cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.3v55p
title: Data from: Estimating the temporal and spatial extent of gene flow among sympatric lizard populations (genus Sceloporus) in the southern Mexican highlands

description: Interspecific gene flow is pervasive throughout the tree of life. Although
 detecting gene flow between populations has been facilitated by new
 analytical approaches, determining the timing and geography of
 hybridization has remained difficult, particularly for historical gene
 flow. A geographically explicit phylogenetic approach is needed to
 determine the overlap of ancestral populations. In this study, we
 performed population genetic analyses, species delimitation, simulations
 and a recently developed approach of species tree diffusion to infer the
 phylogeographic history, timing and geographic extent of gene flow in
 lizards of the Sceloporus spinosus group. The two species in this group,
 S. spinosus and S. horridus, are distributed in eastern and western
 portions of Mexico, respectively, but populations of these species are
 sympatric in the southern Mexican highlands. We generated data consisting
 of three mitochondrial genes and eight nuclear loci for 148 and 68
 individuals, respectively. We delimited six lineages in this group, but
 found strong evidence of mito-nuclear discordance in sympatric populations
 of S. spinosus and S. horridus owing to mitochondrial introgression. We
 used coalescent simulations to differentiate ancestral gene flow from
 secondary contact, but found mixed support for these two models. Bayesian
 phylogeography indicated more than 60% range overlap between ancestral S.
 spinosus and S. horridus populations since the time of their divergence.
 Isolation–migration analyses, however, revealed near-zero levels of gene
 flow between these ancestral populations. Interpreting results from both
 simulations and empirical data indicate that despite a long history of
 sympatry among these two species, gene flow in this group has only
 recently occurred.
description: Concatenated
 DatasetA nexus file of all 8
 nuclear loci concatenated.concatenated.nexIMa2_6popIMa2 input file for the 6-population modelSpecies Tree Diffusion xml fileBEAST xml needed to run species tree diffusion. Other files are needed to run this including a GPS coordinates file delimiting species boundaries, and a posterior distribution of species trees.ST_diffusion.xmlhorridus N .kml distribution fileKML file delineating S. horridus north distribution needed to run a species tree diffusion analysis.hor_N_distribution.kmlPosterior distribution of species treesPosterior distribution of species trees generated in *BEAST needed to run the species tree diffusion analysis.species_tree_posterior.species.treesSTRUCTURAMA input fileInput file for the program STRUCTURAMASTRUCTURAMA.in
DOI: 10.5061/dryad.mj226
title: Data from: Avoiding tipping points in fisheries management through Gaussian process dynamic programming

description: Model uncertainty and limited data are fundamental challenges to robust
 management of human intervention in a natural system. These challenges are
 acutely highlighted by concerns that many ecological systems may contain
 tipping points, such as Allee population sizes. Before a collapse, we do
 not know where the tipping points lie, if they exist at all. Hence, we
 know neither a complete model of the system dynamics nor do we have access
 to data in some large region of state space where such a tipping point
 might exist. We illustrate how a Bayesian non-parametric approach using a
 Gaussian process (GP) prior provides a flexible representation of this
 inherent uncertainty. We embed GPs in a stochastic dynamic programming
 framework in order to make robust management predictions with both model
 uncertainty and limited data. We use simulations to evaluate this approach
 as compared with the standard approach of using model selection to choose
 from a set of candidate models. We find that model selection erroneously
 favours models without tipping points, leading to harvest policies that
 guarantee extinction. The Gaussian process dynamic programming (GPDP)
 performs nearly as well as the true model and significantly outperforms
 standard approaches. We illustrate this using examples of simulated
 single-species dynamics, where the standard model selection approach
 should be most effective and find that it still fails to account for
 uncertainty appropriately and leads to population crashes, while
 management based on the GPDP does not, as it does not underestimate the
 uncertainty outside of the observed data.
description: manuscript source
 .Rmd.Rmd file containing the
 source code for all results presented in the paper, along with raw
 manuscript text documenting the data and figures shown.manuscript.Rmdsupplement source .RmdA plain-text (.Rmd) file containing all code run in the supplement, together with descriptions.supplement.RmdCSV files for figuresAll data tables used to generate figures as CSV files by figure name. (20 files, 13 MB). Note, all data are from simulations, not true observations, and can also be re-generated by running the code provided. See corresponding code blocks of Manuscript.Rmd and Supplement.Rmd for details.data.zipKnitr cache fileThis cache file stores the results of running each of the code chunks in manuscript.Rmd and supplement.Rmd, see http://yihui.name/knitr for details on caching.nonparametric-bayes-cache.tar.gz
DOI: 10.5061/dryad.t64s0
title: Data from: Long-term balanced fertilization improves the soil microbial functional diversity in a phosphorus-limited paddy soil

