cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.nqayn5
title: Occurrence Download

description: A dataset containing 263 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Shorea almon"
 ]
}

 The dataset includes 263 records from 22 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001641-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.8n2d5
title: Data from: The core microbiome bonds the Alpine bog vegetation to a transkingdom metacommunity

description: Bog ecosystems fulfil important functions in Earth's carbon and water
 turnover. While plant communities and their keystone species Sphagnum have
 been well studied, less is known about the microbial communities
 associated with them. To study our hypothesis that bog plants share an
 essential core of their microbiome despite their different phylogenetic
 origins, we analysed four plant community plots with 24 bryophytes,
 vascular plants and lichen species in two Alpine bogs in Austria by 16S
 rDNA amplicon sequencing followed by bioinformatic analyses. The overall
 bog microbiome was classified into 32 microbial phyla, while
 Proteobacteria (30.8%), Verrucomicrobia (20.3%) and Planctomycetes (15.1%)
 belonged to the most abundant groups. Interestingly, the archaeal phylum
 Euryarcheota represented 7.2% of total microbial abundance. However, a
 high portion of micro-organisms remained unassigned at phylum and class
 level, respectively. The core microbiome of the bog vegetation contained
 177 operational taxonomic units (OTUs) (150 526 seq.) and contributed to
 49.5% of the total microbial abundance. Only a minor portion of associated
 core micro-organisms was host specific for examined plant groups
 (5.9–11.6%). Using our new approach to analyse plant–microbial communities
 in an integral framework of ecosystem, vegetation and microbiome, we
 demonstrated that bog vegetation harboured a core microbiome that is
 shared between plants and lichens over the whole ecosystem and formed a
 transkingdom metacommunity. All micro- and macro-organisms are connected
 to keystone Sphagnum mosses via set of microbial species, for example
 Burkholderia bryophila which was found associated with a wide spectrum of
 host plants and is known for a beneficial plant–microbe interaction.
description: Sphagnum_Metacommunity_otu_tableThe complete OTU-table of the partial 16S rRNA genes of the microbiome associated with the vegetation in two Alpine bogs in Austria.
DOI: 10.5061/dryad.gf774
title: Data from: Climate change impacts on bumblebees converge across continents

description: For many species, geographical ranges are expanding toward the poles in
 response to climate change, while remaining stable along range edges
 nearest the equator. Using long-term observations across Europe and North
 America over 110 years, we tested for climate change–related range shifts
 in bumblebee species across the full extents of their latitudinal and
 thermal limits and movements along elevation gradients. We found
 cross-continentally consistent trends in failures to track warming through
 time at species’ northern range limits, range losses from southern range
 limits, and shifts to higher elevations among southern species. These
 effects are independent of changing land uses or pesticide applications
 and underscore the need to test for climate impacts at both leading and
 trailing latitudinal and thermal limits for species.
description: Data and R scripts to
 reproduce figures and analyses appearing in Kerr, Pindar, Galpern et al.,
 2015. Science.This ZIP archive
 contains five files. These are a documented R script and the necessary
 data files required to reproduce figures and analyses appearing in this
 article. Please see the file
 analysisScript_KerrPindarGalpern_etal_Science_2015.R for
 instructions.Data_KerrPindarGalpern_etal_Science_2015.zip
DOI: 10.5061/dryad.v5s13
title: Data from: Fine-scale environmental specialization of reef- building corals might be limiting reef recovery in the Florida Keys

