cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.3q936f7c
title: Data from: Untangling phylogenetical, geometrical and ornamental imprints on Early Triassic ammonoid biogeography: a similarity-distance decay study.

description: Ammonoids are diverse and widespread fossil shelly cephalopods that
 flourished in the world ocean during more than 300 million years before
 their total extinction, 65 million years ago. In spite of two centuries of
 intensive scientific studies, their mode(s) of life, and most particularly
 long-distance dispersal abilities remain poorly known. Here we address
 this question by looking at the latitudinal distribution of Early Triassic
 (~250 Myr) ammonoids through similarity-distance decay analyses. We
 examine and compare how rates of similarity-distance decay differ between
 various systematic, shell geometry and ornamentation groups, during the
 same ~3.5 myr Early Triassic time interval, in order to untangle
 phylogenetical, geometrical and ornamental imprints on the observed
 biogeographical pattern. Our data do not support any phylogenetical and
 shell ornamentation control on the similarity-distance decay, but rather
 evidence a significant effect of (sub-)adult shell geometry: most evolute
 morphs tend to have been more endemic than most involute ones. This result
 contrasts with the classical hypothesis that long-distance ammonoid
 dispersal mainly occurred during the earliest planktonic young stages, and
 thus that (sub-)adult morphological characteristics should not constrain
 large-scale biogeographical patterns of ammonoids. While a direct control
 by Sea Surface Temperature can be discarded, this result may indicate that
 at least some adult Triassic ammonoid morphs were good active swimmers
 able to achieve long-distance migrations, as observed for some present-day
 coleoid cephalopods.
description: Suppl. Figure 1
 Brayard&EscarguelSupplementary figure
 showing the number of Early Triassic ammonoid genera per family according
 to the mean H/D and U/D ratios of the considered familySuppl. Table 1
 Brayard&EscarguelAmmonoid occurrences.
 Updated database from Brayard et al. (2006, 2009c; see text for
 details).Suppl. Table 2
 Brayard&EscarguelSupplementary table with
 categories of H/D, U/D, W/D, W/H, shell ornamentations or features
 determined for each genus. See text and Table 1 for details (v.: venter;
 Y: yes; N: no).Suppl. Table 3
 Brayard&EscarguelMantel tests for the
 correlation between the geographical distance matrix (D) and the matrix of
 differences between two similarity matrices (S1 and S2) computed for two
 distinct phylogenetical, geometrical or ornamental categories. Lower
 triangle: Pearson’s correlation (r); upper triangle: permutation p-value
 (null hypothesis: no linear correlation between D and (S1 – S2), i.e. no
 difference between the SDD rates related to S1 and S2).
DOI: 10.5061/dryad.g645d
title: Data from: Influence of late Quaternary climate change on present patterns of genetic variation in valley oak, Quercus lobata Née