description: The influence of long-term chemical fertilization on soil microbial
 communities has been one of the frontier topics of agricultural and
 environmental sciences and is critical for linking soil microbial flora
 with soil functions. In this study, 16S rRNA gene pyrosequencing and a
 functional gene array, GeoChip 4.0, were used to investigate the shifts in
 microbial composition and functional gene structure in paddy soils with
 different fertilization treatments over a 22-year period. These included a
 control without fertilizers, chemical nitrogen fertilizer (N), N and
 phosphate (NP); N and potassium (NK), and N, P and K (NPK). Based on 16S
 rRNA gene data, both species evenness and key genera were affected by P
 fertilization. Functional gene array-based analysis revealed that
 long-term fertilization significantly changed the overall microbial
 functional structures. Chemical fertilization significantly increased the
 diversity and abundance of most genes involved in C, N, P, and S cycling,
 especially for the treatments NK and NPK. Significant correlations were
 found among functional gene structure and abundance, related soil
 enzymatic activities and rice yield, suggesting that a fertilizer-induced
 shift in the microbial community may accelerate the nutrient turnover in
 soil, which in turn influenced rice growth. The effect of N fertilization
 on soil microbial functional genes was mitigated by the addition of P
 fertilizer in this P-limited paddy soil, suggesting that balanced chemical
 fertilization is beneficial to the soil microbial community and its
 functions.
description: aligned
 sequencealigned 16S rRNA gene
 sequences of all samplesotutableotutable of 16S rRNA gene sequences16S analysisR script for analysis of 16S rRNA gene sequencesgeochip datageochip data, chemical properties and biological properties of soil samples, R script for analysis of geochip datageochip.zip
DOI: 10.5061/dryad.44b4j
title: Data from: Multilocus species trees show the recent adaptive radiation of the mimetic Heliconius butterflies

description: Müllerian mimicry among Neotropical Heliconiini butterflies is an
 excellent example of natural selection, associated with the
 diversification of a large continental-scale radiation. Some of the
 processes driving the evolution of mimicry rings are likely to generate
 incongruent phylogenetic signals across the assemblage, and thus pose a
 challenge for systematics. We use a dataset of 22 mitochondrial and
 nuclear markers from 92% of species in the tribe, obtained by Sanger
 sequencing and de novo assembly of short read data, to re-examine the
 phylogeny of Heliconiini with both supermatrix and multispecies coalescent
 approaches, characterize the patterns of conflicting signal and compare
 the performance of various methodological approaches to reflect the
 heterogeneity across the data. Despite the large extent of reticulate
 signal and strong conflict between markers, nearly identical topologies
 are consistently recovered by most of the analyses, although the
 supermatrix approach failed to reflect the underlying variation in the
 history of individual loci. However, the supermatrix represents a useful
 approximation where multiple rare species represented by short sequences
 can be incorporated easily. The first comprehensive, time-calibrated
 phylogeny of this group is used to test the hypotheses of a
 diversification rate increase driven by the dramatic environmental changes
 in the Neotropics over the past 23 million years, or changes caused by
 diversity-dependent effects on the rate of diversification. We find that
 the rate of diversification has increased on the branch leading to the
 presently most species-rich genus Heliconius, but the change occurred
 gradually and cannot be unequivocally attributed to a specific
 environmental driver. Our study provides comprehensive comparison of
 philosophically distinct species tree reconstruction methods and provides
 insights into the diversification of an important insect radiation in the
 most biodiverse region of the planet.
description: Online Appendix 1
 SpecimensA detailed list of
 specimens and GenBank Accession Numbers.Online Appendix 2
 PartitionsPartitions selected by
 PartitionFinder.Online Appendix 3
 BEASTOnline Appendix 4
 starBEASTSupplementary
 InformationSupplementary data
 (Tables and Figures) for Kozak et al. 2015.
DOI: 10.5061/dryad.v3g17
title: Data from: Rapid and accurate detection of urinary pathogens by mobile IMS-based electronic nose: a proof-of-principle study

