cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.1b5474b
title: Data from: Seasonal dynamics of waterbird assembly mechanisms revealed by phylogenetic and functional diversity in a subtropical wetland

description: Despite growing interest in phylogenetic and functional methods in
 ecological assembly, less attention has been paid to seasonal variation
 patterns of migrant species. Migrants can rapidly mediate influences of
 species interactions and environmental factors through seasonal movement,
 suggesting dynamical relative importance of different assembly mechanisms
 among seasons. Here we describe seasonal dynamics in phylogenetic and
 functional diversity of waterbirds in Mai Po Wetland, in a subtropical
 region with significant predictable temporal variation. Phylogenetic and
 functional structure of α diversity varied seasonally. Specifically,
 phylogenetic structures clustered in summer, while being over-dispersed in
 winter. However, phylogenetic structure in spring and autumn was
 intermediate with a transition to random. Functional structure was
 clustered in spring but showed over-dispersion in the other three seasons.
 For β diversity, summer and winter assemblages had two distinct groups,
 while spring and autumn assemblages were mixed. Thus, waterbird
 assemblages were primarily shaped by interspecific competition in winter.
 Random processes tended to shape assemblage in spring. Environmental
 factors played a more important role in summer . In addition, phylogenetic
 distance of probability of co-occurrence of species pairs was
 significantly larger in winter than in summer. These results suggest that
 the relative importance of assemblage mechanisms can vary seasonally in
 response to changing environmental conditions, suggesting that studies
 attempting to infer a single dominant assembly mechanism may ignore
 important assembly processes. Temporal shifts in assembly mechanisms may
 play an important role in maintaining diversity of subtropical and
 temperate wetlands and perhaps other dynamic systems.
description: waterbird
 communityWaterbird abundance
 recorded in Mai Po Wetland site by site and month by month. Trait (wing
 length) of each species.waterbird communities and
 trait.xlsx
DOI: 10.5061/dryad.m80k750
title: Data from: Fine-scale behavioural adjustments of prey on a continuum of risk

description: In the wild, prey species often live in the vicinity of predators,
 rendering the ability to assess risk on a moment-to-moment basis crucial
 to survival. Visual cues are important as they allow prey to assess
 predator species, size, proximity and behaviour. However, few studies have
 explicitly examined prey’s ability to assess risk based on predator
 behaviour and orientation. Using mosquitofish, Gambusia holbrooki, and
 their predator, jade perch, Scortum barcoo, under controlled conditions,
 we provide some of the first fine-scale characterisation of how prey adapt
 their behaviour according to their continuous assessment of risk based on
 both predator behaviour and angular distance to the predator’s mouth. When
 these predators were inactive and posed less of an immediate threat, prey
 were often found within the attack cone of the predator showing reductions
 in speed and acceleration, characteristic of predator-inspection
 behaviour. However, when predators became active, prey swam faster with
 greater acceleration and were closer together within the attack cone of
 predators. Most importantly, this study provides evidence that prey do not
 adopt a uniform response to the presence of a predator. Instead, we
 demonstrate that prey are capable of rapidly and dynamically updating
 their assessment of risk and showing fine-scale adjustments to their
 behaviour.
description: Kent et
 al_DataDataset containing each
 prey individual's median speed, acceleration and nearest neighbour
 distances based on predator activity state (inactive or active) and
 angular distance to the predator's mouth (in 5º
 bins)MedianStats5degBins.csvKent et al_RcodeR code used to to produce statistics reported in: Fine-scale behavioural adjustments of prey on a continuum of riskKent_Rcode.RKent et al_Data2Data recording the proportion of the trial that each predator spent active or inactive.PropState.csv
DOI: 10.5061/dryad.r0s4ft2
title: Data from: Gene copy number variations as signatures of adaptive evolution in the parthenogenetic, plant-parasitic nematode Meloidogyne incognita

