cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.bp2tg
title: Data from: Evolutionary changes in plant tolerance against herbivory through a resurrection experiment

description: Both theoretical and empirical works have highlighted the difference in
 the evolutionary implications of host resistance and tolerance against
 their enemies. However, it has been difficult to show evolutionary changes
 in host defences in natural populations; thus, evaluating theoretical
 predictions of simultaneous evolution of defences remains a challenge. We
 studied the evolutionary changes in traits related to resistance and
 tolerance against herbivory in a natural plant population using seeds from
 two collections made in a period of 20 years. In a common garden
 experiment, we compared defensive traits of ancestral (1987) and
 descendant (2007) subpopulations of the annual plant Datura stramonium
 that shows genetic variation for tolerance and to which the specialist
 herbivore Lema daturaphila is locally adapted. We also examined the
 effects of different plant genotypes on the herbivore for testing the
 plant genetic variation in resistance. Based on the response to the
 contemporary herbivore populations, results revealed a nonsignificant
 response in plant resistance traits (herbivore consumption, foliar
 trichomes and tropane alkaloids), but a significant one in tolerance. The
 survival of herbivores in laboratory experiments depended on the plant
 genotype, which suggests genetic variation in plant resistance. Although
 we cannot identify the selective agent for the change nor exclude genetic
 drift, the results are consistent with the expectation that when
 resistance fails to control herbivory, tolerance should play a more
 important role in the evolution of the interaction.
description: JEB
 Dryad
DOI: 10.5061/dryad.kh6jg77
title: Data from: Thermal evolution offsets the elevated toxicity of a contaminant under warming: a resurrection study in Daphnia magna

description: Synergistic interactions between temperature and contaminants are a major
 challenge for ecological risk assessment, especially under global warming.
 While thermal evolution may increase the ability to deal with warming, it
 is unknown whether it may also affect the ability to deal with the many
 contaminants that are more toxic at higher temperatures. We investigated
 how evolution of genetic adaptation to warming affected the interactions
 between warming and a novel stressor: zinc oxide nanoparticles (nZnO) in a
 natural population of Daphnia magna using resurrection ecology. We hatched
 resting eggs from two D. magna subpopulations (old: 1955-1965, recent:
 1995-2005) from the sediment of a lake that experienced an increase in
 average temperature and in recurrence of heat waves but was never exposed
 to industrial waste. In the old ‘ancestral’ subpopulation, exposure to a
 sublethal concentration of nZnO decreased the intrinsic growth rate,
 metabolic activity and energy reserves at 24°C but not at 20°C, indicating
 a synergism between warming and nZnO. In contrast, these synergistic
 effects disappeared in the recent ‘derived’ subpopulation that evolved a
 lower sensitivity to nZnO at 24°C, which indicates that thermal evolution
 could offset the elevated toxicity of nZnO under warming. This evolution
 of reduced sensitivity to nZnO under warming could not be explained by
 changes in the total internal zinc accumulation but was partially
 associated with the evolution of the expression of a key metal
 detoxification gene under warming. Our results suggest that the increased
 sensitivity to the sublethal concentration of nZnO under the predicted 4°C
 warming by the end of this century may be counteracted by thermal
 evolution in this D. magna population. Our results illustrate the
 importance of evolution to warming in shaping the responses to another
 anthropogenic stressor, here a contaminant. More general, genetic
 adaptation to an environmental stressor may ensure that synergistic
 effects between contaminants and this environmental stressor will not be
 present anymore.
description: Life history and
 physiology of old and recent sub-populations of Fellbrigg
 clonesThis data file described
 the functional reaction of the Daphnia magna clones in response to nano
 zinc oxide and warming. It includes life history, body energy reserve
 molecules and MT genes expression data.FOFR-all
 data.xlsx
DOI: 10.5061/dryad.7gs24
title: Data from: Temporal variation favors the evolution of generalists in experimental populations of Drosophila melanogaster

