cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.xsj3tx9c2
title: Data from: Environmental context determines the limiting demographic processes for plant recruitment across a species’ elevational range

description: Plant recruitment is a multi-stage process determining population dynamics
 and species distributions. Still, we have limited understanding of how the
 successive demographic processes depend on the environmental context
 across species’ distributional ranges. We conducted a large-scale
 transplant experiment to study recruitment of Pinus cembra over six years.
 We quantified the effects of environmental conditions on four demographic
 processes and identified the most limiting across and beyond the pines’
 elevational range over several years. Realized transition probabilities of
 the demographic processes varied substantially across the species'
 distributional range. Seed deposition decreased from the lower to the
 upper elevational range margin by 90 %, but this reduction was offset by
 increased seed germination and seedling survival. Dispersal limitation at
 the upper range margin potentially stems from unsuitable seed caching
 conditions for the animal seed disperser, whereas increased seed
 germination might result from enemy escape from fungal pathogens and
 favourable abiotic conditions at the upper range margin. Our multi-year
 experiment demonstrates that environmental context is decisive for the
 local relevance of particular demographic processes. We conclude that
 experimental studies identifying the limiting demographic processes
 controlling species distributions are key for projecting future range
 dynamics of plants.
description: Data were collected in the field between 2012-2017 in the Flüela
 and Sertig valley, Davos, Switzerland. Abbreviated headlines are as
 follows: "cache" = presence/absence of caching site,
 "germin1/gemin0" = proportion of seeds germinated,
 "germin0/pred" = proportion of seeds predated, "surv"
 = presence/absence of surving seedling. "cc" = canopy cover (%),
 "veg" = ground vegetation cover (%), "year" = year,
 "site_reg" = site ID, "Ind_RE" = individual level
 random effect
DOI: 10.5061/dryad.xsj3tx9c3
title: Validation of an eDNA-based method for the detection of wildlife pathogens in water

description: Monitoring the occurrence and density of parasites and pathogens can
 identify high infection-risk areas and facilitates disease control and
 eradication measures. Environmental DNA (eDNA) techniques are increasingly
 used for pathogen detection due to their relative ease of application.
 Since many factors affect the reliability and efficacy of eDNA-based
 detection, rigorous validation and assessment of method limitations is a
 crucial first step. We evaluated an eDNA detection method using in-situ
 filtration of large volume water samples, developed to detect and quantify
 aquatic wildlife parasites by qPCR. We assessed method reliability using
 Batrachochytrium dendrobatidis, a pathogenic fungus of amphibians and the
 myxozoan Tetracapsuloides bryosalmonae, causative agent of salmonid
 proliferative kidney disease, in a controlled experimental setup.
 Different amounts of parasite spores were added to tanks containing either
 clean tap water or water from a semi-natural mesocosm community. Overall
 detection rates were higher than 80 %, but detection was not consistent
 among replicate samples. Within tank variation in detection emphasises the
 need for increased site-level replication when dealing with parasites and
 pathogens. Estimated parasite DNA concentrations in water samples were
 highly variable and significant increase with higher spore concentrations
 was observed only for B. dendrobatidis. Despite evidence for PCR
 inhibition in DNA extractions from mesocosm water samples, the type of
 water did not affect detection rates significantly. Direct spiking
 controls revealed that the filtration step reduced detection sensitivity.
 Our study identifies sensitive quantification and sufficient replication
 as major remaining challenges of eDNA-based methods for detection of
 parasites in water.
DOI: 10.5061/dryad.fqz612jqj
title: GPS locations for mechanistic home range analysis reveals drivers of space use patterns for a non-territorial passerine

