cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.c5902
title: Data from: Multicellular group formation in response to predators in the alga Chlorella vulgaris

description: A key step in the evolution of multicellular organisms is the formation of
 cooperative multicellular groups. It has been suggested that predation
 pressure may promote multicellular group formation in some algae and
 bacteria, with cells forming groups to lower their chance of being eaten.
 We use the green alga Chlorella vulgaris and the protist Tetrahymena
 thermophila to test whether predation pressure can initiate the formation
 of colonies. We found that: (1) either predators or just predator
 exoproducts promote colony formation; (2) higher predator densities cause
 more colonies to form; and (3) colony formation in this system is
 facultative, with populations returning to being unicellular when the
 predation pressure is removed. These results provide empirical support for
 the hypothesis that predation pressure promotes multicellular group
 formation. The speed of the reversion of populations to unicellularity
 suggests that this response is due to phenotypic plasticity and not
 evolutionary change.
description: Experimental
 resultsExcel spreadsheet
 showing raw results from all 4 experiments on colony formation in
 Chlorella vulgaris described in the manuscriptresults.xlsx
DOI: 10.5061/dryad.56b81
title: Data from: Generalist predator's niche shifts reveal ecosystem changes in an experimentally fragmented landscape

description: Habitat fragmentation can alter the trophic structure of communities and
 environmental conditions, thus driving changes in biodiversity and
 ecosystem functions. Quantifying niches of generalist predators can reveal
 how fragmentation alters ecosystems. In a habitat fragmentation
 experiment, we used stable isotopes of a generalist predator skink to test
 predictions from spatial theory on trophic structure and to quantify
 abiotic changes associated with fragmentation among continuous forest,
 fragments, and matrix habitats. We predicted that in fragments and the
 matrix, isotopic niches would shift due to decreases in skink trophic
 positions (δ15N) from reductions in trophic structure of arthropod food
 webs and abiotic changes over time (δ13C) relative to continuous forest.
 Contrary to theoretical predictions, we did not find evidence of
 reductions in trophic structure with fragmentation. In fact, skink δ15N
 values were higher in the matrix and fragments than continuous forest,
 likely due to changes in distributions of a detritivorous prey species. In
 addition, δ13C values in the matrix decreased over years since
 fragmentation due to abiotic changes associated with matrix tree
 maturation. We show how isotopic niches are influenced by fragmentation
 via shifts in biotic and abiotic processes. The potential for either or
 both spatial and abiotic effects of fragmentation present a challenge for
 theory to better predict ecological changes in fragmented landscapes.
description: Wog Wog skink stable
 isotope dataCollection information
 and d13C, d15N, [C], and [N] for muscle and liver tissues of pale-flecked
 garden sunskink (Lampropholis guichenoti) from Wog Wog habitat
 fragmentation experiment. See paper and readme for further
 details.Resasco_Skink_Stable_Isotopes.csvWog Wog skink gut contentsPrey orders found in guts of pale-flecked garden sunskink (Lampropholis guichenoti) from Wog Wog habitat fragmentation experiment. 0 = absences, 1 = presence. See paper and readme for further details.Resasco_Skink_Gut_Contents.csv
DOI: 10.5061/dryad.r1k1f
title: Data from: Investigating the production of sexual resting structures in a plant pathogen reveals unexpected self-fertility and genotype-by-environment effects