description: Urinary tract infection (UTI) is a common disease with significant
 morbidity and economic burden, accounting for a significant part of the
 workload in clinical microbiology laboratories. Current clinical chemisty
 point-of-care diagnostics rely on imperfect dipstick analysis which only
 provides indirect and insensitive evidence of urinary bacterial pathogens.
 An electronic nose (eNose) is a handheld device mimicking mammalian
 olfaction that potentially offers affordable and rapid analysis of samples
 without preparation at athmospheric pressure. In this study we demonstrate
 the applicability of ion mobility spectrometry (IMS) –based eNose to
 discriminate the most common UTI pathogens from gaseous headspace of
 culture plates rapidly and without sample preparation. We gathered a total
 of 101 culture samples containing four most common UTI bacteries: E. coli,
 S. saprophyticus, E. faecalis, Klebsiella spp and sterile culture plates.
 The samples were analyzed using ChemPro 100i device, consisting of IMS
 cell and six semiconductor sensors. Data analysis was conducted by linear
 discriminant analysis (LDA) and logistic regression (LR). The results were
 validated by leave-one-out and 5-fold cross validation analysis. In
 discrimination of sterile and bacterial samples sensitivity of 95% and
 specificity of 97% were achieved. The bacterial species were identified
 with sensitivity of 95% and specificity of 96% using eNose as compared to
 urine bacterial cultures. In conclusion: These findings strongly
 demonstrate the ability of our eNose to discriminate bacterial cultures
 and provides a proof of principle to use this method in urinanalysis of
 UTI.
description: PLoS ONE
 dataContains the raw data of
 the measurements and logbook. UT and UU -codes indicate the individual
 sample plates; they are individual samples of the bacteria culture
 described in the header row.PLOS ONE
 DATA.zip
DOI: 10.5061/dryad.pp37p
title: Data from: Spatially heterogeneous impact of climate change on small mammals of montane California

description: Resurveys of historical collecting localities have revealed range shifts,
 primarily leading edge expansions, which have been attributed to global
 warming. However, there have been few spatially replicated community-scale
 resurveys testing whether species' responses are spatially
 consistent. Here we repeated early twentieth century surveys of small
 mammals along elevational gradients in northern, central and southern
 regions of montane California. Of the 34 species we analysed, 25 shifted
 their ranges upslope or downslope in at least one region. However,
 two-thirds of ranges in the three regions remained stable at one or both
 elevational limits and none of the 22 species found in all three regions
 shifted both their upper and lower limits in the same direction in all
 regions. When shifts occurred, high-elevation species typically contracted
 their lower limits upslope, whereas low-elevation species had
 heterogeneous responses. For high-elevation species, site-specific change
 in temperature better predicted the direction of shifts than change in
 precipitation, whereas the direction of shifts by low-elevation species
 was unpredictable by temperature or precipitation. While our results
 support previous findings of primarily upslope shifts in montane species,
 they also highlight the degree to which the responses of individual
 species vary across geographically replicated landscapes.
description: MARK Occupancy Analysis
 Input FileThis file contains the
 site-specific covariates and capture histories for the 34
 occupancy-modeled species. Each row contains a capture history for a
 species at a site along with that site's model covariates, including
 era, region, slope, elevation, elevation squared, T100 (number of traps x
 100), and logT (log of the number of traps). There are also two columns
 for latitude ("lat") and longitude ("long"), but these
 were not used in the occupancy analysis. This file is formatted as it was
 used in the MARK analysis.MARK_Input_File_Capture_Histories_02Mar2011_DRYAD.xls
DOI: 10.5061/dryad.gg8fg
title: Data from: A comprehensive DNA barcode database for Central European beetles with a focus on Germany: adding more than 3,500 identified species to BOLD

