cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.gb7s5
title: Data from: Cryptic habitats and cryptic diversity: unexpected patterns of connectivity and phylogeographic breaks in a Mediterranean endemic marine cave mysid

description: The marine cave-dwelling mysid Hemimysis margalefi is distributed over the
 whole Mediterranean Sea which contrasts with the poor dispersal
 capabilities of this brooding species. In addition, underwater marine
 caves are a highly fragmented habitat which further promotes strong
 genetic structuring, therefore providing highly informative data on the
 levels of marine population connectivity across biogeographic regions.
 This study investigates how habitat and geography have shaped the
 connectivity network of this poor disperser over the entire Mediterranean
 Sea through the use of several mitochondrial and nuclear markers. Five
 deeply divergent lineages were observed among H. margalefi populations
 resulting from deep phylogeographic breaks, some dating back to the
 Oligo-Miocene. Whether looking at the intra-lineage or inter-lineage
 levels, H. margalefi populations present a high genetic diversity and
 population structuring. This study suggests that the five distinct
 lineages observed in H. margalefi actually correspond to as many separate
 cryptic taxa. The nominal species, H. margalefi sensu stricto, corresponds
 to the westernmost lineage here surveyed from the Alboran Sea to
 south-eastern Italy. Typical genetic breaks such as the Almeria-Oran Front
 or the Sicilo-Tunisian Strait do not appear to be influential on the
 studied loci in H. margalefi sensu stricto. Instead, population
 structuring appears more complex and subtle than usually found for model
 species with a pelagic dispersal phase. The remaining four cryptic taxa
 are all found in the eastern basin, but incomplete lineage sorting is
 suspected and speciation might still be in process. Present day population
 structure of the different H. margalefi cryptic species appears to result
 from past vicariance events started in the Oligo-Miocene and maintained by
 present day coastal topography, water circulation and habitat
 fragmentation.
description: Hemimysismargalefi-MolEcol-PhylogeoData files and tree files for assessing the phylogeography of Hemimysis margalefi in the Mediterranean Sea
DOI: 10.5281/zenodo.18382563
title: Pressure-induced phase stability and metallization of monoclinic FeO: Implications for the lower mantle of the Earth

description: The initial structures of two monoclinic phases and the pseudopotential of Fe and O
DOI: 10.5281/zenodo.18382564
title: Pressure-induced phase stability and metallization of monoclinic FeO: Implications for the lower mantle of the Earth

description: The initial structures of two monoclinic phases and the pseudopotential of Fe and O
DOI: 10.5061/dryad.8qb00
title: Data from: Population genetic structure and secondary symbionts in host-associated populations of the pea aphid complex

description: Polyphagous insect herbivores experience different selection pressures on
 their various host plant species. How this affects population divergence
 and speciation may be influenced by the bacterial endosymbionts that many
 harbor. Here, we study the population structure and symbiont community of
 the pea aphid (Acyrthosiphon pisum), which feeds on a range of legume
 species and is known to form genetically differentiated host-adapted
 populations. Aphids were collected from eight legume genera in England and
 Germany. Extensive host plant-associated differentiation was observed with
 this collection of pea aphids comprising nine genetic clusters, each of
 which could be associated with a specific food plant. Compared to host
 plant, geography contributed little to genetic differentiation. The
 genetic clusters were differentiated to varying degrees, but this did not
 correlate with their degree of divergence in host use. We surveyed the pea
 aphid clones for the presence of six facultative (secondary) bacterial
 endosymbionts and found they were non-randomly distributed across the
 aphid genetic clusters and this distribution was similar in the two
 countries. Aphid clones on average carried 1.4 species of secondary
 symbiont with those associated with Lathyrus having significantly fewer.
 The results are interpreted in the light of the evolution of
 specialization and ecological speciation.
description: aphid genotyping
 symbiont dataThis file contains data
 on each aphid clone: Information on origin: country and plant genus.
 Information on performance where applicable: plant species that the aphid
 clone is specialised on (as defined in the paper). Haplotypes for each of
 the nine markers. Presence/absence for each of the six symbiont
 species.survival
 dataThis file contains the
 data on survival on the eight test plants for the English aphid
 clones.
DOI: 10.5061/dryad.8j3s3
title: Data from: Linking social and spatial networks to viral community phylogenetics reveals subtype-specific transmission dynamics in African lions