description: Phylogeography and ecological niche models (ENMs) suggest that late
 Quaternary glacial cycles have played a prominent role in shaping present
 population genetic structure and diversity, but have not applied
 quantitative methods to dissect the relative contribution of past and
 present climate vs. other forces. We integrate multilocus phylogeography,
 climate-based ENMs and multivariate statistical approaches to infer the
 effects of late Quaternary climate change on contemporary genetic
 variation of valley oak (Quercus lobata Née). ENMs indicated that valley
 oak maintained a stable distribution with local migration from the last
 interglacial period (~120 ka) to the Last Glacial Maximum (~21 ka, LGM) to
 the present compared with large-scale range shifts for an eastern North
 American white oak (Quercus alba L.). Coast Range and Sierra Nevada
 foothill populations diverged in the late Pleistocene before the LGM [104
 ka (28–1622)] and have occupied somewhat distinct climate niches,
 according to ENMs and coalescent analyses of divergence time. In
 accordance with neutral expectations for stable populations, nuclear
 microsatellite diversity positively correlated with niche stability from
 the LGM to present. Most strikingly, nuclear and chloroplast
 microsatellite variation significantly correlated with LGM climate, even
 after controlling for associations with geographic location and present
 climate using partial redundancy analyses. Variance partitioning showed
 that LGM climate uniquely explains a similar proportion of genetic
 variance as present climate (16% vs. 11–18%), and together, past and
 present climate explains more than geography (19%). Climate can influence
 local expansion–contraction dynamics, flowering phenology and thus gene
 flow, and/or impose selective pressures. These results highlight the
 lingering effect of past climate on genetic variation in species with
 stable distributions.
description: Aligned, phased
 elongation factor 1-alpha DNA sequencesAligned, phased
 elongation factor 1-alpha (ef1a) DNA sequences in NEXUS
 format.Qlobata_ef1a_forDryad.txtAligned, phased glyceraldehyde 3-phosphate dehydrogenase DNA sequencesAligned, phased glyceraldehyde 3-phosphate dehydrogenase (g3pdh) DNA sequences in NEXUS formatQlobata_g3pdh_forDryad.txtMicrosatellite (SSR) dataSheet 1 contains genotypes for 6 chloroplast microsatellite (cpSSR) loci and Sheet 2 contains genotypes for 6 nuclear microsatellite (nSSR) loci for each valley oak (Quercus lobata) sample. GPS coordinates, sample code and population codes are also given. Sheet 3 is a readme file indicating which additional articles to cite when using the data.Gugger_etal SSR forDryad.xlsxOccurrence points for ecological niche modelsOccurrence points used to construct ecological niche models for Quercus lobata (Sheet 1) and Quercus alba (Sheet 2).Gugger_etal ENM forDryad.xlsx
DOI: 10.5061/dryad.pj76g30
title: Data from: Fertilizer application effects on grain and storage root nutrient concentration

description: Fertilizer application can affect nutrient concentrations of edible plant
 products. Data from 70 crop-nutrient response trials conducted in Mali,
 Niger, Nigeria, and Tanzania were used to evaluate nutrient application
 effects on nutrient concentrations for grain of five pulse and five cereal
 crops and for storage roots of cassava (Manihot esculenta L.). Treatments
 per trial were ≥12 but this study was limited to: no fertilizer applied;
 macronutrients applied (NPK or PK); and the macronutrient treatment plus
 Mg, S, Zn, and B applied (MgSZnB). Dried grain or cassava flour samples
 were analyzed for concentrations of all essential soil nutrients except
 for Ni and Cl. Concentrations of N and K were positively correlated with
 concentrations of most other nutrients. The concentrations were relatively
 low overall for cowpea (Vigna unguiculata L.) and pigeonpea (Cajanus cajan
 L.) compared with other pulse crops and for maize (Zea mays L.) compared
 with other cereal crops. Application of NPK or PK had little effect on
 nutrient concentrations except for increased mean cereal grain
 concentrations for N, Ca, Mg, S, Zn, Cu, and B. Bean (Phaseolus vulgaris
 L.), maize and rice (Oryza sativa L.) grain concentrations were reduced by
 MgSZnB for N, K, S, Cu, Mn, and B. There were no or inconsistent effects
 of MgSZnB on other crop-nutrient concentrations. Nutrient concentrations
 are not reduced by NPK for non-legumes or PK for pulses but MgSZnB often
 reduced bean and cereal nutrient concentrations with greater reductions
 for immobile compared with mobile nutrients.
description: Biofortification through
 fertilizer nutrient application in Tropical AfricaData from 70
 crop-nutrient response trials conducted in Mali, Niger, Nigeria and
 Tanzania were used to evaluate nutrient application effects on nutrient
 concentrations for grain of five pulse and five cereal crops and for
 storage roots of cassava.Grain Nutrient Conc Study for
 Tropical Africa 2018.xlsx
DOI: 10.5061/dryad.2ht78
title: Data from: Seasonal and spatial dynamics of gas ebullition in a temperate water-storage reservoir

