cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.xksn02vbz
title: Context dependency of biotic interactions and its relation to plant rarity

description: Abstract Aim: Biotic interactions can determine rarity and commonness of
 species, however evidence that rare and common species respond differently
 to biotic stress is scarce. This is because biotic interactions are
 notoriously context-dependent and traits leading to success in one habitat
 might be costly or unimportant in another. We aim to identify plant
 characteristics that are related to biotic interactions and may drive
 patterns of rarity and commonness, taking environmental context into
 account. Location: Switzerland Methods: In a multi-species experiment, we
 compared the response to biotic interactions of 19 rare and 21 widespread
 congeneric plant species in Switzerland, while also accounting for
 variation in environmental conditions of the species´ origin. Results: Our
 results restrict the long-standing hypothesis that widespread species are
 superior competitors to rare species to only those species originating
 from resource rich habitats, in which competition is usually strong.
 Tolerance to herbivory and ambient herbivore damage on the other hand, did
 not differ between widespread and rare species. In accordance to the
 resource-availability hypothesis, widespread species from resource rich
 habitats where more damaged by herbivores (less defended) than widespread
 species from resource poor habitats –such a growth-defense tradeoff was
 lacking in rare species. This indicates that the evolutionary important
 tradeoff between traits increasing competitive-ability and defence is
 present in widespread species but may have been lost or never evolved in
 rare species. Main conclusions: Our results indicate that biotic
 interactions, above all competition, might indeed set range limits, and
 underlines the importance of including context-dependency in studies
 comparing traits of common and rare or invasive and non-invasive species.
description: The data are results from a common garden experiment. Details are
 described in the published article.
description: Details are described in the methods section of the article.
DOI: 10.5061/dryad.zgmsbcc75
title: Data from: Animal models to understand the etiology and pathophysiology in polycystic ovary syndrome

description: More than one out of ten women worldwide are diagnosed with the leading
 cause of female reproductive and metabolic dysfunction, polycystic ovary
 syndrome (PCOS). Despite its high prevalence, PCOS and its accompanying
 morbidities are likely under-diagnosed, averaging &gt;2 years and 3
 physicians changes before women are diagnosed. Despite intensive research,
 the underlying cause(s) of PCOS have yet to be defined. In order to
 understand PCOS pathophysiology, its developmental origins, and how to
 predict and prevent PCOS onset, there is urgent need for safe and
 effective markers and treatments. In this review, we detail which animal
 models are more suitable and which are less suitable for contributing to
 our understanding of the etiology and pathophysiology of PCOS. We
 summarize and highlight advantages and limitations of hormonal or genetic
 manipulation of animal models, as well as of naturally occurring PCOS-like
 females.
description: See review article
DOI: 10.5061/dryad.vx0k6djnb
title: Data from: Climate and local environment structure asynchrony and the stability of primary production in grasslands

