cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.12j173m
title: Free‐living and symbiotic lifestyles of a thermotolerant coral endosymbiont display profoundly distinct transcriptomes under both stable and heat stress conditions

description: Reef-building corals depend upon a nutritional endosymbiosis with
 photosynthetic dinoflagellates of the family Symbiodiniaceae for the
 majority of their energetic needs. While this mutualistic relationship is
 impacted by numerous stressors, warming oceans are a predominant threat to
 coral reefs, placing the future of the world’s reefs in peril. Some
 Symbiodiniaceae species exhibit tolerance to thermal stress, but the in
 hospite symbiont response to thermal stress is underexplored. To describe
 the underpinnings of symbiosis and heat stress response, we compared in
 hospite and free-living transcriptomes of Durusdinium trenchii, a
 pan-tropical heat-tolerant Symbiodiniaceae species, under stable
 temperature conditions and acute hyperthermal stress. We discovered that
 symbiotic state was a larger driver of the transcriptional landscape than
 heat stress. The majority of differentially expressed transcripts between
 in hospite and free-living cells were downregulated, suggesting the in
 hospite condition is associated with the shutdown of numerous processes
 uniquely required for a free-living lifestyle. In the free-living state,
 we identified enrichment for numerous cell signaling pathways and other
 functions related to detecting and responding to a changing environment,
 as well as transcripts relating to mitosis, meiosis, and motility. In
 contrast, in hospite cells exhibited enhanced transcriptional activity for
 photosynthesis and carbohydrate transport as well as chromatin
 modifications and a disrupted circadian clock. Hyperthermal stress induced
 drastic alteration of transcriptional activity in hospite, suggesting
 symbiotic engagement with the host elicited an exacerbated stress response
 when compared to free-living D. trenchii. Altogether, the dramatic
 differences in gene expression between in hospite and free-living D.
 trenchii indicate the importance of considering symbiotic state in
 investigations of symbiosis and hyperthermal stress in Symbiodiniaceae.
description: Dtrenchii_rnaseq_assembly_v1.0This is a de novo transcriptome assembly of <i>Durusdinium trenchii</i> from 15 Illumina libraries sequenced across two Illumina HiSeq lanes, using v4 150 base pair paired-end chemistry. The assembly was performed using Trinity and filtered for non-Symbiodiniaceae transcripts.
DOI: 10.5061/dryad.50557nm
title: Breaking ecological barriers: anthropogenic disturbance leads to habitat transitions, hybridization, and high genetic diversity

description: Genetic diversity is expected to erode in disturbed habitats through
 strong selection, local extinctions, and recolonization associated with
 genetic bottlenecks and restricted gene flow. Despite this general
 prediction and over three decades of population genetics studies, our
 understanding of the long-term effect of environmental disturbance on
 local and regional genetic diversity remains limited. We conducted a
 population genetic survey of the microcrustacean Daphnia across a
 landscape subject to anthropogenic stressors from a century of industrial
 mining. At the local scale we found moderate genetic diversity (i.e., low
 clonal diversity), characteristic of habitat-specific selective sweeps and
 local extinctions, but high diversity and strong genetic structure at the
 regional scale despite the shared watershed of many lakes and exceptional
 dispersal ability of daphniids. Many habitats experienced changes in
 species assemblages, with the obligate asexual Daphnia pulex
 lineages—known only to inhabit ponds—dominating disrupted urban lakes.
 This habitat transition (pond to lake) was likely facilitated by the
 disruption of ecological barriers maintaining the genomic separation of
 these young species. Thus, disrupted habitats can exhibit complex and
 unexpected genetic patterns of local extinctions and recolonizations,
 followed by habitat transitions, hybridization and potential speciation
 events that are difficult to predict and should not be underestimated.
description: Microsatellite
 datasetMicrosatellite dataset
 (15 loci; genepop format) for <i>Daphnia</i> populations from
 Sudbury. Additional 'supplemental' populations are included (see
 text).Microsatellite_dataset.gen
DOI: 10.5061/dryad.b0r170c
title: Data from: Assexon: assembling exon using gene capture data

