cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.q3b49
title: Data from: Cryptic diversity, high host specificity and reproductive synchronization in army ant-associated Vatesus beetles

description: Army ants and their arthropod symbionts represent one of the most
 species-rich animal associations on Earth, and constitute a fascinating
 example of diverse host-symbiont interaction networks. However, despite
 decades of research, our knowledge of army ant symbionts remains
 fragmentary due to taxonomic ambiguity and the inability to study army
 ants in the lab. Here we present an integrative approach that allows us to
 reliably determine species boundaries, assess biodiversity, match
 different developmental stages and sexes, and to study the life cycles of
 army ant symbionts. This approach is based on a combination of community
 sampling, DNA barcoding, morphology and physiology. As a test case, we
 applied this approach to the staphylinid beetle genus Vatesus and its
 different Eciton army ant host species at La Selva Biological Station,
 Costa Rica. DNA barcoding led to the discovery of cryptic biodiversity
 and, in combination with extensive community sampling, revealed strict
 host partitioning with no overlap in host range. Using DNA barcoding, we
 were also able to match the larval stages of all focal Vatesus species. In
 combination with studies of female reproductive physiology, this allowed
 us to reconstruct almost the complete life cycles of the different beetle
 species. We show that Vatesus beetles are highly adapted to the symbiosis
 with army ants, in that their reproduction and larval development are
 synchronized with the stereotypical reproductive and behavioral cycles of
 their host colonies. Our approach can now be used to study army
 ant-symbiont communities more broadly, and to obtain novel insights into
 co-evolutionary and ecological dynamics in species-rich host-symbiont
 systems.
description: Alignment
 CAD_winglessAlignment of
 concatenated wg and CAD sequences of Vatesus beetles.Alignment
 COIAlignment of COI
 sequences of Vatesus beetles.CAD_Wingless
 phylogenetic treeNewick tree file of
 concatenated wg and CAD sequences of Vatesus beetles.COI phylogenetic
 treeNewick tree file of COI
 sequences of Vatesus beetles.
DOI: 10.5061/dryad.bh88s
title: Data from: Root morphology and mycorrhizal type strongly influence root production in nutrient hot spots of mixed forests

description: 1. Plants compete for nutrients using a range of strategies. We
 investigated nutrient foraging within nutrient hot-spots simultaneously
 available to plant species with diverse root traits. We hypothesized that
 there would be more root proliferation by thin-root species than by
 thick-root species, and that root proliferation by thin-root species would
 limit root proliferation by thick-root species. 2. We conducted a root
 ingrowth experiment in a temperate forest in eastern USA where root
 systems of different tree species could interact. Tree species varied in
 the thickness of their absorptive roots, and were associated with either
 ectomycorrhizal (EM) or arbuscular mycorrhizal (AM) fungi. Thus, there
 were thin- and thick-root AM and thin- and thick-root EM plant functional
 groups. Half the ingrowth cores were amended with organic nutrients (dried
 green leaves). Relative root length abundance, the proportion of total
 root length in a given soil volume occupied by a particular plant
 functional group, was calculated for the original root population and
 ingrowth roots after 6 months. 3. The shift in relative root length
 abundance from original to ingrowth roots was positive in thin-root
 species but negative in thick-root species (P &lt; 0.001), especially
 in unamended patches (AM: +6% vs. -7%; EM: +8% vs. -9%). Being thin-rooted
 may thus allow a species to more rapidly recolonize soil after a
 disturbance, which may influence competition for nutrients. Moreover, we
 observed that nutrient additions amplified the shift in root length
 abundance of thin over thick roots in AM trees (+13% vs. -14%), but not in
 EM trees (+1% vs -3%). In contrast, phospholipid fatty acid biomarkers
 suggested that EM fungal hyphae strongly proliferated in nutrient
 hot-spots whereas AM fungal hyphae exhibited only modest proliferation. 4.
 We found no evidence that when growing in the shared patch, the
 proliferation of thin roots inhibited the growth of thick roots. 5.
 Synthesis. Knowledge of root morphology and mycorrhizal type of
 co-existing tree species may improve prediction of patch exploitation and
 nutrient acquisition in heterogeneous soils.
description: All
 dataAll data for the
 analyses presented in the article, including root length density and
 fungal biomass indicated by relevant phospholipid fatty acid
 markers
DOI: 10.5061/dryad.66cf7
title: Data from: Experimental evidence for fundamental, and not realised, niche partitioning in a plant-herbivore community interaction network

