cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.m3f26
title: Data from: Global stability of obligate mutualistm in community modules with facultative mutualists

description: Mutualism is a fundamental building block of ecological communities and an
 important driver of biotic evolution. Classic theory suggests that a
 pairwise two-species obligate mutualism is fragile, with a large
 perturbation potentially driving both mutualist populations into
 extinction. In nature, however, there are many cases of pairwise obligate
 mutualism. Such pairwise obligate mutualisms are occasionally associated
 with additional interactions with facultative mutualists. Here, we use a
 mathematical model to show that when a two-species obligate mutualism has
 a single additional link to a third facultative mutualist, the obligate
 mutualism can become permanently persistent. In the model, a facultative
 mutualist interacts with one of two inter-dependent obligate mutualists,
 and the facultative mutualist enhances the persistence not only of its
 directly interacting obligate mutualist, but also that of the other
 obligate mutualist indirectly, enabling the permanent coexistence of the
 three mutualist species. The effect of the facultative mutualist is
 strong; it can allow a three-species permanent coexistence even when two
 obligate mutualists by themselves are not sustainable (i.e. not locally
 stable). These results suggest that facultative mutualists can play a
 pivotal role for the persistence of obligate mutualisms, and contribute to
 a better understanding on the mechanisms maintaining more complex
 mutualistic networks of multiple species.
description: Mathematica file for
 Appendices 1 and 2, and Figures 2, 3, and 4A Mathematica (v9.0)
 file containing the codes for the calculation used in appendices 1 and 2,
 for drawing figures 2, 3, and 4, and for numerical integration of the
 model.Dryad
 file for OIK-02741.R1.nb
DOI: 10.5061/dryad.21s3t
title: Data from: Revisiting the Iberian honey bee (Apis mellifera iberiensis) contact zone: maternal and genome-wide nuclear variation provide support for secondary contact from historical refugia

description: Dissecting diversity patterns of organisms endemic to Iberia has been
 truly challenging for a variety of taxa, and the Iberian honey bee is no
 exception. Surveys of genetic variation in the Iberian honey bee are among
 the most extensive for any honey bee subspecies. From these, differential
 and complex patterns of diversity have emerged, which have yet to be fully
 resolved. Here, we used a genome-wide data set of 309 neutrally tested
 single nucleotide polymorphisms (SNPs), scattered across the 16 honey bee
 chromosomes, which were genotyped in 711 haploid males. These SNPs were
 analysed along with an intergenic locus of the mtDNA, to reveal historical
 patterns of population structure across the entire range of the Iberian
 honey bee. Overall, patterns of population structure inferred from nuclear
 loci by multiple clustering approaches and geographic cline analysis were
 consistent with two major clusters forming a well-defined cline that
 bisects Iberia along a northeastern–southwestern axis, a pattern that
 remarkably parallels that of the mtDNA. While a mechanism of primary
 intergradation or isolation by distance could explain the observed clinal
 variation, our results are more consistent with an alternative model of
 secondary contact between divergent populations previously isolated in
 glacial refugia, as proposed for a growing list of other Iberian taxa.
 Despite current intense honey bee management, human-mediated processes
 have seemingly played a minor role in shaping Iberian honey bee genetic
 structure. This study highlights the complexity of the Iberian honey bee
 patterns and reinforces the importance of Iberia as a reservoir of Apis
 mellifera diversity.
description: mtDNA haplotypes of
 Iberian Honey beeAlignment of mtDNA
 haplotypesmtDNA haplotypes
 A.m.iberiensis.fas
DOI: 10.5061/dryad.520gq
title: Data from: Deep-sea, deep-sequencing: metabarcoding extracellular DNA from sediments of marine canyons

