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

description: A dataset containing 318278 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Country is United States of America",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "StateProvince is California",
 "TaxonKey is one of (Keckiella antirrhinoides, Keckiella rothrockii, Ipomopsis congesta, Eriogonum fasciculatum, Eriogonum latifolium, Eriogonum nudum, Eriogonum umbellatum, Aquilegia coerulea, Clematis ligusticifolia, Ceanothus velutinus, Dasiphora fruticosa, Potentilla fruticosa, Rosa arkansana, Rubus parviflorus, Salix lasiolepis, Pedicularis racemosa, Penstemon strictus, Lantana montevidensis, Larrea tridentata, Agastache urticifolia, Salvia apiana, Salvia carduacea, Salvia columbariae, Salvia mellifera, Salvia polystachya, Salvia sonomensis, Trichostema lanceolatum, Eriodictyon crassifolium, Chamerion angustifolium, Clarkia amoena, Clarkia pulchella, Chamaenerion, Eschscholzia californica, Lathyrus leucanthus, Lupinus arboreus, Lupinus argenteus, Lupinus excubitus, Lupinus formosus, Lupinus nanus, Lupinus succulentus, Medicago sativa, Melilotus albus, Melilotus officinalis, Geranium fremontii, Heliotropium curassavicum, Phacelia ramosissima, Phacelia tanacetifolia, Hypericum perforatum, Mertensia ciliata, Brassica rapa, Cakile maritima, Symphoricarpos albus, Symphoricarpos racemosus, Minuartia cismontana, Peritoma arborea, Wislizenia refracta, Acmispon americanus, Acmispon glaber, Astragalus douglasii, Astragalus pomonensis, Lepidospartum squamatum, Rudbeckia montana, Senecio clarkianus, Senecio flaccidus, Solidago multiradiata, Taraxacum campylodes, Taraxacum officinale, Trifolium pratense, Chilopsis linearis, Amsinckia douglasiana, Chrysothamnus viscidiflorus, Cirsium arvense, Cirsium lanceolatum, Encelia farinosa, Ericameria ericoides, Ericameria nauseosa, Grindelia hirsutula, Grindelia squarrosa, Gutierrezia sarothrae, Haplopappus bloomeri, Haplopappus croceus, Helianthella quinquenervis, Helianthus annuus, Heliomeris multiflora, Helminthotheca echioides, Hymenoxys hoopesii, Asclepias eriocarpa, Asclepias fascicularis, Asclepias speciosa, Centaurea repens, Centaurea solstitialis, Centromadia pungens, Chaenactis fremontii, Chrysopsis villosa, Chrysothamnus nauseosus, Heracleum sphondylium, Foeniculum vulgare)",
 "Year 2016-2026"
 ]
}

 The dataset includes 318278 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002142-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.6wwpzgmtt
title: Potential sex-dependent effects of weather on apparent survival of a high-elevation specialist

description: Mountain ecosystems are inhabited by highly specialised and endemic
 species which are particularly susceptible to climatic changes. However,
 the mechanisms by which climate change affects species population dynamics
 are still largely unknown, particularly for mountain birds. We
 investigated how weather variables correlate with apparent survival of the
 White-winged Snowfinch Montifringilla nivalis, a specialist of
 high-elevation habitat. We analysed a 15-year (2003-2017) mark-recapture
 data set of 671 individuals from the Apennines (Italy), using
 mark-recapture models. We estimated annual apparent survival to be around
 0.44-0.54 for males and around 0.51-0.64 for females. Variance among years
 was high (range: 0.2-0.8), particularly so for females. Apparent survival
 was lower in winter compared to summer. Female annual apparent survival
 was negatively correlated with warm and dry summers, whereas in males
 these weather variables only weakly correlate with apparent survival.
 Remarkably, the average apparent survival measured in this study was lower
 than expected. We suggest that the low apparent survival may be due to
 recent changes in the environment caused by global warming. Possible,
 non-exclusive mechanisms that potentially also could explain sexual
 differential apparent survival act via differential breeding dispersal,
 physiological tolerance of high temperature, weather-dependent food
 availability, and weather-dependent trade-off between reproduction and
 self-maintenance. These results improve our current understanding of the
 mechanisms driving population dynamics in high-elevation specialists,
 which are particularly at risk due to climate change.
description: marking and recapturing by metal rings (see manuscript)
  