description: Patterns of niche partitioning can result from local ecological
 interactions (e.g. interspecific competition) occurring within a
 contemporary time frame (realised niche partitioning). Alternatively they
 may represent the end-product of historical processes acting over long
 time frames (fundamental niche partitioning). Niche partitioning is often
 detected by analysing patterns of resource use within communities, but
 experiments are rarely conducted to test whether patterns of
 non-overlapping resource use reflect realised or fundamental niche
 partitioning. We studied a community of restio leafhoppers from the genus
 Cephalelus, and their host plants, the Restionaceae (restios). We used
 network and experimental approaches to determine whether network
 modularity (a measure of niche partitioning within local communities)
 reflects fundamental or realised niche partitioning. Using a weighted
 modularity index for two party networks (e.g. insect - plant) we
 determined whether the network of this community is modular (i.e. consists
 of groups of species interacting strongly, with weak interactions between
 groups). We also aimed to identify specific Cephalelus - restio modules
 (groups). Using knowledge of module membership to design experiments, we
 tested whether Cephalelus species from two different modules, C. uncinatus
 and C. pickeri, prefer and perform better on restios from their own
 modules versus restios from other modules. These experiments were
 performed under controlled conditions, eliminating the influences of
 competition and predation on host choices. The Cephalelus – restio
 community was modular, implying niche partitioning. Cephalelus also
 preferred and performed better on restios from their own modules in the
 absence of local contemporary factors. Most niche partitioning in the
 investigated Cephalelus community, is not caused by local interactions,
 and thus host use patterns represent fundamental niches. Our findings
 highlight the importance of understanding local community structure in the
 light of processes extrinsic to the local community context.
description: Preference trial
 resultsPreference for one host
 plant over the other for two species, Cephalelus uncinatus and C. pickeri.
 Three host plants were tested Hypodiscus (H), Elegia (E), and Staberoha
 (S).PrefData.xlsxSurvivaldataSurvival on two different host plants, Hypodiscus and Elegia. For adults survival per cage was out of 10, and for C. pickeri larvae it was out of 20.
DOI: 10.5061/dryad.kq2r1
title: Data from: Cost-minimization model of a multidisciplinary antibiotic stewardship team based on a successful implementation on a urology ward of an academic hospital

description: Background: In order to stimulate appropriate antimicrobial use and
 thereby lower the chances of resistance development, an Antibiotic
 Stewardship Team (A-Team) has been implemented at the University Medical
 Center Groningen, the Netherlands. Focus of the A-Team was a pro-active
 day 2 case-audit, which was financially evaluated here to calculate the
 return on investment from a hospital perspective. Methods: Effects were
 evaluated by comparing audited patients with a historic cohort with the
 same diagnosis-related groups. Based upon this evaluation a
 cost-minimization model was created that can be used to predict the
 financial effects of a day 2 case-audit. Sensitivity analyses were
 performed to deal with uncertainties. Finally, the model was used to
 financially evaluate the A-Team. Results: One whole year including 114
 patients was evaluated. Implementation costs were calculated to be
 €17,732, which represent total costs spent to implement this A-Team. For
 this specific patient group admitted to a urology ward and consulted on
 day 2 by the A-Team, the model estimated total savings of €60,306 after
 one year for this single department, leading to a return on investment of
 5.9. Conclusions: The implemented multi-disciplinary A-Team performing a
 day 2 case-audit in the hospital had a positive return on investment
 caused by a reduced length of stay due to a more appropriate antibiotic
 therapy. Based on the extensive data analysis, a model of this
 intervention could be constructed. This model could be used by other
 institutions, using their own data to estimate the effects of a day 2
 case-audit in their hospital.
description: Supplemental
 DataColumn A: 1=Intervention
 patient; 2=Control patient. Column B: Age on submission in years. Column
 C: 1=Male; 2=Female. Column D: LOS in days. Column E: Total nursing time
 for IV treatment in minutes. Column F: Total price of antibiotic therapy
 in Euros. Column G: Total DDDs of antibiotic therapy. Column H: 1=DRG
 Group 1; 2=DRG Group 2.
DOI: 10.5061/dryad.t6d26
title: Data from: Goats display audience-dependent human-directed gazing behaviour in a problem-solving task

