tree density exceeds
 50 stems ha-1. Woodrats reliably collected macrofossils of Pinus edulis,
 P. ponderosa, Juniperus spp., Quercus gambelii, and Opuntia spp. when
 populations of these taxa occur within 20-30 m of a midden site. Woodrats
 did not collect P. ponderosa when the nearest individuals were more than
 30 m away. Low-density populations of these and other species may be
 difficult to detect in fossil woodrat-midden series owing to reduced
 probability that individuals grow within foraging distance of the middens.
 Data from this and similar studies can be used to construct and
 parameterize a forward model of macrofossil representation in woodrat
 middens.
description: 10053
 SupplementaryTable S1. Location,
 presence/absence of species, abundance (%) of species in 30 metres
 surrounding midden and distance of nearest individual of a species the
 midden for 42 collected middens. Table S2. Organs identified in middens
 for each target species.
DOI: 10.5061/dryad.6bs31
title: Data from: Mandated data archiving greatly improves access to research data

description: The data underlying scientific papers should be accessible to researchers
 both now and in the future, but how best can we ensure that these data are
 available? Here we examine the effectiveness of four approaches to data
 archiving: no stated archiving policy, recommending (but not requiring)
 archiving, and two versions of mandating data deposition at acceptance. We
 control for differences between data types by trying to obtain data from
 papers that use a single, widespread population genetic analysis,
 STRUCTURE. At one extreme, we found that mandated data archiving policies
 that require the inclusion of a data availability statement in the
 manuscript improve the odds of finding the data online almost 1000-fold
 compared to having no policy. However, archiving rates at journals with
 less stringent policies were only very slightly higher than those with no
 policy at all. We also assessed the effectiveness of asking for data
 directly from authors and obtained over half of the requested datasets,
 albeit with ∼8 d delay and some disagreement with authors. Given the
 long-term benefits of data accessibility to the academic community, we
 believe that journal-based mandatory data archiving policies and mandatory
 data availability statements should be more widely adopted.
description: Journal
 policiesA file giving the data
 archiving policies from the journals covered in the
 study.Data request
 protocolThe sequence of emails
 used to request data from authors.Vines_et_al_Rcode_4th_JanThe R code used in the statistical analysesVinesetal_data_4th JanThe data used in the statistical analyses
DOI: 10.5061/dryad.5878v18
title: Data from: The influence of cactus spine surface structure on puncture performance and anchoring ability is tuned for ecology

description: Spines are common morphological features found in almost all major
 biological groups offering an opportunity to explore large-scale
 evolutionary convergence across disparate clades. As an example, opuntioid
 cacti have spines with barbed ornamentation that is remarkably similar in
 form and scale to that found on porcupine quills, suggesting specific
 biomechanical convergence across the animal and plant kingdoms. While the
 mechanics of porcupine quills as defensive mechanisms has been previously
 tested, the mechanics of cacti spines (which have evolved to fill a number
 of functions including defense, climbing and dispersal) has not been
 characterized. Here we study the puncturing and anchoring ability of six
 species of cactus, including both barbed and non-barbed spines. We found
 that barbed spines require less work to puncture a variety of targets than
 non-barbed spines. Barbed spines also require more work than non-barbed
 spines to withdraw from biological materials, due to their barbs engaging
 with tissue fibers. These results closely match those found previously for
 barbed vs. non-barbed porcupine quills, implying biomechanical
 convergence. The variation in performance of barbed versus non-barbed
 spines, as well as between barbed spines from different species, is likely
 tied to the diversity of ecological functions of cactus spines.
description: Cactus spine morphology
 and puncture dataData for cactus spine
 tip morphology, puncture and withdraw data for first puncture by spines of
 6 species, and puncture and withdraw data for 5 puncture trials by spines
 of 6 speciesCactus spine
 data.xlsx
DOI: 10.5061/dryad.q8473
title: Data from: Individual performance in relation to cytonuclear discordance in a northern contact zone between long-toed salamander (Ambystoma macrodactylum) lineages

