cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.t29f8
title: Data from: Comparative assessment of SSR and SNP markers for inferring the population genetic structure of the common fungus Armillaria cepistipes

description: During the last years, simple sequence repeats (SSRs, also known as
 microsatellites) and single-nucleotide polymorphisms (SNPs) have become
 the most popular molecular markers for describing neutral genetic
 variation in populations of a wide range of organisms. However, only a
 limited number of studies has focused on comparing the performance of
 these two types of markers for describing the underlying genetic structure
 of wild populations. Moreover, none of these studies targeted fungi, the
 group of organisms with one of the most complex reproductive strategies.
 We evaluated the utility of SSRs and SNPs for inferring the neutral
 genetic structure of Armillaria cepistipes (basidiomycetes) at different
 spatial scales. For that, 407 samples were collected across a small
 (150 km2) area in the Ukrainian Carpathians and a large (41 000 km2) area
 in the Swiss Alps. All isolates were analyzed at 17 SSR loci distributed
 throughout the whole genome and at 24 SNP loci located in different
 single-copy conserved genes. The two markers showed different patterns of
 structure within the two spatial scales studied. The multi-allelic SSR
 markers seemed to be best suited for detecting genetic structure in
 indigenous fungal populations at a rather small spatial scale (radius of
 ~50-100 km). The pattern observed at SNP markers rather reflected ancient
 divergence of distant (~1000 km) populations that in addition are
 separated by mountain ranges. Despite these differences, both marker types
 were suitable for detecting the weak genetic structure of the two A.
 cepistipes populations investigated.
description: Tsykun_at_al_raw_dataThe file has a sheet with SSR genotypes (missing data are coded as "999" allele) and SNP genotypes.
DOI: 10.5061/dryad.3214916
title: Data from: Phagocyte chase behaviors—discrimination between Gram-negative and Gram-positive bacteria by amoebae

description: Phagocytes are cells that pursue, engulf, and kill bacteria. They include
 macrophages and neutrophils of the mammalian immune system, but also
 free-living amoebae that hunt and engulf bacteria for food. Phagocytosis
 can result in diverse outcomes, ranging from sustenance to infection and
 colonization by either pathogens or beneficial symbionts—and thus,
 discrimination may be necessary to seek out good bacteria while avoiding
 bad ones. Here we tested whether the soil amoeba Dictyostelium discoideum
 can discriminate among different types of bacteria, using behavioral
 assays where amoebae were presented with paired choices of different
 bacteria. We observed variation in the extent to which the amoebae pursued
 different types of bacteria, as well as preferential migration towards
 Gram-negative over Gram-positive bacteria. Response profiles were similar
 for amoebae that originated from different geographic locations,
 suggesting that chase preference is conserved across much of the species
 range. While prior work has demonstrated that bacteria will use chemotaxis
 to seek out amoebae they colonize, our work suggests that the opposite
 also occurs—amoebae can preferentially direct themselves to particular
 bacteria in the environment. Preferential sensing and response may help to
 explain why some amoeba-bacterial associations are more common in nature
 than others.
description: bacterial_migrationData from bacterial migration assays, showing the number of amoeba cells (NumCells) that migrated to a particular focal bacteria (Bacteria), the amoeba genotype (Strain), the alternative choice bacteria (Against), the bacterium's gram status (Gram), and the experimental replicate (Block).SAS Analysis MigrationSAS analysis that forms the basis of results presented in Table 1.SAS Analysis.docxSAS Analysis, cAMP migrationSAS analysis that forms the basis of results presented in Table S2.SAS cAMP Analysis.docxcAMP_migration.txtData from cAMP migration assays, comparing response of different D. discoideum strains to strains of E. coli that are wild-type (WT), cAMP non-producers (N), or cAMP overproducers (OE).migration_figures.RR script that produces each results figure from the raw data files.
DOI: 10.5061/dryad.fb1s4
title: Data from: Adaptive shaping of the behavioural and neuroendocrine phenotype during adolescence

