cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.928c32c
title: Data from: Transient synchrony among populations of five foliage-feeding Lepidoptera

description: 1. Studies of transient population dynamics have largely focused on
 temporal changes in dynamical behavior, such as the transition between
 periods of stability and instability. The present study explores a related
 dynamic pattern, namely transient synchrony during a 49-year period among
 populations of five sympatric species of forest insects that share host
 tree resources. The long time-series allows a more comprehensive
 exploration of transient synchrony patterns than most previous studies.
 Considerable variation existed in the dynamics of individual species,
 ranging from periodic to aperiodic. 2. We used time-averaged methods to
 investigate long-term patterns of synchrony and time-localized methods to
 detect transient synchrony. We investigated transient patterns of
 synchrony between species and related these to the species’ varying
 density dependence structures; even species with very different density
 dependence exhibited at least temporary periods of synchrony. Observed
 periods of interspecific synchrony may arise from interactions with host
 trees (e.g. induced host defenses), interactions with shared natural
 enemies, or shared impacts of environmental stochasticity. 3. The
 transient nature of synchrony observed here raises questions both about
 the identity of synchronizing mechanisms and how these mechanisms interact
 with the endogenous dynamics of each species. We conclude that these
 patterns are the result of interspecific interactions that act only
 temporarily to synchronize populations, after which differences in the
 endogenous population dynamics among the species acts to desynchronize
 their dynamics.
description: Damage data for 5
 sympatric lepidopteran defoliators in HungaryData analysed reported
 here consists of annual records of area defoliated by fives species
 feeding on broadleaf trees in Hungary. The time series in the data file
 are comprised of annual values of total damage across Hungary of forest
 areas (in hectares) with defoliation exceeding 20% reduction of all
 foliage. The species that are recorded are lymantria dispar, euproctis
 chrysorrhoea, tortrix viridana, thaumetopoea processionea, malacosoma
 neustria.damage data
 Hungary.csv
DOI: 10.5061/dryad.71jp0
title: Data from: Sweepstake evolution revealed by population-genetic analysis of copy-number alterations in single genomes of breast cancer

description: Single-cell sequencing is a promising technology that can address cancer
 cell evolution by identifying genetic alterations in individual cells. In
 a recent study, genome-wide DNA copy numbers of single cells were
 accurately quantified by single-cell sequencing in breast cancers.
 Phylogenetic tree analysis revealed genetically distinct populations, each
 consisting of homogeneous cells. Bioinformatics methods based on
 population genetics should be further developed to quantitatively analyse
 the single-cell sequencing data. We developed a bioinformatics framework
 that was combined with molecular-evolution theories to analyse copy-number
 losses. This analysis revealed that most deletions in the breast cancers
 at the single-cell level were generated by simple stochastic processes. A
 non-standard type of coalescent theory – the multiple-merger coalescent
 model – aided by approximate Bayesian computation fit well with the data,
 allowing us to estimate the population-genetic parameters in addition to
 false-positive and false-negative rates. The estimated parameters suggest
 that the cancer cells underwent sweepstake evolution, where only 1 or very
 few parental cells produced a descendant cell population. We conclude that
 breast cancer cells successively substitute in a tumour mass, and the high
 reproduction of only a portion of cancer cells may confer high
 adaptability to this cancer.
description: R codes for
 multiple-merger coalescent simulationsR scripts to perform the
 simulations of a beta-coalescent model with a population growth
 termCodesMMC.zip
DOI: 10.5061/dryad.m23c7
title: Data from: Antagonistic versus non-antagonistic models of balancing selection: characterizing the relative timescales and hitchhiking effects of partial selective sweeps

description: Antagonistically selected alleles-–those with opposing fitness effects
 between sexes, environments, or fitness components-–represent an important
 component of additive genetic variance in fitness-related traits, with
 stably balanced polymorphisms often hypothesized to contribute to observed
 quantitative genetic variation. Balancing selection hypotheses imply that
 intermediate-frequency alleles disproportionately contribute to genetic
 variance of life-history traits and fitness. Such alleles may also
 associate with population genetic footprints of recent selection,
 including reduced genetic diversity and inflated linkage disequilibrium at
 linked, neutral sites. Here, we compare the evolutionary dynamics of
 different balancing selection models, and characterize the evolutionary
 timescale and hitchhiking effects of partial selective sweeps generated
 under antagonistic versus nonantagonistic (e.g., overdominant and
 frequency-dependent selection) processes. We show that the evolutionary
 timescales of partial sweeps tend to be much longer, and hitchhiking
 effects are drastically weaker, under scenarios of antagonistic selection.
 These results predict an interesting mismatch between molecular population
 genetic and quantitative genetic patterns of variation. Balanced,
 antagonistically selected alleles are expected to contribute more to
 additive genetic variance for fitness than alleles maintained by classic,
 nonantagonistic mechanisms. Nevertheless, classical mechanisms of
 balancing selection are much more likely to generate strong population
 genetic signatures of recent balancing selection.
description: Transit time
 simulationThis r script simulates
 the number of generations until a successfully invading allele reaches
 polymorphic equilibrium under balancing selection. Output applies to
 figure 1 of the manuscript.transit time
 scriptHitchhiking of a neutral
 alleleThis r script simulates
 the hitchhiking effect caused by a successfully invading allele that
 evolves toward a polymorphic equilibrium. Output applies to figure 2 of
 the manuscript.hitchhiking
 script
DOI: 10.5061/dryad.h0h3b
title: Data from: How can ten fingers shape a pot? Evidence for equivalent function in culturally distinct motor skills

