cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.gmx8ht
title: Occurrence Download

description: A dataset containing 2385 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((16.11946 55.22793,13.90687 54.93962,12.17548 59.21924,10.498 59.67634,9.90348 59.63577,9.98158 56.35524,9.01746 56.10325,9.34483 54.75861,10.92687 53.61318,16.46775 53.18506,16.11946 55.22793))",
 "TaxonKey is Hemigrapsus"
 ]
}

 The dataset includes 2385 records from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001495-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.bm98q
title: Data from: Minimum sample sizes for population genomics: an empirical study from an Amazonian plant species

description: High throughput DNA sequencing facilitates the analysis of large portions
 of the genome in non-model organisms, ensuring high accuracy of population
 genetic parameters. However, empirical studies evaluating the appropriate
 sample size for these kinds of studies are still scarce. In this study, we
 use double digest restriction associated DNA sequencing (ddRADseq) to
 recover thousands of single nucleotide polymorphisms (SNPs) for two
 physically isolated populations of Amphirrhox longifolia (Violaceae), a
 non-model plant species for which no reference genome is available. We
 used resampling techniques to construct simulated populations with a
 random subset of individuals and SNPs to determine how many individuals
 and bi-allelic markers should be sampled for accurate estimates of intra-
 and interpopulation genetic diversity. We identified 3,646 and 4,900
 polymorphic SNPs for the two populations of A. longifolia, respectively.
 Our simulations show that, overall, a sample size greater than eight
 individuals has little impact on estimates of genetic diversity within A.
 longifolia populations, when 1,000 SNPs or higher are used. Our results
 also show that even at a very small sample size (i.e., two individuals),
 accurate estimates of FST can be obtained with a large number of SNPs (≥
 1,500). These results highlight the potential of high-throughput genomic
 sequencing approaches to address questions related to evolutionary biology
 in non-model organisms. Furthermore, our findings also provide insights
 into the optimization of sampling strategies in the era of population
 genomics.
description: Genepop outfile
 generated by Formatomatic V.0.8.1 for A and B populations of Amphirrhox
 longifolia.SNPs for A and B
 populations of Amphirrhox longifolia (Violaceae).Pop A_
 B.xlsx
DOI: 10.5061/dryad.s403s
title: Data from: Quantification of within- and between-farm dispersal of Culicoides biting midges using an immunomarking technique

description: Culicoides biting midges (Diptera, Ceratopogonidae) are vectors of
 arboviruses that cause significant economic and welfare impact.
 Local-scale spread of Culicoides-borne arboviruses is largely determined
 by the between-farm movement of infected Culicoides. Study of the
 dispersal behaviour of Culicoides by capture–mark–recapture (CMR) is
 problematic due to the likelihood of mortality and changes in behaviour
 upon capture caused by the small size and fragility of these insects,
 evidenced by low recapture rates. To counter the problem of using CMR with
 Culicoides, this study utilised an ovalbumin immunomarking technique to
 quantify the within- and between-farm dispersal of Culicoides in southern
 England. Both within- and between-farm dispersal of Culicoides was
 observed. Of the 9058 Culicoides collected over 22 nights of trapping, 600
 ovalbumin-positive Culicoides, of 12 species including those implicated as
 arbovirus vectors, were collected with a maximum dispersal distance of
 3125 m. This study provides the first species-level data on the
 between-farm dispersal of potential bluetongue, Schmallenberg and African
 horse sickness virus vectors in northern Europe. High-resolution
 meteorological data determined upwind and downwind flight by Culicoides
 had occurred. Cumulative collection and meteorological data suggest 15·6%
 of flights over 1 km were upwind of the treatment area and 84·4% downwind.
 Synthesis and applications. The use of immunomarking eliminates the
 potential adverse effects on survival and behaviour of insect collection
 prior to marking, substantially improving the resolution and accuracy of
 estimates of the dispersal potential of small and delicate vector species
 such as Culicoides. Using this technique, quantification of the range of
 Culicoides dispersal with regard to meteorological conditions including
 wind direction will enable improved, data-driven modelling of the spread
 of Culicoides-borne arboviruses and will inform policy response to
 incursions and outbreaks.
description: Culicoides dispersal
 data: ELISA OD, SNV and ovalbumin results with associated trap and
 meterological conditions dataEnzyme-linked
 immunosorbent assay (ELISA) optical density (OD) data, Standard Normal
 Variate (SNV) transformation of OD data, SNV threshold and classical
 thresholds used for data analysis, ovalbumin positive/negative results
 using both SNV and classical thresholds and associated trap and
 meterological data. One record per well/sample. Sanders et al_2017_Journal
 of Applied Ecology_dataSanders et al_2017_Journal of
 Applied Ecology_data.csv
DOI: 10.15468/dl.r4wwt2
title: Occurrence Download

