cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.tmpg4f53j
title: Data from: Plastid phylogenomics of the tribe potentilleae (Rosaceae)

description: The tribe Potentilleae comprises approximately 1700 species in 13 genera,
 making it one of the largest of the 16 tribes in Rosaceae. Our
 understanding of the composition and relationships among members of
 Potentilleae has advanced dramatically with the application of molecular
 markers in the last two decades. Yet there is still much work remaining
 toward a robust phylogenetic framework for the entire Potentilleae and a
 comprehensive genus-level dating framework for the tribe. The goals of the
 present study were to establish a phylogenetic framework for Potentilleae,
 infer the origin and diversification of the tribe using a temporal
 framework, and explore the taxonomic implications in light of the updated
 phylogenetic framework. We used the plastome sequences from 158 accessions
 representing 139 taxa covering all 13 recognized genera of the tribe to
 reconstruct the Potentilleae phylogeny. High phylogenetic resolution was
 recovered along the Potentilleae backbone. Two major clades were recovered
 within Potentilleae, corresponding to two subtribes Fragariinae and
 Potentillinae. Within Fragariinae, two subclades were recovered. In one
 subclade, Sibbaldia sensu stricto is sister to a clade containing
 Sibbaldianthe, Comarum, Farinopsis, and Alchemilla sensu lato. In the
 other subclade, Fragaria is sister to a clade comprising Chamaerhodos,
 Chamaecallis, Drymocallis, Dasiphora, and Potaninia. Within Potentillinae,
 Argentina is sister to Potentilla sensu stricto. Within Potentilla sensu
 stricto, clade Himalaya is sister to Alba, and the Himalayan-Alba clade
 together is sister to a clade comprising Reptans, Potentilla ancistrifolia
 Bunge, Fragarioides, Ivesioid, and Argentea. Divergence time estimates
 indicated that tribe Potentilleae originated during the middle Eocene, and
 subtribes Fragariinae and Potentillinae diverged around the
 Eocene-Oligocene transition, and divergence times dated for Potentilleae
 genera ranged from the early Miocene to the late Pleistocene.
description: # Data from: Plastid phylogenomics of the tribe potentilleae (Rosaceae)
 [https://doi.org/10.5061/dryad.tmpg4f53j](https://doi.org/10.5061/dryad.tmpg4f53j) ## Description of the data and file structure ### Files and variables #### File: gene\_158\_phylogenetic\_analysis\_dataset.fasta **Description:** data matrix used for phylogenetic analysis of Potentilleae. #### File: time2\_molecular\_dating\_dataset.fasta **Description:** data matrix used for molecular dating of Potentilleae. ## Code/software n/a
DOI: 10.5061/dryad.t76hdr855
title: Methane emissions in a subtropical mangrove forest (Ishikaki Island, Japan)

description: The data set provides CH4 flux from buttress roots and stems of
 individuals of Bruguiera gymnorrhiza of different sizes in Ishigaki
 Island, Japan. It also provides CH4 flux from trees and sediments over a
 24-hour cycle.
description: Any program that can read .csv files
description: # Data used in: Variability in methane emissions from stems and buttress
 roots of Bruguiera gymnorrhiza trees in a subtropical mangrove forest
 Daniel Epron, Takumi Mochidome, A.T.M. Zinnatul Bassar, Rempei Suwa CH4
 fluxes were measured using a cavity-enhanced absorption spectroscopy gas
 analyser (Li 7810, Li-Cor; Lincoln, USA) with two 6 mm diameter 2 m long
 PTFE tubes. Changes in the CH4 and CO2 concentrations in the stem chamber
 were recorded for 4 min at a frequency of 1 Hz. For buttress roots and
 stem, a polypropylene chamber bases were affixed to the bark surface with
 neutral seal putty, covering an area of 45 cm2. The stem chambers were
 closed by affixing a polypropylene lid lined with a silicone rubber
 gasket. For sediment, a circular chamber made of clear acrylic resin
 (diameter, 32 cm; height, 14.6 cm) was affixed to PVC collars inserted 10
 cm into the sediment. The slopes of the linear variations in CH4
 concentration in the chambers over time were used to calculate CH4
 emissions, which was expressed per unit area. The experiment was performed
 in July 2022 in a mangrove forest extending about 1500 m along the
 intertidal banks of the Miyara River estuary on Ishigaki Island (Japan,
 2421'N 12412'E). Trees of B. gymnorrhiza were selected in three
 plots. Plot #1 and plot #2 are located near the river mouth on the left
 bank and on the right bank respectively while plot#3 is further upstream
 on the right bank. Trees were selected to cover a large range of diameter
 at breast height (DBH), from 10.5 to 61.5 cm. File 24hhours_flux (data
 used in Figure 5) CH4 fluxes were measured at eight occasions over 24
 hours on two trees at four positions (buttress roots and stems) and on
 three soil collars. Trees were located in plot 1 File Tree_flux.csv (data
 used in Figure 14) CH4 fluxes were measured once on 15 trees at at least
 two positions (buttress roots and lower part of the stems) Column names in
 both files: * Plot ID * Tree ID * DBH: diameter at breast height in cm *
 Position: root, stem or soil * Height: height of the chamber from the soil
 in cm * Time: Time and date of CH4 flux measurement * Flux_CH4: Net CH4
 flux in nmol m-2 s-1, expressed per unit area of either root, stem or soil
 covered by the chamber.
DOI: 10.5061/dryad.h44j0zpqp
title: Data for: Four new species of Viola (Violaceae) from southern China