description: 1. Home ranging is a near-ubiquitous phenomenon in the animal kingdom.
  Understanding the behavioural mechanisms that give rise to
 observed home range patterns is thus an important general question, and
 mechanistic home range analysis (MHRA) provides the tools to address it.
  However, such analysis has hitherto been restricted to
 scent-marking territorial animals, so its potential breadth of application
 has not been tested. 2. Here, we apply MHRA to a population of long-tailed
 tits Aegithalos caudatus a non- territorial passerine, in the
 non-breeding season where there is no clear "central place" near
 which birds need to remain.  The aim is to uncover the principal
 movement mechanisms underlying observed home range formation. 3. Our
 foundational models consist of memory-mediated conspecific avoidance
 between flocks, combined with attraction to woodland.  These are
 then modified to incorporate the effects of flock size and relatedness, to
 uncover the effect of these on the mechanisms of home range formation. 4.
  We found that a simple model of spatial avoidance, together with
 attraction to the central parts of woodland areas, accurately captures
 long-tailed tit home range patterns.  Refining these models
 further, we show that the magnitude of spatial avoidance by a flock is
 negatively correlated to both the relative size of the flock (compared to
 its neighbour) and the relatedness of the flock with its neighbour.
   5. Our study applies MHRA beyond the confines of scent-marking,
 territorial animals, so paves the way for much broader taxonomic
 application.  These could potentially help uncover general
 properties underlying the emergence of animal space use patterns.
  This is also the first study to apply MHRA to questions of
 relatedness and flock size, thus broadening the potential possible
 applications of this suite of analytic techniques.  
description: This file contains the GPS data for flocks of long-tailed tits in
 the non-breeding seasons of 2010-2013 and 2018-19.
DOI: 10.15468/dl.3nshe6
title: Occurrence Download

description: A dataset containing 498 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Observation, Human Observation, Specimen)",
 "Country is Romania",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Erinaceus roumanicus"
 ]
}

 The dataset includes 498 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002414-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.s4mw6m94p
title: Data from: Ecology of domestic dogs (Canis familiaris) as a host for Guinea worm (Dracunculus medinensis) infection in Ethiopia

description: The global programme for the eradication of Guinea worm disease, caused by
 the parasitic nematode Dracunculus medinensis, has been successful in
 driving down human cases, but infections in non-human animals,
 particularly domestic dogs (Canis familiaris), now present a major
 obstacle to further progress. Dog infections have mainly been found in
 Chad and, to a lesser extent in Mali and Ethiopia. While humans
 classically acquire infection by drinking water containing infected
 copepods, it has been hypothesised that dogs might additionally or
 alternatively acquire infection via a novel pathway, such as consumption
 of fish or frogs as possible transport or paratenic hosts. We
 characterised the ecology of free-ranging dogs living in three villages in
 Gog woreda, Gambella region, Ethiopia in April–May 2018. We analysed their
 exposure to potential sources of Guinea worm infection, and investigated
 risk factors associated with infection histories. The home ranges of 125
 dogs and their activity around water sources were described using GPS
 tracking, and the diets of 119 dogs were described using stable isotope
 analysis. Unlike in Chad, where Guinea worm infection is most frequent, we
 found no ecological or behavioural correlates of infection history in dogs
 in Ethiopia. Unlike in Chad, there was no effect of variation among dogs
 in their consumption of aquatic vertebrates (fish or frogs) on their
 infection history, and we found no evidence to support hypotheses for this
 novel transmission pathway in Ethiopia. Dog owners had apparently
 increased the frequency of clean water provision to dogs in response to
 previous infections. Variations in dog ranging behaviour, owner behaviour
 and the characteristics of natural water bodies all influenced the
 exposure of dogs to potential sources of infection. This initial study
 suggests that the classical transmission pathway should be a focus of
 attention for Guinea worm control in non-human animals in Ethiopia.
description: GPS tracking of dogs. Stable isotope analysis of dog diets.
 Epidemiological analysis. Satellite imagery. 
description: See ReadMe.txt file.
DOI: 10.5061/dryad.zcrjdfn88
title: Data from: Investigating cat predation as the cause of bat wing tears using forensic DNA analysis

