cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.th71ss0
title: Data from: The evolutionary history of the Cape hare (Lepus capensis sensu lato): insights for systematics and biogeography

description: Inferring the phylogeography of species with large distributions helps
 deciphering major diversification patterns that may occur in parallel
 across taxa. Here, we infer the evolutionary history of the Cape hare,
 Lepus capensis sensu lato, a species distributed from southern Africa to
 Asia, by analysing variation at 18 microsatellites and 9 DNA (1
 mitochondrial and 8 nuclear) sequenced loci, from field and
 museum-collected samples. Using a combination of assignment and
 coalescent-based methods, we show that the Cape hare is composed of five
 evolutionary lineages, distributed in distinct biogeographic regions –
 north-western Africa, eastern Africa, southern Africa, the Near East and
 the Arabian Peninsula. A deep phylogenetic break possibly dating to the
 Early Pleistocene was inferred between the African and Asian L. capensis
 groups, and the latter appear more closely related to other Eurasian hare
 species than to African Cape hares. The inferred phylogeographic structure
 is shared by numerous taxa distributed across the studied range,
 suggesting that environmental changes, such as the progressive
 aridification of the Saharo-Arabian desert and the fluctuations of
 savannah habitats in Sub-Saharan Africa, had comparable impacts across
 species. Fine-scale analyses of the western Sahara-Sahel populations
 showed rich fragmentation patterns for mitochondrial DNA but not for
 microsatellites, compatible with the environmental heterogeneity of the
 region and female philopatry. The complex evolutionary history of L.
 capensis sensu lato, which possibly includes interspecific gene flow, is
 not reflected by taxonomy. Integrating evolutionary inference contributes
 to an improved characterization of biodiversity, which is fundamental to
 foster the conservation of relevant evolutionary units.
description: GenotypesGenotypes from microsatellite loci.genotypes.xlsx01_CYTB_longCytochrome b long sequence alignment.02_CYTB_shortCytochrome b short sequence alignment.03_DARC_phasedDARC phased sequence alignment.04_HPX_phasedHPX phased sequence alignment.05_SPTBN_phasedSPTBN1 phased sequence alignment.06_TF_phasedTF phased sequence alignment.07_OXA1L_phasedOXA1L phased sequence alignment.08_TG_phasedTG phased sequence alignment.09_TSHB_phasedTSHB phased sequence alignment.10_UCP2_phasedUCP2 phased sequence alignment.
DOI: 10.15468/dl.xz9uqj
title: Occurrence Download

description: A dataset containing 551 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Akodon torques"
 ]
}

 The dataset includes 551 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001681-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.h7b12g4
title: Data from: Long-term shifts in the seasonal abundance of adult Culicoides biting midges and their impact on the potential for arbovirus outbreaks

description: 1. Surveillance of adult Culicoides biting midge flight activity is used
 as an applied ecological method to guide the management of arbovirus
 incursions on livestock production in Europe and Australia. 2. To date the
 impact of changes in the phenology of adult vector activity on arbovirus
 transmission has not been defined. We investigated this at two sites in
 the UK, identifying 150,000 Culicoides biting midges taken from 2867
 collections over a nearly 40 year timescale. 3. Whilst no change in
 seasonal activity was recorded at one site, shifts in first adult
 appearance and last adult appearance increased the seasonal activity
 period of Culicoides species at the other site by 40 days over the time
 period. 4. Lengthening of the adult activity season was driven by an
 increase in abundance of Culicoides and correlated with local increases in
 temperature and precipitation. This diversity in response poses
 significant challenges for predicting future transmission and
 overwintering risk. 5. Policy implications: Our analysis shows a dramatic
 and consistent increase of the adult active period of Culicoides, but also
 that this varies significantly from site to site, suggesting broad-scale
 analyses alone are insufficient to understand the potential impacts of
 changes in climate on arbovirus vector populations.
description: Annual Trends Preston
 and StarcrossThis file contains the
 Culicoides trap collection data for both Preston and Starcross sites and
 source code for analysis using the Bayesian models described in the
 paper.
DOI: 10.5061/dryad.rd00gk7
title: Data from: The impact of bilateral ongoing activity on evoked responses in mouse cortex

