cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.1cm80
title: Data from: Adding landscape genetics and individual traits to the ecosystem function paradigm reveals the importance of species functional breadth

description: Animal pollination mediates both reproduction and gene flow for the
 majority of plant species across the globe. However, past functional
 studies have focused largely on seed production; although useful, this
 focus on seed set does not provide information regarding species-specific
 contributions to pollen-mediated gene flow. Here we quantify pollen
 dispersal for individual pollinator species across more than 690 ha of
 tropical forest. Specifically, we examine visitation, seed production, and
 pollen-dispersal ability for the entire pollinator community of a common
 tropical tree using a series of individual-based pollinator-exclusion
 experiments followed by molecular-based fractional paternity analyses. We
 investigate the effects of pollinator body size, plant size (as a proxy of
 floral display), local plant density, and local plant kinship on seed
 production and pollen-dispersal distance. Our results show that while
 large-bodied pollinators set more seeds per visit, small-bodied bees
 visited flowers more frequently and were responsible for more than 49% of
 all long distance (beyond 1 km) pollen-dispersal events. Thus, despite
 their size, small-bodied bees play a critical role in facilitating
 long-distance pollen-mediated gene flow. We also found that both plant
 size and local plant kinship negatively impact pollen dispersal and seed
 production. By incorporating genetic and trait-based data into the
 quantification of pollination services, we highlight the diversity in
 ecological function mediated by pollinators, the influential role that
 plant and population attributes play in driving service provision, and the
 unexpected importance of small-bodied pollinators in the recruitment of
 plant genetic diversity.
description: Correlation between tree
 size and floral displayThis data file has the
 diameter at breast height and the number of inflorescences per individual
 for 146 trees of populations Gamboa and Camino de Plantaciones (GB and CP
 respectively).correlation_dbh_number of
 inflorescences.xlsxGenotypes of
 reproductive trees and seeds of Miconia affinisThis data file has two
 spreadsheets, one with the genotypes for reproductive trees used in our
 paternity analysis for 8 microsatellite markers. We also included the
 geographic coordinates for each tree. The other spreadsheet has the
 genotypes for the seeds collected in our single pollinator visit
 experiment.genotypes_Miconia
 affinis.xlsxPollen dispersal
 analysisThis data file has all
 the variables that we used in our pollen dispersal
 model.pollen_dispersal_analysis_data.xlsxSeed viability analysisThis data file has all the variables used in our seed viability model.seed_viability_analysis_data.xlsx
DOI: 10.5061/dryad.2v7m4
title: Data from: Long-term environmental monitoring for assessment of change: measurement inconsistencies over time and potential solutions

description: The importance of long-term environmental monitoring and research for
 detecting and understanding changes in ecosystems and human impacts on
 natural systems is widely acknowledged. Over the last decades a number of
 critical components for successful long-term monitoring have been
 identified. One basic component is quality assurance/quality control
 protocols to ensure consistency and comparability of data. In Norway, the
 authorities require environmental monitoring of the impacts of the
 offshore petroleum industry on the Norwegian continental shelf, and in
 1996 a large-scale regional environmental monitoring program was
 established. As a case study, we used a sub-set of data from this
 monitoring to explore concepts regarding best practices for long-term
 environmental monitoring. Specifically, we examined data from physical and
 chemical sediment samples and benthic macro-invertebrate assemblages from
 11 stations from six sampling occasions during the period 1996-2011.
 Despite the established quality assessment and quality control protocols
 for this monitoring program, we identified several data challenges, such
 as, missing values and outliers, discrepancies in variable and station
 names, changes in procedures without calibration, and different taxonomic
 resolution. Furthermore, we show that the use of different laboratories
 over time makes it difficult to draw conclusions with regard to some of
 the observed changes. We offer recommendations to facilitate comparison of
 data over time. We also present a new procedure to handle different
 taxonomic resolution so valuable historical data is not discarded. These
 topics have a broader relevance and application than for our case study.
description: Faunal data: Long-term
 environmental monitoring for assessment of change: measurement
 inconsistencies over time and potential solutionsData on soft-sediment
 macrobenthos from 11 regional stations collected at the southern part of
 the Norwegian continental shelf (Region I, i.e. the Ekofisk-region) from
 six sampling occasions during the period 1996-2011. The data were
 extracted from the Environmental Monitoring Database (the MOD-database),
 owned by the Norwegian Oil and Gas Association. We used a version of the
 MOD-database from March 2013.R1Bio_22.09.14.txtR script: Long-term environmental monitoring for assessment of change: measurement inconsistencies over time and potential solutionsData analyses, including the procedure of lumping/splitting taxa in the species list prior to data analyses. All analyses were done using R. Data on soft-sediment macrobenthos from 11 regional stations collected at the southern part of the Norwegian continental shelf (Region I, i.e. the Ekofisk-region) from six sampling occasions during the period 1996-2011 are given in the file “Faunal data”.MOD-DRYAD.R
DOI: 10.5061/dryad.rk280
title: Data from: Correlations between heterozygosity and reproductive success in the blue tit (Cyanistes caeruleus): an analysis of inbreeding and single locus effects