description: Marine sediments are home to one of the richest species pools on Earth,
 but logistics and a dearth of taxonomic work-force hinders the knowledge
 of their biodiversity. We characterized α- and β-diversity of deep-sea
 assemblages from submarine canyons in the western Mediterranean using an
 environmental DNA metabarcoding. We used a new primer set targeting a
 short eukaryotic 18S sequence (ca. 110 bp). We applied a protocol designed
 to obtain extractions enriched in extracellular DNA from replicated
 sediment corers. With this strategy we captured information from DNA
 (local or deposited from the water column) that persists adsorbed to
 inorganic particles and buffered short-term spatial and temporal
 heterogeneity. We analysed replicated samples from 20 localities including
 2 deep-sea canyons, 1 shallower canal, and two open slopes (depth range
 100–2,250 m). We identified 1,629 MOTUs, among which the dominant groups
 were Metazoa (with representatives of 19 phyla), Alveolata, Stramenopiles,
 and Rhizaria. There was a marked small-scale heterogeneity as shown by
 differences in replicates within corers and within localities. The spatial
 variability between canyons was significant, as was the depth component in
 one of the canyons where it was tested. Likewise, the composition of the
 first layer (1 cm) of sediment was significantly different from deeper
 layers. We found that qualitative (presence-absence) and quantitative
 (relative number of reads) data showed consistent trends of
 differentiation between samples and geographic areas. The subset of
 exclusively benthic MOTUs showed similar patterns of β-diversity and
 community structure as the whole dataset. Separate analyses of the main
 metazoan phyla (in number of MOTUs) showed some differences in
 distribution attributable to different lifestyles. Our results highlight
 the differentiation that can be found even between geographically close
 assemblages, and sets the ground for future monitoring and conservation
 efforts on these bottoms of ecological and economic importance.
description: obitools commands used
 in the analysis of dataThis file contains the
 obitools commands used to manipulate sequence reads, filter sequences, and
 assign taxonomyobitools
 commands.txtDatabase of MOTUs and
 sequencesThis database contains
 the number of reads of the different MOTUs in the samples studied,
 together with information on taxonomic assignment and the sequences
 themselvesdatabase
 corrected.txt
DOI: 10.5061/dryad.m663t
title: Data from: Flowering time QTL in natural populations of Arabidopsis thaliana and implications for their adaptive value

description: The genetic basis of phenotypic traits is of great interest to
 evolutionary biologists, but their contribution to adaptation in nature is
 often unknown. To determine the genetic architecture of flowering time in
 ecologically relevant conditions, we used a recombinant inbred line
 population created from two locally adapted populations of Arabidopsis
 thaliana from Sweden and Italy. Using these RILs, we identified flowering
 time QTL in growth chambers that mimicked the natural temperature and
 photoperiod variation across the growing season in each native
 environment. We also compared the genomic locations of flowering time QTL
 to those of fitness (total fruit number) QTL from a previous three-year
 field study. Ten total flowering time QTL were found, and in all cases,
 the Italy genotype caused early flowering regardless of the conditions.
 Two QTL were consistent across chamber environments and these had the
 largest effects on flowering time. Five of the fitness QTL co-localized
 with flowering time QTL found in the Italy conditions, and in each case
 the local genotype was favored. In contrast, just two flowering time QTL
 found in the Sweden conditions co-localized with fitness QTL and in only
 one case was the local genotype favored. This implies that flowering time
 may be more important for adaptation in Italy than Sweden. Two candidate
 genes (FLC and VIN3) underlying the major flowering time QTL found in the
 current study are implicated in local adaptation.
description: Experimental Chamber
 ConditionsGrowth chamber
 conditions used to simulate the native photoperiod and temperature
 fluctuations across the growing season for both the Sweden and Italy
 populationschamber_conditions.xlsxFlowering Time for all RILs and parentsOne tab contains the mean flowering time for all RILs in the experiment in both conditions. The number of replicates that survived to flower is also indicated. Another tab gives the mean flowering time for both parents in both conditions.Chamber_FloweringTime.xlsxGenotype DataThis data file is formatted for use in R/qtlgeno_DTFF_CHAMB.csv
DOI: 10.5061/dryad.424tb
title: Data from: Semisynthesis and insecticidal activity of some novel fraxinellone-based thioethers containing 1,3,4-oxadiazole moiety

description: Two series of novel fraxinellone-based thioethers containing
 1,3,4-oxadiazole moiety were prepared as insecticidal agents against the
 oriental armyworm, Mythimna separata Walker. The structural assignment was
 based on the spectroscopic and X-ray analysis data. Among all the target
 compounds, compounds 4b, 4k, 5b, 5j and 5k exhibited more potent
 insecticidal activity with final mortality rates (FMRs) of &gt; 65%,
 especially 4k with the FMR of 75.9%, when compared with toosendanin. Some
 interesting results of structure–activity relationships were also
 discussed.
description: Semisynthesis and
 insecticidal activity of some novel fraxinellone-based thioethers
 containing 1,3,4-oxadiazole moietySpectra data of
 compounds 4e-4k and 5e-5k.Supporting
 information-YG.doc
DOI: 10.5061/dryad.n2q57qn
title: Data from: Phylotocol: promoting transparency and overcoming bias in phylogenetics

