cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.fk7bh24
title: Data from: Root responses to elevated CO2, warming, and irrigation in a semi-arid grassland: integrating biomass, length, and life span in a 5‐year field experiment

description: Plant roots mediate the impacts of environmental change on ecosystems, yet
 knowledge of root responses to environmental change is limited because few
 experiments evaluate multiple environmental factors and their
 interactions. Inferences about root functions are also limited because
 root length dynamics are rarely measured. Using a five‐year experiment in
 a mixed‐grass prairie, we report the responses of root biomass, length,
 and lifespan to elevated carbon dioxide (CO2), warming, elevated CO2 and
 warming combined, and irrigation. Root biomass was quantified using soil
 cores and root length dynamics were assessed using minirhizotrons. By
 comparing root dynamics with published results for soil resources and
 aboveground productivity, we provide mechanistic insights into how climate
 change might impact grassland ecosystems. In the upper soil layer, 0–15 cm
 depth, both irrigation and elevated CO2 alone increased total root length
 by two‐fold, but irrigation decreased root biomass and elevated CO2 had
 only small positive effects on root biomass. The large positive effects of
 irrigation and elevated CO2 alone on total root length were due to
 increases in both root length production and root lifespan. The increased
 total root length and lifespan under irrigation and elevated CO2 coincided
 with apparent shifts from water‐limitation of plant growth to
 nitrogen‐limitation. Warming alone had minimal effects on root biomass,
 length, and lifespan in this shallow soil layer. Warming and elevated CO2
 combined increased root biomass and total root length by ~25%, but total
 root length in this treatment was lower than expected if the effects of
 CO2 and warming alone were additive. Treatment effects on total root
 length and root lifespan varied with soil depth and root diameter.
 Synthesis. Sub‐additive effects of CO2 and warming suggest studies of
 elevated CO2 alone might overestimate the future capacity of grassland
 root systems to acquire resources. In this mixed‐grass prairie, elevated
 CO2 with warming stimulated total root length and root lifespan in deeper
 soils, likely enhancing plant access to more stable pools of
 growth‐limiting resources, including water and phosphorus. Thus, these
 root responses help explain previous observations of higher, and more
 stable, aboveground productivity in these projected climate conditions.
description: individual_roots_lifespan_survivorship_length_diameter Data used for analyses of root lifespan and survivorship     total_root_length_production_mortality Data used for analyses of total 'standing' root length, total root production, and total root mortality
DOI: 10.5061/dryad.16g72gk
title: Data from: Linkage disequilibrium clustering-based approach for association mapping with tightly linked genome-wide data

description: Genome-wide association studies (GWAS) aim to identify genetic markers
 strongly associated with quantitative traits by utilizing linkage
 disequilibrium (LD) between candidate genes and markers. However, because
 of LD between nearby genetic markers, the standard GWAS approaches
 typically detect a number of correlated SNPs covering long genomic
 regions, making corrections for multiple testing overly conservative.
 Additionally, the high dimensionality of modern GWAS data poses
 considerable challenges for GWAS procedures such as permutation tests,
 which are computationally intensive. We propose a cluster-based GWAS
 approach that first divides the genome into many large non-overlapping
 windows, and uses linkage disequilibrium network analysis in combination
 with principal component (PC) analysis as dimensional reduction tools to
 summarize the SNP data to independent PCs within clusters of loci
 connected by high LD. We then introduce single- and multi-locus models
 that can efficiently conduct the association tests on such high
 dimensional data. The methods can be adapted to different model
 structures, and used to analyse samples collected from the wild or from
 bi-parental F2 populations, which are commonly used in ecological genetics
 mapping studies. We demonstrate the performance of our approaches with two
 publicly available data sets from a plant (Arabidopsis thaliana) and a
 fish (Pungitius pungitius), as well as with simulated data.
description: R script and code for
 cluster-based association and QTL mappingR script and example data for
 cluster-based association and QTL
 mapping.zip
DOI: 10.5061/dryad.9b4g92k
title: Data from: Survival estimates strongly depend on capture-recapture designs in a disturbed environment inducing dispersal