description: Exon capture across species has been one of the most broadly applied
 approaches to acquire multi-locus data in phylogenomic studies of
 non-model organisms. Methods for assembling loci from short-read sequences
 (eg, Illumina platforms) that rely on mapping reads to a reference genome
 may not be suitable for studies comprising species across a wide
 phylogenetic spectrum; thus, de novo assembling methods are more generally
 applied. Current approaches for assembling targeted exons from short reads
 are not particularly optimized as they cannot (1) assemble loci with low
 read depth, (2) handle large files efficiently, and (3) reliably address
 issues with paralogs. Thus, we present Assexon: a streamlined pipeline
 that de novo assembles targeted exons and their flanking sequences from
 raw reads. We tested our method using reads from Lepisosteus osseus
 (4.37 Gb) and Boleophthalmus pectinirostris (2.43 Gb), which are captured
 using baits that were designed based on genome sequence of Lepisosteus
 oculatus and Oreochromis niloticus, respectively. We compared performance
 of Assexon to PHYLUCE and HybPiper, which are commonly used pipelines to
 assemble ultra-conserved element (UCE) and Hyb-seq data. A custom exon
 capture analysis pipeline (CP) developed by Yuan et al was compared as
 well. Assexon accurately assembled more than 3400 to 3800 (20%-28%) loci
 than PHYLUCE and more than 1900 to 2300 (8%-14%) loci than HybPiper across
 different levels of phylogenetic divergence. Assexon ran at least twice as
 fast as PHYLUCE and HybPiper. Number of loci assembled using CP was
 comparable with Assexon in both tests, while Assexon ran at least 7 times
 faster than CP. In addition, some steps of CP require the user’s
 interaction and are not fully automated, and this user time was not
 counted in our calculation. Both Assexon and CP retrieved no paralogs in
 the testing runs, but PHYLUCE and Hybpiper did. In conclusion, Assexon is
 a tool for accurate and efficient assembling of large read sets from exon
 capture experiments. Furthermore, Assexon includes scripts to filter
 poorly aligned coding regions and flanking regions, calculate summary
 statistics of loci, and select loci with reliable phylogenetic signal.
 Assexon is available at https://github.com/yhadevol/Assexon.
description: Supplementary file
 2-5A
 package comprising Supplementary file 2-5.Supplementary2-5.zip
DOI: 10.5061/dryad.tr87dh0
title: Data from: Adapterama III: quadruple-indexed, double/triple-enzyme RADseq libraries (2RAD/3RAD)

description: Molecular ecologists frequently use genome reduction strategies that rely
 upon restriction enzyme digestion of genomic DNA to sample consistent
 portions of the genome from many individuals (e.g., RADseq, GBS). However,
 researchers often find the existing methods expensive to initiate and/or
 difficult to implement consistently, especially due to the inability to
 highly-multiplex samples to fill entire sequencing lanes. Here, we
 introduce a low-cost and highly robust approach for the construction of
 dual-digest RADseq libraries that relies on adapters and primers designed
 in Adapterama I. Major features of our method include: 1) minimizing the
 number of processing steps; 2) focusing on a single strand of sample DNA
 for library construction, allowing the use of a non-phosphorylated adapter
 on one end; 3) ligating adapters in the presence of active restriction
 enzymes, thereby reducing chimeras; 4) including an optional third
 restriction enzyme to cut apart adapter-dimers formed by the
 phosphorylated adapter, thus increasing the efficiency of adapter ligation
 to sample DNA, which is particularly effective when only low
 quantity/quality DNA samples are available; 5) interchangeable adapter
 designs; 6) incorporating variable-length internal indexes within the
 adapters to increase the scope of sample indexing, facilitate pooling, and
 increase sequence diversity; 7) maintaining compatibility with universal
 dual-indexed primers and thus, Illumina sequencing reagents and libraries;
 and, 8) easy modification for the identification of PCR duplicates. We
 present eight adapter designs that work with 72 restriction enzyme
 combinations. We demonstrate the efficiency of our approach by comparing
 it with existing methods, and we validate its utility through the
 discovery of many variable loci in a variety of non-model organisms. Our
 2RAD/3RAD method is easy to perform, has low startup costs, produces
 libraries that can be highly-multiplexed and pooled with other Illumina
 libraries, and 3RAD has increased utility with low-concentration input
 DNA.
description: Ki_ssp_Commands_and_OutputCommand-line code (e.g., ipyrad, Stacks) and selected output for Ki_ssp and St_de.Ticks_ssp_Commands_and_OutputCommand-line code (e.g., Stacks) and select output for Ticks_spp and Am_am example.Eu_bi_Commands_and_OutputCommand-line code (e.g., Stacks) and select output for Eu_bi example.Wi_sp_Commands_and_OutputCommand-line code (e.g., Stacks) and select output for Wi_sp example.Rh_pa_Commands_and_OutputCommand-line code (e.g., Stacks) and select output for Rh_pa example.Ga_af_Commands_and_OutputCommand-line code (e.g., Stacks) and select output for Ga_af example.Sp_ti_Commands_and_OutputCommand-line code (e.g., Stacks) and select output for Sp_ti example.Sp_le_Commands_and_OutputCommand-line code (e.g., Stacks) and select output for Sp_le example.
DOI: 10.5061/dryad.g884q70
title: Data from: Microbial and volatile profiling of soils suppressive to Fusarium culmorum of wheat

