cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.dm94c
title: Data from: Stoichiometric imbalances between detritus and detritivores are related to shifts in ecosystem functioning

description: How are resource consumption and growth rates of litter-consuming
 detritivores affected by imbalances between consumer and litter C:N:P
 ratios? To address this question, we offered leaf litter as food to three
 aquatic detritivore species, which represent a gradient of increasing body
 N:P ratios: a crustacean, a caddisfly and a stonefly. The detritivores
 were placed in microcosms and submerged in a natural stream. Four
 contrasting leaf species were offered, both singly and in two-species
 mixtures, to obtain different levels of stoichiometric imbalance between
 the resources and their consumers. The results suggest that detritivore
 growth was constrained by N rather than C or P, even though 1) the N:P
 ratios of the consumers’ body tissue was relatively low and 2) microbial
 leaf conditioning during the experiment reduced the N:P imbalance between
 detritivores and leaf litter. This surprisingly consistent N limitation
 may be a consequence of cumulative N-demand arising from the production of
 N-rich chitin in the exoskeletons of all three consumer species, which is
 lost during regular moults, in addition to N-demand for silk production by
 the caddisfly. These N requirements are not commonly quantified in
 stoichiometric analyses of arthropod consumers. There was no evidence for
 compensatory feeding, but when offered mixed-species litter varying in
 C:N:P ratios, detritivores consumed more of the litter species showing the
 highest N:P and lowest C:N ratio, accelerating the mass loss of the
 preferred leaf species in the litter mixture. These results show that
 imbalances in consumer–resource stoichiometry can have contrasting effects
 on coupled processes, highlighting a challenge in developing a mechanistic
 understanding of the role of stoichiometry in regulating ecosystem
 processes such as leaf litter decomposition.
description: InvAllometric
 FraineretalOikos2015Data on invertebrate
 length and dry mass used for calculating allometric
 relationships.InvertebrateFinalLength
 FraineretalOikos2015Data on invertebrate
 length measured at the end of the experiment, using high-quality digital
 photographs and software analyzer ImageJ.LitterFinalNP
 FraineretalOikos2015Nitrogen and phosphorus
 concentration in the leaf litter at the end of the
 experiment.LitterMassLoss
 FraineretalOikos2015Initial and final dry
 mass of the leaf litter.
DOI: 10.5061/dryad.3k5v6
title: Data from: Identifying patterns and drivers of coral diversity in the Central Indo-Pacific marine biodiversity hotspot

description: Biodiversity hotspots are increasingly recognized as areas of high
 taxonomic and functional diversity. These hotspots are dynamic and shift
 geographically over time in response to environmental change. To identify
 drivers of the origin, evolution, and persistence of diversity hotspots,
 we investigated the diversity patterns of reef-building corals
 (Scleractinia) in the Central Indo-Pacific, a marine biodiversity hotspot
 for the last 25 Myr. We used the scleractinian fossil record (based on
 literature and a newly acquired fossil collection) to examine the
 taxonomic and functional diversity of corals from the Eocene to Pliocene.
 Our data identify potential drivers of coral diversity through time (and
 space) in the Central Indo-Pacific by constraining the timing of taxonomic
 turnover events and correlating them with known environmental changes.
 Increases in taxonomic diversity, high origination rates, and changes in
 abundance of functional character states indicate that the origin of the
 Central Indo-Pacific hotspot occurred during the Oligocene, initially
 through proliferation of pre-existing taxa and then by origination of new
 taxa. In contrast to taxonomic diversity, overall functional diversity of
 Central Indo-Pacific reef-building corals remained constant from the
 Eocene to the Pliocene. Our results identify global sea level as a main
 driver of diversity increase that, together with local tectonics,
 regulates availability of suitable habitats. Moreover, marine biodiversity
 hotspots develop from both the accumulation of taxa from older
 biodiversity hotspots and origination of new taxa. Our study demonstrates
 the utility of a combined literature-based and new collection approach for
 gaining new insights into the timing, drivers, and development of tropical
 biodiversity hotspots.
description: Mihaljevic et al 2017
 Paleobiology_ Supplementary materialThe uploaded zip file
 contains one Appendix, two Supplementary Figures, and three Supplementary
 Tables. They are all referred to in the manuscript "Identifying
 patterns and drivers of coral diversity in the Central Indo-Pacific marine
 biodiversity hotspot" by Mihaljevic et al. 2017 published in
 Paleobiology. Figure captions can be found below the Supplementary Figures
 and Table captions above the Supplementary Tables.
DOI: 10.5061/dryad.293hd
title: Data from: Farmers without borders - genetic structuring in century old barley (Hordeum vulgare)