description: Capture‐Recapture (CR) approaches are extensively used to estimate
 demographic parameters. Their robustness relies on the selection of
 suitable statistical models, but also on the sampling design and effort
 deployed in the field. In colonial or territorial species showing breeding
 site fidelity, recurrent local perturbations, such as predation‐induced
 breeding failure, may lead individuals to disperse locally or regionally.
 This might induce heterogeneity in individual CR histories and biases in
 demographic parameter estimates. Here, we assessed the effect of buffer
 areas and multi‐site designs on annual survival estimate accuracy and
 precision. First, using simulated data with and without a multi‐site
 design, we compared survival estimates for different scenarios involving
 contrasted local and regional dispersal. Then, using data from a local
 multi‐site long‐term monitoring survey carried out in a colony of
 black‐legged kittiwakes, we tested the homogeneity of individual CR
 histories and compared survival estimates from three datasets including
 one or several breeding cliffs with or without buffer areas. Results from
 simulations highlighted that a single‐site design consistently led to
 underestimated or less precise survival values compared to a multi‐site
 design. Similarly, a multi‐site design allowed detecting significant
 temporal trends while a single‐site one did not. In the field‐based study,
 adding buffer areas reduced individual heterogeneity, but all three
 datasets suffered from strong trap‐dependence possibly due to individual
 breeding success affecting nest‐site fidelity. Implementing a multi‐site
 design significantly improved the accuracy and precision of annual
 survival estimates, regardless of CR models applied. Adapting the spatial
 scale of sampling design to the local environment and species behaviour is
 essential to provide robust parameters of key relevance for population
 monitoring and management. We show that implementing buffer areas and/or
 multi‐site designs may be especially beneficial for long‐lived species
 facing regular local perturbation events leading to local dispersal.
description: Field-based and
 simulated datasetsThese are all the
 datasets used in the simulated and field-based studies. The simulated data
 were obtained from M-Surge software. The field-based data have been
 collected from a long-term monitoring survey carried out in the
 black-legged kittiwake colony of Hornøya, Norway.Field-based ans simulated
 datasets.zip
DOI: 10.5061/dryad.kk628dt
title: Data from: The polyphyly of Plasmodium: comprehensive phylogenetic analyses of the malaria parasites (order Haemosporida) reveal widespread taxonomic conflict

description: The evolutionary relationships among the apicomplexan blood pathogens
 known as the malaria parasites (order Haemosporida), some of which infect
 nearly 200 million humans each year, has remained a vexing phylogenetic
 problem due to limitations in taxon sampling, character sampling, and the
 extreme nucleotide base composition biases that are characteristic of this
 clade. Previous phylogenetic work on the malaria parasites has often
 lacked sufficient representation of the broad taxonomic diversity within
 the Haemosporida or the multi-locus sequence data needed to resolve deep
 evolutionary relationships, rendering our understanding of haemosporidian
 life history evolution and the origin of the human malaria parasites
 incomplete. Here we present the most comprehensive phylogenetic analysis
 of the malaria parasites conducted to date, using samples from a broad
 diversity of vertebrate hosts that includes numerous enigmatic and poorly
 known haemosporidian lineages in addition to genome-wide multi-locus
 sequence data. We find that if base composition differences were corrected
 for during phylogenetic analysis, we recovered a well-supported topology
 indicating that the evolutionary history of the malaria parasites was
 characterized by a complex series of transitions in life history
 strategies and host usage. Notably we find that Plasmodium, the malaria
 parasite genus that includes the species of human medical concern, is
 polyphyletic with the life history traits characteristic of this genus
 having evolved in a dynamic manner across the phylogeny. We find support
 for multiple instances of gain and loss of asexual proliferation in host
 blood cells and production of hemozoin pigment, two traits that have been
 used for taxonomic classification as well as considered to be important
 factors for parasite virulence and used as drug targets. Lastly, our
 analysis illustrates the need for a widespread reassessment of malaria
 parasite taxonomy.
description: all_phylogenetic_treesThe results of all 19 phylogenetic analyses conducted in this study. Each tree corresponds to an analysis described in Supplementary Table 4.phylogenetic_trees.taramino_acid_gene_treesGene trees for all 21 loci sequenced in this study produced from amino acid alignmentsnucleotide_gene_treesGene trees for all 21 loci sequenced in this study produced from codon alignmentsall_alignmentsAll alignments (codon and amino acid) used for phylogenetic analysesalignments.tar
DOI: 10.5061/dryad.240t21v
title: Data from: Resilience to fire of phylogenetic diversity across biological domains

