cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.r5j0s3n
title: Data from: Applying modern coexistence theory to priority effects

description: Modern coexistence theory is increasingly used to explain how differences
 between competing species lead to coexistence versus competitive
 exclusion. Although research testing this theory has focused on
 deterministic cases of competitive exclusion, in which the same species
 always wins, mounting evidence suggests that competitive exclusion is
 often historically contingent, such that whichever species happens to
 arrive first excludes the other. Coexistence theory predicts that
 historically contingent exclusion, known as priority effects, will occur
 when large destabilizing differences (positive frequency-dependent growth
 rates of competitors), combined with small fitness differences
 (differences in competitors’ intrinsic growth rates and sensitivity to
 competition), create conditions under which neither species can invade an
 established population of its competitor. Here we extend the empirical
 application of modern coexistence theory to determine the conditions that
 promote priority effects. We conducted pairwise invasion tests with four
 strains of nectar-colonizing yeasts to determine how the destabilizing and
 fitness differences that drive priority effects are altered by two abiotic
 factors characterizing the nectar environment: sugar concentration and pH.
 We found that higher sugar concentrations increased the likelihood of
 priority effects by reducing fitness differences between competing
 species. In contrast, higher pH did not change the likelihood of priority
 effects, but instead made competition more neutral by bringing both
 fitness differences and destabilizing differences closer to zero. This
 study demonstrates how the empirical partitioning of priority effects into
 fitness and destabilizing components can elucidate the pathways through
 which environmental conditions shape competitive interactions.
description: Data from Grainger et
 al. 2019 PNASDensities of four yeast
 species when grown in monoculture (densities measured at 0h, 48h and 96h)
 and when invading each of four competitors (densities measured at 48h and
 96h).
DOI: 10.5061/dryad.qp7539t
title: Data from: Genetic introgression among differentiated clades is lower among clades exhibiting different parity modes

description: Mechanisms leading to sympatric speciation are diverse and may build up
 reproductive isolation. Reproductive isolation among differentiated clades
 may exist due to genetic incompatibilities, sexual selection, differences
 in parity mode, reduced post-zygotic survival or reproductive success of
 hybrids. Here we test whether differences in parity mode lead to
 reproductive isolation by investigating introgression in Zootoca vivipara,
 a lizard species exhibiting oviparous and viviparous reproduction. We
 measured introgression in transects spanning different viviparous clades,
 different oviparous subclades, transects containing oviparous and
 viviparous clades, and transects within the same subclade (control
 transects). Introgression in transects spanning oviparous and viviparous
 clades was one order of magnitude smaller than transects spanning the same
 reproductive mode and no statistical differences existed between transects
 spanning the same reproductive mode and contr ol transects. Among types of
 transects, no significant differences existed in genetic and geographic
 distances, nor number of detected alleles. Moreover, hybrids were detected
 in all types of transects, showing that parity mode alone does not
 necessarily lead to complete reproductive isolation, which suggests that
 reinforcement may play an important role. The evolution of different
 parity modes together with reinforcement may thus promote reproductive
 isolation and rapid speciation, potentially explaining why only six of the
 almost 40’000 vertebrates belonging to groups consisting of viviparous and
 oviparous species exhibit bimodal reproduction.
description: dataset Horreo et al
 2019 HeredityGenepop formate - text
 file
DOI: 10.5061/dryad.66bp77v
title: Data from: Range expansion is associated with increased survival and fecundity in a long-lived bat species