description: Gas ebullition of river impoundments plays an increasingly significant
 role, particularly in transporting methane CH4 from their sediments to the
 atmosphere, and contributing to the global carbon budget and global
 warming. Quantifying stochastic and episodic nature of gas ebullition is
 complicated especially when conventionally conducted by using
 coverage-limited gas traps. Current knowledge of seasonality in a
 reservoir’s gas ebullition is lacking in the literature. For this reason,
 advanced acoustic surveying was intensively applied to determine
 spatiotemporal distributions of gas ebullition in a European water-storage
 reservoir for two years. Additionally, the sampling was accompanied with
 gas collecting for analyzing gas composition. The gas released from the
 reservoir was primarily composed of CH4 (on average 52%, up to 94%). The
 longitudinal distribution of gas ebullition was mainly determined by a
 proximity to the river inflow as a source of organic matter. A magnitude
 of ebullitive fluxes within the reservoir varied up to 1,300 mL m-2 d-1(30
 mmol CH4 m-2 d-1). The most significant period of ebullition has turned
 out to be in fall, on average reaching a sevenfold ebullitive flux (70 mL
 m-2 d-1, 1.6 mmol CH4 m-2 d-1) higher than in the rest of the season. A
 substantial contribution to the fall peak was induced by an expansion of
 gas ebullition into greater depths, covering two thirds of the reservoir
 in late fall. The study demonstrates that the ebullitive fluxes of the
 temperate water storage reservoir were correlated to season, depth, and
 inflow proximity.
description: Tuser et al -
 dataThese data were resource
 data for figures in the manuscript. They include both background data from
 the field and data which arised after proccesing of acoustical data in
 Sonar5 software (see methodical chapter of the ms).
DOI: 10.5061/dryad.8vt6s95
title: Data from: Tracing the diversification history of a Neogene rodent invasion into South America

description: We investigated spatial patterns of evolutionary relatedness and
 diversification rates to test hypotheses about the historical
 biogeographic processes underlying the radiation of Neotropical rats and
 mice (Sigmodontinae, ~400 species). A negative correlation between mean
 phylogenetic distance and diversification rates of rodent assemblages
 reveals a pattern of species co-occurrence in which assemblages of closely
 related species are also the fastest diversifying ones. Subregions of the
 Neotropics occupied by distantly related species that are on average more
 slowly diversifying include Central America, northern South America, and
 the Atlantic forest. In southern South America, recent species turnover
 appears to have been higher. Ancestral locations for the main tribes of
 sigmodontines were also estimated, suggesting eastern South America and
 the Amazonian lowlands were colonized before some central Andean regions,
 even though the latter are now centers of species richness for these
 rodents. Moreover, a past connection between the tropical Andes and the
 Atlantic Forest is suggested by our results, highlighting a role for a
 hypothetical arc connecting the two biomes, which would have impacted many
 other groups of organisms. Whether rapid, recent speciation in some
 regions is related to Quaternary climatic fluctuations and the young age
 of sigmodontines (~12.7 Ma crown age) or instead to intrinsic traits of
 these rodents remains an open question. If the former is true, we
 hypothesize that contrasting trends will characterize older Neotropical
 clades.
description: Biogeographic regions
 for Sigmodontinae.A shapefile containing
 the bioregions for sigmodontines across the Neotropical
 region.Bioregions_Sigmodontinae.rarGeographic range maps for South American CricetidaeDigitized range maps of species of cricetid rodents in South America; taxonomy and distributions follow accounts in Patton, Pardiñas & D'Elia (eds.). 2015. Mammals of South America, Vol 2: Rodents, University of Chicago Press.Shapefiles_Cricetidae.rar
DOI: 10.5061/dryad.2r05d
title: Data from: Measuring CO2 and HCO3- permeabilities of isolated chloroplasts using a MIMS-18O approach

