cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.34tmpg4pk
title: Experimental reduction of haemosporidian infection affects maternal reproductive investment, parental behaviour, and offspring condition

description: When hosts have a long coevolutionary history with their parasites,
 fitness costs of chronic infection have often been assumed to be
 negligible. Yet, experimental manipulation of infections sometimes reveals
 effects of parasites on their hosts, particularly during reproduction.
 Whether these effects translate into fitness costs remains unclear. Here,
 we present the results of an experimental study conducted in a
 free-ranging population of red-winged blackbirds (Agelaius phoeniceus)
 naturally experiencing a high prevalence of haemosporidian infections,
 with &gt; 95% of breeding adults infected with parasites from one or
 more haemosporidian genus. To assess effects of infection during
 reproduction, we manipulated adult red-winged blackbird females’ parasite
 burden by administering an anti-haemosporidian medication before onset of
 egg-laying. Experimental reduction of infection resulted in significant
 benefits to mothers and their offspring. Medicated females laid heavier
 clutches, invested more in incubation and provisioning behaviour, and
 produced more fledglings than control females. Nestlings of medicated
 females had higher haematocrit, higher blood glucose, and lower reactive
 oxygen metabolites than nestlings of control females. Overall, our results
 provide evidence that, even in a species with a long history of high
 prevalence of infection, parasites can lead to decreased maternal
 investment and offspring quality, substantially reducing fitness.
DOI: 10.6084/m9.figshare.31143889.v2
title: Reactive-infiltration instabilities and pattern transitions in heterogeneous porous media with finite extent

description: This is the dateset for "Reactive-infiltration instabilities and pattern transitions in heterogeneous porous media with finite extent" by Li et al.
DOI: 10.5061/dryad.ngf1vhhxw
title: COI-barcoding evidences mislabelling and the use of endangered species in German shark products

description: Recent estimations categorize about 37% of all cartilaginous fish species
 (sharks, rays and chimaeras) as endangered. Especially sharks show severe
 population declines and many species are protected by CITES and other
 international conventions. Shark meat and other body parts are sold as
 various products internationally, often via complex trade routes. As most
 shark products (like cartilage pills, liver oil or smoked meat) are
 heavily processed, correct species identification can only be achieved via
 DNA-based methods. It has been shown that a large proportion of shark
 products ends up mislabelled to the consumer in Europe. Moreover,
 fraudulent and economically motivated substitution with cheaper meat is a
 strong driver for illegal and non-transparent shark trade. Interestingly,
 the German market is one of the most significant key drivers of the legal
 trade with Squalus acanthias, the spiny dogfish, which is appreciated in
 gastronomy as ‘Schillerlocken’ although the species is listed as
 vulnerable by the IUCN. Additionally, cartilage pills are a popular
 ‘health’ product in ‘alternative medicine’. We wanted to find out whether
 mislabelled and substituted shark products exist in the German market.
 Hence seven ‘Schillerlocken’ and 17 products of ‘shark cartilage pills’
 were analysed by DNA-Barcoding. We used various primer cocktails to
 amplify and sequence between 127 bp (‘minibarcodes’) and 650 bp of the
 mitochondrial Cytochrome C Oxidase subunit I. We identified 45.8% Squalus
 acanthias (including all ‘Schillerlocken’) and 8.3% critically endangered
 shark species (Galeorhinus galeus), as well as 4.2% Prionace glauca. In
 addition, we report 70.6% of the cartilage pills as mislabelled or
 substituted. The analysis revealed the use of an undeclared teleost
 species (Merluccius merluccius, European hake), as well as Gallus gallus
 (chicken) and Solanum sp. (potato). Our results support earlier demands
 for better transparency and stronger regulation of the shark product
 market and hold implications for conservation as well as for
 consumers' health.
description: DNA was extracted from either fermented shark abdominal flaps or
 shark cartilage food supplements (N=23). PCRs were conducted targeting
 between 127 and 650 bp of the mitochondrial Cytochrome C Oxidase subunit
 I. Sequences were obtained by Sanger sequencing.
DOI: 10.5061/dryad.v6wwpzh0h
title: Country‐wide genetic monitoring over 21 years reveals lag in genetic recovery despite spatial connectivity in an expanding carnivore (Eurasian otter, Lutra lutra) population