description: Aim: Climate variability threatens to destabilize production in many
 ecosystems. Asynchronous species dynamics may buffer against such
 variability when decreased performance by some species is offset by
 increased performance of others. However, high climatic variability can
 eliminate species through stochastic extinctions or cause similar stress
 responses among species, reducing buffering. Local conditions, such as
 soil nutrients, can further alter production stability directly or by
 influencing asynchrony. We test these hypotheses using a globally
 distributed sampling experiment. Location: Grasslands in North America,
 Europe and Australia. Time period: Annual surveys over five-year intervals
 occurring between 2007 and 2014. Major taxa studied: Herbaceous plants.
 Methods: We annually sampled per-species cover and aboveground community
 biomass (net primary productivity; NPP), plus soil chemical properties, in
 twenty-nine grasslands. We tested how soil conditions, combined with
 precipitation and temperature variability, affect species richness,
 asynchrony and temporal stability of primary productivity. We used
 bivariate relationships and structural equation modeling to examine
 proximate and ultimate relationships. Results: Climate variability
 strongly predicted asynchrony, whereas NPP stability was more related to
 soil conditions. Species richness was structured by both climate
 variability and soils, and in turn increased asynchrony. Temperature and
 precipitation variability caused a unimodal asynchrony response, with
 asynchrony lowest at low and high climate variability. Climate impacted
 stability indirectly through its effect on asynchrony, with stability
 increasing at higher asynchrony due to lower inter-annual NPP variability.
 Soil conditions had no detectable effect on asynchrony but increased
 stability by increasing mean NPP, especially when soil organic matter was
 high. Main Conclusions: We found globally consistent evidence that climate
 modulates species asynchrony, but that the direct effect on stability is
 low relative to local soil conditions. Nonetheless, our observed
 unimodal responses to temperature and precipitation variability
 suggest asynchrony thresholds, beyond which there are detectable
 destabilizing impacts of climate on primary productivity.
description: The dataset contains site information, years of survey and
 climate data, and summary data for species asynchrony, stability, climate
 means and variability. Most data are processed to provide the indices and
 summary statistics used in the published paper, and allow reproduction of
 the published figures and statistics reported. Raw data containing annual
 species abundances and monthly climate measurements for each site and plot
 are available from the NutNet database (https://nutnet.org/).
DOI: 10.5061/dryad.dv41ns1v4
title: Enhanced recruitment of larger predators in the presence of large prey

description: Most carnivores undergo diet shift from smaller to larger prey items
 during ontogeny. The trophic relationship between a growing carnivore and
 larger prey is representative of a size-structured predator-prey
 interaction. The strength of this interaction is, in part, determined by
 the recruitment of individuals from smaller predatory size classes into
 larger predatory size classes. Therefore, it is interesting to investigate
 how larger prey alter the recruitment of smaller predator size classes
 into larger predator size classes, since this can affect their own future
 predation risk.  Past empirical studies have exclusively
 documented that large prey reduce predator recruitment by decreasing
 growth and/or survival of the smaller predators. In this study, we provide
 empirical evidence of the contrasting pattern: large prey enhance the
 recruitment of smaller predators into larger predators even though they
 increase cannibalism mortality of the smaller predators. We have done this
 here by studying the trophic interaction between predatory salamander
 larvae (Hynobius retardatus) and the frog tadpoles (Rana pirica) that
 represent their large prey.  In a field experiment in which
 salamander hatchlings were exposed to the presence or absence of large
 frog tadpoles, we found that more giant salamanders emerged in the
 presence of frog tadpoles than in their absence. Re-assignment of frog
 tadpoles (to both treatments) in the subsequent experimental period showed
 that the enhanced emergence of giant salamanders in the presence of frog
 tadpoles leads to the intensification of salamander predation on the frog
 tadpoles.  In an additional laboratory experiment, to better
 understand the underlying mechanisms, we manipulated both the presence of
 frog tadpoles and the occurrence of cannibalism between salamander
 hatchlings. This experiment revealed that frog tadpoles intensify the
 cannibalism of salamander larvae during their hatchling stage, thus
 allowing more salamander larvae to become large-sized predators. Our
 results suggest that frog tadpoles can inadvertently intensify their own
 future predation risk by intensifying cannibalistic interactions among
 predatory salamander hatchlings, thereby enhancing the degree of predator
 recruitment to a larger size class. Hence, large prey can enhance the
 recruitment of individuals from small predator size classes into larger
 predator size classes.
DOI: 10.5061/dryad.vq83bk3pj
title: Hydrogen sulfide exposure reduces thermal set point in zebrafish

