cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.jm63xsj65
title: Estimating survival for elusive juvenile pond‐breeding salamanders

description: Juvenile vital rates have important effects on population dynamics for
 many species, but this demographic is often difficult to locate and track.
 As such, we frequently lack reliable estimates of juvenile survival, which
 are necessary for accurately assessing population stability and potential
 management approaches to conserve biodiversity. We empirically estimated
 survival rates for elusive juveniles of 3 complex lifecycle species of
 salamanders (ringed salamander [Ambystoma annulatum], spotted slamander
 [A. maculatum], and small-mouthed slamander [A. texanum]) using 2
 approaches. First, we conducted an 11-month mark-recapture study within
 semi-natural enclosures and used Bayesian Cormack-Jolly-Seber models to
 estimate survival and recapture probabilities. Second, we inferred the
 expected annual juvenile survival rate given published vital rates for
 pre-metamorphic and adult ambystomatids assuming stable population growth.
 For all 3 species, juvenile survival probabilities were constant across
 recapture occasions, while recapture probability estimates were
 time-dependent. Further, survival and recapture probabilities among study
 species did not significantly differ. Post-study sampling revealed that
 the initial study period median estimate of annual survival probability
 (0.39) underestimated the number of salamanders known alive at 11 months.
 We therefore appended approximately 1 year of opportunistic data, which
 produced a median annual survival probability of 0.50, encompassing
 salamanders that we knew to have been alive. Calculation from literature
 values suggested a mean annual terrestrial juvenile ambystomatid survival
 probability of 0.45. Similar results among our approaches indicated that
 juvenile survival estimates for the study species were robust and likely
 comparable to rates in nature. These estimates can now be confidently
 applied to research, monitoring, and management efforts for the study
 species and ecologically similar taxa. Our data indicated that similarly
 robust vital rate estimates for subsets of ecologically and
 phylogenetically similar species can provide reasonable surrogate
 demographic information to advance conservation efforts for data-deficient
 species.
description: We collected these data during an 11-month capture-mark-recapture
 study under semi-natural conditions. We used the Bayesian jagsUI package
 (Kellner 2017) in R Software 3.5.1 (R Core Team 2018) to build
 Cormack-Jolly-Seber models to analyze our data.
DOI: 10.5061/dryad.4j0zpc86z
title: Parentage Assignment in Brown trout strains (Salmo trutta) and their hybrids using microsatellite markers

description: Brown trout, Salmo trutta is a widespread fish species throughout the
 Europe yet most of the natural populations of the species is in decline
 due to the anthropogenic pressures. Hatchery based stock enhancement is
 commonly used to restore depleted populations. Tracking pedigree
 information is useful for evaluating performance of stocked offspring and
 for examining introgression where hatchery-based stocking programs are
 being implemented. In this study, parentage assignment powers of 16
 previously developed microsatellite markers have been evaluated in four
 brown trout strains and their hybrids. The number of alleles per locus
 ranged between 3 (Str73INRA) -24 (T3-13). Observed (HO) and expected
 heterozygosity HE were between 0.188-0.854 and 0.175-0.903, respectively.
 According to the simulation analysis with prior known parental and filial
 information, of the 204 offspring tested, correct assignment rate of 8
 most informative microsatellite marker to their parental pairs was 96.08%
 and that of 15 loci was 98.04%. Having more than 8 markers boosted only
 1.96% extra power of assignment. Meanwhile correct assignment rate of 5
 loci was resulted only 85.29%. Our results demonstrate that microsatellite
 markers are reliable and effective tools for the parentage assignment in
 brown trout strains and their hybrids. The findings obtained in the
 present study also indicates that parentage assignment in brown trout
 strains would be useful for examining introgression into natural
 populations or to evaluate performance of stocked fish.
DOI: 10.5061/dryad.mgqnk98vz
title: Inferring competitive outcomes, ranks and intransitivity from empirical data: A comparison of different methods