description: 1.Heterogeneity within pathogen species can have important consequences
 for how pathogens transmit across landscapes; however, discerning
 different transmission routes is challenging. 2.Here we apply both
 phylodynamic and phylogenetic community ecology techniques to examine the
 consequences of pathogen heterogeneity on transmission by assessing
 subtype specific transmission pathways in a social carnivore. 3.We use
 comprehensive social and spatial network data to examine transmission
 pathways for three subtypes of feline immunodeficiency virus (FIVPle) in
 African lions (Panthera leo) at multiple scales in the Serengeti National
 Park, Tanzania. We used FIVPle molecular data to examine the role of
 social organization and lion density in shaping transmission pathways and
 tested to what extent vertical (i.e., father and/or mother offspring
 relationships) or horizontal (between unrelated individuals) transmission
 underpinned these patterns for each subtype. Using the same data, we
 constructed subtype specific FIVPle co-occurrence networks and assessed
 what combination of social networks, spatial networks, or co-infection
 best structured the FIVPle network. 4.While social organization (i.e.,
 pride) was an important component of FIVPle transmission pathways at all
 scales, we find that FIVPle subtypes exhibited different transmission
 pathways at within- and between-pride scales. A combination of social and
 spatial networks, coupled with consideration of subtype co-infection, was
 likely to be important for FIVPle transmission for the two major subtypes,
 but the relative contribution of each factor was strongly subtype
 specific. 5.Our study provides evidence that pathogen heterogeneity is
 important in understanding pathogen transmission, which could have
 consequences for how endemic pathogens are managed. Furthermore, we
 demonstrate that community phylogenetic ecology coupled with phylodynamic
 techniques can reveal insights into the differential evolutionary
 pressures acting on virus subtypes, which can manifest into
 landscape-level effects.
description: Lion FIV
 metadataMetadata associated for
 'pride or density' (Tab 1), within pride (Tab 2) and between
 pride (Tabs 3-12) analyses. Associated sequence data can be found on
 GenBank (accession numbers AY549217-537 AY549304, AY552614 to AY552683,
 and AY552684 - AY552748, and AY878208 - AY878235). "Ple numbers"
 attached to sequence data match to the first column of Tab 1. Please see
 README for information about each tab.Fountain-Jones et al
 Data.xlsx
DOI: 10.5061/dryad.8bk7d72
title: Data from: Interaction networks of macrofungi and mycophagous beetles reflect diurnal variation and the size and spatial arrangement of resources

description: Ecological networks are useful for characterizing interspecific
 associations and predicting the resilience of ecological communities. We
 evaluated how such networks vary with the size, spatial distribution, and
 timing of availability of resources, with a focus on beetle-macrofungal
 associations. We used 2 y of field experiments to construct ecological
 networks based on manipulated sporocarp baits (resources; Pleurotus
 ostreatus) and natural communities of beetles (consumers) in a temperate
 forest. Centrality and interaction strength increased with resource size,
 but were associated weakly with resource density and isolation, and not at
 all with position within patches. Whole-network connectance was greater in
 mornings (when beetle richness and abundance were high) than evenings.
 Interannual differences in networks were consistent with differences in
 beetle communities between years. The capacity of networks to vary
 temporally, spatially, and as a function of resource traits is examined in
 light of understanding beetle-macrofungal associations, which are
 important components of fungal ecology.
description: 2010
 MatricesData represent abundance
 matrices with columns representing species or morphospecies of adult
 beetles found on baits of mature, fresh sporocarps of _Pleurotus
 ostreatus_ mushrooms. Each entry represents the number of individuals of
 that beetle species found on a particular bait type (see paper for
 experimental design of bait arrays). Rows represent individual mushroom
 baits, with letter codes corresponding to positions in experimental arrays
 as described in the manuscript. Each tab in the data file represents a
 different census. Adult beetles were censused mornings and evenings on
 consecutive days.2010_Matrices for
 Dryad.xlsx2011
 MatricesData represent abundance
 matrices with columns representing species or morphospecies of adult
 beetles found on baits of mature, fresh sporocarps of _Pleurotus
 ostreatus_ mushrooms. Each entry represents the number of individuals of
 that beetle species found on a particular bait type (see paper for
 experimental design of bait arrays). Rows represent individual mushroom
 baits, with letter codes corresponding to positions in experimental arrays
 as described in the manuscript. Each tab in the data file represents a
 different census. Adult beetles were censused mornings and evenings on
 consecutive days.2011_Matrices for
 Dryad.xlsx
DOI: 10.5061/dryad.kv145
title: Data from: Bryophyte traits explain climate-warming effects on tree seedling establishment