description: Beetles are the most diverse group of animals and are crucial for
 ecosystem functioning. In many countries, they are well established for
 environmental impact assessment, but even in the well-studied Central
 European fauna, species identification can be very difficult. A
 comprehensive and taxonomically well-curated DNA barcode library could
 remedy this deficit and could also link hundreds of years of traditional
 knowledge with next generation sequencing technology. However, such a
 beetle library is missing to date. This study provides the globally
 largest DNA barcode reference library for Coleoptera for 15 948
 individuals belonging to 3514 well-identified species (53% of the German
 fauna) with representatives from 97 of 103 families (94%). This study is
 the first comprehensive regional test of the efficiency of DNA barcoding
 for beetles with a focus on Germany. Sequences ≥500 bp were recovered from
 63% of the specimens analysed (15 948 of 25 294) with short sequences from
 another 997 specimens. Whereas most specimens (92.2%) could be
 unambiguously assigned to a single known species by sequence diversity at
 CO1, 1089 specimens (6.8%) were assigned to more than one Barcode Index
 Number (BIN), creating 395 BINs which need further study to ascertain if
 they represent cryptic species, mitochondrial introgression, or simply
 regional variation in widespread species. We found 409 specimens (2.6%)
 that shared a BIN assignment with another species, most involving a pair
 of closely allied species as 43 BINs were involved. Most of these taxa
 were separated by barcodes although sequence divergences were low. Only
 155 specimens (0.97%) show identical or overlapping clusters.
description: Appendix
 S1Appendix S1: Compendium
 of all German beetle species used in this study including information on
 their geographical distribution, specimen count, BIN, Mean and Max ISD,
 Nearest-Neighbor(NN) species and Distance to NN.Appendix
 S2Appendix S2: Accession
 numbers, BOLD Sample-IDs and species names for all specimens used in this
 study.Appendix
 S3CO1-5P
 Alignments15 files of 1000 aligned
 CO1 sequencesAlignments.zip
DOI: 10.5061/dryad.qc700
title: Data from: Untangling human and environmental effects on geographical gradients of mammal species richness: a global and regional evaluation

description: Different hypotheses (geographic, ecological, evolutionary or a
 combination of them) have been suggested to account for the spatial
 variation in species richness. However, the relative importance of
 environment and human impacts in explaining these patterns, either
 globally or at the biogeographic region level, remains largely unexplored.
 Here we jointly evaluate how current environmental conditions and human
 impacts shape global and regional gradients of species richness in
 terrestrial mammals. We processed IUCN global distributional data for 3939
 mammal species and a set of seven environmental and two human impact
 variables at a spatial resolution of 96.5x 96.5 km. We used simple,
 multiple and partial regression techniques to evaluate environmental and
 human effects on species richness. Actual evapotranspiration is the main
 driver of mammal species richness globally. Together with our results at
 the biogeographic realm level, this lends strong support for the Hawkins
 et al. (2003) conjecture (i.e. global diversity gradients are best
 explained by the interaction of water and energy, with a latitudinal shift
 in the relative importance of ambient energy vs. water as we move from the
 poles to the equator). While human effects on species richness are not
 easily detected at a global scale due to the large proportion of shared
 variance with the environment, these effects significantly emerge at the
 regional level. In the Nearctic, Palearctic and Oriental regions, the
 independent contribution of human impacts is almost as important as
 current environmental conditions in explaining richness patterns. The
 intersection of human impacts with climate drives the geographic variation
 in mammal species richness in the Palearctic, Nearctic and Oriental
 regions. Using a human accessibility variable we show, for the first time,
 that the zones most accessible to humans are often those where we find
 lower mammal species richness.
description: mammal species richness
 and environmental variables at global scaleInclude database of the
 species richness of mammals and different environmental variables at
 global scaleglobal_dryad.csv
DOI: 10.5061/dryad.t75c4
title: Data from: Species richness of wild bees, but not the use of managed honey bees, increases fruit set of a pollinator-dependent crop

