cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.76mg6
title: Data from: Yet another empty forest: considering the conservation value of a recently established tropical nature reserve

description: The primary approach used to conserve tropical biodiversity is in the
 establishment of protected areas. However, many tropical nature reserves
 are performing poorly and interventions in the broader landscape may be
 essential for conserving biodiversity both within reserves and at large.
 Between October 2010 and 2012, we conducted bird surveys in and around a
 recently established nature reserve in Xishuangbanna, China. We
 constructed a checklist of observed species, previously recorded species,
 and species inferred to have occurred in the area from their distributions
 and habitat requirements. In addition, we assessed variation in community
 composition and habitat specificity at a landscape-scale. Despite the fact
 that the landscape supports a large area of natural forest habitat
 (~50,000 ha), we estimate that &gt;40% of the bird fauna has been
 extirpated and abundant evidence suggests hunting is the primary cause. A
 large proportion (52%) of the bigger birds (&gt;20 cm) were extirpated
 and for large birds there was a U-shaped relationship between habitat
 breadth and extirpation probability. Habitat specificity was low and bird
 communities were dominated by widespread species of limited conservation
 concern. We question whether extending tropical protected area networks
 will deliver desired conservation gains, unless much greater effort is
 channeled into addressing the hunting problem both within existing
 protected areas and in the broader landscape.
description: R
 scriptR script for the
 analysis of data files supplied here.Another empty
 forest.Rcom_2Site by species matrix
 for all bird speciescomfive2Site by species matrix for bird species with 5 or more individualshab_2Habitat categories (open land, disturbed forest or primary forest) for plotslargeres_2Site by species matrix for large range bird speciesmedsmallres_2Site by species matrix for small and medium range bird speciesmengsongBird species, response (extant or extirpated) and functional trait dateframems_laiForest structural data for plotsms_landuseLanduse history for plotsms_topoTopographical data for plotsvar3Summary table of plot variables used in multivariate modeling
DOI: 10.5061/dryad.22tg2
title: Data from: Task-dependent workload adjustment of female breeders in a cooperatively breeding fish

description: Parental investment affects the future survival and reproductive success
 of breeders. Therefore, breeders should optimize the amount of care they
 invest into the current offspring. In cooperative breeding systems, the
 amount of breeders’ parental care is influenced by the behavior of
 brood-care helpers. Such workload adjustment is expected to depend on the
 task that needs to be fulfilled. While investment rules of breeders in
 respect to single tasks are well investigated in many bird and mammal
 species, little is known about behavioral adjustment of breeders when
 dealing with multiple tasks. Here, we examined the workload adjustment in
 multiple tasks of female breeders in the cooperatively breeding fish
 Neolamprologus obscurus. By combining behavioral observations with helper
 removal experiments in a wild population, we found that female territory
 defense and offspring care significantly decreased with increasing helper
 number. Furthermore, the workload invested in these tasks significantly
 increased after the removal of a helper, suggesting load-lightening
 effects in territory defense and offspring care. On the other hand, female
 territory maintenance behavior (i.e. excavating sand from the breeding
 shelter) did not correlate with helper number. While sand excavation
 significantly increased after the helper removal experiment, the size of
 the excavated stone area decreased after the helper removal in the recent
 study, suggesting that sand excavation may have additive effects for the
 breeders. These results demonstrate and underline the importance of task
 dependent workload adjustment in cooperative breeders.
description: Driad Tanaka et
 al.
DOI: 10.5061/dryad.nr2cf12
title: Data from: Predicting bioprocess targets of chemical compounds through integration of chemical-genetic and genetic interactions

