cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.79cnp5hvw
title: Fruit hardness, size, and weight for wild fruits in Uganda and Madagascar

description: Fleshy fruits have evolved to be attractive to frugivorous seed
 dispersers. As a result, many fruit traits like size, color, scent and
 nutritional content are assumed to be the result of selective pressures
 exerted by frugivores. At the same time, fruit traits are also subjected
 to a set of other selective pressures and constraints. One such trait is
 fruit hardness. On one hand, haptic cues have been suggested to play a
 role in frugivore behavior, potentially driving selection on fruit skin
 traits, including hardness. On the other hand, fruit skin traits also
 interact with antagonists, e.g., seed predators and microbes, which can
 also impose selective pressures, particularly with respect to fruit
 hardness.  Yet skin hardness may also be driven not by adaptive
 response to biotic pressures, but rather a mechanical constraint: fruits
 are packed with water-rich pulp and seeds which exert mechanical pressure
 on the skin. Skin hardness may simply result from the need for fruits to
 withhold internal pressure to maintain fruit integrity. We test the fruit
 mechanical constraint hypothesis on a set of 95 native Malagasy plant
 species. We used a theoretical structural formula to model internal
 pressure experienced by fruit skins to test whether variation in pressure
 predicts fruit hardness. We find that, while positively correlated,
 internal stress explains very little of the variance in fruit hardness.
 This suggests that mechanical constraints play a minor role in driving
 fruit hardness, and that biotic factors may therefore contribute
 substantially to variation in fruit hardness.
DOI: 10.5061/dryad.cc2fqz668
title: Data from: Reproductive tradeoffs and phenotypic selection change with body condition, but not with predation regime, across island lizard populations

description: Tradeoffs between reproduction and survival are central to life-history
 theory and are expected to shape patterns of phenotypic selection, but the
 ecological factors structuring these tradeoffs and resultuant patterns of
 selection are generally unknown. We manipulated reproductive investment
 and predation regime in island populations of brown anole lizards (Anolis
 sagrei) to test (1) whether previously documented increases in the
 survival of experimentally non-reproductive females (OVX = ovariectomy)
 reflect the greater susceptibility of reproductive females (SHAM =
 control) to predation, and (2) whether phenotypic selection differs as a
 function of reproductive investment and predation regime. OVX females
 exceeded SHAM controls in growth, mass gain, and body condition,
 indicating pronounced energetic costs of reproduction. Although mortality
 was greatest in the presence of bird and snake predators, differences in
 survival between OVX and SHAM were unrealted to predation regime, as were
 patterns of natural selection on body size. Instead, we found that body
 condition at the conclusion of the experiment differed significantly
 across populations, suggesting that local environments varied in their
 ability to support mass gain and positive energy balance. As mean body
 condition improved across populations, the magnitude of the
 survival cost of reproduction increased, linear selection on body size
 shifted from positive to negative, and quadratic selection shifted from
 stabilizing to weakly disruptive. Our results suggest that reproductive
 tradeoffs and patterns of phenotypic selection in female brown anoles are
 more sensitive to inferred variation in environmental quality than to
 experimentally induced variation in predation.
description: Data were collected as records of size and survival of individual
 lizards in the field, then entered into Excel files. These primary data
 have been used to calculate additional measures such as body condition
 residuals, and to derive means, standard errors, least-square means, and
 other summary statistics for populations.
description: See associated ReadMe file. Methods of analysis are described in
 the associated manuscript.
DOI: 10.5061/dryad.f1vhhmgx6
title: Recent natural variability in global warming weakened phenological mismatch and selection on seasonal timing in great tits (Parus major)