description: Adaptation to changing environmental conditions represents a challenge to
 parthenogenetic organisms and until now, how phenotypic variants are
 generated in clones in response to the selection pressure of their
 environment remains poorly known. The obligatory parthenogenetic root-knot
 nematode species Meloidogyne incognita has a worldwide distribution and is
 the most devastating plant-parasitic nematode. Despite its asexual
 reproduction, this species exhibits an unexpected capacity of adaptation
 to environmental constraints, e.g., resistant hosts. Here we used a
 genome-wide comparative hybridization strategy to evaluate variations in
 gene copy numbers between genotypes of M. incognita resulting from two
 parallel experimental evolution assays on a susceptible vs. resistant host
 plant. We detected gene copy number variations (CNVs) associated with the
 ability of the nematodes to overcome resistance of the host plant, and
 this genetic variation may reflect an adaptive response to host resistance
 in this parthenogenetic species. The CNV distribution throughout the
 nematode genome is not random and suggests the occurrence of genomic
 regions more prone to undergo duplications and losses in response to the
 selection pressure of the host resistance. Furthermore, our analysis
 revealed an outstanding level of gene loss events in nematode genotypes
 that have overcome the resistance. Overall, our results support the view
 that gene loss could be a common class of adaptive genetic mechanism in
 response to a challenging new biotic environment in clonal animals.
description: aCGH_Raw_Data
DOI: 10.5281/zenodo.18261256
title: Data for paper "Main phase transition of hydroperoxidized SOPC bilayers"

description: Data set for paper "Main phase transition of hydroperoxidized SOPC bilayers". The data concerns four techniques: small angle neutron scattering (SANS), differential scanning calorimetry (DSC), and spectrophotometric data from vesicles with the probe laurdan (Laurdan) and probe A10 (A10). Data from each technique is stored as a compressed zip file containing the data and a readme.txt file with the corresponding data information.
DOI: 10.5061/dryad.m8hb503
title: Data from: Digit ratio predicts the number of lifetime recruits in female collared flycatchers

description: The early environment in which an organism grows can have long-lasting
 impact on both its phenotype and fitness. However, assessing this
 environment comprehensively is a formidable task. The relative length of
 the second to the fourth digit (2D:4D) is a broadly studied skeletal trait
 that is fixed for life during ontogeny. 2D:4D has been shown to indicate
 various early effects including the perinatal steroid milieu in both
 humans and non-human animals. However, the fitness relevance of the early
 effects indicated by 2D:4D remains unknown. Here, we investigated hindlimb
 2D:4D and measures of lifetime performance in wild collared flycatcher
 (Ficedula albicollis) females. We found that females with higher 2D:4D had
 a greater number of recruiting offspring to the breeding population. This
 was the case despite the fact that such females did not lay more eggs or
 breed more times during their reproductive life. Our results support that
 2D:4D, known to be a retrospective marker of perinatal development,
 positively associates with female quality in the collared flycatcher.
description: Long-term breeding data
 and 2D:4D measures from collared flycatchers.Long-term breeding data
 and 2D:4D measures from a Hungarian population of collared flycatchers.
 Variables are detailed in the sheet named
 "variables".RSBL-2019-0051_data.xls
DOI: 10.5281/zenodo.18261255
title: Data for paper "Main phase transition of hydroperoxidized SOPC bilayers"

description: Data set for paper "Main phase transition of hydroperoxidized SOPC bilayers". The data concerns four techniques: small angle neutron scattering (SANS), differential scanning calorimetry (DSC), and spectrophotometric data from vesicles with the probe laurdan (Laurdan) and probe A10 (A10). Data from each technique is stored as a compressed zip file containing the data and a readme.txt file with the corresponding data information.
DOI: 10.5061/dryad.92m95r1
title: Data from: Spatial variation in anuran richness, diversity, and abundance across montane wetland habitat in Volcanoes National Park, Rwanda