description: The integrity of science requires that the process be based on sound
 experimental design and objective methodology. Strategies that increase
 reproducibility and transparency in science protect this integrity by
 reducing conscious and unconscious biases. Given the large number of
 analysis options and the constant development of new methodologies in
 phylogenetics, this field is one that would particularly benefit from more
 transparent research design. Here, we introduce phylotocol
 (fī·lō·´tə·kôl), an a priori protocol-driven approach in which all
 analyses are planned and documented at the start of a project. The
 phylotocol template is simple and the implementation options are flexible
 to reduce administrative burdens and allow researchers to adapt it to
 their needs without restricting scientific creativity. While the primary
 goal of phylotocol is to increase transparency and accountability, it has
 a number of auxiliary benefits including improving study design and
 reproducibility, enhancing collaboration and education, and increasing the
 likelihood of project completion. Our goal with this Point of View article
 is to encourage a dialogue about transparency in phylogenetics and the
 best strategies to bring transparent research practices to our field.
description: Appendix_1Blank phylotocol template in Word formatAppendix_2Blank phylotocol template in markdown formatAppendix_3Example phylotocol in markdown format. This document describes the analysis plan for an empirical phylogenomic study. Title: Planned analysis for testing holothurian phylogeny and developing target enrichment baitsAppendix_4Example phylotocol in PDF format. This document describes the analysis plan for a phylogenetic simulation study. Title: An extension of testing 6-state recoding strategies to address substitution bias and compositional heterogeneityAppendix_5Example phylotocol in PDF format. This document describes the analysis plan for an empirical phylogenomic study. Title: Planned analyses for testing existence of sponge parahox
DOI: 10.5061/dryad.qk826
title: Data from: Recombinant DNA modification of gibberellin metabolism alters growth rate and biomass allocation in Populus

description: Overexpression of genes that modify gibberellin (GA) metabolism and
 signaling have been previously shown to produce trees with improved
 biomass production but highly disturbed development. To examine if more
 subtle types of genetic modification of GA could improve growth rate and
 modify tree architecture, we transformed a model poplar genotype (Populus
 tremula × P. alba) with eight genes, including two cisgenes (intact copies
 of native genes), four intragenes (modified copies of native genes), and
 two transgenes (from sexually incompatible species), and studied their
 effects under greenhouse and field conditions. In the greenhouse, four out
 of the eight tested genes produced a significant and often striking
 improvement of stem volume, and two constructs significantly modified the
 proportion of root or shoot biomass. Characterization of GA concentrations
 in the cisgenic population that had an additional copy of a poplar
 GA20-oxidase gene showed elevated concentrations of 13-hydroxylated GAs
 compared to wild-type poplars. In the field, we observed growth
 improvement for three of the six tested constructs, but it was
 significantly greater for only one of the constructs, a pRGL:GA20-oxidase
 intragene. The greenhouse and field responses were highly variable,
 possibly to due to cross-talk among the GA pathway and other stress
 response pathways, or due to interactions between the cisgenes and
 intragenes with highly similar endogenes. Our results indicate that
 extensive field trials, similar to those required for conventional
 breeding, will be critical to evaluating the value and pleiotropic effects
 of GA-modifying genes.
description: Lu_poplar GA raw
 data
DOI: 10.5061/dryad.f94f2
title: Data from: A new species of Peckoltia from the Upper Orinoco (Siluriformes: Loricariidae)

