cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.0cfxpnw15
title: Migration without interbreeding: Evolutionary history of a highly selfing Mediterranean grass inferred from whole genomes

description: Wild plant populations show extensive genetic subdivision and are far from
 the ideal of panmixia which permeates population genetic theory.
 Understanding the spatial and temporal scale of population structure is
 therefore fundamental for empirical population genetics – and of interest
 in itself, as it yields insights into the history and biology of a
 species. In this study we extend the genomic resources for the wild
 Mediterranean grass Brachypodium distachyon to investigate the scale of
 population structure and its underlying history at whole-genome
 resolution. 86 accessions were sampled at local and regional scales in
 Italy and France, which closes a conspicuous gap in the collection for
 this model organism. The analysis of 196 accessions, spanning the
 Mediterranean from Spain to Iraq, suggests that the interplay of high
 selfing and seed dispersal rates has shaped genetic structure in B.
 distachyon. At the continental scale, the evolution in B. distachyon is
 characterized by the independent expansion of three lineages during the
 Upper Pleistocene. Today, these lineages may occur on the same meadow yet
 do not interbreed. At the regional scale, dispersal and selfing interact
 and maintain high genotypic diversity, thus challenging the textbook
 notion that selfing in finite populations implies reduced diversity. Our
 study extends the population genomic resources for B. distachyon and
 suggests that an important use of this wild plant model is to investigate
 how selfing and dispersal, two processes typically studied separately,
 interact in colonizing plant species.
DOI: 10.5061/dryad.n02v6www7
title: Study of the genetic and phenotypic variation among wild and cultivated clary sages provides interesting avenues for breeding programs of a perfume, medicinal and aromatic plant

description: A road-map of the genetic and phenotypic diversities in both crops and
 their wild-related species can help identifying valuable genetic resources
 for further crop breeding. The clary sage (Salvia sclarea L.), a perfume,
 medicinal and aromatic plant, is used for sclareol production and
 ornamental purposes. Despite its wide use in the field of cosmetics, the
 phenotypic and genetic diversity of wild and cultivated clary sage remains
 to be explored. We characterized the genetic and phenotypic variation of a
 collection of six wild S. sclarea populations from Croatia, sampled along
 an altitudinal gradient, and of populations of three S. sclarea cultivars.
 We showed low level of genetic diversity for the two S. sclarea
 traditional cultivars used for essential oil production and for ornamental
 purposes, respectively. In contrast, a recent cultivar resulting from new
 breeding methods, which involve hybridizations among several genotypes
 rather than traditional recurrent selection and self-crosses over time,
 showed high genetic diversity. We also observed a marked phenotypic
 differentiation for the ornamental clary sage compared with other
 cultivated and wild clary sages. Instead, the two cultivars used for
 essential oil production, a traditional and a recent, respectively, were
 not phenotypically differentiated from the wild Croatian populations. Our
 results also featured some wild populations with high sclareol content and
 early-flowering phenotypes as good candidates for future breeding
 programs. This study opens up perspectives for basic research aiming at
 understanding the impact of breeding methods on clary sage evolution, and
 highlights interesting avenues for clary breeding programs.
DOI: 10.15468/dl.hm5t76
title: Occurrence Download

description: A dataset containing 70 species occurrences available in GBIF matching the query:
{
 "and" : [
 "CoordinateUncertaintyInMeters 0.0-5000.0",
 "TaxonKey is Elaeagnus conferta"
 ]
}

 The dataset includes 70 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002731-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.sxksn0325
title: Prospects for the natural distribution of crop wild-relatives with limited adaptability: The case of the wild pea Pisum fulvum