description: Environmental conditions during early life can adaptively shape the
 phenotype for the prevailing environment. Recently, it has been suggested
 that adolescence represents an additional temporal window for adaptive
 developmental plasticity, though supporting evidence is scarce. Previous
 work has shown that male guinea pigs living in large mixed-sex colonies
 develop a low-aggressive phenotype as part of a queuing strategy that is
 adaptive for integrating into large unfamiliar colonies. By contrast,
 males living in pairs during adolescence become highly aggressive towards
 strangers. Here, we tested whether the high-aggressive phenotype is
 adaptive under conditions of low population density, namely when directly
 competing with a single opponent for access to females. For that purpose,
 we established groups of one pair-housed male (PM), one colony-housed male
 (CM) and two females. PMs directed more aggression towards the male
 competitor and more courtship and mating towards females than did CMs. In
 consequence, PMs attained the dominant position in most cases and sired
 significantly more offspring. Moreover, they showed distinctly higher
 testosterone concentrations and elevated cortisol levels, which probably
 promoted enhanced aggressiveness while mobilizing necessary energy. Taken
 together, our results provide the clearest evidence to date for adaptive
 shaping of the phenotype by environmental influences during adolescence.
description: Zimmermann et al Proc B
 2017 - Behavioural measuresLatencies and
 frequencies of behavioural measures.Behavioural
 measures.xlsxZimmermann et al Proc B
 2017 - Hormones, body weights, and paternitiesPlasma concentrations of
 cortisol and testosterone, body weights, and number of sired litters and
 offspring.Hormones, body weights, and
 paternities.xlsx
DOI: 10.5061/dryad.3274k
title: Data from: Dysregulation of valvular interstitial cell let-7c, miR-17, miR-20a, and miR-30d in naturally occurring canine myxomatous mitral valve disease

description: Canine myxomatous mitral valve disease (MMVD) resembles the early stages
 of myxomatous pathology seen in human non-syndromic mitral valve prolapse,
 a common valvular heart disease in the adult human population. Canine MMVD
 is seen in older subjects, suggesting age-related epigenetic dysregulation
 leading to derangements in valvular cell populations and matrix synthesis
 or degradation. We hypothesized that valvular interstitial cells (VICs)
 undergo disease-relevant changes in miRNA expression. In primary VIC lines
 from diseased and control valves, miRNA expression was profiled using
 RT-qPCR and next generation sequencing. VICs from diseased valves showed
 phenotypic changes consistent with myofibroblastic differentiation
 (vimentinlow+, a-SMAhigh+), increases in senescence markers (p21,
 SA-b-gal), and decreased cell viability and proliferation potential.
 RT-qPCR and miRNA sequencing analyses both showed significant
 (p&lt;0.05) downregulation of let-7c, miR-17, miR-20a, and miR-30d in
 VICs from diseased valves compared to controls. Decreased let-7c, miR-17,
 and miR-20a may contribute to myofibroblastic differentiation in addition
 to cell senescence, and decreased miR-30d may disinhibit cell apoptosis.
 These data support the hypothesis that epigenetic dysregulation plays an
 important role in age-related canine MMVD.
description: RNAseq
 dataExcel data file with
 RNAseq count dataDESeq2_normalized_data.xlsxRT-qPCR DataPCR data with Ct numbersVICs PCR Data.xlsx
DOI: 10.5061/dryad.2v3p5
title: Data from: Life history of the Glanville fritillary butterfly in fragmented versus continuous landscapes

