cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.v9s4mw712
title: Data for: Tree-ring 15N isotope of red alder

description: Nitrogen (N) accretion rates under N2-fixing tree species can vary with
 site condition and possibly decline over time with down-regulation of N
 fixation. Tree-ring δ15N may depict these site-specific, long-term
 patterns in N dynamics, but field trials with N2-fixing tree species are
 lacking. We examined whether tree-ring δ15N of N2-fixing red alder (Alnus
 rubra) would mirror N accretion rates and δ15N of soils. We sampled a
 27-year-old replacement series trial on southeastern Vancouver Island with
 red alder and coastal Douglas-fir (Pseudotsuga menziesii) in five
 proportions (0/100, 11/89, 25/75, 50/50, and 100/0, respectively). An
 escalation in forest floor N content was evident with an increasing
 proportion of red alder, equivalent to a difference of approximately 750
 kg N ha-1 between 100% Douglas-fir vs. 100% alder. The forest floor
 horizon was also enriched in δ15N under denser red alder treatments. Red
 alder had a consistent quadratic fit in tree-ring δ15N over time, with a
 net increase of 1.5‰, on average, before declining slightly.
 Douglas-fir tree-ring δ15N, in contrast, was largely unchanged over time
 (in 3 of 4 plots) but significantly enriched in the 50/50 mix. The minor
 differences in current litter N content and leaf δ15N between alder and
 Douglas-fir suggests the declining trend in alder tree-ring δ15N could
 coincide with lower N-fixation rates, either by down-regulation via
 nitrate availability or loss in alder vigour with shading and drought. We
 suggest tree-ring δ15N can provide insights into the abiotic constraints
 and facultative/obligate nature of N fixation for N2-fixing trees.
description: # Nitrogen dynamics under N2-fixing Alnus rubra *** Included are the soil,
 litter and tree ring data for the replacement series trial with red alder
 and coastal Douglas-fir. Results are focused on nitrogen concentrations
 and delta 15 nitrogen isotope. ## Description of the data and file
 structure Column one is the treatment code, the proportion of alder and
 fir. Column two is the subplot with each treatment. The remaining columns
 are the data, including mass and chemical concentrations. A missing data
 point is referenced by 'n/a'. The main data sets are the forest
 floors (or organic horizons as the surface), the underlying mineral soil,
 the leaf litter collected over the growing season, and the increment cores
 taken from the trees ## Sharing/Access information All data used in the
 manuscript are included in this Dryad submission. Further questions about
 the data can be made through the British Columbia Ministry of Forests
DOI: 10.5061/dryad.g79cnp5v0
title: Annotated VCF of 192 Verticillium dahliae isolates

description: Verticillium dahliae is an important soil-borne pathogen causing
 Verticillium wilt. It is also the primary causal agent of the Potato Early
 Dying, a disease complex involving the root-lesion nematode. Here, we
 report the whole-genome sequencing of 192 isolates of V. dahliae
 originating from the major potato production areas across Canada. Our
 results yielded a resource of  277,010 genetic
 variations that will be useful for genetic analyses and revealed
 the presence of two major lineages, both present in all provinces but
 exhibiting differences in regional prevalence.
description: Filtered WGS reads (fastp) aligned on <em>Verticillium
 dahliae</em> reference (https://www.ncbi.nlm.nih.gov/assembly/95341/GCA_000150675.2) with BWA. VCF called with freebayes v1.3.6 and annotated with snpeff.
DOI: 10.5061/dryad.mkkwh714j
title: Genomic analysis of geographical structure and diversity in the capercaillie (Tetrao urogallus)