description: Despite decades of monitoring global reef decline, we are still largely
 unable to explain patterns of reef deterioration at local scales, which
 precludes the development of effective management strategies. Offshore
 reefs of the Florida Keys, USA, experience milder temperatures and lower
 nutrient loads in comparison to inshore reefs yet remain considerably more
 degraded than nearshore patch reefs. A year-long reciprocal transplant
 experiment of the mustard hill coral (Porites astreoides) involving four
 source and eight transplant locations reveals that corals adapt and/or
 acclimatize to their local habitat on a &lt;10-km scale. Surprisingly,
 transplantation to putatively similar environmental types (e.g., offshore
 corals moved to a novel offshore site, or along-shore transplantation)
 resulted in greater reductions in fitness proxies, such as coral growth,
 than cross-channel transplantation between inshore and offshore reefs. The
 only abiotic factor showing significantly greater differences between
 along-shore sites was daily temperature range extremes (rather than the
 absolute high or low temperatures reached), providing a possible
 explanation for this pattern. Offshore-origin corals exhibited significant
 growth reductions at sites with greater daily temperature ranges, which
 explained up to 39% of the variation in their mass gain. In contrast,
 daily temperature range explained at most 9% of growth variation in
 inshore-origin corals, suggesting that inshore corals are more tolerant of
 high-frequency temperature fluctuations. Finally, corals incur trade-offs
 when specializing to their native reef. Across reef locations the
 coefficient of selection against coral transplants was 0.07 ± 0.02 (mean ±
 SE). This selection against immigrants could hinder the ability of corals
 to recolonize devastated reefs, whether through assisted migration efforts
 or natural recruitment events, providing a unifying explanation for
 observed patterns of coral decline in this reef system.
description: Supplementary Data and R
 scriptThis file contains raw
 data in comma-separated format and R code for replicating statistical
 models and figures. Please see the ReadMe file for more detailed
 information.Supplement1.zip
DOI: 10.5061/dryad.q202d
title: Data from: Using the Spatial Population Abundance Dynamics Engine for conservation management

description: 1. An explicit spatial understanding of population dynamics is often
 critical for effective management of wild populations. Sophisticated
 approaches are available to simulate these dynamics, but are largely
 either spatially homogeneous or agent-based, and thus best suited to small
 spatial or temporal scales. These approaches also often ignore financial
 decisions crucial to choosing management approaches on the basis of
 cost-effectiveness. 2. We created a user-friendly and flexible modelling
 framework for simulating these population issues at large spatial scales –
 the Spatial Population Abundance Dynamics Engine (SPADE). SPADE is based
 on the STAR model (McMahon et al. 2010) and uses a reaction-diffusion
 approach to model population trajectories and a cost-benefit analysis
 technique to calculate optimal management strategies over long periods and
 across broad spatial scales. It expands on STAR by incorporating species
 interactions and multiple concurrent management strategies, and by
 allowing full user control of functional forms and parameters. 3. We used
 SPADE to simulate the eradication of feral domestic cats Felis catus on
 sub-Antarctic Marion Island (Bester et al. 2002) and compared modelled
 outputs to observed data. The parameters of the best-fitting model
 reflected the conditions of the management programme, and the model
 successfully simulated the observed movement of the cat population to the
 southern and eastern portion of the island under hunting pressure. We
 further demonstrated that none of the management strategies would likely
 have been successful within a reasonable timeframe if performed in
 isolation. 4. SPADE is applicable to a wide range of population management
 problems, and allows easy generation, modification and analysis of
 management scenarios. It is a useful tool for the planning, evaluation and
 optimisation of the management of wild populations, and can be used
 without specialised training.
description: Marion Island case
 studyData files from the
 Marion Island feral cat eradication covering hunting, killing, sighting
 and trapping events. Includes files used in order to prepare this dataset
 for analysis in SPADE.case
 study.zip
DOI: 10.5061/dryad.9116
title: Data from: Fine-scale population structure, inbreeding risk and avoidance in a wild insect population