description: Habitat loss and fragmentation threaten the long-term viability of
 innumerable species of plants and animals. At the same time, habitat
 fragmentation may impose strong natural selection and lead to evolution of
 life histories with possible consequences for demographic dynamics. The
 Baltic populations of the Glanville fritillary butterfly (Melitaea cinxia)
 inhabit regions with highly fragmented habitat (networks of small dry
 meadows) as well as regions with extensive continuous habitat (calcareous
 alvar grasslands). Here, we report the results of common garden studies on
 butterflies originating from two highly fragmented landscapes (FL) in
 Finland and Sweden and from two continuous landscapes (CL) in Sweden and
 Estonia, conducted in a large outdoor cage (32 by 26 m) and in the
 laboratory. We investigated a comprehensive set of 51 life-history traits,
 including measures of larval growth and development, flight performance,
 and adult reproductive behavior. Seventeen of the 51 traits showed a
 significant difference between fragmented versus CL. Most notably, the
 growth rate of postdiapause larvae and several measures of flight
 capacity, including flight metabolic rate, were higher in butterflies from
 fragmented than CL. Females from CL had shorter intervals between
 consecutive egg clutches and somewhat higher life-time egg production, but
 shorter longevity, than females from FL. These results are likely to
 reflect the constant opportunities for oviposition in females living in
 continuous habitats, while the more dispersive females from FL allocate
 more resources to dispersal capacity at the cost of egg maturation rate.
 This study supports theoretical predictions about small population sizes
 and high rate of population turnover in fragmented habitats selecting for
 increased rate of dispersal, but the results also indicate that many other
 life-history traits apart from dispersal are affected by the degree of
 habitat fragmentation.
description: egg
 weightData on egg weight
 experiment.Clutch-Rank12-19April-Spring2011.xlsxBody PartsData on dry body part and wing sizeBodyParts-Pure_May2011.xlsxOviposition-ALOLSAUPData on clutches from AL, OL, UP and SA populationsLife-HistoryTraits_ALOLSAUPData on life history traits (larval and adult) for AL, OL, UP and SA populations
DOI: 10.5061/dryad.qt984
title: Data from: Seasonal dynamics of Atlantic herring (Clupea harengus L.) populations spawning in the vicinity of marginal habitats

description: Gillnet sampling and analyses of otolith shape, vertebral count and growth
 indicated the presence of three putative Atlantic herring (Clupea harengus
 L.) populations mixing together over the spawning season February–June
 inside and outside an inland brackish water lake (Landvikvannet) in
 southern Norway. Peak spawning of oceanic Norwegian spring spawners and
 coastal Skagerrak spring spawners occurred in March–April with small
 proportions of spawners entering the lake. In comparison, spawning of
 Landvik herring peaked in May–June with high proportions found inside the
 lake, which could be explained by local adaptations to the environmental
 conditions and seasonal changes of this marginal habitat. The 1.85 km2
 lake was characterized by oxygen depletion occurring between 2.5 and 5 m
 depth between March and June. This was followed by changes in salinity
 from 1–7‰ in the 0–1 m surface layer to levels of 20–25‰ deeper than 10 m.
 In comparison, outside the 3 km long narrow channel connecting the lake
 with the neighboring fjord, no anoxic conditions were found. Here salinity
 in the surface layer increased over the season from 10 to 25‰, whereas
 deeper than 5 m it was stable at around 35‰. Temperature at 0–5 m depth
 increased significantly over the season in both habitats, from 7 to 14°C
 outside and 5 to 17°C inside the lake. Despite differences in peak
 spawning and utilization of the lake habitat between the three putative
 populations, there was an apparent temporal and spatial overlap in
 spawning stages suggesting potential interbreeding in accordance with the
 metapopulation concept.
description: Data 2012
 Landvik
DOI: 10.5061/dryad.4v268
title: Data from: Female mating preferences and offspring survival: testing hypotheses on the genetic basis of mate choice in a wild lekking bird

description: Indirect benefits of mate choice result from increased offspring genetic
 quality and may be important drivers of female behaviour.
 ‘Good-genes-for-viability’ models predict that females prefer mates of
 high additive genetic value, such that offspring survival should correlate
 with male attractiveness. Mate choice may also vary with genetic diversity
 (e.g. heterozygosity) or compatibility (e.g. relatedness), where the
 female's genotype influences choice. The relative importance of these
 nonexclusive hypotheses remains unclear. Leks offer an excellent
 opportunity to test their predictions, because lekking males provide no
 material benefits and choice is relatively unconstrained by social
 limitations. Using 12 years of data on lekking lance-tailed manakins,
 Chiroxiphia lanceolata, we tested whether offspring survival correlated
 with patterns of mate choice. Offspring recruitment weakly increased with
 father attractiveness (measured as reproductive success, RS), suggesting
 attractive males provide, if anything, only minor benefits via offspring
 viability. Both male RS and offspring survival until fledging increased
 with male heterozygosity. However, despite parent–offspring correlation in
 heterozygosity, offspring survival was unrelated to its own or maternal
 heterozygosity or to parental relatedness, suggesting survival was not
 enhanced by heterozygosity per se. Instead, offspring survival benefits
 may reflect inheritance of specific alleles or nongenetic effects.
 Although inbreeding depression in male RS should select for inbreeding
 avoidance, mates were not less related than expected under random mating.
 Although mate heterozygosity and relatedness were correlated, selection on
 mate choice for heterozygosity appeared stronger than that for relatedness
 and may be the primary mechanism maintaining genetic variation in this
 system despite directional sexual selection.
description: zip folder of data
 filesDatafiles
 zip.zip
DOI: 10.5061/dryad.3mb30
title: Data from: Budget constraints affect male rats’ choices between differently priced commodities