description: Above the alpine tree line, bryophytes cover much of the tundra soil
 surface in dense, often monospecific carpets. Therefore, when climate
 warming enables tree seedling establishment above the tree line,
 interaction with the bryophyte layer is inevitable. Bryophytes are known
 to modify their environment in various ways. However, little is known
 about to which extent and by which mechanisms bryophytes affect the
 response of tree seedlings to climate warming. We aimed to assess and
 understand the importance of bryophyte species identity and traits for
 tree seedling performance at tree line temperatures and their response to
 warmer conditions. Seedlings of two common, tree line-forming tree species
 (Betula pubescens and Pinus sylvestris) were planted into intact cushions
 of eight common tundra bryophyte species and bryophyte-free soil and grown
 for 18 weeks at current (7·0 °C) and near-future (30–50 years; 9·2 °C)
 tree line average growing-season temperatures. Seedling performance
 (biomass increase and N-uptake) was measured and related to bryophyte
 species identity and traits indicative of their impact on the environment.
 Tree seedlings performed equally well or better in the presence of
 bryophytes than in bryophyte-free soil, which contrasts to their usually
 negative effects in milder climates. In addition, seedling performance and
 their response to higher temperatures depended on bryophyte species and
 seedlings of both species grew largest in the pan-boreal and subarctic
 bryophyte Hylocomium splendens. However, B. pubescens seedlings showed
 much stronger responses to higher temperatures when grown in bryophytes
 than in bryophyte-free soil, while the opposite was true for P. sylvestris
 seedlings. For B. pubescens, but not for P. sylvestris, available organic
 nitrogen of the bryophyte species was the trait that best predicted
 seedling responses to higher temperatures, likely because these seedlings
 had increased N-demands. Synthesis. Climatically driven changes in
 bryophyte species distribution may not only have knock-on effects on
 vascular plant establishment, but temperature effects on seedling
 performance are themselves moderated by bryophytes in a species-specific
 way. Bryophyte traits can serve as a useful tool for understanding and
 predicting these complex interactions.
description: Tree seedling growth
 responses to temperature and bryophyte traitstree seedling responses
 (biomass and N uptake) to growing in 8 bryophyte species at 7.2 and 9.0 °C
 for 4 months plus data for 6 traits of the 8 bryophyte species. Bryophyte
 Traits are: water holding capacity, density, height and water extractable
 NH4+ and dissolved organic N and total phenolsDATA for Lett et al.
 .xls
DOI: 10.15468/dl.2by6da
title: Occurrence Download

description: A dataset containing 832 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Country is Mexico",
 "TaxonKey is Leptophis mexicanus",
 "Year 1960-2026"
 ]
}

 The dataset includes 832 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000815-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.1d8761h1
title: Data from: Evolution of stenophagy in spiders (Araneae): evidence based on the comparative analysis of spider diets

description: Stenophagy (narrow diet breadth) represents an extreme of trophic
 specialization in carnivores, but little is known about the forces driving
 its evolution. We used spiders, the most diversified group of terrestrial
 predators, to investigate whether stenophagy 1) promoted diversification,
 2) was phylogenetically conserved and evolutionarily derived state, and 3)
 was determined either by geographical distribution and foraging guild. We
 utilized published data on the prey of almost 600 species. Six categories
 of stenophagy were found: myrmecophagy, araneophagy, lepidopterophagy,
 termitophagy, dipterophagy and crustaceophagy. We found that the species
 diversity of euryphagous genera and families was similar to stenophagous
 genera and families. At the family level, stenophagy evolved repeatedly
 and independently. Within families, the basal condition was oligophagy or
 euryphagy. Most types of stenophagy were clearly derived: myrmecophagy in
 Zodariidae; lepidopterophagy in Araneidae; dipterophagy in Theridiidae. In
 contrast, araneophagy was confined to basal and intermediate lineages,
 suggesting its ancestral condition. The diet breadth of species from the
 tropics and subtropics was less diverse than species from the temperate
 zone. Diet breadth was lower in cursorial spiders compared to web-building
 species. Thus, the evolution of stenophagy in spiders appears to be
 complex and governed by phylogeny as well as by ecological determinants.
description: dataAll data were extracted
 from the literature or unpublished sources.
DOI: 10.5061/dryad.86q4k
title: Data from: Passive restoration of sub-tropical grassland after abandonment of cultivation