description: Behavioural flexibility allows ectotherms to exploit the environment to
 govern their metabolic physiology, including in response to environmental
 stress. Hydrogen sulfide (H2S) is a widespread environmental toxin that
 can lethally inhibit metabolism. However, H2S can also alter behaviour and
 physiology, including a hypothesised induction of hibernation-like states
 characterised by downward shifts of the innate thermal setpoint
 (anapyrexia). Support for this hypothesis has proved controversial because
 it is difficult to isolate active and passive components of
 thermoregulation, especially in animals with high resting metabolic heat
 production. Here, we directly test this hypothesis by leveraging the
 natural behavioural thermoregulatory drive of fish to move between
 environments of different temperatures in accordance with their current
 physiological state and thermal preference. We observed a decrease in
 adult zebrafish (Danio rerio) preferred body temperature with exposure to
 0.02% H2S, which we interpret as a shift in thermal setpoint. Individuals
 exhibited consistent differences in shuttling behaviour and preferred
 temperatures, which were reduced by a constant temperature magnitude
 during H2S exposure. Seeking lower temperatures alleviated H2S-induced
 metabolic stress, as measured by reduced rates of aquatic surface
 respiration. Our findings highlight the interactions between individual
 variation and sublethal impacts of environmental toxins on behaviour.
DOI: 10.7272/q64j0c9d
title: Cardiovascular risk factors and accelerated cognitive decline in midlife

description: ObjectiveIncreasing evidence supports an association between midlife
 cardiovascular risk factors (CVRFs) and risk of dementia, but less is
 known about whether CVRFs influence cognition in midlife. We examined the
 relationship between CVRFs and midlife cognitive decline.MethodsIn 2,675
 black and white middle-aged adults (mean age 50.2 ± 3.6 years, 57% female,
 45% black), we measured CVRFs at baseline: hypertension (31%), diabetes
 mellitus (11%), obesity (43%), high cholesterol (9%), and current
 cigarette smoking (15%). We administered cognitive tests of memory,
 executive function, and processing speed at baseline and 5 years later.
 Using logistic regression, we estimated the association of CVRFs with
 accelerated cognitive decline (race-specific decline ≥1.5 SD from the mean
 change) on a composite cognitive score.ResultsFive percent (n = 143) of
 participants had accelerated cognitive decline over 5 years. Smoking,
 hypertension, and diabetes mellitus were associated with an increased
 likelihood of accelerated decline after multivariable adjustment (adjusted
 odds ratio [AOR] 1.65, 95% confidence interval [CI] 1.00–2.71; AOR 1.87,
 95% CI 1.26–2.75; AOR 2.45, 95% CI 1.54–3.88, respectively), while obesity
 and high cholesterol were not associated with risk of decline. These
 results were similar when stratified by race. The likelihood of
 accelerated decline also increased with greater number of CVRFs (1–2
 CVRFs: AOR 1.77, 95% CI 1.02–3.05; ≥3 CVRFs: AOR 2.94, 95% CI 1.64–5.28)
 and with Framingham Coronary Heart Disease Risk Score ≥10 (AOR 2.29, 95%
 CI 1.21–4.34).ConclusionsMidlife CVRFs, especially hypertension, diabetes
 mellitus, and smoking, are common and associated with accelerated
 cognitive decline at midlife. These results identify potential modifiable
 targets to prevent midlife cognitive decline and highlight the need for a
 life course approach to cognitive function and aging.
description: CARDIA is a multicenter
 longitudinal study designed to measure risk factors for coronary artery
 disease in a cohort of black and white women and men (n=5115), initially
 aged 18 to 30 years and healthy at enrollment. To assess the effect of CVRF
 exposure on cognitive changes during midlife, we included participants who
 completed cognitive testing at Year 25 (2010-11), our study’s baseline,
 and five years later (follow up mean (SD)=5.02 (0.34) years,
 range=3.90-6.11 years) .
description: The are supplemetary tables with showing results from sensitvity
 analyses described in the published manuscript.
DOI: 10.5061/dryad.7h44j0zr2
title: Speciation rate and the diversity of fishes in freshwaters and the oceans