description: Plant breeders and conservationists depend on knowledge about the genetic
 variation of their species of interest. Pisum fulvum, a wild
 relative of domesticated pea, has attracted attention as a genetic
 resource for crop improvement, yet little information about its diversity
 in the wild has been published hitherto. We sampled 15 populations
 of P. fulvum from Israeli natural habitats and
 conducted genotyping by sequencing to analyse their genetic diversity and
 adaptive state. We also attempted to evaluate the species past demography
 and the prospects of its future reaction to environmental changes. The
 results suggest that genetic diversity of P. fulvum is low to
 medium and is distributed between well diverged populations. Surprisingly,
 with 56 % in the total population, the selfing rate was found to
 be significantly lower than expected from a species that is commonly
 assumed to be a predominant selfer. We found a strong genetic bottleneck
 during the last glacial period and only limited patterns of isolation by
 distance and environment, which explained 13 % - 18 % of the
 genetic variation. Despite the weak signatures of genome-wide IBE, 1354
 markers were significantly correlated with environmental factors, 1233 of
 which were located within known genes with a nonsynonymous to synonymous
 ratio of 0.382. Species distribution modelling depicted an ongoing
 fragmentation and decreased habitable area over the next 80 years under
 two different socio-economic pathways. Our results suggest that complex
 interactions of substantial drift and selection shaped the genome
 of P. fulvum. Climate change is likely to cause further erosion
 of genetic diversity in P. fulvum. Systematic ex-situ
 conservation may be advisable to safeguard genetic variability for future
 utilization of this species.
description: <strong>VCF files
 description</strong> 
 File Description 
 Pfulvum_raw.vcf.gz
 raw vcf file from Elshire, where I extracted the fulvum samples,
 but did not apply any filters 
 Pfulvum.vcf Filtered Pfulvum.raw.vcf as
 follow: Biallelic SNPs with minor allele frequency (MAF) ≥ 0.01, minimum
 depth ≥ 3, minimum mean depth across samples ≥ 5, minimum genotype quality
 ≥ 25, and genotype calls ≥ 40%.<br>                      Applied by
 runnig: vcftools --gzvcf ../data/Pfulvum_raw.vcf.gz --remove-indels
 --min-alleles 2 --max-alleles 2 --maf 0.01 --max-missing 0.6 --minGQ 25
 --min-meanDP 5 --minDP 3 --recode 
 Pfulvum.imputed.vcf Imputed version of
 Pfulvum.vcf.   <br> Applied by running: java -jar
 ../../software/beagle/beagle.18May20.d20.jar gt=Pfulvum.vcf iterations=30
 burnin=10 ap=true gp=true ne=50000 seed=170887 out=Pfulvum.imputed.nohead
 nthreads=6 
 Pfulvum.LDpruned.vcf  LD pruned
 (r^2&gt;0.5) version of Pfulvum.vcf. the outcome of a
 script 
 Pfulvum.imputed.LDpruned.vcf  LD pruned
 (r^2&gt;0.5) version of Pfulvum.imputed.vcf.
DOI: 10.5061/dryad.280gb5mp5
title: Data from: Passive skeletal muscle can function as an osmotic engine

description: Muscles are composite structures. The protein filaments responsible for
 force production are bundled within fluid-filled cells, and these cells
 are wrapped in ordered sleeves of fibrous collagen. Recent models suggest
 that the mechanical interaction between intracellular fluid and
 extracellular collagen is essential to force production in passive
 skeletal muscle, ultimately allowing the material stiffness of
 extracellular collagen to contribute to passive muscle force at
 physiologically relevant muscle lengths. Such models lead to the
 prediction, tested here, that expansion of the fluid compartment within
 muscles should drive forceful shortening of muscle tissue, resulting in
 the production of mechanical work unassociated with contractile activity.
 We tested this prediction by experimentally increasing the fluid volumes
 of isolated bullfrog semimembranosus muscles via osmotically hypotonic
 bathing solutions. Over time, passive muscles bathed in hypotonic solution
 widened by 16.44 ± 3.66% as they took on fluid. At the same time, muscles
 shortened by 2.13 ± 0.75% (mean ± SD) along their line of action,
 displacing a force-regulated servomotor and doing measurable mechanical
 work. This behavior suggests a functional mechanism analogous to that of
 engineered pneumatic actuators and highlights the significance of
 three-dimensional processes of force transmission in skeletal muscle.
description: This data table contains the width and length data from figures
 1a and 1b, as well as the strain data for all eight individuals in
 figure 2b. In figure 2b, strain is reported as a percentage, so the raw
 data must be multiplied by 100 to match the presentation in the main
 text.
DOI: 10.5061/dryad.rjdfn2z97
title: Data from: Physical and ecological isolation contribute to maintain genetic differentiation between fire salamander subspecies