description: ITS sequences for the article 'Four new species of Viola (Violaceae)
 from southern China'. Our sequences are for 4 new species, i.e. Viola
 heyuanensis, V.
 chaozhouensis, V.qingruii and V. longissima.
description: This tree was generated by Mrbayes, and the ITS sequences were
 downloaded from NCBI Genbank or sequenced by our lab.
DOI: 10.5061/dryad.ttdz08m3b
title: High promiscuity among females of the invasive pest species Drosophila suzukii

description: Drosophila suzukii (Matsumura, 1931), the spotted-wing drosophila, is a
 highly invasive fruit fly that spread from Southern Asia across most
 regions of Asia, and in the last fifteen years has invaded Europe and the
 Americas. It is an economically important pest of small fruits such as
 berries and stone fruits. Drosophila suzukii speciated by adapting to
 cooler, mountainous and forest environments. In temperate regions, it
 evolved seasonal polyphenism traits which enhanced its survival during
 stressful winter population bottlenecks. Consequently, in these temperate
 regions, the populations undergo seasonal reproductive dynamics. Despite
 its economic importance, no data are available on the behavioural
 reproductive strategies of this fly. The presence of polyandry, for
 example, has not been determined despite the important role it might play
 in the reproductive dynamics of the populations. We explored the presence
 of polyandry in an established population in Trentino, a region in North
 Italy. In this area, D. suzukii overcomes the winter bottleneck and
 undergoes a seasonal reproductive fluctuation. We observed a high remating
 frequency in females during the late spring demographic explosion that led
 to the abundant summer population. The presence of a high degree of
 polyandry and shared paternity associated with the post-winter population
 increase raises the question of the possible evolutionary adaptive role of
 this reproductive behaviour in D. suzukii.
description: Multilocus genotyping was
 performed using four dinucleotide repeat microsatellite loci: DS05, DS09,
 DS15 and DS22 chosen from the previously characterized SSR sequences
 (Fraimount et al., 2015). Genotypes were determined for each mother and
 her progeny.
description: Simple text editor or Microsoft Excel.
description: # *Drosophila suzukii* mother and progeny genotype data The genotypes of
 12 *Drosophila suzukii* mothers and their progenies are provided at 4 SSR
 loci. ## Description of the data and file structure The first column
 contains each mother's indicator code (U3 etc.) followed by her
 progeny (U3-1..U3-20). The second and third columns contain the two SSR
 alleles present at the first SSR locus (Ds05) The fourth and fifth columns
 contain the two SSR alleles present at the second SSR locus (Ds09) The
 sixth and seventh columns contain the two SSR alleles present at the third
 SSR locus (Ds15) The eighth and ninth columns contain the two SSR alleles
 present at the fourth SSR locus (Ds22)
DOI: 10.7488/ds/8072
title: The effects of pressure on immiscibility in metallic, core–forming liquids: implications for protoplanetary differentiation