description: The four rda files can be loaded into R using the function
 "load". Each vile contains an R-object called
 "datax". "datax" is a list that
 contains: - the capture history: a matrix with one row
 for each individual and one column for each capture occasion (4-month
 period or year). 0 = the indivdiual was not captured during that capture
 occasion, 1 = individual was captured - the vector
 first: gives the capture occasion number during which the individual was
 marked (full data set) or at which the sex was first identified (reduced
 data set) - number of individuals "nind": in
 the full data set nindi = number of individuals with identified sex,
 nindni = number of individuals with non-identified sex.
 - number of capture occasion - age matrix: 1 =
 first year, 2 = after first year - transients matrix:
 indicator of the occasion when the individual was first captured
 - sex: 1 = males, 2 = females - tempsu:
 z-transformed average summer temperature (see manuscript)
 - tempwi: z-transformed average winter temperature (see
 manuscript) The data is formatted so that the models of
 which the Stan code is given in the supplementary material of the
 manuscript can be fitted.
DOI: 10.5061/dryad.j6q573n94
title: Simulations of planetary-scale collisions between rotating, differentiated bodies

description: In the late stages of terrestrial planet formation, pairwise collisions
 between planetary-sized bodies act as the fundamental agent of planet
 growth. These collisions can lead to either growth or disruption of the
 bodies involved and are largely responsible for shaping the final
 characteristics of planets. Despite their critical role in planet
 formation, an accurate treatment of collisions has yet to be realized.
 Therefore, we simulated a new set of 10,700 smoothed-particle
 hydrodynamics (SPH) simulations of pairwise collisions between rotating,
 differentiated bodies. This dataset is an order of magnitude larger than
 any previous collision dataset and is intended to serve as a training
 dataset for machine learning models, so that accurate surrogate models for
 planetary-scale collisions can be developed.
description: Each collision is uniquely defined by a set of 12 pre-impact
 parameters. Together, these parameters define the geometry of the impact
 and the physical and rotational characteristics of the bodies involved in
 the collision. The colliding bodies are referred to as the
 <em>target</em> and <em>projectile</em>, where the
 target is the more massive of the two. The pre-impact parameter space was
 constructed using Latin hypercube sampling (LHS). For the LHS10K set, a
 LHS-based adaptive surface response method (ARSM) was used to
 progressively enrich the sample from an initial LHS sample of 1000
 collisions. The collisions were simulated with
 Gasoline, a massively-parellel smoothed-particle hydrodynamics (SPH) code
 (Wadsley et al. 2004). The number of particles in each collision is set by
 the ratio of the projectile mass to target mass, whereby the projectile
 always contains 10,000 particles and the number of particles in the target
 is scaled relative to its mass. Each collision was simulated for 100 times
 its collision timescale, which is equivalent to the crossing time of the
 encounter.
description: The files provided here include the Gasoline runtime parameter
 files (collision.param), initial conditions (collision.std), final outputs
 (outcome.std), and SKID group finding files (*.grp). The parameter and
 initial condition files are sufficient to run the simulations with
 Gasoline and the appropriate Tillotson equation of state (EOS). The
 associated outputs and group finding files are those on which the analysis
 was carried out. Users can explore and analyze the input and output files
 using a number of open-source software packages, but we suggest
 Python's pynbody package
 (https://pynbody.github.io/pynbody/). In the course of
 simulating the datasets, a small number of collisions failed to complete.
 These failures were either a result of hardware failures during
 integration, interruptive maintenence downtimes, or the result of a
 pre-impact body (i.e., target or projectile) that was rotationally
 unstable. Therefore, in the LHS10K set, there are 9978 collisions, 499
 collisions in the LHS500 dataset, and 199 collisions in the LHS200
 dataset.
DOI: 10.5061/dryad.ht76hdrbr
title: Fine-scale seascape genomics of an exploited marine species, the common cockle Cerastoderma edule, using a multi-modelling approach

