cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.gf1vhhmnf
title: Winter moth in Scandinavia: structure file

description: The frequency and severity of outbreaks by pestiferous insects is
 increasing globally, likely as a result of human-mediated introductions of
 non-native organisms. However, it is not always apparent whether an
 outbreak is the result of a recent introduction of an evolutionarily naïve
 population, or of recent disturbance acting on an existing population that
 arrived previously during natural range expansion.  Here we use
 approximate Bayesian computation to infer the colonization history of a
 pestiferous insect, the winter moth, Operophtera brumata L. (Lepidoptera:
 Geometridae), which has caused widespread defoliation in northern
 Fennoscandia. We generated genotypes using a suite of 24 microsatellite
 loci and find that populations of winter moth in northern Europe can be
 assigned to five genetically distinct clusters that correspond with 1)
 Iceland, 2) the British Isles, 3) Central Europe and southern
 Fennoscandia, 4) Eastern Europe, and 5) northern Fennoscandia. We find
 that the northern Fennoscandia winter moth cluster is most closely related
 to a population presently found in the British Isles, and that these
 populations likely diverged around 2,900 years ago. This result suggests
 that current outbreaks are not the result of a recent introduction, but
 rather that recent climate or habitat disturbance is acting on existing
 populations that may have arrived to northern Fennoscandia via pre-Roman
 traders from the British Isles, and/or by natural dispersal across the
 North Sea likely using the Orkney Islands of northern Scotland as a
 stepping-stone before dispersing up the Norwegian coast.
description: Single line formatted structure file based on microsatellite
 genotyping of 24 polymorphic loci from winter moth individuals collected
 from northern Europe.
description: Single line structure format with putative population IDs.
 Missing values coded as "-9."
DOI: 10.5061/dryad.3ffbg79gv
title: Data from: Beyond a single patch: local and regional processes explain diversity patterns in a seagrass epifaunal metacommunity

description: Ecological communities are jointly structured by dispersal,
 density-independent responses to environmental conditions and
 density-dependent biotic interactions. Metacommunity ecology provides a
 framework for understanding how these processes combine to determine
 community seagrass meadows along the British Columbia coast, we tested the
 hypothesis that eelgrass (Zostera marina L.) epifaunal invertebrate
 assemblages are influenced by local environmental conditions, but that
 high dispersal rates at larger spatial scales dampen effects of
 environmental differences. We used hierarchical joint species distribution
 modelling to understand the contribution of environmental conditions,
 spatial distance between meadows, and species co-occurrences to epifaunal
 invertebrate abundance and distribution across the region. We found that
 patterns of taxonomic compositional similarity among meadows were
 inconsistent with dispersal limitation, and meadows in the same region
 were often no more similar to each other than meadows over 1000 km away.
 Abiotic environmental conditions (temperature, dissolved oxygen) explained
 a small fraction of variation in taxonomic abundances patterns across the
 region. We found novel co-occurrence patterns among taxa that could not be
 explained by shared responses to environmental gradients, suggesting the
 possibility that interspecific interactions influence seagrass
 invertebrate abundance and distribution. Our results suggest that
 biodiversity and ecosystem functions provided by seagrass meadows reflect
 ecological processes occurring both within meadows and across seascapes,
 and that management of eelgrass habitat for biodiversity may be most
 effective when both local and regional processes are considered.
description: There are three datasets: eelgrass-associated invertebtrate
 biodiversity data, environmental data, and spatial coordinates. There were
 17 sites in the study across the coast of British Columbia, and we sampled
 6 quadrats in each in a 2x3 array (see Fig. 1 in Supplement of Stark et
 al. for schematic diagram and specific sampling details).
 Y_matrix.csv is a diversity dataset, with species counts for
 every quadrat in the study. X_matrix.csv is the
 environmental data, with temperature, salinity, nitrates, and seagrass
 biometrics for each quadrat. spatial.csv provides
 spatial coordinates for each quadrat in the study.
DOI: 10.5061/dryad.dz08kprwc
title: Association of gyrification pattern, white matter changes and phenotypic profile in patients with Parkinson’s disease

