cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.6cn04
title: Data from: Genomic collinearity and the genetic architecture of floral differences between the homoploid hybrid species I. nelsonii and one of its progenitors, I. hexagona

description: Hybrid speciation represents a relatively rapid form of diversification.
 Early models of homoploid hybrid speciation suggested that reproductive
 isolation between the hybrid species and progenitors primarily resulted
 from karyotypic differences between the species. However, genic
 incompatibilities and ecological divergence may also be responsible for
 isolation. Iris nelsonii is an example of a homoploid hybrid species that
 is likely isolated from its progenitors primarily by strong prezygotic
 isolation, including habitat divergence, floral isolation, and
 post-pollination prezygotic barriers. Here, we used linkage mapping and
 QTL mapping approaches to investigate genomic collinearity and the genetic
 architecture of floral differences between I. nelsonii and one of its
 progenitor species I. hexagona. The linkage map produced from this cross
 is highly collinear with another linkage map produced between I. fulva and
 I. brevicaulis (the two other species shown to have contributed to the
 genomic makeup of I. nelsonii), suggesting that karyotypic differences do
 not contribute substantially to isolation in this homoploid hybrid
 species. Similar to other studies of the genetic architecture of floral
 characteristics, at least one QTL was found that explained &gt;20%
 variance in each color trait, while minor QTLs were detected for each
 morphological trait. These QTLs will serve as hypotheses for regions under
 selection by pollinators.
description: data for
 dryadData file includes
 individual genotypes at the mapped loci in the first tab and individual
 phenotypes for the floral traits in the second tab. Individuals are in the
 same order in each tab.
DOI: 10.15468/dl.4bwxme
title: Occurrence Download

description: A dataset containing 1811 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Piptanthus"
 ]
}

 The dataset includes 1811 records from 76 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000750-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.kc680
title: Data from: Neonicotinoid pesticides and nutritional stress synergistically reduce survival in honey bees

description: The honey bee (Apis mellifera L.) is a major pollinator whose health is of
 global concern. Declines in honey bee health are related to multiple
 factors, including resource quality and pesticide contamination. Intensive
 agricultural areas with crop monocultures potentially reduce the quality
 and quantity of available nutrients and expose bee foragers to pesticides.
 However, there is, to date, no evidence for synergistic effects between
 pesticides and nutritional stress in animals. The neonicotinoids
 clothianidin (CLO) and thiamethoxam (TMX) are common systemic pesticides
 that are used worldwide and found in nectar and pollen. We therefore
 tested if nutritional stress (limited access to nectar, and access to
 nectar with low sugar concentrations) and sublethal, field-realistic acute
 exposures to two neonicotinoids (CLO and TMX at 1/5 and 1/25 of LD50)
 could alter bee survival, food consumption, and hemolymph sugar levels.
 Bee survival was synergistically reduced by the combination of poor
 nutrition and pesticide exposure (-50%). Nutritional and pesticide
 stressors reduced also food consumption (-48%) and hemolymph levels of
 glucose (-60%) and trehalose (-27%). Our results provide the first
 demonstration that field-realistic nutritional stress and pesticide
 exposure can synergistically interact and cause significant harm to animal
 survival. These findings have implications for current pesticide
 risk-assessment procedures and pollinator protection.
description: SurvivalSurvival datasetConsumptionConsumption datasetHemolymphHemolymph dataset
DOI: 10.5061/dryad.70d46
title: Data from: Biodiverse cities: the nursery industry, homeowners, and neighborhood differences drive urban tree composition