description: A dataset containing 759 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Pentachondra pumila",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 759 records from 24 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001497-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.75265
title: Data from: Predicting the spread of all invasive forest pests in the United States

description: We tested whether a general spread model could capture macroecological
 patterns across all damaging invasive forest pests in the United States.
 We showed that a common constant dispersal kernel model, simulated from
 the discovery date, explained 67.94% of the variation in range size across
 all pests, and had 68.00% locational accuracy between predicted and
 observed locational distributions. Further, by making dispersal a function
 of forest area and human population density, variation explained increased
 to 75.60%, with 74.30% accuracy. These results indicated that a single
 general dispersal kernel model was sufficient to predict the majority of
 variation in extent and locational distribution across pest species and
 that proxies of propagule pressure and habitat invasibility – well-studied
 predictors of establishment – should also be applied to the dispersal
 stage. This model provides a key element to forecast novel invaders and to
 extend pathway-level risk analyses to include spread.
description: Species and site
 characteristics used to fit dispersal modelsThis data file is a
 multi-tab spreadsheet that describes the characteristics of the 64 species
 and the 3372 50 x 50 km grid cells spanning the contiguous United States
 used in the spread models (where spatial data are calculated as the grid
 cell area-weighted average of county-level data used in Liebhold et al.
 (2013)). Within the spreadsheet, the 'griddata' tab includes
 scaled and unscaled spatial variables by grid cell,
 'scaledhostden' includes scaled host density by grid cell,
 'gridtreevolume' includes raw tree volume by grid cell as
 measured by the Forest Inventory and Analysis National Program (FIA),
 'FIAcodes' lists the host FIA codes by pest species, and
 'pestdata' includes scaled and unscaled pest
 characteristics.dryad_data.xlsx
DOI: 10.5061/dryad.hq67g
title: Data from: A student-centered framework for teaching undergraduate parasitology

description: Many biology subdisciplines are re-evaluating their undergraduate
 curriculum amid changing student attitudes towards education. However, a
 modern framework for undergraduate parasitology has yet to be formally
 outlined. We present a student-centered approach to teaching parasitology,
 which diminishes the power of the lectern and emphasizes the use of active
 learning techniques.
description: Parasitology Selected
 Course MaterialsSelected exercises and
 problem sets for starting a student-centered course in undergraduate
 Parasitology
DOI: 10.5061/dryad.g8h54
title: Data from: Analysis of local-scale background concentrations of methane and other gas-phase species in the Marcellus Shale