description: 1. Native, wild bees are important pollinators for both crop and wild
 plants. With concerns over the availability and cost of managed honey
 bees, attention has turned to native, wild bees as crop pollinators.
 However, the ability of native, wild bees to provide sufficient
 pollination may depend on their populations at local scales. 2. Therefore,
 at the farm scale, we examined the pollination contribution of both
 native, wild bees and managed honey bees to apples, and assessed the
 relative importance of bee abundance versus species richness. Over three
 growing seasons, apple fruit set, bee abundance, and bee species richness
 were measured at orchards in Wisconsin, half of which used managed honey
 bees, thus allowing us to independently examine the contribution of
 native, wild bees to fruit set. We additionally conducted observations of
 honey bees and wild bees foraging on apple blossoms in order to examine
 functional complementarity. 3. We found that apples are highly dependent
 on animal pollinators. However, fruit set was not significantly higher at
 orchards with managed honey bees, nor did it increase with the number of
 honey bees per orchard. Instead, fruit set significantly increased with
 the species richness of native, wild bees during bloom. 4. Honey bees and
 wild bees showed different foraging preferences: honey bees more
 frequently visited apple flowers on densely blooming trees, while wild
 bees showed no preference for floral density, thereby evenly visiting
 trees throughout the orchard. 5. Synthesis and applications. Our results
 show that native, wild bees play a significant and unique role in apple
 pollination within our region, and cannot therefore be replaced by managed
 bees. Moreover, our findings suggest that bee conservation efforts should
 focus specifically on maintaining or increasing bee species richness in
 order to improve pollination and crop yields.
description: bee visitation/floral
 densityVisitation rates of
 different bees (wild, honey, unique morphospecies) to apple trees of
 varying floral densitybeevisitation.xlsxfruitsetbeesProportion fruit set, honey bee abundance, wild bee abundance, wild bee species richness and site characteristics at apple orchards in southern WisconsinspecieslistList of all collected wild and honey bees identified to species
DOI: 10.5061/dryad.n3215
title: Data from: Dissecting the phenotypic components of crop plant growth and drought responses based on high-throughput image analysis

description: Significantly improved crop varieties are urgently needed to feed the
 rapidly growing human population under changing climates. While genome
 sequence information and excellent genomic tools are in place for major
 crop species, the systematic quantification of phenotypic traits or
 components thereof in a high-throughput fashion remains an enormous
 challenge. In order to help bridge the genotype to phenotype gap, we
 developed a comprehensive framework for high-throughput phenotype data
 analysis in plants, which enables the extraction of an extensive list of
 phenotypic traits from nondestructive plant imaging over time. As a proof
 of concept, we investigated the phenotypic components of the drought
 responses of 18 different barley (Hordeum vulgare) cultivars during
 vegetative growth. We analyzed dynamic properties of trait expression over
 growth time based on 54 representative phenotypic features. The data are
 highly valuable to understand plant development and to further quantify
 growth and crop performance features. We tested various growth models to
 predict plant biomass accumulation and identified several relevant
 parameters that support biological interpretation of plant growth and
 stress tolerance. These image-based traits and model-derived parameters
 are promising for subsequent genetic mapping to uncover the genetic basis
 of complex agronomic traits. Taken together, we anticipate that the
 analytical framework and analysis results presented here will be useful to
 advance our views of phenotypic trait components underlying plant
 development and their responses to environmental cues.
description: tpc129601_SupplementalDataSupplemental Data Sets