description: In variable environments, selection should favor generalists that maintain
 fitness across a range of conditions. However, costs of adaptation may
 generate fitness trade-offs and lead to some compromise between
 specialization and generalization that maximizes fitness. Here, we
 evaluate the evolution of specialization and generalization in 20
 populations of Drosophila melanogaster experimentally evolved in constant
 and variable thermal environments for 3 years. We developed genotypes from
 each population at two temperatures after which we measured fecundity
 across eight temperatures. We predicted that constant environments would
 select for thermal specialists and that variable environments would select
 for thermal generalists. Contrary to our predictions, specialists and
 generalists did not evolve in constant and spatially variable
 environments, respectively. However, temporal variation produced a type of
 generalist that has rarely been considered by theoretical models of
 developmental plasticity. Specifically, genotypes from the temporally
 variable selective environment were more fecund across all temperatures
 than were genotypes from other environments. These patterns suggest
 certain allelic effects and should inspire new directions for modeling
 adaptation to fluctuating environments.
description: Fecundity
 datadevelopment, selective
 environment, population, isofemale line, centroid size, fecundity at 14C,
 16C, 20.5C, 25C, 28C, 320C, 32C, 36C.Fecunditydata.csv
DOI: 10.5061/dryad.26p87
title: Data from: Learned parasite avoidance is driven by host personality and resistance to infection in a fish–trematode interaction

description: Cognitive abilities related to the assessment of risk improve survival.
 While earlier studies have examined the ability of animals to learn to
 avoid predators, learned parasite avoidance has received little interest.
 In a series of behavioural trials with the trematode parasite Diplostomum
 pseudospathaceum, we asked whether sea trout (Salmo trutta trutta) hosts
 show associative learning in the context of parasitism and if so, whether
 learning capacity is related to the likelihood of infection mediated
 through host personality and resistance. We show that animals are capable
 of learning to avoid visual cues associated with the presence of
 parasites. However, avoidance behaviour ceased after the likely activation
 of host resistance following consecutive exposures during learning,
 suggesting that resistance to infection outweighs avoidance. Further, we
 found a positive relationship between learning ability and boldness,
 suggesting a compensation of risky lifestyles through increased investment
 in cognitive abilities. By contrast, an increased risk of infection due to
 low resistance was not balanced by learning ability. Instead, these traits
 were positively related, which may be explained by inherent physiological
 qualities controlling both traits. Overall, the results demonstrate that
 parasitism, in addition to other biological interactions such as
 predation, is an important selective factor in the evolution of animal
 cognition.
description: dataset for Klemme &
 Karvonen 2016Complete dataset for
 study by Klemme & Karvonen, including fish morphometric data, results
 from repeated personality tests and from repeated avoidance learning tests
 as well as parasite numbers acquired before the behavioural tests, during
 the behavioural tests and during a resistance test.data_Klemme&Karvonen.xlsx
DOI: 10.5061/dryad.s8fn4
title: Data from: Baby fish working out: an epigenetic source of adaptive variation in the cichlid jaw

description: Understanding the developmental processes that underlie the production of
 adaptive variation (i.e. the ‘arrival of the fittest’) is a major goal of
 evolutionary biology. While most evo-devo studies focus on the genetic
 underpinnings of adaptive phenotypic variation, factors beyond changes in
 nucleotide sequence can also play a major role in shaping developmental
 outcomes. Here, we document a vigorous but enigmatic gaping behaviour
 during the early development of Lake Malawi cichlid larvae. The onset of
 the behaviour precedes the formation of bone, and we predicted that it
 might influence craniofacial shape by affecting the mechanical environment
 in which bone develops. Consistent with this, we found that both natural
 variation and experimental manipulation of this behaviour induced
 differential skeletal development that foreshadows adaptive variation in
 adult trophic morphology. In fact, the magnitude of difference in skeletal
 morphology induced by these simple shifts in behaviour was similar to
 those predicted to be caused by genetic factors. Finally, we demonstrate
 that this mechanical-load-induced shift in skeletal development is
 associated with differences in ptch1 expression, a gene previously
 implicated in mediating between-species differences in skeletal shape. Our
 results underscore the complexity of development, and the importance of
 epigenetic (sensu Waddington) mechanisms in determining adaptive
 phenotypic variation.
description: cichlid gaping
 dataThis excel file contains
 data associated with the paper titled "Baby fish working out: An
 epigenetic source of adaptive variation in the cichlid jaw". The
 first tab contains cichlid larvae gaping frequency (times/minute) during
 early developmental stages (6 days to 10 days post fertilization) in three
 Lake Malawi cichlid species (LF, MZ and TT). The second tab contains
 results of the gaping manipulation experiment in MZ. The third tab
 contains results of the interopercle-mandibular ligament surgery in
 LF.
DOI: 10.5061/dryad.6ps78
title: Data from: Evolutionary divergence in life history traits among populations of the Lake Malawi cichlid fish Astatotilapia calliptera