description: In arid and semi-arid regions, where few if any trees are native, city
 trees are largely human-planted. Societal factors such as resident
 preferences for tree traits, nursery offerings, and neighborhood
 characteristics are potentially key drivers of urban tree community
 composition and diversity, however they remain critically understudied. We
 investigated patterns of urban tree structure in residential neighborhoods
 of the Salt Lake Valley, Utah, combining biological variables, such as
 neighborhood and plant nursery tree species and trait composition, and
 sociological data comprised of resident surveys and U.S. Census data. We
 sampled nine neighborhoods that varied in household income and age of
 homes. We found more tree species were offered in locally-owned nurseries
 compared with mass merchandiser stores and yard trees at private
 residences were more diverse than public street trees in the same
 neighborhoods. There were significant differences among neighborhoods in
 street and yard tree composition. Newer neighborhoods differed from older
 neighborhoods in street tree species composition and trait diversity,
 while neighborhoods varying in affluence differed in yard tree
 composition. Species richness of yard trees was positively correlated with
 neighborhood household income, while species richness of street trees was
 negatively correlated with home age of neighborhood residences. Tree
 traits differed across neighborhoods of varying ages, suggesting different
 tree availability and preferences over time. Lastly, there was a positive
 correlation between resident preferences for tree attributes and the
 number of trees that had those attributes both in residential yards and in
 nursery offerings. Strong relationships between social variables and urban
 tree composition provides evidence that resident preferences and nursery
 offerings affect patterns of biodiversity in cities across Salt Lake
 Valley. These findings can be applied toward efforts to increase taxonomic
 and functional diversity of city trees in semi-arid regions in ways that
 will also provide ecosystem services of most interest to residents.
description: NeighborhoodSurveySurvey on tree attributes sent to 100 homes in each neighborhood. See Table 3 for more details and appendix S2 for survey questions.YardSurveySurvey given only to homes where we collected tree data. See table 3 for details and appendix S2 for questions.TreeDataTree species data including both street and residential trees and their traits. See tables 2 and 3 for more details.NurseryDataSpecies inventory for visited nurseries. See text for more details.
DOI: 10.5061/dryad.7vg42
title: Data from: Evaluating fish scale preservation in sediment records from the oxygen minimum zone off Peru

description: Fish scales accumulating in marine laminated sediments can provide a
 record of population variability of small pelagic fishes. Although some
 studies have noted signs of scale degradation that could affect estimates
 of population variability, there are presently no well-developed means to
 evaluate degradation. We developed several indices as indicators of fish
 scale preservation in two box-cores that we collected off Pisco (14ºS),
 one at 301 m near the center of the oxygen minimum zone (OMZ), and the
 other at 201 m near the upper limit of the OMZ. These indices include (1)
 an index of fish scale integrity (estimate of scale wholeness relative to
 fragmentation), (2) the fungi-free area of fish scales and vertebrae, (3)
 the ratio of fish scales to vertebrae (as well as fish scales to vertebrae
 and bones), and (4) the ratio of whole scales to fragments. We address
 whether lower numbers of anchovy scales occurring in association with
 reduced total organic carbon fluxes and higher bottom-water oxygen
 concentrations are due entirely to lower abundances of anchovy or whether
 differential preservation of the fish scales in the sediments plays an
 important role in reduced scale abundances. Comparison of temporal
 sequences between the two cores provides the means to assess whether there
 are differences in the preservation of fish scales. The combined indices
 indicate that the lower numbers of fish scales in the earliest period have
 been affected by degradation, and to a greater degree in the box-core from
 201 meters, which can be subject to higher oxygen concentrations. On the
 other hand, decadal-scale variations in fish scale abundance within the
 period of better preservation are unlikely to be caused by degradation. We
 discuss the utility and drawbacks of different indices of preservation for
 reconstructing past changes in fish population sizes with fluxes of fish
 debris and also briefly discuss the utility of these indices to other
 paleobiological systems.
description: Ms 10045 data Salvatteci
 et al
DOI: 10.15468/dl.m3uchn
title: Occurrence Download

description: A dataset containing 46 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Country is Mexico",
 "TaxonKey is Bogertophis subocularis",
 "Year 1960-2026"
 ]
}