description: The sexual stage of pathogens governs recombination patterns and often
 also provides means of surviving the off-season. Despite its importance
 for evolutionary potential and between-season epidemiology, sexual systems
 have not been carefully investigated for many important pathogens, and
 what generates variation in successful sexual reproduction of pathogens
 remains unexplored. We surveyed the sexually produced resting structures
 (chasmothecia) across 86 natural populations of fungal pathogen
 Podosphaera plantaginis (Ascomycota) naturally infecting Plantago
 lanceolata in the Åland archipelago, southwest of Finland. For this
 pathosystem, these resting structures are a key life-history stage, as
 more than half of the local pathogen populations go extinct every winter.
 We uncovered substantial variation in the level of chasmothecia produced
 among populations, ranging from complete absence to presence on all
 infected leaves. We found that chasmothecia developed within clonal
 isolates (single strain cultures). Additionally, these clonal isolates all
 contained both MAT1-1-1 and MAT1-2-1 genes that characterize mating-types
 in Ascomycetes. Hence, contrary to expectations, we conclude that this
 species is capable of haploid selfing. In controlled inoculations we
 discovered that pathogen genotypes varied in their tendency to produce
 chasmothecia. Production of chasmothecia was also affected by ambient
 temperature (E), and by the interaction between temperature and pathogen
 genotype (G × E). These G, E and G × E effects found both at a European
 scale, as well as within Åland, may partly explain the high variability
 observed among populations in chasmothecia levels. Consequently, they may
 be key drivers of the evolutionary potential and epidemiology of this
 highly dynamic pathosystem.
description: dryad_expExcel file contening the results of the experiment described in the article as: "Experiment assessing the effect of pathogen genotype, environmental conditions and their interaction on chasmothecia production"
DOI: 10.5061/dryad.t72kr
title: Data from: Assessing risks of invasion through gamete performance: farm Atlantic salmon sperm and eggs show equivalence in function, fertility, compatibility and competitiveness to wild Atlantic salmon

description: Adaptations at the gamete level (a) evolve quickly, (b) appear sensitive
 to inbreeding and outbreeding and (c) have important influences on
 potential to reproduce. We apply this understanding to problems posed by
 escaped farm salmon and measure their potential to reproduce in the wild.
 Farm Atlantic salmon (Salmo salar) are a threat to biodiversity, because
 they escape in large numbers and can introgress, dilute or disrupt locally
 adapted wild gene pools. Experiments at the whole fish level have found
 farm reproductive potential to be significant, but inferior compared to
 wild adults, especially for males. Here, we assess reproductive
 performance at the gamete level through detailed in vitro comparisons of
 the form, function, fertility, compatibility and competitiveness of farm
 versus wild Atlantic salmon sperm and eggs, in conditions mimicking the
 natural gametic microenvironment, using fish raised under similar
 environmental conditions. Despite selective domestication and reduced
 genetic diversity, we find functional equivalence in all farm fish gamete
 traits compared with their wild ancestral strain. Our results identify a
 clear threat of farm salmon reproduction with wild fish and therefore
 encourage further consideration of using triploid farm strains with
 optimized traits for aquaculture and fish welfare, as triploid fish remain
 reproductively sterile following escape.
description: DRYAD DATA FARM V
 WILDRaw data supporting all
 analyses and Figures 1 to 4
DOI: 10.5061/dryad.g2785
title: Data from: Evaluation of novel large cut-off ultrafiltration membranes for adenovirus serotype 5 (Ad5) concentration.

description: The purification of virus particles and viral vectors for vaccine and gene
 therapy applications is gaining increasing importance in order to deliver
 a fast, efficient, and reliable production process. Ultrafiltration (UF)
 is a widely employed unit operation in bioprocessing and its use is
 present in several steps of the downstream purification train of
 biopharmaceuticals. However, to date few studies have thoroughly
 investigated the performance of several membrane materials and cut-offs
 for virus concentration/diafiltration. The present study aimed at
 developing a novel class of UF cassettes for virus
 concentration/diafiltration. A detailed study was conducted to evaluate
 the effects of (i) membrane materials, namely polyethersulfone (PES),
 regenerated cellulose (RC), and highly cross-linked RC (xRC), (ii) nominal
 cut-off, and (iii) UF device geometry at different production scales. The
 results indicate that the xRC cassettes with a cut-off of approximately
 500 kDa are able to achieve a 10-fold concentration factor with 100%
 recovery of particles with a process time twice as fast as that of a
 commercially available hollow fiber. DNA and host cell protein clearances,
 as well as hydraulic permeability and fouling behavior, were also
 assessed.
description: Figure raw
 dataThe file provides the
 raw data of the figures 2-9
DOI: 10.5061/dryad.1513
title: Data from: Genetic approaches refine ex situ lowland tapir (Tapirus terrestris) conservation