description: Population dynamics of marine species that are sessile as adults are
 driven by oceanographic dispersal of larvae from spawning to nursery
 grounds. This is mediated by life-history traits such as the timing and
 frequency of spawning, larval behaviour and duration, and settlement
 success. Here, we use 1725 single nucleotide polymorphisms (SNPs) to study
 the fine scale spatial genetic structure in the commercially important
 cockle species Cerastoderma edule and compare it to environmental
 variables and current-mediated larval dispersal within a modelling
 framework. Hydrodynamic modelling employing the NEMO Atlantic Margin Model
 (AMM15) was used to simulate larval transport and estimate connectivity
 between populations during spawning months (April - September), factoring
 in larval duration and inter-annual variability of ocean currents. Results
 at neutral loci reveal the existence of three separate genetic clusters
 (mean FST=0.021) within a relatively fine spatial scale in the northwest
 Atlantic. Environmental Association analysis indicates that oceanographic
 currents and geographical proximity explain over 20% of the variance
 observed at neutral loci, while genetic variance (71%) at outlier loci was
 explained by sea surface temperatures extremes. These results fill an
 important knowledge gap in the management of a commercially important and
 overexploited species, bringing us closer to understanding the role of
 larval dispersal in connecting populations at a fine geographical scale.
description: This repository contains the files used to run the analyses for
 this paper, as follows: 1. 1711Neutral_STR.str:
 genotypes of putatively neutral SNPs, in Structure format
 2. 14Outlier_STR.str:
 genotypes of putatively outliers, in Structure format
 3. MAF_per_population.txt: the genomic input file for the environmental association analysis 4.edges-to-nodes2.csv: the matrix of connectivity used for SEA 5.edges_weights2.csv: the weights associated to the above matrix (derived by connectivity matrices) 6.Environmental_data_by_location.csv: Environmental data used forthe environmental association analysis
DOI: 10.15468/dl.e7gha3
title: Occurrence Download

description: A dataset containing 46 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "PublishingOrg is one of (c2ecae57-6701-485e-9ebd-5f87b2945cb2, f9b67ad0-9c9b-11d9-b9db-b8a03c50a862, 6ea87510-0561-11d8-b851-b8a03c50a862)",
 "TaxonKey is Melanoplus davisi",
 "Year 1900-2026"
 ]
}

 The dataset includes 46 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002179-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.w6m905qkx
title: Identification of hidden population structure in time-scaled phylogenies