description: Data used for the publication "The effects of pressure on immiscibility in metallic, core–forming liquids: implications for protoplanetary differentiation". Data obtained as part of an investigation of liquid compositions and liquid immiscibility at high-pressure (up to 5.0 GPa) in the system Fe-Ni-S-P-C (+ minor O and N). Data is used in the publication to assess the importance of immiscibility and liquid unmixing during protoplanetary melting and differentiation. This study was funded by the the Royal Society (International Exchange grant IEC\R3\213008) and Leverhulme Trust (RPG–2021–015).
DOI: 10.5061/dryad.j6q573nk3
title: Phylogenomics resolves the Himalayan endemic Brachymeniopsis gymnostoma (Bryophyta, Funariaceae), rediscovered after almost a century, as a species of Entosthodon

description: Traits of the spore-bearing generation have historically provided the
 basis for systematic concepts across the phylogenetic spectrum and depth
 of mosses. Whether taxa characterized by a simple sporophytic architecture
 are closely related or emerged from independent reduction is often
 ambiguous. Phylogenomic inferences in the Funariaceae, which hold the
 model taxon Physcomitrium patens, revealed that several such shifts in
 sporophyte complexity occurred, mostly within the
 Entosthodon-Physcomitrium complex. Here, we report the rediscovery, nearly
 100 years after its description, of the Chinese endemic and monospecific
 genus Brachymeniopsis, which is characterized by, among other traits, its
 short sporophytes lacking the sporangial peristome teeth controlling spore
 dispersal. Phylogenomic inferences reveal that its sole species, B.
 gymnostoma arose within the clade of Entosthodon sensu stricto, a genus
 with typically long-exerted capsules. We therefore propose to transfer B.
 gymnostoma to the genus Entosthodon, as E. gymnostomus. Furthermore,
 Clavitheca poeltii, the sole species of the genus, is morphologically
 highly similar to E. gymnostomus, and should also be transferred to
 Entosthodon, but is retained as a distinct taxon, E. poeltii, until
 additional populations allow for testing the robustness of the observed
 divergence in costa and seta length between the Nepalese and Chinese
 populations.
description: Targeted DNA sequencing of nuclear loci was carried out using
 similar protocols to (Medina et al., 2019). We extracted DNA from
 gametophyte tissue of a sample of <em>Brachymeniopsis</em>
 herbarium specimen <em>Zhang</em> <em>9430</em>
 (conn) using the modified CTAB/chloroform method (Doyle and Doyle, 1987).
 We prepared an Illumina library for high-throughput sequencing using
 NEB-Next Ultra II DNA with fragmentase in 1/2 volumes. We performed target
 enrichment on 809 nuclear protein-coding genes (Medina et al., 2019) and
 included the sample with 95 other enriched libraries libraries (but no
 <em>Entosthodon</em> to avoid contamination) on an Illumina
 MiSeq 2x300 paired end sequencing. We extracted the 809 protein-coding
 genes plus flanking regions "supercontigs" with HybPiper v 1.3.1
 (Johnson et al., 2016). This Dryad repository contains the alignments,
 gene trees, and species trees with the Medina et al., (2019) samples
 plus<em> Zhang 9430</em>.
DOI: 10.5066/p1dedkqv
title: Hydrologic scenarios and ecological model output used to explore potential sea-level rise scenarios on ecological models used in Everglades restoration planning