description: Domestication is an important factor driving changes in animal cognition
 and behaviour. In particular, the capacity of dogs to communicate in a
 referential and intentional way with humans is considered a key outcome of
 how domestication as a companion animal shaped the canid brain. However,
 the lack of comparison with other domestic animals makes general
 conclusions about how domestication has affected these important cognitive
 features difficult. We investigated human-directed behaviour in an
 ‘unsolvable problem’ task in a domestic, but non-companion species: goats.
 During the test, goats experienced a forward-facing or an away-facing
 person. They gazed towards the forward-facing person earlier and for
 longer and showed more gaze alternations and a lower latency until the
 first gaze alternation when the person was forward-facing. Our results
 provide strong evidence for audience-dependent human-directed visual
 orienting behaviour in a species that was domesticated primarily for
 production, and show similarities with the referential and intentional
 communicative behaviour exhibited by domestic companion animals such as
 dogs and horses. This indicates that domestication has a much broader
 impact on heterospecific communication than previously believed.
description: Dataset
 "Human-directed behaviour in livestock"data_goats look
 back.xlsx
DOI: 10.5061/dryad.6t5n0
title: Data from: Epigenetic alterations and decreasing insecticide sensitivity of the Asian tiger mosquito Aedes albopictus

description: A range of environmental factors, including chemicals, can affect
 epigenetic processes in organisms leading to variations in phenotype.
 Thus, epigenetics displays an important environmentally responsive
 element. The transgenerational impact of environmental stressors on DNA
 methylation and phenotype was the focus of this study. The influence of
 two known DNA methylation-changing agents, the phytoestrogen genistein and
 the fungicide vinclozolin, on the overall DNA methylation level in the
 Asian tiger mosquito Aedes albopictus was investigated. The experiment
 comprised four generations in a full life-cycle design with an exposed
 parental generation and three consecutive non-exposed offspring
 generations. Application of the methylation agents to the parental
 generation of the study led to an alteration of the global DNA methylation
 level of the exposed individuals and those in two subsequent generations.
 The phenotypic variability of the offspring generations was assessed by
 examining their insecticide sensitivity. Here, a significant decrease in
 sensitivity (p&lt;0.01) towards the model insecticide imidacloprid
 revealed alterations of the mosquito's phenotype in two subsequent
 generations. Thus, the evaluation of A. albopictus from an epigenetic
 perspective can contribute important information to the study of the high
 adaptability of this invasive disease vector to new environments, and its
 underlying mechanisms.
description: Oppold et al.
 2015_Figure 2_methylation dataRaw data and statistics
 of global DNA methylation levels in Aedes albopictus.Oppold et al.
 2015_Figure 3_toxicity dataRaw data and statistics
 of imidacloprid insecticide sensitivity of Aedes
 albopictus.
DOI: 10.5061/dryad.k4g78
title: Data from: Phylogenetic relationships of toads of the Rhinella granulosa group (Anura: Bufonidae): a molecular perspective with comments on hybridization and introgression

description: The Rhinella granulosa group consists of 13 species of toads distributed
 throughout open areas of South America and Panama. In this paper we
 perform a phylogenetic analysis considering all but one species of the
 group, employing five nuclear and four mitochondrial genes, for up to 7910
 bp per specimen. Separate phylogenetic analyses under direct optimization
 (DO) of nuclear and mitochondrial sequences recovered the R. granulosa
 group as monophyletic and revealed topological incongruence that can be
 explained mainly by multiple events of hybridization and introgression,
 both mitochondrial and nuclear. The DO combined analysis, after the
 exclusion of putatively introgressed or heterozygous genomes, resulted in
 a phylogenetic hypothesis for the R. granulosa group in which most of the
 species are recovered as monophyletic, but with interspecific
 relationships poorly supported. The optimization of morphological (adult
 and larval), chromosomal, and behavioural characters resulted in 12
 putative phenotypic synapomorphies for this species group and some other
 synapomorphies for internal clades. Our results indicate the need for
 additional population genetic studies on R. dorbignyi and R. fernandezae
 to corroborate the taxonomic status of both taxa. Finally, we discuss
 biological and genetic characteristics of Bufonidae, as possible
 explanations for the common occurrence of hybridization and introgression
 observed in some lineages of this family.
description: DNA
 sequencesCompressed zip file
 containing the alignments of DNA sequences used in the study in FASTA
 formatalignments.zip
DOI: 10.5061/dryad.rh460
title: Data from: Environmental factors and traits that drive plant litter decomposition do not determine home-field advantage effects