description: The spatial distribution of species has long sparked interest among
 ecologists and biogeographers, increasingly so in studies of species
 responses to climate change. However, field studies on spatial patterns of
 distribution, useful to inform conservation actions at local scales, are
 still lacking for many regions, especially the tropics. We studied
 elevational trends and species‐area relationships among anurans in wetland
 habitats within Volcanoes National Park (VNP) in Rwanda, part of the
 biodiverse Albertine Rift region. In VNP, wetlands are key sites for
 anuran reproduction, and anurans are likely threatened by wetland
 desiccation which has occurred for the last few decades. Between 2012 and
 2017, we sampled anuran communities in ten VNP wetlands located along an
 elevational gradient of c. 600 m (from 2,546 to 3,188 m a.s.l.) and found
 at least eight species, including at least two Albertine Rift Endemics. We
 show that species richness, diversity, and abundance likely decline with a
 decrease in wetland size and with an increase in elevation, though
 additional sampling (e.g., at night) might be needed to derive definite
 conclusions. Larger wetlands at lower elevations contained most species
 and individuals, which indicates the potential threat of wetland size
 reduction (through desiccation) for anuran conservation. However, we also
 found that wetlands differed in species composition and that some species
 (e.g., Sclerophrys kisoloensis) were likely restricted in distribution to
 only a few of the smaller wetlands—suggesting that the conservation of
 each individual wetland should be prioritized, regardless of size. We
 propose that all wetlands in VNP require additional conservation measures,
 which should be based on knowledge gathered through long‐term monitoring
 of anuran communities and research on drivers of wetland decline. Only
 such extended research will allow us to understand the response of anurans
 in VNP to threats such as climate change and wetland desiccation.
description: Appendix
 S1Species
 records.AppendixS1.xlsxAppendix S2Species photographic material.
DOI: 10.5281/zenodo.18386086
title: Levy Time Crystals

description: We introduce Levy time crystals, driven many-body systems where subharmonic order is controlledby heavy-tailed control statistics rather than Gaussian noise. Levy-distributed pulse errorslead to a non-analytic scaling of the decay rate, providing a direct dynamical signature of rareeventfluctuations. When the drive timing is heavy-tailed, renewal dynamics produces algebraicdecay without a characteristic timescale. Heavy-tailed control noise thus places temporal order ina regime governed by rare events rather than heating. Here is the Python code we used to perform the research.
DOI: 10.5281/zenodo.18386087
title: Levy Time Crystals

description: We introduce Levy time crystals, driven many-body systems where subharmonic order is controlledby heavy-tailed control statistics rather than Gaussian noise. Levy-distributed pulse errorslead to a non-analytic scaling of the decay rate, providing a direct dynamical signature of rareeventfluctuations. When the drive timing is heavy-tailed, renewal dynamics produces algebraicdecay without a characteristic timescale. Heavy-tailed control noise thus places temporal order ina regime governed by rare events rather than heating. Here is the Python code we used to perform the research.
DOI: 10.5061/dryad.g75r459
title: Data from: Environmental sources of bacteria and genetic variation in behavior influence host-associated microbiota

description: In many organisms, host-associated microbial communities are acquired
 horizontally after birth. This process is believed to be shaped by a
 combination of environmental and host genetic factors. We examined whether
 genetic variation in animal behavior could affect the composition of the
 animal’s microbiota in different environments. The freshwater crustacean
 Daphnia magna is primarily planktonic but exhibits variation in the degree
 to which it browses in benthic sediments. We performed an experiment with
 clonal lines of D. magna showing different levels of sediment-browsing
 intensity exposed to either bacteria-rich or bacteria-poor sediment or
 whose access to sediments was prevented. We found that the bacterial
 composition of the environment and genotype-specific browsing intensity
 together influence the composition of the Daphnia-associated bacterial
 community. Exposure to more diverse bacteria did not lead to a more
 diverse microbiome, but greater abundances of environment-specific
 bacteria were found associated with host genotypes that exhibited greater
 browsing behavior. Our results indicate that, although there is a great
 deal of variation between individuals, behavior can mediate
 genotype-by-environment interaction effects on microbiome composition.
description: MAPFILESample descriptionsOTU tablep303_run34_map97_ab5_utax.tabOTU consensus sequencesp303_run34_OTU_ab5.faOTU tree filep303_run34_OTU_ab5.treAnalysis scriptBehaviorMicrobiota_2018.R
DOI: 10.5061/dryad.29h669c
title: Data from: Fitness of an allopolyploid rupicolous fern compared to its diploid progenitors: From sporogenesis to sporophyte formation