description: Landscape features shape patterns of gene flow among populations,
 ultimately determining where taxa lay along the continuum between panmixia
 to complete reproductive isolation. Gene flow can be restricted leading to
 population differentiation in two non-exclusive ways: “physical
 isolation”, in which geographic distance in combination with the landscape
 features restricts movement of individuals promoting genetic drift, and
 “ecological isolation”, in which adaptive mechanisms constrain gene flow
 between different environments via divergent natural selection. In central
 Iberia, two fire salamander subspecies occur in parapatry across elevation
 gradients along the Iberian Central System mountains, while in adjacent
 Mountains of Toledo Region only one of them occurs. By integrating
 population and landscape genetic analyses, we show a ubiquitous role of
 physical isolation between and within mountain ranges, with unsuitable
 landscapes increasing differentiation between populations. However, across
 the Iberian Central System, we found strong support for a significant
 contribution of ecological isolation, with low genetic differentiation in
 environmentally homogeneous areas, but high differentiation across sharp
 transitions in precipitation seasonality. These patterns are consistent
 with a significant contribution of ecological isolation in restricting
 gene flow among subspecies. Overall, our results suggest that ecological
 divergence contributes to reduce genetic admixture, creating an
 opportunity for lineages to follow distinct evolutionary trajectories.
description: For sampling and genotyping details see associated
 publication.
description: genotype_data.xlsx Genotype profiles (13
 microsatellites) obtained from fire salamanders (<em>Salamandra
 salamandra</em>) sampled across the Iberian Central System. For
 direct use we provide GenAlEx format. Sheet 1 -
 genotype_data_info Sheet 2 -
 genotype_data_GenAlEx
DOI: 10.5061/dryad.j6q573ncp
title: Cercarial behaviour alters the consumer functional response of three-spined sticklebacks

description: 1. Free-living parasite life stages may contribute substantially to
 ecosystem biomass and thus represent a significant source of energy flow
 when consumed by non-host organisms. However, ambient temperature and the
 predator’s own infection status may modulate consumption rates towards
 parasite prey. 2. We investigated the combined effects of temperature and
 predator infection status on the consumer functional response of
 three-spined sticklebacks towards the free-living cercariae stages of two
 common freshwater trematode parasites (Plagiorchis, Trichobilharzia). 3.
 Our results revealed genera-specific functional responses and consumption
 rates towards each parasite prey: Type II for Plagiorchis and Type III for
 Trichobilharzia, with an overall higher consumption rate on
 Trichobilharzia. Elevated temperature (13 ºC) increased the consumption
 rate on Plagiorchis prey for sticklebacks with mild cestode infections
 (&lt;5% fish body weight) only. 4. High consumption of cercarial prey
 by sticklebacks may impact parasite population dynamics by severely
 reducing or even functionally eliminating free-living parasite life stages
 from the environment. This supports the potential role of fish as
 biocontrol agents for cercariae with similar dispersion strategies, in
 instances where functional response relationships have been established.
 5. Our study demonstrates how parasite consumption by non-host organisms
 may be shaped by traits inherent to parasite transmission and dispersal,
 and emphasizes the need to consider free-living parasite life stages as
 integral energy resources in aquatic food webs.
DOI: 10.15468/dl.5c5zgj
title: Occurrence Download

description: A dataset containing 1141 species occurrences available in GBIF matching the query:
{
 "and" : [
 "CoordinateUncertaintyInMeters 0.0-5000.0",
 "TaxonKey is Eleocharis dulcis"
 ]
}