description: In disease-suppressive soils, microbiota protect plants from root
 infections. Bacterial members of this microbiota have been shown to
 produce specific molecules that mediate this phenotype. To date, however,
 studies have focused on individual suppressive soils and the degree of
 natural variability of soil suppressiveness remains unclear. Here, we
 screened a large collection of field soils for suppressiveness to Fusarium
 culmorum using wheat (Triticum aestivum) as a model host plant. A high
 variation of disease suppressiveness was observed, with 14% showing a
 clear suppressive phenotype. The microbiological basis of suppressiveness
 to F. culmorum was confirmed by gamma sterilization and soil
 transplantation. Amplicon sequencing revealed diverse bacterial taxonomic
 compositions and no specific taxa were found exclusively enriched in all
 suppressive soils. Nonetheless, co-occurrence network analysis revealed
 that two suppressive soils shared an overrepresented bacterial guild
 dominated by various Acidobacteria. In addition, our study revealed that
 volatile emission may contribute to suppression, but not for all
 suppressive soils. Our study raises new questions regarding the possible
 mechanistic variability of disease-suppressive phenotypes across
 physico-chemically different soils. Accordingly, we anticipate that
 larger-scale soil profiling, along with functional studies, will enable a
 deeper understanding of disease-suppressive microbiomes.
description: Ossowicki&Tracanna 16S amplicon data, part 1 Raw FASTQ files of 16S amplicon data. Part 1 of 2-part tarball. Join the two parts using 'cat' before extracting. Ossowicki_Tracanna_16S_amplicon_data.tar.gz.part_aa Ossowicki&Tracanna 16S amplicon data, part 2 Raw FASTQ files of 16S amplicon data. Part 1 of 2-part tarball. Join the two parts using 'cat' before extracting. Ossowicki_Tracanna_16S_amplicon_data.tar.gz.part_ab
DOI: 10.5061/dryad.40qc27m
title: Data from: The early elasmobranch Phoebodus: phylogenetic relationships, ecomorphology, and a new time-scale for shark evolution

description: Anatomical knowledge of early chondrichthyans and estimates of their
 phylogeny are improving, but many taxa are still known only from
 microremains. The nearly cosmopolitan and regionally abundant Devonian
 genus Phoebodus has long been known solely from isolated teeth and fin
 spines. Here, we report the first skeletal remains of Phoebodus from the
 Famennian (Late Devonian) of the Maïder region of Morocco, revealing an
 anguilliform body, specialized braincase, hyoid arch, elongate jaws and
 rostrum, complementing its characteristic dentition and ctenacanth fin
 spines preceding both dorsal fins. Several of these features corroborate a
 likely close relationship with the Carboniferous species Thrinacodus
 gracia, and phylogenetic analysis places both taxa securely as members of
 the elasmobranch stem lineage. Identified as such, phoebodont teeth
 provide a plausible marker for range extension of the elasmobranchs into
 the Middle Devonian, thus providing a new minimum date for the origin of
 the chondrichthyan crown-group. Among pre-Carboniferous jawed vertebrates,
 the anguilliform body shape of Phoebodus is unprecedented, and its
 specialized anatomy is, in several respects, most easily compared with the
 modern frilled shark Chlamydoselachus. These results add greatly to the
 morphological, and by implication ecological, disparity of the earliest
 elasmobranchs.
description: PLY-files of all single
 elements of Phoebodus saidselachusHere, we provide
 PLY-files of the endocast, braincase, endolymphatic recess,
 glossopharyngeal recess, branchial elements, ceratohyals,
 ceratobranchials, epibranchials, hyoid arches, palatoquadrate,
 pharyngobranchial, Meckel's cartilage, and the notochord as well as
 other small elements visible in specimen PIMUZ A/I 4711 of the Famennian
 (Late Devonian) chondrichthyan Phoebodus saidselachus. The specimen was
 found at Madene El Mrakib near Tafraoute in the eastern
 Anti-Atlas.PLYforReconstruction.zipPhoebodus2_1Nov17_01Original TIFF-image stack of the main specimen of Phoebodus saidselachus.Nexus fileThis file was used for our phylogenetic analyses.Phoebo7.nex
DOI: 10.5061/dryad.c4798q5
title: Inhibition of Cdc42 activity extends lifespan and decreases circulating inflammatory cytokines in aged female C57BL/6 mice

