cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.9feqex
title: Occurrence Download

description: A dataset containing 270 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Demosthenesia mandonii",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 270 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001267-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.8g55g
title: Data from: Studies in lichens and lichenicolous fungi – No. 19: further notes on species from the Coastal Plain of southeastern North America

description: Geographically disjunct and ecologically unusual populations of Cladonia
 apodocarpa from hardwood swamps are reported from southeastern North
 Carolina, and assignment to that species is confirmed with analyses of
 nrITS sequence data. The separation of Lecanora cinereofusca var.
 cinereofusca and L. cinereofusca var. appalachensis is discussed in the
 light of analyses of mtSSU and nrITS sequence data. Lecanora cinereofusca
 var. appalachensis is considered to merit recognition at the species
 level, for which the name L. saxigena Lendemer & R.C. Harris
 (nomen novum pro L. appalachensis (Brodo) non L. appalachensis Lendemer
 & R.C. Harris) is introduced. Phlyctis ludoviciensis is formally
 placed in synonymy with P. boliviensis. Phlyctis willeyi is shown to
 belong to the genus Leucodecton and the new combination L. willeyi (Tuck.)
 R.C. Harris is proposed. Piccolia nannaria is hypothesized to be a
 parasite on Pyrrhospora varians and is shown to be more widespread in the
 Coastal Plain than previously thought. Schismatomma rappii is revised,
 illustrated, and shown to be widespread in the Coastal Plain of
 southeastern North America. Tylophoron hibernicum is confirmed to be the
 correct name for all North American records of T. protrudens.
description: changes_MACP_datapacketThis is a zipped folder containing the following items: 1) alignments of Cladonia nrITS sequences used in Bayesian Inference (BI), maximum likelihood (ML), and maximum parsimony (MP) analyses in this study; 2) alignment of nrITS sequences of Lecanora cinereofusca s.l. used for examination of genetic distance; 3) alignments of mtSSU sequences of Lecanoraceae illustrating the monophyly and phylogenetic placement of Lecanora cinereofusca s.l. used in in Bayesian Inference (BI) and maximum likelihood (ML) analyses in this study.
DOI: 10.5061/dryad.m77j0
title: Data from: MotionMeerkat: integrating motion video detection and ecological monitoring

description: 1. Human observation is expensive and limits the breadth of data
 collection. For this reason, remotely placed video cameras are
 increasingly used to monitor animals. One drawback of field-based video
 recordings is extensive review time. Computer vision can mitigate this
 cost and enhance data collection by extracting biological information from
 images with minimal time investment. 2. MotionMeerkat is a new standalone
 program that identifies motion events from a video stream. After running a
 video, the user reviews a folder of candidate motion frames for the target
 organism. This tool reduces the time needed to review videos and
 accommodates a variety of inputs. 3. I tested MotionMeerkat using
 hummingbird-plant videos recorded in a tropical montane forest. To
 validate the optimal parameter set for finding motion events, I counted
 hummingbirds observed from direct video review compared to events found in
 images returned from MotionMeerkat. To show the generality of the
 approach, MotionMeerkat was tested on a set of terrestrial and underwater
 videos. To assess the performance of the background subtraction for
 further image analysis, I hand counted the number of frames with target
 organisms and compared them to the MotionMeerkat output. 4. MotionMeerkat
 was highly successful in finding motion events and often reduced the
 number of frames needed to capture hummingbird visitation by over 90%.
 Both background approaches effectively found a variety of organisms in
 ecological videos. I provide general recommendations for parameter
 settings and extending this approach in the future.
description: MotionTestData used to testing background subtraction.AcctestingR script for running performance analysis.
DOI: 10.5061/dryad.627sf
title: Data from: Aboveground mammal and invertebrate exclusions cause consistent changes in soil food webs of two subalpine grassland types, but mechanisms are system-specific