description: Chemical-genetic interactions–observed when the treatment of mutant cells
 with chemical compounds reveals unexpected phenotypes–contain rich
 functional information linking compounds to their cellular modes of
 action. To systematically identify these interactions, an array of mutants
 is challenged with a compound and monitored for fitness defects,
 generating a chemical-genetic interaction profile that provides a
 quantitative, unbiased description of the cellular function(s) perturbed
 by the compound. Genetic interactions, obtained from genome-wide
 double-mutant screens, provide a key for interpreting the functional
 information contained in chemical-genetic interaction profiles. Despite
 the utility of this approach, integrative analyses of genetic and
 chemical-genetic interaction networks have not been systematically
 evaluated. We developed a method, called CG-TARGET (Chemical Genetic
 Translation via A Reference Genetic nETwork), that integrates large-scale
 chemical-genetic interaction screening data with a genetic interaction
 network to predict the biological processes perturbed by compounds. In a
 recent publication, we applied CG-TARGET to a screen of nearly 14,000
 chemical compounds in Saccharomyces cerevisiae, integrating this dataset
 with the global S. cerevisiae genetic interaction network to prioritize
 over 1500 compounds with high-confidence biological process predictions
 for further study. We present here a formal description and rigorous
 benchmarking of the CG-TARGET method, showing that, compared to
 alternative enrichment-based approaches, it achieves similar or better
 accuracy while substantially improving the ability to control the false
 discovery rate of biological process predictions. Additional investigation
 of the compatibility of chemical-genetic and genetic interaction profiles
 revealed that one-third of observed chemical-genetic interactions
 contributed to the highest-confidence biological process predictions and
 that negative chemical-genetic interactions overwhelmingly formed the
 basis of these predictions. We also present experimental validations of
 CG-TARGET-predicted tubulin polymerization and cell cycle progression
 inhibitors. Our approach successfully demonstrates the use of genetic
 interaction networks in the high-throughput functional annotation of
 compounds to biological processes.
description: All chemical-genetic
 interaction profilesCG-interaction-mat.txt.gzAll compound-bioprocess predictionsBioprocess-predictions-all.txt.gzGenetic interaction profilesGenetic-interaction-mat.txt.gzGene Ontology biological process termsGO-BP-mat.txt.gzBioprocess predictions for compounds, FDR &lt;= 25%Bioprocess-predictions-cpds-FDR25.txt.gz
DOI: 10.5061/dryad.3q471
title: Data from: Crossing the divide: admixture across the Antarctic Polar Front revealed by the brittle star Astrotoma agassizii

description: The Antarctic Polar Front (APF) is one of the most well-defined and
 persistent oceanographic features on the planet and serves as a barrier to
 dispersal between the Southern Ocean and lower latitudes. High levels of
 endemism in the Southern Ocean have been attributed to this barrier,
 whereas the accompanying Antarctic Circumpolar Current (ACC) likely
 promotes west-to-east dispersal. Previous phylogeographic work on the
 brittle star Astrotoma agassizii Lyman, 1875 based on mitochondrial genes
 suggested isolation across the APF, even though populations in both South
 American waters and the Southern Ocean are morphologically
 indistinguishable. Here, we revisit this finding using a high-resolution
 2b-RAD (restriction-site-associated DNA) single-nucleotide polymorphism
 (SNP)-based approach, in addition to enlarged mitochondrial DNA data sets
 (16S rDNA, COI, and COII), for comparison to previous work. In total, 955
 biallelic SNP loci confirmed the existence of strongly divergent
 populations on either side of the Drake Passage. Interestingly, genetic
 admixture was detected between South America and the Southern Ocean in
 five individuals on both sides of the APF, revealing evidence of recent or
 ongoing genetic contact. We also identified two differentiated populations
 on the Patagonian Shelf with six admixed individuals from these two
 populations. These findings suggest that the APF is a strong but imperfect
 barrier. Fluctuations in location and strength of the APF and ACC due to
 climate shifts may have profound consequences for levels of admixture or
 endemism in this region of the world.
description: README_AstrotomaREADME file describing the details of all uploaded dataastrotoma_94_955This is the main data matrix file, ready for downstream analyses.Astrotoma_cleaned_fastaThis file contains all sample files. All files have be checked for quality, size, and the presence of the restriction enzyme AlfI. Samples are ready for further processing through custom pipelines or through programs such as STACKS.
DOI: 10.5061/dryad.kp6n4
title: Data from: Spatial representativeness of environmental DNA metabarcoding signal for fish biodiversity assessment in a natural freshwater system