description: Cat predation upon bat species has been reported to have significant
 effects on bat populations in both rural and urban areas. The majority of
 research in this area has focussed on observational data from bat
 rehabilitators documenting injuries, and cat owners, when domestic cats
 present prey. However, this has the potential to underestimate the number
 of bats killed or injured by cats. Here, we use forensic DNA analysis
 techniques to analyse swabs taken from injured bats in the United Kingdom,
 mainly including Pipistrellus pipistrellus (40 out of 72 specimens). Using
 quantitative PCR, cat DNA was found in two-thirds of samples submitted by
 bat rehabilitators. Of these samples, short tandem repeat analysis
 produced partial DNA profiles for approximately one-third of samples,
 which could be used to link predation events to individual cats. The use
 of genetic analysis can complement observational data, and potentially
 provide additional information to give a more accurate estimation of cat
 predation.      
description: Bat wing swabs samples were subject to DNA extraction, followed
 by either qPCR or PCR and capillary electrophoresis for cat specific DNA
 markers.
DOI: 10.5061/dryad.cc2fqz645
title: No net insect abundance and diversity declines across US Long Term Ecological Research sites

description: Recent reports of dramatic declines in insect abundance suggest grave
 consequences for global ecosystems and human society. Most evidence comes
 from Europe, however, leaving uncertainty about insect population trends
 worldwide. We used &gt; 5,300 time series for insects and other
 arthropods, collected over 4-36 years at monitoring sites representing 68
 different natural and managed areas, to search for evidence of declines
 across the United States. Some taxa and sites showed decreases in
 abundance and diversity while others increased or were unchanged, yielding
 net abundance and biodiversity trends generally indistinguishable from
 zero. This lack of overall increase or decline was consistent across
 arthropod feeding groups, and was similar for heavily disturbed versus
 relatively natural sites. The apparent robustness of U.S. arthropod
 populations is reassuring. Yet, this result does not diminish the need for
 continued monitoring and could mask subtler changes in species composition
 that nonetheless endanger insect-provided ecosystem services. 
description: Data curated from NSF Long-Term Ecological Research Site public
 repositories.
description: R code used to curate and analyze data is included.
DOI: 10.5061/dryad.jwstqjq6f
title: Hamlet aggressive mimicry: permanovas and bootstraps results on dS, dL

description: We tested the potential for aggressive mimicry by a group of coral reef
 fishes, the colour polymorphic Hypoplectrus hamlets, from the point of
 view of their most common prey, small epibenthic gobies and mysid shrimp.
 We build visual models based on the visual pigments and spatial resolution
 of the prey, the underwater light spectrum and colour reflectances of
 putative models and their hamlet mimics. We apply Maia & White
 2018 two-step statistical approach to estimate statistical and perceptual
 separation based on noise-corrected colour distances. The results of the
 PERMANOVAs and related bootstrap procedures on dS, dL from visual
 modelling of Mysidium shrimp and masked goby (Coryphopterus personatus)
 are presented here. Our results are consistent with a proposed mimic-model
 relationship between the butter hamlet H. unicolor and its model the
 butterflyfish Chaetodon capistratus but do not support a second proposed
 mimic-model pair between the black hamlet H. nigricans and the dusky
 damselfish Stegastes adustus.
DOI: 10.5061/dryad.k0p2ngf5x
title: Data from: Contrasting population structure and demographic history of cereal aphids in different environmental and agricultural landscapes