description: Cytonuclear discordance in contact zones between related lineages is
 common, with mitochondrial clines often being displaced from clines in
 nuclear allele frequency. Proposed explanations for such a pattern include
 adaptive introgression of mtDNA or a neutral wake of mtDNA being left
 behind following hybrid zone movement. However, studies investigating
 these hypotheses are rare. Our previous survey of genetic variation in the
 long-toed salamander (Ambystoma macrodactylum) highlighted a potential
 case of cytonuclear discordance between two lineages in western Canada.
 Here, we use additional markers and samples to clarify the extent of this
 discordance. We simultaneously assess the feeding performance of
 individuals in a common environment to test for an association between
 mitotype and individual performance. The genetic results confirm a general
 pattern of cytonuclear discordance in the focal region. However, we also
 observed more limited introgression of a diagnostic nuclear marker.
 Intriguingly, although there were differences in individual performance
 associated with the transition between mitotypes, these differences were
 not fully explained by mitotype. Instead, the lowest performance was
 observed in individuals demonstrating the greatest mismatch between mtDNA
 and all nuclear markers, suggesting the potential for cytonuclear
 incompatibilities to be acting. These results highlight the complexity of
 understanding the causes and consequences of mtDNA introgression and
 cytonuclear discordance in contact zones.
description: Genetic data and results
 from feeding experimentThe main folder contains
 a spreadsheet (saved as both and Excel file and a csv file) that lists the
 genetic ancestry of individuals in terms of mistype and three nuclear
 markers. This file also contains the details of the feeding experiment,
 including weekly mass measurements and final calculations of conversion
 efficiency. The main folder contains a subfolder called
 "AFLPs_Structure_Distruct". Within this folder the input file
 for the STRUCTURE analyses ("structureMatrix") is saved as both
 and Excel and text file. Input parameter files for the STRUCTURE analysis
 are also provided. The file "Distruct_K2_outfile.txt" lists the
 final STRUCTURE ancestry scores used in Fig.2 with individuals in the same
 order as listed in STRUCTURE input file (this file was produced after
 running the STRUCTURE output through StructureHarvester, CLUMPP and
 DISTRUCT).Lee-Yaw_Jacobs_Irwin_MEC2014.zip
DOI: 10.5061/dryad.mk3tj78
title: Data from: Phytochemical changes in milkweed induced by elevated CO2 alter wing morphology but not toxin sequestration in monarch butterflies

description: 1. Environmental change has the potential to influence trophic
 interactions by altering the defensive phenotype of prey. 2. Here, we
 examine the effects of a pervasive environmental change driver, elevated
 atmospheric concentrations of CO2 (eCO2), on toxin sequestration and
 flight morphology of a specialist herbivore. 3. We fed monarch butterfly
 larvae, Danaus plexippus, foliage from four milkweed, Asclepias, species
 of varying chemical defense profiles grown under either ambient or eCO2.
 We also infected a subset of these herbivores with a protozoan parasite,
 Ophryocystis elektroscirrha, to understand how infection and environmental
 change combine to alter herbivore defenses. We measured changes in
 phytochemistry induced by eCO2 and assessed cardenolide, toxic steroid,
 sequestration and wing morphology of butterflies. 4. Monarchs compensated
 for lower plant cardenolide concentrations under eCO2 by increasing
 cardenolide sequestration rate, maintaining similar cardenolide
 composition and concentrations in their wings under both CO2 treatments.
 We suggest that these increases in sequestration rate are a byproduct of
 compensatory feeding aimed at maintaining a nutritional target in response
 to declining dietary quality. 5. Monarch wings were more suitable for
 sustained flight (more elongated) when reared on plants grown under eCO2
 or when reared on A. syriaca or A. incarnata rather than on A. curassavica
 or A. speciosa. Parasite infection engendered wings less suitable for
 sustained flight (wings became rounder) on three of four milkweed species.
 Wing loading (associated with powered flight) was higher on A. syriaca
 than on other milkweeds, whereas wing density was lower on A. curassavica.
 Monarchs that fed on high cardenolide milkweed developed rounder, thinner
 wings, which are less efficient at gliding flight. 6. Ingesting foliage
 from milkweed high in cardenolides may provide protection from enemies
 through sequestration yet come at a cost to monarchs manifested as lower
 quality flight phenotypes: rounder, thinner wings with lower wing loading
 values. 7. Small changes in morphology may have important consequences for
 enemy evasion and migration success in many animals. Energetic costs
 associated with alterations in defense and morphology may, therefore, have
 important consequences for trophic interactions in a changing world.
description: wing.morphoDataset that accompanies: Decker, LE; Soule, AJ; de Roode, JC; Hunter, MD, 2018ms. Phytochemical changes in milkweed induced by elevated CO2 alter wing morphology but not toxin sequestration in monarch butterflies. Functional Ecology. We examined the indirect effects of elevated CO2 on toxin sequestration and flight morphology of the monarch butterfly mediated by plant quality. We measured the concentration of cardenolides sequestered by the monarchs fed plants grown under ambient or elevated CO2 and also examined aspects of butterfly wing morphology.
DOI: 10.5061/dryad.k5b0j
title: Data from: Ontogenetic trajectories of septal spacing in Early Jurassic belemnites from Germany and France, and their palaeobiological implications