description: The Marcellus Shale is a rapidly developing unconventional natural gas
 resource found in part of the Appalachian region. Air quality and climate
 concerns have been raised regarding development of unconventional natural
 gas resources. Two ground-based mobile measurement campaigns were
 conducted to assess the impact of Marcellus Shale natural gas development
 on local scale atmospheric background concentrations of air pollution and
 climate relevant pollutants in Pennsylvania. The first campaign took place
 in Northeastern and Southwestern PA in the summer of 2012. Compounds
 monitored included methane (CH4), ethane, carbon monoxide (CO), nitrogen
 dioxide, and Proton Transfer Reaction Mass Spectrometer (PTR-MS) measured
 volatile organic compounds (VOC) including oxygenated and aromatic VOC.
 The second campaign took place in Northeastern PA in the summer of 2015.
 The mobile monitoring data were analyzed using interval percentile
 smoothing to remove bias from local unmixed emissions to isolate
 local-scale background concentrations. Comparisons were made to other
 ambient monitoring in the Marcellus region including a NOAA SENEX flight
 in 2013. Local background CH4 mole fractions were 140 ppbv greater in
 Southwestern PA compared to Northeastern PA in 2012 and background CH4
 increased 100 ppbv from 2012 to 2015. CH4 local background mole fractions
 were not found to have a detectable relationship between well density or
 production rates in either region. In Northeastern PA, CO was observed to
 decrease 75 ppbv over the three year period. Toluene to benzene ratios in
 both study regions were found to be most similar to aged rural air masses
 indicating that the emission of aromatic VOC from Marcellus Shale activity
 may not be significantly impacting local background concentrations. In
 addition to understanding local background concentrations the ground-based
 mobile measurements were useful for investigating the composition of
 natural gas emissions in the region.
description: Goetz_etal_2017_dataThe zip file holds six tab delimited text files that contain 1 Hz mobile lab data and accompanying local background estimates from 2012 measurements in SW PA and NE PA and 2015 measurements in NE PA. See publication for more details. The provided local background data is derived from 20 minute 35th percentile smoothing. All time information is in military format. Date information is in mm/dd/yy. Concentration data is in units of ppbv. GPS data is in units of decimal degrees and in datum WGS84. Please contact authors if additional information is needed. All use of the provided data should be accompanied by the proper citations.
DOI: 10.5061/dryad.3r1v5
title: Data from: Finding the best management policy to eradicate invasive species from spatial ecological networks with simultaneous actions

description: 1. Spatial management of invasive species is more likely to be successful
 when multiple locations are treated simultaneously. However, selecting the
 best locations to act is difficult due to the many options available at
 any time. 2. We design a near-optimal policy for applying multiple actions
 simultaneously for faster invasive species control within a network. Our
 method uses a recent optimisation tool, the Graph-based Markov decision
 process (GMDP). Since the policy can be difficult to interpret, we
 extracted a simpler policy using classification trees. We applied our
 approach to the eradication of invasive mosquitofish (Gambusia holbrooki)
 from the habitat of the red-finned blue-eye (Scaturiginichthys
 vermeilipinnis), a critically endangered fish with a global population
 that is restricted to seven artesian springs in Queensland, Australia. 3.
 The policy returned by the GMDP was to manage springs occupied by
 mosquitofish and their connected neighbours, unless the neighbours were
 occupied by red-finned blue-eyes. 4. Simultaneous management resulted in
 rapid declines in simulated mosquitofish occupancy even if eradication
 effectiveness was low; however the cost of simultaneous eradication was
 high and sustained eradication effort was necessary to maintain low
 mosquitofish occupancy. 5. Synthesis and applications. Our paper finds a
 near-optimal, multi-action control policy to remove an invasive species
 from a multi-species spatial network. We introduce the Graph-based Markov
 decision process (GMDP) and apply it to a real case study – eradication of
 invasive mosquitofish from the habitat of the red-finned blue-eye. We find
 that the GMDP can generate policies for networks with extremely large
 state spaces, however it works best when nodes have fewer than five
 neighbours. We conclude that simultaneous eradications are effective for
 rapid control of invasive species; however, managers should consider the
 cost and time required for an effective eradication program.
description: Supplementary
 information S1-S6This file contains
 supplementary information S1-S6 referred to in the main text of the
 manuscript. File format is Microsoft Word (docx).Supplementary_information_S1-S6_revised4.docxSupporting info S7: Data and Matlab/R codeThis folder contains the Matlab files used to run the GMDP and create the figures in the paper. It also contains the R code required to parameterise the likelihood function and the R code for drawing the classification trees. Occupancy data for RFBE and Gambusia are contained in the excel file 'Edgbaston Presence Data.xlsx'. See the included readme file for details of the code.Supporting info s7.tar
DOI: 10.5061/dryad.j0p8c
title: Data from: Characterization of a transgenic mouse model exhibiting spontaneous lung adenocarcinomas with a metastatic phenotype