description: The inference of pairwise competitive outcomes (PCO) and multispecies
 competitive ranks and intransitivity from empirical data is essential to
 evaluate how competition shapes plant communities. Three categories of
 methods, differing in theoretical background and data requirements, have
 been used: (a) theoretically sound coexistence theory‐based methods, (b)
 index‐based methods, and (c) ‘process‐from‐pattern’ methods. However, how
 they are related is largely unknown. In this study, we explored the
 relations between the three categories by explicitly comparing three
 representatives of them: (a) relative fitness difference (RFD), (b)
 relative yield (RY), and (c) a reverse‐engineering approach (RE).
 Specifically, we first conducted theoretical analyses with Lotka–Volterra
 competition models to explore their theoretical linkages. Second, we used
 data from a long‐term field experiment and a short‐term greenhouse
 experiment with eight herbaceous perennials to validate the theoretical
 findings. The theoretical analyses showed that RY or RE applied with
 equilibrium data indicated equivalent, or very similar, PCO respectively
 to RFD, but these relations became weaker or absent with data further from
 equilibrium. In line with this, both RY and RE converged with RFD in
 indicating PCO over time in the field experiment as the communities became
 closer to equilibrium. Moreover, the greenhouse PCO (far from equilibrium)
 were only similar to the field PCO of earlier rather than later years.
 Intransitivity was more challenging to infer because it could be
 reshuffled by even a small competitive shift among similar competitors.
 For example, the field intransitivity inferred by three methods differed
 greatly: no intransitivity was detected with RFD; intransitivity detected
 with RY and RE was poorly correlated, changed substantially over time
 (even after equilibrium) and failed to explain coexistence. Our findings
 greatly help the comparison and generalization of studies using different
 methods. For future studies, if equilibrium data are available, one can
 infer PCO and multispecies competitive ranks with RY or RE. If not, one
 should apply RFD with density gradient or time‐series data. Equilibria
 could be evaluated with T tests or standard deviations. To reliably infer
 intransitivity, one needs high quality data for a given method to first
 accurately infer PCO, especially among similar competitors.
description: This file includes the data of diallel greenhouse experiment for
 the 8 species of the dominance experiment within the Jena Experiment. The
 data were collected by Enrica De Luca and Bernhard Schmid.
DOI: 10.6071/m3nd50
title: Data from: An initial comparative genomic autopsy of wasting disease in sea stars

description: Beginning in 2013, sea stars throughout the Eastern North Pacific were
 decimated by wasting disease, also known as ‘asteroid idiopathic wasting
 syndrome’ (AIWS) due to its elusive etiology. The geographic extent and
 taxonomic scale of AIWS meant events leading up to the outbreak were
 heterogeneous, multifaceted, and oftentimes unobserved; progression from
 morbidity to death was rapid, leaving few tell-tale symptoms. Here we take
 a forensic genomic approach to discover candidate genes that may help
 explain sea star wasting syndrome. We report the first genome and
 annotation for P. ochraceus, along with differential gene expression (DGE)
 analyses in four size classes, three tissue types, and in symptomatic and
 asymptomatic individuals. We integrate nucleotide polymorphisms associated
 with survivors of the wasting disease outbreak, DGE associated with
 temperature treatments in P. ochraceus, and DGE associated with wasting in
 another asteroid Pycnopodia helianthoides. In P. ochraceus, we find DGE
 across all tissues, among size classes, and between asymptomatic and
 symptomatic individuals; the strongest wasting-associated DGE signal is in
 pyloric caecum. We also find previously identified outlier loci co-occur
 with differentially expressed genes. In cross-species comparisons of
 symptomatic and asymptomatic individuals, consistent responses distinguish
 genes associated with invertebrate innate immunity and chemical defense,
 consistent with context-dependent stress responses, defensive apoptosis,
 and tissue degradation. Our analyses thus highlight genomic constituents
 that may link suspected environmental drivers (elevated temperature) with
 intrinsic differences among individuals (age/size, alleles associated with
 susceptibility) that elicit organismal responses (e.g. coelomocyte
 proliferation) and manifest as sea star wasting mass mortality.
description: See manuscript.
DOI: 10.5061/dryad.ksn02v70b
title: Data from: Ecological drivers of jellyfish blooms – the complex life history of a 'well-known' medusa (Aurelia aurita)