description: Based on well-preserved belemnites, the ontogenetic trajectories of septal
 spacing between succeeding chambers were analysed. In the examined species
 (Passaloteuthis laevigata, Parapassaloteuthis zieteni and Pseudohasitites
 longiformis) that come from Buttenheim, Germany, and Lixhausen, France,
 the ontogenetic trajectories of septal spacing follow exponentially
 increasing trends with no decreasing phase of septal crowding during the
 earliest ontogenetic stage. The absence of a decreasing trend at the
 earliest ontogenetic stage is a unique character in contrast with those in
 modern cuttlefish and ancient and modern nautiloids, in which the
 decreasing trends are related to hatching events. These ontogenetic septal
 spacing trends suggest that the belemnite hatchlings had only a protoconch
 with no chamber. These belemnite hatchlings with no chamber and therefore
 small embryonic shell diameter are similar to those of ammonoids.
 Significant difference in a statistical test that compared the protoconch
 size between the two localities, might suggest that there was limited
 transportation at the embryonic stage, although it could also just
 indicate differences in regional environmental conditions, age and/or
 degree of time averaging which might differ between the examined taxa.
description: Supplementary
 data
DOI: 10.5061/dryad.nb85p
title: Data from: Save your host, save yourself? caste-ratio adjustment in a parasite with division of labor and snail host survival following shell damage

description: Shell damage and parasitic infections are frequent in gastropods,
 influencing key snail host life-history traits such as survival, growth,
 and reproduction. However, their interactions and potential effects on
 hosts and parasites have never been tested. Host–parasite interactions are
 particularly interesting in the context of the recently discovered
 division of labor in trematodes infecting marine snails. Some species have
 colonies consisting of two different castes present at varying ratios;
 reproductive members and nonreproductive soldiers specialized in defending
 the colony. We assessed snail host survival, growth, and shell
 regeneration in interaction with infections by two trematode species,
 Philophthalmus sp. and Maritrema novaezealandense, following damage to the
 shell in the New Zealand mud snail Zeacumantus subcarinatus. We
 concomitantly assessed caste-ratio adjustment between nonreproductive
 soldiers and reproductive members in colonies of the trematode
 Philophthalmus sp. in response to interspecific competition and shell
 damage to its snail host. Shell damage, but not parasitic infection,
 significantly increased snail mortality, likely due to secondary
 infections by pathogens. However, trematode infection and shell damage did
 not negatively affect shell regeneration or growth in Z. subcarinatus;
 infected snails actually produced more new shell than their uninfected
 counterparts. Both interspecific competition and shell damage to the snail
 host induced caste-ratio adjustment in Philophthalmus sp. colonies. The
 proportion of nonreproductive soldiers increased in response to
 interspecific competition and host shell damage, likely to defend the
 parasite colony and potentially the snail host against increasing threats.
 These results indicate that secondary infections by pathogens following
 shell damage to snails both significantly increased snail mortality and
 induced caste-ratio adjustments in parasites. This is the first evidence
 that parasites with a division of labor may be able to produce
 nonreproductive soldiers according to environmental factors other than
 interspecific competition with other parasites.
description: Data MacLeod et
 al_ECE-2017-08-01014.R1Data used in the
 analyses for the article published in Ecology and
 Evolution
DOI: 10.5061/dryad.10b86
title: Data from: Hard and soft selection on phenology through seasonal shifts in the general and social environments: a study on plant emergence time

description: The timing of transition out of one life history phase determines where in
 the seasonal succession of environments the next phase is spent. Shifts in
 the general environment (e.g., seasonal climate) affect the expected
 fitness for particular transition dates. Variation in transition date also
 leads to temporal variation in the social environment. For instance, early
 transition may confer a competitive advantage over later individuals. If
 so, the social environment will impose frequency- and density-dependent
 selection components. In effect, the general environment imposes hard
 selection while the social environment imposes soft selection on
 phenology. We examined hard and soft selection on seedling emergence time
 in an experiment on Brassica rapa. In monoculture (uniform social
 environment), early emergence results in up to a 1.5-fold increase in seed
 production. In bi-cultures (heterogeneous social environment),
 early-emerging plants capitalized on their head start, suppressing their
 late neighbors and increasing their fitness advantage to as much as
 38-fold, depending on density. We devised a novel adaptation of contextual
 analysis to partition total selection (i.e., Cov(ω, z)) into the hard and
 soft components. Hard and soft components had similar strengths at low
 density, whereas soft selection was five times stronger than hard at high
 density.
description: Experiment to estimate
 hard and soft selection on seedling emergence timeThe experiment explored
 the impact of the general environment (climate) and the social environment
 (density and frequency of alternate phenotypes) on the selective advantage
 of early seedling emergence. Two emergece phenotype, early and late, were
 generated by planting seeds on two dates weeks apart. File contains
 indentifiers, stem size, leaf size and final seed pod production data by
 desinty, frequency and individual phenotype classes.BASIC.DATA.Sep2104.txt
DOI: 10.5061/dryad.dj6p6
title: Data from: Centromere–associated meiotic drive and female fitness variation in Mimulus