description: The ecological and evolutionary importance of fine scale genetic structure
 within populations is increasingly appreciated. However, available data
 are largely restricted to wild vertebrates and eusocial insects. In
 addition there is the expectation that most insects tend to have such
 large and high density populations and are so mobile that they are
 unlikely to face inbreeding risks through fine scale population
 structuring. This has made the growing body of evidence for inbreeding
 avoidance in insects and its implication in mating systems evolution
 somewhat enigmatic. We present a four year study of a natural population
 of field crickets. Using detailed video monitoring combined with
 genotyping we track the movement of all adults within the population and
 investigate genetic structure at a fine scale. We find some evidence for
 relatives being found in closer proximity, both across generations and
 within a single breeding season. Whilst incestuous matings are not
 avoided, population inbreeding is low, suggesting that mating is close to
 random and the limited fine scale structure is does not create significant
 inbreeding risk. Hence there is little evidence for selective pressures
 associated with the evolution of inbreeding avoidance mechanisms in a
 closely related species.
description: Bretman et al
 MEC-11-0191 dataExcel file contains
 spatial distance and relatedness for pairs of crickets, maximum adult
 distance moved, distance between offspring first sighting and
 mother's mean position and full genotypes at 13 microsatellite loci
 for all individuals.
DOI: 10.5061/dryad.0cr7d
title: Data from: High speciation rate at temperate latitudes explains unusual diversity gradients in a clade of ectomycorrhizal fungi

description: Understanding the patterns of biodiversity through time and space is a
 challenging task. However, phylogeny-based macroevolutionary models allow
 us to account and measure many of the processes responsible for diversity
 build-up, namely speciation and extinction. The general latitudinal
 diversity gradient (LDG) is a well-recognized pattern describing a decline
 in species richness from the equator pole-wards. Recent macroecological
 studies in ectomycorrhizal (EM) fungi have shown that their LDG is
 shifted, peaking at temperate rather than tropical latitudes. Here we
 investigate this phenomenon from a macroevolutionary perspective, focusing
 on a well-sampled group of edible EM edible mushrooms from the genus
 Amanita –the Caesar's mushrooms, which follow similar diversity
 patterns. Our approach consisted in applying a suite of models including:
 (1) non-trait-dependent time-varying diversification (BAMM), (2)
 continuous trait-dependent diversification (QuaSSE), and (3)
 diversity-dependent diversification (DDD). In short, results give strong
 support for high speciation rates at temperate latitudes (BAMM and
 QuaSSE). We also find some evidence for different diversity-dependence
 thresholds in ‘temperate’ and ‘tropical’ subclades, and little differences
 in diversity due to extinction. We conclude that our analyses on the
 Caesar's mushrooms give further evidence of a temperate-peaking LDG
 in EM fungi, highlighting the importance and the implications of
 macroevolutionary processes in explaining diversity gradients in
 microorganisms.
description: Main compressed
 fileIn this compressed
 folder ("Dryad") you will find three subfolders: (1)
 "Data" with phylogenetic trees, including the section-level MCC
 and the 100 posterior subtrees of clade 'Caesarea'. This
 subfolder also contains the tip latitudinal traits. (2)
 "Results" with three other subfolders, each one with raw result
 files from BAMM, QuaSSE, and DDD. Lastly, (3) "Simulations"
 contains the R script used for QuaSSE simulations.Dryad.zip
DOI: 10.5061/dryad.05pk3
title: Data from: Contrasting responses of male and female foraging effort to year-round wind conditions

description: 1. There is growing interest in the effects of wind on wild animals, given
 evidence that wind speeds are increasing and becoming more variable in
 some regions, particularly at temperate latitudes. Wind may alter movement
 patterns or foraging ability, with consequences for energy budgets and,
 ultimately, demographic rates. 2. These effects are expected to vary among
 individuals due to intrinsic factors such as sex, age or feeding
 proficiency. Furthermore, this variation is predicted to become more
 marked as wind conditions deteriorate, which may have profound
 consequences for population dynamics as the climate changes. However, the
 interaction between wind and intrinsic effects has not been
 comprehensively tested. 3. In many species, in particular those showing
 sexual size dimorphism, males and females vary in foraging performance.
 Here, we undertook year-round deployments of data loggers to test for
 interactions between sex and wind speed and direction on foraging effort
 in adult European shags Phalacrocorax aristotelis, a pursuit-diving
 seabird in which males are c. 18% heavier. 4. We found that foraging time
 was lower at high wind speeds but higher during easterly (onshore) winds.
 Furthermore, there was an interaction between sex and wind conditions on
 foraging effort, such that females foraged for longer than males when
 winds were of greater strength (9% difference at high wind speeds vs. 1%
 at low wind speeds) and when winds were easterly compared with westerly
 (7% and 4% difference, respectively). 5. The results supported our
 prediction that sex-specific differences in foraging effort would become
 more marked as wind conditions worsen. Since foraging time is linked to
 demographic rates in this species, our findings are likely to have
 important consequences for population dynamics by amplifying sex-specific
 differences in survival rates.
description: Lewis et al for
 Dryad
DOI: 10.5061/dryad.61691
title: Data from: From promise to practice: pairing non-invasive sampling with genomics in conservation