description: In the absence of external stimuli or overt behavior, the activity of the
 left and right cortical hemispheres shows fluctuations that are largely
 bilateral. Here we show that these fluctuations are largely responsible
 for the variability observed in cortical responses to sensory stimuli.
 Using widefield imaging of voltage and calcium signals, we measured
 activity in the cortex of mice performing a visual detection task.
 Bilateral fluctuations invested all areas, particularly those closest to
 the midline. Activity was less bilateral in the monocular region of
 primary visual cortex and, especially during task engagement, in secondary
 motor cortex. Ongoing bilateral fluctuations dominated unilateral visual
 responses, and interacted additively with them, explaining much of the
 variance in trial-by-trial activity. Even though these fluctuations
 occurred in regions necessary for the task, they did not affect detection
 behavior. We conclude that bilateral ongoing activity continues during
 visual stimulation and has a powerful additive impact on visual responses.
description: datasetShimaoka_etal_2019_eLife.mat
DOI: 10.15468/dl.8t5xfp
title: Occurrence Download

description: A dataset containing 725 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Schizopepon bryoniifolius",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 725 records from 52 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001682-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.8ts30t5
title: Data from: Degradation of internal organic matter is the main control on pteropod shell dissolution after death

description: The potential for preservation of thecosome pteropods is thought to be
 largely governed by the chemical stability of their delicate aragonitic
 shells in seawater. However, sediment trap studies have found that
 significant carbonate dissolution can occur above the carbonate saturation
 horizon. Here we present the results from experiments conducted on two
 cruises to the Scotia Sea to directly test whether the breakdown of the
 organic pteropod body influences shell dissolution. We find that, on the
 timescales of three to thirteen days, the oxidation of organic matter
 within the shells of dead pteropods is a stronger driver of shell
 dissolution than the saturation state of seawater. Three to four days
 after death, shells became milky white and nano‐SEM images reveal
 smoothing of internal surface features and increased shell porosity, both
 indicative of aragonite dissolution. These findings have implications for
 the interpretation of the condition of pteropod shells from sediment traps
 and the fossil record, as well as for understanding the processes
 controlling particulate carbonate export from the surface ocean.
description: Ambient seawater (omega
 1.40) - liveFile contains 5 folders
 with the reconstructed CT data (*.DICOM format) and scan set-up
 information (*.pca format) for the 5 live specimens of L.helicina
 antarctica incubated for 13 days in ambient seawater (omega aragonite =
 1.40)1)
 Ambient seawater (omega 1.40) - live.zipAmbient seawater (omega
 1.40) - decayFile contains 5 folders
 with the reconstructed CT data (*.DICOM format) and scan set-up
 information (*.pca format) for the 5 decaying specimens of L.helicina
 antarctica incubated for 13 days in ambient seawater (omega aragonite =
 1.40)2)
 Ambient seawater (omega 1.40) - decay.zipSlightly undersaturated
 seawater (omega 0.89) - decayFile contains 5 folders
 with the reconstructed CT data (*.DICOM format) and scan set-up
 information (*.pca format) for the 5 decaying specimens of L.helicina
 antarctica incubated for 13 days in seawater adjusted to an aragonite
 saturation of 0.893) Slightly undersaturated
 seawater (omega 0.89) - decay.zipHighly undersaturated
 seawater (omega 0.78) - decayFile contains 5 folders
 with the reconstructed CT data (*.DICOM format) and scan set-up
 information (*.pca format) for the 5 decaying specimens of L.helicina
 antarctica incubated for 13 days in seawater adjusted to an aragonite
 saturation of 0.784) Highly undersaturated
 seawater (omega 0.78) - decay.zip
DOI: 10.5281/zenodo.18391559
title: ИДИОМАЛАРНИНГ ТАРЖИМА МАСАЛАЛАРИ: ТЎҒРИ ТАРЖИМА, МОС ЭКВИВАЛЕНТ, ТАФОВУТЛАР

description:  Мазкур мақола идиомаларни таржимада мос эквивалентлар орқали узатиш масалаларини қамраб олади. Идиомаларнинг маъно тузилиши, компонент таркиби ва функционал хусусиятлари тадқиқ этилиб, эквивалент танлашдаги мезонлар: семантик яқинлик, стиллик мувофиқлик ва прагматик адекватлик кўриб чиқилади. Муаллиф ўзбек ва инглиз тиллари материаллари асосида турли турдаги эквивалентлар — тўлиқ, қисман ва функционал эквивалентлар мисолларини таҳлил қилади. Мақолада таржимон учун амалий тавсиялар ҳам берилади.
DOI: 10.5281/zenodo.18391558
title: ИДИОМАЛАРНИНГ ТАРЖИМА МАСАЛАЛАРИ: ТЎҒРИ ТАРЖИМА, МОС ЭКВИВАЛЕНТ, ТАФОВУТЛАР