description: The capercaillie is widespread throughout the boreal forests of northern
 Eurasia but faces serious conservation challenges in the southernmost
 mountain ranges, where the populations are fragmented and some are
 critically endangered. To develop effective conservation strategies for
 these populations, it is essential to have information on both their
 genetic diversity and the genetic structure of the species. In this work,
 we used a reduced representation (ddRAD) genomic sequencing technique to
 analyze the genetic structure of the capercaillie across its European
 range and to assess the inbreeding levels in some of the most threatened
 populations. Our population structure analysis suggested the existence of
 two evolutionarily significant units, one formed by the two populations
 from the Iberian Peninsula and the other by the populations from the rest
 of Europe. Genetic diversity showed a significant decrease in the Iberian
 populations with respect to the other European populations. An
 isolation-with-migration model supported these results and allowed us to
 estimate the parameters of the population tree. The inbreeding
 coefficients estimated for the Iberian capercaillies showed relatively low
 levels in the Pyrenees. However, some individuals with very high
 inbreeding values were detected in the Cantabrian Mountains, suggesting
 that some of its subpopulations are substantially isolated. The population
 structure results and the genomic monitoring method we used to assess
 inbreeding levels may be crucial for the conservation and recovery of the
 most endangered capercaillie populations.
description: Title: Genomic analysis of geographical structure and diversity in the
 capercaillie (Tetrao urogallus) Authors: Lidia Escoda, Josep Pique,
 Ladislav Paule, Kevin Foulche, Emmanuel Menoni, Jose Castresana
 Quality-filtered ddRAD reads for each individual in FASTQ format:
 ddRAD\_reads.zip
DOI: 10.5061/dryad.xksn02vkx
title: Data from: Plant–moth community relationships at the degraded urban peat-bog in Central Europe

description: Peatlands have their own, specific insect fauna. They are a habitat not
 only for ubiquistic but also stenotopic moths that feed on plants limited
 to wet, acid and oligotrophic habitats. In the past, raised bogs and fens
 were widely distributed in Europe. This has changed since 20th c. Due to
 irrigation, modern forestry and increasing human settlement, peatlands
 have become isolated islands in agricultural and urban landscape. Here we
 analyse the flora in a degraded bog situated in a large Lodz city
 agglomeration in Poland in relation to the diversity and composition of
 moth fauna. Over the last 40 years since the bog has been protected as a
 nature reserve, birch, willow and alder shrubs replaced the typical raised
 bog plant communities due to the decreased water level. The analysis of
 moth communities sampled in 2012 and 2013 indicates dominance of
 ubiquistic taxa associated with deciduous wetland forests and rushes.
 Tyrphobiotic and tyrphophile moth taxa were not recorded. We conclude that
 the absence of moths typical of bog habitats and the dominance of common,
 woodland species are associated with hydrological changes, the expansion
 of trees and brushes over typical bog plant communities and light
 pollution.
description: The material was collected
 from spring of 2011 to late autumn of 2012. At the Różana 30B street
 (51˚48'00"N; 19˚18'42") (R) site, a Robinson trap with
 mercury bulb was used, and sampling took place from spring 2011 to spring
 2012. Catching was carried out regularly at two-week intervals from 9:00
 pm to 3:00 am. The catch at Torfowa Street (T) (51˚48'08"N;
 19˚17'38") took place by a standard light trap with
 mercury-incandescent bulb and white canvas from spring to autumn 2012 at
 two-week intervals. The light trap at Torfowa st. took place between 10.00
 pm and 12.00 pm. The data matrix presenting a list of taxa collected at R
 and T sites is included in appendices Tab. S1 and Tab. S2. The Heterocera
 were poisoned with ethyl acetate and then frozen until preparation. The
 habitat and host plant preferences of collected moth species were obtained
 from literature data, especially those focused on central European
 fauna.  To recognise
 an assemblage pattern in caterpillar host plants of the reported taxa, a
 series of analysis was used. 1) NMDS analysis based on Bray-Curtis formula
 was conducted on all collected moth species as “samples”, and for each
 species up to three main host plants as “variables”. As NMDS divided taxa
 into two main moth groups – A and B, and the out-group O, 2) one-way
 SIMPER analysis indicating main host plants for each of group was
 conducted using Bray-Curtis similarity index and 100%
 cut-off. 
description: The files are in .pdf and .xlsx formats.
DOI: 10.5061/dryad.v9s4mw714
title: Urbanization can accelerate climate change by increasing soil N2O emission while reducing CH4 uptake