 The dataset includes 46 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000751-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.b952b
title: Data from: Queen pheromones modulate DNA methyltransferase activity in bee and ant workers

description: DNA methylation is emerging as an important regulator of polyphenism in
 the social insects. Research has concentrated on differences in
 methylation between queens and workers, though we hypothesized that
 methylation is involved in mediating other flexible phenotypes, including
 pheromone-dependent changes in worker behaviour and physiology. Here, we
 find that exposure to queen pheromone affects the expression of two DNA
 methyltransferase genes in Apis mellifera honeybees and in two species of
 Lasius ants, but not in Bombus terrestris bumblebees. These results
 suggest that queen pheromones influence the worker methylome, pointing to
 a novel proximate mechanism for these key social signals.
description: Holman et al DNMT gene
 expression - DataDryadRaw data for the qPCR
 experiments. See readme file for a list of the columns'
 contents.
DOI: 10.5061/dryad.5k7b5
title: Data from: Limitations of species delimitation based on phylogenetic analyses: a case study in the (Hypogymnia hypotrypa) group (Parmeliaceae, Ascomycota)

description: Delimiting species boundaries among closely related lineages often
 requires a range of independent data sets and analytical approaches.
 Similar to other organismal groups, robust species circumscriptions in
 fungi are increasingly investigated within an empirical framework. Here we
 attempt to delimit species boundaries in a closely related clade of
 lichen-forming fungi endemic to Asia, the Hypogymnia hypotrypa group
 (Parmeliaceae). In the current classification, the Hypogymnia hypotrypa
 group includes two species: H. hypotrypa and H. flavida, which are
 separated based on distinctive reproductive modes, the former producing
 soredia but absent in the latter. We reexamined the relationship between
 these two species using phenotypic characters and molecular sequence data
 (ITS, GPD, and MCM7 sequences) to address species boundaries in this
 group. In addition to morphological investigations, we used Bayesian
 clustering to identify potential genetic groups in the H. hypotrypa/H.
 flavida clade. We also used a variety of empirical, sequence-based species
 delimitation approaches, including: the “Automatic Barcode Gap Discovery”
 (ABGD), the Poisson tree process model (PTP), the General Mixed Yule
 Coalescent (GMYC), and the multispecies coalescent approach BPP. Different
 species delimitation scenarios were compared using Bayes factors
 delimitation analysis, in addition to comparisons of pairwise genetic
 distances, pairwise fixation indices (FST). The majority of the species
 delimitation analyses implemented in this study failed to support H.
 hypotrypa and H. flavida as distinct lineages, as did the Bayesian
 clustering analysis. However, strong support for the evolutionary
 independence of H. hypotrypa and H. flavida was inferred using BPP and
 further supported by Bayes factor delimitation. In spite of rigorous
 morphological comparisons and a wide range of sequence-based approaches to
 delimit species, species boundaries in the H. hypotrypa group remain
 uncertain. This study reveals the potential limitations of relying on
 distinct reproductive strategies as diagnostic taxonomic characters for
 Hypogymnia and also the challenges of using popular sequence-based species
 delimitation methods in groups with recent diversification histories.
description: 3genelocusalignmentDNA sequences alignment
DOI: 10.5061/dryad.mj5vs
title: Data from: Trophic and non-trophic interactions influence the mechanisms underlying biodiversity–ecosystem functioning relationships under different abiotic conditions

description: Plant diversity effects on ecosystem functioning usually have been studied
 from a plant perspective. However, the mechanisms underlying
 biodiversity–ecosystem functioning relationships may also depend on
 positive or negative interactions between plants and other biotic and
 abiotic factors, which remain poorly understood. Here we assessed whether
 plant–herbivore and/or plant–detritivore interactions modify the
 biodiversity–ecosystem functioning relationship and the mechanisms
 underlying biodiversity effects, including complementarity and selection
 effects, biomass allocation, vertical distribution of roots, and plant
 survival using a microcosm experiment. We also evaluated to what extent
 trophic and non-trophic interactions are affected by abiotic conditions by
 studying drought effects. Our results show that biotic and abiotic
 conditions influence the shape of the biodiversity–ecosystem function
 relationship, varying from hump-shaped to linear. For instance, total
 biomass increased linearly with plant richness in the presence of
 detritivores, but not in the absence of detritivores. Moreover,
 detritivore effects on belowground plant productivity were highly context
 dependent, varying in the presence of herbivores. Plant interactions with
 soil biota, especially with herbivores, influenced the mechanisms
 underlying diversity effects. Herbivores increased plant complementarity
 and modified biomass allocation and vertical distribution of roots.
 Furthermore, biotic–abiotic interactions influenced plant productivity
 differently across plant functional groups. Our findings emphasize the
 importance of complex biotic interactions underlying biodiversity effects,
 and that these biotic interactions may change with abiotic conditions.
 Despite minor changes in productivity in the short-term, soil
 biota-induced changes in plant–plant interactions and plant survival are
 likely to have significant long-term consequences for ecosystem
 functioning. Considering the context-dependency of multichannel
 interactions may contribute to reconciling differences among observed
 patterns in biodiversity studies. Further, abiotic conditions modified the
 effects of biotic interactions, suggesting that changes in environmental
 conditions may not only affect ecosystems directly, but also change the
 biotic composition of and dynamics within ecosystems.
description: Raw data used in the
 analysis at the microcosm and the species levelsRaw data from the
 microcosm experiment using six plant species, belowground herbivores, and
 detritivores under normal and drought conditions. The data include plant
 biomass (shoots, roots, dead, and total) at the microcosm level as well as
 at the species level. Plant survival per species is also included. The
 weight at the beginning and at the end of the experiment of each
 belowground herbivore and detritivore has been also
 included.Guerrero_Eisenhauer_Oikos_Data.xls
DOI: 10.5061/dryad.1c3k32r
title: Data from: Divergent in shape and convergent in function: adaptive evolution of the mandible in Sub-Antarctic mice