description: Ex situ conservation management remains an important tool in the face of
 continued habitat loss and global environmental change. Here, we use
 microsatellite marker variation to evaluate conventional assumptions of
 pedigree-based ex situ population management and directly inform a captive
 lowland tapir breeding program within a range country. We found relatively
 high levels of genetic variation (Ntotal = 41; mean HE = 0.67 over 10
 variable loci) and little evidence for relatedness among founder
 individuals (Nfounders = 10; mean relatedness = -0.05). Seven of 29
 putative parent-offspring relationships were excluded by parentage
 analysis based on allele-sharing, and we identified two individuals of
 high genetic value to the population (mk ≤ 0.007) that would otherwise
 have been excluded from the breeding program. Traditional assumptions of
 founders being unrelated and individuals of unknown origin being highly
 related led to overestimates of mean kinship and inbreeding, and
 underestimates of gene diversity, when compared to values found when
 genetic markers were used to inform kinship. We discuss our results within
 the context of recent studies that have assessed the utility of neutral
 molecular markers for ex situ conservation.
description: Microsatellite genotypes
 of captive lowland tapirs in ArgentinaLength, in base-pairs,
 of alleles at 13 microsatellite loci in 41 individuals of captive lowland
 tapirs. Missing data coded as -9. Data collected with funds from the
 Copenhagen Zoo, Martha Pipper Research Award, and Canadian Foundation for
 Innovation.ArgTapirs_genotypes_Final
 March10.xls
DOI: 10.5061/dryad.m1k5m
title: Data from: Towards a mechanistic understanding of thermal niche partitioning

description: We develop a theoretical framework to elucidate the mechanistic basis of
 thermal niche partitioning in ectotherms. Using a food web module of two
 consumers competing for a biotic resource, we investigate how temperature
 effects on species' attack and mortality rates scale up to
 population-level outcomes of coexistence and exclusion. We find that
 species' differences in competitive effects arise from asymmetries
 generated by the non-linear temperature response of mortality:
 cold-adapted species experience stronger intra-specific competition than
 warm-adapted species; they also exert weaker competition on, and
 experience stronger competition from, warm-adapted species. These
 asymmetries become greater as seasonal fluctuations increase, generating
 latitudinal variation in coexistence and priority effects. Characterizing
 species' thermal niches in terms of mechanistic descriptions of trait
 responses allows for testable predictions about population-level
 competitive outcomes based solely on three fundamental, and easily
 measurable, quantities: attack rate optima, response breadths and
 temperature sensitivity of mortality. We test our predictions with data
 from an insect host-parasitoid community. By quantifying the three basic
 quantities we predict that priority effects cannot occur, which is borne
 out by population-level experiments showing that the outcome of
 competition does not depend on initial conditions. More broadly, our
 framework can predict the conditions under which exotic invasive species
 can exclude, or coexist with, native biota, and the effects of climate
 warming on competitive communities across latitudinal gradients.
description: data_Smith&AmarasekareMean parasitism rates at each temperature
DOI: 10.5061/dryad.js7r696
title: Data from: Local persistence of Mann’s soft-haired mouse Abrothrix manni (Rodentia, Sigmodontinae) during Quaternary glaciations in southern Chile

description: Quaternary climatic oscillations have impacted Patagonian sigmodontine
 fauna, leaving traceable genetic footprints. In southern Chile, changes in
 the landscape included transitions to different vegetation formations as
 well as the extension of ice sheets. In this study, we focus on the
 Valdivian forest endemic and recently described sigmodontine species
 Abrothrix manni. We aim to assess the genetic structure of this species,
 testing for the existence of intraspecific lineages, and inferring the
 recent demographic history of the species. Analyses were based on the
 first 801 bp of the mitochondrial gene Cytocrhome-b from 49 individuals of
 A. manni collected at 10 localities that covers most part of its
 geographic distribution. Genealogical analyses recovered two main
 intraspecific lineages that are geographically segregated and present an
 intermediate site of secondary contact. Historical demography shows signal
 of recent population decrease. Based on these results, we proposed that
 current genetic diversity of A. manni differentiated in at least two
 distinct refugial areas in southern Chile. This scenario, in addition to
 be unique among those uncovered for the so far studied Valdivian forest
 rodents, is noteworthy because of the reduced geographic scale inhabited
 by the species.
description: Cytochrome-b_alignment_Abrothrix_manniDNA sequences of the first 801bp of the gene Cytochrome-b of specimens of Abrothrix manni. This is a non-redundant alignment, i.e., only one sequence representative of each haplotypic class is included. These sequences were also deposited in GenBank. Accession numbers area provided as sequence header in this file.manni_NR_xa_dryad.txt
DOI: 10.5061/dryad.c2v56
title: Data from: Ancient DNA provides new insight into the maternal lineages and domestication of Chinese donkeys