description: Objective: To investigate the cortical gyrification changes as well as
 their relationships with white matter (WM) microstructural abnormalities
 in the akinetic-rigid (AR) and tremor-dominant (TD) subtypes of
 Parkinson's disease (PD). Methods: Sixty-four patients with the AR
 subtype, 26 patients with the TD subtype and 56 healthy controls (HCs)
 were included in this study. High-resolution T1-weighted and
 diffusion-weighted images were acquired for each participant. We computed
 local gyrification index (LGI) and fractional anisotropy (FA) to identify
 the cortical gyrification and WM microstructural changes in the AR and TD
 subtypes. Results: Compared with HCs, patients with the AR subtype showed
 decreased LGI in the precentral, postcentral, inferior and superior
 parietal, middle and superior frontal/temporal, anterior and posterior
 cingulate, orbitofrontal, supramarginal, precuneus, and some visual
 cortices, and decreased FA in the corticospinal tract, inferior and
 superior longitudinal fasciculus, inferior fronto-occipital fasciculus,
 forceps minor/major, and anterior thalamic radiation. Decreases in LGI and
 FA of the AR subtype were found to be tightly coupled. LGIs of the left
 inferior and middle frontal gyrus correlated with the mini-mental state
 examination and the Hoehn and Yahr scores of patients with the AR subtype.
 Patients with the TD subtype showed no significant change in the LGI and
 FA compared with patients with the AR subtype and HCs. Conclusions: Our
 results suggest that cortical gyrification changes in PD are motor
 phenotype-specific and are possibly mediated by the microstructural
 abnormalities of the underlying WM tracts.
description: Supplemental data corresponding to research paper
 "Association of gyrification pattern, white matter changes and
 phenotypic profile in patients with Parkinson's
 disease". It contains Appendix_e-1 and Figure_e-1
 for this paper.
DOI: 10.5061/dryad.c59zw3r65
title: Males respond to substrate-borne, not airborne, female chemical cues in the jumping spider, Habronattus pyrrithrix

description: Jumping spiders are known for complex courtship displays with both visual
 and vibratory components, but increasing evidence shows they also use
 chemoreception in intraspecific communication. We conducted two
 experiments using Habronattus pyrrithrix (Chamberlin, 1924) to assess male
 response to substrate-borne or airborne chemical cues produced by virgin
 females. First, we tested the effect of substrate-borne cues by allowing
 males to inspect two pieces of filter paper that had either been exposed
 to a female (thus covered in silk and/or excreta) or not (control).
 Second, we used a Y-tube olfactometer to test male response to female
 airborne cues versus a no-odor control in the absence of substrate-borne
 cues. Males responded to substrate-borne cues (spending more time
 traversing and palpating female-treated filter paper compared with the
 control) but did not respond to airborne cues alone. Together, these
 experiments suggest male H. pyrrithrix may use contact chemical cues from
 female silk to locate or assess females.
description: Please see ReadMe file included here
 ('README.txt')
DOI: 10.5061/dryad.pnvx0k6kj
title: Evolutionary and morphological patterns underlying carnivoran body shape diversity

description: The diversity of body shapes is one of the most prominent features of
 phenotypic variation in vertebrates. Biologists, however, still lack a
 full understanding of the underlying morphological components that
 contribute to its diversity, particularly in endothermic vertebrates such
 as mammals. In this study, I tested hypotheses pertaining to the evolution
 of the cranial and axial components that contribute to the diversity of
 carnivoran body shapes. I found three trends in the evolution of
 carnivoran body shapes: 1) carnivorans exhibit diverse body shapes with
 intrafamilial variation predicted best by family clade age, 2) body shape
 is driven by strong allometric effects of body size where species become
 more elongate with decreasing size, and 3) the thoracic and lumbar regions
 and rib length contribute the most to body shape variation, albeit
 pathways differ between different families. These results reveal the
 morphological patterns that led to increased diversity in carnivoran body
 shapes and provide elucidate the similarities and dissimilarities that
 govern body shape diversity across vertebrates.
DOI: 10.5061/dryad.vq83bk3rc
title: Complex post-breeding moult strategies in a songbird migrating along the East Asian flyway, the Pallas’s Grasshopper Warbler Locustella certhiola