description: To support photosynthetic CO2 fixation by Rubisco, the chloroplast must be
 fed with inorganic carbon in the form of CO2 or bicarbonate. However, the
 mechanisms allowing the rapid passage of this gas and this charged
 molecule through the bounding membranes of the chloroplast envelope are
 not yet completely elucidated. We describe here a method allowing us to
 measure the permeability of these two molecules through the chloroplast
 envelope using a membrane inlet mass spectrometer and 18O-labelled
 inorganic carbon. We established that the internal stromal carbonic
 anhydrase activity is not limiting for this technique, and precisely
 measured the chloroplast surface area and permeability values for CO2 and
 bicarbonate. This was performed on chloroplasts from several plant
 species, with values ranging from 2.3 × 10–4 m s–1 to 8 × 10–4 m s–1
 permeability for CO2 and 1 × 10–8 m s–1 for bicarbonate. We were able to
 apply our method to chloroplasts from an Arabidopsis aquaporin mutant, and
 this showed that CO2 permeability was reduced 50% in the mutant compared
 with the wild-type reference.
description: Tolleter et al_highly
 enrichedCOPASI file of numerical
 modelling used for the the generation of time courses for changes in
 dually labelled CO2 (highly enriched 18O bicarbonate)Tolleter et al_lowly
 enrichedCOPASI file of numerical
 modelling used for the generation of times courses for changes in singly
 labelled CO2 species (lowly enriched 18O bicarbonate)
DOI: 10.5061/dryad.8172
title: Data from: Evaluation of candidate DNA barcoding loci for economically important timber species of the mahogany family (Meliaceae)

description: There has been considerable debate regarding locus choice for DNA
 barcoding land plants. This is partly attributable to a shortage of
 comparable data from proposed candidate loci on a common set of samples.
 In this study, we evaluated main candidate plastid regions (rpoC1, rpoB,
 accD) and additional plastid markers (psbB, psbN, psbT exons and the
 trnS-trnG spacer) as well as the nuclear ribosomal spacer region
 (ITS1-5.8S-ITS2) in a group of land plants belonging to the mahogany
 family, Meliaceae. Across these samples, only ITS showed high levels of
 resolvability. Interspecific sharing of sequences from individual plastid
 loci was common. The combination of multiple loci did not improve
 performance. DNA barcoding with ITS alone revealed cryptic species and
 proved useful in identifying species listed in Convention on International
 Trade of Endangered Species appendixes.
description: GenBank_Accessions
DOI: 10.5061/dryad.gr883k8
title: Data from: The increasing disconnection of primary biodiversity data from specimens: how does it happen and how to handle it?

description: Abstract.—Primary biodiversity data represent the fundamental elements of
 any study in systematics and evolution. They are, however, no longer
 gathered as they used to be and the mass-production of observation-based
 occurrences is overthrowing the collection of specimen-based occurrences.
 Although this change in practice is a major upheaval with significant
 consequences in the study of biodiversity, it remains understudied and has
 not attracted yet the attention it deserves. Analyzing 536 million
 occurrences from the Global Biodiversity Information Facility (GBIF)
 mediated data, we show that this spectacular change affects the 24
 eukaryote taxonomic classes we targeted: from 1970 to 2016 the proportion
 of occurrences marked as traceable to tangible material (i.e.
 specimen-based occurrences) fell from 68 to 18 %; moreover, most of those
 specimen based-occurrences cannot be readily traced back to a specimen
 because the necessary information is missing. Ethical, practical or legal
 reasons responsible for this shift are known, and this situation appears
 unlikely to be reversed. Still, we urge scholars to acknowledge this
 dramatic change, embrace it and actively deal with it. Specifically, we
 emphasize why specimen-based occurrences must be gathered, as a warrant to
 allow both repeating evolutionary studies and conducting rich and diverse
 investigations. When impossible to secure, voucher specimens must be
 replaced with observation-based occurrences combined with ancillary data
 (e.g. pictures, recordings, samples, DNA sequences). Ancillary data are
 instrumental for the usefulness of biodiversity occurrences and we show
 that, despite improving technologies to collate them, they remain rarely
 shared. The consequences of such a change are not yet clear but we
 advocate collecting material evidence or ancillary data to ensure that
 primary biodiversity data collected lately do not partly become obsolete
 when doubtful.
description: Figure
 S1Figure S1: Accumulation
 curve of collected species occurrences from 1900 to today. The plot shows
 the cumulated number of occurrences available between 1900 and
 2016.supplementary_1.pngFigure S2Figure S2: Average completeness of the GBIF mediated data per year does not evolve along time. The blue line represents the average proportion of columns filled in the DarwinCore format. The blue area represents the standard deviation of this value. The average completeness of the data does not change much over the years and is never above 25 %.supplementary_2.png
DOI: 10.5061/dryad.6t779
title: Data from: Estimation of mating system parameters in an evolving gynodioecous population of cultivated sunflower (Helianthus annuus L.)

