cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.x95x69pp0
title: Dataset on how mesopredator-mediated trophic cascade can break persistent phytoplankton blooms in coastal waters

description: Managing eutrophied systems using only nutrient decreases to impose
 bottom-up control can be economically and ecologically challenging.
 Top-down controls through increased consumption have sometimes effectively
 controlled phytoplankton blooms. However, mechanistic insights, especially
 on possible trophic cascades, are less understood in brackish,
 species-poor coastal waters, where large cladocera are absent. In this
 study, we set up large mesocosms for three consecutive years during the
 growing season. One set of mesocosms contained mesopredators (gobies and
 shrimps), whereas the other mesocosms had no such mesopredator present.
 The results were standardized to monitoring data from the ecosystem to
 track possible differences between treatments and the system. We found
 that mesopredator mesocosms showed lower turbidity, phytoplankton biomass,
 and nutrients compared to no-mesopredator mesocosms, and compared to the
 ecosystem. This decrease allowed macrophytes to colonize water depths only
 sparsely colonized in the ecosystem. Rotifer biomass increased in
 mesopredator mesocosms compared to the ecosystem and to the
 no-mesopredator mesocosms. Likewise, copepod biomass that potentially
 grazes upon rotifers and other microzooplankton decreased in mesopredator
 mesocosms. No-mesopredator mesocosms were colonized by an omnivorous
 mesograzer (Gammarus tigrinus), potentially creating additional pressure
 on macrophytes and increasing grazing-mediated nutrient release.
 Zooplankton was not able to control the non-nutrient-limited
 phytoplankton. We propose a new mechanism, where a higher mesopredator
 density will increase grazing on phytoplankton by promoting
 microzooplankton capable of grazing on picophytoplankton. This proposed
 mechanism would contrast with freshwater systems, where a decrease of
 zooplanktivorous fish would promote larger phytoplankton grazer like
 cladocerans. Biomanipulation in such species-poor eutrophic coastal waters
 may be more successful, due to fewer trophic pathways, that can cause
 complex top-down controls like in other systems. Stocking eutrophic
 coastal waters with gobies and shrimps may be an alternative
 biomanipulative approach rather than selectively removing large
 piscivorous or omnivorous fish from eutrophic coastal waters.
description: This dataset includes monitoring data from the Biological Station
 Zingst, experimental set-ups and field data. Data collection spanned
 several years and sampling was conducted according to HELCOM protocols.
 For more details, please read the Material and Methods section of the
 publication. Data was processed using R and RStudio.
 Data is presented as raw data and partially converted to fresh mass per
 square meter.
description: All datasets can be opened using R/RStudio.
DOI: 10.5061/dryad.6t1g1jx32
title: Periodically disturbing biofilms reduces expression of quorum sensing regulated virulence factors in Pseudomonas aeruginosa

description: The opportunistic pathogen Pseudomonas aeruginosa uses quorum
 sensing to control the expression of multiple virulence factors. In this
 dataset, we provide raw data demonstrating that periodically disturbing
 biofilms composed of P. aeruginosa using a physical force reduces
 the expression of multiple quorum sensing regulated virulence factors from
 the three major regulons. This dataset also contains cell density
 measurements of bacteria both the in biofilm and planktonic state under a
 variety of conditions that use physical force to manipulate the spatial
 positioning of bacteria. Finally, the data set contains raw outputs from a
 network logic model that described the core quorum sensing network. This
 data is affiliated with the manuscript entitled "Periodically
 disturbing biofilms reduces expression of quorum sensing regulated
 virulence factors in Pseudomonas aeruginosa."
DOI: 10.5061/dryad.jsxksn0dw
title: Fourier transform infrared spectroscopy as a non-destructive method for analysing herbarium specimens