description: In order to understand the mechanisms behind heterozygosity-fitness
 correlations (HFC), it is necessary to employ large numbers of markers
 with known function and to independently estimate the variation in
 inbreeding in the population. Here we genotyped 794 blue tits with 79
 microsatellites that were distributed across 25 chromosomes and that were
 classified either as "functional" (N = 58) or
 "neutral" (N = 21). We found a positive effect of individual
 heterozygosity at multiple loci on clutch size, on the number of eggs
 sired by males, and on the number of recruits produced by males and
 females. We documented the occurrence of some consanguineous matings and
 found evidence for a particular type of population structure that can
 contribute to the occurrence of inbreeding. As the set of
 "neutral" loci provided more power to detect HFC and identity
 disequilibrium, we argue that "neutral" markers are better
 predictors of the effects of inbreeding. The number of significant effects
 at single loci did not exceed the expected number of false positives and
 no strong effects were associated with heterozygosity at
 "functional" markers. Thus, the HFC found here cannot be
 attributed to strong effects of the loci under study.
description: Single-locus
 heterozygosity of all individualsHeterozygosity
 information is given as homozygote (0) or heterozygote (1) for all loci.
 Loci names see publication, table 1.Olano_etal_heterozygosity.txtClutch sizes of all females and breeding seasonsClutch sizes (no. of eggs) per female and breeding season are listed. Age of the female is coded as 1 (one year old) or 2 (two or more years old).Olano_etal_clutch_size.txtSired eggs of all males and breeding seasonsNumber sired eggs per male and breeding season is listed. Age of the male is coded as 1 (one year old) or 2 (two or more years old).Olano_etal_sired_eggs.txtReproductive success of each nest (breeding pair)Reproductive success information per nest is given as clutch size, no. of hatchlings, no. of fledglings and no. of recruits to the next breeding season. Age is coded as 1 (one year old) or 2 (two or more years old).Olano_etal_nest_success.txt
DOI: 10.5061/dryad.t6g5t
title: Data from: Geographical matching of volatile signals and pollinator olfactory responses in a cycad brood-site mutualism