description: Single Nucleotide Polymorphisms files and phylogonetic trees of
 S. miscanthi samples collected in China and S. avenae from the UK used to
 study the population genetics analyses of these species. These are:
 China_samples_vcf.zip: dataset of SNPs from S. miscanthi sampled in 10
 populations of China obtained using FreeBayes (in vcf format).
 China_samples_vcf_filtered.zip: SNPs from S. miscanthi after
 filtering the file China_samples_vcf.zip using vcftools (max-missing 0.75,
 minDP 3, mac 3, minQ 30, remove-indels, thin 2000, max-missing 0.9, thin
 5000). This file was used in all population genetic analyses of the
 Chinese populations in the paper, transforming to the appropriate formats.
 China_samples_SNPs.fas: fasta file of phased SNPs used to estimate the
 phylogeny of S. miscanthi haplotypes using RAxML.
 China_RAxML_phylogeny_newick.tre: RAxML phylogenetic tree in newick format
 obtained with China_samples_SNPs.fas. England_samples_vcf.zip: dataset of
 SNPs from S. avenae sampled in 12 populations of
 England obtained using FreeBayes (in vcf format).
 England_samples_vcf_filtered.zip: SNPs from S. avenae after
 filtering the file England_samples_vcf.zip using vcftools (max-missing
 0.5, mac 3, minQ 30, minDP 3, max-missing 0.5, exclude individuals with
 50% missing data, max-missing 0.75, remove-indels, thin 2000). This file
 was used in all population genetic analyses of the English populations in
 the paper, transforming the vcf to the corresponding formats.
 England_samples_SNPs.fas: fasta file of phased SNPs.
 England_samples_SNPs_polymorphic.fas: fasta file of phased SNPs used in
 the phylogenetic reconstruction of S. avenae
 haplotypes using RAxML. This file is the same as
 England_samples_SNPs.fas after removing sites which were not polymorphic
 (e.g. a site that contains N and T in different samples is not considered
 polymorphic for RAxML and has to be removed)
 England_RAxML_phylogeny_newick.tre: RAxML phylogenetic tree in newick
 format obtained with England_samples_SNPs_polymorphic.fas.
DOI: 10.5061/dryad.cfxpnvx37
title: Lupclip: Annual mowing has the potential to reduce the invasion of herbaceous Lupinus polyphyllus

description: In order to manage invasive plant species efficiently, it is necessary to
 have a thorough understanding of different strategies of population
 control, including the underlying mechanisms of action and the
 consequences for target populations. Here, I explored the effectiveness of
 biomass removal as a method of control for the invasive perennial herb
 Lupinus polyphyllus. More specifically, using seed material from 11
 populations, I assessed among-population variation (if any) in plant
 compensatory growth as a response to annual biomass removal under
 standardised growing conditions over two consecutive years, and quantified
 the demographic effects of a single biomass-removal event. In all study
 populations, annual biomass removal reduced plant size, flowering
 probability, and shoot and root biomass. Biomass removal also reduced
 plant survival and the number of flowering shoots, but these effects were
 pronounced at certain time points only. A population-level demographic
 analysis revealed that a single biomass-removal event considerably
 decreased the long-term population growth rate (λ); this decline in λ was
 due to a reduction in plant fecundity followed by survival and growth.
 These findings suggest that annual mowing has the potential to curb
 invasions of L. polyphyllus because plants are not able to fully
 compensate for drastic biomass loss.
description: This dataset of Lupinus polyphyllus was collected
 based on a common garden study in the Ruissalo Botanical Garden of the
 University of Turku, Finland during 2017-2018. Individuals that died
 before the first clipping treatment in June 2017 (n = 40 individuals out
 of 880) have been deleted from the data.
description: Lupclip_README.txt:<br>
 Readme file a detailed description of the variables in each
 file. Lupclip_time.xlsx:<br>
 Measurements of individual plants of <i>Lupinus
 polyphyllus</i> in four time points. Lupclip_biomass.xlsx:<br>
 Plant dry biomass at the end of the experiment. Lupclip_IPMdata.xlsx:<br>
 Demographic data of <i>Lupinus polyphyllus</i> from two
 consecutive years. Lupclip_IPM.txt:<br> An
 R-code to construct an integral projection model and calculate the
 deterministic population growth rate with 95% confidence intervals based
 on bootstrapping.
DOI: 10.15468/dl.tcmcgm
title: Occurrence Download

description: A dataset containing 11 species occurrences available in GBIF matching the query:
{
 "CatalogNumber" : [
 "is one of (K-M000820309, K-M000772199, K-M000868903, K-M000235252, K-M000769752, K-M000951317, K-M000235258, K-M000193560, K-M000822527, K-M001441780, K-M000193561)"
 ]
}