description: Jellyfish blooms are conspicuous demographic events with significant
 ecological and socio-economic impact. Despite worldwide concern about an
 increased frequency and intensity of such mass occurrences, predicting
 their booms and busts remains challenging. Forecasting how jellyfish
 populations may respond to environmental change requires considering their
 complex life histories. Metagenic life cycles, which include a benthic
 polyp stage, can boost jellyfish mass occurrences via asexual recruitment
 of pelagic medusae. Here we present stage-structured matrix population
 models with monthly, individual-based demographic rates of all life stages
 of the moon jellyfish Aurelia aurita L. (sensu stricto). We investigate
 the life stage-dynamics of these complex populations under low and high
 food conditions to illustrate how changes in medusa density depend on
 non-medusa stage dynamics. We show that increased food availability can be
 an important ecological driver of jellyfish mass occurrences, as it can
 temporarily shift the population structure from polyp- to medusa-
 dominated. Projecting populations for a winter warming scenario enhanced
 the booms and busts of jellyfish blooms. We identify demographic key
 variables that control the intensity and frequency of jellyfish blooms in
 response to environmental drivers such as habitat eutrophication and
 climate change. By contributing to an improved understanding of mass
 occurrence phenomena, our findings provide perspective for future
 management of ecosystem health.
DOI: 10.5061/dryad.98sf7m0dv
title: Correlation between internal pudendal artery stenosis and erectile dysfunction in patients with suspected coronary artery disease

description: Background Stenoses of internal pudendal arteries (IPAs) appear to be
 related to erectile dysfunction (ED). Nevertheless, the correlation
 between the severity of ED and stenosis of the IPAs is not well
 established. Objectives To evaluate angiographic findings of IPAs in
 patients with suspected coronary artery disease (CAD) and to assess the
 correlation between the severity of ED and IPA stenosis. Materials and
 methods Ninety-one patients who were scheduled for cardiac angiogram (CAG)
 because of suspected CAD participated. ED was assessed using the
 International Index of Erectile Function (IIEF) questionnaire. Erectile
 function (EF) domain scoring was used to assess the severity of ED: severe
 (EF score = 1-10); moderate (11-16); mild-moderate (17-21); mild (22-25);
 and no ED (26-30). Angiography was performed in bilateral common, internal
 iliac, and IPAs and the location and extent of stenoses were measured. We
 divided patients according to those with maximum stenosis of less than 50%
 (Group I) and those with more than 50% (Group II), regardless of
 direction. Results We diagnosed 88 patients (88/91, 96.70%) with ED. There
 was no correlation between increasing age and severity of ED (r = - 0.063,
 p = 0.555). There were 72 patients in Group I and 19 in Group II. In Group
 I, 62 patients were diagnosed with ED even though there was no stenosis.
 There was no significant correlation between the severity of ED and the
 extent of stenosis in IPAs (r = -0.118, p = 0.265). Conclusions There was
 no significant correlation between the severity of ED and the extent of
 stenosis of IPAs. We believe that this is because the progression of ED is
 induced by endothelial cell dysfunction, not by mechanical obstruction
 leading to blood flow reduction. Key words; angiography; coronary artery
 disease; endothelial cells; erectile dysfunction; vascular disease
DOI: 10.5061/dryad.8pk0p2nht
title: SNP dataset for Buchenavia oxycarpa