description: Ungulates, smaller mammals, and invertebrates can each affect soil biota
 through their influence on vegetation and soil characteristics. However,
 direct and indirect effects of the aboveground biota on soil food webs
 remain to be unraveled. We assessed effects of progressively excluding
 aboveground large-, medium- and small-sized mammals as well as
 invertebrates on soil nematode diversity and feeding type abundances in
 two subalpine grassland types: short- and tall-grass vegetation. We
 explored pathways that link exclusions of aboveground biota to nematode
 feeding type abundances via changes in plants, soil environment, soil
 microbial biomass, and soil nutrients. In both vegetation types,
 exclusions caused a similar shift toward higher abundance of all nematode
 feeding types, except plant feeders, lower Shannon diversity, and lower
 evenness. These effects were strongest when small mammals, or both small
 mammals and invertebrates were excluded in addition to excluding larger
 mammals. Exclusions resulted in a changed abiotic soil environment that
 only affected nematodes in the short-grass vegetation. In each vegetation
 type, exclusion effects on nematode abundances were mediated by different
 drivers related to plant quantity and quality. In the short-grass
 vegetation, not all exclusion effects on omni–carnivorous nematodes were
 mediated by the abundance of lower trophic level nematodes, suggesting
 that omni–carnivores also depended on other prey than nematodes. We
 conclude that small aboveground herbivores have major impacts on the soil
 food web of subalpine short- and tall-grass ecosystems. Excluding
 aboveground animals caused similar shifts in soil nematode assemblages in
 both subalpine vegetation types, however, mechanisms turned out to be
 system-specific.
description: Data_OIK-03341.R2Data_OIK-03341.R2.csv contains the data on nematode feeding type abundances and community indices, as well as the data used in the Structural Equation Models of the progressive aboveground mammal and invertebrate exclusion effects on the abundance of bacterivorous, fungivorous, plant-feeding and omni-carnivorous nematode abundance via pathways of plants, soil nutrients, soil microbial biomass, and soil environment in both short- and tall-grass vegetation.
DOI: 10.5061/dryad.s3mr73b
title: Data from: Masculinisation of gene expression is associated with male quality in Drosophila melanogaster

description: The signature of sexual selection has been revealed through the study of
 differences in patterns of genome-wide gene expression, both between the
 sexes and between alternative reproductive morphs within a single sex.
 What remains unclear, however, is whether differences in gene expression
 patterns between individuals of a given sex consistently map to variation
 in individual quality. Such a pattern, particularly if found in males,
 would provide unambiguous evidence that the phenotypic response to sexual
 selection is shaped through sex-specific alterations to the transcriptome.
 To redress this knowledge gap, we explored whether patterns of sex-biased
 gene expression are associated with variation in male reproductive quality
 in Drosophila melanogaster. We measured two male reproductive phenotypes,
 and their association with sex-biased gene expression, across a selection
 of inbred lines from the Drosophila Genetic Reference Panel. Genotypes
 with higher expression of male-biased genes produced males exhibiting
 shorter latencies to copulation, and higher capacity to inseminate
 females. Conversely, female-biased genes tended to show negative
 associations with these male reproductive traits across genotypes. We
 uncovered similar patterns, by reanalysing a published dataset from a
 second D. melanogaster population. Our results reveal the footprint of
 sexual selection in masculinising the male transcriptome.
description: PhenotypeData_33DGRPMale reproductive phenotype data for 33 of the DGRP lines. Phenotypes include male latency to copulation and male insemination capacity.
DOI: 10.5061/dryad.gr3p6
title: Data from: Living on the edge: parasite prevalence changes dramatically across a range edge in an invasive gecko

