cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.g3psf6
title: Occurrence Download

description: A dataset containing 7394 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Magnolia acuminata"
 ]
}

 The dataset includes 7394 records from 255 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001810-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.h3tema
title: Occurrence Download

description: A dataset containing 271 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is India",
 "OccurrenceStatus is Present",
 "TaxonKey is Shorea robusta"
 ]
}

 The dataset includes 271 records from 29 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001815-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.rd838k2
title: Data from: Linking intra-specific trait variation and plant function: seed size mediates performance trade-offs within species

description: Substantial intra-specific trait variation exists within plant
 communities, and in theory this variation could influence community
 dynamics. Although recent research has focused on intra-specific variation
 in traits themselves, it is the influence of this variation on plant
 performance that makes intra-specific trait variation relevant to
 ecological dynamics within or among species. Understanding the links
 between trait and performance variation, and the role of traits in
 mediating relationships among multiple components of performance, is
 critical for assessing the importance of intra-specific trait variation
 for community dynamics. Seed size is thought to affect aspects of plant
 performance including fecundity, seedling growth, dispersal, and tolerance
 of natural enemies. For two tropical tree species, we assessed how seed
 size was related to performance variation within each species and
 determined whether intra-specific trait variation mediates intra-specific
 performance trade-offs. We used field seed rain collection to characterize
 size-dependent outcomes of dispersal, sowed seeds of known size in soil
 collected near or far from conspecifics to characterize susceptibility to
 soil pathogens, and monitored growth of seedlings from seeds of known
 size. We found that intra-specific seed size variation caused
 intra-specific performance variation. The degree of trait-based
 performance variation was consistently smaller than the degree of trait
 variation, and seed size influenced different components of performance
 for each species. One species exhibited a trade-off in which small seeds
 had a fecundity advantage (more seedlings per unit reproductive mass) but
 produced smaller seedlings, whereas the other species exhibited a
 trade-off in which small seeds dispersed to areas of low conspecific
 density but were less tolerant of density-responsive natural enemies. Our
 results indicate that a single trait can influence multiple components of
 performance and can mediate different trade-offs in co-occurring species.
 Complex and heterogeneous effects of a single trait in multidimensional
 niche space may favour inter-specific niche differentiation and
 coexistence.
description: Seed size variation and
 functional variationZip file contains R
 project with data as CSV files and analysis R code.
DOI: 10.5061/dryad.n1701c9
title: Data from: Variation in sexual dimorphism in a wind-pollinated plant: the influence of geographical context and life-cycle dynamics

description: Understanding the mechanisms causing phenotypic differences between
 females and males has long fascinated evolutionary biologists. An
 extensive literature exists on animal sexual dimorphism but less is known
 about sex differences in plants, particularly the extent of geographical
 variation in sexual dimorphism and its life-cycle dynamics. Here, we
 investigate patterns of genetically-based sexual dimorphism in vegetative
 and reproductive traits of a wind-pollinated dioecious plant, Rumex
 hastatulus, across three life-cycle stages using open-pollinated families
 from 30 populations spanning the geographic range and chromosomal
 variation (XY and XY1Y2) of the species. The direction and degree of
 sexual dimorphism was highly variable among populations and life-cycle
 stages. Sex-specific differences in reproductive function explained a
 significant amount of temporal change in sexual dimorphism. For several
 traits, geographical variation in sexual dimorphism was associated with
 bioclimatic parameters, likely due to the differential responses of the
 sexes to climate. We found no systematic differences in sexual dimorphism
 between chromosome races. Sex-specific trait differences in dioecious
 plants largely result from a balance between sexual and natural selection
 on resource allocation. Our results indicate that abiotic factors
 associated with geographical context also play a role in modifying sexual
 dimorphism during the plant life cycle.
description: Phenotypic data of R.
 hastatulusPhenotypic data across
 three time points for thirty populations across two chromosome races of
 Rumex hastatulus.pheno_Rumex_hastatulus.csvGeographic and demographic data of R. hastatulus populationsGeographic and demographic data of Rumex hastatulus sampled populations.populations_Rumex_hastatulus.csv
DOI: 10.5061/dryad.3b65k44
title: Data from: Reverting ontogeny: rapid phenotypic plasticity of color vision in cichlid fish

