cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.4g503
title: Data from: Using long-term experimental evolution to uncover the patterns and determinants of molecular evolution of an Escherichia coli natural isolate in the streptomycin treated mouse gut

description: Though microbial ecology of the gut is now a major focus of interest,
 little is known about the molecular determinants of microbial adaptation
 in the gut. Experimental evolution coupled with whole genome sequencing
 can provide insights of the adaptive process. In vitro experiments have
 revealed some conserved patterns: intermediate convergence, epistatic
 interactions between beneficial mutations and mutations in global
 regulators. To test the relevance of these patterns and to identify the
 selective pressures acting in vivo, we have performed a long-term
 adaptation of an E. coli natural isolate, the streptomycin resistant
 strain 536, in the digestive tract of streptomycin treated mice. After a
 year of evolution, a clone from 15 replicates was sequenced. Consistently
 with in vitro observations, the identified mutations revealed a strong
 pattern of convergence at the mutation, gene, operon and functional
 levels. Yet, the rate of molecular evolution was lower than in in vitro
 and no mutations in global regulators were recovered. More specific
 targets were observed: the dgo operon, involved in the galactonate pathway
 that improved growth on D-galactonate, and rluD and gidB, implicated in
 the maturation of the ribosomes, which mutations improved growth only in
 the presence of streptomycin. As in vitro, the non-random associations of
 mutations within the same pathways suggested a role of epistasis in
 shaping the adaptive landscape. Overall, we show that “evolve and
 sequence” approach coupled to an analysis of convergence, when applied to
 a natural isolate, can be used to study adaptation in vivo and uncover the
 specific selective pressures of that environment.
description: data of figure
 1Quantification of E.
 coli 536 in the feces in each mouse along the
 experimentDfquant.txtdata of figure 4The results of flux cytometry are presented in this tabledataCMF.txtdata of figure 5The data used to produce the box plots of the figure 5 are presented in this tableCC536Galmix14.txtdata of figure 6The data used to produce the figure 6 are presented in this tableCC536MutATB1214mix.txt
DOI: 10.5061/dryad.j1c4t
title: Data from: The Trojan Female Technique for pest control: a candidate mitochondrial mutation confers low male fertility across diverse nuclear backgrounds in Drosophila melanogaster

description: Pest species represent a major ongoing threat to global biodiversity.
 Effective management approaches are required that regulate pest numbers,
 while minimizing collateral damage to nontarget species. The Trojan Female
 Technique (TFT) was recently proposed as a prospective approach to
 biological pest control. The TFT draws on the evolutionary hypothesis that
 maternally inherited mitochondrial genomes are prone to the accumulation
 of male, but not female, harming mutations. These mutations could be
 harnessed to provide trans-generational fertility-based control of pest
 species. A candidate TFT mutation was recently described in the fruit fly,
 Drosophila melanogaster, which confers male-only sterility in the specific
 isogenic nuclear background in which it is maintained. However,
 applicability of the TFT relies on mitochondrial mutations whose
 male-sterilizing effects are general across nuclear genomic contexts. We
 test this assumption, expressing the candidate TFT-mutation bearing
 haplotype alongside a range of nuclear backgrounds and comparing its
 fertility in males, relative to that of control haplotypes. We document
 consistently lower fertility for males harbouring the TFT mutation, in
 both competitive and noncompetitive mating contexts, across all nuclear
 backgrounds screened. This indicates that TFT mutations conferring reduced
 male fertility can segregate within populations and could be harnessed to
 facilitate this novel form of pest control.
description: Data associated with
 Dowling et al, The Trojan Female Technique for pest
 control:All the column headers
 are self explanatory. mtDNA is the mtDNA haplotype, and paternal line is
 the strain to which females of each mtDNA line were crossed. In the
 competitive assays, the response variable is a binomial vector comprising
 the number of offspring sired by the focal male, and the number sired by
 the tester male. The column 'wild type offspring' denotes those
 offspring sired by the focal males, and the column 'brown eye
 offspring' denotes those offspring sired by the tester males. In the
 non-competitive assays, the column "total offspring" denotes the
 reproductive success of the focal males.Dowling et al TFT data
 files.xlsx
DOI: 10.5061/dryad.cd7467n6
title: Data from: Genetic and maternal effects on tail spine and body length in the invasive spiny water flea (Bythotrephes longimanus)