description: Population structure influences genealogical patterns, however data
 pertaining to how populations are structured are often unavailable or not
 directly observable. Inference of population structure is highly important
 in molecular epidemiology where pathogen phylogenetics is increasingly
 used to infer transmission patterns and detect outbreaks. Discrepancies
 between observed and idealised genealogies, such as those generated by the
 coalescent process, can be quantified, and where significant differences
 occur, may reveal the action of natural selection, host population
 structure, or other demographic and epidemiological heterogeneities. We
 have developed a fast non-parametric statistical test for detection of
 cryptic population structure in time-scaled phylogenetic trees. The test
 is based on contrasting estimated phylogenies with the theoretically
 expected phylodynamic ordering of common ancestors in two clades within a
 coalescent framework. These statistical tests have also motivated the
 development of algorithms which can be used to quickly screen a
 phylogenetic tree for clades which are likely to share a distinct
 demographic or epidemiological history. Epidemiological applications
 include identification of outbreaks in vulnerable host populations or
 rapid expansion of genotypes with a fitness advantage. To demonstrate the
 utility of these methods for outbreak detection, we applied the new
 methods to large phylogenies reconstructed from thousands of HIV-1 partial
 pol sequences. This revealed the presence of clades which had grown
 rapidly in the recent past, and was significantly concentrated in young
 men, suggesting recent and rapid transmission in that group. Furthermore,
 to demonstrate the utility of these methods for the study of antimicrobial
 resistance, we applied the new methods to a large phylogeny reconstructed
 from whole genome Neisseria gonorrhoeae sequences. We find that population
 structure detected using these methods closely overlaps with the
 appearance and expansion of mutations conferring antimicrobial resistance.
description: Simulation code and output:<br> ot2.1.datadryad.R<br>
 ot2.1.tar.gz <br> HIV-1 sequences: <br>
 vb2017-genbank.fasta<br> vb2017-genbank.nex
 Neisseria sequences:<br> ngono-gisp-align.nex.gz
DOI: 10.5061/dryad.3xsj3txbz
title: Data from: Genetic architecture influences when and how hybridization contributes to colonization

description: The role of genetic architecture in adaptation to novel environments has
 received considerable attention when the source of adaptation variation is
 de novo mutation. Relatively less is known when the source of adaptive
 variation is inter- or intraspecific hybridization. We model hybridization
 between divergent source populations and subsequent colonization of an
 unoccupied novel environment using individual-based simulations in order
 to understand the influence of genetic architecture on the timing of
 colonization and the mode of adaptation. We find that two distinct
 categories of genetic architecture facilitate rapid colonization but that
 they do so in qualitatively different ways. For few and/or tightly linked
 loci, the mode of adaptation is via the recovery of adaptive parental
 genotypes. With many unlinked loci, the mode of adaptation is via the
 generation of novel hybrid genotypes. The first category results in the
 shortest colonization lag phases across the widest range of parameter
 space, but further adaptation is mutation limited. The second category
 takes longer and is more sensitive to genetic variance and dispersal rate,
 but can facilitate adaptation to environmental conditions which exceed the
 tolerance of parental populations. These findings have implications for
 understanding the origins of biological invasions and the success of
 hybrid populations.
description: This dataset was collected using the simulation software
 quantiNemo version 2.0.0, the documentation for which is available
 at https://www2.unil.ch/popgen/softwares/quantinemo/. The dataset was analysed using custom python and R scripts which are included here.
description: Please see the README.txt file for usage information on the files
 and scripts included in this dataset.
DOI: 10.5061/dryad.cc2fqz638
title: Habitat suitability analysis reveals high ecological flexibility in a "strict" forest primate

description: Background: Research of many mammal species tends to focus on single
 habitats, reducing knowledge of ecological flexibility. The Javan
 lutung (Trachypithecus auratus) is considered a strict forest primate, and
 little is known about populations living in savannah. In 2017–2018, we
 investigated the density and distribution of Javan lutung in Baluran
 National Park, Indonesia. We conducted ad libitum follows and line
 transect distance sampling with habitat suitability analysis of Javan
 lutung. Results: Estimated density was 14.91 individuals km− 2 (95% CI
 7.91–28.08), and estimated population size was 3727 individuals
 (95% CI 1979 – 7019). Long-tailed macaque (Macaca fascicularis) habitat
 suitability was the main driver of lutung habitat suitability as
 the probability of lutung occurrence increased greatly with macaque
 habitat suitability. Distance to roads, and distance to secondary
 forest had a negative relationship with lutung occurrence. Lutung habitat
 suitability decreased with increasing elevation, however, Mt Baluran and
 the primary forest on Mt Baluran was under-sampled due to treacherous
 conditions. Follows of six focus groups revealed considerable use of
 savannah, with terrestrial travel. The follows also revealed polyspecific
 associations with long-tailed macaques through shared sleeping
 sites and inter-specific vocalisations.  Conclusions: Our study
 provides new knowledge on the general ecology of Javan lutung, such as use
 of savannah habitats, underlining our need to branch out in our study
 sites to understand the flexibility and adaptability of our study species.
 Another undocumented behaviour is the polyspecific association with
 long-tailed macaques. We encourage more research on this subject.
description: Line transect distance sampling Species
 distribution modelling, MaxEnt algorithm R
 code
DOI: 10.5061/dryad.wwpzgmsg3
title: Data from: Blue crab abundance and survival in a fragmenting coastal marsh system