description: Convergent evolution in similar environments constitutes strong evidence
 of adaptive evolution. Transported with people around the world, house
 mice colonized even remote areas, such as Sub-Antarctic islands. There,
 they returned to a feral way of life, shifting towards a diet enriched in
 terrestrial macroinvertebrates. Here, we test the hypothesis that this
 triggered convergent evolution of the mandible, a morphological character
 involved in food consumption. Mandible shape from four Sub-Antarctic
 islands was compared to phylogeny, tracing the history of colonization,
 and climatic conditions. Mandible shape was primarily influenced by
 phylogenetic history, thus discarding the hypothesis of convergent
 evolution. The biomechanical properties of the jaw were then investigated.
 Incisor in-lever and temporalis out-lever suggested an increase in the
 velocity of incisor biting, in agreement with observations on various
 carnivorous and insectivorous rodents. The mechanical advantage related to
 incisor biting also revealed an increased functional performance in
 Sub-Antarctic populations, and appears to be an adaptation to catch prey
 more efficiently. The amount of change involved was larger than expected
 for a plastic response, suggesting microevolutionary processes were
 evolved. This study thus denotes some degree of adaptive convergent
 evolution related to changes in habitat-related changes in dietary items
 in Sub-Antarctic mice, but only regarding simple, functionally relevant
 aspects of mandible morphology.
description: Mandible descriptors and
 PCs for comparisonSheet 1: Mandible area
 and Fourier coefficients from A0 to B7 describing size and shape of the
 mandible. Sheet 2: Mechanical advantages (MAs) and axes for comparisons:
 PCclimate, PC for D-loop analysis, and PC for mitochondrial
 analysis.Md_FCs_MAs_PCs.xls
DOI: 10.5061/dryad.39qf1
title: Data from: Hybridization, natural selection and evolution of reproductive isolation: a 25-years survey of an artificial sympatric area between two mosquito sibling species of the Aedes mariae complex