description: Interest in the evolution of invasive species has grown in recent years,
 yet few studies have investigated sources of variation in invasive species
 traits experiencing natural selection. The spiny water flea, Bythotrephes
 longimanus, is an invasive zooplankton in the Great Lakes that exhibits
 seasonal changes in tail spine and body length consistent with natural
 selection. Evolution of Bythotrephes traits, however, depends on the
 presence and magnitude of quantitative genetic variation, which could
 change within or across years. Clonal analysis of wild-captured
 Bythotrephes indicated that variance components for distal spine length
 were variable among but not within years. Spine length was always
 heritable but was not always influenced by maternal effects. In contrast,
 variance components for body length varied both within and among years,
 but likewise body length was always heritable and not always influenced by
 maternal effects. Results indicate that important Bythotrephes traits have
 heritable variation comparable to native species and other invasive
 species that would enable an evolutionary response to natural selection.
 This evolutionary capacity could contribute to the widespread success and
 dramatic effects of Bythotrephes invasion in systems with diverse biotic
 and abiotic conditions.
description: Miehls et al. Evol Appl
 DataThe Miehls et al. Evol
 Appl Data.csv file contains the data used to quantify genetic, maternal,
 and environmental variation in distal spine and body length of
 Bythotrephes longimanus (the spiny water flea) in Lake Michigan (USA).
 Each row in the spreadsheet includes field and laboratory information
 (including clonal line relationships and trait measurements) for a single
 F2 Bythotrephes born in our laboratory clonal lines. All analyses were
 completed using data from F2 individuals.
DOI: 10.5061/dryad.b1m1h
title: Data from: Direct and indirect effects of native range expansion on soil microbial community structure and function

description: Analogous to the spread of non-native species, shifts in native species’
 ranges resulting from climate and land use change are also creating new
 combinations of species in many ecosystems. These native range shifts may
 be facilitated by similar mechanisms that provide advantages for
 non-native species and may also have comparable impacts on the ecosystems
 they invade. Soil biota, in particular bacteria and fungi, are important
 regulators of plant community composition and below-ground ecosystem
 function. Compared to non-native plant invasions, there have been
 relatively few studies examining how soil biota influence – or are
 influenced by – native species range shifts. Here, we examined how a
 native range-expanding sagebrush species (Artemisia rothrockii) affects
 below-ground abiotic conditions and microbial community structure and
 function using next-generation sequencing coupled with other biotic and
 abiotic soil analyses. We utilized a range-expansion gradient, together
 with a shrub removal experiment and structural equation models, to
 determine the direct and indirect drivers of these interconnected
 processes. Sagebrush colonization increased bacterial and archaeal
 richness and diversity and altered community composition across the
 expansion gradient. Soil organic C and N and soil moisture increased with
 sagebrush presence; however, results varied across the expansion gradient.
 We found no relationship between sagebrush and soil pH; however, pH
 strongly influenced microbial richness and diversity. Microbial
 (substrate-induced) respiration was influenced by soil organic N, as well
 as microbial diversity and functional group relative abundances,
 highlighting direct and indirect effects of sagebrush on microbial
 community structure and function. Microbial community composition of soils
 after 4 years of sagebrush removal was more similar to communities in
 shrub interspaces than underneath shrubs, suggesting microbial community
 resilience. Synthesis. Our results suggest that native range expansions
 can have important impacts on soil biological communities, soil chemistry
 and hydrology which can further impact below-ground ecosystem processes
 such as nutrient cycling and litter decomposition. The combination of
 high-throughput sequencing and structural equation modelling used here
 offers an exciting yet underutilized approach to understanding how both
 native and non-native species’ range expansions may affect the structure
 and function of soil ecosystems.
description: Soil biotic and abiotic
 dataSIR, microbial biomass
 C, N, TOC,TON, pH, VWC.mappingfile_5_9_dryad.xlsxmycorrhizaeData_dryadAMF colonization (%)baseline C-N_dryadtotal (bulk) soil C, NSequence data16S alpha, beta diversity indices, and oligotrophic, copiotrophic group abundancesmicrobedata_dryad.csv
DOI: 10.5061/dryad.vf8d2
title: Data from: Asymmetric sensitivity of ecosystem carbon and water processes in response to precipitation change in a semi-arid steppe