description: During the early stages of adaptive radiation, populations diverge in life
 history traits such as egg size and growth rates, in addition to
 eco-morphological and behavioral characteristics. However, there are few
 studies of life history divergence within ongoing adaptive radiations.
 Here, we studied Astatotilapia calliptera, a maternal mouthbrooding
 cichlid fish within the Lake Malawi haplochromine radiation. This species
 occupies a rich diversity of habitats, including the main body of Lake
 Malawi, as well as peripheral rivers and shallow lakes. We used common
 garden experiments to test for life history divergence among populations,
 focussing on clutch size, duration of incubation, egg mass, offspring
 size, and growth rates. In a first experiment, we found significant
 differences among populations in average clutch size and egg mass, and
 larger clutches were associated with smaller eggs. In a second experiment,
 we found significant differences among populations in brood size, duration
 of incubation, juvenile length when released, and growth rates. Larger
 broods were associated with smaller juveniles when released and shorter
 incubation times. Although juvenile growth rates differed between
 populations, these were not strongly related to initial size on release.
 Overall, differences in life history characters among populations were not
 predicted by major habitat classifications (Lake Malawi or peripheral
 habitats) or population genetic divergence (microsatellite-based FST). We
 suggest that the observed patterns are consistent with local selective
 forces driving the observed patterns of trait divergence. The results
 provide strong evidence of evolutionary divergence and covariance of life
 history traits among populations within a radiating cichlid species,
 highlighting opportunities for further work to identify the processes
 driving the observed divergence.
description: Environmental
 DataEnvironmental data
 relating to source locations of experimental
 populations.EnvironmentalData.txtExperiment 2 DataExperiment 2 Data: Female size and brood dataExperiment2Data.txtExperiment 1 DataExperiment 1 Data: Female size and egg dataExperiment1Data.txtMicrosatellite DataMicrosatellite Data: Genepop formatMicrosatelliteData_Genepop.txt
DOI: 10.5061/dryad.300gs
title: Data from: Contrasting effects of ammonium and nitrate additions on the biomass of soil microbial communities and enzyme activities in subtropical China