description: Fire alters the structure and composition of above- and belowground
 communities with concurrent shifts in phylogenetic diversity. The
 inspection of post-fire trends in the diversity of ecological communities
 incorporating phylogenetic information allows to better understand the
 mechanisms driving fire resilience. While fire reduces plant phylogenetic
 diversity based on the recruitment of evolutionarily-related species with
 post-fire seed persistence, it increases that of soil microbes by limiting
 soil resources and changing the dominance of competing microbes. Thus,
 during post-fire community reassembly, plant and soil microbes might
 experience opposing temporal trends in their phylogenetic diversity that
 are linked through changes in the soil conditions. We tested this
 hypothesis by investigating the post-fire evolution of plant and soil
 microbial (fungi, bacteria and archaea) communities across three 20-year
 chronosequences. Plant phylogenetic diversity increased with time since
 fire as pioneer seeders facilitate the establishment of distantly-related
 late-successional shrubs. The post-fire increase in plant phylogenetic
 diversity fostered plant productivity, eventually recovering soil organic
 matter. These shifts over time in the soil conditions explained the
 post-fire restoration of fungal and bacterial phylogenetic diversity,
 which decreased to pre-fire levels, suggesting that evolutionarily-related
 taxa with high relative fitness recover their competitive superiority
 during community reassembly. The resilience to fire of phylogenetic
 diversity across biological domains helps preserve the evolutionary
 history stored in our ecosystems.
description: Phylogenetic trees of
 archaea, bacteria, fungi and plantsRData containing
 phylogenetic trees of archaea, bacteria, fungi and plants. Five
 independent phylogenetic trees per biological group are provided. Plant
 and fungal phylogenies were reconstructed after grafting our study species
 in a supertree derived from the literature. Archaeal and bacterial
 phylogenies were reconstructed from 16S rRNA sequences using maximum
 likelihood.Phylogenies_Perez-Valera_et_al.RData
DOI: 10.5061/dryad.hm249b5
title: Data from: Stable coexistence of genetically divergent Atlantic cod ecotypes at multiple spatial scales

description: Coexistence in the same habitat of closely related yet genetically
 different populations is a phenomenon that challenges our understanding of
 local population structure and adaptation. Identifying the underlying
 mechanisms for such coexistence can yield new insight into adaptive
 evolution, diversification, and the potential for organisms to adapt and
 persist in response to a changing environment. Recent studies have
 documented cryptic, sympatric populations of Atlantic cod (Gadus morhua)
 in coastal areas. We analyzed genetic origin of 6483 individual cod
 sampled annually over 14 years from 125 locations along the Norwegian
 Skagerrak coast and document stable coexistence of two genetically
 divergent Atlantic cod ecotypes throughout the study area and study
 period. A ‘fjord’ ecotype dominated in numbers deep inside fjords while a
 'North Sea' ecotype was the only type found in offshore North
 Sea. Both ecotypes coexisted in similar proportions throughout coastal
 habitats at all spatial scales. The size-at-age of the North Sea ecotype
 on average exceeded that of the fjord ecotype by 20% in length and 80% in
 weight across all habitats. Different growth and size among individuals of
 the two types might be one of several ecologically significant variables
 that allow for stable coexistence of closely related populations within
 the same habitat. Management plans, biodiversity initiatives, and other
 mitigation strategies that do not account for the mixture of species
 ecotypes are unlikely to meet objectives related to the sustainability of
 fish and fisheries.
description: 26snp_reference data for
 analysis of assignmentReference data
 (individual genetic data (26 SNP's for each ind) for the North sea
 and coastal component). SNP's are described in paper.The other file
 contains inds that was genetically assigned to either of
 the"populations" in this file (North Sea or coastal
 component)26snp_reference.genepopBeachSeine_26SNP_all26 SNP loci for all beach seine dataindividual_informationInformation on all individuals (length position, aso)r_data3-6.csv
DOI: 10.5061/dryad.5b8n621
title: Data from: Dynamics of investor spanning trees around dot-com bubble