description: Background: The donkey (Equus asinus) is an important domestic animal that
 provides a reliable source of protein and method of transportation for
 many human populations. However, the process of domestication and the
 dispersal routes of the Chinese donkey are still unclear, as donkey
 remains are sparse in the archaeological record and often confused with
 horse remains. To explore the maternal origins and dispersal route of
 Chinese donkeys, both mitochondrial DNA D-loop and cytochrome b gene
 fragments of 21 suspected donkey remains from four archaeological sites in
 China were amplified and sequenced.Results: Molecular methods of species
 identification show that 17 specimens were donkeys and three samples had
 the maternal genetic signature of horses. One sample that dates to about
 20,000 years before present failed to amplify. In this study, the
 phylogenetic analysis reveals that ancient Chinese donkeys have high
 mitochondrial DNA diversity and two distinct mitochondrial maternal
 lineages, known as the Somali and Nubian lineages. These results indicate
 that the maternal origin of Chinese domestic donkeys was probably related
 to the African wild ass, which includes the Nubian wild ass (Equus
 africanus africanus) and the Somali wild ass (Equus africanus
 somaliensis). Combined with historical records, the results of this study
 implied that domestic donkeys spread into west and north China before the
 emergence of the Han dynasty. The number of Chinese domestic donkeys had
 increased primarily to meet demand for the expansion of trade, and they
 were likely used as commodities or for shipping goods along the Silk Road
 during the Tang Dynasty, when the Silk Road reached its golden age.
 Conclusions: This study is the first to provide valuable ancient animal
 DNA evidence for early trade between African and Asian populations. The
 ancient DNA analysis of Chinese donkeys also sheds light on the dynamic
 process of the maternal origin, domestication, and dispersal route of
 ancient Chinese donkeys.
description: ancient DNA of Chinese
 donkeysSamples were collected
 from four archaeological sites in China. 17 samples (L1- L9 and L11-L18)
 were from the Yanjialiang site in Inner Mongolia, which dates to 800-600
 yr BP, during the Yuan dynasty. Sample L10 was from the Jinsitai cave site
 in Inner Mongolia, which dates to 18,000-20,000 yr BP. L21 was from the
 Lantianxinjie site in Shaanxi province. The date of the sample was
 determined to be about 568 (+/-50) yr BP using C14
 dating.40
 sequences.txt
DOI: 10.5061/dryad.28v5c
title: Data from: Disruption of plant-soil-microbial relationships influences plant growth

description: Differential dispersal of plant and microbial propagules may result in the
 geographical disassociation of plant populations from their local abiotic
 conditions and microbial communities, especially in the face of species
 introductions and changing climates. To assess the potential consequences
 of disrupting historical relationships between plant populations,
 microbial communities, and soil conditions, we grew Carpinus caroliniana
 seedlings from populations across the species range in combinations of
 sterilized soils and soil microbial communities, in soils collected from
 sites with or without conspecific trees. This controlled environment study
 simulated the consequences for seedling growth of independently or jointly
 disrupting the historical plant population-soil match, plant
 population-microbial community match, and microbial community-soil match.
 Seedlings grown in soils from areas without conspecifics had lower
 biomass, but benefited from inoculation with their historical microbial
 communities. For conspecific-cultured soils, growth was optimized when
 seedlings grew with novel microbial communities, but only when microbial
 communities were local with respect to abiotic soil conditions.
 Correlative evidence suggests that this may stem from alignment of
 ectomycorrhizal fungal communities to abiotic soil conditions. Synthesis:
 Maintaining historical plant-microbial community relationships may benefit
 plant species spreading into new areas; however, for movement within
 current ranges, maintaining the historical relationship between microbial
 communities and the abiotic aspects of soils may have more important
 consequences for early growth.
description: C. caroliniana seedling
 performance, tissue chemistry, and fungal community
 dissimilaritiesThis file contains all
 of the data necessary to replicate the analyses in the associated article,
 including seedling biomass data, tissue chemistry data, and measures of
 community dissimilarity between ancestral and experimental fungal
 communities.finaldatafordryad.xlsx
DOI: 10.15468/dl.47xkqe
title: Occurrence Download

description: A dataset containing 6 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Moroteuthopsis longimana",
 "HasCoordinate is true",
 "DecimalLatitude is greater than -90",
 "DecimalLatitude is less than 10",
 "DecimalLongitude is greater than -180",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 2015"
 ]
}