 The dataset includes 1141 records from 32 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002732-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.ncjsxkstb
title: eDNA sampled from stream networks correlates with camera trap detection rates of terrestrial mammals

description: Biodiversity monitoring delivers vital information to those making
 conservation decisions. Comprehensively measuring terrestrial biodiversity
 usually requires costly methods that can rarely be deployed at large
 spatial scales over multiple time periods, limiting conservation
 efficiency. Here we investigated the capacity of environmental DNA (eDNA)
 from stream water samples to survey terrestrial mammal diversity at
 multiple spatial scales within a large catchment. We compared biodiversity
 information recovered using an eDNA metabarcoding approach with data from
 a dense camera trap survey, as well as the sampling costs of both methods.
 Via the sampling of large volumes of water from the two largest streams
 that drained the study area, eDNA metabarcoding provided information on
 the presence and detection probabilities of 35 mammal taxa, 25% more than
 camera traps and for half the cost. While eDNA metabarcoding had limited
 capacity to detect felid species and provide individual-level demographic
 information, it is a cost-efficient method for large-scale monitoring of
 terrestrial mammals that can offer sufficient information to solve many
 conservation problems.
description: Compressed files containing forward and reverse Illumina sequence
 files after adapter trimming and text files containing the correspondence
 between sample code, the code of the library in which it was sequenced and
 the tag used for PCR.
DOI: 10.5061/dryad.4mw6m908m
title: Reconstructing dietary ecology of extinct strepsirrhines (Primates, Mammalia) with new approaches for characterizing and analyzing tooth shape

description: The morphological and ecological diversity of lemurs and lorisiformes once
 rivalled the rest of the primate order. Here, we assemble a dataset of 3D
 models representing the second mandibular molars of a wide range of extant
 and fossil strepsirrhines encompassing this diversity. We use these models
 to distill quantitative descriptors of tooth form and then analyze these
 data using new analytical methods. We employ a recently developed dental
 topography metric (ariaDNE), which is less sensitive to details of random
 error in 3D model quality than previously used metrics (e.g., DNE);
 Bayesian multinomial modelling with metrics designed to measure
 overfitting risk; and a tooth segmentation algorithm that allows the
 shapes of disaggregated tooth surface features to be quantified using
 dental topography metrics. This approach is successful at reclassifying
 extant strepsirrhine primates to known dietary ecology and indicates that
 the averaging of morphological information across the tooth surface does
 not interfere with the ability of dental topography metrics to predict
 dietary adaptation. When applied to extinct species, many subfossil lemurs
 and the most basal fossil strepsirrhines are predicted to have been
 primarily frugivorous or gummivorous. This supports an ecological
 contraction among the extant lemurs and the importance of frugivory in the
 origins of crown Strepsirrhini, potentially to avoid competition with more
 insectivorous and folivorous members of Paleogene Afro-Arabian primate
 faunas.
description: This data includes four result readouts from Bayesian model
 comparisions; information on sources for dietary classifications;
 summaries of dental topography metric values calculated on extant and
 fossil strepsirrhines; and dental topography metrics calculated by
 specimen.
DOI: 10.5061/dryad.wpzgmsbm0
title: Data from: Dung beetle activity had no positive effect on nutrient concentration or performance of established rainforest seedlings

description: All five datasets from this study correspond to field observations
 collected for seedlings of six tree species (Brosimum alicastrum,
 Calophyllum brasiliense, Cymbopetalum baillonii, Diospyros digyna,
 Omphalea oleifera and Poulsenia armata) in a tropical rainforest (Los
 Tuxtlas, Mexico). We estimated the concentrations of foliar nitrogen (N)
 and phosphorus (P), resource allocation (the ratio of biomass allocated to
 shoot vs root), seedling survival, and growth. Experimental seedlings were
 subject to three treatment levels: (a) feces added and beetles active, (b)
 feces added and beetles excluded, and (c) no feces added (and consequently
 no beetles active). We analyzed data at two levels: community (all plant
 species together) and individual species. For resource allocation
 (ESM_Dataset1_RootShoot) we weighed aerial parts (stem and leaves) and
 roots, separately, and calculated the root/shoot biomass ratio for each
 seedling. For foliar nutrients (ESM_Dataset2_FoliarNutrients) we obtained
 N and P concentrations using a Kjeldahl wet digestion and colorimetric
 analysis; for the analyses four outlier values were removed (for Brosimum
 one P value; for Calophyllum two P values and one N value). We analyzed
 foliar nutrients for all plant species. In the case of seedling survival
 (ESM_Dataset3_Survival) we registered seedling survival weekly during six
 weeks for Cymbopetalum, and during 26 weeks for the other five species.
 The response variable was the number of days elapsed until death;
 seedlings alive by the end of the experiment were included as
 right-censored data. For seedling growth in height
 (ESM_Dataset4_GrowthHeight; measured in all plant species except
 Cymbopetalum) we measured seedling height to the nearest centimeter every
 four or five weeks during 26 weeks. For this variable we calculated net
 growth in height (final height minus initial height). Finally, for the
 growth in the number of leaves (ESM_Dataset5_GrowthLeaves; measured in all
 plant species except Cymbopetalum) we counted the number of leaves lost
 and number of new leaves, every four or five weeks during 26 weeks; the
 response variable was the net growth in the number of leaves (final number
 of leaves minus initial number of leaves). All analyses were conducted in
 R. Detailed information about dataset structure and contents can be found
 in file ESM_Metadata.
DOI: 10.5061/dryad.qv9s4mwd8
title: Retention behavior of analytes applying three micellar mobile phases