description: Numerous terrestrial mammal species have experienced extensive population
 declines during past centuries, due largely to anthropogenic pressures.
 For some species, including the Eurasian otter (Lutra lutra),
 environmental and legal protection has more recently led to population
 growth and recolonisation of parts of their historic ranges. While
 heralded as conservation successes, only a few such recoveries have been
 examined from a genetic perspective, i.e. whether genetic variability and
 connectivity have been restored. We here use large-scale and long-term
 genetic monitoring data from UK otters, whose population underwent a
 well-documented population decline between the 1950s to 1970s, to explore
 the dynamics of a population re-expansion over a 21-year period. We
 genotyped otters from across Wales and England at five time points between
 1994 and 2014 using 15 microsatellite loci. We used this combination of
 long-term temporal and large-scale spatial sampling to evaluate 3
 hypotheses relating to genetic recovery; that (i) gene flow between
 sub-populations would increase over time, (ii) genetic diversity of
 previously isolated populations would increase, and that (iii) genetic
 structuring would weaken over time. Although we found an increase in
 inter-regional gene flow and admixture levels among subpopulations, there
 was no significant temporal change in either heterozygosity or allelic
 richness. Genetic structuring among the main sub-populations hence
 remained strong and showed a clear historical continuity. These findings
 highlight an underappreciated aspect of population recovery of endangered
 species, that genetic recovery may often lag behind the processes of
 spatial and demographic recovery. In other words, the restoration of
 physical connectivity of populations does not necessarily lead to genetic
 connectivity. Our findings emphasise the need for genetic data as an
 integral part of conservation monitoring, to enable the potential
 vulnerability of populations to be evaluated.
description: DNA extracted from muscle tissue samples, PCR of microsatellite
 loci, fragment analysis with fluorescent labels on capillary instrument,
 manual genotype calling.
description: Text editor or spreadsheet software such as Excel.
DOI: 10.15468/dl.gve2x5
title: Occurrence Download

description: A dataset containing 2925 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Zeltus amasa"
 ]
}

 The dataset includes 2925 records from 37 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003352-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.rjdfn2zfw
title: Simulated pollinator decline has similar effects on seed production of female and hermaphrodite Lobelia siphilitica, but different effects on selection on floral traits

description: PREMISE: Pollinator decline, by reducing seed production, is predicted to
 strengthen natural selection on floral traits. However, the effect of
 pollinator decline on gender dimorphic species (such as gynodioecious
 species, where plants produce female or hermaphrodite flowers) may differ
 between the sex morphs: if pollinator decline reduces the seed production
 of females more than hermaphrodites, then it should also have a larger
 effect on selection on floral traits in females than in hermaphrodites.
 RESULTS: Experimentally reducing pollination decreased seed production of
 both females and hermaphrodites by ~21%. Reducing pollination also
 strengthened selection on floral traits, but this effect was not larger in
 females than in hermaphrodites. Instead, reducing pollination intensified
 selection for taller inflorescences in hermaphrodites, but did not
 intensify selection on any floral trait in females. CONCLUSIONS: Our
 results suggest that pollinator decline will not have a larger effect on
 either seed production or selection on floral traits of female plants. As
 such, any effect of pollinator decline on seed production may be similar
 for gender dimorphic and monomorphic species. However, the potential for
 floral traits of females (and thus of gender dimorphic species) to evolve
 in response to pollinator decline could be limited.
description: To simulate pollinator decline, we experimentally reduced
 pollinator access to female and hermaphrodite Lobelia siphilitica plants.
 We compared the seed production of plants in the reduced pollination
 treatment to plants that were exposed to ambient pollination conditions.
 Within each treatment we also measured directional selection on four
 floral traits of females and hermaphrodites.
DOI: 10.15468/dl.ajr3mr
title: Occurrence Download

description: A dataset containing 20 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Astragalus membranaceus mongholicus"
 ]
}