description: Climate change has led to phenological shifts in many species, but with
 large variation in magnitude among species and trophic levels. The poster
 child example of the resulting phenological mismatches between the
 phenology of predators and their prey is the great tit (Parus major),
 where this mismatch led to directional selection for earlier seasonal
 breeding. Natural climate variability can obscure the impacts of climate
 change over certain periods, weakening phenological mismatching and
 selection. Here, we show that selection on seasonal timing indeed weakened
 significantly over the past two decades as increases in late spring
 temperatures have slowed down. Consequently, there has been no further
 advancement in the date of peak caterpillar food abundance, while great
 tit phenology has continued to advance, thereby weakening the phenological
 mismatch. We thus show that the relationships between temperature,
 phenologies of prey and predator, and selection on predator phenology are
 robust, also in times of a slowdown of warming. Using projected
 temperatures from a large ensemble of climate simulations that take
 natural climate variability into account, we show that prey phenology is
 again projected to advance faster than great tit phenology in the coming
 decades, and therefore that long-term global warming will intensify
 phenological mismatches.
description: Data was collected in our long-term population of great tits
 (Parus major) at the Hoge Veluwe population (Netherlands).
 It was processed using ACCESS database queries and
 R-scripts.
description: See the ReadMe file.
DOI: 10.5061/dryad.c2fqz6188
title: P-elements strengthen reproductive isolation within the Drosophila simulans species complex

description: Determining mechanisms that underlie reproductive isolation is key to
 understanding how species boundaries are maintained in nature.
 Transposable elements (TEs) are ubiquitous across eukaryotic genomes.
 However, the role of TEs in modulating the strength of reproductive
 isolation between species is poorly understood. Several species of
 Drosophila have been found to harbor P-elements (PEs), yet only D.
 simulans is known to be currently polymorphic for their presence in wild
 populations. PEs can cause reproductive isolation between PE-containing
 (P) and PE-lacking (M) lineages of the same species. Here, we use the
 simulans species complex to assess whether differences in PE status
 between D. simulans and its sister species, which do not harbor PEs,
 contribute to multiple barriers to gene flow between species. We show that
 crosses involving a P-D. simulans father and an M-mother from a sister
 species exhibit lower F1 female fecundity than crosses involving an M-D.
 simulans father and an M-sister-species mother. We also find that another
 TE, I-element, might play a minor role on determining the frequency of
 dysgenesis between species. Our results suggest that the presence of PEs
 in a species can strengthen isolation from its sister species, providing
 evidence that TEs can play a role in isolation. --
DOI: 10.5061/dryad.t1g1jwt2m
title: Nitrogen fixation and crop productivity enhancements codriven by intercrop root exudates and key rhizosphere bacteria

description: 1. Crop diversity management is widely used to increase agricultural
 productivity and sustainability. Recent studies have demonstrated that
 maize root exudates can drive interspecific facilitation to enhance N2
 fixation of bean in intercropping systems. However, the mechanisms of N2
 fixation enhancement stimulated by root exudates in the intercropping
 systems remain unclear. 2. Four experiments were designed to provide a
 progressively deeper understanding of how root exudates stimulate
 microbial-mediated N2 fixation. First, the effects of faba bean/maize
 intercropping on yields and soil microbial communities were determined in
 a field experiment. Second, root-derived interspecific facilitation was
 evaluated using a root partitioning approach. Third, the key microbial
 taxa in the faba bean rhizosphere were traced using 13C-labeled maize root
 exudates. Fourth, the codriven mechanism of maize root exudates and
 microorganisms in the faba bean rhizosphere were explored. 3. Faba
 bean/maize intercropping with maize residue return increased the yields of
 faba bean (26%), maize (27%), and broccoli (9.1%) compared to that under
 monocropping. Nodulin-like 4 (NODL4), chalcone-flavanone isomerase (CFI),
 and early nodulin-like (ENODL2) gene expression in faba bean roots
 intercropped with maize increased by 1.5-2.3-fold compared to that
 observed under monoculture. More than half of the N2 fixation of faba bean
 increase under intercropping was due to interactions with microorganisms.
 Nine key bacterial genera in the faba bean rhizosphere were identified by
 13C-DNA based stable isotope probing analysis. Among them Agromyces,
 Arthrobacter, Bacillus, Lysobacter, and Paenibacillus directly fix N2,
 while Gemmatimonas, Heliobacillus, Natronocella, and Sorangium increase
 the N2 fixation capacity of Azotobacter by providing additional carbon
 sources. These key bacteria triggered by maize root exudates played an
 important role in the rhizosphere facilitation of intercropping. 4.
 Synthesis and applications. We demonstrated a novel root-root facilitation
 of N2 fixation and increased crop yields codriven by root exudates and
 rhizosphere bacteria under faba bean/maize intercropping, and nine key
 bacteria associated with this process were identified by 13C-DNA based
 stable isotope probing. We recommend the adoption and optimization of
 intercropping systems with residue return to reduce the shortcomings of
 continuous cropping and to increase the sustainability of crop production.
DOI: 10.5061/dryad.6wwpzgmzq
title: Literature based occurrence locations of Aedes aegypti and Aedes albopictus in India since 2015