description: Brood-site mutualisms represent extreme levels of reciprocal
 specialization between plants and insect pollinators, raising questions
 about whether these mutualisms are mediated by volatile signals and
 whether these signals and insect responses to them covary geographically
 in a manner expected from coevolution. Cycads are an ancient plant lineage
 in which almost all extant species are pollinated through brood-site
 mutualisms with insects. We investigated whether volatile emissions and
 insect olfactory responses are matched across the distribution range of
 the African cycad Encephalartos villosus. This cycad species is pollinated
 by the same beetle species across its distribution, but cone volatile
 emissions are dominated by alkenes in northern populations, and by
 monoterpenes and a pyrazine compound in southern populations. In
 reciprocal choice experiments, insects chose the scent of cones from the
 local region over that of cones from the other region. Antennae of beetles
 from northern populations responded mainly to alkenes, while those of
 beetles from southern populations responded mainly to pyrazine. In
 bioassay experiments, beetles were most strongly attracted to alkenes in
 northern populations and to the pyrazine compound in southern populations.
 Geographical matching of cone volatiles and pollinator olfactory
 preference is consistent with coevolution in this specialized mutualism.
description: Data on GEOGRAPHICAL
 RESPONSE OF CYCAD INSECTS TO CONE VOLATILE COMPOUNDSData on GEOGRAPHICAL MATCHING
 OF VOLATILE SIGNALS AND POLLINATOR OLFACTORY RESPONSES IN A CYCAD
 BROOD-SITE MUTUALISM TNS et al..xls
DOI: 10.5061/dryad.85kc60b
title: Data from: Density-dependent fitness, not dispersal movements, drives temporal variation in spatial genetic structure in dark-eyed juncos (Junco hyemalis)

description: Some studies have found that dispersal rates and distances increase with
 density, indicating that density-dependent dispersal likely affects
 spatial genetic structure. In an 11-year mark-recapture study on a
 passerine, the dark-eyed junco, we tested whether density affected
 dispersal distance and/or fine-scale spatial genetic structure. Contrary
 to expectations, we found no effect of pre-dispersal density on dispersal
 distance or the proportion of locally-produced juveniles returning to the
 population from which they hatched. However, even though density did not
 affect dispersal distance or natal return rates, we found that density
 still did affect spatial genetic structure. We found significant positive
 spatial genetic structure at low densities of (post-dispersal) adults but
 not at high densities. In years with high post-dispersal (adult) densities
 that also had high pre-dispersal (juvenile) densities in the previous
 year, we found negative spatial genetic structure, indicating high levels
 of dispersal. We found that density also affected fitness of recruits, and
 fitness of immigrants, potentially linking these population parameters
 with the spatial genetic structure detected. Immigrants and recruits
 rarely nested in low post-dispersal density years. In contrast, in years
 with high post-dispersal density, recruits were common and immigrants had
 equal success to local birds, so novel genotypes diluted the gene pool and
 effectively eliminated positive spatial genetic structure. In relation to
 fine-scale spatial genetic structure, fitness of immigrants and new
 recruits is poorly understood compared to dispersal movements, but we
 conclude that it can have implications for the spatial distribution of
 genotypes in populations.
description: ME-18-0878-raw genetic
 data.Raw genetic data and
 geographic locations (UTMs) for all Junco individuals (Junco hyemalis)
 captured each year from 1997-2007.ME-18-0878-nesting vs
 non-nesting male genotypes by year.Male Junco hyemalis
 genotypes (separated nesting and non-nesting) from
 1997-2007.ME-18-0878 Liebgold et
 al 2019-mark-recapture dataUTM locations and band
 numbers of Junco nestlings and return locations (recapture and/or adult
 nesting location).
DOI: 10.5061/dryad.89735cr0
title: Data from: Human impacted landscapes facilitate hybridization between a native and an introduced tree

description: Spatial and temporal dynamics of hybridization, in particular the
 influence of local environmental conditions, are well studied for
 sympatric species but less is known for native-introduced systems,
 especially for long-lived species. We used microsatellite and chloroplast
 DNA markers to characterize the influence of anthropogenic landscapes on
 the extent, direction, and spatial distribution of hybridization between a
 native North American tree Juglans cinerea (butternut) and an introduced
 tree Juglans ailantifolia (Japanese walnut) for 1363 trees at 48 locations
 across the native range of butternut. Remarkably, admixture in
 anthropogenic sites reached nearly 70%, while fragmented and continuous
 forests showed minimal admixture (7.5% and 2.5%, respectively).
 Furthermore, more hybrids in anthropogenic sites had J. ailantifolia seed
 parents (95%) than hybrids in fragmented and continuous forests (69% and
 59%, respectively). Our results show a strong influence of landscape on
 rate and direction of realized gene flow. While hybridization is clearly
 rampant in anthropogenic landscapes, our results suggest that even small
 forested landscapes serve as substantial barriers to hybridization, a key
 consideration for conservation planning for butternut, a species already
 exhibiting severe decline, and for other North American forest trees that
 hybridize with introduced congeners.
description: Hoban_EvolApps_microsat_Data_For_DryadThe genotypes for trees used in this study for all analyses, after clones, etc. have been removed. The data are referred to in the publication as "1515 unique genotypes for analysis: 79 J. ailantifolia reference, 7 hybrid 231 reference, 66 J. cinerea reference, and 1363 naturally occurring trees." The names of the populations are as in table one, or similar abbreviation. File format is Convert, tab delimited. All 12 microsatellite loci. Missing data with a '?'. Details about collections are in the manuscript.
DOI: 10.5061/dryad.vg75p
title: Data from: Sleepless in town – drivers of the temporal shift in dawn song in urban European Blackbirds