description:  Мазкур мақола идиомаларни таржимада мос эквивалентлар орқали узатиш масалаларини қамраб олади. Идиомаларнинг маъно тузилиши, компонент таркиби ва функционал хусусиятлари тадқиқ этилиб, эквивалент танлашдаги мезонлар: семантик яқинлик, стиллик мувофиқлик ва прагматик адекватлик кўриб чиқилади. Муаллиф ўзбек ва инглиз тиллари материаллари асосида турли турдаги эквивалентлар — тўлиқ, қисман ва функционал эквивалентлар мисолларини таҳлил қилади. Мақолада таржимон учун амалий тавсиялар ҳам берилади.
DOI: 10.18167/dvn1/8r3ot1
title: Family farming in Santarém region, Brazilian Amazon: survey with rural community representatives (Odyssea project, 2019)
title: Agriculture familiale dans la région de Santarém, Amazonie Brésilienne: enquêtes avec des représentants de communautés rurales (projet Odyssea, 2019)
title: Agricultura familiar na região de Santarém, Pará, Amazonia Brasileira: enquetes com representantes de comunidades rurais (projeto Odyssea, 2019)

description: This data was collected during the project Odyssea - Observatory of the Dinamics of Societies and Environments in the Amazon. Through a partnership with Family Farmer Unions (STTR), community researchers realized surveys with kobotoolbox application in 32 rural communities in the Santarem Planalto, in April-June 2019. 
The research, built through a citizen science process, involving farmer unions and community leaders, aimed at understanding the impact on smallholders of global changes, in particular agrobusiness pressure (soy).
description: This data was collected as part of two projects: Odyssea - Observatory of the Dynamics of Societies and their Environments in the Amazon (H2020-RISE, 2016-2019; see: https://www.odyssea-amazonia.org) and INCT Odisseia - Instituto Nacional de Ciencia e Tecnologia "Observatório das Dinâmicas Socioambientais" (CNPq-CAPES-FAP, 2018-2022; see: http://inct-odisseia.i3gs.org)
description: KoboToolBox, Excel, SPSS, 16.16.27
DOI: 10.5061/dryad.88h3gp6
title: Data from: Queen execution, diploid males, and selection for and against polyandry in the Brazilian stingless bee Scaptotrigona depilis

description: Female mating frequency varies. Determining the causes of this variation
 is an active research area. We tested the hypothesis that in stingless
 bees, Meliponini, single mating is due to the execution of queens that
 make a matched mating at the CSD (complementary sex determination) locus
 and have diploid male offspring. We studied the Brazilian species
 Scaptotrigona depilis. We made up 70 test colonies so that 50% (single
 matched mating), 25% (double mating), 12.5% (4-mating), or 0% (single
 non-matched mating) emerging brood were diploid males. Queen execution
 following diploid male emergence was equal and high in colonies producing
 50% (77% executed) and 25% (75%) diploid males, versus equal and low in
 colonies producing 12.5% (7%) and 0% (0%) diploid males. These results
 show that queens that mate with two males with similar paternity suffer an
 increased chance of being executed, which selects against double mating.
 However, double mating with unequal paternity (e.g., 25:75), which
 occasionally occurs in S. depilis, is selectively neutral. Single mating
 and double mating with unequal paternity form one adaptive peak. The
 results show a second adaptive peak at 4-mating. However, this is
 inaccessible via gradual evolutionary change in a selective landscape with
 reduced fitness at double mating.
description: Raw data queen
 executionThis datasheet provided
 the information for the Figure 2 of the manuscript, basically the only
 result presented. This table shows the queen execution (0 = no; 1 = yes)
 on colonies under different treatments (proportion of diploid males
 emerging on the brood). It also includes the queen that produced the
 diploid males, as well as the time in which the queen execution was
 observed. The survival rate that was used for the Figure 2 prodution is
 also presented for each group of treatment.Dryad_58836R2.xlsx
DOI: 10.5061/dryad.c5f0ps6
title: Data from: Outstanding intraindividual genetic diversity in fissiparous planarians (Dugesia, Platyhelminthes) with facultative sex