description: Urban land use change has the potential to affect local to global
 biogeochemical carbon (C) and nitrogen (N) cycles and associated
 greenhouse gas (GHG) fluxes. We conducted a meta-analysis to 1) assess the
 effects of urbanization-induced land-use conversion on soil nitrous oxide
 (N2O) and methane (CH4) fluxes, 2) quantify direct N2O emission factors
 (EFd) of fertilized urban soils used e.g., as lawns or forests, and 3)
 identify the key drivers leading to flux changes associated with
 urbanization. On average, urbanization increases soil N2O emissions by
 153%, to 3.0 kg N ha-1 yr-1, while rates of soil CH4 uptake are reduced by
 50%, to 2.0 kg C ha-1 yr-1. The mean annual N2O EFd of fertilized lawns
 and urban forests is 1.4%, suggesting that urban soils can be regional
 hotspots of N2O emissions. On a global basis, conversion of land to urban
 greenspaces has increased soil N2O emission by 0.46 Tg N2O-N yr-1 and
 decreased soil CH4 uptake by 0.58 Tg CH4-C yr-1. Urbanization-driven
 changes in soil N2O emission and CH4 uptake are associated with changes in
 soil properties (bulk density, pH, total N content and C/N ratio),
 increased temperature, and management practices, especially fertilizer
 use. Overall, our meta-analysis shows that urbanization increases soil N2O
 emissions and reduces the role of soils as a sink for atmospheric CH4.
 These effects can be mitigated by avoiding soil compaction, reducing
 fertilization of lawns, and restoring native ecosystems in urban
 landscapes.
DOI: 10.6078/d1k992
title: Hyperlocal monitoring of traffic-related air pollution to assess near-term impacts of sustainable transportation interventions

description: Traffic and air pollution are two of the South Coast Air Basin’s most
 difficult challenges for environmental sustainability. This challenge also
 exists at local levels, such as in the City of Riverside, where two major
 highways service the area (CA 60/I-215 and CA 91), and background air
 pollution is high in the afternoons due to pollution transport and
 photochemistry. The South Coast Air Quality Management District predicts
 continued increases in VMT in the Basin, while secondary ozone levels are
 also beginning to increase after decades-long reductions. Heavy-duty trips
 are also increasing due to increasing goods movement activity in inland
 Southern California. Therefore, it can be conjectured that traffic-related
 air pollution will continue to be a challenge for the City of Riverside,
 whose corridors service a high volume of logistics activity. This project
 proposes a low-cost, measurement-based approach for assessing the impacts
 of sustainable traffic interventions on local air pollution.
 Traffic-related air pollutions, NO2 and PM2.5, will be measured along an
 urban corridor while simultaneously implementing eco-driving strategies as
 vehicles pass through signalized intersections. The chosen testbed
 location is the City of Riverside Innovation Corridor, a six-mile roadway
 that services downtown Riverside, the University of California, Riverside,
 and several businesses and community organizations. Evaluation of traffic
 and air quality feedbacks in the testbed will provide insight into the
 effectiveness of wider-scale implementation of smart transportation
 technologies in the City of Riverside for the improvement of local air
 quality.
description: Data were derived from the following sources:
 Clarity Node S measurements along University Avenue
 in Riverside, California (USA) California Air
 Resources Board AQMIS2 online database
 Openweathermap.org GridSmart traffic
 monitoring at Iowa Avenue and University Avenue in Riverside, California
 (USA) Caltrans Performance Measurement
 System Google Maps trip time data
DOI: 10.5061/dryad.931zcrjq6
title: Rice grain weight and candidate gene marker dataset

description: It is hypothesized that the genome-wide genic markers may increase the
 prediction accuracy of genomic selection for quantitative traits. To test
 this hypothesis, a set of candidate gene based markers for yield and grain
 traits-related genes cloned across the rice genome were custom-designed. A
 multi-model, multi-locus genome-wide association study (GWAS) was
 performed using new genic markers developed to test their effectiveness
 for gene discovery. Two multi-locus models, FarmCPU and mrMLM, along with
 a single-locus mixed linear model (MLM), identified 28 significant marker
 trait associations. These associations revealed novel causative alleles
 for grain weight and pleiotropic associations with other traits. For
 instance, the marker YD91 derived from the gene OsAAP3 on chromosome 1 was
 consistently associated with grain weight, while the gene has a
 significant effect on grain yield. Furthermore, nine genomic selection
 methods, including regression-based and machine learning-based models,
 were used to predict grain weight using a leave-one-out five-fold cross
 validation approach to optimize the genomic selection model with genic
 markers. Among nine prediction models, Kernel Hilbert Space Regression
 (RKHS) is the best among regression-based models, and Random Forest
 Regression (RFR) is the best among machine learning-based models. Genomic
 prediction accuracies with and without GWAS significant markers were
 compared to assess the effectiveness of markers. The rapid decreases in
 prediction accuracy upon dropping GWAS significant markers indicate the
 effectiveness of new genic markers in genomic selection. Apart from that,
 the candidate gene-based markers were found to be more effective in
 genomic selection programs for better accuracy.
DOI: 10.5061/dryad.w6m905qtg
title: Sexual dimorphism in specialist pollinated dioecious species with complex flowers