description: The nitrate to ammonium ratios in nitrogen (N) compounds in wet
 atmospheric deposits have increased over the recent past, which is a cause
 for some concern as the individual effects of nitrate and ammonium
 deposition on the biomass of different soil microbial communities and
 enzyme activities are still poorly defined. We established a field
 experiment and applied ammonium (NH4Cl) and nitrate (NaNO3) at monthly
 intervals over a period of 4 years. We collected soil samples from the
 ammonium and nitrate treatments and control plots in three different
 seasons, namely spring, summer, and fall, to evaluate the how the biomass
 of different soil microbial communities and enzyme activities responded to
 the ammonium (NH4Cl) and nitrate (NaNO3) applications. Our results showed
 that the total contents of phospholipid fatty acids (PLFAs) decreased by
 24 and 11 % in the ammonium and nitrate treatments, respectively. The
 inhibitory effects of ammonium on Gram-positive bacteria (G+) and
 bacteria, fungi, actinomycetes, and arbuscular mycorrhizal fungi (AMF)
 PLFA contents ranged from 14 to 40 % across the three seasons. We also
 observed that the absolute activities of C, N, and P hydrolyses and
 oxidases were inhibited by ammonium and nitrate, but that nitrate had
 stronger inhibitory effects on the activities of acid phosphatase (AP)
 than ammonium. The activities of N-acquisition specific enzymes (enzyme
 activities normalized by total PLFA contents) were about 21 and 43 % lower
 in the ammonium and nitrate treatments than in the control, respectively.
 However, the activities of P-acquisition specific enzymes were about 19 %
 higher in the ammonium treatment than in the control. Using redundancy
 analysis (RDA), we found that the measured C, N, and P hydrolysis and
 polyphenol oxidase (PPO) activities were positively correlated with the
 soil pH and ammonium contents, but were negatively correlated with the
 nitrate contents. The PLFA biomarker contents were positively correlated
 with soil pH, soil organic carbon (SOC), and total N contents, but were
 negatively correlated with the ammonium contents. The soil enzyme
 activities varied seasonally, and were highest in March and lowest in
 October. In contrast, the contents of the microbial PLFA biomarkers were
 higher in October than in March and June. Ammonium may inhibit the
 contents of PLFA biomarkers more strongly than nitrate because of
 acidification. This study has provided useful information about the
 effects of ammonium and nitrate on soil microbial communities and enzyme
 activities.
description: Biomass of soil
 microbial communities and enzyme activities in subtropical
 ChinaIncluding three times
 data for three treatment (CK, ammonium addition, nitrate addtion) in
 subtropical forest soils. Data including carbon, nitrogen and phosphorus
 hydrolase and oxidase, soil PLFAs and nutrient contentsBiogeoscience- original
 data.xlsx
DOI: 10.5061/dryad.sb560
title: Data from: Conflict between morphological and molecular data: a case study of Ficus krishnae (Moraceae)

description: Ficus krishnae, considered as highly sacred plant species in India, is
 well known for its peculiar nature of cup-shaped leaves. The species
 distinctly differs from its allied species F. benghalensis not only in the
 cup formation in leaves but also in the height of plants, aerial roots,
 stipules, petiole and its leafy appendages, ostiolar bracts of the
 receptacle and pollinator wasps, in addition to slight differences in the
 karyotype, DNA contents, stomatal and parenchymatous cells and nodal
 anatomy. In spite of having several morphological differences, F. krishnae
 is considered by some authors as a synonym of F. benghalensis, which does
 not seem to be convincing. Contrary to the morphological differences, the
 sequence analysis of nuclear and plastid regions of both the species
 conducted in the present study does not reveal any significant variations
 and thus infers no differentiation between the species at molecular level.
 This may be due to mutations at one or few coding loci or differences in
 gene expression associated with morphogenesis with significant phenotypic
 appearance.
description: Supplementary figure
 1Multiple alignment of
 ITS region of two accessions of Ficus krishnae (FK) and F. benghalensis
 (FB)ITS
 (1).alnSupplementary figure
 2aMultiple alignment of
 atpB region of two accessions of Ficus krishnae (FK) and F. benghalensis
 (FB).atpB(2a)
 .alnSupplementary figure
 2bMultiple alignment of
 rps16 region of two accessions of Ficus krishnae (FK) and F. benghalensis
 (FB).RPS16(2b)
 .alnSupplementary figure
 2cMultiple alignment of
 trnL-F region of two accessions of Ficus krishnae (FK) and F. benghalensis
 (FB).trnL-F
 (2c).alnSupplementary figure
 2dMultiple alignment of
 psbM-trnD region of two accessions of Ficus krishnae (FK) and F.
 benghalensis (FB).psbM-trnD(2d).aln
DOI: 10.5061/dryad.5m30d
title: Data from: Phylogenetic diversity is maintained despite richness losses over time in restored tallgrass prairie plant communities