description: Background: Predicted genetic consequences of asexuality include high
 intraindividual genetic diversity (i.e., the Meselson effect) and
 accumulation of deleterious mutations (i.e., Muller’s Ratchet), among
 others. These consequences have been largely studied in parthenogenetic
 organisms, but studies on fissiparous species are scarce. Differing from
 parthenogens, fissiparous organisms inherit part of the soma of the
 progenitor, including somatic mutations. Thus, in the long term,
 fissiparous reproduction may also result in genetic mosaicism, besides the
 presence of the Meselson effect and Muller’s Ratchet. Dugesiidae
 planarians show outstanding regeneration capabilities, allowing them to
 naturally reproduce by fission, either strictly or combined with sex
 (facultative). Therefore, they are an ideal model to analyze the genetic
 footprint of fissiparous reproduction, both when it is alternated with sex
 and when it is the only mode of reproduction. Results: In the present
 study, we generate and analyze intraindividual cloned data of a nuclear
 and a mitochondrial gene of sexual, fissiparous and facultative wild
 populations of the species Dugesia subtentaculata. We find that most
 individuals, independently of their reproductive strategy, are mosaics.
 However, the intraindividual haplotype and nucleotide diversity of
 fissiparous and facultative individuals is significantly higher than in
 sexual individuals, with no signs of Muller’s Ratchet. Finally, we also
 find that this high intraindividual genetic diversity of fissiparous and
 facultative individuals is composed by different combinations of ancestral
 and derived haplotypes of the species. Conclusions: The intraindividual
 analyses of genetic diversity point out that fissiparous reproduction
 leaves a very special genetic footprint in individuals, characterized by
 mosaicism combined with the Meselson effect (named in the present study as
 the mosaic Meselson effect). Interestingly, the different intraindividual
 combinations of ancestral and derivate genetic diversity indicate that
 haplotypes generated during periods of fissiparous reproduction can be
 also transmitted to the progeny through sexual events, resulting in
 offspring showing a wide range of genetic diversity and putatively
 allowing purifying selection to act at both intraindividual and individual
 level. Further investigations, using Dugesia planarians as model
 organisms, would be of great value to delve into this new model of genetic
 evolution by the combination of fission and sex.
description: Cox1_DryadCox1 alignment in fasta format used to infer the phylogenetic treeTMED9_DryadTMED9 alignment in fasta format used to infer the phylogenetic tree
DOI: 10.5061/dryad.3pm80bp
title: Data from: Species-specific calcification response of Caribbean corals after two-year transplantation to low aragonite saturation submarine springs

description: Coral calcification is expected to decline as atmospheric carbon dioxide
 concentration increases. We assessed the potential of Porites astreoides,
 Siderastrea siderea and Porites porites to survive and calcify under
 acidified conditions in a two-year field transplant experiment around
 low-pH, low aragonite saturation (Ωarag) submarine springs. Slow-growing
 S. siderea had the highest post-transplantation survival and showed an
 increase in tissue concentrations of Symbiodiniaceae, chlorophyll a, and
 protein at the low Ωarag site. Nubbins of P. astreoides had 20% lower
 survival and higher chlorophyll a concentration at the low Ωarag site.
 Only 33% of P. porites nubbins survived at low Ωarag and their linear
 extension and calcification rates were reduced. The density of skeletons
 deposited after transplantation was 15-30% lower for all species at the
 low Ωarag spring. These results suggest that corals with slow
 calcification rates and high Symbiodiniaceae, chlorophyll a and protein
 concentrations may be less susceptible to ocean acidification, albeit with
 reduced skeletal density. We postulate that corals in the springs are
 responding to greater energy demands for overcoming larger differences in
 carbonate chemistry between the calcifying medium and the external
 environment. The differential mortality, growth rates and physiological
 changes may impact future coral species assemblage and the reef framework
 robustness.
description: MartinezEtAl2019_CaribbeanCoralCalcification1_Martinez2019_coral_survival2_Martinez2019_coral_density3_Martinez2019_coral_extension4_Martinez2019_coral_calcification5_Martinez2019_coral_multiplotSkeleton6_Martinez2019_coral_zoox7_Martinez2019_coral_chlorophyll8_Martinez2019_coral_protein9_Martinez2019_coral_multiplotTissue
DOI: 10.5061/dryad.v7fp8ms
title: Data from: Discovering floristic and geoecological gradients across Amazonia