description: Conservation genomics has become an increasingly popular term, yet it
 remains unclear whether the non-invasive sampling that is essential for
 many conservation-related studies is compatible with the minimum
 requirements for harnessing next-generation sequencing technologies. Here,
 we evaluated the feasibility of using genotyping-by-sequencing of
 non-invasively collected hair samples to simultaneously identify and
 genotype single nucleotide polymorphisms (SNPs) in a climate
 change-sensitive mammal, the American pika (Ochotona princeps). We
 identified and genotyped 3,803 high-confidence SNPs across eight sites
 distributed along two elevational transects using starting DNA amounts as
 low as 1 nanogram. Fifty-five outlier loci were detected as candidate gene
 regions under divergent selection, constituting potential targets for
 future validation. Genome-wide estimates of gene diversity significantly
 and positively correlated with elevation across both transects, with all
 low elevation sites exhibiting significant heterozygote deficit likely due
 to inbreeding. More broadly, our results highlight a range of issues that
 must be considered when pairing genomic data collection with non-invasive
 sampling, particularly related to field sampling protocols for minimizing
 exogenous DNA, data collection strategies and quality control steps for
 enhancing target organism yield, and analytical approaches for maximizing
 cost-effectiveness and information content of recovered genomic data.
description: SNP genotypic data from
 American pika in North Cascades National ParkExcel file including
 genotypes at 9825 SNPs for 67 American pika sampled in North Cascades
 National Park, Washington, USA. The first column is contig name. The
 second column is SNP position within the contig. Every two columns after
 is an individual. Each row is a locus. Sample names include the transect
 identifier (PP=Pyramid Peak; TL=Thornton Lake), site name (ex. 1A), and
 individual number (ex. 20a). Allele calls are as follows: 1=A, 2=C, 3=G,
 4=T.PikaNextRAD_SNP.xlsx
DOI: 10.5061/dryad.rg7s7
title: Data from: Population-level consequences of herbivory, changing climate and source-sink dynamics on a long-lived invasive shrub

description: Long-lived plant species are highly valued environmentally, economically,
 and socially, but can also cause substantial harm as invaders. Realistic
 demographic predictions can guide management decisions, and are
 particularly valuable for long-lived species where population response
 times can be long. Long-lived species are also challenging, given
 population dynamics can be affected by factors as diverse as herbivory,
 climate, and dispersal. We developed a matrix model to evaluate the
 effects of herbivory by a leaf-feeding biological control agent released
 in Australia against a long-lived invasive shrub (mesquite, Leguminoseae:
 Prosopis spp.). The stage-structured, density-dependent model used an
 annual time step and 10 climatically diverse years of field data. Mesquite
 population demography is sensitive to source–sink dynamics as most seeds
 are consumed and redistributed spatially by livestock. In addition,
 individual mesquite plants, because they are long lived, experience
 natural climate variation that cycles over decadal scales, as well as
 anthropogenic climate change. The model therefore explicitly considered
 the effects of both net dispersal and climate variation. Herbivory
 strongly regulated mesquite populations through reduced growth and
 fertility, but additional mortality of older plants will be required to
 reach management goals within a reasonable time frame. Growth and survival
 of seeds and seedlings were correlated with daily soil moisture. As a
 result, population dynamics were sensitive to rainfall scenario, but
 population response times were typically slow (20–800 years to reach
 equilibrium or extinction) due to adult longevity. Equilibrium population
 densities were expected to remain 5% higher, and be more dynamic, if
 historical multi-decadal climate patterns persist, the effect being
 dampened by herbivory suppressing seed production irrespective of
 preceding rainfall. Dense infestations were unlikely to form under a drier
 climate, and required net dispersal under the current climate. Seed input
 wasn't required to form dense infestations under a wetter climate.
 Each factor we considered (ongoing herbivory, changing climate, and
 source–sink dynamics) has a strong bearing on how this invasive species
 should be managed, highlighting the need for considering both ecological
 context (in this case, source–sink dynamics) and the effect of climate
 variability at relevant temporal scales (daily, multi-decadal, and
 anthropogenic) when deriving management recommendations for long-lived
 species.
description: Field data used to
 parameterise the mesquite population modelAn overview of what
 field data was used to estimate each parameter is provided in the first
 tab. Subsequent tabs contain the raw field data that was collected,
 including a text box providing a brief description of the data source.
 Notes on column headings provide information on data fields where it is
 not self-explanatory.Dryad Data only
 V4a.xlsx
DOI: 10.5061/dryad.n27h3
title: Data from: No deep diving: evidence of predation on epipelagic fish for a stem beaked whale from the late Miocene of Peru