 The dataset includes 6 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001226-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.20bm4
title: Data from: Mutualism effectiveness of a fungal endophyte in an annual grass is impaired by ozone

description: 1. Ozone is an increasing tropospheric contaminant of climate change.
 Exposure to ozone may affect the symbiotic relationship between plants and
 beneficial microorganisms. In particular, the herbivore resistance
 mechanism conferred by fungal endophytes (defensive mutualism) may be
 affected, as any of the ozone-triggered effects (such as elicitation of
 defence mechanisms against biotrophic fungi or oxidative stress in the
 apoplastic space) may target the symbiont. 2. Symbiotic and non-symbiotic
 Lolium multiflorum plants were exposed to ozone for two consecutive days
 (2 h per day), after which half were infested with 10 aphids
 (Rhopalosiphum padi). We measured variables related to performance of
 plants, the endophyte symbiont (alkaloids) and the herbivores. 3. Aphid
 populations were smaller on symbiotic plants than in non-symbiotic plants
 in low-ozone conditions. However, this difference disappeared in exposed
 plants to high-ozone conditions. Under low-ozone conditions, structure of
 aphid populations on endophyte-symbiotic plants was characterized by a low
 number of nymphs and a high number of adults. This pattern was not
 observed with high-ozone exposure. Level of fungal alkaloids (lolines) was
 not affected by either ozone or herbivory. 4. Results indicate that ozone
 impairs the grass-endophyte symbiosis without affecting production of
 alkaloids generally linked with aphids’ response to endophyte presence.
 Since neither plant biomass nor alkaloid level were affected by ozone,
 other ozone-mediated mechanisms at molecular or biochemical level may
 underlie plant-herbivore interaction mediated by fungal endophytes. Thus,
 the mechanism behind this effect must be determined in future experiments.
description: FE-Ueno A. et al.,
 DatabaseThis file contains the
 data that was used in the analyses.Ueno A. etal., Measurements
 (database).xlsx
DOI: 10.5061/dryad.1qb31
title: Data from: Carotenoids and amphibians: effects on life history and susceptibility to the infectious pathogen, Batrachochytrium dendrobatidis

description: Carotenoids are considered beneficial nutrients because they provide
 increased immune capacity. Although carotenoid research has been conducted
 in many vertebrates, little research has been done in amphibians, a group
 that is experiencing global population declines from numerous causes,
 including disease. We raised two amphibian species through metamorphosis
 on three carotenoid diets to quantify the effects on life-history traits
 and post-metamorphic susceptibility to a fungal pathogen (Batrachochytrium
 dendrobatidis; Bd). Increased carotenoids had no effect on survival to
 metamorphosis in gray treefrogs (Hyla versicolor) but caused lower
 survival to metamorphosis in wood frogs [Lithobates sylvaticus (Rana
 sylvatica)]. Increased carotenoids caused both species to experience
 slower development and growth. When exposed to Bd after metamorphosis,
 wood frogs experienced high mortality, and the carotenoid diets had no
 mitigating effects. Gray treefrogs were less susceptible to Bd, which
 prevented an assessment of whether carotenoids could mitigate the effects
 of Bd. Moreover, carotenoids had no effect on pathogen load. As one of
 only a few studies examining the effects of carotenoids on amphibians and
 the first to examine potential interactions with Bd, our results suggest
 that carotenoids do not always serve amphibians in the many positive ways
 that have become the paradigm in other vertebrates.
description: Bd_loadgray tree frog_survival during Bd challengegray tree frog_time to metamorphosissurvival from initiation of experiment to metamorphosiswood frog_survival during Bd challengewood frog_time to metamorphosis