description: Premise Pollinators with flower constancy and long nectar-feeding organs
 should favour less or no sexual dimorphism in the individual flowers of
 dioecious plants. This hypothesis is deduced because such pollinators can
 discriminate between intersexual flower size differences, and
 morphological differences between male and female flowers often diminish
 pollen transfer. Methods We compared floral traits and pollinator
 behaviour between sexes in the hawkmoth-pollinated
 species, Trichosanthes cucumeroides. We focused on the roles of
 elaborate petal fringes in pollinator attraction and pollination success
 of female and male flowers by conducting field pollinator observations and
 fringe removal experiments. Results Female flowers had a similar front
 flower size and fringe extension as male flowers, supporting our
 hypothesis. In contrast, females allocated fewer resources to floral
 biomass. Additionally, they had smaller and narrower petal lobes, lower
 fringe density, shorter tubes with inferior nectar rewards, and lower
 display size than males, which is inconsistent with the hypothesis.
 Nocturnal hawkmoths prefer flowers with long fringe extensions. Fringe
 removal significantly decreased hawkmoth visitations to both female and
 male flowers but reduced success only in females. A literature survey
 indicated that specialist-pollinated species tend to exhibit similar or
 larger female attraction to floral organs more frequently than
 generalist-pollinated species. Conclusions Female flowers have evolved
 similar fringe extensions to male flowers, likely increasing pollinator
 attraction even slightly, and exhibited lower biomass of other floral
 parts and nectar production than male flowers. Our findings imply that
 female-biased resource limitation and flower-size-sensitive pollinators
 together exert sex-specific selection of floral traits in T.
 cucumeroides.
description: Please see detail in paper "Sexual dimorphism in specialist pollinated
 dioecious species with complex flowers" in <em>American Journal
 of Botany</em>.
DOI: 10.5061/dryad.pg4f4qrv4
title: Unravelling the genetic diversity of water yam (Dioscorea alata L.) accessions from Tanzania using simple sequence repeat (SSR) markers

description: Water yam (Dioscorea alata L.) is among the most cultivated
 species used as a source of food and income for small-scale farmers in
 Tanzania. However, little is documented about Dioscorea species available
 in Tanzania, including their genetic diversity. This study used ten
 polymorphic microsatellite markers to determine the genetic diversity and
 relationship of 63 D. alata accessions from six major
 producing regions. Results revealed a polymorphic information content
 (PIC) of 0.63, while the number of alleles per locus ranged from 4 to 12
 with a mean of 7.60. The expected heterozygosity ranged from 0.17 to 0.74,
 with a mean of 0.49, which suggests moderate genetic diversity
 of D. alata accessions. Kagera region had the highest mean number
 of (1.5) private alleles. Analysis of molecular variance revealed that 91%
 of the variation was attributed to within-population while
 among-population contributed 9% of the total variation. The highest
 Nei's genetic distance (0.65) was for accessions sampled from Arusha
 and Mtwara regions. Principal coordinate analysis and cluster analysis
 using Unweighted Paired Group Method using Arithmetic (UPGMA) grouped D.
 alata accessions into two major clusters regardless of
 geographical origin and local names. The Bayesian structure analysis
 confirmed the two clusters obtained in UPGMA and revealed an admixture
 of D. alata accessions in all six regions suggesting
 farmers' extensive exchange of planting materials. These results are
 helpful in the selection of D. alata accessions for
 breeding programs in Tanzania.
DOI: 10.5061/dryad.vhhmgqnzc
title: Original data of heterospecific pollen in three Silene species