description: Passive restoration of grasslands after the abandonment of cultivation may
 be a viable restoration option where seed sources from remnant grasslands
 are available, and if the risk of deflected succession is low. Passive
 restoration of subtropical grassland in Queensland, Australia was
 evaluated along a chronosequence of abandoned cultivation (fallow)
 paddocks. Plant communities in fallow paddocks were compared with nearby
 remnant grassland. On average, species richness recovers after 60 years of
 abandonment and floristic composition shows affinities with nearby remnant
 grassland (Bray-Curtis ˜ 0·6). The risk of deflected succession, such as
 dominance by exotic grasses, has apparently been low in this ecosystem.
 Annual grasses and forbs are rapid colonizers of the abandoned fields, and
 richness of perennial forbs exhibits near-linear recovery. Perennial
 grasses are relatively slow to establish but all except two species have
 statistically insignificant differences in abundance between remnant
 grassland and fallow fields after 20 years. The perennial grasses that
 recover most rapidly in fallow paddocks have disseminules that are adorned
 with appendages for wind dispersal including the most important dominant
 grass, Dichanthium sericeum. The perennial grasses that are slowest to
 recover are probably less effective dispersers. Synthesis and
 applications. Passive restoration of grasslands after the abandonment of
 cultivation can be a viable contribution to grassland conservation where
 there is an adequate matrix of remnant grasslands in the vicinity of
 fallows, perennial exotic species do not monopolize fallows and the
 dominant native grasses are well dispersed.
description: fallow_data
DOI: 10.5061/dryad.db40s
title: Data from: Intergenerational effects of inbreeding in Nicrophorus vespilloides: offspring suffer fitness costs when either they or their parents are inbred

description: Inbreeding depression is the reduction in fitness caused by mating between
 related individuals. Inbreeding is expected to cause a reduction in
 offspring fitness when the offspring themselves are inbred, but outbred
 individuals may also suffer a reduction in fitness when they depend on
 care from inbred parents. At present, little is known about the
 significance of such intergenerational effects of inbreeding. Here, we
 report two experiments on the burying beetle Nicrophorus vespilloides, an
 insect with elaborate parental care, in which we investigated inbreeding
 depression in offspring when either the offspring themselves or their
 parents were inbred. We found substantial inbreeding depression when
 offspring were inbred, including reductions in hatching success of inbred
 eggs and survival of inbred offspring. We also found substantial
 inbreeding depression when parents were inbred, including reductions in
 hatching success of eggs produced by inbred parents and survival of
 outbred offspring that received care from inbred parents. Our results
 suggest that intergenerational effects of inbreeding can have substantial
 fitness costs to offspring, and that future studies need to incorporate
 such costs to obtain accurate estimates of inbreeding depression.
description: MatteyStruttSmisethJEB2013Data from two experiments testing for effects on inbreeding in offspring and inbreeding in parents on offspring fitness in the burying beetle Nicrophorus vespilloides
DOI: 10.5061/dryad.q8292
title: Data from: Plasmodium infection brings forward mosquito oviposition