description: We identify temporal investor networks for Nokia stock by constructing
 networks from correlations between investor-specific net-volumes and
 analyze changes in the networks around dot-com bubble. The analysis is
 conducted separately for households, financial, and non-financial
 institutions. Our results indicate that spanning tree measures for
 households reflected the boom and crisis: the maximum spanning tree
 measures had a clear upward tendency in the bull markets when the bubble
 was building up, and, even more importantly, the minimum spanning tree
 measures pre-reacted the burst of the bubble. At the same time, we find
 less clear reactions in the minimal and maximal spanning trees of
 non-financial and financial institutions around the bubble, which suggests
 that household investors can have a greater herding tendency around
 bubbles.
description: financial
 institutiondata in financial
 institution file contains investors links between financial institutional
 investors.non-financial
 institutiondata in non-financial
 institution file contains investors links between non-financial
 institutional investors.households_part1data in households_par1 file contains investors links between household investors until 2000.households_part2data in households_part2 file contains investors links between household investors between 2001-2002.
DOI: 10.5061/dryad.g85t15k
title: Data from: Nest boxes increase reproductive output for Tree Swallows in a forest grassland matrix in central British Columbia

description: Secondary cavity-nesting birds depend on tree cavities for nesting and
 roosting, but many studies of these birds are conducted using nest boxes.
 Implementation of effective conservation strategies for cavity-nesting
 species such as nest-site supplementation requires careful comparisons of
 fecundity and other vital rates for birds using both natural and
 artificial nest site types. We compared breeding phenology, clutch and
 brood sizes, and fledging success of Tree Swallows (Tachycineta bicolor)
 nesting in tree cavities and nest boxes during 2001–2003 in British
 Columbia, Canada. Swallows using nest boxes initiated egg-laying and
 hatched young at approximately the same time as those in tree cavities (2
 June, 23 June, respectively). Female Tree Swallows in boxes laid larger
 clutches (5.9 ± 0.9 eggs, N = 76) than those in tree cavities (4.2 ± 1.6
 eggs, N = 67). The mean number of nestlings hatched was greater in nest
 boxes (5.2 ± 1.1 nestlings, N = 67) than in tree cavities (2.6 ± 2.0
 nestlings, N = 58). Pairs in boxes were over twice as successful in
 producing fledglings (93.4%; 57 of 61 pairs fledged &gt; 1 young) than
 those in tree cavities (35.8%; 19 of 53 pairs). Of those successful nests,
 pairs nesting in boxes fledged 5.1 ± 1.1 young (N = 57), whereas those in
 tree cavities fledged 3.5 ± 1.2 young (N = 18). Because cavities in nest
 boxes averaged 60% larger in volume and 1.8 cm wider internally than tree
 cavities, we suggest that increased reproductive output was correlated
 with boxes enabling a larger clutch size. In previous research, we found
 that Tree Swallows were a poor competitor with other cavity-nesting
 passerines for tree cavities. The addition of nest boxes may serve as an
 effective way to supplement local reproduction for secondary
 cavity-nesting bird populations by reducing competition for limited nest
 sites. This is especially true in regions where the availability of
 natural nesting sites is highly variable, and where species compete with
 many other cavity-nesting passerines using a similar ecological niche and
 nesting cavities.
description: PLOS_for_upload_TRES_cavboxNorrisetalData includes tree cavity and nest box information for 2001-2003
DOI: 10.5061/dryad.b71g0gr
title: Data from: Fitness consequences of interspecific nesting associations among cavity-nesting birds