description: Dried plant specimens stored in herbaria are an untapped treasure chest of
 information on environmental conditions, plant evolution and change over
 many hundreds of years. Due to their delicate nature and irreplaceability,
 there is limited access for analysis to these sensitive samples,
 particularly where chemical data is obtained using destructive techniques.
 Fourier transform infrared spectroscopy (FTIR) is a chemical analysis
 technique that can be applied non-destructively to understand chemical
 bonding information and therefore functional groups within the sample.
 This provides the potential for understanding geographic, spatial and
 species-specific variation in plant biochemistry. Here we demonstrate the
 use of mid-FTIR microspectroscopy for the analysis of Drosera rotundifolia
 herbaria specimens, which were collected 100 years apart from different
 locations. Principal component and hierarchical clustering analysis
 enabled successful differentiation between three main regions on the plant
 (lamina, tentacle stalk and tentacle head), and between the different
 specimens. Lipids and protein spectral regions were particularly sensitive
 differentiators of plant tissues. Differences between the different sets
 of specimens were smaller. This study demonstrates that relevant
 information can be extracted from herbarium specimens using FTIR, with
 little impact on the specimens. FTIR therefore provides the potential as a
 powerful tool to unlock historic information within herbaria.
description: <strong>Sample Collection</strong>
 Four <em>D. rotundifolia</em> herbarium specimens
 were used in this study (Table 1, Figure S1). Two of the specimens were
 plants collected in 2021 from the same location, at the same time by the
 same collector. The other two specimens were collected from a different
 location but were collected at the same place on the same date in 1934.
 All samples were in dried form with no observable moisture.
 <strong>FTIR</strong> Specimens
 were carefully removed from the herbarium sheet and placed onto the sample
 stage. FTIR spectra were taken for each of three tissue types (Fig. 1:
 lamina, tentacle stalk, tentacle head), on two leaves, for each of the
 four specimens. In each area, three replica FTIR spectra maps were
 produced. Each map consisted of roughly 15 points depending on area size
 (minimum = 8, maximum = 20). Infrared spectra were taken using a Thermo
 Nicolet iN10mx spectrometer fitted with a liquid-nitrogen-cooled MCT
 detector. Spectra were captured in transmission mode, with an 80 × 80 µm
 aperture size and 4 cm-1 resolution. Background spectra were taken in air
 before each sample, with 64 scans averaged at each map point; samples were
 suspended enabling direct transmission of IR.
DOI: 10.5061/dryad.3ffbg79nf
title: Replaced feathers, degree of bill corrugation, and bill coloration in 19 Central American hummingbird species

description: We document molt extent; age-specific molt patterns, plumages, and percent
 of the bill with corrugations; the presence or absence of delayed plumage
 maturation and bill color changes in males of some species; and molt
 timing in the 19 resident hummingbird species of Belize. Molt strategies
 and rates of bill smoothing were similar to North American species, with
 all species showing limited to partial preformative molts, replacing only
 body feathers and some wing coverts and retaining all remiges and
 rectrices. Extent of bill corrugations reduced to ≤10% of bill length in
 all species by the time definitive cycle basic plumage is achieved. Males
 in sexually dichromatic species showed delayed maturation in plumage
 characteristics and/or bill coloration, and in two dichromatic species,
 some older females showed male-like plumage. Nine species representing
 multiple clades showed advanced timing to the second prebasic molt,
 indicating that this trait may be a proximal response to individuals not
 breeding during the first molt cycle. Species with advanced second
 prebasic molts replaced fewer wing coverts during the preformative molt
 than species with later molt timing.
description: Data was collected at 5 MoSI bird-banding stations in Belize, and
 also through analysis of photographs in the Cornell Laboratory of
 Ornithology's Macaulay Library.
DOI: 10.5061/dryad.jdfn2z3f8
title: An aphid symbiont confers protection against a specialized RNA virus, another increases vulnerability to the same pathogen