description: Demand theory can be applied to analyse how a human or animal consumer
 changes her selection of commodities within a certain budget in response
 to changes in price of those commodities. This change in consumption
 assessed over a range of prices is defined as demand elasticity.
 Previously, income-compensated and income-uncompensated price changes have
 been investigated using human and animal consumers, as demand theory
 predicts different elasticities for both conditions. However, in these
 studies, demand elasticity was only evaluated over the entirety of choices
 made from a budget. As compensating budgets changes the number of
 attainable commodities relative to uncompensated conditions, and thus the
 number of choices, it remained unclear whether budget compensation has a
 trivial effect on demand elasticity by simply sampling from a different
 total number of choices or has a direct effect on consumers’ sequential
 choice structure. If the budget context independently changes choices
 between commodities over and above price effects, this should become
 apparent when demand elasticity is assessed over choice sets of any
 reasonable size that are matched in choice opportunities between budget
 conditions. To gain more detailed insight in the sequential choice
 dynamics underlying differences in demand elasticity between budget
 conditions, we trained N=8 rat consumers to spend a daily budget by making
 a number of nosepokes to obtain two liquid commodities under different
 price regimes, in sessions with and without budget compensation. We
 confirmed that demand elasticity for both commodities differed between
 compensated and uncompensated budget conditions, also when the number of
 choices considered was matched, and showed that these elasticity
 differences emerge early in the sessions. These differences in demand
 elasticity were driven by a higher choice rate and an increased
 reselection bias for the preferred commodity in compensated compared to
 uncompensated budget conditions, suggesting a budget context effect on
 relative valuation.
description: dataset of choices per
 phaseThis dataset contains
 the raw choices, response times, budgets and spent nosepokes for all
 rat/session combinations, per phase. See ReadMe for
 details.data_vanWingerden.mat
DOI: 10.5061/dryad.2pm21
title: Data from: Inorganic fungicides as routinely applied in organic and conventional agriculture can increase palatability but reduce microbial decomposition of leaf litter

description: 1. The application of fungicides is considered an indispensable measure to
 secure crop production. These substances, however, may unintentionally
 enter surface waters via runoff, potentially affecting the microbial
 community. To assess such risks adequately, authorities recently called
 for suitable test designs involving relevant aquatic microorganisms. 2. We
 assessed the structural and functional responses of leaf-associated
 microbial communities, which play a key role in the breakdown of
 allochthonous leaf material in streams, towards the inorganic fungicides
 copper (Cu) and elemental sulphur (S). These substances are of particular
 interest as they are authorized for both conventional and organic farming
 in many countries of the world. We used the food-choice of the amphipod
 shredder Gammarus fossarum (indicative for microorganism-mediated leaf
 palatability) as well as microbial leaf decomposition as functional
 endpoints. Moreover, the leaf-associated microbial communities were
 characterized by means of bacterial density, fungal biomass and community
 composition facilitating mechanistic understanding of the observed
 functional effects. 3. While Gammarus preferred Cu-exposed leaves over
 unexposed ones, microbial leaf decomposition was reduced by both Cu and S
 (up to 30%). Furthermore, Cu-exposure decreased bacterial densities (up to
 60%), stimulated the growth of leaf-associated fungi (up to 100%) and
 altered fungal community composition, while S did not affect any of the
 assessed structural endpoints. 4. Synthesis and applications. We observed
 both structural and functional changes in leaf-associated microbial
 communities at inorganic fungicide concentrations realistic for surface
 water bodies influenced by conventional and organic farming. Our data
 hence justify a careful re-evaluation of the environmental safety of the
 agricultural use of these compounds. Moreover, inclusion of an
 experimental design similar to the one used in the present study in
 lower-tier environmental risk assessments of antimicrobial compounds may
 aid to safeguard the integrity of aquatic microbial communities and the
 functions they provide.
description: Data for Zubrod et al.
 2015 (Journal of Applied Ecology)This file contains all
 data used for analyses presented in the associated paper by Zubrod et
 al.Data_JAPPL_Zubrod_2015.xlsx
DOI: 10.5061/dryad.cr3ft
title: Data from: Hotspots of mutualistic networks