 The dataset includes 20 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003353-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gf2x7q
title: Occurrence Download

description: A dataset containing 61 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "GadmGid is BRA.13_1",
 "TaxonKey is Melanoxylon brauna"
 ]
}

 The dataset includes 61 records from 25 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003354-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.vq83bk3xb
title: Simulations scripts for: Strain localization patterns and thrust propagation in 3-D discrete element method (DEM) models of accretionary wedges

description: High-resolution three-dimensional discrete element method (DEM)
 simulations of sandbox-scale models of accretionary wedges performed in
 this study suggest thrusts follow a variety of propagation processes and
 orientations in the wedges depending on a number of factors including the
 stage of development of the wedge (precritical vs. critical), basal
 friction, and type of thrust (forward vs. backward-vergent). In terms of
 propagation processes, two clear mechanisms are identified. The first
 involves propagation from the decollement to the wedge top, similar to the
 standard model of thrust propagation seen in many kinematic models, and in
 the second, thrusts grow downward from an initial nucleation point just
 below the top surface of the wedge as well as upward from the decollement
 joining in the middle. In terms of orientation, forward-vergent thrusts
 initially form at  Roscoe or Arthur orientations, and over
 shortening, form at Coulomb orientations. To arrive at these results, a
 wide array of continuum parameters and fields were extracted from the
 granular assembly of the DEM simulations, including stress, strain, strain
 rate, kinetic energy, Mohr-Coulomb parameters, and proximity to yielding
 using the Drucker-Prager criterion to visualize thrust nucleation and
 propagation. Lastly, the advantages and disadvantages of these continuum
 proxies for discerning failure in the granular assembly are considered,
 and the spatial and temporal relationship between proximity to yielding
 and strain localization (both pre-peak and persistent shear banding) in
 the granular model of an accretionary wedge is explored.
description: This repository contains the LAMMPS simulation scripts used for
 running all granular simulations whose results are reported in the
 manuscript titled " Strain localization patterns and thrust
 propagation in 3-D discrete element method (DEM) models of accretionary
 wedges." These include the simple shear simulations and the
 accretionary wedge simulations. The repository also contains the scripts
 used for calculating continuum fields from the discrete grains of the
 LAMMPS simulation results, such as stress, strain, strain rate, and
 kinetic energy. These files are available as Jupyter notebooks.
DOI: 10.5061/dryad.k0p2ngfc4
title: Genomic analyses of hair from Ludwig van Beethoven

description: Ludwig van Beethoven (1770–1827) remains among the most influential and
 popular classical music composers. Health problems significantly impacted
 his career as a composer and pianist, including progressive hearing loss,
 recurring gastrointestinal complaints and liver disease. In 1802,
 Beethoven requested that following his death, his disease be described and
 made public. Medical biographers have since proposed numerous hypotheses,
 including many substantially heritable conditions. Here we attempt a
 genomic analysis of Beethoven in order to elucidate potential underlying
 genetic and infectious causes of his illnesses. We incorporated
 improvements in ancient DNA methods into existing protocols for ancient
 hair samples, enabling the sequencing of high-coverage genomes from small
 quantities of historical hair. We analyzed eight independently sourced
 locks of hair attributed to Beethoven, five of which originated from a
 single European male. We deemed these matching samples to be almost
 certainly authentic and sequenced Beethoven’s genome to 24-fold genomic
 coverage. Although we could not identify a genetic explanation for
 Beethoven's hearing disorder or gastrointestinal problems, we found
 that Beethoven had a genetic predisposition for liver disease. Metagenomic
 analyses revealed furthermore that Beethoven had a hepatitis B infection
 during at least the months prior to his death. Together with the genetic
 predisposition and his broadly accepted alcohol consumption, these present
 plausible explanations for Beethoven’s severe liver disease, which
 culminated in his death. Unexpectedly, an analysis of Y-chromosomes
 sequenced from five living members of the Van Beethoven patrilineage
 revealed the occurrence of an extra-pair paternity event in Ludwig van
 Beethoven’s patrilineal ancestry.
description: For all methodology, see the article, Supplementary Information,
 and/or STAR methods.
description: For usage, see the README.md file and GGT.R help menu.
DOI: 10.5061/dryad.z08kprrh5
title: Data for: Identification of integrons and gene cassette-associated recombination sites in bacteriophage genomes