description: The geographic distribution of genetic diversity can reveal the
 evolutionary history of a species. For crop plants, phylogeographic
 patterns also indicate how seed has been exchanged and spread in agrarian
 communities. Such patterns are, however, easily blurred by the intense
 seed trade, plant improvement and even genebank conservation during the
 twentieth century, and discerning fine-scale phylogeographic patterns is
 thus particularly challenging. Using historical crop specimens, these
 problems are circumvented and we show here how high-throughput genotyping
 of historical nineteenth century crop specimens can reveal detailed
 geographic population structure. Thirty-one historical and nine extant
 accessions of North European landrace barley (Hordeum vulgare L.), in
 total 231 individuals, were genotyped on a 384 single nucleotide
 polymorphism assay. The historical material shows constant high levels of
 within-accession diversity, whereas the extant accessions show more
 varying levels of diversity and a higher degree of total genotype sharing.
 Structure, discriminant analysis of principal components and principal
 component analysis cluster the accessions in latitudinal groups across
 country borders in Finland, Norway and Sweden. FST statistics indicate
 strong differentiation between accessions from southern Fennoscandia and
 accessions from central or northern Fennoscandia, and less differentiation
 between central and northern accessions. These findings are discussed in
 the context of contrasting historical records on intense within-country
 south to north seed movement. Our results suggest that although seeds were
 traded long distances, long-term cultivation has instead been of locally
 available, possibly better adapted, genotypes.
description: Barley genotype
 dataSNP genotype data for
 historical and genebank landrace barley. DNA was extracted from seed of
 historical collections and leaf tissue from genebank material. File was
 created in Microsoft Excel 2010.
DOI: 10.5061/dryad.72m15
title: Data from: The genetic architecture of freezing tolerance varies across the range of Arabidopsis thaliana

description: The capacity to tolerate freezing temperatures limits the geographical
 distribution of many plants, including several species of agricultural
 importance. However, the genes involved in freezing tolerance remain
 largely unknown. Here, we describe the variation in constitutive freezing
 tolerance that occurs among worldwide accessions of Arabidopsis thaliana.
 We found that although plants from high latitudes tend to be more freezing
 tolerant than plants from low latitudes, the environmental factors that
 shape cold adaptation differ across the species range. Consistent with
 this, we found that the genetic architecture of freezing tolerance also
 differs across its range. Conventional genome-wide association studies
 helped identify a priori and other promising candidate genes. However,
 simultaneously modelling climate variables and freezing tolerance together
 pinpointed other excellent a priori candidate genes. This suggests that if
 the selective factor underlying phenotypic variation is known, multi-trait
 mixed models may aid in identifying the genes that underlie adaptation.
description: reportsReports (top candidates from GWAS), manhattan/eps files, and phenotypes.freezing.tgz
DOI: 10.5061/dryad.g40n0
title: Data from: Size-dependent mortality and competition interactively shape community diversity