description: Semi-arid ecosystems play an important role in regulating the dynamics of
 the global terrestrial CO2 sink. These dynamics are mainly driven by
 increasing inter-annual precipitation variability. However, how ecosystem
 carbon processes respond to changes in precipitation is not well
 understood, due to a lack of substantial experimental evidence that
 combines increased and decreased precipitation treatments. This study, a
 3-year field manipulation experiment with five precipitation levels
 conducted in a semi-arid steppe, examined the impacts of increased and
 decreased precipitation on ecosystem CO2 (GEP: gross ecosystem
 photosynthesis; ER: ecosystem respiration; NEE: net ecosystem CO2
 exchange), water exchange (ET: evapotranspiration), and resource use
 efficiency (CUE: carbon use efficiency; WUE: water use efficiency). We
 found that decreased precipitation reduced ecosystem CO2, water exchange
 and resource use efficiency significantly, while increased precipitation
 did not cause significant influence on them. That is, they responded more
 sensitively to decreased precipitation. Soil water availability was the
 most important driver determining changes in GEP, ER and ET. Changes in
 NEE, CUE and WUE were predominately regulated by soil temperature.
 Photosynthesis at leaf and ecosystem levels showed significantly greater
 sensitivity to changed precipitation than respiration and ET, and
 therefore determined the trends of net carbon uptake and resource use
 efficiency. This study highlighted an asymmetric response of ecosystem
 carbon and water processes to altered precipitation. This is potentially
 important for improving our understanding of how possible future changes
 in precipitation will affect the carbon cycle. Taking this asymmetric
 response into consideration will inevitably reduce uncertainties in
 predicting the dynamics of the global carbon cycle.
description: FE-2016-00613-sup-DataGross (GEP) and net (NEE) ecosystem photosynthesis, ecosystem respiration (ER), evapotranspiration (ET),carbon (CUE) and water (WUE) use efficiency, related abiotic and biotic factors under five precipitation levels in a semiarid steppe from 2012 to 2014.
DOI: 10.5061/dryad.2n0v8
title: Data from: Simplified models of the symmetric single-pass parallel-plate counterflow heat exchanger: a tutorial

description: The heat exchanger is important in practical thermal processes, especially
 those of (i) the molten-salt storage schemes, (ii) compressed air energy
 storage schemes, and (iii) other load-shifting thermal storage presumed to
 undergird a Smart Grid. Such devices, although central to the utilization
 of energy from sustainable (but intermittent) renewable sources, will be
 unfamiliar to many scientists, who nevertheless need a working knowledge
 of them. This tutorial paper provides a largely self-contained conceptual
 introduction for such persons. It begins by modelling a novel quantized
 exchanger , impractical as a device, but useful for comprehending the
 underlying thermophysics. It then reviews the one-dimensional steady-state
 idealization which demonstrates that effectiveness of heat transfer
 increases monotonically with (device length)/(device throughput). Next it
 presents a two-dimensional steady-state idealization for plug flow and
 from it derives a novel formula for effectiveness of transfer; this
 formula is then shown to agree well with a finite-difference time-domain
 (FDTD) solution of the two-dimensional idealization under Hagen-Poiseuille
 flow. These results are consistent with a conclusion that effectiveness of
 heat exchange can approach unity, but may involve unwelcome tradeoffs
 amongst device cost, size, and throughput.
description: FDS4dThis is the code, which
 we used to generate the blue points in Fig. 5INSTRUCTIONS -- Program
 FDS4d.mINSTRUCTIONS -- Program FDS4d.m
 -- revision 1.doc
DOI: 10.15468/dl.29cvqf
title: Occurrence Download