description: Incorporating interactions into a biogeographical framework may serve to
 understand how such interactions and the services they provide are
 distributed in space. We begin by simulating the spatiotemporal dynamics
 of realistic mutualistic networks inhabiting spatial networks of habitat
 patches. We proceed by comparing these predictions with the empirical
 results of a set of pollination networks in isolated hills of the
 Argentinian Pampas. We first find that one needs to sample up to five
 times as much area to record interactions as would be needed to sample the
 same proportion of species. Second, we find that peripheral patches have
 fewer interactions and harbor less nested networks ---therefore
 potentially less resilient communities--- compared to central patches. Our
 results highlight the important role played by the structure of dispersal
 routes on the spatial distribution of community patterns. This may help to
 understand the formation of biodiversity hotspots.
description: Networks and
 coordinatesThis datafile contains
 the plant pollinator network at each of the 12 "sierras"
 sampled. Also the metaweb is provided along with the geographical
 coordinates of each of the "sierras" and their
 area.Datos
 Sierras.xlsx
DOI: 10.5061/dryad.56v1c
title: Data from: Human-mediated and natural dispersal of an invasive fish in the eastern Great Lakes

description: The globally invasive Round Goby (Neogobius melanostomus) was introduced
 to the Great Lakes around 1990, spreading widely and becoming the dominant
 benthic fish in many areas. The speed and scope of this invasion is
 remarkable and calls into question conventional secondary spread models
 and scenarios. We utilized 9 microsatellites to identify large-scale
 genetic structure in Round Goby populations in the eastern Great Lakes,
 and assessed the role of colonization versus secondary transport and
 dispersal in developing this structure. We identified three clusters,
 corresponding with Lake Huron, eastern Lake Erie, and western Lake Erie
 plus eastern Lake Ontario, along with three highly-divergent populations.
 Bottleneck analysis identified founder effects in two divergent
 populations. Regression analyses of isolation-by-distance and allelic
 richness vs. distance from the initial invasion site were consistent with
 limited migration. However, some populations in eastern Lake Erie and Lake
 Ontario showed anomalously low genetic distance from the original site of
 colonization, consistent with secondary transport of large numbers of
 individuals via ballast water. Genetic structure of Round Goby in the
 Great Lakes principally resulted from long-distance secondary transport
 via ballast water with additional movement of individual via bait buckets
 and natural dispersal. The success of Round Gobies represents an
 interesting model for colonization characterization; however, those same
 attributes present significant challenges for conservation and fisheries
 management. Current management likely prevents many new species from
 arriving in the Great Lakes, but fails to address the transport of species
 within the lakes after they arrive; an issue of clear and pressing
 importance.
description: Round Goby
 Microsatellite DataMicrosatellite data for
 Round Goby in the eastern Great Lakes. Nine markers: (Nme10, Nme4, Nme9,
 Nme7, Nme5, Nme2, Nme3, Nme1, Nme6) and 32 population (location) samples.
 Locations sampled are identified with geographical coordinates in the
 associated manuscript.Microsatellite
 Data.txtPopulation Pairwise
 DistancesShortest distances over
 water between all pairs of populations, in matrix
 format.Pairwise
 Distances.txt