description: The ‘home-field advantage’ (HFA) hypothesis predicts that plant litter is
 decomposed faster than expected underneath the plant from which it
 originates (‘home’) than underneath other plants (‘away’), because
 decomposer communities are specialized to break down litter from the
 plants they associate with. However, empirical evidence shows that the
 occurrence of HFA is highly variable, and the reasons for this are little
 understood. In our study we progress our understanding by investigating
 whether HFA is stronger for more recalcitrant litter types and under
 colder conditions and how soil properties and plant functional traits
 affect the magnitude and direction of HFA. In subarctic tundra in northern
 Sweden we set up a reciprocal transplant litter decomposition experiment
 along an elevational gradient where three highly contrasting vegetation
 types (heath, meadow and Salix) occur at all elevations, and where
 temperature decreases strongly with elevation. In this study, we used a
 litter bag approach where litters from each elevation × vegetation type
 combination were decomposed in all combinations of elevation × vegetation
 type. We also measured community-level plant functional traits, such as
 leaf and litter nutrient content. We determined soil biotic and abiotic
 properties, such as microbial biomass and soil nutrient content, in soil
 cores collected for each elevation × vegetation type combination. We found
 that mass loss increased with plant and litter nutrient content and with
 soil temperature. In contrast, the occurrence of HFA was limited in our
 study system, and its magnitude and direction could not be explained by
 vegetation type, elevation, plant traits or soil properties, despite these
 factors serving as powerful drivers of litter mass loss in our study. We
 conclude that although vegetation type and climate are major drivers of
 litter mass loss, they do not emerge as important determinants of HFA.
 Therefore, while rapid shifts in plant community composition or
 temperature due to global change are likely to influence litter mass loss
 directly by altering environmental conditions, plant trait spectra and
 litter quality, indirect effects of global change resulting from
 decoupling of specialist interactions between litter and decomposer
 communities appears to be of less importance.
description: Veen et al-environmental
 dataEnvironmental data
 collected at the plot level: soil abiotic properties, soil biotic
 properties, plant leaf traits, plant litter traits, litter mass loss of
 litter originating from the plot and percentage of additional
 decomposition at home.Veen-FE2014-00722_environmental
 data.txtVeen-FE2014-00722_litter
 mass lossLitter mass loss of each
 litter transplant.
DOI: 10.5061/dryad.rn0198d
title: Data from: Application of a novel molecular method to age free-living wild Bechstein’s bats

description: The age profile of populations fundamentally affects their conservation
 status. Yet age is frequently difficult to assess in wild animals. Here,
 we assessed the use of DNA methylation of homologous genes to establish
 the age structure of a rare and elusive wild mammal: the Bechstein’s bat
 (Myotis bechsteinii). We collected 62 wing punches from individuals whose
 ages were known as a result of a long-term banding study. DNA methylation
 was measured at seven CpG sites from three genes which have previously
 shown age-associated changes in humans and laboratory mice. All CpG sites
 from the tested genes showed a significant relationship between DNA
 methylation and age, both individually and in combination (multiple linear
 regression R2=0.58, p&lt;0.001). Despite slight approximation around
 estimates, the approach is sufficiently precise to place animals into
 practically useful age cohorts. This method is of considerable practical
 benefit as it can reliably age individual bats. It is also much faster
 than traditional capture-mark-recapture techniques, with the potential to
 collect information on the age structure of an entire colony from a single
 sampling session to better inform conservation actions for Bechstein’s
 bats. By identifying three genes where DNA methylation correlates with age
 across distantly related species, this study also suggests that the
 technique can potentially be applied across a wide range of mammals.
description: DNA methylation
 dataDNA methylation dataset
 for all Bechstein's bats of known age with data from duplicates and
 stool samplesMbechsteinii_EpigeneticsR script used for the data analysis (linear regression, multiple linear regression, LOOCV).
DOI: 10.5061/dryad.j054r
title: Data from: Fatty acid profiles of five farmed Brazilian freshwater fish species from different families