description: Bacteriophages are versatile mobile genetic elements that play key roles
 in driving the evolution of their bacterial hosts through horizontal gene
 transfer. Phages co-evolve with their bacterial hosts and have plastic
 genomes with extensive mosaicism. In this study, we present bioinformatic
 and experimental evidence that temperate and virulent (lytic) phages carry
 integrons, including integron-integrase genes, attC/attI recombination
 sites and gene cassettes. Integrons are normally found in Bacteria, where
 they capture, express and re-arrange mobile gene cassettes via
 integron-integrase activity. We demonstrate experimentally that a panel of
 attC sites carried in virulent phage can be recognized by the bacterial
 class 1 integron-integrase (IntI1) and then integrated into the
 paradigmatic attI1 recombination site using an attC x attI recombination
 assay. With an increasing number of phage genomes projected to become
 available, more phage-associated integrons and their components will
 likely be identified in the future. The discovery of integron components
 in bacteriophages establishes a new route for lateral transfer of these
 elements and their cargo genes between bacterial host cells.
description: All bacteriophage genomes with the descriptions
 “complete genomes” or “genomic sequences” were downloaded from the NCBI
 Genome database (last accessed on 1 May 2022). “Unverified”, “partial” or
 “incomplete” phage genomes were excluded. IntegronFinder 2.0 was used to
 detect complete integrons, CALINs (clusters of <em>attC</em>s
 lacking an associated integron-integrase) and In0 elements
 (integron-integrase that does not carry any gene cassettes) in the 10,705
 downloaded phage genomes, using default parameters.  In addition, every phage genome was screened
 for integron <em>attC</em> sites using a previously described
 HattCI + INFERNAL pipeline. For the HattCI + INFERNAL analysis, the
 minimum bit-score threshold was set to 20, and a minimum of two predicted
 <em>attC</em> sites were required in each candidate CALIN
 according to previously published methods. All predicted <em>attC </em>sites
 that were located within 3 kB of another <em>attC </em>site
 were used in subsequent analysis. Annotations of <em>attC</em>
 sites were based on the results from both sets of bioinformatic
 predictions (i.e. IntegronFinder and HattCI + INFERNAL). ORF annotations
 were based on IntegronFinder results and the original GenBank annotations
 for the respective phages from NCBI. An in-house script attC-taxa.sh
 (https://github.com/timghaly/attC-taxa) was used to classify the phage-associated <em>attC</em> sites according to sequence and structural homologies of chromosomal <em>attC</em> sequences in eleven bacterial taxa.
description: Supplementary File 1 can be opened using Geneious or
 SnapGene.
DOI: 10.5061/dryad.4tmpg4fdx
title: Lianas have a faster resource acquisition strategy than trees: belowground evidence from root traits, phylogeny, and the root economics space