description: Invertebrate hosts often bring forward their reproductive effort in
 response to a parasitic infection. This is widely interpreted as a
 host-driven response aimed at compensating for the expected losses in
 future fitness as a result of parasitism. Here we report that mosquitoes
 bring forward their oviposition schedule when they are infected with
 Plasmodium, a parasite known to severely curtail mosquito fecundity. This
 response could aim at compensating for a negative time-dependent effect of
 the parasite on mosquito fitness, as infected mosquitoes seem to display a
 strong and progressive decrease in the quality of the eggs they lay. In
 addition, we show that this shift in oviposition date is dependent on
 mosquito strain: a comparison of several isogenic mosquitoes strains, one
 insecticide-susceptible and two insecticide-resistant ones, reveals that
 only the former shift their oviposition strategy when infected. This
 pattern suggests the existence of a costly host-driven response to
 parasitism, as insecticide-resistant mosquitoes have been shown to be in
 generally poorer condition.
description: Description of the
 columns headersoviposition.data (first
 tab in the Excel file) has 12 columns : - mosquito number - the
 experimental cage the mosquito comes from (where he bloodfed) - whether
 the bird he fed on was infected or not : infection - the identity of that
 bird (ring color and number) - the parasitaemia of that bird (when he is
 infected) at the acute phase of the infection (10 days after the infection
 onset) : J10 - the color of the mosquito (to identify which strains it
 belongs to) - mosquito strain - the egg-laying date (to which 6 days
 should be removed to get the graphs in the article) : lay - the number of
 eggs laid by the females : eggs - eggs hatching date : hatch - the number
 of larvae hatched from those eggs - if and when mosquito died in the water
 before egg laying : drown oocyst.data (second tab) has 5 columns : - the
 experimental infected cage the mosquito comes from (where he bloodfed) -
 mosquito strain (bas4 = SA4B4, aslab = SLAB, csr = SR) - the number of
 oocysts counted after dissection - the number of eggs laid by the females
 : eggs - the number of larvae hatched from those eggsOviposition.data.xlsx
DOI: 10.5061/dryad.2mn480b
title: Data from: Spatial, temporal, and experimental: three study design cornerstones for establishing defensible numeric criteria in freshwater ecosystems

description: 1.Nutrient over‐enrichment increasingly threatens global water resources.
 Stressor‐response studies specifically designed to identify levels of
 nutrients strongly associated with undesirable ecological conditions are
 needed to inform numeric nutrient criteria that protect inland waters.
 2.Diatoms are important components of aquatic life, which support higher
 trophic levels and are sensitive to nutrient enrichment. We tested a
 framework that relies on stressor‐response modelling of phosphorus (P)
 enrichment and stream diatom assemblages across many field locations,
 multiple years and seasons within years, and under controlled experimental
 conditions to inform nutrient criteria development. 3.Diatom species
 composition was nonlinearly correlated with total phosphorus (TP)
 throughout the two‐year field study. This occurred despite temporal shifts
 in species composition between two hydrologically distinct years and over
 eight seasons. 4.Species assemblages on rocks transplanted from a low P
 stream to mesocosms representing a P enrichment gradient (8, 20 and 100 μg
 L−1) shifted into two groups over time. Species composition on rocks in
 low (20 μg L−1) and high (100 μg L−1) P mesocosms was consistent with
 assemblages at P‐enriched field sites, whereas rocks in control (8 μg L−1)
 mesocosms had significantly different species composition, consistent with
 low P field sites. Species composition on rocks transplanted from high P
 streams did not shift as dramatically and were not significantly different
 after exposure to different P treatments in mesocosms. 5.Threshold
 Indicator Taxa Analysis identified synchronous declines in several diatom
 species that culminated in assemblage thresholds associated with TP
 concentrations &gt; 20 and 25 μg L−1 for 2006 and 2007 respectively.
 6.Synthesis and applications. Diatom assemblages show consistent responses
 to nutrient enrichment despite temporal shifts associated with confounding
 factors common in stream ecosystems. Regulators should include diatom
 assemblage responses when developing numeric nutrient criteria. We present
 a framework that includes spatial, temporal and experimental components,
 and has broad applicability for use in different ecological settings to
 evaluate ecological endpoints and set limits for a variety of contaminants
 threatening freshwater ecosystems throughout the world.
description: TaylorDiatomAssemblageMultivariate2018This file explains all of the variables in each of the datasets that accompany: Taylor J, Back J, Brooks B, King R 2018ms. Spatial, temporal, experimental: three study design cornerstones for establishing defensible numeric criteria for freshwater ecosystems. Each dataset is a separate workbook in a single excel file (TaylorDiatomAssemblageMultivariate2018.xlsx).