cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.h32p6
title: Data from: Spartina alterniflora genotypic identity affects plant and consumer responses in an experimental marsh community

description: 1. Competition and herbivory are ubiquitous processes known to
 interactively shape plant performance, distribution and community
 assembly. Likewise, plant genetic variation and associated trait
 differences can impact both plant-plant and plant-herbivore interactions
 individually, yet few studies have explored these interactions
 simultaneously. 2. Salt marsh communities are an ideal system to study
 these questions, as they are dominated along the Atlantic and Gulf coasts
 of the United States by a foundation plant species, Spartina alterniflora,
 with high levels of genetically-based trait variation. Furthermore,
 consumer pressure and plant competitors are known to influence both the
 distribution and production of Spartina. We manipulated Spartina genetic
 identity, neighbor identity (needlerush, Juncus roemerianus), and consumer
 presence (snail, Littoraria irrorata) in a one-year field experiment in
 St. Joseph Bay, FL to test how the strength and direction of neighbor and
 consumer interactions vary by plant genotype. 3. Consumer effects on
 Spartina were generally stronger and more variable than those of the plant
 neighborhood, and these effects were generally consistent across Spartina
 genotypes. However, genotype-specific variation in morphology, phenology,
 and palatability significantly influenced both consumer and neighbor
 responses to Spartina: the consumer Littoraria was more likely to climb
 palatable Spartina genotypes, and neighboring Juncus had shorter stems in
 the presence of highly productive Spartina genotypes. 4. Synthesis. Our
 results add to the growing list of examples highlighting the role of
 intraspecific variation in species interactions, and suggest that
 variation in these interactions may promote the maintenance of plant
 genetic variation and community composition.
description: Zerebeckietal_1-5Zerebeckietal_1-5.zip contains 5 consecutively numbered csv files which contain the data presented in the manuscript and appendices.
DOI: 10.5061/dryad.7h554
title: Data from: Geographic variation and trade-offs in parasitoid virulence

description: Host–parasitoid systems are characterized by a continuous development of
 new defence strategies in hosts and counter-defence mechanisms in
 parasitoids. This co-evolutionary arms race makes host–parasitoid systems
 excellent for understanding trade-offs in host use caused by evolutionary
 changes in host immune responses and parasitoid virulence. However,
 knowledge obtained from natural host–parasitoid systems on such trade-offs
 is still limited. In this study, the aim was to examine trade-offs in
 parasitoid virulence in Asecodes parviclava (Hymenoptera: Eulophidae) when
 attacking three closely related beetles: Galerucella pusilla, Galerucella
 calmariensis and Galerucella tenella (Coleoptera: Chrysomelidae). A second
 aim was to examine whether geographic variation in parasitoid infectivity
 or host immune response could explain differences in parasitism rate
 between northern and southern sites. More specifically, we wanted to
 examine whether the capacity to infect host larvae differed depending on
 the previous host species of the parasitoids and if such differences were
 connected to differences in the induction of host immune systems. This was
 achieved by combining controlled parasitism experiments with cytological
 studies of infected larvae. Our results reveal that parasitism success in
 A. parviclava differs both depending on previous and current host species,
 with a higher virulence when attacking larvae of the same species as the
 previous host. Virulence was in general high for parasitoids from G.
 pusilla and low for parasitoids from G. calmariensis. At the same time, G.
 pusilla larvae had the strongest immune response and G. calmariensis the
 weakest. These observations were linked to changes in the larval hemocyte
 composition, showing changes in cell types important for the encapsulation
 process in individuals infected by more or less virulent parasitoids.
 These findings suggest ongoing evolution in parasitoid virulence and host
 immune response, making the system a strong candidate for further studies
 on host race formation and speciation.
description: Raw data hemocyte
 counts_Fors et alThis file contains raw
 data for hemocyte counts of infected G. pusilla and G. tenella larvae. The
 data from each experimental group (larvae from either northern or southern
 localities infected with parasitoids of different origin) of the two
 species are shown in separate excel sheets named accordingly. The tables
 include image file names, date for the parasitism experiments,
 identification data for each sample, geographic origin of the beetles, the
 raw hemocyte counts subdivided into hemocyte classes and the calculated
 percentages. On average 700 hemocytes from 9 images were counted per
 individual.
DOI: 10.5061/dryad.hj4t4
title: Data from: Fine-scale spatiotemporal patterns of genetic variation reflect budding dispersal coupled with strong natal philopatry in a cooperatively breeding mammal