description: Aim: The number of fish taxa that occur exclusively in marine biomes is
 approximately equal to the number that occur in freshwater biomes. Both
 the geographic area and habitable volume of the marine realm are vastly
 greater than for Earth's freshwater ecosystems, suggesting that the
 density of marine species is proportionately much lower in the oceans.
 Because freshwater lineages are relatively recently derived from older
 marine lineages, this difference in species density suggests that
 speciation rates might be elevated in freshwater systems. I tested whether
 speciation rates differ systematically between freshwater and marine
 habitats. Location: Aquatic ecosystems worldwide Taxon: Ray-finned fishes
 (Actinopterygii) Methods: Marine-freshwater transitions were tabulated
 from literature survey and from ancestral state reconstruction. I tested
 for repeated effects of salinity transitions on speciation rate using
 formal state-dependent diversification methods (STRAPP, FiSSE). Using
 maximum likelihood, I then tested for absolute (unreplicated) differences
 in speciation rate between marine and freshwater lineages. Results:
 Ray-finned fishes have undergone numerous transitions from marine to
 freshwater systems, but the vast majority of freshwater species richness
 has resulted from a handful of freshwater colonization events. Speciation
 rates in freshwater lineages are substantially faster on average than
 those of marine lineages, but transitions to freshwaters do not lead to
 elevated rates of speciation in general. This paradox of state-dependent
 diversification arises because of the disproportionate effect of several
 freshwater clades with high species richness and fast rates of
 speciation.  Main Conclusions: Transitions to freshwater do not
 cause faster rates of speciation, but freshwater ecosystems worldwide are
 dominated by several clades with relatively fast rates of speciation.
 There is no evidence that invasion of a novel habitat (freshwater) is
 generally sufficient to trigger a burst of speciation in colonizing
 lineages. These results raise an important conceptual problem for the
 interpretation of state-dependent diversification analyses.
DOI: 10.5061/dryad.8w9ghx3hn
title: Cassowary gloss and a novel form of structural color in birds

description: One of the two lineages of extant birds resulting from its deepest split,
 Palaeognathae, has been reported not to exhibit structural
 coloration in feathers, affecting inferences of ancestral
 coloration mechanisms in extant birds. Structural coloration in facial
 skin and eggshells have been shown in the lineage, but not
 feathers. Here, we report the first evidence for two distinct
 mechanisms of structural color in palaeognath feathers.
 One extinct volant clade, Lithornithidae, shows evidence of
 elongate melanin-containing organelles uniquely associated with
 glossy/iridescent color. This mechanism of structural color is
 present in fossil outgroups and neognath birds. Second, we demonstrate
 a structural basis of exceptional gloss in extant cassowary
 feathers. Gloss is proposed to be an intermediate phenotype
 between matte and iridescent plumage, conferred by a thick and
 smooth feather rachis. Rachis-based structural color has not been
 previously investigated. The new data inform relationships
 between avian melanin-based coloration and feather structure.
description: Dataset (trait dataset, and time-calibrated phylogeny) and R code
 used in analyses within the manuscript.
DOI: 10.5061/dryad.qrfj6q5br
title: Panmixia in a sea ice-associated marine mammal: evaluating genetic structure of the Pacific walrus (Odobenus rosmarus divergens) at multiple spatial scales

description: The dataset includes 5303 Pacific walrus genotypes for 114 single
 nucleotide polymorphisms used in the manuscript "Panmixia in a sea
 ice-associated marine mammal:  evaluating genetic structure of
 the Pacific walrus (Odobenus rosmarus divergens) at multiple spatial
 scales".  Biopsy samples were collected from Pacific
 walruses hauled-out on sea ice in the Bering and Chukchi seas from
 2013-2017 in June of each year.  Genotypes are presented in two
 columns per locus and missing data is coded as "N".
DOI: 10.7280/d11960
title: CA1 20-40 Hz oscillatory dynamics reflect trial-specific information processing supporting nonspatial sequence memory