description: The speed and dynamics of range expansions shape species distributions and
 community composition. Despite the critical impact of population growth
 rates for range expansion, they are neglected in existing empirical
 studies, which focus on the investigation of selected life history traits.
 Here, we present an approach based on non-invasive genetic
 capture-mark-recapture data for the estimation of adult survival,
 fecundity, and juvenile survival, which determine population growth. We
 demonstrate the reliability of our method with simulated data, and use it
 to investigate life history changes associated with range expansion in 35
 colonies of the bat species Rhinolophus hipposideros. Comparing the
 demographic parameters inferred for 19 of those colonies which belong to
 an expanding population with those inferred for the remaining 16 colonies
 from a non-expanding population reveals that range expansion is associated
 with higher net reproduction. Juvenile survival was the main driver of the
 observed reproduction increase in this long-lived bat species with low per
 capita annual reproductive output. The higher average growth rate in the
 expanding population was not associated with a trade-off between increased
 reproduction and survival, suggesting that the observed increase in
 reproduction stems from a higher resource acquisition in the expanding
 population. Environmental conditions in the novel habitat hence seem to
 have an important influence on range expansion dynamics, and warrant
 further investigation for the management of range expansion in both native
 and invasive species.
description: Capture
 historySampled individuals’
 capture history. 13-1 = first sampling session in year 2013; 17-2 = second
 sampling session in year 2017, etc. . ‘1’ denotes detection in the
 according sampling session; ‘0’ denotes no detectionDRYAD_Capture-History.xlsxMultilocus genotypesSampled individuals’ genotypes. See Zarzoso-Lacoste et al. 2018 [25] for information on the microsatellite markers used. 0 = missing dataDRYAD_Genotypes.xlsxMother-daughter pairs detected per yearMother-daughter pairs detected per year.DRYAD_Pedigree.xlsx
DOI: 10.5061/dryad.cb74s0q
title: Data from: Effects of landscape complexity on pollinators are moderated by pollinators’ association with mass-flowering crops

description: Conserving and restoring semi-natural habitat, i.e. enhancing landscape
 complexity, is one of the main strategies to mitigate pollinator decline
 in agricultural landscapes. However, we still have limited understanding
 of how landscape complexity shapes pollinator communities in both crop and
 non-crop habitat, and whether pollinator responses to landscape complexity
 vary with their association with mass-flowering crops. Here, we surveyed
 pollinator communities on mass-flowering leek crops and in nearby
 semi-natural habitat in landscapes of varying complexity. Surveys were
 done before and during crop bloom and distinguished between pollinators
 that visit the crop frequently (dominant), occasionally (opportunistic) or
 not at all (non-crop). Forty-four percent of the species in the wider
 landscape were also observed on leek flowers. Crop pollinator richness
 increased with local pollinator community size and increasing landscape
 complexity, but relationships were stronger for opportunistic than for
 dominant crop pollinators. Relationships between pollinator richness in
 semi-natural habitats and landscape complexity differed between groups
 with the most pronounced positive effects on non-crop pollinators. Our
 results indicate that while dominant crop pollinators are core components
 of crop pollinator communities in all agricultural landscapes,
 opportunistic crop pollinators largely determine species-richness
 responses and complex landscapes are local hotspots for both biodiversity
 conservation and potential ecosystem service-provision.
description: Description of the
 datafilesThese file describes the
 data in the separate data files providedmetadata.datafiles.xlsxBootstrapped species richness estimatesBootstrapped estimates of species richness for the sampled survey periods and transect locations. A distinction is made for each functional group of pollinators.bootstrapped.species.richness.csvAverage flower coverThe average flower cover per transect in the wider landscape over the whole survey period.flower.cover.average.csvAverage flower cover per survey periodThe average flower cover per transect in the wider landscape separate for the two survey periods.flower.cover.period.csvAverage pollinator densities per survey periodThe average pollinator densities per survey period and for both the wider landscape transects and the crop transects for each agricultural landscape. A distinction is made for each functional group of pollinators.mean.densities.csvAverage pollinator densities over the whole survey periodThe average pollinator densities over the whole survey period, separate for wider landscape transects and crop transects. A distinction is made for each functional group of pollinators.total.densities.csvR ScriptThe R Script used to perform the statistics in the manuscript, and to reproduce figures 2-5.Fijen et al Proceedings B - Script.R
DOI: 10.5061/dryad.7k7s800
title: Data from: Neural structure mapping in human probabilistic reward learning