description: Phenotypic plasticity, particularly during development, allows organisms
 to rapidly adjust to different environmental conditions. Yet, it is often
 unclear whether the extent and direction of plastic changes are restricted
 by an individual’s ontogeny. Many species of cichlid fishes go through
 ontogenetic changes in visual sensitivity, from short to long wavelengths,
 by switching expression of cone opsin genes crucial for color vision.
 During this progression, individuals often exhibit phenotypic plasticity
 to the ambient light conditions. However, it is commonly assumed that once
 an adult visual phenotype is reached, reverting to an earlier ontogenetic
 state with higher sensitivity at shorter wavelengths is not common. In
 this study, we experimentally demonstrate that four-month-old Midas
 cichlid fish (Amphilophus astorquii) show plasticity in single cone opsin
 expression after experiencing drastic changes in light conditions.
 Resulting shifts of visual sensitivity occurred presumably in an adaptive
 direction - towards shorter or longer wavelengths when exposed to short or
 long wavelength light, respectively. Single cone opsin expression changed
 within only a few days and went through a transitional phase of
 co-expression. When the environment was experimentally enriched in long
 wavelength light, the corresponding change occurred gradually along a
 dorsoventral gradient within the retina. This plasticity allowed
 individuals to revert earlier ontogenetic changes and return to a more
 juvenile visual phenotype demonstrating previously unrecognized insights
 into temporal and spatial dynamics of phenotypic plasticity of the visual
 system in response to ambient light.
description: qpcr_dataThis file contains data on raw and mean critical threshold values (Cq) determined by quantitative RT-PCR as well as primer efficiencies for all genes investigated in this study.
DOI: 10.5061/dryad.b3k21db
title: Data from: Nonconsumptive effects of hunting on a nontarget game bird

description: 1. Human hunting activity and disturbance can significantly impact prey
 species through both consumptive and nonconsumptive effects. The
 nonconsumptive effects of rabbit hunting on Northern Bobwhite (Colinus
 virginianus; hereafter, bobwhite) are currently unknown. Increased
 perceived risk of predation by bobwhite during rabbit hunting events may
 elicit anti-predator responses among bobwhite that impact fitness via
 changes in behavior that ultimately impact population growth. 2. We
 estimated the nonconsumptive effects of rabbit hunting on bobwhite
 behavior using telemetry across varying rabbit hunting intensities.
 Movements were analyzed using Bayesian hierarchical modeling with a
 before-after-control-impact (BACI) design to determine the effect of
 rabbit hunting on bobwhite. 3. We observed an overall reduction in
 bobwhite movement in the presence of rabbit hunting, with a 38% (Posterior
 Overlap = 0.01) increase in bobwhite step length in the absence of rabbit
 hunting. We also observed bobwhite maintaining closer proximity to
 hardwood and escape cover under high rabbit hunting intensity, with a 59%
 (Posterior Overlap = 0.03) increase in distance from hardwood and a 28%
 (Posterior Overlap = 0.14) increase in distance from escape cover when
 rabbit hunting was removed. 4. Synthesis and applications. Heightened
 antipredator behavior through decreased movement may assist with bobwhite
 predator avoidance. However, decreased movement and increased use of poor
 habitats may also have negative effects as a result of reduced foraging
 time or increased susceptibility to other predators. Future research
 should attempt to quantify the effect of decreased movement on bobwhite
 fitness through the evaluation of foraging time and survival in order to
 continue to improve management efforts for the species.
description: Northern Bobwhite
 movement metrics in relation to rabbit huntingNorthern Bobwhite
 telemetry data gathered in the field via VHF-telemetry. Movement metrics
 described from the telemetry data were determined through analysis in
 ArcGIS and package "trajr" in R Statistical Software. Additional
 information on the attached files are described in the "README"
 text file.Mohlman_BobwhiteMovement_DataSubmission.zip
DOI: 10.5061/dryad.2jq5027
title: Data from: Dynamic changes in DNA methylation during embryonic and postnatal development of an altricial wild bird