description: Moult strategies have received relatively little attention in current
 ornithology, and knowledge concerning the evolution, variability, and
 extent of moult is sparse in many bird species. This is especially true
 for East Asian Locustella species where assumptions on moult patterns are
 based on incomplete information. We provide evidence indicating a complex
 post-breeding moult strategy and variable moult extent among Pallas’s
 Grasshopper Warbler Locustella certhiola, based on data from six ringing
 sites situated along its flyway from the breeding grounds to the wintering
 areas. A detailed study revealed for the first time that in most
 individuals wing feather moult proceeds from the centre both towards the
 body and the wing-tip, a moult pattern known as partial divergent moult
 (which is rare among Palaearctic passerines). In the Russian Far East,
 where both breeding birds and passage migrants occur, a third of the adult
 birds were moulting in late summer. In Central Siberia, at the
 northwestern limit of its distribution, adult individuals commenced their
 primary moult partly divergently and partly with unknown sequence. During
 migration in Mongolia, only descendantly (i.e. from the body towards the
 wing-tip) moulting birds were observed, while further south in Korea, Hong
 Kong and Thailand the proportion of potential eccentric and divergent
 feather renewal was not identifiable since the renewed feathers were
 already fully grown as expected. We found an increase in the mean number
 of moulted primaries during the progress of the autumn migration. Moderate
 body mass levels and low fat and muscle scores were observed in moulting
 adult birds, without any remarkable increase in the later season.
 According to optimality models, we suggest that an extremely short season
 of high food abundance in tall grass habitats and a largely overland route
 allow autumn migration with low fuel loads combined with moult-migration
 in at least a part of the population. This study highlights the importance
 of further studying moult strategy as well as stopover behaviour decisions
 and the trade-offs among migratory birds that are now facing a panoply of
 anthropogenic threats along their flyways.
description: Birds were
 caught with mist-nets without using playback.
description: Additional information on all individuals (e.g. wing length) is
 available upon request from the authors.
DOI: 10.5061/dryad.76hdr7svb
title: Data and R Code for publication: Should dispersers be fast learners? Modelling the role of cognition in dispersal

description: Both cognitive abilities and dispersal tendencies can vary strongly
 between individuals. Since cognitive abilities may help dealing with
 unknown circumstances it is conceivable that dispersers may rely
 more heavily on learning abilities than residents. However, cognitive
 abilities are costly and leaving a familiar place might result in losing
 the advantage of having learned to deal with local conditions. Thus,
 individuals which invested in learning to cope with local conditions may
 be more reluctant to leave their natal place. In order to disentangle the
 complex relationship between dispersal and learning abilities we
 implemented individual-based simulations. By allowing for developmental
 plasticity, individuals could either develop a
 "resident" or "dispersal" cognitive
 phenotype. In line with our expectations, the correlation between learning
 abilities and dispersal could take any direction, depending how much time
 individuals had to recoup their investment in cognition. Both, longevity
 and the timing of dispersal within lifecycles determine the time
 individuals have to recoup that investment and thus crucially influence
 this correlation. We therefore suggest that
 species' life-history will strongly impact the expected
 cognitive abilities of dispersers, relative to their resident
 conspecifics, and that cognitive abilities might be an integral part of
 dispersal syndromes.
description: Data were optained from running a compelx function written in
 R.  The funciton is published in this deposit alonge
 side the data. Data was analyises and plots were
 created using R.
DOI: 10.5061/dryad.r7sqv9s9x
title: Implications for the mesopelagic microbial gardening hypothesis as determined by experimental fragmentation of Antarctic krill faecal pellets