description: Organisms living in urban environments are exposed to different
 environmental conditions compared to their rural conspecifics. Especially
 anthropogenic noise and artificial night light are closely linked to
 urbanization and pose new challenges to urban species. Songbirds are
 particularly affected by these factors, because they rely on the spread of
 acoustic information and adjust their behaviour to the rhythm of night and
 day, e.g. time their dawn song according to changing light intensities.
 Our aim was to clarify the specific contributions of artificial night
 light and traffic noise on the timing of dawn song of urban European
 Blackbirds (Turdus merula). We investigated the onset of blackbird dawn
 song along a steep urban gradient ranging from an urban forest to the city
 centre of Leipzig, Germany. This gradient of anthropogenic noise and
 artificial night light was reflected in the timing of dawn song. In the
 city centre, blackbirds started their dawn song up to 5 hours earlier
 compared to those in semi-natural habitats. We found traffic noise to be
 the driving factor of the shift of dawn song into true night, although it
 was not completely separable from the effects of ambient night light. We
 additionally included meteorological conditions into the analysis and
 found an effect on the song onset. Cloudy and cold weather delayed the
 onset, but cloud cover was assumed to reflect night light emissions, thus,
 amplified sky luminance and increased the effect of artificial night
 light. Beside these temporal effects, we also found differences in the
 spatial autocorrelation of dawn song onset showing a much higher
 variability in noisy city areas than in rural parks and forests. These
 findings indicate that urban hazards such as ambient noise and light
 pollution show a manifold interference with naturally evolved cycles and
 have significant effects on the activity patterns of urban blackbirds.
description: Song onset of urban
 blackbirdsdata.csv
DOI: 10.5061/dryad.918bg
title: Data from: Genome reorganization in F1 hybrids uncovers the role of retrotransposons in reproductive isolation

description: Interspecific hybridization leads to new interactions among divergent
 genomes, revealing the nature of genetic incompatibilities having
 accumulated during and after the origin of species. Conflicts associated
 with misregulation of transposable elements (TEs) in hybrids expectedly
 result in their activation and genome-wide changes that may be key to
 species boundaries. Repetitive genomes of wild wheats have diverged under
 differential dynamics of specific long terminal repeat retrotransposons
 (LTR-RTs), offering unparalleled opportunities to address the
 underpinnings of plant genome reorganization by selfish sequences. Using
 reciprocal F1 hybrids between three Aegilops species, restructuring and
 epigenetic repatterning was assessed at random and LTR-RT sequences with
 amplified fragment length polymorphism and sequence-specific amplified
 polymorphisms as well as their methylation-sensitive counterparts,
 respectively. Asymmetrical reorganization of LTR-RT families predicted to
 cause conflicting interactions matched differential survival of F1
 hybrids. Consistent with the genome shock model, increasing divergence of
 merged LTR-RTs yielded higher levels of changes in corresponding genome
 fractions and lead to repeated reorganization of LTR-RT sequences in F1
 hybrids. Such non-random reorganization of hybrid genomes is coherent with
 the necessary repression of incompatible TE loci in support of hybrid
 viability and indicates that TE-driven genomic conflicts may represent an
 overlooked factor supporting reproductive isolation.
description: datasetsThis compressed folder contains all AFLP, SSAP, MSAP and MSTD datasets in .txt
DOI: 10.5061/dryad.2ph0t
title: Data from: The effect of taxonomic corrections on Phanerozoic generic richness trends in marine bivalves with a discussion on the clade’s overall history