description: In the last few years, the study of environmental DNA (eDNA) has drawn
 attention for many reasons, including its advantages for monitoring and
 conservation purposes. So far, in aquatic environments, most of eDNA
 research has focused on the detection of single species using
 species-specific markers. Recently, species inventories based on the
 analysis of a single generalist marker targeting a larger taxonomic group
 (eDNA metabarcoding) have proven useful for bony fish and amphibian
 biodiversity surveys. This approach involves in situ filtering of large
 volumes of water followed by amplification and sequencing of a short
 discriminative fragment from the 12S rDNA mitochondrial gene. In this
 study, we went one step further by investigating the spatial
 representativeness (i.e. ecological reliability and signal variability in
 space) of eDNA metabarcoding for large-scale fish biodiversity assessment
 in a freshwater system including lentic and lotic environments. We tested
 the ability of this approach to characterize large-scale organization of
 fish communities along a longitudinal gradient, from a lake to the
 outflowing river. First, our results confirm that eDNA metabarcoding is
 more efficient than a single traditional sampling campaign to detect
 species presence, especially in rivers. Second, the species list obtained
 using this approach is comparable to the one obtained when cumulating all
 traditional sampling sessions since 1995 and 1988 for the lake and the
 river, respectively. In conclusion, eDNA metabarcoding gives a faithful
 description of local fish biodiversity in the study system, more
 specifically within a range of a few kilometers along the river in our
 study conditions, i.e. longer than a traditional fish sampling site.
description: Run1Compressed file
 containing: 1) Forward sequence file 2) Reverse sequence file 3) File with
 experiment name, sample name and the tags, the forward primer and the
 reverse primer sequence associated.Run2Compressed file
 containing: 1) Forward sequence file 2) Reverse sequence file 3) File with
 experiment name, sample name and the tags, the forward primer and the
 reverse primer sequence associated.
DOI: 10.5061/dryad.7q3m05fm
title: Data from: Rapid evolution of an adaptive cyanogenesis cline in introduced North American white clover (Trifolium repens L.)

description: White clover is polymorphic for cyanogenesis (HCN production after tissue
 damage), and this herbivore defense polymorphism has served as a classic
 model for studying adaptive variation. The cyanogenic phenotype requires
 two interacting biochemical components; the presence/absence of each
 component is controlled by a simple Mendelian gene (Ac/ac and Li/li).
 Climate-associated cyanogenesis clines occur in both native (Eurasian) and
 introduced populations worldwide, with cyanogenic plants predominating in
 warmer locations. Moreover, previous studies have suggested that epistatic
 selection may act within populations to maintain cyanogenic (AcLi) plants
 and acyanogenic plants that lack both components (acli plants) at the
 expense of plants possessing a single component (Acli and acLi plants).
 Here we examine the roles of selection, gene flow, and demography in the
 evolution of a latitudinal cyanogenesis cline in introduced North American
 populations. Using 1,200 plants sampled across a 1,650 km transect, we
 determine the distribution of cyanogenesis variation across the central
 U.S. and investigate whether clinal variation is adaptive or an artifact
 of population introduction history. We also test for evidence of epistatic
 selection. We detect a clear latitudinal cline, with cyanogenesis
 frequencies increasing from 11% to 86% across the transect. Population
 structure analysis using nine microsatellite loci indicates that the cline
 is adaptive and not a byproduct of demographic history. However, we find
 no evidence for epistatic selection within populations. Our results
 provide strong evidence for rapid adaptive evolution in these introduced
 populations, and they further suggest that the mechanisms maintaining
 adaptive variation may vary among populations of a species.
description: Microsatellite_Data_for_Central_US_ClineThis is a comma delimited file (.csv) which contains the microsatellite data for 349 Trifolium repens (white clover) individuals from 38 subpopulations (7 populations) located across the Central U.S.Microsatellite_Data_for CentralUS_Cline.csv
DOI: 10.5061/dryad.69r593t
title: Data from: Folivory has long-term effects on sexual but not on asexual reproduction in woodland strawberry