description: Louisiana’s coastal marshes are becoming increasingly fragmented due to
 sea level rise, subsidence, reduced sediment inflow from the Mississippi
 River, and saltwater intrusion. Many commercially and recreationally
 fished species rely on the marsh system as nursery habitat, and the
 resilience of species to further marsh loss and marsh fragmentation is
 uncertain. We examined the impacts of marsh fragmentation on the blue
 crab, Callinectes sapidus, a species supporting one of the largest
 fisheries in coastal Louisiana, which uses marsh edge as nursery habitat.
 Juvenile and adult abundances were quantified in multiple habitats (bare
 sediment, marsh edge, and submerged aquatic vegetation [SAV]) within an
 actively fragmenting coastal marsh. Adult blue crabs were sampled using
 crab pots, while juveniles were sampled using a throw trap. In general,
 blue crab density was unrelated to the ranges of marsh fragmentation
 sampled here, but were instead related to local-scale patterns of habitat
 availability, including presence and type of vegetation. In tethering
 experiments to examine predation rates on juvenile blue crabs across
 habitats, predation rates were lowest in SAV compared to marsh edge or
 bare sediment. While direct effects of marsh fragmentation on local-scale
 patterns of blue crab abundance were not observed, marsh fragmentation
 will likely have indirect effects on blue crab populations through changes
 in habitat availability. Unless SAV expands into newly created open water
 areas, providing an alternative nursery habitat for blue crabs, continued
 marsh fragmentation and loss is expected to have negative impacts on
 future blue crab populations and fisheries through a decrease in available
 nursery habitat.
description: Please see the published paper:
 <strong>Shakeri et al. 2020. Blue crab abundance and
 survival in a fragmenting coastal marsh system. <em>Estuaries and
 Coasts</em>.
 https://doi.org/10.1007/s12237-020-00738-9</strong>
 For more information, contact M. Zachary Darnell
 (zachary.darnell@usm.edu).
description: Please see README.txt.
DOI: 10.15468/dl.nwttv8
title: Occurrence Download

description: A dataset containing 72 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Chamaecyparis lawsoniana",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Country is United States of America",
 "Year is greater than or equal to 2000",
 "Year is less than or equal to 2010"
 ]
}

 The dataset includes 72 records from 35 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002180-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.h9w0vt4f5
title: An experimental test of the role of male mating history on paternal effects in the livebearer fish, Gambusia holbrooki

description: We experimentally tested if differences in the mating history of old males
 affects their offsprings’ performance in the mosquitofish, Gambusia
 holbrooki. Upon maturation, males were housed for the duration of a
 natural field breeding season (23 weeks) either with mating access to
 females (‘lifetime mating’) or with visual but no physical access to
 females (‘no mating’). We then paired these males with a female to test
 whether male mating history had a significant effect on their mate’s
 breeding success or offspring performance. The daughters, but not the
 sons, of ‘no mating’ treatment males matured significantly sooner, and at
 a significantly smaller size, than those of ‘lifetime mating’ treatment
 males. There was, however, no effect of male mating history on their
 daughters’ initial fecundity, or on proxy measures of their sons’
 reproductive success. These results, when combined with earlier studies
 showing effects of male mating history on sperm quality, growth and
 immunity, suggest that variation in paternal effects currently attributed
 to male age could partly arise simply because older males have usually
 mated more often than younger males.