description: DNA methylation could shape phenotypic responses to environmental cues and
 underlie developmental plasticity. Environmentally induced changes in DNA
 methylation during development can give rise to stable phenotypic traits
 and thus affect fitness. In the laboratory, it has been shown that the
 vertebrate methylome undergoes dynamic reprogramming during development,
 creating a critical window for environmentally induced epigenetic
 modifications. Studies of DNA methylation in the wild are lacking, yet are
 essential for understanding how genes and the environment interact to
 affect phenotypic development and ultimately fitness. Furthermore, our
 knowledge of the establishment of methylation patterns during development
 in birds is limited. We quantified genome-wide DNA methylation at various
 stages of embryonic and postnatal development in an altricial passerine
 bird, the great tit Parus major. While there was no change in global DNA
 methylation in embryonic tissue during the second half of embryonic
 development, a two-fold increase in DNA methylation in blood occurred
 between 6 and 15 d posthatch. Though not directly comparable, DNA
 methylation levels were higher in the blood of nestlings compared with
 embryonic tissue at any stage of prenatal development. This provides the
 first evidence that DNA methylation undergoes global change during
 development in a wild bird, supporting the hypothesis that methylation
 mediates phenotypic development. Furthermore, the plasticity of DNA
 methylation demonstrated during late postnatal development, in the present
 study, suggests a wide window during which DNA methylation could be
 sensitive to environmental influences. This is particularly important for
 our understanding of the mechanisms by which early-life conditions
 influence later-life performance. While we found no evidence for
 differences in genome-wide methylation in relation to habitat of origin,
 environmental variation is likely to be an important driver of variation
 in methylation at specific loci.
description: Watson_2019_developmental_methylationPlease refer to README file for further information.
DOI: 10.5061/dryad.r1r839d
title: Data from: Adaptive phenotypic divergence in an annual grass differs across biotic contexts

description: Climate is a powerful force shaping adaptation within species, yet
 adaptation to climate occurs against a biotic background: species
 interactions can filter fitness consequences of genetic variation by
 altering phenotypic expression of genotypes. We investigated this process
 using populations of teosinte, a wild annual grass related to maize (Zea
 mays ssp. mexicana), sampling plants from ten sites along an elevational
 gradient as well as rhizosphere biota from three of those sites. We grew
 half-sibling teosinte families in each biota to test whether trait
 divergence among teosinte populations reflects adaptation or drift, and
 whether rhizosphere biota affect expression of diverged traits. We further
 assayed the influence of rhizosphere biota on contemporary additive
 genetic variation. We found that adaptation across environment shaped
 divergence of some traits, particularly flowering time and root biomass.
 We also observed that different rhizosphere biota shifted expressed values
 of these traits within teosinte populations and families and altered
 within-population genetic variance and covariance. In sum, our results
 imply that changes in trait expression and covariance elicited by
 rhizosphere communities could have played a historical role in teosinte
 adaptation to environments and that they are likely to play a role in the
 response to future selection.
description: Data and analysis
 scripts, zip archiveThe zip archive includes
 the original data collected for this paper, as well as supporting analysis
 files. Each script used in the analysis is included here. Scripts include
 line commenting. Software packages are listed in the README, but must be
 downloaded separately to run. The zip archive also includes a README file,
 specifying input and output and purpose of each script. Scripts also
 available via https://github.com/amob/GenoPheno, although github scripts
 could possibly become altered from the manuscript versions in the future.
 Please see Figshare for sequences generated as part of this work
 https://doi.org/10.6084/m9.figshare.4714030.v1. Please see cited sources
 in manuscript for publicly available data that are required to repeat
 analysis, sources are listed in the README.GenoPheno-master.zip
DOI: 10.5061/dryad.2df6h8k
title: Data from: Evolution of a soft-tissue foraging adaptation in African cichlids: roles for novelty, convergence, and constraint