description: A new species of the suckermouth armored catfish genus Peckoltia is
 described from the lower Ventuari River, a tributary of the upper Orinoco
 River in Amazonas State, Venezuela. Specimens of this species were
 formerly included in the wide-ranging Amazonian species P. vittata, but a
 recent molecular phylogeny found Orinoco individuals to be distantly
 related to Amazon Basin individuals spanning the range of P. vittata
 syntypes. Detailed morphological examination confirmed distinctiveness of
 Orinoco specimens, and found them to be diagnosable from true P. vittata
 by having generally greater than 25 teeth (vs. less), spots on the nape
 (vs. nape lacking spots), the upper lip with two to three black bar-shaped
 markings in a line like a moustache (vs. lips generally with a hyaline
 wash), and by the snout having a medial black line disconnected from the
 moustache markings (vs. medial snout stripe connected to a bar just above
 the lip). Peckoltia wernekei displays remarkable genetic similarity to its
 sister species, P. lujani, but differs morphologically by having dentary
 tooth rows meet at an angle less than 90° (vs. &gt;90°), by having
 large faint blotches on the abdomen (vs. abdomen with no blotches), by a
 smaller internares width (21.2–26.6% vs. 28.5–46.5% of interorbital
 width), and a larger dorsal spine (148.1–178.6% vs. 80.1–134.5% of
 abdominal length).
description: Peckoltia
 MorphometricsMorphometrics for all
 species examined of PeckoltiaPeckoltia
 2015.xls
DOI: 10.5061/dryad.f5c60
title: Data from: Molecular data and ecological niche modeling reveal population dynamics of widespread shrub Forsythia suspensa (Oleaceae) in China’s warm-temperate zone in response to climate change during the Pleistocene

description: Background: Despite its high number of endemic deciduous broad-leaved
 species in China’s warm-temperate zone, far less attention has been paid
 to phylogeographic studies in this region. In this work, the
 phylogeographic history of Forsythia suspensa endemic to China’s
 warm-temperate zone was investigated to explore the effect of climate
 change during the Pleistocene on the distribution of this deciduous
 broad-leaved species in China. Results: The cpDNA data revealed seven
 phylogeographical groups corresponding to geographical regions. By
 contrast, the nrDNA data supported the samples clustered into three
 groups, which was inconsistent with separate geographical regions
 supported by cpDNA data. Ecological niche modeling showed that the
 climatically suitable area during the cold period was larger than that
 during the warm period. Conclusions: Both molecular data and ecological
 niche modeling indicated that F. suspensa expanded to nearby low-elevation
 plains in the glacial periods, and retreated to mountaintops during
 interglacial warmer stages. This study thus supported that F. suspensa
 persisted in situ during the glacial of the Pleistocene with enlarged
 distribution area, contrary to the hypothesis of long distance southward
 migration or large-scale range contraction.
description: 7 trnL-F chlorotype
 sequencesC1.txt11 psbA-trnH chlorotype sequencesC2.txt74 ribotype sequencesR.txtGeographic characteristics of 50 F. suspensa presence points used in this studyAdditional file 3.pdfNuclear DNA sequence polymorphisms detected in internal transcribed spacer (ITS) regions of F. suspensa identifying seventy-four ribotypes (R1–R74)Additional file 2.pdfChloroplast DNA sequence polymorphisms detected in two intergenic spacer (IGS) regions of F. suspensa identifying thirteen chlorotypes (C1–C13)Additional file 1.pdf
DOI: 10.5061/dryad.3b15s
title: Data from: Landscape variation in tree regeneration and snag fall drive fuel loads in 25-yr old post-fire lodgepole pine forests

description: Escalating wildfire in subalpine forests with stand-replacing fire regimes
 is increasing the extent of early-seral forests throughout the western US.
 Post-fire succession generates the fuel for future fires, but little is
 known about fuel loads and their variability in young post-fire stands. We
 sampled fuel profiles in 24-year-old post-fire lodgepole pine (Pinus
 contorta var. latifolia) stands (n=82) that regenerated from the 1988
 Yellowstone Fires to answer three questions. (1) How do canopy and surface
 fuel loads vary within and among young lodgepole pine stands? (2) How do
 canopy and surface fuels vary with pre- and post-fire lodgepole pine stand
 structure and environmental conditions? (3) How have surface fuels changed
 between 8 and 24 years post-fire? Fuel complexes varied tremendously
 across the landscape despite having regenerated from the same fires.
 Available canopy fuel loads and canopy bulk density averaged 8.5 Mg ha-1
 [range 0.0-46.6] and 0.24 kg m3 [range: 0.0-2.3], respectively, meeting or
 exceeding levels in mature lodgepole pine forests. Total surface-fuel
 loads averaged 123 Mg ha-1 [range: 43 - 207], and 88% was in the 1000-hr
 fuel class. Litter, 1-hr, and 10-hr surface fuel loads were lower than
 reported for mature lodgepole pine forests, and 1000-hr fuel loads were
 similar or greater. Among-plot variation was greater in canopy fuels than
 surface fuels, and within-plot variation was greater than among-plot
 variation for nearly all fuels. Post-fire lodgepole pine density was the
 strongest positive predictor of canopy and fine surface fuel loads.
 Pre-fire successional stage was the best predictor of 100-hr and 1000-hr
 fuel loads in the post-fire stands and strongly influenced the size and
 proportion of sound logs (greater when late successional stands had
 burned) and rotten logs (greater when early successional stands had
 burned). Our data suggest that 76% of the young post-fire lodgepole pine
 forests have 1000-hr fuel loads that exceed levels associated with
 high-severity surface fire potential, and 63% exceed levels associated
 with active crown fire potential. Fire rotations in Yellowstone National
 Park are predicted to shorten to a few decades and this prediction cannot
 be ruled out by a lack of fuels to carry repeated fires.
description: Stand structure and
 live/dead biomass in 24 year old lodgepole pine forestsIncludes: stand
 structure, derived topographic and environmental variables, live and dead
 forest fuels, 83 plots collected across the 1988 wildfire footprint within
 Yellowstone National Park. Full metadata available in the readme
 file.FUEL_DATA_NELSONETAL_ECOAPPS_2016.xlsx
DOI: 10.5061/dryad.77bt2
title: Data from: Multiple global radiations in tadpole shrimps challenge the concept of ‘living fossils’