description: Body size is recognized as a major factor in evolutionary processes
 mediating sympatric diversification and community structuring.
 Life-history types with distinct body sizes can result from two
 fundamental mechanisms, size-dependent competition and size-dependent
 mortality. While previous theoretical studies investigated these two
 processes in separation, the model analyzed here allows both selective
 forces to affect body-size evolution interactively. Here we show for the
 first time that in the presence of size-dependent competition,
 size-dependent mortality can give rise to multiple, coexisting size morphs
 representing the final outcomes of evolution. Moreover, our results
 demonstrate that interactions between size-dependent competition and
 mortality can create characteristic abrupt changes in size structure and
 non-monotonic patterns of biological diversity along continuous and
 monotonic environmental gradients. We find that the two selective forces
 differentially affect the body-size ratios of coexisting morphs:
 size-dependent competition results in small and relatively constant
 ratios, whereas size-dependent mortality can open niches for morphs that
 greatly differ in body size. We show that these differential effects
 result in characteristic distributions of size ratios across communities,
 which we suggest can help detect the concurrent action and relative
 influence of size-dependent competition and mortality in nature.
description: Data for Taborsky et al.
 Evolution, Fig. 5
DOI: 10.5061/dryad.v751b
title: Data from: Overview of animal rabies in Kinshasa Province in the Democratic Republic of Congo

description: Introduction: Rabies is one of the major public health problems mostly
 affecting developing countries in Africa and Asia where 99.9% of all
 rabies related human deaths are recorded each year. In Democratic Republic
 of Congo, repeated outbreaks have been reported. Despite this, there is
 little reliable epidemiological data about rabies in the country for the
 development of effective control strategies. Materials and Methods: A
 retrospective study was carried out in Kinshasa Province during a period
 of five years (2009–2013) to describe the proportion of rabid animals and
 the species involved in rabies transmission and maintenance. The survey
 also aimed at describing the spatial-temporal distribution of rabies. To
 gather information, the daily registers of institutions involved in rabies
 diagnosis were reviewed and each rabies case was traced back to area of
 occurrence for collection of geographic coordinates. Results and
 Discussion: A total of 5,053 attacks were registered involving six animal
 species including dog, cat, monkey, rabbit, rat, and pig. Based on
 clinical observations, rabies was reported in dogs and cats while data
 obtained from the laboratory confirmed rabies cases included dogs, cats
 and a goat. The annual distribution showed a significant decrease of
 rabies cases from 2009 up to 2011 and a later increase up to 2013. There
 was no difference in rabies occurrence between seasons (p = 0.721). Rabies
 cases were three times higher in peri-urban zone than in urban zone OR =
 3.4 (95% CI: 2.3–5.1). The positive proportion of rabies was 2.6% (95% CI:
 2.1–3) based on clinical evidence and 65.9% (95% CI: 50–79.5) for
 laboratory confirmed cases. Conclusion and Suggestion: This study confirms
 the endemicity of rabies in Kinshasa where occurrence of rabies cases was
 related to human population density and lifestyle. In order to control
 rabies, there is need to set up a surveillance program and implement
 efficient mass vaccination campaigns of susceptible animals.
description: Species and
 Spatio-temporal distribution of animal rabiesData collected in daily
 registers of institutions dealing with rabies from 2009 to 2013. Data are
 coded according to the variables corresponding to the column heading as
 shown for each column when mouse passes.Database_Rabies_Kinshasa_DRC.xls
DOI: 10.5061/dryad.rb237
title: Data from: Logging, exotic plant invasions, and native plant reassembly in a lowland tropical rain forest