description: This dataset contains data representing the retention behavior obtained
 upon utilizing three micellar based mobile phases for the simultaneous
 determination of certain partial dopamine agonists that are used to
 overcome the withdrawal symptoms of abused drugs, namely aripiprazole,
 pramipexole, and piribedil. The studied drugs were separated using
 micellar liquid chromatography (MLC), hybrid micellar liquid
 chromatography (HMLC), and micro emulsion liquid chromatography (MELC).
 The resultant retention behavior of the studied drugs applying the three
 developed mobile phases were mathematically manipulated to select the
 suitable mobile phase for log p measurement of the concerned
 pharmaceuticals. Experimental determination of log Pm/w values using the
 three mobile phases demonstrates that HMLC is the mobile phase of choice
 since the obtained practical log Pm/w values were in accordance with the
 reported log P values, and calculated log P and log D values.
description: The
 dataset was collected during separation and optimization of aripiprazole,
 pramipexole, and piribedil applying MLC, HMLC, and MELC in Central
 Laboratory at Faculty of Pharmacy Delta University for Science and
 Technology. Simple mathematical calculations of the obtained retention
 parameters were manipulated to select the most appropriate mobile phase
 for log P estimation.
DOI: 10.5061/dryad.wstqjq2kb
title: Dark extinction: The problem of unknown historical extinctions

description: The extinction of species before they are discovered and named (dark
 extinction, DE) is widely inferred as a significant part of species loss
 in the ‘pre-taxonomic’ period (approx. 1500–1800 CE) and, to some extent,
 in the ‘taxonomic period’ (approx. 1800–present) as well. The discovery of
 oceanic islands and other pristine habitats by European navigators and the
 consequent introduction of destructive mammals, such as rats and goats,
 started a process of anthropogenic extinction. Much ecosystem change
 happened before systematic scientific recording, so has led to DE.
 Statistical methods are available to robustly estimate DE in the
 ‘taxonomic period’. For the ‘pre-taxonomic period’, simple extrapolation
 can be used. The application of these techniques to world birds, for
 example, suggests that approximately 56 DEs occurred in the ‘taxonomic
 period’ (1800–present) and approximately 180 in the ‘pre-taxonomic period’
 (1500–1800). Targeting collection activities in extinction hotspots, to
 make sure organisms are represented in collections before their
 extinction, is one way of reducing the number of extinct species without a
 physical record (providing that collection efforts do not themselves
 contribute to species extinction).
description: List of all birds (csv format) known to exist after 1500 CE with:
 whether extant, extinction date (if extinct), date of first taxonomic
 description. The dataset is compiled from various publically available
 sources mainly: Szabo, J.K., Khwaja, N., Garnett, S.T.
 & Butchart, S.H.M. 2012 Global Patterns and Drivers of Avian
 Extinctions at the Species and Subspecies Level. Plos One 7.
 (doi:10.1371/journal.pone.0047080). BirdLife. 2019
 Handbook of the Birds of the World and BirdLife International digital
 checklist of the birds of the world. Version 4.
description: This list is compiled as of 2019. Birds extant in 2019 are given
 a placeholder date of last record ("extinction date") of
 2019.