description: Although modern beaked whales (Ziphiidae) are known to be highly
 specialized toothed whales that predominantly feed at great depths upon
 benthic and benthopelagic prey, only limited palaeontological data
 document this major ecological shift. We report on a ziphiid–fish
 assemblage from the Late Miocene of Peru that we interpret as the first
 direct evidence of a predator–prey relationship between a ziphiid and
 epipelagic fish. Preserved in a dolomite concretion, a skeleton of the
 stem ziphiid Messapicetus gregarius was discovered together with numerous
 skeletons of a clupeiform fish closely related to the epipelagic extant
 Pacific sardine (Sardinops sagax). Based on the position of fish
 individuals along the head and chest regions of the ziphiid, the lack of
 digestion marks on fish remains and the homogeneous size of individuals,
 we propose that this assemblage results from the death of the whale
 (possibly via toxin poisoning) shortly after the capture of prey from a
 single school. Together with morphological data and the frequent discovery
 of fossil crown ziphiids in deep-sea deposits, this exceptional record
 supports the hypothesis that only more derived ziphiids were regular deep
 divers and that the extinction of epipelagic forms may coincide with the
 radiation of true dolphins.
description: Lambert et al_suppl
 material1. Supplementary Figures
 2. Size and Weight Estimates for Messapicetus gregarius 3. Size and Weight
 Estimates for Sardinops sp. cf S. sagax 4. Comparison of Cervical
 Vertebrae Ankylosis and Size among Ziphiidae 5. Comparison of Relative
 Humeral Length among Ziphiidae 6. Abbreviations for Institutions 7.
 Supplementary References
DOI: 10.5061/dryad.q5h96
title: Data from: Evolution of increased competitiveness in cows trades offs with reduced milk yield, fertility and more masculine morphology

description: In some species females compete for food, foraging territories, mating,
 and nesting sites. Competing females can exhibit morphological,
 physiological and behavioral adaptations typical of males, which are
 commonly considered as secondary sexual traits. Competition and the
 development of traits increasing competitiveness require much energy and
 may exert adverse effects on fecundity and survival. From an evolutionary
 perspective, positive selection for increased competitiveness would then
 result in evolution of reduced values for traits related to fitness such
 as fecundity and survival. There is recent evidence for such evolutionary
 trade-offs involving male competition, but no study has considered
 competing females so far. Using data from competitions for dominance in
 cows (Bos taurus), we found negative genetic correlations between traits
 providing success in competition, i.e., fighting ability, and fitness
 traits related to milk production and with fertility (the inverse of
 parity-conception interval). Fighting ability also showed low but positive
 genetic correlations with “masculine” morphological traits, and negative
 correlations with “feminine” traits. A genetic change in traits over time
 has occurred due to selection on competitiveness, corresponding to an
 evolutionary process of “masculinization” counteracting the official
 selection for milk yield. Similar evolutionary trade-off between success
 in competition and fitness components may be present in various species
 experiencing female competition.
description: Data_for_dryadDatasets and pedigrees used in the studydata for dryad.zip