description: The relatedness structure of animal populations is thought to be a
 critically important factor underlying the evolution of mating systems and
 social behaviours. While previous work has shown that population structure
 is shaped by many biological processes, few studies have investigated how
 these factors vary over time. Consequently, we explored the fine-scale
 spatiotemporal genetic structure of an intensively studied population of
 cooperatively breeding banded mongooses (Mungos mungo) over a ten-year
 period. Overall population structure was strong (average Fst = 0.129) but
 groups with spatially overlapping territories were not more genetically
 similar to one another than non-contiguous groups. Instead, genetic
 differentiation was associated with historical group-fission (budding)
 events, with new groups diverging from their parent groups over time.
 Within groups, relatedness was high within but not between the sexes,
 although the latter increased over time since group formation due to group
 founders being replaced by philopatric young. This trend was not mirrored
 by a decrease in average offspring heterozygosity over time, suggesting
 that close inbreeding may often be avoided, even when immigration into
 established groups is virtually absent and opportunities for extra-group
 matings are rare. Fine-scale spatiotemporal population structure could
 have important implications in social species, where relatedness between
 interacting individuals is a vital component in the evolution of patterns
 of inbreeding avoidance, reproductive skew and kin-selected helping and
 harming.
description: Life-history data and
 genotypes of a population of banded mongooses in Western
 UgandaLife-history data on a
 population of banded mongooses including the sex, group of birth (social
 group) and year of birth for each individual (one individual per row),
 followed by the 14-locus genotype of each individual. Genotypes are given
 in two columns per locus, one representing each allele. Genotype columns
 are labelled with the name of the locus followed by 'a' or
 'b', representing the first and second alleles. Zeros indicate
 cases where genotyping failed.Dryad
 file.xlsx
DOI: 10.5061/dryad.0nr5s
title: Data from: Eutherians experienced elevated evolutionary rates in the immediate aftermath of the Cretaceous–Palaeogene mass extinction

description: The effect of the Cretaceous–Palaeogene (K–Pg) mass extinction on the
 evolution of many groups, including placental mammals, has been hotly
 debated. The fossil record suggests a sudden adaptive radiation of
 placentals immediately after the event, but several recent quantitative
 analyses have reconstructed no significant increase in either clade
 origination rates or rates of character evolution in the Palaeocene. Here
 we use stochastic methods to date a recent phylogenetic analysis of
 Cretaceous and Palaeocene mammals and show that Placentalia likely
 originated in the Late Cretaceous, but that most intraordinal
 diversification occurred during the earliest Palaeocene. This analysis
 reconstructs fewer than 10 placental mammal lineages crossing the K–Pg
 boundary. Moreover, we show that rates of morphological evolution in the 5
 Myr interval immediately after the K–Pg mass extinction are three times
 higher than background rates during the Cretaceous. These results suggest
 that the K–Pg mass extinction had a marked impact on placental mammal
 diversification, supporting the view that an evolutionary radiation
 occurred as placental lineages invaded new ecological niches during the
 Early Palaeocene.
description: PhylogeniesSix sets of phylogenetic trees derived from differing data sets and levels of constraint. Analyses were conducted on all sets of trees.File S1 - Phylogenies.zipDiscrete character-taxon matrixCharacter-taxon matrix used for the reconstruction of character transitions on the tree, and the subsequent calculation of rates.File S7 - Discrete character-taxon matrix.txtR CodeCode used to run the dating and evolutionary rates analyses in R.File S8 - R Code.txt
DOI: 10.15468/dl.y42n9b
title: Occurrence Download

description: A dataset containing 19746 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Hedychium gardnerianum"
 ]
}