description: Interspecific aggregations of prey may provide benefits by mitigating
 predation risk, but they can also create costs if they increase
 competition for resources or are more easily detectable by predators.
 Variation in predation risk and resource availability may influence the
 occurrence and fitness effects of aggregating in nature. Yet, tests of
 such possibilities are lacking. Cavity nesting birds provide an
 interesting test case. They compete aggressively for resources and
 experience low nest predation rates, which might predict dispersion, but
 we found they commonly aggregate by sharing nest trees across 19 years of
 study. Tree sharing was more common when aspen were more abundant and
 somewhat more common in years with higher nest predation risk. Nest
 success was higher in shared trees when nest predation risk was higher
 than average. Ultimately, the costs and benefits of aggregating (nest tree
 sharing) varied across years and we outline hypotheses for future studies.
description: Mouton_Martin_2018_AmNat_MantelTestAndHeightDifferenceData used to examine the frequency species share nest trees together and the vertical distance between nests. Note: Phlyogenetic distances are in a separate file.Mouton_Martin_2018_AmNat_MantelTestPhyloDistancePhylogenetic distances between species. Phylogenetic distances were obtained from a majority rules consensus tree constructed from 1000 trees using program Mesquite (Maddison and Maddison 2011). Phylogenetic trees were downloaded from www.birdtree.org (Jetz et al 2012) using the Hackett et al. (2008) backbone.Mouton_Martin_2018_AmNat_SharingAcrossYearsData used to examine whether nest tree sharing is related to variation in ecological variables across years.Mouton_Martin_2018_AmNat_HabitatAndNestSuccessData used to examine (1) habitat covariates related to shared nest trees and (2) the relationship between nest tree sharing and nest success.
DOI: 10.5061/dryad.96dn293
title: Data from: Weak interspecific interactions in a sagebrush steppe? Conflicting evidence from observations and experiments

description: Stable coexistence requires intraspecific limitations to be stronger than
 interspecific limitations. The greater the difference between intra- and
 interspecific limitations, the more stable the coexistence, and the weaker
 the competitive release any species should experience following removal of
 competitors. We conducted a removal experiment to test whether a
 previously estimated model, showing surprisingly weak interspecific
 competition for four dominant species in a sagebrush steppe, accurately
 predicts competitive release. Our treatments were 1) removal of all
 perennial grasses and 2) removal of the dominant shrub, Artemisia
 tripartita. We regressed survival, growth and recruitment on the
 locations, sizes, and species identities of neighboring plants, along with
 an indicator variable for removal treatment. If our ``baseline"
 regression model, which accounts for local plant-plant interactions,
 accurately explains the observed responses to removals, then the removal
 coefficient should be non-significant. For survival, the removal
 coefficients were never significantly different from zero, and only A.
 tripartita showed a (negative) response to removals at the recruitment
 stage. For growth, the removal treatment effect was significant and
 positive for two species, Poa secunda and Pseudoroegneria spicata,
 indicating that the baseline model underestimated interspecific
 competition. For all three grass species, population models based on the
 vital rate regressions that included removal effects projected 1.4 to
 3-fold increases in equilibrium population size relative to the baseline
 model (no removal effects). However, we found no evidence of higher
 response to removal in quadrats with higher pretreatment cover of A.
 tripartita, or by plants experiencing higher pre-treatment crowding by A.
 tripartita, raising questions about the mechanisms driving the positive
 response to removal. While the experimental results showed greater
 competitive release than our baseline models predicted, we will need more
 tightly controlled experiments focused on underlying mechanisms to
 conclusively validate or reject our model's predictions.
description: Data and R
 codeThe zip archive contains
 the data and R code used to conduct the analyses reported in the
 publication. Readme files in the subdirectories contain metadata and
 instructions for running the code. Note that changing the directory
 structure will cause the R scripts to fail.removals_data&code.zip