description: A dataset containing 169 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Galax urceolata",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 169 records from 35 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001138-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.49f83
title: Data from: A revision of the Leptogium saturninum group in North America

description: A revision of the North American members of the Leptogium saturninum group
 (i.e. species with long lower-surface hairs, isidia, and usually smooth
 upper surface) is presented based on molecular phylogenetic analyses of
 mtSSU and nrITS sequence data, together with an extensive morphological
 study. Three species supported by both molecular and morphological
 characteristics are recognized: L. acadiense sp. nov. (distinguished by
 granular saturninum-type isidia, medulla composed of irregularly arranged
 or perpendicular hyphae), L. cookii sp. nov. (distinguished by cylindrical
 saturninum-type isidia) and L. hirsutum (distinguished by hirsutum-type
 isidia and medulla composed of loosely intertwined hyphae). One species
 supported by morphological characteristics, but for which no molecular
 data could be generated, is also recognized: L. compactum sp. nov.
 (distinguished by hirsutum-type isidia and medulla composed of tightly
 packed hyphae). Finally, L. saturninum (distinguished by granular
 saturninum-type isidia and medulla composed of perpendicular and parallel
 hyphae) is supported by morphological characteristics but molecular data
 from geographically diverse populations, including those near the type
 locality, indicate that the morphologically defined species is
 paraphyletic. Leptogium burnetiae is excluded from North American based on
 morphological study of the type. The species are described and illustrated
 in detail, and are distinguished morphologically by their isidium
 development, morphology of mature isidia, and pattern of hyphae in the
 medulla in transverse sections near lobe margins. A key to the members of
 the L. saturninum group and related species is also presented.
description: data_packetThis is a datapacket that contains the input files for all analyses performed in this study as described in the publication. This includes input files for maximum parsimony, maximum likelihood and Bayesian inference analyses of mtSSU; maximum liklihood and Bayesian inference input files for a partitioned ITS dataset; and the distance table of computed ITS Jukes Cantor sequences distances calculated in PAUP.
DOI: 10.5061/dryad.63124
title: Data from: Rapid evolution of symbiont-mediated resistance compromises biological control of aphids by parasitoids

description: There is growing interest in biological control as a sustainable and
 environmentally friendly way to control pest insects. Aphids are among the
 most detrimental agricultural pests worldwide, and parasitoid wasps are
 frequently employed for their control. The use of asexual parasitoids may
 improve the effectiveness of biological control because only females kill
 hosts and because asexual populations have a higher growth rate than
 sexuals. However, asexuals may have a reduced capacity to track
 evolutionary change in their host populations. We used a factorial
 experiment to compare the ability of sexual and asexual populations of the
 parasitoid Lysiphlebus fabarum to control caged populations of black bean
 aphids (Aphis fabae) of high and low clonal diversity. The aphids came
 from a natural population, and one third of the aphid clones harbored
 Hamiltonella defensa, a heritable bacterial endosymbiont that increases
 resistance to parasitoids. We followed aphid and parasitoid population
 dynamics for three months but found no evidence that the reproductive mode
 of parasitoids affected their effectiveness as biocontrol agents,
 independent of host clonal diversity. Parasitoids failed to control aphids
 in most cases, because their introduction resulted in strong selection for
 clones protected by H. defensa. The increasingly resistant aphid
 populations escaped control by parasitoids and we even observed parasitoid
 extinctions in many cages. The rapid evolution of symbiont-conferred
 resistance in turn imposed selection on parasitoids. In cages where
 asexual parasitoids persisted until the end of the experiment, they became
 dominated by a single genotype able to overcome the protection provided by
 H. defensa. Thus there was evidence for parasitoid counteradaptation, but
 it was generally too slow for parasitoids to regain control over aphid
 populations. It appears that when pest aphids possess defensive symbionts,
 the presence of parasitoid genotypes able to overcome symbiont-conferred
 resistance is more important for biocontrol success than their
 reproductive mode.
description: DRYAD_aphid_and_parasitoid_densitiesSee README file.DRYAD_infection_matrixSee README file.DRYAD_genotype_frequenciesSee README file.
DOI: 10.5061/dryad.fh8b8
title: Data from: Structural diversity of naturally regenerating Chinese yew (Taxus wallichiana var. mairei) populations in an ex situ conservation