description: One of the largest and most expensive restoration efforts in the world is occurring in the Everglades, a sub-tropical freshwater wetland system located in southern Florida. This unique ecosystem supports several endemic and endangered species, provides flood control for Florida’s large urban population, and provides water for both agriculture and drinking supply within the state. The Comprehensive Everglades Restoration Plan (CERP), authorized by Congress in 2000, guides federal, state, and local efforts to build the infrastructure necessary to bring more water into the Everglades and restore its ecological integrity. The Everglades encompasses the southern coast of Florida and restoration efforts are likely to be impacted by climate-induced sea-level rise. However, currently, many project planning studies do not formally incorporate the potential impacts of sea-level rise when evaluating restoration plan outcomes. Resource managers and project planners require methods and tools to confidently incorporate scenarios of sea-level rise into their evaluations. This effort demonstrates how incorporating sea-level rise scenarios into Everglades restoration project planning can help managers decide whether projects will maintain or improve the ecological integrity of this critical system and ensure water availability for wildlife and humans. The following model outputs were generated to explore how sea-level rise may impact ecological models: two sea-level rise scenarios (an intermediate scenario of 53 cm and a high scenario of 152 cm) using the BISECT hydrodynamic model, and the Everglades Vulnerability Analysis vegetation sub-model outputs generated using the baseline, intermediate, and high sea-level rise hydrologic scenarios. We also provide R code used to visualize the outputs.
DOI: 10.5061/dryad.zpc866tcz
title: Data for: Widespread wood placement and regrading drive lateral connectivity and reworking of the channel and floodplain in a valley bottom reset to stage 0

description: Valley bottom process reset, or the excavation of high surfaces and fill
 of incised channels combined with large wood addition, is a new method for
 creating multi-channel river-wetland corridors (also referred to as Stage
 0 valley bottoms). Valley bottom process reset seeks to increase lateral
 flow and sediment connectivity to retain flow and sediment and kickstart
 geomorphic processes that may sustain aquatic and riparian habitats. This
 anthropogenic intervention provides an opportunity to examine
 relationships among wood-induced hydraulic roughness, valley bottom
 topography, and geomorphic processes such as overbank flow and sediment
 transport, avulsion, sediment retention, and pool scour. Here, I present a
 6-year case study of a two-phase valley bottom process reset along Deer
 Creek, OR which indicates that kickstarting processes that reshape the
 floodplain requires a substantial increase in roughness and hydrologic
 connectivity. A first phase of construction enhanced hydrologic but not
 sediment connectivity, largely failing to kickstart avulsion and
 floodplain reworking even during a likely 2- to 5-year recurrence interval
 flood. A second, more intensive phase of construction substantially
 reduced the threshold flow necessary for overbank flow and incision of
 floodplain reworking, as evidenced by the occurrence of these processes
 after only a &lt; 2-year recurrence interval flood. During this flood,
 a spatially distributed wood lattice rearranged into discrete jams that
 scoured pools, retained sediment, and drove geomorphically effective
 overbank flows. While valley bottom regrading likely contributed to these
 geomorphic effects, the spatial correlation between newly incised
 floodplain channels and areas of wood aggregation indicates a substantial
 role of wood-induced hydraulic roughness and channel blockage. Wood drove
 floodplain reworking via two mechanisms: in-channel wood jams backwatered
 and constructed flow into the floodplain, and small wood jams formed in
 the floodplain forest further constricted flow through nascent channels to
 facilitate channel incision.
DOI: 10.5061/dryad.866t1g1vr
title: Supplementary information to: Recalibrating the significance of the decline effect in fish ocean acidification research

description: This data set represents a reanalysis of the work of Clements et al. 2022
 (Meta-analysis reveals an extreme “decline effect” in the impacts of ocean
 acidification on fish; PLOS Biology) wherein effect sizes initially
 presented as LnRR were converted to % impairment relative to a control
 value of 100%. The meta-analysis data set includes citation meta-data,
 relevant individual study information, and ocean-acidification-induced
 effect sizes. Three files are provided: 1) meta-data, 2) all individual
 data sets, and 3) data sets presented as study/paper means. 
description: This data set is a meta-analysis originally published by Clements
 et al. 2022 (Meta-analysis reveals an extreme “decline effect” in the
 impacts of ocean acidification on fish; PLOS Biology). New additions to
 the data set as presented here include re-analysis of effect size by
 converting LnRR to a percent impairment metric. No original data
 collection or other processing was undertaken. Analyses were performed on
 data as individual collected experimental data (one file) and as study
 means per publication (one file). 
description: The files are provided as CSV files.
DOI: 10.5061/dryad.02v6wwq7c
title: Gill morphology data and geometric morphometric data of Enteromius spp. in relation to dissolved oxygen gradients