description: India has witnessed a five-fold increase in dengue incidence in the past
 decade. However, the nation-wide distribution of dengue vectors, and the
 impacts of climate change are not known. Species distribution models are a
 novel approach for determining the distribution of species based on
 biologically relevant environmental factors, and relies on known presence
 and absence locations of the species. The Global Biodiversity Information
 Facility (GBIF) contains 562 records of Aedes aegypti occurrence
 and 207 records of Aedes albopictus occurrence in India, most of which are
 derived from a large scale study that compiled the global geographic
 database of Aedes aegypti and Aedes albopictus locations up to 2014, based
 on peer reviewed literature, national entomological surveys and expert
 networks. However, there was a need to update the occurrence locations
 after 2014. To overcome this knowledge gap, we compiled data on
 the occurrences of Aedes aegypti and Aedes albopictus in India, based on
 published literature after 2014 that carried out entomological surveys in
 India. This dataset was combined with data from GBIF to map the present
 and future distributions of Aedes aegypti and Aedes albopictus in India
 based on different scenarios for climate change.
description: An extensive survey of all dengue entomological studies conducted
 in India after 2014 was carried out. The search terms ‘India’, ‘aegypti’
 and ‘albopictus’ were used to find relevant peer reviewed literature in
 NCBI - PubMed (https://www.ncbi.nlm.nih.gov/pubmed), Science Direct
 (https://www.sciencedirect.com/) and grey literature in Google Scholar
 https://scholar.google.com/). Only those studies were included where the
 exact coordinates of the survey were clearly mentioned. In total, 128 new
 occurrence locations of Aedes aegypti and 127 occurrence locations of
 Aedes albopictus were obtained. The data was then compiled in the Darwin
 core format.
DOI: 10.5061/dryad.8sf7m0cnj
title: Chesapeake Bay and Baltic Sea phytoplankton sample metadata

description: We analyze the relationship between species richness, salinity and
 resource use efficiency from 10712 summer (June to September) surface
 phytoplankton samples from the Chesapeake Bay (n=3967) and the Baltic Sea
 (n=6745). As sample species richness (alpha diversity) has a U-shape
 distribution along an estuarine salinity gradient and species richness is
 known to scale with resource use efficiency – an important ecosystem
 function, we hypothesized that the ecosystem function can be predicted
 from salinity.
description: Samples from Chesapeake Bay were taken from fixed statutory
 monitoring station. From The Baltic Sea samples represented a combination
 of fixed and spatially scattered locations. Sampling
 and sample processing details are given in respective program manuals
 (Michaels and Kahrr 2010; HELCOM 2014). Aliquots of surface layer samples
 were preserved with acid Lugol’s solution or formalin, and cells were
 enumerated from aliquots of 10–50 mL using inverted microscopes. The
 counting effort varied but in general was better than 100 cells of the
 most numerous taxon. Michaels, B., and R. Kahrr. 2010.
 Maryland Chesapeake Bay water quality monitoring program: phytoplankton
 component. https://
 www.chesapeakebay.net/documents/3684/3_mdphdoc.pdf.
 HELCOM. 2014. Manual for marine monitoring in the COMBINE pro-
 gramme. http://www.helcom.fi/Lists/Publications/Manual%20for%20
 Marine%20Monitoring%20in%20the%20COMBINE%20Programme %20of%20HELCOM.pdf.
 HELCOM, Helsinki.
description: UTF-8 text file with LF line endings. Missing
 values denoted with NA Geographic range of
 data: Chesapeake Bay (USA); Baltic Sea. The sampling station coordinates
 are given in the data table in columns lat and lon
 Temporal coverage: 1984-06-06 to 2008-09-30
DOI: 10.5061/dryad.70rxwdbxq
title: Model data for: Drawdown of atmospheric pCO2 via dynamic particle export stoichiometry in the ocean twilight zone