description: Natural selection can act against maladaptive hybridization between
 co-occurring divergent populations leading to evolution of reproductive
 isolation among them. A critical unanswered question about this process
 that provides a basis for the theory of speciation by reinforcement, is
 whether natural selection can cause hybridization rates to evolve to zero.
 Here we investigated this issue in two sibling mosquitoes species, Aedes
 mariae and Ae. zammitii, that show post-mating reproductive isolation (F1
 males sterile) and partial pre-mating isolation (different height of
 mating swarms) that could be reinforced by natural selection against
 hybridization. In 1986, we created an artificial sympatric area between
 the two species and sampled about 20,000 individuals over the following 25
 years. Between 1986 to 2011, the composition of mating swarms and the
 hybridization rate between the two species were investigated across time
 in the sympatric area. Our results showed that Ae. mariae and Ae. zammitii
 have not completed reproductive isolation since their first contact in the
 artificial sympatric area. We have discussed the relative role of factors
 such as time of contact, gene flow, strength of natural selection, and
 biological mechanisms causing prezygotic isolation to explain the observed
 results.
description: Simulated multilocus
 genotypes of Aedes mariae and Aedes zammitiiSimulated multilocus
 genotypes of Aedes mariae and Aedes zammitii for six allozymic loci. From
 multilocus genotypes of 100 individuals of Ae. mariae from Circeo and
 Scauri populations and 100 individuals of Ae. zammitii from Peschici and
 Baia dei Campi populations sampled in 1985, we simulated 1000 individuals
 of each of five genotypic class (parental Ae. mariae and Ae. zammitti, F1,
 F2 and first-generation backcrosses) using the software hybridlab version
 1.0. z0s = Ae. zammitii from Peschici and Baia dei Campi populations; z1s
 = Ae. mariae from Circeo and Scauri populations.simulated data_Aedes
 mariae_Aedes zammitii.dat
DOI: 10.3535/59m-4wp-nea
title: Corythornis leucogaster leopoldi

description: Digital Specimen for the physical specimen hosted at Natural History Museum of Denmark.
DOI: 10.3535/s6d-sbn-8y8
title: Alcedo euryzona

description: Digital Specimen for the physical specimen hosted at Natural History Museum of Denmark.
DOI: 10.3535/k50-924-7wq
title: Alcedo semitorquata

description: Digital Specimen for the physical specimen hosted at Natural History Museum of Denmark.
DOI: 10.3535/dky-jcp-ab1
title: Corythornis cristatus

description: Digital Specimen for the physical specimen hosted at Natural History Museum of Denmark.
DOI: 10.3535/lsd-pj0-0ar
title: Corythornis cristatus thomensis

description: Digital Specimen for the physical specimen hosted at Natural History Museum of Denmark.
DOI: 10.5061/dryad.js47k
title: Data from: Cross-scale interactions and the distribution-abundance relationship

description: Positive interspecific relationships between local abundance and extent of
 regional distribution are among the most ubiquitous patterns in ecology.
 Although multiple hypotheses have been proposed, the mechanisms underlying
 distribution-abundance (d-a) relationships remain poorly understood. We
 examined the intra- and interspecific distribution-abundance relationships
 for a metacommunity of 13 amphibian species sampled for 15 consecutive
 years. Mean density of larvae in occupied ponds was positively related to
 number of ponds occupied by species; employing the fraction of ponds
 uniquely available to each species this same relationship sharply
 decelerates. The latter relationship suggested that more abundant species
 inhabited most available habitats annually, whereas rarer species were
 dispersal limited. We inferred the mechanisms responsible for this pattern
 based on the dynamics of one species, Pseudacris triseriata, which
 transitioned between a rare, narrowly distributed species to a common,
 widely distributed species and then back again. Both transitions were
 presaged by marked changes in mean local densities driven by climatic
 effects on habitat quality. We identified threshold densities separating
 these population regime shifts that differed with landscape configuration.
 Our data suggest that these transitions were caused by strong cross-scale
 interactions between local resource/niche processes and larger scale
 metapopulation processes. The patterns we observed have relevance for
 understanding the mechanisms of interspecific d-a relationships and
 critical thresholds associated with habitat fragmentation.
description: Amphibian abundance and
 occupancy dataThese data are the
 abundance and occupancy patterns for amphibian species on the ES George
 Reserve (Michigan, USA) over multiple yearsWerner_etal_ESGR_PLOS_data_Files.xlsxAmphibian phylogenyThis is the amphibian phylogeny used in the independent contrasts analysis.ESGRAmphibianPhylogeny.nex
DOI: 10.3535/dfy-dh6-3f9
title: Corythornis cristatus

description: Digital Specimen for the physical specimen hosted at Natural History Museum of Denmark.
DOI: 10.3535/wgl-8bh-kk6
title: Alcedo meninting

description: Digital Specimen for the physical specimen hosted at Natural History Museum of Denmark.
DOI: 10.3535/whw-hd3-4xy
title: Alcedo meninting

description: Digital Specimen for the physical specimen hosted at Natural History Museum of Denmark.