description: Insects often harbor heritable symbionts that provide defense against
 specialized natural enemies, yet little is known about symbiont protection
 when hosts face simultaneous threats. In pea aphids (Acyrthosiphon pisum),
 the facultative endosymbiont Hamiltonella defensa confers protection
 against the parasitoid, Aphidius ervi, and Regiella insecticola protects
 against aphid-specific fungal pathogens, including Pandora neoaphidis.
 Here we investigated whether these two common aphid symbionts protect
 against a specialized virus A. pisum virus (APV), and whether their
 anti-fungal and anti-parasitoid services are impacted by APV infection. We
 found that APV imposed large fitness costs on symbiont-free aphids and
 these costs were elevated in aphids also housing H. defensa. In contrast,
 APV titers were significantly reduced and costs to APV infection were
 largely eliminated in aphids with R. insecticola. To our knowledge, R.
 insecticola is the first aphid symbiont shown to protect against a viral
 pathogen, and only the second arthropod symbiont reported to do so. In
 contrast, APV infection did not impact the protective services of either
 R. insecticola or H. defensa. To better understand APV biology, we
 produced five genomes and examined transmission routes. We found that
 moderate rates of vertical transmission, combined with horizontal transfer
 through food plants, were the major route of APV spread, although lateral
 transfer by parasitoids also occurred. Transmission was unaffected by
 facultative symbionts. In summary, the presence and species identity of
 facultative symbionts resulted in highly divergent outcomes for aphids
 infected with APV, while not impacting defensive services that target
 other enemies. These findings add to the diverse phenotypes conferred by
 aphid symbionts, and to the growing body of work highlighting extensive
 variation in symbiont-mediated interactions.
description: Please see refer to the accompanying published article:Higashi,
 C. H. V., Nichols, W. L., Chevignon, G., Patel, V., Allison, S. E., Kim,
 K. L., ... & Oliver, K. M. (2022). An aphid symbiont confers
 protection against a specialized RNA virus, another increases
 vulnerability to the same pathogen. Molecular Ecology.
DOI: 10.5061/dryad.866t1g1tv
title: Eyes on the future: buffering increased costs of incubation by abandoning offspring

description: Abstract Life history theory states that the resources invested in current
 reproduction must be traded off against resources needed for survival and
 future reproduction. Long-lived organisms have a higher residual
 reproductive value and are therefore expected to be sensitive to
 reproductive investments that may reduce survival and future reproduction.
 Individuals within a population may vary in phenotypic quality,
 experience, access to resources etc. This may affect their optimal
 reproductive investment level. In this study we manipulated reproductive
 costs by shortening and extending the incubation period in common eiders
 Somateria mollissima without altering clutch size. Females whose
 incubation time was prolonged experimentally, suffered higher mass loss
 and increased clutch loss/nest desertion. These females were also more
 prone to abandon their brood after hatching. Both clutch loss and brood
 abandonment decreased with clutch size in all treatment categories,
 indicating higher phenotypic quality and/or better access to resources for
 females producing more eggs. However, although females with prolonged
 incubation were lighter at hatching, their return rate and breeding
 performance in the following year were unaffected. These results show that
 individual quality as expressed through clutch size and body mass is
 affecting current reproductive investment level as well as future survival
 and breeding performance. The results also show that individual birds are
 sensitive to changes in their own condition, and when reproductive effort
 is approaching a level where survival or future survival may be
 compromised, they respond by terminating their current reproductive
 attempt.
description: The dataset contains four
 files:  (1) README.pdf
 (explanations) (2) eider.xlsx (microsoft excel spreadsheet
 workbook) (3) eider.csv (experimental data file as
 semicolon-delimited plain text) (4) eider.inp (capture-mark-recapture data as
 whitespace-delimited plain text)
   The
 experimental data are provided both in "eider.csv" and in the
 "Experiment" sheet of
 "eider.xlsx". The capture-mark-recapture data are provided
 both in "eider.inp" and in the "CMR" sheet of
 "eider.xlsx". The information needed to interpret the data is
 provided both in "README.pdf" and in
 "eider.xlsx".   For questions on these files, please contact the
 first author (sveinn.a.hanssen@nina.no).
DOI: 10.5061/dryad.mgqnk9935
title: Quantitative assessment of the dispersal of soil-dwelling oribatid mites via rodents in restored heathlands