description: Aim: To map and interpret floristic and geoecological patterns across the
 Amazon basin by combining extensive field data with basin-wide Landsat
 imagery and climatic data Location: Amazonia Taxon: Ground truth data on
 ferns and lycophytes; remote sensing results reflect forest canopy
 properties Methods: We used field plot data to assess main ecological
 gradients across Amazonia and to relate floristic ordination axes to soil
 base cation concentration, CHELSA climatic variables and reflectance
 values from a basin-wide Landsat image composite with generalized linear
 models (GLM). Ordination axes were then predicted across all Amazonia
 using Landsat and CHELSA, and a regional subdivision was obtained using
 k-medoid classification. Results: The primary floristic gradient was
 strongly related to base cation concentration in the soil, and the
 secondary gradient to climatic variables. The Landsat image composite
 revealed a tapestry of broad-scale variation in canopy reflectance
 characteristics across Amazonia. Ordination axis scores predicted using
 Landsat and CHELSA variables produced spatial patterns consistent with
 existing knowledge on soils, geology and vegetation, but also suggested
 new floristic patterns. The clearest dichotomy was between central
 Amazonia and the peripheral areas, and the available data supported a
 classification into at least eight subregions. Main conclusions Landsat
 data are capable of predicting soil-related species compositional patterns
 of understory ferns and lycophytes across the Amazon basin with
 surprisingly high accuracy. Although the exact floristic relationships may
 differ among plant groups, the observed ecological gradients must be
 relevant for other plants as well, since surface reflectance recorded by
 satellites is mostly influenced by the tree canopy. This opens exciting
 prospects for species distribution modelling, conservation planning, and
 biogeographical and ecological studies on Amazonian biota. Our maps
 provide a preliminary geoecological subdivision of Amazonia that can now
 be tested and refined using field data of other plant groups and from
 hitherto unsampled areas.
description: Environmental and fern
 species data for Amazonian plotsSpecies and soil data
 were collected in the field by the researchers mentioned as data providers
 for each plot. Reflectance data come from a Landsat TM/ETM+ image
 composite based on images acquired in 2000-2009 and processed using R code
 written by Jasper Van doninck. CHELSA and SRTM data come from respective
 online portals. See README file for explanation of the data contained in
 each column.Tuomisto_etal_JBI-18-0631_data.csv
DOI: 10.5061/dryad.27812c7
title: Data from: Reconstruction of larval origins based on genetic relatedness and biophysical modeling

description: The assessment of the mechanisms and patterns of larval connectivity
 between geographically separated populations leads to a better
 understanding of benthic marine population dynamics, especially in
 commercially valuable species. This study investigated for the first time
 the fine-scale temporal genetic variability of new settlers and their
 origins in a benthic marine organism with one of the longest pelagic
 larval phases, the Caribbean spiny lobster (Panulirus argus). We genotyped
 newly settled postlarvae in the Florida Keys and adults of spiny lobster
 from the Florida Keys and throughout the Caribbean Sea. We identified
 strong larval connectivity between Dominican Republic, Belize, Nicaragua,
 the Florida Keys, and West-Florida. The larval dispersal modeling suggests
 that Florida’s lobster population could receive recruits from within and
 from other areas outside its state and national maritime boundaries. The
 genetic analyses refine the oceanographic model indicating that the
 connectivity patterns described could also result from unknown parental
 populations sourcing adults and postlarvae in different spawning seasons
 to the Florida Keys. We discuss the importance of small temporal scales to
 identify patterns in larval export. Our findings are significant on two
 levels. From the larval dispersal perspective, genetic results and
 biophysical modeling identify patterns of gene flow enhancing persistence
 of local populations. From an economic and fishery perspective, P. argus
 is the most important commercial species in the Caribbean and our results
 inform how considering larval source and sink dynamics across
 international boundaries could improve management plans at local,
 national, and regional levels.
description: Microsatellite genotypes
 from Caribbean spiny lobsterGenotypes from 14
 microsatellite loci from adult and postlarvae population of the Caribbean
 spiny lobster, Panulirus argus.Genotype data_Panulirus
 argus.txt