description: Wallace’s (1854) Riverine Barrier hypothesis is one of the earliest
 explanations for Amazon biotic diversification. Despite the importance of
 this hypothesis for explaining speciation in some animal groups, it has
 not been studied extensively for plant species. In this study we use a
 prominent Amazon tree, Buchenavia oxycarpa (Mart.) Eichler (Combretaceae),
 to evaluate Wallace’s hypothesis along the Rio Negro, a major Amazon
 tributary that has driven allopatric speciation for several animal taxa.
 We sampled six individuals from sixteen localities along both river banks,
 and used a modified ddRADseq protocol to identify SNP markers. Our
 population genomic data revealed strong genetic structure for B. oxycarpa
 sampled across banks of the Rio Negro (ϕCT = 0.576, P &lt; 0.001),
 supporting the hypothesis that the Rio Negro acted as a significant
 genetic barrier for B. oxycarpa. Our study shows that gene flow
 for this large and well-dispersed Amazon tree is impeded by riverine
 barriers though this has not yet resulted in speciation. Future studies
 focused on species with different life histories, including species
 restricted to non-flooded forests, are need to further advance our
 understanding of Amazon rivers as drivers of biotic diversification.
description: SNP dataset for Buchenavia oxycarpa
DOI: 10.5061/dryad.51c59zw4h
title: Leaf resistance traits influence endophytic fungi colonization and community composition in a South American temperate rainforest

description: Despite the ubiquitous presence of fungal endophytes in woody plants,
 mechanisms underlying variation in foliar fungal endophyte communities are
 poorly understood. Given that endophytes in woody plants are predominantly
 horizontally transmitted, fungal endophyte colonization of foliar tissues
 is likely to be influenced by plant resistance traits. Here, we evaluated
 the association between leaf resistance traits and colonization and
 community composition of horizontally transmitted endophytes (HTE) in ten
 dominant trees species in a temperate rainforest in Southern Chile.
 Because resistance traits might restrict colonization of HTE, it was
 hypothesized that host trees with similar leaf resistance traits would
 show similar HTE communities. We measured leaf traits with reported roles
 in plant resistance against pathogens and/or herbivores: cell wall
 polysaccharides, leaf toughness, flavonoids, anthocyanins, terpenoids and
 chitinases. We also determined variation in fungal read counts, number of
 operational taxonomic units (OTUs), diversity and community structure
 across tree species. Foliar fungal endophyte communities were
 characterized using Illumina MiSeq sequencing of tagged amplicons of the
 ITS1 region. Fungal read counts were significantly different among host
 trees, while number of OTUs and diversity were similar among them.
 Multivariate analyses showed that community composition of endophytic
 fungi significantly differed among hosts, and that variation in cell wall,
 flavonoids, anthocyanins and terpenoids was associated with differences in
 HTE communities. We found that host trees sharing leaf resistance traits
 harbor similar HTE communities. Fungal read counts decreased with
 increasing content of cell wall polysaccharides, while endophyte diversity
 decreased with increasing anthocyanin levels. Fungal read counts, in
 contrast, were positively associated with terpenoids. Additionally,
 culture-based data indicated that some HTE strains inhibited the growth of
 the common fungal pathogen Botrytis cinerea. Synthesis: Overall, we found
 that leaf resistance traits may influence fungal endophyte colonization
 and community composition in tree species, likely through deterrent
 effects of structural and chemical traits. We suggest that endophytic
 fungi that overcome resistance traits might play a role in plant
 protection.
DOI: 10.5061/dryad.3n5tb2rcf
title: Data from: Ocean warming increases availability of crustacean prey via riskier behaviour

description: Marine prey and predators will respond to future climate through
 physiological and behavioural adjustments. However, our understanding of
 how such direct effects may shift the outcome of predator-prey
 interactions is still limited. Here, we investigate the effects of ocean
 warming and acidification on foraging behaviour and biomass of a common
 prey (shrimps, Palaemon spp.) tested in large mesocosms harbouring natural
 resources and habitats. Acidification did not alter foraging behaviour in
 prey. Under warming, however, prey showed riskier behaviour by foraging
 more actively and for longer time periods, even in the presence of a live
 predator. No effects of longer-term exposure to climate stressors were
 detected on prey biomass. Our findings suggest that ocean warming may
 increase the availability of some prey to predators via a behavioural
 pathway (i.e. increased risk-taking by prey), likely by elevating
 metabolic demand of prey species.
DOI: 10.5061/dryad.6hdr7sqwg
title: Exceptional preservation of comma shrimp from a mid-Cretaceous Lagerstätte of Colombia, and the origins of crown Cumacea