description: Understanding the origins of biodiversity demands consideration of both
 extrinsic (e.g., ecological opportunity) and intrinsic (e.g.,
 developmental constraint) factors. Here we use a combination of
 phylogenetic and genetic tools to address the origin of novelty in African
 cichlids. In particular, we focus on an extreme hypertrophied snout that
 is structurally integrated with the upper jaw. We show that this bizarre
 trait has evolved independently in at least two distinct and ecologically
 successful cichlid clades. We find that snout dimensions are decoupled
 both phenotypically and genetically, which has enabled it to evolve
 independently in multiple directions. Further, patterns of variation among
 species and within a genetic mapping pedigree suggest that relative to
 snout length, depth is under greater genetic and/or developmental
 constraint. Models of evolution suggest that snout shape is under
 selection for feeding behavior, with snout depth being important for algae
 scraping and snout length for sand sifting. Indeed, the deep snout of some
 algivores is achieved via an expansion of the intermaxillary ligament,
 which is important for jaw stability and may increase feeding performance.
 Overall, our data imply that the evolution of exaggerated snout depth
 required overcoming a genetic/developmental constraint, which led to
 expanded ecological opportunity via foraging adaptation.
description: CichlidFemaleMean_20181126Data for comparative analyses, female Ophthalmotilapia nasutaCichlidMaleMean_20181126Data for comparative analyses, male Ophthalmotilapia nasutaLTandLM_conNexus file for comparative analyses, both Lake Malawi and Lake Tanganyika taxaLTandLM_conTree file for comparative analyses, both Lake Malawi and Lake Tanganyika taxaMalawiTangNasutaFemalesOnlyRaw phenotypic data, female Ophthalmotilapia nasutaMalawiTangNasutaMaleOnlyRaw phenotypic data, male Ophthalmotilapia nasutaEctodini_SOURCESource code for comparative analysesEctodiniCompMethsComparative methods codePhylogeneticTreeTree files
DOI: 10.5061/dryad.ct7dg14
title: Data from: Geo-clustered chronic affinity: pathways from socio-economic disadvantages to health disparities

description: Objective: Our objective was to develop and test a new concept (affinity)
 analogous to multimorbidity of chronic conditions for individuals at
 census tract level in Memphis, TN. The use of affinity will improve the
 surveillance of multiple chronic conditions and facilitate the design of
 effective interventions. Methods: We used publicly available chronic
 condition data (Center for Disease Control and Prevention (CDC) 500 Cities
 project), socio-demographic data (U.S. Census Bureau) and demographics
 data (Environmental Systems Research Institute; ESRI). We examined the
 geographic pattern of the affinity of chronic conditions using global
 Moran’s I and Getis-Ord Gi statistics and its association with
 socio-economic disadvantage (poverty, unemployment, and crime) using
 robust regression models. We also used the most common behavioral factor,
 smoking, and other demographic factors (percent of the male population,
 percent of the population 67 years and over and total population size) as
 control variables in the model. Results: A geo-distinctive pattern of
 clustered chronic affinity associated with socio-economic deprivation was
 observed. Statistical results confirmed that neighborhoods with higher
 rates of crime, poverty, and unemployment were associated with an
 increased likelihood of having a higher affinity among major chronic
 conditions. With the inclusion of smoking in the model, however, only the
 crime prevalence was statistically significantly associated with the
 chronic affinity. Conclusion: Chronic affinity disadvantages were
 disproportionately accumulated in socially disadvantaged areas. We showed
 links between commonly co-observed chronic diseases at the population
 level and systematically explored the complexity of affinity and
 socio-economic disparities. Our affinity score, based on publicly
 available datasets, served as a surrogate for multimorbidity at the
 population level, which may assist policymakers and public health planners
 to identify urgent hot spots for chronic disease and allocate clinical,
 medical and healthcare resources efficiently.
description: Affinity
 DATA
DOI: 10.5061/dryad.4pf04c0
title: Data from: Winter corticosterone and body condition predict subsequent breeding investment in nonmigratory bird