description: Cdc42 is a small RhoGTPase regulating multiple functions in eukaryotic
 cells. The activity of Cdc42 is significantly elevated in several tissues
 of aged mice, while the Cdc42 gain-of-activity mouse model presents with a
 pre-mature aging-like phenotype and with decreased lifespan. These data
 suggest a causal connection between elevated activity of Cdc42, aging and
 reduced lifespan. Here, we demonstrate that systemic treatment of aged
 (75-week old) female C57BL/6 mice with a Cdc42 activity specific inhibitor
 (CASIN) for 4 consecutive days significantly extends average and maximum
 lifespan. Moreover, aged CASIN-treated animals displayed a youthful level
 of the aging-associated cytokines IL-1b, IL-1a and INFg in serum and a
 significantly younger epigenetic clock as based on DNA methylation levels
 in blood cells.  Overall, our data show that systemic
 administration of CASIN to reduce Cdc42 activity in aged mice extends
 murine lifespan.
description: Fig. S1
 Raw data related
 to graphs in supplementary fig. 1c-k. Data refer to: (<b>c)
 </b>Weight in grams of the mice included in the lifespan study.
 (<b>d-e</b>) White blood cell (WBC) count (1000 cells/µl of
 blood) and red blood cell (RBC) count ( million of cells/µl).
 (<b>f-h</b>) Flow cytometry analysis of PB from mice of the
 lifespan study. Data are plotted as percentage of B220+, Cd3+ and Gr1+,
 Mac1+ and Gr1+Mac1+ cells among all white blood cells (WBCs).
 (<b>i-k</b>) Lymphocytes (Ly), Neutrophils (NE) and Monocyte
 (Mo) cell count.   
 Fig. S2
 Cytokine array
 dataset. Data represent serum cytokine amount per mouse in
 pg/ml.   
 Fig. 1
 Raw data related
 to graphs displayed in figure 1.
DOI: 10.5061/dryad.1tm8705
title: Data from: To remain or leave: dispersal variation and its genetic consequences in benthic freshwater invertebrates

description: Variation in dispersal capacity may influence population genetic variation
 and relatedness of freshwater animals and hence provide insights on
 patterns and processes that influence biodiversity. The majority of
 studies addressing this issue have focused on dispersal variation in in
 fish inhabiting riverine systems whose dendritic nature and
 upstream/downstream gradients facilitate characterizing populations along
 networks. We undertook extensive, large-scale investigations of two
 freshwater bryozoans species whose dispersive propagules (statoblasts) are
 either attached to surfaces (Fredericella sultana) or are released as
 buoyant stages (Cristatella mucedo). Characterizing population genetic
 structure in multiple sites within each of three (or four) UK regions
 enabled us to test hypotheses regarding how dispersal variation and
 hydrological connectivity impact genetic variation in colonial freshwater
 invertebrates that primarily inhabit lotic (F. sultana) or lentic (C.
 mucedo) habitats. We found that hydrological connectivity enhanced genetic
 diversity and gene flow in and amongst C. mucedo populations but not in F.
 sultana. Higher overall measures of clonal diversity and greater genetic
 divergence suggest accumulation of genetic variation over time within F.
 sultana populations – perhaps reflecting constraints of releasing
 propagules that might eventually be swept to sea. Our study provides more
 nuanced views about drivers of population genetic structures in freshwater
 invertebrates and illustrates how a range of demographic and evolutionary
 processes reflect life history attributes. Growing evidence that genetic
 divergence may commonly characterise populations of a diversity of
 riverine taxa highlights how organisms inhabiting lotic systems may be
 particularly challenged by environmental change.
description: Genotype datafiles for
 the manuscript "To remain or leave: dispersal variation and its
 genetic consequences in benthic freshwater invertebrates", Ruggeri
 Paolo, Pasternack Ellen, Okamura BethThe Excel file contains
 two folders with monoclone multilocus genotypes per individual at the 10
 microsatellite loci typed. The first column indicates the sample ID. Names
 in the first row are referring to the names of the microsatellite loci
 here used. The last folder contains a summary of general infomation
 concerning the localities associated with the samples ID in the folders C.
 mucedo and F. sultana.Dryad_CrisFred.xlsx
DOI: 10.5061/dryad.1cn681t
title: Data from: How do predators generalize warning signals in simple and complex prey communities? Insights from a videogame