description: The proximate composition and fatty acid (FA) profiles of five Brazilian
 freshwater fish species, namely Brycon cephalus (BC), Cichla ocellaris
 (CO), Prochilodus lineatus (PL), Leporinus friderici (LF) and
 Pseudoplatystoma corruscans (PCO), were investigated. CO and LF exhibited
 the highest (p &lt; 0.05) moisture content, as well as one of the
 lowest (p &lt; 0.05) lipid values, whereas BC presented the lowest (p
 &lt; 0.05) moisture and, alongside PL, the highest (p &lt; 0.05)
 lipid content. The predominant FAs in the evaluated fish species were
 palmitic, oleic, linoleic and docosahexaenoic acids. BC and CO presented
 high n-3 PUFA content, especially DHA, and demonstrated superior
 nutritional quality indices compared to the other evaluated fish species.
 Furthermore, a significant relationship was observed among these species,
 suggesting they possess similar nutritional lipid values. Thus, BC and CO
 were proven to be an excellent matrix with relevant lipid quality,
 desirable for human health.
description: Fatty acid and proximate
 composition data of Brazilian freshwater fish species from different
 familiesProximate composition,
 fatty acid profile (% of total fatty acids) and nutritional quality
 indices in fillets of five Brazilian freshwater fish species from
 different familiesData
 file.xlsx
DOI: 10.15468/dl.ry5ejq
title: Occurrence Download

description: A dataset containing 1202 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Galiteuthis glacialis",
 "HasCoordinate is true",
 "DecimalLatitude is greater than -90",
 "DecimalLatitude is less than 10",
 "DecimalLongitude is greater than -180",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 1950",
 "Year is less than or equal to 2014"
 ]
}

 The dataset includes 1202 records from 23 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001139-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.8bp5pp44
title: Data from: The relation between the neutrality index for mitochondrial genes and the distribution of mutational effects on fitness

description: We explore factors affecting patterns of polymorphism and divergence (as
 captured by the neutrality index) at mammalian mitochondrial loci. To do
 this, we develop a population genetic model that incorporates a fraction
 of neutral amino acid sites, mutational bias, and a probability
 distribution of selection coefficients against new nonsynonymous
 mutations. We confirm, by reanalyzing publicly available data sets, that
 the mitochondrial cyt-b gene shows a broad range of neutrality indices
 across mammalian taxa, and explore the biological factors that can explain
 this observation. We find that observed patterns of differences in the
 neutrality index, polymorphism and divergence are not caused by
 differences in mutational bias. They can, however, be explained by a
 combination of a small fraction of neutral amino acid sites, weak
 selection acting on most amino acid mutations, and differences in
 effective population size among taxa.
description: Bernardo_data_plusnewKs2FS = synonymous substitutions | FN = nonsynonymous substitutions | PS = synonymous polymorphisms | PN = nonsynonymous polymorphisms | Pa = pairwise nucleotide diversity (pi) at amino acid sites | Ps = pairwise nucleotide diversity (pi) at synonymous sites | JC = Jukes-Cantor corrected values | GY.HKY = Goldman-Yang corrected values using the HKY85 model for DNA substitution | Pa.over.Ps = Pa.JC/Ps.JC | p.val = p-value of Fisher's Exact test on FS, FN, PS, and PN values | NI = Pa.over.Ps/ka_ks_JC | newNI = Pa.over.Ps/Ka_Ks_GY.HKY | gccontent1, etc. = fraction of sites that are GC at 1st position in the codon | DOS = direction of selection statistic of Stoletzki and Eyre-Walker 2011