description: Reproduction is an energetically-demanding life history stage that
 requires costly physiological and behavioral changes, yet some individuals
 will invest more into reproduction and breed more successfully than
 others. To understand variation in reproductive investment, previous
 studies have evaluated factors during breeding, but conditions outside of
 this life history stage may also play a role. Using a free-ranging
 population of black-capped chickadees (Poecile atricapillus), we assessed
 the repeatability of plastic traits relating to energetic condition
 (circulating initial corticosterone concentrations and body condition)
 during the non-breeding season and evaluated whether these traits
 predicted reproductive investment in the subsequent breeding season. We
 found that initial corticosterone concentrations and an index of body
 condition, but not fat score, were moderately repeatable over a one-week
 period in winter. This trait repeatability supports the interpretation
 that among-individual variation in these phenotypic traits could reflect
 an intrinsic strategy to cope with challenging conditions across life
 history stages. We found that females with larger fat reserves during
 winter laid eggs sooner and tended to spend more time incubating their
 eggs and feeding their offspring. In contrast, we found that females with
 higher residual body mass delayed breeding, after controlling for the
 relationship between fat score and timing of breeding. Additionally,
 females with higher initial corticosterone in winter laid lighter eggs.
 Our findings suggest that conditions experienced outside of the breeding
 season may be important factors explaining variation in reproductive
 investment.
description: Rchickadees_RepeatabilityData associated with the trait repeatability portion of our study. We evaluated the degree to which among-individual variation in corticosterone, scaled mass index, and fat score is attributable to individual identity or, conversely, due to environmental plasticity by using estimates of agreement repeatability. In all repeatability calculations, we only included data from individuals caught twice during the winter (2nd measurements were done at least 6 days after first measurements).Rchickadees_Cross_SeasonsData associated with the cross-seasonal portion of our study. We evaluated whether initial corticosterone and estimates of body condition (i.e., scaled mass index and fat score) measured during winter predicted reproductive investment in the subsequent breeding season. Some birds were sampled twice during winter, but we only used the first measurement of winter CORT, fat, and scaled mass index to investigate these cross-seasonal relationships. The data file also contains a README tab containing variable definitions.
DOI: 10.5061/dryad.rd435pq
title: Data from: Cross-scale dynamics in community and disease ecology: relative timescales shape the community ecology of pathogens

description: Communities of free-living organisms are shaped by processes operating
 within and among patches of habitat, while pathogen communities are shaped
 by analogous processes operating within and among hosts. Resource
 competition (R) theory can describe dynamics within patches or hosts,
 while metacommunity dynamics describe competition-colonization tradeoffs,
 extinction debts, and superinfection. However, models at this broader
 scale often assume instantaneous competitive exclusion in co-inhabited
 patches or coinfected hosts. Impacts of more gradual competitive exclusion
 on the abundance, distribution, and diversity of species are less clear.
 Here, we nest a general resource competition model within a metacommunity
 framework and manipulate the relative timescales for processes operating
 within and among patches/hosts. We focus on superinfection in pathogen
 communities. We compare cases where transmission depends on infection
 prevalence versus the abundance of pathogens within hosts. Surprisingly,
 slowing the relative pace of competitive exclusion within hosts can
 decrease infection prevalence of the inferior competitor and increase
 prevalence of the superior competitor, depending on transmission and
 virulence. Slower dynamics reduce the abundance of both pathogens within
 hosts and promote diversity at multiple scales: coinfections within
 individual hosts and co-occurrence in the host population. These results
 highlight surprising feedbacks that can emerge across scales and reinforce
 the rich cross-scale connections between community and disease ecology.
description: Simulation of the
 hierarchical model with frequency-dependent
 transmission.Simulation of the
 hierarchical model with frequency-dependent
 transmission.sim.eg.tr.freq.RSimulation of the hierarchical model with transmission that depends on the abundance of pathogens within hosts.Simulation of the hierarchical model with transmission that depends on the abundance of pathogens within hosts.sim.eg.tr.abun.R