description: Habitat modification and biological invasions are key drivers of global
 environmental change. However, the extent and impact of exotic plant
 invasions in modified tropical landscapes remains poorly understood. We
 examined whether logging drives exotic plant invasions, and whether their
 combined influences alter understory plant community composition in
 lowland rain forests in Borneo. We tested the relationship between
 understory communities and local- and landscape-scale logging intensity,
 using leaf area index (LAI) and above-ground biomass (AGB) data from 192
 plots across a logging-intensity gradient from primary to
 repeatedly-logged forests. Overall, we found relatively low levels of
 exotic plant invasions, despite an intensive logging history. Exotic
 species were more speciose, had greater cover, and more biomass in sites
 with more local-scale canopy loss. Surprisingly, though, exotic species
 invasion was not related to either landscape-scale canopy loss nor road
 configuration. Moreover, logging and invasion did not seem to be acting
 synergistically on native plant composition, except that seedlings of the
 canopy-dominant Dipterocarpaceae family were less abundant in areas with
 higher exotic plant biomass. Current low levels of invasion, and limited
 association with native understory community change, suggest there is a
 window of opportunity to manage invasive impacts. We caution about
 potential lag effects and the possibly severe negative impacts of exotic
 plant invasions on the long-term quality of tropical forest, particularly
 where agricultural plantations function as permanent seed sources for
 recurrent dispersal along logging roads. We therefore urge prioritization
 of strategic management plans to counter the growing threat of exotic
 plant invasions in modified tropical landscapes.
description: PlotDataBiotropicaThis csv file contains the full database of characteristics for each of 159 vegetation plots including logging metrics, environmental variables as well as specific data on native and exotic plants.SpeciesDataBiotropicaThis csv file contains the complete list of species (723) sampled across 192 vegetation plots (2 x 2m) located at the Stability of Altered Forest Ecosystems (SAFE) project in Sabah, Malaysia, including a distinction between native and exotic species origin.PlotSpeciesDataBiotropicaThis csv file contains a matrix of biomass values for 723 plant taxa sampled across 192 vegetation plots (2 x 2m) located at the Stability of Altered Forest Ecosystems (SAFE) project in Sabah, Malaysia.
DOI: 10.5061/dryad.584m3
title: Data from: The behavior of Metropolis-coupled Markov chains when sampling rugged phylogenetic distributions

description: Bayesian phylogenetic inference involves sampling from posterior
 distributions of trees, which sometimes exhibit local optima, or peaks,
 separated by regions of low posterior density. Markov chain Monte Carlo
 (MCMC) algorithms are the most widely used numerical method for generating
 samples from these posterior distributions, but they are susceptible to
 entrapment on individual optima in rugged distributions when they are
 unable to easily cross through or jump across regions of low posterior
 density. Ruggedness of posterior distributions can result from a variety
 of factors, including unmodeled variation in evolutionary processes and
 unrecognized variation in the true topology across sites or genes.
 Ruggedness can also become exaggerated when constraints are placed on
 topologies that require the presence or absence of particular bipartitions
 (often referred to as positive or negative constraints, respectively).
 These types of constraints are frequently employed when conducting tests
 of topological hypotheses (Bergsten et al. 2013; Brown and Thomson 2017).
 Negative constraints can lead to particularly rugged distributions when
 the data strongly support a forbidden clade, because monophyly of the
 clade can be disrupted by inserting outgroup taxa in many different ways.
 However, topological moves between the alternative disruptions are very
 difficult, because they require swaps between the inserted outgroup taxa
 while the data constrain taxa from the forbidden clade to remain close
 together on the tree. While this precise form of ruggedness is particular
 to negative constraints, trees with high posterior density can be
 separated by similarly complicated topological rearrangements, even in the
 absence of constraints.
description: Unconstrained
 exampleNexus file containing
 the DNA alignment from the unconstrained phylogenetic
 example.tetrapods.nexConstrained exampleNexus file containing the DNA alignment for the constrained phylogenetic example.top5.nex
DOI: 10.5061/dryad.hd2g2
title: Data from: Not seeing the grass for the trees: timber plantations and agriculture shrink tropical montane grassland by two-thirds over four decades in the Palani Hills, a Western Ghats Sky Island

description: Tropical montane habitats, grasslands, in particular, merit urgent
 conservation attention owing to the disproportionate levels of endemic
 biodiversity they harbour, the ecosystem services they provide, and the
 fact that they are among the most threatened habitats globally. The Shola
 Sky Islands in the Western Ghats host a matrix of native forest-grassland
 matrix that has been planted over the last century, with exotic timber
 plantations. The popular discourse on the landscape change is that mainly
 forests have been lost to the timber plantations and recent court
 directives are to restore Shola forest trees. In this study, we examine
 spatiotemporal patterns of landscape change over the last 40 years in the
 Palani Hills, a significant part of the montane habitat in the Western
 Ghats. Using satellite imagery and field surveys, we find that 66% of
 native grasslands and 31% of native forests have been lost over the last
 40 years. Grasslands have gone from being the dominant, most contiguous
 land cover to one of the rarest and most fragmented. They have been
 replaced by timber plantations and, to a lesser extent, expanding
 agriculture. We find that the spatial pattern of grassland loss to
 plantations differs from the loss to agriculture, likely driven by the
 invasion of plantation species into grasslands. We identify remnant
 grasslands that should be prioritised for conservation and make specific
 recommendations for conservation and restoration of grasslands in light of
 current management policy in the Palani Hills, which favours large-scale
 removal of plantations and emphasises the restoration of native forests.
description: Palani Hills Landscape
 change mapThis study examines
 landscape change in the Palani Hills using LANDSAT imageries. Study was
 funded by INTACH Kodaikanal and IISER TIRUPATI.2014_GCS.rar
DOI: 10.15468/dl.2n9z3m
title: Occurrence Download