 The dataset includes 19746 records from 134 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000762-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.908g4
title: Data from: Genetic isolation between coastal and fishery-impacted, offshore bottlenose dolphin (Tursiops spp.) populations

description: The identification of species and population boundaries is important in
 both evolutionary and conservation biology. In recent years, new
 population genetic and computational methods for estimating population
 parameters and testing hypotheses in a quantitative manner have emerged.
 Using a Bayesian framework and a quantitative model-testing approach, we
 evaluated the species status and genetic connectedness of bottlenose
 dolphin (Tursiops spp.) populations off remote northwestern Australia,
 with a focus on pelagic 'offshore' dolphins subject to
 incidental capture in a trawl fishery. We analysed 71 dolphin samples from
 three sites beyond the 50 m depth contour (the inshore boundary of the
 fishery) and up to 170 km offshore, including incidentally caught and
 free-ranging individuals associating with trawl vessels, and 273 dolphins
 sampled at 12 coastal sites inshore of the 50 m depth contour and within
 10 km of the coast. Results from 19 nuclear microsatellite markers showed
 significant population structure between dolphins from within the fishery
 and coastal sites, but also among dolphins from coastal sites, identifying
 three coastal populations. Moreover, we found no current or historic gene
 flow into the offshore population in the region of the fishery, indicating
 a complete lack of recruitment from coastal sites. Mitochondrial DNA
 corroborated our findings of genetic isolation between dolphins from the
 offshore population and coastal sites. Most offshore individuals formed a
 monophyletic clade with common bottlenose dolphins (T. truncatus), while
 all 273 individuals sampled coastally formed a well-supported clade of
 Indo-Pacific bottlenose dolphins (T. aduncus). By including a quantitative
 modelling approach, our study explicitly took evolutionary processes into
 account for informing the conservation and management of protected
 species. As such, it may serve as a template for other, similarly
 inaccessible study populations.
description: Allen_et_al_IBDIBD analysis using microsatellite data and geographic distancesAllen_et_al_Microsat_DataMicrosatellite data (recoded). For original scores please contact Michael Krützen (michael.kruetzen@aim.uzh.ch)Allen_et_al_infile_migrate-n_analysisInput_file_migrate_analysisAllen_et_al_mtDNA_treeNexus mtDNA input file. Identical haplotypes are collapsed.
DOI: 10.5061/dryad.8fp2v06
title: Data from: Expression of and choice for condition-dependent carotenoid-based color in an urbanizing context

description: Urban environments create a unique suite of conditions, leading to changes
 in animal behavior, morphology, phenology or physiology.
 Condition-dependent traits such as the carotenoid-based coloration offer a
 unique opportunity to assess the impacts of urbanization on organisms
 because they reflect the nutrition, health or other resource-based
 attributes of their bearers and they play an essential role in intra- and
 inter-sex interactions. To determine if and how the carotenoid-based
 coloration of male house finches (Haemorhous mexicanus) varies along a
 gradient of urbanization, we quantified the plumage coloration of more
 than 1200 individuals in urban, suburban, rural and desert habitats over
 the course of 17 months. We also examined for the first time the
 preference of females for male plumage coloration across the urban-rural
 gradient, to test if and how female preferences varied relative to the
 range of plumage coloration displayed by males in their local population.
 We found that carotenoid-based coloration decreased along the gradient of
 urbanization, suggesting that the enzyme-driven metabolic conversion of
 dietary carotenoids into red carotenoids used to color plumage is
 sensitive to urban stressors. The stronger negative effect of urbanization
 on carotenoid-based plumage colouration during breeding than during molt
 and winter suggests that urbanization affects colour fading rate, maybe
 through modifications of feather-degrading bacterial load. Finally, we
 have shown that urbanization influences female mate choice behavior,
 suggesting that female color preferences may track the variation in male
 coloration across the gradient of urbanization.
description: Giraudeau et al. 2018
 Behavioral Ecology Field DataIncludes data on
 carotenoid-based plumage hue for three separate regions (crown, breast,
 rump), body mass, site of capture, and urbanization indices for each
 individual bird.Giraudeau et al. 2018
 Behavioral Ecology Data.csvGiraudeau et al. 2018
 Behavioral Ecology Mate Choice DataData file includes, for
 each female, the capture site, observation and experiment number,
 observation date, and time near each male and the respective male's
 identity and plumage hue.Mate_Choice_Exps.csv
DOI: 10.5061/dryad.5d2d7
title: Data from: Multilocus analysis of nucleotide variation and speciation in three closely related Populus (Salicaceae) species