description: We explored how range expansion of freshwater fishes coincident with
 climate warming is affected by, and then in turn affects, responses to a
 second environmental gradient – dissolved oxygen. Traits related to
 hypoxia tolerance, specifically various metrics of gill size and geometric
 morphometric proxies of gill size were quantified for a range-expanding
 cyprinid fish (Enteromius apleurogramma) in both its historical and novel
 ranges in the Mpanga River drainage of Uganda, East Africa. We found that
 E. apleurogramma followed patterns previously established in the congener
 E. neumayeri. Gill filament length and some other metrics were strongly
 divergent in long-established populations of both E. apleurogramma and E.
 neumayeri, with larger gills in hypoxic populations compared to normoxic
 ones. Range-expanding populations were intermediate to the two
 long-established populations, but divergent between themselves. Other gill
 traits such as filament number were weakly or not divergent. Furthermore,
 we show that grosser morphological traits such as opercular area can be
 successfully used as a proxy for gill size, both by direct measurement as
 well as using geometric morphometric techniques. Finally, we show that
 both parapatric conspecific populations and sympatric heterospecific
 populations can be used as reference points to approximate the “target” of
 adaptation to hypoxic conditions.
description: Some data are presented as .csv files which should be usable in
 any spreadsheet or data analysis software. Other data for geometric
 morphometrics are presented as .tps files, and can be opened as a flat
 text file, or read by the geomorph package in R.
DOI: 10.5061/dryad.1jwstqk0g
title: SNP table and metadata for: Geographically consistent hybridization dynamics between the Black-crested and Tufted Titmouse with evidence of hybrid zone expansion

description: We studied hybridization between the Black-crested and Tufted titmouse
 across two geographically distinct transects that differ in the timing of
 secondary contact by hundreds to thousands of years. We found that
 hybridization patterns correspond to localized hybrid swarms and that the
 titmouse hybrid zone is likely slowly expanding over time, a product of
 short post-natal dispersal distances coupled with weak or absent selection
 against admixture.
DOI: 10.15468/dl.yc6h5s
title: Occurrence Download

description: A dataset containing 25553756 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Passer domesticus"
 ]
}

 The dataset includes 25553756 records from 5287 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002957-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17632/mfr3x33rtd
title: Preguntas de los test y de la evocación el proyecto de innovación docente de 24/25

description: Preguntas contestadas por los estudiantes en los test tradicionales de clases y en los nuevos test de evocación. Pertenecen al proyecto de innovación docente del 24/25 desarrollado en la asignatura «Software para Robots» del Grado en Ingeniería Informática del Software de la Universidad de Oviedo.
DOI: 10.17632/mfr3x33rtd.1
title: Preguntas de los test y de la evocación el proyecto de innovación docente de 24/25

description: Preguntas contestadas por los estudiantes en los test tradicionales de clases y en los nuevos test de evocación. Pertenecen al proyecto de innovación docente del 24/25 desarrollado en la asignatura «Software para Robots» del Grado en Ingeniería Informática del Software de la Universidad de Oviedo.
DOI: 10.15468/dl.p5wha4
title: Occurrence Download

description: A dataset containing 104 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Nouelia insignis",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 104 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010262-260120142942310/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.3886/e112458v1-198069
title: Replication data for: Nudging Farmers to Use Fertilizer: Theory and Experimental Evidence from Kenya

description: We model farmers as facing small fixed costs of purchasing fertilizer and assume some are stochastically present biased and not fully sophisticated about this bias. Such farmers may procrastinate, postponing fertilizer purchases until later periods, when they may be too impatient to purchase fertilizer. Consistent with the model, many farmers in Western Kenya fail to take advantage of apparently profitable
fertilizer investments, but they do invest in response to small, time-limited discounts on the cost of acquiring fertilizer (free delivery) just after harvest. Calibration suggests that this policy can yield
higher welfare than either laissez-faire policies or heavy subsidies. (JEL Q13, Q12, Q16, Q18)
DOI: 10.15468/dl.wmxhme
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Novaguinea rudalliae",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 8 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010263-260120142942310/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.72pjxq
title: Occurrence Download

description: A dataset containing 1179542 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Psittaciformes",
 "Country is Brazil",
 "HasCoordinate is true",
 "Year is greater than or equal to 2000"
 ]
}

 The dataset includes 1179542 records from 60 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010209-260120142942310/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.