description: PREMISE OF THE STUDY: When two populations of related cytotypes grow in
 sympatry, the rarer cytotype tends to be excluded due to a
 frequency-dependent mating disadvantage. Evolutionary models predict that
 polyploids, which are typically the rarer cytotype upon first formation,
 should have higher relative fitness and/or higher selfing rates to
 establish and then coexist with diploid parents. METHODS: We compared
 performance in early recruitment among three co-occurring rupicolous fern
 species: the allotetraploid Cheilanthes tinaei and its diploid ancestors,
 C. hispanica and C. maderensis. We made culture experiments with fresh
 spores and samples of soil spore banks to test for variation among
 cytotypes in germination, survival, growth and fecundity, and mating
 system of gametophytes. KEY RESULTS: Compared to its diploid parents, C.
 tinaei fresh spores had: higher abortion percentages, worselower dispersal
 ability due to larger spores, and similar vigor at germination. As for
 gametophytes from soil spore banks, C. tinaei showed high survival as C.
 maderensis, but its , similar germination percentage and similar time
 taken to germinate at each incubation temperature. Regarding soil spore
 banks, C. tinaei showed more abundant germination than both diploids,
 which supports greater spore deposition under sporophytes of the
 allotetraploid. Its gender expression resembles that of C. hispanica, with
 a high proportion of males. Patterns of sporophyte formation by females
 and bisexuals indicate that the polyploid does not have increased
 intragametophytic selfing rates. Gametophytes were larger in C. tinaei,
 but its reproductive success (sporophyte formation) was intermediate
 relative to diploids. CONCLUSIONS: Our results indicate that the
 allopolyploid show similar or even lower fitness than diploid progenitors
 show no evidence of higher selfing or fitness advantage of the
 allopolyploid over both diploid parents at any stage of early recruitment.
 In addition, all three species may have similar selfing rates. These two
 unexpected findings suggest that further factors, such as niche
 differentiation, play a more important role in cytotype coexistence.
description: Data from: Fitness of an
 allopolyploid rupicolous fern compared to its diploid progenitors: From
 sporogenesis to sporophyte formationPangua et al. 2019 Fitness of a
 fern polyploid complex.xlsx
DOI: 10.5061/dryad.jd71434
title: Data from: Plant selection initiates alternative successional trajectories in the soil microbial community after disturbance

description: Because interactions between plants and microbial organisms can influence
 species diversity and rates of nutrient cycling, how plants shape
 microbial communities is fundamental to understanding the structure of
 ecosystems. Despite this, the spatial and temporal scales over which
 plants influence microbial communities is poorly understood, particularly
 whether past abiotic or biotic legacies strongly constrain microbial
 community development. We examined biogeochemical cycling and microbial
 community structure in a coastal landscape where historical patterns of
 vegetation transition after a large fire in 1995 are well known, allowing
 us to account for past abiotic and biotic conditions. We found that
 alternative states in microbial community structure and ecosystem
 processes emerged under different plant species, regardless of past
 conditions. Greenhouse studies further demonstrated that these differences
 arise from direct plant selection of microbes, with selection stronger in
 roots compared with soils, especially for bacteria. Correlation of
 microbial community structure with seedling growth rates was also stronger
 for fungi compared to bacteria. Despite these effects, minimal overlap
 between seedling and field microbial communities indicates that the
 effects of initial plant selection are not stable, rather plant selection
 initiated alternative successional trajectories after the fire. Using data
 from a guild where we have abundant natural history information -
 ectomycorrhizal fungi - we show that greenhouse communities are dominated
 by ruderal taxa that are also common in the field after the fire, and that
 these ruderal fungi strongly alter spatial patterns in plant-soil
 feedback, enabling invasion and transformation of soils previously
 occupied by heterospecific plants, thus potentially acting as keystone
 mutualists.
description: Field Data for Plots
 Surveyed in Duhamel et al.Contains all of the
 vegetation and soil attributes measured at our field
 sites.Duhamel_PlotData_22FEB19.csv
DOI: 10.5061/dryad.6qf743b
title: Data from: Increases in local richness (α-diversity) following invasion are offset by biotic homogenization in a biodiversity hotspot