description: Cultivated plants have been molded by human-induced selection, including
 manipulations of the mating system in the twentieth century. How these
 manipulations have affected realized parameters of the mating system in
 freely evolving cultivated populations is of interest for optimizing the
 management of breeding populations, predicting the fate of escaped
 populations and providing material for experimental evolution studies. To
 produce modern varieties of sunflower (Helianthus annuus L.),
 self-incompatibility has been broken, recurrent generations of selfing
 have been performed and male sterility has been introduced. Populations
 deriving from hybrid-F1 varieties are gynodioecious because of the
 segregation of a nuclear restorer of male fertility. Using both phenotypic
 and genotypic data at 11 microsatellite loci, we analyzed the
 consanguinity status of plants of the first three generations of such a
 population and estimated parameters related to the mating system. We
 showed that the resource reallocation to seed in male-sterile individuals
 was not significant, that inbreeding depression on seed production
 averaged 15–20% and that cultivated sunflower had acquired a mixed-mating
 system, with ~50% of selfing among the hermaphrodites. According to
 theoretical models, the female advantage and the inbreeding depression at
 the seed production stage were too low to allow the persistence of male
 sterility. We discuss our methods of parameter estimation and the
 potential of such study system in evolutionary biology.
description: Genotypic_dataGenotypic data for 11 microsatellites; missing data coded as NAPhenotypic_dataThe excel file has both the data, and a worksheet explaining each of the columns/fields.
DOI: 10.5061/dryad.h748c88
title: Data from: Frugivore biodiversity and complementarity in interaction networks enhance landscape-scale seed dispersal function

description: 1. Animal biodiversity matters for the provision of ecosystem functions
 derived from trophic activity. However, the mechanisms underlying this
 pattern remain elusive since animal abundance and diversity, which are the
 components commonly used for representing biodiversity, provide poor
 information about ecological complementarity in species assemblages. An
 approach based on species interaction networks may overcome this
 constraint. 2. Here, we relate frugivore biodiversity and frugivore-plant
 network structure with landscape-scale seed dispersal function. We
 sampled, for two years, and at fourteen plots with variable assemblages of
 frugivores and plants in the Cantabrian Range (N Spain), data on the
 abundance and diversity of frugivorous birds, the consumption of fleshy
 fruits of woody plants, and the landscape-scale patterns of avian seed
 deposition. As a measure of interaction complementarity in seed dispersal
 networks, we estimated the degree to which frugivore and plant species
 specialize in their interacting partners. 3. Specialization varied
 strongly across the seed dispersal networks of the different plots, being
 higher in networks harboring smaller bird species that dispersed mostly
 small-fruited plants, and also in networks with late-ripening, dominant
 fruiting species dispersed mostly by wintering birds. 4. Bird abundance
 markedly affected seed deposition. Plots harboring more birds received a
 higher density of dispersed seeds, and showed higher probabilities of seed
 arrival and seed deposition in open microhabitats. Bird diversity also had
 a positive effect on the density of dispersed seed and, to a lesser
 extent, seed arrival probability. Independently of frugivore abundance and
 diversity, the density of dispersed seeds increased in plots where seed
 dispersal networks showed a higher degree of specialization. 5. This study
 considers the structure of interaction networks to re-address the
 relationship between biodiversity and ecosystem functionality, evidencing
 that specialization in frugivore-plant networks drives the large-scale
 process of seed dispersal. These results encourage the consideration of
 interaction complementarity as an underlying mechanism linking animal
 biodiversity and trophic-related functions.
description: Abundance of birds and
 fruitsSee README file for a
 description of the content of all datafiles.Abundance.csvFruit consumption observations eventsSee README file for a description of the content of all datafiles.Fruit_Consumption.csvSeed deposition by birds in different yearsSee README file for a description of the content of all datafiles.Seed_Dispersal_Year.csvSeed deposition by birds, sampling years pooled.See README file for a description of the content of all datafiles.Seed_Dispersal_Pooled.csv