description: Historical tectonism and climate oscillations can isolate and contract the
 geographical distributions of many plant species, and they are even known
 to trigger species divergence and ultimately speciation. Here, we
 estimated the nucleotide variation and speciation in three closely related
 Populus species, Populus tremuloides, P. tremula and P. davidiana,
 distributed in North America and Eurasia. We analysed the sequence
 variation in six single-copy nuclear loci and three chloroplast (cpDNA)
 fragments in 497 individuals sampled from 33 populations of these three
 species across their geographic distributions. These three Populus species
 harboured relatively high levels of nucleotide diversity and showed high
 levels of nucleotide differentiation. Phylogenetic analysis revealed that
 P. tremuloides diverged earlier than the other two species. The cpDNA
 haplotype network result clearly illustrated the dispersal route from
 North America to eastern Asia and then into Europe. Molecular dating
 results confirmed that the divergence of these three species coincided
 with the sundering of the Bering land bridge in the late Miocene and a
 rapid uplift of the Qinghai-Tibetan Plateau around the Miocene/Pliocene
 boundary. Vicariance-driven successful allopatric speciation resulting
 from historical tectonism and climate oscillations most likely played
 roles in the formation of the disjunct distributions and divergence of
 these three Populus species.
description: locithe aligned sequences
 for all individuals and locitreefilethe input and resulting tree files underlying the phylogeniesinput files used for analysesinput files for Arlequin, BEAST, DNAsp, MLHKA and NETWORK analysis in the manuscriptinput_files_used_for_analyses.rarthe code and GPS coordinates for all of the sampled individualsthe code and GPS coordinate for all the sampled individualsGPS coordinates for all of the sampled individuals.xlsx
DOI: 10.15468/dl.xkhgcs
title: Occurrence Download

description: A dataset containing 781 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is one of (North America, South America)",
 "TaxonKey is Sprekelia formosissima"
 ]
}

 The dataset includes 781 records from 85 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000763-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.jr107
title: Data from: Long-term effective population size dynamics of an intensively monitored vertebrate population

description: Long-term genetic data from intensively monitored natural populations are
 important for understanding how effective population sizes (Ne) can vary
 over time. We therefore genotyped 1622 common buzzard (Buteo buteo) chicks
 sampled over 12 consecutive years (2002–2013 inclusive) at 15
 microsatellite loci. This data set allowed us to both compare
 single-sample with temporal approaches and explore temporal patterns in
 the effective number of parents that produced each cohort in relation to
 the observed population dynamics. We found reasonable consistency between
 linkage disequilibrium-based single-sample and temporal estimators,
 particularly during the latter half of the study, but no clear
 relationship between annual Ne estimates (hdy201667e1gif(239)1917) and
 census sizes. We also documented a 14-fold increase in
 hdy201667e2gif(239)1917 between 2008 and 2011, a period during which the
 census size doubled, probably reflecting a combination of higher adult
 survival and immigration from further afield. Our study thus reveals
 appreciable temporal heterogeneity in the effective population size of a
 natural vertebrate population, confirms the need for long-term studies and
 cautions against drawing conclusions from a single sample.
description: Microsatellite sequences
 Buteo buteoYear of sampling,
 microsatellite sequences and morph of individual of Buteo
 buteoBuzzardSequencesDRYAD.txt
DOI: 10.5061/dryad.7t23j
title: Data from: Larval nutritional stress affects vector life history traits and human malaria transmission