description: 1. Detritivores need to upgrade their food to increase its nutritional
 value. One method is to fragment detritus promoting the colonisation­ of
 nutrient-rich microbes, which consumers then ingest along with the
 detritus; so-called microbial gardening. Observations and numerical models
 of the detritus-dominated ocean mesopelagic zone have suggested microbial
 gardening by zooplankton is a fundamental process in the ocean carbon
 cycle leading to increased respiration of carbon-rich detritus. However,
 no experimental evidence exists to demonstrate that microbial respiration
 rates are higher on recently fragmented sinking detrital particles. 2.
 Using aquaria-reared Antarctic krill faecal pellets we showed
 fragmentation increased microbial particulate organic carbon (POC)
 turnover by 1.8x, but only on brown faecal pellets, formed from the
 consumption of other pellets. Microbial POC turnover on un-and fragmented
 green faecal pellets, formed from consuming fresh phytoplankton, was
 equal. Thus, POC content, fragmentation, and potentially nutritional value
 together drive POC turnover rates. 3. Mesopelagic microbial gardening
 could be a risky strategy, as the dominant detrital food source is
 settling particles. Even though fragmentation decreases particle size and
 sinking rat, it is unlikely that an organism would remain with the
 particle long enough to nutritionally benefit from attached microbes. We
 propose ‘communal gardening’ occurs whereby additional mesopelagic
 organisms nearby or below the site of fragmentation consume the particle
 and the colonised microbes. 4. To determine how fragmentation impacts the
 remineralisation of sinking carbon-rich detritus, and to parameterise
 microbial gardening in mesopelagic carbon models, three key metrics from
 further controlled experiments and observations are needed; how particle
 composition (here, pellet colour/krill diet) impacts the response of
 microbes to the fragmentation of particles; the nutritional benefit to
 zooplankton from ingesting microbes after fragmentation along with
 identification of which essential nutrients are being targeted; how both
 these factors vary between physical (shear) and biological particle
 fragmentation.
description: Data on oxygen uptake by microbes on fragmented and unfragmented
 feacal pellets in a laboratory experiment (O2_FP.csv), the size of the
 faecal pellets (csv files BL1...GS4.csv) and the particulate organic
 carbon content of the faecal pellets (POC_FP.csv). R
 code to analyse the data and make the figures from the publication will be
 available at www.github.com/e-cavan.
DOI: 10.25345/c5k64b663
title: MassIVE MSV000100611 - Carbon source-driven metabolic and regulatory remodeling defines phenomic states in Lipomyces starkeyi
title: Multi-PTM dataset including global proteomics, cysteine oxidation, and phosphorylation for oleaginous yeast Lipomyces starkeyi. Samples were processed using the multi-PTM workflow, including SP3-based cleanup, digestion with trypsin and LysC, enrichment of the peptides. Final peptide samples were analyzed by LC-MS/MS on an Orbitrap 480. Data was searched with MS-GF+ using PNNL's DMS processing pipeline.
DOI: 10.15468/dl.g7gxz5
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Coronilla valentina",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002671-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.prr4xgxkb
title: Data from: Density-dependent adaptive topography in a small passerine bird, the collared flycatcher

description: The adaptive topography is a central concept in evolutionary biology,
 describing how the mean fitness of the population changes with gene
 frequencies or mean phenotypes. We use expected population size as
 quantity to be maximized by natural selection to show that selection on
 pairwise combinations of reproductive traits of collared flycatchers
 caused by fluctuations in population size generated an adaptive topography
 with distinct peaks often located at intermediate phenotypes. This
 occurred because r- and K-selection made phenotypes favored at small
 densities different from those with higher fitness at population sizes
 close to the carrying capacity K. The fitness decreased rapidly with a
 delay in the timing of egg-laying with a density-dependent effect
 especially occurring among early-laying females. The number of fledglings
 maximizing fitness was larger at small population sizes than close to K.
 Finally, there was directional selection for large fledglings independent
 of population size. We suggest that these patterns can be explained by
 increased competition for some limiting resources or access to favorable
 nest sites at high population densities. Thus, r- and K-selection based on
 expected population size as evolutionary maximization criterion may
 influence life history evolution and constrain the selective responses to
 changes in the environment.
DOI: 10.5061/dryad.sxksn031s
title: Data from: Plasticity matches phenotype to local conditions despite genetic homogeneity across 13 snake populations