description: ‘Living fossils’, a phrase first coined by Darwin, are defined as species
 with limited recent diversification and high morphological stasis over
 long periods of evolutionary time. Morphological stasis, however, can
 potentially lead to diversification rates being underestimated.
 Notostraca, or tadpole shrimps, are an ancient, globally distributed order
 of branchiopod crustaceans regarded as ‘living fossils’ because their rich
 fossil record dates back to the early Devonian and their morphology is
 highly conserved. Recent phylogenetic reconstructions have shown a strong
 biogeographic signal, suggesting diversification due to continental
 breakup, and widespread cryptic speciation. However, morphological
 conservatism makes it difficult to place fossil taxa in a phylogenetic
 context. Here we reveal for the first time the timing and tempo of tadpole
 shrimp diversification by inferring a robust multilocus phylogeny of
 Branchiopoda and applying Bayesian divergence dating techniques using
 reliable fossil calibrations external to Notostraca. Our results suggest
 at least two bouts of global radiation in Notostraca, one of them recent,
 so questioning the validity of the ‘living fossils’ concept in groups
 where cryptic speciation is widespread.
description: Supermatrix
 alignmentSupermatrix alignment of
 7 genes as used for phylogenetic and divergence time analysis. Please see
 readme file for details of gene partitions.Branchiopoda_Art_and_Strep_OG_Muscle_no_introns.fasBEAST xml file for divergence time analysisThis is the BEAST xml file used to run the divergence time analysis.Run_with_data_1.xml
DOI: 10.5061/dryad.15d2p
title: Data from: Urbanization drives the evolution of parallel clines in plant populations

description: Urban ecosystems are an increasingly dominant feature of terrestrial
 landscapes. While evidence that species can adapt to urban environments is
 accumulating, the mechanisms through which urbanization imposes natural
 selection on populations are poorly understood. The identification of
 adaptive phenotypic changes (i.e. clines) along urbanization gradients
 would facilitate our understanding of the selective factors driving
 adaptation in cities. Here, we test for phenotypic clines in urban
 ecosystems by sampling the frequency of a Mendelian-inherited
 trait—cyanogenesis—in white clover (Trifolium repens L.) populations along
 urbanization gradients in four cities. Cyanogenesis protects plants from
 herbivores, but reduces tolerance to freezing temperatures. We found that
 the frequency of cyanogenic plants within populations decreased towards
 the urban centre in three of four cities. A field experiment indicated
 that spatial variation in herbivory is unlikely to explain these clines.
 Rather, colder minimum winter ground temperatures in urban areas compared
 with non-urban areas, caused by reduced snow cover in cities, may select
 against cyanogenesis. In the city with no cline, high snow cover might
 protect plants from freezing damage in the city centre. Our study suggests
 that populations are adapting to urbanization gradients, but regional
 climatic patterns may ultimately determine whether adaptation occurs.
description: Master ZIP File
 (Contains data, script, metadata)This ZIP folder contains
 all datasets associated with the publication (.csv format), metadata
 (.rtf), and R analysis script (.R). Descriptions of datasets are included
 in metadata.Thompson_et_al_DryadPackage.zip