description: A dataset containing 21883 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Observation, Human Observation, Specimen)",
 "Geometry POLYGON((-127.08 59.12,-84.39 59.12,-84.39 70.13,-127.08 70.13,-127.08 59.12))",
 "HasCoordinate is true",
 "License is one of (CC-BY-NC 4.0, CC-BY 4.0, CC0 1.0)",
 "OccurrenceStatus is Present",
 "TaxonKey is Fungi"
 ]
}

 The dataset includes 21883 records from 101 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000593-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.jn14d
title: Data from: How stock of origin affects performance of individuals across a meta-ecosystem: an example from Sockeye salmon

description: Connectivity among diverse habitats can buffer populations from adverse
 environmental conditions, influence the functioning of meta-ecosystems,
 and ultimately affect the reliability of ecosystem services. This
 stabilizing effect on populations is proposed to derive from
 complementarity in growth and survival conditions experienced by
 individuals in the different habitats that comprise meta-ecosystems. Here
 we use the fine scale differentiation of salmon populations between
 diverse lake habitats to assess how rearing habitat and stock of origin
 affect the body condition of juvenile sockeye salmon. We use genetic
 markers (single nucleotide polymorphisms) to assign individuals of unknown
 origin to stock group and in turn characterize ecologically relevant
 attributes across habitats and stocks. Our analyses show that body
 condition of juvenile salmon is related to the productivity of alternative
 habitats across the watershed, irrespective of their stock of origin.
 Emigrants and residents with genetic origins in the high productivity lake
 were also differentiated by their body condition, poor and high
 respectively. These emigrants represented a substantial proportion of
 juvenile sockeye salmon rearing in the lower productivity lake habitat.
 Despite emigrants originating from the more productive lake, they did not
 differ in body condition from the individuals spawned in the lower
 productivity, recipient habitat. Genetic tools allowed us to assess the
 performance of different stocks groups across the diverse habitats
 comprising their meta-ecosystem. The ability to characterize the
 ecological consequences of meta-ecosystem connectivity can help develop
 strategies to protect and restore ecosystems and the services they provide
 to humans.
description: Griffiths2013Genotypes2010ChignikLakeSingle-nucleotide polymorphism (SNP) genotypes for juvenile sockeye salmon (Oncorhynchus nerka) collected in 2010 in Chignik Lake, AK.Griffiths2013Genotypes2011ChignikLakeSingle-nucleotide polymorphism (SNP) genotypes for juvenile sockeye salmon (Oncorhynchus nerka) collected in 2011 in Chignik Lake, AK.Griffiths2013LengthMass2010BlackLakeLength and mass for juvenile sockeye salmon (Oncorhynchus nerka) collected in 2010 in Black Lake, AK.Griffiths2013LengthMass2010ChignikLakeLength and mass for juvenile sockeye salmon (Oncorhynchus nerka) collected in 2010 in Chignik Lake, AK.Griffiths2013LengthMass2011BlackLakeLength and mass for juvenile sockeye salmon (Oncorhynchus nerka) collected in 2011 in Black Lake, AK.Griffiths2013LengthMass2011ChignikLakeLength and mass for juvenile sockeye salmon (Oncorhynchus nerka) collected in 2010 in Chignik Lake, AK.