description: Ecosystem restoration is an important tool for mitigating biodiversity
 loss and recovering critical ecosystem services to humanity, but
 restoration rarely takes into account the evolutionary attributes of the
 community being restored. Phylogenetic diversity (PD) represents a
 potentially valuable measure of restoration success because it can
 correlate with functional trait diversity that drives ecosystem function.
 However, PD patterns in restored communities are rarely assessed. We
 surveyed plant communities in restored tallgrass prairies 2–19 years old
 and calculated two PD measures, SESMNTD and SESMPD, of the communities and
 seed mixture applied to sites. We also identified high-threat exotic
 species present in each site to determine whether PD of the seed mixture
 applied was related to resistance against invasion. We show that PD in
 North American tallgrass prairie restorations, as measured by both SESMNTD
 and SESMPD, is maintained over time even as richness declines. Neither the
 resulting community PD nor invasion by high-threat exotic species was
 affected by PD of the seed mixture used in site restoration. Thus, simply
 maximizing PD of seed mixtures without considering the particular
 component species is unlikely to help achieve restoration goals. Synthesis
 and applications. These results suggest that species losses over time are
 not biased towards species with or without close relatives in the
 community. If phylogenetic diversity (PD) reflects functional trait
 diversity in communities, then local declines in species richness may not
 necessarily mean the loss of ecosystem function in restoration projects.
 However, PD of restored communities may be limited by low establishment
 rates for most species. Conservation practitioners should consider PD with
 careful planning to maintain overall community diversity and potentially
 maximize ecosystem function and services in restorations. This perspective
 will require a deeper understanding of the relationships between
 phylogenetic relatedness and traits associated with competition and
 fitness.
description: Nachusa_site_characteristicsCharacteristics of each site in the study, including age, species richness, MPD and MNTD of plant community and seed mixture applied, summer precipitation in the first year of growth, and number of high-priority exotic plant species present.Nachusa_plant_communitiesPresence/absence of plant species in each survey site.Nachusa_seed_mixesSpecies included in seed mixes applied to 16 of 19 surveyed restoration sites.
DOI: 10.15468/dl.dstr6z
title: Occurrence Download

description: A dataset containing 4699 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Specimen)",
 "TaxonKey is Acacia confusa"
 ]
}

 The dataset includes 4699 records from 123 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001257-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.arfb2j
title: Occurrence Download

description: A dataset containing 333 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cyathodes glauca",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 333 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001258-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.k785p43
title: Data from: Hot temperatures during the dry season reduce survival of a resident tropical bird

description: Understanding how climate change will shape species distributions in the
 future requires a functional understanding of the demographic responses of
 animals to their environment. For birds, most of our knowledge of how
 climate influences population vital rates stems from research in temperate
 environments, even though most of the Earth’s avian diversity is
 concentrated in the tropics. We evaluated effects of Southern Oscillation
 Index (SOI) and local temperature and rainfall at multiple temporal scales
 on sex-specific survival of a resident tropical bird, the Rufous-and-White
 Wren Thryophilus rufalbus, studied over 15 years in the dry forests of
 northwestern Costa Rica. We found that annual apparent survival of males
 was 8% higher than females, more variable over time, and responded more
 strongly to environmental variation than female survival, which did not
 vary strongly with SOI or local weather. For males, mean and maximum local
 temperatures were better predictors of survival than either rainfall or
 SOI, with high temperatures during the dry season and early wet season
 negatively influencing survival. These results suggest that, even for
 species adapted to hot environments, further temperature increases may
 threaten the persistence of local populations in the absence of
 distributional shifts.
description: Mark-recapture/re-sighting data and model codeThis file contains: (1) mark-recapture/re-sighting data summarized in m-array format for Rufous-and-white Wrens (Thryophilus rufalbus) from Sector Santa Rosa of the Area de Conservación Guanacaste in northwestern, Costa Rica (10°52’N, 85°36’W) collected from 2003-2017; (2) a description of the climate and weather covariates included in survival analyses; and (3) R and JAGS code for estimating effects of climate and weather on sex-specific survival of Rufous-and-white Wrens.Woodworth_et_al_CMR_DATA_AND_MODEL_CODE.txtClimate and weather dataThe contents and structure of this file are described in Woodworth_et_al_CMR_DATA_AND_MODEL_CODE.txtWoodworth_et_al_CLIMATE_AND_WEATHER_DATA.csv