description: 1. Heathland restoration using topsoil removal requires the
 re-colonisation of above- and belowground communities. Oribatid mites play
 a key role in the comminution of organic matter and are frequently early
 colonizers during succession despite their limited mobility. Whereas the
 assembly of their communities may take decades, passive dispersal likely
 dominates colonisation processes, but especially dispersal via other
 animals (phoresy) remains poorly studied. Compared to other potential
 hosts, movement habits and ecology of small rodents may provide dispersal
 advantages to oribatid communities. 2. We studied dispersal of oribatid
 mites via small rodents in restored heathland sites of different age. We
 measured movement patterns of small rodents and extracted mites from their
 pelts and nests to estimate annual contributions of these rodents to the
 dispersal of oribatids. We also discussed phoretic estimates reported on
 other host groups as a reference. 3. Probability estimates of oribatids in
 pelts and nests showed lower occurrence frequencies compared to other
 reported phoretic hosts. However, local rodent communities may aid the
 dispersal of up to 41,000 oribatid mites per year. We highlight the high
 diversity of oribatid species mounting rodents, unlike strong
 species-specific filters reported in other passive pathways. We found that
 over  half (58%) of the oribatid species reproduced asexually and
 over a third (34%) had a soil-dwelling lifestyle. We also observed that
 rodents often travel short distances below 40m, but occasionally reach
 distances of up to 100m, especially in earlier successional stages. 4.
 Synthesis and applications. Our results suggest that rodents may
 contribute to assembly processes of soil-dwelling oribatid communities
 given the slow turnover rate of this group in heathlands. This is
 accomplished through short-distance dispersal, and especially in sites at
 early stages of succession. To our knowledge, we are the first to
 quantitatively assess the potential dispersal of oribatid mites via
 rodents.
DOI: 10.5061/dryad.44j0zpchw
title: Using DNA metabarcoding to explore spatial variation in diet across European Hawfinch populations

description: The investigation of diet in avian species is essential to an
 understanding of their ecology and local adaptations, as well as long-term
 conservation. This can be particularly challenging due to the wide
 distribution and high ecological plasticity of many bird species. Dietary
 richness and variation are under-studied in woodland bird species, due
 primarily to challenges in accurately identifying plant and invertebrate
 taxa consumed. Within Europe, Hawfinch (Coccothraustes coccothraustes)
 have shown variation in population trends, with moderate declines across
 central and eastern Europe, while western European populations have shown
 moderate increases. Ecological drivers behind this differing trend are
 still unknown; one possibility is differences in diet, yet little research
 has been conducted into Hawfinch diet in mainland Europe or elsewhere.
 This study aimed to present the first molecular dietary analysis of
 Hawfinch populations across two European countries. Faecal samples were
 collected between January and July of 2019 from Hawfinch caught at six
 artificial feed sites: two in Denmark and four in Germany. DNA was
 successfully extracted from 80 samples and plant Internal Transcribed
 Spacer 2 (ITS2) and invertebrate Cytochrome Oxidase Subunit 1 (COI)
 barcodes were amplified. A total of 35 plant and 37 invertebrate taxa were
 found across the 80 Hawfinch faecal samples, with plant and insect orders
 Fagales and Lepidoptera respectively the most frequently detected.
 Hawfinch dietary composition differed significantly between European
 countries, suggesting Hawfinch can make use of available food resources
 which are likely to differ spatially. Our study shows how DNA
 metabarcoding can be used to provide novel ecological information
 associated with under-studied bird species, thus providing essential
 information for future management and conservation of Hawfinch and their
 habitats.
description: Files containing raw Illumina sequencing data regarding Hawfinch
 diet described in Stenhouse et al. 2023.
DOI: 10.5061/dryad.x3ffbg7p8
title: Data for: The biomechanics of tooth strength: testing the utility of simple models for predicting fracture in geometrically complex teeth

description: Teeth must fracture foods while avoiding being fractured themselves. This
 study evaluated dome biomechanical models used to describe tooth
 strength.  Finite element analysis (FEA) tested whether the
 predictions of the dome models applied to the complex geometry of an
 actual tooth. A finite element model (FEM) was built from microCT scans of
 a human M3. The FEA included three loading regimes simulating contact
 between 1) a hard object and a single cusp tip, 2) a hard object and all
 major cusp tips, and 3) a soft object and the entire occlusal basin. Our
 results corroborate the dome models with respect to the distribution and
 orientation of tensile stresses, but document heterogeneity of stress
 orientation across the lateral enamel. This implies that high stresses
 might not cause fractures to fully propagate between cusp tip and cervix
 under certain loading conditions. The crown is most at risk of failing
 during hard object biting on a single cusp. Geometrically simple
 biomechanical models are valuable tools for understanding tooth function
 but do not fully capture aspects of biomechanical performance in actual
 teeth whose complex geometries may reflect adaptations for strength.
DOI: 10.5061/dryad.5qfttdz99
title: Data from: Pathogen reduction of monkeypox virus in plasma and whole blood using riboflavin and UV light