description: PREMISE: In communities with multiple co-flowering species, those species
 that have not evolved an avoidance mechanism may exhibit tolerance to
 heterospecific pollen (HP) deposition as an adaptive strategy to minimize
 any deleterious effects of HP transfer, but empirical evidence for the
 tolerance hypothesis remains scarce. METHODS: To estimate the potential
 effects of heterospecific pollen deposition (HPD) on female reproductive
 success, we counted conspecific (CP) and HP pollen grains deposited on
 stigmas and assessed subsequent seed sets of both open- and
 hand-pollinated flowers in three co-flowering Silene species with exposed
 stigmas that usually received numerous HP grains in nature. RESULTS: HP
 percent per flower varied from 16.6% to 43.0% among the three species.
 Silene chungtienensis experienced lower HP percent and the CP-HP
 relationship was neutral, S. gracilicaulis and S. yunnanensis experienced
 relatively higher HP percent and the CP-HP relationship was positive.
 Positive effects of CP and HP number on natural seed set were observed in
 all three species, but stronger negative effects of HP percent in S.
 chungtienensis and S. gracilicaulis. In hand-pollinated flowers of the
 three Silene species, there was no decrease in seed set with HP whether CP
 was in excess or insufficient, indicating no negative effects of HPD on
 seed production. CONCLUSIONS: Consistent with the tolerance hypothesis,
 our results indicated that species experiencing higher HP interference are
 likely to be tolerant to an increase of HP percent. These species with
 generalist-pollinated flowers may benefit from an increase in conspecific
 pollen deposition, despite the associated increase in heterospecific
 pollen deposition.
DOI: 10.5061/dryad.dz08kps1z
title: Effects of warming on structure of aquatic communities in tropical bromeliad microecosystems

description: Freshwaters are among the most vulnerable ecosystems to climate warming,
 with projected temperature increases over the coming decades leading to
 significant losses of aquatic biodiversity. Experimental studies that
 directly warm entire natural ecosystems in the tropics are needed, for
 understanding the disturbances in aquatic communities. Therefore, we
 conducted an experiment to test the impacts of predicted future warming on
 density, alpha diversity, and beta diversity of freshwater aquatic
 communities, inhabiting natural microecosystems – Neotropical tank
 bromeliads. Aquatic communities within the tank bromeliads were
 experimentally exposed to warming, temperatures ranging from 23.58 to
 31.72°C. Linear regression analysis was used to test the impacts of
 warming. Next, distance-based redundancy analysis was performed to assess
 how warming might alter total beta diversity and its components. This
 experiment was conducted across a gradient of habitat size (bromeliad
 water volume) and availability of detrital basal resources. A combination
 of the highest detritus biomass and higher experimental temperatures
 resulted in the greatest density of flagellates. However, the density of
 flagellates declined in bromeliads with higher water volume and lower
 detritus biomass. Moreover, the combination of the highest water volume
 and high temperature reduced density of copepods. Finally, warming changed
 microfauna species composition, mostly through species substitution (βrepl
 component of total beta-diversity). These findings indicate that warming
 strongly structures freshwater communities by reducing or increasing
 densities of different aquatic community groups. It also enhances
 beta-diversity, and many of these effects are modulated by habitat size or
 detrital resources.
description: Further methodological details on data collection can be found
 within the published paper and its supplementary material.
description: This archive contains the dataset used for all analyses and
 plotting carried out in this paper. Please see the "ReadMe"
 sheet within the Excel file for further descriptive information on the
 contents of the dataset and the units of each column. All additional
 methodological details are present in the main and supplementary
 components of the published paper.
DOI: 10.15468/dl.rdwue5
title: Occurrence Download

description: A dataset containing 66355 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Bidens frondosa L."
 ]
}

 The dataset includes 66355 records from 517 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0149763-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5tu4qx
title: Occurrence Download

description: A dataset listing the 65083 species recorded in GBIF matching the query:
{
 "and" : [
 "Country is United Kingdom of Great Britain and Northern Ireland",
 "BasisOfRecord is one of (Human Observation)"
 ]
}

 The dataset's 65083 records were derived from 1244 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025683-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.