description: 1. Plant fitness is often a result of both sexual and asexual reproductive
 success and, in perennial plants, over several years. Folivory can affect
 both modes of reproduction. However, little is known about the effects of
 folivory on resource allocation to the two modes of reproduction
 simultaneously and across years. 2. In a two-year common garden experiment
 we examined the effects of different levels of folivory by the strawberry
 leaf beetle, Galerucella tenella, on current growth, as well as current
 and future sexual and asexual reproduction (runners) of perennial woodland
 strawberry, Fragaria vesca. In addition, we measured the chlorophyll
 content in leaves in the year of experimental damage to determine whether
 there was increased photosynthetic activity, and, thus, a compensatory
 response to herbivory. 3. In the year of experimental damage, plants that
 were exposed to moderate and high levels of folivory (25% and 50 % leaf
 area consumed, respectively) increased their photosynthetic activity
 compared to control plants. However, only plants exposed to high folivory
 exhibited negative effects, with a lower probability of flowering compared
 to control plants, indicating that plants exposed to low or moderate
 folivory were able to compensate for the damage. Negative effects of
 folivory were carried over to the subsequent year. Plants that were
 exposed to moderate folivory (25 % leaf area consumed) during one year
 produced fewest flowers and fruits in the subsequent year. Runner
 production was consistently unaffected by folivory. 4. Synthesis. Our
 results show that the negative effects of folivory only influence sexual
 reproduction in woodland strawberry. Furthermore, even though woodland
 strawberry can tolerate moderate amounts of folivory in the short term,
 the negative effects on fitness appear later; this highlights the
 importance of studying the effects of herbivory over consecutive years in
 perennial plants.
description: Long-term effects of
 folivory on Fragaria vesca fitnessData on the effects of
 leaf damage by Galerucella tenella on survival, growth, chlorophyll
 content and sexual and clonal reproduction of woodland strawberry
 (Fragaria vesca) during the year of damage and year after
 damage.
DOI: 10.5061/dryad.5h6q8
title: Data from: Evaluation of the implementation fidelity of the seasonal malaria chemoprevention intervention in Kaya health district, Burkina Faso

description: Background: Burkina Faso implemented the seasonal malaria chemoprevention
 (SMC) in 2014 in seven pilot health districts, following the new
 recommendation by the WHO in 2012 for the prevention of the disease in
 children under five years old, for areas of highly seasonal malaria
 transmission. The objective of this study was to assess the implementation
 fidelity of the seasonal malaria chemoprevention strategy in one of the
 districts, Kaya Health District. Methodology: We conducted a case study,
 with a quantitative and qualitative mixed methods. Data were collected
 after two campaigns of implementation of the intervention, in 2014 and
 2015, through a review of specific documents of SMC intervention, and
 individual interview with key informants (n = 21) involved at various
 levels in the implementation of the strategy and a household survey with
 the parents (n = 284) of eligible children for the SMC strategy in 2015 in
 the Kaya health district. The analysis framework focused on the fidelity
 of the intervention's content, its coverage, and its schedule, as
 well as the potential moderating factors, using the model proposed by
 Hasson, originally from Carroll. Results: All components of the
 intervention were implemented. Villages and sectors were covered at 100%.
 In terms of intervention doses received, less than one-third of eligible
 children (32.3%) received the recommended four doses in 2015.
 Implementation of the strategy faced some difficulties due to insufficient
 training of community distributors, inadequate supply of inputs and
 insufficient financial resources for remuneration, advocacy and
 supervision, but also because of the contextual constraints due to the
 rainy season. Moreover, an interaction between the different moderating
 factors, influencing the degree of implementation of the strategy was
 noted. Conclusion: Taking into account the moderating factors of the
 implementation is necessary for achieving the highest possible degree of
 implementation fidelity and then, reach the expected beneficial effects.
description: CONTENT ADHERENCE TO
 FIDELITYContent adherence of
 seasonal malaria chemoprevention intervention's activities to
 implementation fidelity in Kaya health district in 2014 and
 2015SCHEDULE ADHERENCE TO
 IMPLEMENTATION FIDELITYSchedule adherence of
 seasonal malaria chemoprevention intervention's activities to
 implementation fidelity in Kaya health district in 2014 and
 2015
DOI: 10.5061/dryad.6hs29
title: Data from: Evolutionary history of the Maltese wall lizard Podarcis filfolensis: insights on the ‘Expansion-Contraction’ model of Pleistocene biogeography