description: Female meiotic drive, in which chromosomal variants preferentially
 segregate to the egg pole during asymmetric female meiosis, is a
 theoretically pervasive but still mysterious form of selfish evolution.
 Like other selfish genetic elements, driving chromosomes may be maintained
 as balanced polymorphisms by pleiotropic or linked fitness costs. A
 centromere-associated driver (D) with a ∼58:42 female-specific
 transmission advantage occurs at intermediate frequency (32-40%) in the
 Iron Mountain population of the yellow monkeyflower, Mimulus guttatus.
 Previously determined male fertility costs are sufficient to prevent the
 fixation of D, but predict a higher equilibrium frequency. To better
 understand the dynamics and effects of D, we developed a new population
 genetic model and measured genotype-specific lifetime female fitness in
 the wild. In three of four years, and across all years, D imposed
 significant recessive seedset costs, most likely due to hitchhiking by
 deleterious mutations. With both male and female costs as measured, and
 58:42 drive, our model predicts an equilibrium frequency of D (38%) very
 close to the observed value. Thus, D represents a rare selfish genetic
 element whose local population genetic dynamics have been fully
 parameterized, and the observation of equilibrium sets the stage for
 investigations of co-evolution with suppressors.
description: Female fitness data and
 D genotype for Iron Mountain M. guttatus (2010-2014)This Excel file includes
 lifetime female fitness (seedset; 2010-2013), fruit numbers (2010-2013),
 and flower numbers (2012-2013), as well as LG11 centromere associated
 drive genotype (D = driver, determined by lb5a marker genotype), for
 individuals sampled from the Iron Mountain, OR population of Mimulus
 guttatus. All individuals sampled survived to produce at least 1 fruit, so
 these data do not include variation in survival to reproduction that may
 be present in the population.DriveCostsforDryad2015.xlsx
DOI: 10.5061/dryad.0mq34
title: Data from: Desiccation resistance and mating behavior in laboratory populations of Drosophila simulans originating from the opposing slopes of Lower Nahal Oren (Israel)

description: Lower Nahal Oren in Northern Israel, often referred to as "Evolution
 Canyon", has been proposed as a microscale model site for ecological
 evolution. However, conflicting mating assay and stress-resistance
 contribute to controversy over the Nahal Oren model. In this study we
 further tested the Nahal Oren model, while extending its focus from
 Drosophila melanogaster to its sister species, D. simulans. Using fly
 populations derived from the opposing canyon slopes and acclimated to
 laboratory conditions for 11-22 generations we did not find a significant
 slope effect on desiccation resistance (p=0.96) or body metabolic fuel
 content (p&gt;0.43) which would indicate a genetic basis for
 adaptation to local resource limitation. Multiple-choice mating assays
 (47-48% homotypic couples in two replicate populations) did not indicate
 divergence from a random mating pattern between north and south-facing
 slope flies. In conclusion, our findings do not support divergence of D.
 simulans populations across Lower Nahal Oren.
description: Nahal_Oren_D_simulans
DOI: 10.5061/dryad.n5q26
title: Data from: Direct benefits of choosing a high fitness mate can offset the indirect costs associated with intralocus sexual conflict

description: Intralocus sexual conflict generates a cost to mate choice: high fitness
 partners transmit genetic variation that confers lower fitness to
 offspring of the opposite sex. Our earlier work in the fruit fly,
 Drosophila melanogaster, revealed that these indirect genetic costs were
 sufficient to reverse potential “good genes” benefits of sexual selection.
 However, mate choice can also confer direct fitness benefits by inducing
 larger numbers of progeny. Here, we consider whether direct benefits
 through enhanced fertility could offset the costs associated with
 intralocus sexual conflict in D. melanogaster. Using hemiclonal analysis,
 we found that females mated to high fitness males produced 11% more
 offspring compared to those mated to low fitness males, and high fitness
 females produced 37% more offspring than low fitness females. These direct
 benefits more than offset the reduction in offspring fitness caused by
 intralocus sexual conflict, creating a net fitness benefit for each sex to
 pairing with a high fitness partner. Our findings highlight the need to
 consider both direct and indirect effects when investigating the fitness
 impacts of mate choice. Direct fitness benefits may shelter sexually
 antagonistic alleles from selection, suggesting a novel mechanism for the
 maintenance of fitness variation.
description: Pischedda &
 Chippindale 2017 Evolution Data