description: The persistence of distinct warning signals within and between sympatric
 mimetic communities is a puzzling evolutionary question because selection
 favours convergence of colour patterns among toxic species. Such
 convergence is partly shaped by predators’ reaction to similar but not
 identical stimulus, i.e. generalization behaviour. And generalisation by
 predators is likely to be shaped by the diversity of local prey.
  However, studying generalization behaviour is generally limited
 to simple variations of prey colour patterns. Here, we used a computer
 game played by humans as surrogate predators to investigate generalization
 behaviours on simple (4 morphs) and complex (10 morphs) communities of
 unprofitable (associated with a penalty) and profitable butterflies.
 Colour patterns used in the game are observed in the natural populations
 of unprofitable butterfly species such as Heliconius numata. Analyses of
 449 game participants’ behaviours show that players avoided unprofitable
 prey more readily in simple than in complex communities. However,
 generalization was observed only in players that faced complex
 communities, enhancing the protection of profitable prey that looked
 similar to at least one unprofitable morph. Additionally, similarity among
 unprofitable prey also reduced attack rates only in complex communities.
 These results are consistent with previous studies using avian predators
 but artificial colour patterns and suggest that mimicry is more likely to
 evolve in complex communities where increases in similarity are more
 likely to be advantageous.
description: AriasetalDataDescription Data from experiment in the first sheet and description of variables in the second sheet.
DOI: 10.5061/dryad.fr8pm0n
title: Data from: Modified antibiotic adjuvant ratios can slow and steer the evolution of resistance: Co-amoxiclav as a case study

description: As antibiotic resistance spreads, developing sustainable methods to
 restore the efficacy of existing antibiotics is increasingly important.
 One widespread method is to combine antibiotics with synergistically
 acting adjuvants that inhibit resistance mechanisms, allowing drug
 killing. Here we use co-amoxiclav (a clinically important combination of
 the -lactam antibiotic amoxicillin and the -lactamase inhibitor
 clavulanate) to ask whether treatment efficacy and resistance evolution
 can be decoupled via component dosing modifications. A simple mathematical
 model predicts that different ratios of these two drug components can
 produce distinct evolutionary responses irrespective of initial efficacy.
 We test this hypothesis by selecting Escherichia coli with a plasmid
 encoded -lactamase (CTX-M-14), against different compositions of
 amoxicillin and clavulanate. Consistent with our theory, we found that
 while resistance evolved under all conditions, the component ratio
 influenced both the rate and mechanism of resistance evolution.
 Specifically, we found that the current clinical practice of high
 amoxicillin to clavulanate ratios resulted in the most rapid adaptation to
 antibiotics via gene dosing responses. Increased plasmid copy number
 allowed E. coli to increase -lactamase dosing and effectively titrate out
 low quantities of clavulanate, restoring amoxicillin resistance. In
 contrast, high clavulanate ratios were more robust - plasmid copy number
 did not increase, although porin or efflux resistance mechanisms were
 found, as in all drug ratios. Our results indicate that by changing the
 ratio of adjuvant to antibiotic we can slow and steer the path of
 resistance evolution. We therefore suggest using increased adjuvant dosing
 regimens to slow the rate of resistance evolution.
description: Data_Files for
 "Modified Antibiotic Adjuvant Ratios Can Slow and Steer the Evolution
 of Resistance: Co-amoxiclav as a Case Study"All data files required
 to produce statistics and analysis for the paper.Data_Files.zip