description: Humans can learn abstract concepts that describe invariances over
 relational patterns in data. One such concept, known as magnitude, allows
 stimuli to be compactly represented on a single dimension (i.e. on a
 mental line). Here, we measured representations of magnitude in humans by
 recording neural signals whilst they viewed symbolic numbers. During a
 subsequent reward-guided learning task, the neural patterns elicited by
 novel complex visual images reflected their payout probability in a way
 that suggested they were encoded onto the same mental number line, with
 'bad' bandits sharing neural representation with
 'small' numbers and 'good' bandits with
 'large' numbers. Using neural network simulations, we provide a
 mechanistic model that explains our findings and shows how structural
 alignment can promote transfer learning. Our findings suggest that in
 humans, learning about reward probability is accompanied by structural
 alignment of value representations with neural codes for the abstract
 concept of magnitude.
description: Bandit_modelParameter fits and model estimates from RL model.Numbers_modelParameter fits and model estimates of psychometric model.Numbers_EEGPreprocessed EEG data for the Numerical task of all subjects.Bandit_EEGPreprocessed EEG data from the test phase of the Bandit task for all subjects.Bandit_behavBehavioural data of Bandit task.Numbers_behavBehavioural data of Numerical task.
DOI: 10.5061/dryad.m592p4g
title: Data from: Experimental evidence of frequency-dependent selection on group behaviour

description: Evolutionary ecologists often seek to identify the mechanisms maintaining
 intraspecific variation. In social animals, whole groups can exhibit
 between-group differences in their collective traits. We examined whether
 negative frequency-dependent selection (i.e., a rare-type advantage) could
 help to maintain between-group variation. We engineered neighborhoods of
 social spider colonies bearing bold or shy foraging phenotypes and
 monitored their fecundity in situ. We found that bold colonies enjoyed a
 rare-type advantage that is lost as the frequency of bold colonies in a
 neighborhood increases. The success of shy colonies was not
 frequency-dependent. These dynamics appear driven by a foraging advantage
 of bold colonies that is lost in bold neighborhoods because prey become
 scarce, and shy colonies perform better than bold colonies under
 low-resource conditions. Thus, to understand selection on collective
 traits, it is insufficient to examine groups in isolation. One must
 consider the phenotypic environment in which groups reside and compete.
description: Dryad_Frequency
 Histogram Data
DOI: 10.5061/dryad.n410g85
title: Data from: Intraspecific and interspecific trait variability in tadpole metacommunities from the Brazilian Atlantic rainforest

description: 1. A better understanding of species coexistence and community dynamics
 may benefit from more insights on trait variability at the individual and
 species levels. 2. Tadpole assemblages offer an excellent system to
 understand the relative influence of intra- and interspecific variability
 on community assembly, due to their high phenotypic plasticity, and the
 strong influence that environmental variables have on their spatial
 distribution and individual performance. 3. Here we quantified the intra-
 and interspecific components of tadpoles’ trait variability in order to
 investigate their relative role in shaping tadpole communities. 4. We
 selected eight functional traits related to microhabitat use, foraging
 strategies and swimming ability. We measured these traits on 678
 individuals from 22 species captured in 43 ponds in the Atlantic Forest.
 We used single- and multi-trait analyses to decompose trait variability.
 To explore the action of external and internal filtering on community
 assembly, we used a variance decomposition approach that compares
 phenotypic variability at the individual, population, community and
 regional levels. 5. On average, 33% of trait variability was due to within
 species variation. This decomposition varied widely among traits. We found
 only a reduced effect of external filtering (low variation in the height
 of the ventral fin within ponds in comparison to the total variation),
 whereas the internal filtering was stronger than expected. Traits related
 to the use of different micro-habitats through the water column were
 generally less variable than traits related to swimming ability to escape
 of predators, with tail traits being highly variable within species. 6.
 Our study highlights the importance of incorporating both intra- and
 interspecific, trait differences and of focusing on a diversity of traits
 related to both stabilizing niche and fitness differences in order to
 better understand how trait variation relates to species coexistence.
description: data_Atlantic_ForestData of pond-dweeling tadpoles collected in 43 ponds from Atlantic Rain Forest (2011-2013) in four different localities (Ubatuba, Bertioga, Itanhaém, and Iguape municipalities) in São Paulo state, southeastern Brazil. A standadized protocol was used to measure XX morphological traits on 678 tadpoles from 22 anuran species. Abbreviations: estagio = tadpole developement stage; BCI = body compression index; RDE = Relative diameter of the eyes; HDF= Relative height of the dorsal fin; HVF = Relative height of the ventral fin; RWT = Relative width of the tail; TCI = Tail compression index; DNS = Distance from nares to snout; RDN = Relative diameter of the nares; Numb_species = species richness by pond; Numb_individuals = total abundance by pond; Minimum_individual_per_species = minimum number of individual per species by pond.
DOI: 10.5061/dryad.nf63rb8
title: Data from: HIV infection is an independent risk factor for decreased 6-minute walk test distance