description: Exposure to stress during an insect’s larval development can have
 carry-over effects on many adult life history traits and affect host
 susceptibility to pathogens. Studies on mosquitoes have shown that the
 larval environment impacts on components of vectorial capacity such as
 vector competence and adult survival. We investigated the carry-over
 effects of larval nutritional stress for the first time on a natural
 mosquito vector-malaria parasite association: Anopheles coluzzii exposed
 to field isolates of Plasmodium falciparum. In contrast to previous
 studies, we show that larval nutritional stress may affect human to
 mosquito transmission antagonistically: nutritionally deprived larvae
 showed lower parasite prevalence only on a subset of gametocyte carriers;
 they also had lower fecundity. However, they had greater survival rates
 that were even higher when infected. We combined these opposing effects
 into epidemiological models to show that they depend on mosquito
 densities. Larval nutritional stress induced a decrease in malaria
 transmission at low mosquito density and an increase in transmission at
 high mosquito densities, whereas transmission by mosquitoes from well-fed
 larvae was stable. Our work underscores the importance of including larval
 ecological factors towards understanding host – parasite dynamics, and the
 need to confirm findings from artificial models on natural systems to
 improve disease transmission models and control.
description: Raw data of mosquito
 life history traits measurementsLaboratory data form
 experimental infections of Anopheles coluzzii mosquitoes with Plasmodium
 falciparum malaria parasitesdata diet
 dryad.xlsx
DOI: 10.5061/dryad.gb9534p
title: Data from: Artificial lighting at night alters aquatic-riparian invertebrate food webs

description: Artificial lighting at night (ALAN) is a global phenomenon that can be
 detrimental to organisms at individual and population levels, yet
 potential consequences for communities and ecosystem functions are less
 resolved. Riparian systems may be particularly vulnerable to ALAN. We
 investigated the impacts of ALAN on invertebrate community composition and
 food-web characteristics for linked aquatic-terrestrial ecosystems. We
 focused on food-chain length (FCL) - a central property of ecological
 communities that can influence their structure, function and stability –
 and the contribution of aquatically-derived energy (i.e., nutritional
 subsidies originating from stream periphyton). We collected terrestrial
 arthropods and emergent aquatic insects from a suite of stream and wetland
 sites in Columbus, Ohio, USA. Stable isotopes of carbon (13C) and nitrogen
 (15N) were used to infer FCL and contribution of aquatically-derived
 energy. We found that moderate to high levels of ALAN altered invertebrate
 community composition, favoring primarily predators and detritivores.
 Impacts of ALAN, however, were very taxon specific as illustrated, for
 example, by the negative impact of ALAN on the abundance of orb-web
 spiders belonging to the families Tetragnathidae and Araneidae – key
 invertebrate riparian predators. Most notably, we observed decreases in
 both invertebrate FCL and reliance on aquatically-derived energy under
 ALAN (although aquatic energetic contributions appeared to increase again
 at higher levels of ALAN), in addition to shifts in the timing of
 reciprocal nutritional subsidies. Our study demonstrates that ALAN can
 alter the flows of energy between aquatic and terrestrial systems, thereby
 representing an environmental perturbation that can cross ecosystem
 boundaries. Given projections for global increases in ALAN, both in terms
 of coverage and intensity, these results have broad implications for
 stream ecosystem structure and function.
description: Sullivan_EAP18-0555_WetlandFieldExperiment_2013This dataset contains all response and predictor variables associated with the Wetland Field Experiment from the Sullivan et al. Ecological Applications publication to enable replication of the corresponding statistical analyses and Figs. 1, 3 and S7B,C.Sullivan_EAP18-0555_UrbanStreamCategories_2010This dataset contains all response and predictor variables associated with the Urban Stream Categories field study from the Sullivan et al. Ecological Applications publication to enable replication of the corresponding statistical analyses and Figs. 4, 5, and S4-6.Sullivan_EAP18-0555_UrbanStreamGradient_2010-2011This dataset contains all response and predictor variables associated with the Urban Stream Gradient field study from the Sullivan et al. Ecological Applications publication to enable replication of the corresponding statistical analyses and Figs. 2, S2 and S3.