description: Species interactions can determine range limits, and parasitism is the
 most intimate of such interactions. Intriguingly, the very conditions on
 range edges likely change host-parasite dynamics in nontrivial ways. Range
 edges are often associated with clines in host density and with
 environmental transitions, both of which may affect parasite transmission.
 On advancing range edges, founder events and fitness/dispersal costs of
 parasitism may also cause parasites to be lost on range edges. Here we
 examine the prevalence of three species of parasite across the range edge
 of an invasive gecko, Hemidactylus frenatus, in northeastern Australia.
 The gecko’s range edge spans the urban-woodland interface at the edge of
 urban areas. Across this edge, gecko abundance shows a steep decline,
 being lower in the woodland. Two parasite species (a mite and a
 pentastome) are coevolved with H. frenatus, and these species become less
 prevalent as the geckos become less abundant. A third species of parasite
 (another pentastome) is native to Australia and has no coevolutionary
 history with H. frenatus. This species became more prevalent as the geckos
 become less abundant. These dramatic shifts in parasitism (occurring over
 3.5 km) confirm that host-parasite dynamics can vary substantially across
 the range edge of this gecko host.
description: Geckos parasitised with
 three species of parasitesDataset of geckos
 collected and scored for the study. list refers to distance from the urban
 edge for each collection site; sex refers to the sex of the gecko (j
 denotes juvenile); mite refers to counts and presence absence of Geckobia
 mites; pent refers to presence/absence of Raillietiella eggs in the faeces
 (pent.eggs) is the egg count in the faecal float); waddy refers to
 intensity and presence absence of Waddycephalus; abund refers to the
 relative abundance of geckos at the site.comb.data.csvZip file with data and scriptsHere is the dataset and all analysis scripts (in R and JAGS) for the paper.dataAndScriptsCoatesetal.zip
DOI: 10.5061/dryad.k2v04
title: Data from: Biodiversity inventories and conservation of the marine fishes of Bootless Bay, Papua New Guinea

description: BACKGROUND: The effective management and conservation of biodiversity is
 predicated on clearly defined conservation targets. Species number is
 frequently used as a metric for conservation prioritization and monitoring
 changes in ecosystem health. We conducted a series of synoptic surveys
 focusing on the fishes of the Bootless Bay region of Papua New Guinea to
 generate a checklist of fishes of the region. Bootless Bay lies directly
 south of Port Moresby, the capital of Papua New Guinea, and experiences
 the highest human population density of any marine area in the country.
 Our checklist will set a baseline against which future environmental
 changes can be tracked RESULTS: We generated a checklist of 488 fish
 species in 72 families found in Bootless Bay during a two-week sampling
 effort. Using incident-based methods of species estimation, we extrapolate
 there to be approximately 940 fish species in Bootless Bay, one of the
 lowest reported numbers in Papua New Guinea. CONCLUSIONS: Our data suggest
 that the Bootless Bay ecosystem of Papua New Guinea, while diverse in
 absolute terms, has lower fish biodiversity compared to other shallow
 marine areas within the country. These differences in faunal diversity,
 are most likely a combination of unequal sampling effort as well as
 biophysical factors within Bootless Bay compounded by historical and/or
 contemporary anthropogenic disturbances.
description: FishListA list of marine fish species identified as occurring in Bootless Bay, Papua New Guinea. Species in BOLD were not observed during the January 2011 survey, but reported in the literature or in museum collections Species were identified to the finest taxonomic resolution possible.
DOI: 10.5061/dryad.6cr82
title: Data from: The challenge of accurately documenting bee species richness in agroecosystems: bee diversity in eastern apple orchards

description: Bees are important pollinators of agricultural crops, and bee diversity
 has been shown to be closely associated with pollination, a valuable
 ecosystem service. Higher functional diversity and species richness of
 bees have been shown to lead to higher crop yield. Bees simultaneously
 represent a mega-diverse taxon that is extremely challenging to sample
 thoroughly and an important group to understand because of pollination
 services. We sampled bees visiting apple blossoms in 28 orchards over 6
 years. We used species rarefaction analyses to test for the completeness
 of sampling and the relationship between species richness and sampling
 effort, orchard size, and percent agriculture in the surrounding
 landscape. We performed more than 190 h of sampling, collecting 11,219
 specimens representing 104 species. Despite the sampling intensity, we
 captured &lt;75% of expected species richness at more than half of the
 sites. For most of these, the variation in bee community composition
 between years was greater than among sites. Species richness was
 influenced by percent agriculture, orchard size, and sampling effort, but
 we found no factors explaining the difference between observed and
 expected species richness. Competition between honeybees and wild bees did
 not appear to be a factor, as we found no correlation between honeybee and
 wild bee abundance. Our study shows that the pollinator fauna of
 agroecosystems can be diverse and challenging to thoroughly sample. We
 demonstrate that there is high temporal variation in community composition
 and that sites vary widely in the sampling effort required to fully
 describe their diversity. In order to maximize pollination services
 provided by wild bee species, we must first accurately estimate species
 richness. For researchers interested in providing this estimate, we
 recommend multiyear studies and rarefaction analyses to quantify the gap
 between observed and expected species richness.
description: DataforDryad_netmaludomeMatrix of taxa (bee species) by apple orchard localities in New York (coded alphabetically by size). Cells in the matrix include the abundance of the bee species collected at each orchard over a period of six years, from 2008-2013. Bees were net collected on and between apple blossoms.
DOI: 10.5061/dryad.66jn7g7
title: Data from: Integrating morphological characters, molecular markers, and distribution patterns to assess the identity of Blepharis species from Jordan