description: Background: Ambulatory function predicts morbidity and mortality and may
 be influenced by cardiopulmonary dysfunction. Persons living with HIV
 (PLWH) suffer from a high prevalence of cardiac and pulmonary
 comorbidities that may contribute to higher risk of ambulatory dysfunction
 as measured by 6-minute walk test distance (6-MWD). We investigated the
 effect of HIV on 6-MWD. Methods: PLWH and HIV-uninfected individuals were
 enrolled from 2 clinical centers and completed a 6-MWD, spirometry,
 diffusing capacity for carbon monoxide (DLCO) and St. George’s Respiratory
 Questionnaire (SGRQ). Results of 6-MWD were compared between PLWH and
 uninfected individuals after adjusting for confounders. Multivariable
 linear regression analysis was used to determine predictors of 6-MWD.
 Results: Mean 6-MWD in PLWH was 431 meters versus 462 in 130
 HIV-uninfected individuals (p = 0.0001). Older age, lower forced
 expiratory volume (FEV1)% or lower forced vital capacity (FVC)%, and
 smoking were significant predictors of decreased 6-MWD in PLWH, but not
 HIV-uninfected individuals. Lower DLCO% and higher SGRQ were associated
 with lower 6-MWD in both groups. In a combined model, HIV status remained
 an independent predictor of decreased 6-MWD (Mean difference = -19.9
 meters, p = 0.005). Conclusions: HIV infection was associated with
 decreased ambulatory function. Airflow limitation and impaired diffusion
 capacity can partially explain this effect. Subjective assessments of
 respiratory symptoms may identify individuals at risk for impaired
 physical function who may benefit from early intervention.
description: Data for HIV 6MW PLOS
 ONETwo sheets one data and
 one code books included in this file.
DOI: 10.5061/dryad.rq3jc84
title: Data from: Synchrony is more than its top-down and climatic parts: interacting Moran effects on phytoplankton in British seas

description: Large-scale spatial synchrony is ubiquitous in ecology. We examined 56
 years of data representing chlorophyll density in 26 areas in British seas
 monitored by the Continuous Plankton Recorder survey. We used wavelet
 methods to disaggregate synchronous fluctuations by timescale and
 determine that drivers of synchrony include both biotic and abiotic
 variables. We tested these drivers for statistical significance by
 comparison with spatially synchronous surrogate data. We generated
 timescale-specific models, accounting for 61% of long-timescale (&gt;
 4yrs) synchrony in a chlorophyll density index, but only 3% of observed
 short-timescale (&lt; 4yrs) synchrony. The dominant source of
 long-timescale chlorophyll synchrony was closely related to sea surface
 temperature, through a Moran effect, though likely via complex
 oceanographic mechanisms. The top-down action of Calanus finmarchicus
 predation enhances this environmental synchronising mechanism and
 interacts with it non-additively to produce more long-timescale synchrony
 than top-down and climatic drivers would produce independently. Thus we
 demonstrate interaction effects between Moran drivers of synchrony, a new
 mechanism for synchrony that may affect many ecosystems at large spatial
 scales.
description: Plankton and
 oceanographic time-seriesThis zip file includes
 annualized Plankton Colour Index time-series, annualized plankton species
 abundance time-series, and annualized oceanographic variables. See
 readme.txt file.planktontimeseries.zip
DOI: 10.5061/dryad.dp13668
title: Data from: Climate change, extinction, and Sky Island biogeography in a montane lizard