description: The hippocampus is known to play a critical role in processing information
 about the temporal context in which our experiences occur. However, it
 remains unclear how hippocampal oscillations are associated with
 this type of information processing, and how their
 functional organization is influenced by connectivity gradients.
 Here we investigate these issues by examining local field
 potential activity recorded across the proximodistal axis of CA1 as
 rats performed a complex odor sequence memory task. More
 specifically, we took advantage of the paradigm’s precise
 time-locking and diverse cognitive demands to evaluate the
 correspondence between specific patterns of oscillatory activity
 and specific forms of information processing. Our first main
 finding is that spectral content differed between behavioral states (odor
 sequence processing epochs vs running epochs) and that, for each
 behavioral state, the power of recruited oscillations showed
 significantly distinct gradients along the proximodistal axis. Odor
 sequence processing epochs were characterized by increased power in the
 4-8 Hz and 20-40 Hz range, with 20-40 Hz oscillations showing a
 power gradient increasing toward proximal CA1. In contrast,
 running epochs were characterized by increased power in the 8-12 Hz range
 and in a broad but modest increase in power across higher
 frequency ranges (&gt;24 Hz), with power gradients increasing
 toward proximal and distal CA1, respectively. Our second main finding
 is the discovery that 20-40 Hz oscillations were specifically and
 significantly modulated by sequence memory performance. We found
 that 20-40 Hz power increased with knowledge of the sequence and carried
 trial-type-specific information. These results link 20-40 Hz oscillations
 with trial-specific processing of nonspatial information critical for
 order memory judgments, which is consistent with the demonstrated role of
 the hippocampus in processing temporal relationships among events. The
 prominence of such oscillations in proximal CA1 is also consistent with
 evidence that medial entorhinal input is important for the processing of
 temporal information in CA1.
description: Data was initially collected using a Plexon MAP system and then
 processed in Matlab. Data (behavioral and neural) from the original .plx
 files was organized in a format used by the Fortin lab and collaborators
 and stored as a .mat file. Behavioral and neural data are stored in
 separate files with a common organization. For each session the data was
 arranged in an NxM matrix where rows indicate a timestamp and columns
 represent different events and/or data collected at that time. Further
 description of the data organization can be found in the ReadMe and at
 https://github.com/FortinLab/statMatrixNeuralAnalysis.
description: Associated code located at https://github.com/FortinLab/Gattas_et_al_2020. A readme (Filenames README.txt) is included to indicate the naming convention for the associated files.
DOI: 10.5061/dryad.zw3r22854
title: Efficacy of metabarcoding for identification of fish eggs evaluated with mock communities

description: There is urgent need for effective and efficient monitoring of marine fish
 populations. Monitoring eggs and larval fish may be more informative that
 traditional fish surveys since ichthyoplankton surveys reveal the
 reproductive activities of fish populations, which directly impact their
 population trajectories.  Ichthyoplankton surveys have turned to
 molecular methods (DNA barcoding & metabarcoding) for
 identification of eggs and larval fish due to challenges of morphological
 identification. In this study we examine the effectiveness of using
 metabarcoding methods on mock communities of known fish egg DNA. We
 constructed six mock communities with known ratios of species. In addition
 we analyzed two samples from a large field collection of fish eggs and
 compared metabarcoding results with traditional DNA barcoding results. We
 examine the ability of our metabarcoding methods to detect species and
 relative proportion of species identified in each mock community. We found
 that our metabarcoding methods were able to detect species at very low
 input proportions, however levels of successful detection depended on the
 markers used in amplification, suggesting that the use of multiple markers
 is desirable. Variability in our quantitative results may result from
 amplification bias as well as interspecific variation in mitochondrial DNA
 copy number.  Our results demonstrate that there remain
 significant challenges to using metabarcoding for estimating proportional
 species composition; however the results provide important insights into
 understanding how to interpret metabarcoding data. This study will aid in
 the continuing development of efficient molecular methods of biological
 monitoring for fisheries management.