description: Understanding the global carbon cycle is key to understanding the climate
 system. One of the large unknowns is the processes happening in the
 twilight zone of the ocean. Here, we focus on how elemental stoichiometry
 of particulate organic matter in the twilight zone affects the strength of
 the biological pump and atmospheric CO2. We show through modeling that
 atmospheric CO2 is very sensitive to the change in C:P ratio in the
 twilight zone. Numerous model studies study the link between the
 carbon cycle and flexible elemental stoichiometry of organic matter in the
 surface ocean. However, our model study is unique. It investigates the
 effects of stoichiometric changes both at the surface and in the
 subsurface ocean that also involve stoichiometric interaction between
 phytoplankton and zooplankton. We use a 3D numerical model to illustrate
 how C:P variability in the twilight zone can significantly modulate the
 strength of carbon sequestration and atmospheric CO2. We used the
 biogeochemical model MOPS (Kriest and Oschlies, Geosci. Model Dev., 8,
 2929–2957, 2015) coupled to ECCO Transport Matrices. This repository
 contains model input and output files for each sensitivity run outlined in
 the paper. The run ID corresponds to different sensitivity run. See README
 for more details.
DOI: 10.15468/dl.njywps
title: Occurrence Download

description: A dataset containing 45924 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is iNaturalist Research-grade Observations",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Country is one of (Canada, Mexico, United States of America)",
 "EventDate is greater than or equal to 2026-01-02",
 "EventDate is less than or equal to 2026-02-01",
 {
 "not" : {
 "Issue" : [
 "is one of (Basis of record invalid, Coordinate reprojection failed, Coordinate reprojection suspicious, Coordinate precision invalid, Coordinate uncertainty meters invalid, Country mismatch, Country invalid, Geodetic datum invalid, Presumed swapped coordinate, Presumed negated longitude, Presumed negated latitude, Country coordinate mismatch)"
 ]
 }
 },
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 45924 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002859-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.vx0k6djrv
title: Stresses affect inbreeding depression in complex ways: Disentangling stress-specific genetic effects from effects of initial size in plants

description: The magnitude of inbreeding depression (ID) varies unpredictably among
 environments. ID often increases in stressful environments suggesting that
 these expose more deleterious alleles to selection or increase their
 effects. More simply, ID could increase under conditions that amplify
 phenotypic variation (CV²), e.g. by accentuating size hierarchies among
 plants. These mechanisms are difficult to distinguish when stress
 increases both ID and phenotypic variation. We grew in- and outbred
 progeny of Mimulus guttatus under six abiotic stress treatments (control,
 waterlogging, drought, nutrient deficiency, copper addition and clipping)
 with and without competition by the grass Poa palustris. ID differed
 greatly among stress treatments with δ varying from 7% (control) to 61%
 (waterlogging) but did not consistently increase with stress intensity.
 Poa competition increased ID under nutrient deficiency but not other
 stresses. Analyzing effects of initial size on performance of outbred
 plants suggests that under some conditions (low N, clipping) competition
 increased ID by amplifying initial size differences. In other cases (e.g.,
 high ID under waterlogging), particular environments amplified the
 deleterious genetic effects of inbreeding suggesting differential gene
 expression. Interestingly, conditions that increased the phenotypic
 variability of inbred progeny regularly increased ID whereas variability
 among outbred progeny showed no relationship to ID. Our study reconciles
 the stress- and phenotypic variability hypotheses by demonstrating how
 specific conditions (rather than stress per se) act to increase ID.
 Analyzing CV² separately in inbred and outbred progeny while including
 effects of initial plant size improve our ability to predict how ID and
 gene expression vary across environments.
description: The dataset contains the results of a greenhouse experiment with
 inbred and outbred <em>Mimulus guttatus</em> plants grown
 under different experimental stress treatments, see publication for
 details.
DOI: 10.5061/dryad.000000040
title: Frequency and characterization of movement disorders in anti-IgLON5 disease