description: Around the world, many species are confined to “Sky Islands,” with
 different populations in isolated patches of montane habitat. How does
 this pattern arise? One scenario is that montane species were widespread
 in lowlands when climates were cooler, and were isolated by local
 extinction caused by warming conditions. This scenario implies that many
 montane species may be highly susceptible to anthropogenic warming. Here,
 we test this scenario in a montane lizard (Sceloporus jarrovii) from the
 Madrean Sky Islands of southeastern Arizona. We combined data from field
 surveys, climate, population genomics, and physiology. Overall, our
 results support the hypothesis that this species’ current distribution is
 explained by local extinction caused by past climate change. However, our
 results for this species differ from simple expectations in several ways:
 (1) their absence at lower elevations is related to warm winter
 temperatures, not hot summer temperatures; (2) they appear to exclude a
 low-elevation congener from higher elevations, not the converse; (3) they
 are apparently absent from many climatically suitable but low mountain
 ranges, seemingly “pushed off the top” by climates even warmer than those
 today; (4) despite the potential for dispersal among ranges during recent
 glacial periods (~18,000 years ago), populations in different ranges
 diverged ~4.5–0.5 million years ago and remained largely distinct; and (5)
 body temperatures are inversely related to climatic temperatures among
 sites. These results may have implications for many other Sky Island
 systems. More broadly, we suggest that Sky Island species may be relevant
 for predicting responses to future warming.
description: Supplementary
 MaterialDatafile_S1Datafile_S1: Data matrix for RAxML analysis for single batch RADseq dataDatafile_S2Datafile_S2: Data matrix for RAxML analysis for combined-batch RADseq data
DOI: 10.5061/dryad.966ff04
title: Data from: Experimental removals reveal dietary niche partitioning facilitates coexistence between native and introduced species

description: Niche overlap between native species and ecologically similar invaders can
 lead to competitive exclusion of threatened native species, but if two
 such species also co‐occur naturally elsewhere, interactions between
 native and introduced populations may mirror coevolved niche partitioning
 that reduces competition and promotes coexistence. A single, insular
 population of Fremont’s squirrel (Tamiasciurus fremonti) the Mount Graham
 red squirrel (MGRS; T. f. grahamensis) in the Pinaleño Mountains, Arizona,
 USA, is critically endangered and resource competition with introduced
 Abert’s squirrels (Sciurus aberti) may threaten its long‐term persistence.
 The species are naturally synoptic in other mountain sites, and both
 consume diets comprised primarily of conifer seeds and fungi. We conducted
 experimental removals of introduced Abert’s squirrels and used stable
 isotope analysis of diets before and after removals, and of diets in
 naturally syntopic populations to test the hypothesis that dietary niche
 partitioning can facilitate coexistence between native and introduced
 species. We also developed a novel approach to determine the influence of
 fluctuating food availability on carbon enrichment in consumers. Mount
 Graham red squirrels and introduced Abert’s squirrels partitioned the
 dietary niche similarly to naturally syntopic populations. Removals had no
 apparent effect. Diet of MGRS was more closely linked to availability of
 resources than to presence of Abert’s squirrels. Flexible dietary niche of
 introduced Abert’s squirrels may have allowed them to exploit a resource
 opportunity in syntopy with MGRS. Variable food production of MGRS habitat
 may intensify competition in poor years, and territorial defense against
 non‐native Abert’s squirrels likely imposes fitness costs on individual
 MGRS. Similarity in our model species’ diets may make MGRS more vulnerable
 to competition if climate change eliminates the advantages of
 larder‐hoarding. Where introduced populations of ecologically similar
 species are better adapted to changing conditions, they may ultimately
 replace southern peripheral populations of native species.
description: all_MG_food_dataC & N stable isotope data of squirrel diet items, Mount Graham, AZnonMG_redsquirrel_dataC & N stable isotope data of red squirrel, San Francisco Peaks and White Mountains, AZnonMG_Abert_dataC & N stable isotope data of Abert's squirrels, San Francisco Peaks and White Mountains, AZMG_Aberts_dataC & N stable isotope data of Abert's squirrels, Mount Graham, AZMGRS_dataC & N stable isotope data of Mount Graham red squirrels, Mount Graham, AZ