description: This study uses a comprehensive, revised, and updated global bivalve
 dataset combining information from two major databases available to study
 temporal trends in Phanerozoic bivalve richness: the Sepkoski Compendium
 and the Paleobiology Database. This compilation results in greater
 taxonomic and stratigraphic coverage than possible with either of the two
 databases alone. However, there are challenges in directly comparing these
 two sources due to differences in their taxonomic designations and
 stratigraphic range information. Moreover, both of these datasets are
 fraught with a number of taxonomic errors, which can significantly bias
 the overall richness estimate. Additionally, a substantial number of
 taxonomic corrections were made before a new Phanerozoic bivalve richness
 curve was produced. The new generic taxonomic curve is comparable with the
 trajectory of the Sepkoski’s modern fauna and shows rapid and substantial
 diversification through the Ordovician, followed by a Paleozoic plateau, a
 Mesozoic high, and Cenozoic diversification after a small reduction in
 richness associated with the K/Pg extinction. The steep Cenozoic rise
 documented in the raw richness curve derived from the new dataset is
 likely real, and reflects the overall robustness and completeness of the
 bivalve fossil record.
description: Phanerozoic Marine
 Bivalve DatasetSupplementary Table 1:
 The newly revised and updated database used in this study based on a
 critical compilation of data from the Sepkoski Compendium and the
 Paleobiology Database. FADs and LADs indicate first and last appearances,
 respectively, in Ma based on the Geological Society of America Geological
 Time scale (v. 4.0) as compiled from Gradstein et al. (2012) and Cohen et
 al. (2012).Mondal and
 Harries_Paleobiology_Supplementary Table
 1.docx
DOI: 10.5061/dryad.304pm
title: Data from: Asymmetric adaptation to indolic- and aliphatic-glucosinolates in the B and Q sibling species of Bemisia tabaci (Hemiptera: Aleyrodidae)

description: The role glucosinolates play in defending plants against delicate phloem
 feeders such as aphids and whiteflies is currently not clear as these
 herbivores may avoid bringing glucosinolates from the phloem sap into
 contact with myrosinase enzymes. Here, we investigated the effects of high
 levels of aliphatic- and indolic-glucosinolates on life history traits and
 detoxification gene expression in two sibling species, B and Q, of the
 whitefly Bemisia tabaci. High levels of aliphatic-glucosinolates decreased
 the average oviposition rate of both species, and reduced the survival and
 developmental rate of Q nymphs. High levels of indolic-glucosinolates
 decreased the oviposition rate and survival of nymphal stages of the B
 species and the developmental rate of both species. Molecular analyses
 revealed two major asymmetries between the B and Q species. First,
 specific GST genes (BtGST1 and BtGST2) were significantly induced during
 exposure to indolic-glucosinolates only in Q. This may reflect the genes
 putative involvement in indolic-glucosinolates detoxification and explain
 the species' good performance on plants accumulating
 indolic-glucosinolates. Second, the constitutive expression of eight of
 the ten detoxification genes analyzed was higher in the Q species than in
 the B species. Interestingly, four of these genes were induced in B in
 response to high levels of glucosinolates. It seems, therefore, that the B
 and Q species differ in their "optimal defense strategy". B
 utilizes inducible defenses which are profitable if the probability of
 experiencing the stress is small and its severity is low, while Q invests
 significant resources in being always "ready" for a challenge.
description: Choice
 ovipositionNo choice oviposition
 BNo choice oviposition
 QSurvival on
 sinigrinDevelopment
 BDevelopment
 QEgg and nymph survival
 BEgg and nymph survival
 Q