description: Objective: Anti-IgLON5 disease is a recently described neurological
 disease that shares features of autoimmunity and neurodegeneration.
 Abnormal movements appear to be frequent and important but have not been
 characterized and are under-reported. Here we describe the frequency and
 types of movement disorders in a series of consecutive patients with this
 disease. Methods: In this retrospective, observational study, the presence
 and phenomenology of movement disorders were assessed with a standardized
 clinical questionnaire. Available videos were centrally reviewed by three
 experts in movement disorders. Results: Seventy two patients were
 included. In 41 (57%) the main reason for initial consultation was
 difficulty walking along with one or several concurrent movement
 disorders. At the time of anti-IgLON5 diagnosis, 63 (87%) patients had at
 least one movement disorder with a median of three per patient. The most
 frequent abnormal movements were gait and balance disturbances (52
 patients, 72%), chorea (24, 33%), bradykinesia (20, 28%), dystonia (19,
 26%), abnormal body postures or rigidity (18, 25%), and tremor (15, 21%).
 Other hyperkinetic movements (myoclonus, akathisia, myorhythmia, myokymia,
 or abdominal dyskinesias) occurred in 26 (36%) patients. The craniofacial
 region was one of the most frequently affected by multiple concurrent
 movement disorders (23 patients, 32%) including dystonia (13), myorhythmia
 (6), chorea (4) or myokymia (4). Considering any body region, the most
 frequent combination of multiple movement disorders consisted of gait
 instability or ataxia associated with craniofacial dyskinesias or
 generalized chorea observed in 31(43%) of patients. In addition to
 abnormal movements, 87% of patients had sleep alterations, 74% bulbar
 dysfunction, and 53% cognitive impairment. Fifty-five (76%) patients were
 treated with immunotherapy, resulting in important and sustained
 improvement of the movement disorders in only seven (13%) cases.
 Conclusions: Movement disorders are a frequent and leading cause of
 initial neurological consultation in patients with anti-IgLON5 disease.
 Although multiple types of abnormal movements can occur, the most
 prevalent are disorders of gait, generalized chorea, and dystonia and
 other dyskinesias that frequently affect craniofacial muscles. Overall,
 anti-IgLON5 disease should be considered in patients with multiple
 movement disorders, particularly if they occur in association with sleep
 alterations, bulbar dysfunction, or cognitive impairment.
DOI: 10.5061/dryad.9s4mw6mgt
title: Scripts and metadata of the manuscript: Characterization of tmt-opsin2 in medaka fish provides insight into the interplay of light and temperature for behavioral regulation

description: One of the big challenges in the study of animal behavior is to combine
 the molecular-level questions of functional genetics, typically performed
 in the lab, with meaningful combinations of environmental stimuli. Light
 and temperature are important external cues, influencing the behaviors of
 organisms. Thus, understanding the combined effect of light and
 temperature changes on wildtype versus genetically modified animals is a
 first step to understand the role of individual genes in the ability of
 animals to cope with changing environments. Many behavioral traits can be
 extrapolated from behavioral tests performed from automated motion
 tracking combined with machine learning. The acquired datasets, typically
 complex and large, can be challenging for subsequent quantitative
 analyses. Here we investigate medaka behavior of tmt-opsin2 mutants versus
 corresponding wildtypes under different light and temperature conditions
 using automated tracking combined with a convolutional neuronal network
 and a Hidden Markov model-based approach. The temperatures in this study
 can occur in summer versus fall/winter in the natural habitat of
 medakafish. Under summer-like temperature, tmt-opsin2 mutants did
 not exhibit changes in overall locomotion, consistent with previous
 observations. However, detailed analyses of fish position revealed that
 tmt-opsin2 mutants spent more time in central locations of the dish,
 possibly due to decreased anxiety. Furthermore, a clear difference in
 location and overall movement was obvious between mutant and wildtypes
 under colder conditions. These data indicate a role of tmt-opsin2 in
 behavioral adjustment, at least in part depending on the season.