description: The world’s ecosystems are experiencing unparalleled rates of biodiversity
 change with invasive species implicated as one of the drivers that
 restructure local assemblages. Here we focus on the processes leading to
 biodiversity change in a biodiversity hotspot, the Brazilian Cerrado. The
 null expectation that invasion leads to increase in local species richness
 is supported by our investigation of the grass layer in two key habitats
 (campo sujo and campo úmido). Our analysis uncovered a linear relationship
 between total richness and invasive richness at the plot level. However,
 because the invasive species – even though few in number - are widespread,
 their contribution to local richness (α-diversity) is offset by their
 homogenizing influence on composition (β-diversity). We thus identify a
 mechanism that can help explain the paradox that species richness is not
 declining in many local assemblages, yet compositional change is exceeding
 the predictions of ecological theory. As such, our results emphasize the
 importance of quantifying both α-diversity and β-diversity in assessments
 of biodiversity change in the contemporary world.
description: Data from: Increases in
 local richness (alpha-diversity) following invasion are offset by biotic
 homogenization in a biodiversity hotspotDataKortzMagurranBL.xlsx
DOI: 10.5061/dryad.pm793v8
title: Data from: The prevalence of MS in the United States: a population-based estimate using health claims data

description: Objective: To generate a national multiple sclerosis (MS) prevalence
 estimate for the United States by applying a validated algorithm to
 multiple administrative health claims (AHC) datasets. Methods: A validated
 algorithm was applied to private, military, and public AHC datasets to
 identify adult cases of MS between 2008 and 2010. In each dataset, we
 determined the 3-year cumulative prevalence overall and stratified by age,
 sex, and census region. We applied insurance-specific and stratum-specific
 estimates to the 2010 US Census data and pooled the findings to calculate
 the 2010 prevalence of MS in the United States cumulated over 3 years. We
 also estimated the 2010 prevalence cumulated over 10 years using 2 models
 and extrapolated our estimate to 2017. Results: The estimated 2010
 prevalence of MS in the US adult population cumulated over 10 years was
 309.2 per 100,000 (95% confidence interval [CI] 308.1–310.1), representing
 727,344 cases. During the same time period, the MS prevalence was 450.1
 per 100,000 (95% CI 448.1–451.6) for women and 159.7 (95% CI 158.7–160.6)
 for men (female:male ratio 2.8). The estimated 2010 prevalence of MS was
 highest in the 55- to 64-year age group. A US north-south decreasing
 prevalence gradient was identified. The estimated MS prevalence is also
 presented for 2017. Conclusion: The estimated US national MS prevalence
 for 2010 is the highest reported to date and provides evidence that the
 north-south gradient persists. Our rigorous algorithm-based approach to
 estimating prevalence is efficient and has the potential to be used for
 other chronic neurologic conditions.
description: Prev of MS in the
 US-E-Appendix-Feb-19-2018
DOI: 10.5061/dryad.t1k42p8
title: Data from: A new way to estimate neurologic disease prevalence in the United States

description: Objective: Considerable gaps exist in knowledge regarding the prevalence
 of neurologic diseases, such as multiple sclerosis (MS), in the United
 States. Therefore, the MS Prevalence Working Group sought to review and
 evaluate alternative methods for obtaining a scientifically valid estimate
 of national MS prevalence in the current health care era. Methods: We
 carried out a strengths, weaknesses, opportunities, and threats (SWOT)
 analysis for 3 approaches to estimate MS prevalence: population-based MS
 registries, national probability health surveys, and analysis of
 administrative health claims databases. We reviewed MS prevalence studies
 conducted in the United States and critically examined possible methods
 for estimating national MS prevalence. Results: We developed a new 4-step
 approach for estimating MS prevalence in the United States. First,
 identify administrative health claim databases covering publicly and
 privately insured populations in the United States. Second, develop and
 validate a highly accurate MS case-finding algorithm that can be
 standardly applied in all databases. Third, apply a case definition
 algorithm to estimate MS prevalence in each population. Fourth, combine MS
 prevalence estimates into a single estimate of US prevalence, weighted
 according to the number of insured persons in each health insurance
 segment. Conclusions: By addressing methodologic challenges and proposing
 a new approach for measuring the prevalence of MS in the United States, we
 hope that our work will benefit scientists who study neurologic and other
 chronic conditions for which national prevalence estimates do not exist.
description: Nelson_SupplementalTable_E1Nelson_SupoplementalTable_E1.docx