description: Mesozoic rocks with exceptional preservation of marine arthropods are
 known worldwide but largely restricted to high latitudes. The scarcity of
 assemblages with exceptional preservation in low latitudes greatly limits
 our understanding of the origins of several modern groups and the
 evolution of tropical biotas through time. Here we report the oldest
 Cumacea, or “comma” shrimp (Arthropoda: Eumalacostraca: Peracarida) with
 modern affinities, from a new mid-Cretaceous (95–90 Mya) Lagerstätte in
 tropical South America. Cumaceans have one of the poorest fossil records
 among marine arthropods, despite today being abundant and speciose benthic
 organisms associated with fine-grained sediments with high fossilization
 potential. Eobodotria muisca gen. et sp. nov., found in mass-accumulation
 surfaces, preserves with stunning detail the gut, mouth parts, legs,
 pleopods, uropods bearing setae, antennal flagella, and even small eyes
 bearing ommatidia. These features, rarely preserved in fossil crustaceans,
 plus the large sample size (&gt;200 individuals, ~8 mm long), allow us
 to discuss phylogenetic/systematic aspects of the oldest modern cumacean
 known, and explore possible mechanisms behind their unusual accumulation.
 Eobodotria bridges a ~165 My gap in the cumacean fossil record, provides a
 reliable calibration point for molecular studies, and expands our
 understanding of exceptional preservation in past and present tropical
 settings.
DOI: 10.5061/dryad.73n5tb2sj
title: Empirical evidence of disturbance interactions: examples from Australian ecosystems

description: Ecosystems are shaped by a range of drivers including natural and human
 disturbances. Many natural disturbances such as fire, insect attack and
 windstorms are increasing in frequency and severity. At the same time,
 human disturbances like logging, land clearing and plantation
 establishment are expanding. Co-occurring disturbances can interact with
 far-reaching consequences, including altered ecological processes and
 losses of biodiversity. Whilst the importance of interacting disturbances
 is increasingly recognized, the majority of empirical studies focus only
 on a single driver of change. We evaluate evidence for interacting drivers
 of change, including natural and human disturbances, in 57 empirical
 studies completed within two markedly different ecosystems in southern
 Australia that had been subject to large-scale, long-term research
 programs. These programs have documented the ecological effects of fire,
 native forest logging, post-fire (salvage) logging, browsing by native
 herbivores, and invasive species control. We found effects of interactions
 among disturbances on every vertebrate class that we examined (mammals,
 birds, reptiles and amphibians), as well as on vegetation and ecosystem
 processes (e.g. tree germination and tree mortality). Interactions between
 disturbances were often statistically significant when tested for.
 Similarly, where tested, environmental context often significantly
 modified disturbance effects. Finally, we found evidence of one
 disturbance affecting the likelihood or intensity of a subsequent
 disturbance (viz: an interaction chain or linked disturbances), and of the
 order in which disturbances occurred altering biotic responses. Synthesis
 and applications. Interactions between disturbances warrant more attention
 in empirical studies because they can be common and have substantial
 impacts over large spatial scales, and prolonged timeframes. Approaches to
 limit adverse impacts of interacting disturbances include eliminating some
 drivers if possible (particularly where interaction chains are present),
 reducing the spatial overlap of disturbances (e.g. by protecting key
 refugia), reducing the potential for temporal overlap of multiple
 disturbances, and identifying key leverage points where actions are most
 effective.
description: These data consist of summaries from previously published
 research that quantified the effects of disturbance on
 biodiversity.