description: In a widespread species, a matching of phenotypic traits to local
 environmental optima is generally attributed to site-specific adaptation.
 However, the same matching can occur via adaptive plasticity, without
 requiring genetic differences among populations. Adult sea kraits
 (Laticauda saintgironsi) are highly philopatric to small islands, but the
 entire population within the Neo-Caledonian lagoon is genetically
 homogenous because females migrate to the mainland to lay their eggs at
 communal sites; recruits disperse before settling, mixing up alleles.
 Consequently, any adaptive matching between local environments (e.g., prey
 sizes) and snake phenotypes (e.g., body sizes and relative jaw sizes) must
 be achieved via phenotypic plasticity rather than spatial heterogeneity in
 gene frequencies. We sampled 13 snake colonies spread along a ~200km
 northwest-southeast gradient (N&gt;4,500 individuals) to measure two
 morphological features that affect maximum ingestible prey size in
 gape-limited predators: body size and relative jaw size. As proxies of
 habitat quality, we used protection status, fishing pressure and lagoon
 characteristics (lagoon width and distance of islands to the barrier
 reef). In both sexes, spatial variation in body sizes and relative jaw
 sizes was linked to habitat quality; albeit in different ways, consistent
 with sex-based divergences in foraging ecology. Strong spatial divergence
 in morphology among snake colonies, despite genetic homogeneity, supports
 the idea that phenotypic plasticity can facilitate speciation by creating
 multiple phenotypically distinct sub-populations shaped by their
 environment.
description: In the field during long term mark recapture study (2002-2002) on
 sea snakes. Initiated and supervisedby XB.
description: The data set provided is extracted from the main data base.
 Further details can be obtained by contacting XB.
DOI: 10.5061/dryad.3tx95x6f1
title: Morphology and mini-barcodes: The inclusion of larval sampling and NGS-based barcoding improves robustness of ecological analyses of mosquito communities

description: A significant proportion of vector-borne diseases are transmitted by
 blood-sucking dipterans, including mosquitoes. Understanding transmission
 risks requires accurate identification of species across heterogenous
 habitats, but many cryptic and polymorphic species are overlooked when
 using morphological identification. Estimates of mosquito diversity are
 typically based on adult female trapping methods which tend to target
 host-seeking species and may represent a biased snapshot of community
 structure. Unfortunately, diversity estimates based on larval data are
 rarely included in mosquito ecological analyses. We carried out adult and
 larval sampling over six months in Singapore using an integrative approach
 of morphological identification and molecular delineation with
 mini-barcodes (313 bp) generated on a Next Generation Sequencing platform
 to obtain species estimates. We collected 3201 mosquitoes across 58
 species (14 genera). Notably, 16 species were collected only through
 larval sampling and 22 species were only resolved using mini-barcodes. Of
 the latter we identified three morphologically similar species groups and
 documented several intraspecific polymorphisms. We compared adult-only
 data against a full dataset (adult + larval + mini-barcode). The species
 accumulation curves reached an asymptote for all but one site when using
 the latter; non-metric multidimensional scaling (NMDS) revealed that
 mosquito communities were only well separated when using the full dataset.
 Overall, the latter reflects a more defined and accurate community
 structure across all sites. We find that several mosquito species were
 generally influenced by tree cover, rainfall and presence of large water
 bodies, further supporting the idea that many species are
 niche-specific. Synthesis and applications. We report the first
 successful use of mini-barcodes on mosquitoes and demonstrate its utility
 in delineating multiple challenging species groups. We recommend the use
 of both morphological and molecular identification methods for ecological
 studies and vector surveillance. Misidentification in species estimation,
 especially for medically relevant insect groups can lead to conflicting
 reports and slows down vector control efforts. We provide evidence that
 varying sampling techniques, particularly of the larval stages for
 holometabolous insects, is important in generating a robust dataset for
 downstream analyses. Together with DNA barcoding, this integrative
 approach helps to minimize error cascades when designing management
 strategies.