description: Developing lung cancer in mouse models that display similarities of both
 phenotype and genotype will undoubtedly provide further and better
 insights into lung tumor biology. Moreover, a high degree of
 pathophysiological similarity between lung tumors from mouse models and
 their human counterparts will make it possible to use these mouse models
 for preclinical tests. Ovine pulmonary adenocarcinomas (OPAs) present the
 same symptoms as adenocarcinomas in humans and are caused by a
 betaretrovirus. OPAs have served as an exquisite model of carcinogenesis
 for human lung adenocarcinomas. In this study, we characterized the
 histopathology and genetic profiles of a jaagsiekte sheep retrovirus
 (JSRV)-envelope protein (Env) transgenic mouse model with spontaneous lung
 tumors, and associations of the genetic profiles with tumor metastasis,
 especially the phenomenon of the epithelial-mesenchymal transition (EMT).
 Genetic information obtained from an expression array was analyzed using
 an ingenuity pathways analysis (IPA) and human disease database
 (MalaCards). By careful examination, several novel EMT-related genes were
 identified from tumor cells using an RT-qPCR, and these genes also scored
 high in MalaCards. We concluded that the JSRV-Env mouse model could serve
 as a spontaneous lung adenocarcinoma model with a metastatic phenotype,
 which will benefit the study of early-onset and progression of lung
 adenocarcinoma. In addition, it can also be a valuable tool for biomarkers
 and drug screening, which will be helpful in developing intervention
 therapies.
description: Microarray_deposit to
 Dryad online
DOI: 10.5061/dryad.fj043
title: Data from: Measuring site fidelity and spatial segregation within animal societies

description: 1.Animals often display a marked tendency to return to previously-visited
 locations that contain important resources, such as water, food, or
 developing brood that must be provisioned. A considerable body of work has
 demonstrated that this tendency is strongly expressed in ants, which
 exhibit fidelity to particular sites both inside and outside the nest.
 However, thus far many studies of this phenomena have taken the approach
 of reducing an animal's trajectory to a summary statistic, such as
 the area it covers. 2.Using both simulations of biased random walks, and
 empirical trajectories from individual rock ants, Temnothorax albipennis,
 we demonstrate that this reductive approach suffers from an unacceptably
 high rate of false negatives. 3.To overcome this, we describe a
 site-centric approach which, in combination with a spatially-explicit null
 model, allows the identification of the important sites towards which
 individuals exhibit statistically significant biases. 4.Using the ant
 trajectories we illustrate how the site-centric approach can be combined
 with social network analysis tools to detect groups of individuals whose
 members display similar space-use patterns. 5.We also address the
 mechanistic origin of individual site fidelity; by examining the sequence
 of visits to each site, we detect a statistical signature associated with
 a self-attracting walk - a non-Markovian movement model that has been
 suggested as a possible mechanism for generating individual site fidelity.
description: Ant
 TrajectoriesWithin-nest ant
 trajectories. Trajectories obtained from digital images, with a 10 minute
 interval between successive photographs.Ant_Trajectories.txtBrood LocationsWithin-nest locations of ant brood items, that is, immature ants (eggs, larvae, pupae). Coordinates correspond to the coordinates in the accompanying Ant_Trajectories.txt file. Photographs are taken every 50 photographs, as indicated by the 'brood_photo' column. These photographs correspond to the Ant_Z column in the accompanying Ant_Trajectories.txt file.Brood_Locations.txt
DOI: 10.15468/dl.9q3haj
title: Occurrence Download

description: A dataset containing 4921733 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-20 -38,55 -38,55 38,-20 38,-20 -38))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Pelecaniformes"
 ]
}