description: The Chinese yew (Taxus wallichiana var. mairei) is ranked among the first
 class of important wild endangered plants in China. However, due to its
 overexploitation, it now occurs scattered in the forest undergrowth along
 the Yangtze River Valley. To improve this tree’s conservation management,
 we used structural indices to investigate the structural diversity of
 naturally regenerating yew populations that have established via ex situ
 conservation. The results show that most yews had larger non-yew tree
 neighbors; these were 30–70% larger than their reference trees.
 Collectively, the average distances between the yews and the three
 nearest-neighboring trees were short (&lt;3 m). This result suggests
 that the yews likely face strong interspecific competition from neighbors.
 In these two forest stands, most of the pole-sized yews are found beneath
 a single tall neighboring tree (height ≥10 m), and their growth was
 enhanced under a single neighboring tree but not under two, three or zero
 neighboring trees. Finally, we recommend simple silvicultural treatments
 to reduce interspecific competition; specifically, the cutting or pruning
 of branches of large neighboring trees in tandem with the thinning of
 canopy trees growing next to the mother yews.
description: 20171212 Raw data of
 Chinese Yew ManuscriptThis file includes raw
 data concerning Chinese yews' structural diversity and regenerating
 plots of the manuscript entitled "Structural diversity of naturally
 regenerating Chinese yew (Taxus wallichiana var. mairei) populations in an
 ex situ conservation".
DOI: 10.5061/dryad.g8143
title: Data from: Differential impact of the dual CCR2/CCR5 inhibitor cenicriviroc on migration of monocyte and lymphocyte subsets in acute liver injury

description: A hallmark of acute hepatic injury is the recruitment of neutrophils,
 monocytes and lymphocytes, including natural killer (NK) or T cells,
 towards areas of inflammation. The recruitment of leukocytes from their
 reservoirs bone marrow or spleen into the liver is directed by chemokines
 such as CCL2 (for monocytes) and CCL5 (for lymphocytes). We herein
 elucidated the impact of chemokine receptor inhibition by the dual CCR2
 and CCR5 inhibitor cenicriviroc (CVC) on the composition of myeloid and
 lymphoid immune cell populations in acute liver injury. CVC treatment
 effectively inhibited the migration of bone marrow monocytes and splenic
 lymphocytes (NK, CD4 T-cells) towards CCL2 or CCL5 in vitro. When liver
 injury was induced by an intraperitoneal injection of carbon tetrachloride
 (CCl4) in mice, followed by repetitive oral application of CVC, flow
 cytometric and unbiased t-SNE analysis of intrahepatic leukocytes
 demonstrated that dual CCR2/CCR5 inhibition in vivo significantly
 decreased numbers of monocyte derived macrophages in acutely injured
 livers. CVC also reduced numbers of Kupffer cells (KC) or monocyte derived
 macrophages with a KC-like phenotype, respectively, after injury. In
 contrast to the inhibitory effects in vitro, CVC had no impact on the
 composition of hepatic lymphoid cell populations in vivo. Effective
 inhibition of monocyte recruitment was associated with reduced
 inflammatory macrophage markers and moderately ameliorated hepatic
 necroses at 36h after CCl4. In conclusion, dual CCR2/CCR5 inhibition
 primarily translates into reduced monocyte recruitment in acute liver
 injury in vivo, suggesting that this strategy will be effective in
 reducing inflammatory macrophages in conditions of liver disease.
description: PlosOne_supporting_information_filesNanoString gene analysis raw data files