description: Background: Blepharis constitutes an important vegetative part of the
 Jordanian arid and semi-arid regions, yet whether one or more species
 occurs in this area is debatable. We addressed this question by assessing
 morphological characters and employing Inter-Simple Sequence Repeat (ISSR)
 markers on three populations of Blepharis: two Northern (lower slopes of
 Kufranjah valley and the Dead Sea region) and one Southern (Wadi al Yutm).
 Results: Shoots from 19 randomly chosen Blepharis plants per population
 were harvested for morphological and molecular analyses. Spikes were lax
 and bract width was considerably shorter than length of the longest
 lateral spine in the Northern populations compared to the Southern
 population (P &lt; 0.001). A multivariate linear discriminant analysis
 (LDA) distinguished the Northern populations from the Southern one largely
 by internode length, bract width, longest lateral spine length, and bract
 width to spine length ratio (P &lt; 0.001). The ISSR analysis revealed
 that 44 markers across eight primers were polymorphic with major allele
 frequency of 83.6% and an average of 5.5 polymorphic markers per primer.
 The genetic resemblance among individuals ranged from 0.27 to 0.96. The
 three Blepharis populations were accordingly clustered into two distinct
 groups, similar to the analysis of morphological differences. Conclusions:
 Our results strongly indicate the occurrence of two discrete Blepharis
 species in Jordan and the hypothesis that the genus is represented by only
 one species is not supported. The species in Jordan are B. attenutata
 Napper (represented by the Northern populations) and B. ciliaris [L.] B.
 L. Burtt (represented by the Southern population). These findings are
 important for informing floristic work within the region and an updated
 key has been included in our findings.
description: Morphological
 DataMorphological data (see
 README.md for variable description). All data & analysis files
 available as an .Rproj project file from GitHub:
 https://github.com/ColauttiLab/BlepharisMorphDataMuhaidatEtAl_MorphData.csvLDA.RR code for Linear Discriminant AnalysisLDAvsISSRR code for comparing LDA with NMDS from ISSR genotype dataMuhaidatEtAl_ISSRDataISSR genotype data
DOI: 10.5061/dryad.4291n
title: Data from: A quantitative test of the predicted relationship between countershading and lighting environment.

description: Countershading, a vertical luminance gradient from a dark back to a light
 belly, is perhaps the most common coloration phenotype in the animal
 kingdom. Why? We investigated whether countershading functions as
 self-shadow concealment (SSC) in ruminants. We calculated “optimal”
 countershading for SSC by measuring illumination falling onto a model
 ruminant as a function of time of day and lighting environment. Calibrated
 images of 114 species of ruminant were compared to the countershading
 model, and phylogenetic analyses were used to find the best predictors of
 coats’ countershading characteristics. In many species, countershading was
 close to the model’s prediction of “optimal” countershading for SSC.
 Stronger countershading was associated with increased use of open lighting
 environments, living closer to the equator, and small body size. Abrupt
 transitions from dark to light tones were more common in open lighting
 environments but unassociated with group size or antipredator behavior.
 Though the SSC hypothesis prediction for stronger countershading in
 diurnal species was not supported and noncountershaded or
 reverse-countershaded species were unexpectedly common, this basic pattern
 of associations is explained only by the SSC hypothesis. Despite extreme
 variation in lighting conditions, many terrestrial animals still find
 protection from predation by compensating for their own shadows.
description: WA_countershading_in_ruminants_comparative_dataColumn A contains species names. The corresponding phylogenetic tree can be obtained at: (http://purl.org/phylo/treebase/phylows/study/TB2:S12968). Columns B-I are the countershading measures taken from analysis of calibrated images of museum specimens. Columns J-O are ecological and beavioural predictors of countershading variation. Column headings are self-explanatory. Can be saved as a tab-delimited .txt file.TreeBASE S12968
DOI: 10.5061/dryad.d18r8
title: Data from: Pleistocene range dynamics in the eastern Greater Cape Floristic Region: a case study of the Little Karoo endemic Berkheya cuneata (Asteraceae)