 The dataset includes 4921733 records from 289 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001453-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.1365
title: Data from: Genetic uniformity characterizes the invasive spread of water hyacinth (Eichhornia crassipes), a clonal aquatic plant

description: Aquatic plant invasions are often associated with long-distance dispersal
 of vegetative propagules and prolific clonal reproduction. These
 reproductive features combined with genetic bottlenecks have the potential
 to severely limit genetic diversity in invasive populations. To
 investigate this question we conducted a global scale population genetic
 survey using Amplified Fragment Length Polymorphism (AFLP) markers of the
 world’s most successful aquatic plant invader – Eichhornia crassipes
 (water hyacinth). We sampled 1140 ramets from 54 populations from the
 native (South America) and introduced range (Asia, Africa, Europe, North
 America, Central America and the Caribbean). Although we detected 49
 clones, introduced populations exhibited very low genetic diversity and
 little differentiation compared with those from the native range, and ~80%
 percent of introduced populations were composed of a single clone. A
 widespread clone (‘W’) detected in two Peruvian populations accounted for
 70.9% of the individuals sampled and dominated in 74.5% of the introduced
 populations. However, samples from Bangladesh and Indonesia were composed
 of different genotypes, implicating multiple introductions to the
 introduced range. Nine of 47 introduced populations contained clonal
 diversity suggesting that sexual recruitment occurs in some invasive sites
 where environmental conditions favor seedling establishment. The global
 patterns of genetic diversity in E. crassipes likely result from severe
 genetic bottlenecks during colonization and prolific clonal propagation.
 The prevalence of the “W” genotype throughout the invasive range may be
 explained by stochastic sampling, or possibly because of pre-adaptation of
 the “W” genotype to tolerate low temperatures.
description: AFLP data matrix of
 Eichhornia crassipesAFLP data matrix of 49
 water hyacinth (Eichhornia crassipes) populations from its native and
 introduced ranges. If you have any problem with the data, please contact
 zhang@ips.unibe.ch.water hyacinth AFLP
 data.xls
DOI: 10.5061/dryad.4h0d0
title: Data from: Genetic architecture of threshold reaction norms for male alternative reproductive tactics in Atlantic salmon (Salmo salar L.)

description: Alternative mating tactics have important ecological and evolutionary
 implications and are determined by complex interactions between
 environmental and genetic factors. Here, we study the genetic effect and
 architecture of the variability in reproductive tactics among Atlantic
 salmon males which can either mature sexually early in life in freshwater
 or more commonly only after completing a migration at sea. We applied the
 latent environmental threshold model (LETM), which provides a conceptual
 framework linking individual status to a threshold controlling the
 decision to develop alternative traits, in an innovative experimental
 design using a semi-natural river which allowed for ecologically relevant
 phenotypic expression. Early male parr maturation rates varied greatly
 across families (10 to 93%) which translated into 90% [64–100%] of the
 phenotypic variation explained by genetic variation. Three significant
 QTLs were found for the maturation status, however only one collocated
 with a highly significant QTL explaining 20.6% of the variability of the
 maturation threshold located on chromosome 25 and encompassing a locus
 previously shown to be linked to sea age at maturity in anadromous
 Atlantic salmon. These results provide new empirical illustration of the
 relevance of the LETM for a better understanding of alternative mating
 tactics evolution in natural populations.
description: Accompanying data of the
 article "Genetic architecture of threshold reaction norms for male
 alternative reproductive tactics in Atlantic salmon (Salmo salar
 L.)"Accompanying data of the
 article "Genetic architecture of threshold reaction norms for male
 alternative reproductive tactics in Atlantic salmon (Salmo salar L.)"
 . Includes ReadMe sheet.DataForDRYAD_Lepais-et-al.xlsx