description: The Expansion-Contraction (EC) model predicts demographic and range
 contraction of temperate species during Pleistocene glaciations as a
 consequence of climate-related habitat changes, and provides a paradigm
 for explaining the high intraspecific diversity found in refugia in terms
 of long-term demographic stability. However, recent evidence has revealed
 a weak predictive power of this model for terrestrial species in insular
 and coastal settings. We investigated the Pleistocene EC dynamics and
 their evolutionary consequences on temperate species using the Maltese
 archipelago and its endemic lizard Podarcis filfolensis as a model system.
 The evolutionary and demographic history of P. filfolensis as inferred
 from mitochondrial and nuclear sequences data does not conform to the EC
 model predictions, supporting (i) demographic and spatial stability or
 expansion, rather than contraction, of the northern and southern lineages
 during the last glacial period, and (ii) a major role for allopatric
 differentiation primed by sea-level dynamics, rather than prolonged
 demographic stability, in the formation of the observed genetic diversity.
 When combined with evidence from other Mediterranean refugia, this study
 shows how the incorporation of Pleistocene sea-level variations in the EC
 model accounts for a reverse demographic and range response of insular and
 coastal temperate biotas relative to continental ones. Furthermore, this
 cross-archipelago pattern in which allopatric diversity is formed and
 shaped by EC cycles resembles that seen between isolated populations
 within mainland refugia and suggests that the EC model, originally
 developed to explain population fluctuations into and out-of refugia, may
 be appropriate for describing the demographic and evolutionary dynamics
 driving the high genetic diversity observed in these areas.
description: ALIGNEMENTS nd4, mc1r,
 pod55, pod15bFasta files used for TCS
 network analyses and diversity estimates for each locus (nd4, mc1r, pod55,
 pod15b)ALNs_nd4_mc1r_pod55_pod15b.rarinput and output files DAMBEdatingAlignement, input tree, and dated tree of dating analysis carried out in DAMBEinput_outputTree_DAMBEdating.rarInput and output files BEASTdatingBeauty input files of the two runs of BEAST and resulting combined treeinput_outputTree_BEASTdating.rar
DOI: 10.5061/dryad.jb78964
title: Data from: Differences in Al sensitivity affect establishment of Populus genotypes on acidic forest land

description: Forest lands hold great potential for Populus plantations, but in native
 boreal forests, soils normally have low pH and thus higher levels of
 aluminum ions (Al3+ and hydroxides). Aluminum (Al) is one of the major
 factors limiting plant growth on these soils by inhibiting root growth,
 thus reducing water and nutrient uptake and slowing growth. There is a
 large variation in Al resistance both among and within species. In this
 study, growth responses of greenhouse-grown hybrid aspen (P. tremula ×
 tremuloides) and poplar (P. trichocarpa hybrids) were monitored in
 relation to changes in Al concentrations. In quartz sand, hybrid aspen was
 more tolerant to exogenous application of Al than P. trichocarpa hybrids.
 This difference in Al-tolerance was further confirmed by hematoxylin
 staining of the roots, with hybrid aspen displaying less staining after Al
 treatment than poplar clones. When planted on forest land with low pH,
 hybrid aspen increased growth after planting and showed low mortality.
 This was not the case for poplar clones; plant height decreased after
 planting and mortality increased. Together, our results suggest that
 differences in initial growth and survival on forest land among hybrid
 aspen and the tested poplar clones may be connected to differences in Al
 tolerance. Our findings that staining with hematoxylin can identify
 Al-tolerant Populus genotypes may help identify Al-tolerant genotypes
 suitable for forest land.
description: Data For Depositony
 Böhlenius etal 2018Data sheet “Al
 experiment” contains growth response of four Populus genotypes during
 exposure to Al treatments, which included 6 concentrations 10-300 mg/l.
 Plants were grown in sand and irrigated with nutrient solutions
 supplemented with A. Data sheet “field experiment” contains growth
 response during the first two years of the same Populus genotypes when
 planted at two forest sites.
DOI: 10.15468/dl.2tbycv
title: Occurrence Download

description: A dataset containing 218 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Globodera rostochiensis"
 ]
}

 The dataset includes 218 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001081-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.