description: The glacial–interglacial climate cycles of the Pleistocene played a
 significant role in dramatically altering species distributions across the
 globe. However, the climate of the Greater Cape Floristic Region is
 thought to have been decoupled from global fluctuations and the current
 Mediterranean climate remained relatively buffered during this period.
 Here we explore the roles of climate stability and the topographic
 complexity of the region on the range history of an endemic Little Karoo
 plant, Berkheya cuneata, using ensemble species distribution modelling and
 multi-locus phylogeography. The species distribution models projected onto
 downscaled climate simulation of the Last Glacial Maximum demonstrated a
 considerable range contraction and fragmentation into the western and
 eastern Little Karoo, separated by the Rooiberg inselberg. This population
 fragmentation is mirrored in the phylogeographic structuring of both
 chloroplast and nuclear DNA. These results suggest that sufficient
 climatic buffering coupled with regionally complex topography ensured the
 localised population persistence during Pleistocene climate cycles but
 these features have also promoted population vicariance in this, and
 likely other, Little Karoo lowland species.
description: DNA.alignmentsThe zip file contains the DNA alignments used for analyses. This submission includes the original unedited alignments plus the gap-coded alignments (with gaps removed). See the original publication for details regarding collection, DNA extraction, amplification and sequencing.
DOI: 10.5061/dryad.2sk69c4
title: Data from: Catechol-O-Methyltransferase moderates effect of stress mindset on affect and cognition

description: There is evidence that altering stress mindset— the belief that stress is
 enhancing vs. debilitating —can change cognitive, affective and
 physiological responses to stress. However individual differences in
 responsiveness to stress mindset manipulations have not been explored.
 Given the previously established role of catecholamines in both placebo
 effects and stress, we hypothesized that genetic variation in
 catechol-O-methyltransferase (COMT), an enzyme that metabolizes
 catecholamines, would moderate responses to an intervention intended to
 alter participants’ mindsets about stress. Participants (N=107) were
 exposed to a stress mindset manipulation (videos highlighting either the
 enhancing or debilitating effects of stress) prior to engaging in a Trier
 Social Stress task and subsequent cognitive tasks. The associations of the
 COMT rs4680 polymorphism with the effect of stress mindset video
 manipulations on cognitive and affective responses were examined. Genetic
 variation at rs4680 modified the effects of stress mindset on affective
 and cognitive responses to stress. Individuals homozygous for rs4680
 low-activity allele (met/met) were responsive to the stress-is-enhancing
 mindset manipulation as indicated by greater increases in positive affect,
 improved cognitive functioning, and happiness bias in response to stress.
 Conversely, individuals homozygous for the high-activity allele (val/val)
 were not as responsive to the stress mindset manipulation. These results
 suggest that responses to stress mindset intervention may vary with COMT
 genotype. These findings contribute to the understanding of gene by
 environment interactions for mindset interventions and stress reactivity
 and therefore warrant further investigations.
description: Crumetal2018_COMTSMM_PLOSONEData from Crum, Akinola, Turnwald, Kaptchuk & Hall (2018) PLOS ONE article: Catechol-O-Methyltransferase moderates effect of stress mindset on affect and cognition