description: Background Monkeypox virus has recently emerged from endemic foci in
 Africa and, to date, several hundred human infections have been reported
 from at least 16 non-African countries.  The detection
 of virus in skin lesions, blood, semen, and saliva of infected patients
 with monkeypox infections raises the potential for disease transmission
 via routes that have not been previously documented, including by blood
 and plasma transfusions.  Methods for protecting the
 blood supply against the threats of newly emerging disease agents exist
 and include Pathogen Reduction Technologies (PRT) which utilize
 photochemical treatment processes to inactivate pathogens in blood while
 preserving the integrity of plasma and cellular
 components.  Such methods have been employed broadly for
 over 15 years, but effectiveness of these methods under routine use
 conditions against monkeypox virus has not been reported. Results The
 levels of spiked virus present in whole blood and plasma samples exceeded
 103 infectious particles per dose, corresponding to greater than
 105 DNA copies per mL.  Treatment of whole
 blood and plasma units under standard operating procedures for the Mirasol
 PRT System resulted in complete inactivation of infectivity to the limits
 of detection.  This is equivalent to a reduction
 of ≥ 2.86 +/- 0.73 log10 pfu/mL of infectivity
 in whole blood and ≥ 3.47 +/-0.19 log10 pfu/mL
 of infectivity in plasma under standard operating conditions for those
 products.  Conclusion Based on this data and corresponding
 studies on infectivity in patients with monkeypox infections, use of
 Mirasol PRT would be expected to significantly reduce the risk of
 transfusion transmission of monkeypox.
description: Monkeypox virus (strain USA_2003) was used to inoculate plasma
 and whole blood units that were then treated with riboflavin and UV light
 (Mirasol Pathogen Reduction Technology System, Terumo BCT, Lakewood, CO).
 The infectious titers of monkeypox virus in the samples before and after
 riboflavin + UV treatment were determined by plaque assay on Vero
 cells.
DOI: 10.5061/dryad.9kd51c5n2
title: Including environmental covariates clarifies the relationship between endangered Atlantic salmon (Salmo salar) abundance and environmental DNA

description: Collecting environmental DNA (eDNA) as a nonlethal sampling approach has
 been valuable in detecting the presence/absence of many imperiled taxa;
 however, its application to indicate species abundance poses many
 challenges. A deeper understanding of eDNA dynamics in aquatic systems is
 required to better interpret the substantial variability often associated
 with eDNA samples. Our sampling design took advantage of natural variation
 in juvenile Atlantic salmon (Salmo salar) distribution and abundance along
 9 km of a single river in the Province of New Brunswick (Canada), covering
 different spatial and temporal scales to address the unknown seasonal
 impacts of environmental variables on the quantitative relationship
 between eDNA concentration and species abundance. First, we asked whether
 accounting for environmental variables strengthened the relationship
 between eDNA and salmon abundance by sampling eDNA during their spring
 seaward migration. Second, we asked how environmental variables affected
 eDNA dynamics during the summer as the parr abundance remained relatively
 constant. Spring eDNA samples were collected over a 6‐week period (12
 times) near a rotary screw trap that captured approximately 18.6% of
 migrating smolts, whereas summer sampling occurred (i) at three distinct
 salmon habitats (9 times) and (ii) along the full 9 km (3 times). We
 modeled eDNA concentration as a product of fish abundance and
 environmental variables, demonstrating that (1) with inclusion of
 abundance and environmental covariates, eDNA was highly correlated with
 spring smolt abundance and (2) the relationships among environmental
 covariates and eDNA were affected by seasonal variation with relatively
 constant parr abundance in summer. Our findings underscore that with
 appropriate study design that accounts for seasonal environmental
 variation and life history phenology, eDNA salmon population assessments
 may have the potential to evaluate abundance fluctuations in spring and
 summer.
description: Data provided include field sample metadata, qPCR results, and
 calculated eDNA concentrations. Standard curve data are included as
 well.
description: MS Excel/Google Sheets. All missing data are denoted with
 NA.