 The dataset includes 11 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002416-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.4xgxd256h
title: Data from: Detection of the endangered European weather loach (Misgurnus fossilis) via water and sediment samples: testing multiple eDNA workflows.

description: The European weather loach (Misgurnus fossilis) is classified as highly
 endangered in several countries of Central Europe. Populations of M.
 fossilis are predominantly found in ditches with low water levels and
 thick sludge layers and are thus hard to detect using conventional fishing
 methods. Therefore, environmental DNA (eDNA) monitoring appears
 particularly relevant for this species. In previous studies, M. fossilis
 was surveyed following eDNA water sampling protocols, which were not
 optimized for this species. Therefore, we created two full factorial study
 designs to test six different eDNA workflows for sediment samples and
 twelve different workflows for water samples. We used qPCR to compare the
 Threshold cycle (Ct) values of the different workflows, which indicate the
 target DNA amount in the sample, and spectrophotometry to quantify and
 compare the total DNA amount inside the samples. We analyzed 96 water
 samples and 48 sediment samples from a pond with a known population of M.
 fossilis. We tested several method combinations for long-term sample
 preservation, DNA capture and DNA extraction. Additionally, we analyzed
 the DNA yield of samples from a ditch with a natural M. fossilis
 population monthly over one year to determine the optimal sampling period.
 Our results showed that the long-term water preservation method commonly
 used for eDNA surveys of M. fossilis did not lead to optimal DNA yields,
 and we present a valid long-term sample preservation alternative. A
 cost-efficient high salt DNA extraction led to the highest target DNA
 yields and can be used for sediment and water samples. Furthermore, we
 were able to show that in a natural habitat of M. fossilis, total and
 target eDNA were higher between June and September, which implies that
 this period is favorable for eDNA sampling. Our results will help to
 improve the reliability of future eDNA surveys of M. fossilis.
DOI: 10.15468/dl.j9kzsr
title: Occurrence Download

description: A dataset containing 330 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Barbieria pinnata",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 330 records from 53 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002417-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.mgqnk98x3
title: Data from: Model egg rejection by Eastern Bluebirds

description: Brood parasitism results in substantial costs to hosts, yet not all
 species eject foreign eggs. Because the costs of mistakenly ejecting one’s
 own eggs are high, selection may favor ejection behavior only if it is
 unlikely a host will incorrectly eject her own eggs. Eastern Bluebirds are
 currently subject to relatively low levels of interspecific brood
 parasitism but still sometimes eject parasitic eggs. Therefore, we tested
 which visual cues they use to eject foreign eggs with the prediction that
 only the most dissimilar eggs would be ejected, reducing the likelihood of
 a female’s making a mistake. House Sparrows, which occasionally parasitize
 bluebirds, lay eggs that have an off-white ground color with brown
 speckling. Therefore, to test which colors or patterns allow for
 discrimination of parasitic eggs, we generated 3D-printed model House
 Sparrow eggs and painted them entirely off-white, entirely brown, half
 off-white and half brown, or off-white with brown speckling. We then
 sequentially placed these four different model eggs in the nests of
 Eastern Bluebirds, with each nest receiving all treatments over the course
 of four days. After watching females enter and leave the nest box just one
 time after placement of the model egg, we found that speckled eggs were
 ejected half the time (7 of 14 nests), while no other treatment was
 ejected more than three times. Thus, Eastern Bluebird females eject eggs
 based primarily on color patterning (i.e., a speckled pattern) rather than
 coloration per se, and that they can do so very quickly, as the average
 female had removed the model egg within six minutes of entering the nest.
 Because Eastern Bluebirds do not lay speckled eggs, but some brood
 parasites (e.g., House Sparrows, Brown-headed Cowbirds) do, selection may
 specifically favor ejection of eggs with a speckled pattern, not just eggs
 that have within-egg color contrasts.
description: Collected by observation (behavior) and Photoshop (eggshell color
 quantifcation).  Processed in EXCEL and SAS.
description: Labels in dataset.