description: 1. The competitive advantage of lianas over trees has been widely
 documented in studies of their leaf functional traits across diverse
 habitats; however, the relative contribution of root functional traits to
 the competitive superiority of lianas over trees has not yet been
 evaluated. The aim of this study was to explore the root functional
 traits, phylogenetic structure of these traits, and root trait dimensions
 of lianas to clarify why lianas can outperform trees. 2. We sampled 69
 liana species from tropical and temperate forests in China and measured
 nine key functional traits of first-order roots of each species, including
 morphological, architectural, anatomical, and chemical traits, as well as
 the percentage of mycorrhizal colonization. Data on these traits were then
 compared with similar data of 127 tree species from the same biome
 obtained from the Global Root Traits (GRooT) database and our previous
 studies. 3. Liana roots had lower construction costs and could acquire
 resources more rapidly compared with tree roots. Significant differences
 were observed in most tree root traits between tropical and temperate
 sites. However, no significant differences were observed in any of the
 liana root traits between tropical and temperate sites, apart from the
 root branching ratio. 4. Lianas showed much weaker phylogenetic
 conservatism in their root traits than trees when species were pooled
 across sites. Phylogenetic constraint was lower for nearly all root traits
 of both temperate lianas and trees compared with those of tropical lianas
 and trees. 5. The root economics space of lianas and trees had two
 orthogonal dimensions with “conservation” and “collaboration” axes.
 However, lianas occupied the trait space with higher root nitrogen
 concentration and greater specific root length, showing “fast” resource
 acquisition strategy, while trees placed opposite space and exhibited
 relatively “slow” strategy. 6. Synthesis. The ability of lianas to
 outcompete trees in harsh environments might be explained by their faster
 resource acquisition strategy and the lower phylogenetic constraint in
 root traits. Generally, lianas might play an increasingly important role
 in the structure and function of forest ecosystems in the future with
 ongoing habitat fragmentation and climate change.
DOI: 10.15468/dl.gkeh9j
title: Occurrence Download

description: A dataset containing 981 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is French Guiana",
 "OccurrenceStatus is Present",
 "TaxonKey is Anopheles darlingi"
 ]
}

 The dataset includes 981 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003355-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.5hqbzkh97
title: Phylogenomic data of Camellia section Paracamellia based on transcriptomes and plastomes

description: Camellia section Paracamellia of the genus Camellia (Theaceae) includes
 major woody oil crops in China and relative wild species as valuable
 genetic resources for breeding. However, the phylogeny and origin of C.
 oleifera and its relative species are still uncertain. In this study, the
 transcriptomes of 22 samples and plastomes of 19 samples were sequenced
 and assembled. Finally, the dataset of phylogenomic matrices was
 generated, including 982 and 326 single-copy orthologous (SCO) genes
 generated from transcriptomes data and the plastid matrix used for
 phylogenetic analysis. Please cite this article as doi:
 10.1111/jse.12948.
DOI: 10.5061/dryad.h70rxwdnh
title: Data from: Infection by a helminth parasite is associated with changes in DNA methylation in the house sparrow

description: Parasites can exert strong selective pressures on their hosts and
 influence the evolution of host immunity. While several studies have
 examined the genetic basis for parasite resistance, the role of
 epigenetics in the immune response to parasites is less understood. Yet,
 epigenetic modifications, such as changes in DNA methylation, may allow
 species to respond rapidly to parasite prevalence or virulence. To test
 the role of DNA methylation in relation to parasite infection we examined
 genome-wide DNA methylation before and during infection by a parasitic
 nematode, Syngamus trachea, in a natural population of house sparrows
 (Passer domesticus) using reduced representation bisulfite sequencing
 (RRBS). We found that DNA methylation levels were slightly lower in
 infected house sparrows, and identified candidate genes relating to the
 initial immune response, activation of innate and adaptive immunity, and
 mucus membrane functional integrity that were differentially methylated
 between infected and control birds. Subsequently, we used
 methylation-sensitive high-resolution melting (MS-HRM) analyses to verify
 the relationship between methylation proportion and Syngamus trachea
 infection status at two candidate genes in a larger sample dataset. We
 found that methylation level at NR1D1, but not CLDN22, remained related to
 infection status, and that juvenile recruitment probability was positively
 related to methylation level at NR1D1. This underscores the importance of
 performing follow up studies on candidate genes. Our findings demonstrate
 that plasticity in the immune response to parasites can be epigenetically
 mediated, and highlight the potential for epigenetic studies in natural
 populations to provide further mechanistic insight into host-parasite
 interactions.
description: Please see the README document ("README.md") and the
 accompanying published article: Lundregan, S.L., Mäkinen, H., Buer, A.,
 Holand, H., Jensen, H. and Husby, A. 2022. Infection by a helminth
 parasite is associated with changes in DNA methylation in the house
 sparrow. Ecology and Evolution. Accepted. DOI: 10.1002/ECE3.9539