description: Behavioural variability is likely to emerge when a particular task is
 performed in different cultural settings, assuming that part of human
 motor behaviour is influenced by culture. In analysing motor behaviour it
 is useful to distinguish how the action is performed from the result
 achieved. Does cultural environment lead to specific cultural motor
 skills? Are there differences between cultures both in the skills
 themselves and in the corresponding outcomes? Here we analyse the skill of
 pottery wheel-throwing in French and Indian cultural environments. Our
 specific goal was to examine the ability of expert potters from distinct
 cultural settings to reproduce a common model shape (a sphere). The
 operational aspects of motor performance were captured through the
 analysis of the hand positions used by the potters during the fashioning
 process. In parallel, the outcomes were captured by the geometrical
 characteristics of the vessels produced. As expected, results revealed a
 cultural influence on the operational aspects of the potters’ motor skill.
 Yet, the marked cultural differences in hand positions used did not give
 rise to noticeable differences in the shapes of the vessels produced.
 Hence, for the simple model form studied, the culturally-specific motor
 traditions of the French and Indian potters gave rise to an equivalent
 outcome, that is shape uniformity. Further work is needed to test whether
 such equivalence is also observed in more complex ceramic shapes.
description: ShapeDescriptorsThis zip file contains two MATLAB .m files which will convert a shape to a set of elliptical fourier coefficients, which uniquely describe its shape. The other file converts back to the shape using few to all of the coefficients.
DOI: 10.5061/dryad.7mk1v
title: Data from: Reconstructing the origins of high-alpine niches and cushion life form in the genus Androsace s.l. (Primulaceae)

description: Relatively few species have been able to colonize extremely cold alpine
 environments. We investigate the role played by the cushion life form in
 the evolution of climatic niches in the plant genus Androsace s.l., which
 spreads across the mountain ranges of the Northern Hemisphere. Using
 robust methods that account for phylogenetic uncertainty, intraspecific
 variability of climatic requirements and different life history evolution
 scenarios, we show that climatic niches of Androsace s.l. exhibit low
 phylogenetic signal and that they evolved relatively recently and
 punctually. Models of niche evolution fitted onto phylogenies show that
 the cushion life form has been a key innovation providing the opportunity
 to occupy extremely cold environments, thus contributing to rapid climatic
 niche diversification in the genus Androsace. We then propose a plausible
 scenario for the adaptation of plants to alpine habitats.
description: Consensus Chronogram for
 the Androsace genusThis consensus tree is
 rooted and ultrametric. The outgroups were trimmed.chrono_consensus_Androsace_noutg_nosp_lackinfo.tre
DOI: 10.5061/dryad.r5s08
title: Data from: Can biosecurity and local network properties predict pathogen species richness in the salmonid industry?

description: Salmonid farming in Ireland is mostly organic, which implies limited
 disease treatment options. This highlights the importance of biosecurity
 for preventing the introduction and spread of infectious agents.
 Similarly, the effect of local network properties on infection spread
 processes has rarely been evaluated. In this paper, we characterized the
 biosecurity of salmonid farms in Ireland using a survey, and then
 developed a score for benchmarking the disease risk of salmonid farms. The
 usefulness and validity of this score, together with farm indegree
 (dichotomized as ≤ 1 or &gt; 1), were assessed through generalized
 Poisson regression models, in which the modeled outcome was pathogen
 richness, defined here as the number of different diseases affecting a
 farm during a year. Seawater salmon (SW salmon) farms had the highest
 biosecurity scores with a median (interquartile range) of 82.3 (5.4),
 followed by freshwater salmon (FW salmon) with 75.2 (8.2), and freshwater
 trout (FW trout) farms with 74.8 (4.5). For FW salmon and trout farms, the
 top ranked model (in terms of leave-one-out information criteria, looic)
 was the null model (looic = 46.1). For SW salmon farms, the best ranking
 model was the full model with both predictors and their interaction (looic
 = 33.3). Farms with a higher biosecurity score were associated with lower
 pathogen richness, and farms with indegree &gt; 1 (i.e. more than one
 fish supplier) were associated with increased pathogen richness. The
 effect of the interaction between these variables was also important,
 showing an antagonistic effect. This would indicate that biosecurity
 effectiveness is achieved through a broader perspective on the subject,
 which includes a minimization in the number of suppliers and hence in the
 possibilities for infection to enter a farm. The work presented here could
 be used to elaborate indicators of a farm's disease risk based on its
 biosecurity score and indegree, to inform risk-based disease surveillance
 and control strategies for private and public stakeholders.
description: Pathogen richness models
 dataPathogen richness and
 biosecurity score based on field work carried out in Ireland during
 2015.Data_PLOS.csv
DOI: 10.5061/dryad.52064
title: Data from: A new taxon of cynodont from the Tropidostoma Assemblage Zone (upper Permian) of South Africa, and the early evolution of Cynodontia

description: A new taxon of early cynodont, Abdalodon diastematicus gen. et sp. nov.,
 is described. The new taxon is represented by a single skull from the
 upper Permian Tropidostoma Assemblage Zone (AZ) of the Beaufort Group
 (Karoo Basin, South Africa), which was previously referred to
 Procynosuchus delaharpeae. Abdalodon is distinguished from Procynosuchus
 by the presence of only four upper and three lower incisors, fewer
 postcanines, a well-developed depression on the lateral surface of the
 maxilla posterior to the canine root, a tall mandibular symphysis forming
 a distinct ‘chin’, a relatively short snout, and weak or absent
 interdigitation of sutures in the interorbital region. These features are
 shared with the only other Tropidostoma AZ cynodont, Charassognathus
 gracilis. Abdalodon is distinguished from Charassognathus by its
 postcanine morphology, the presence of an expanded masseteric fossa, inset
 postcanine tooth rows, a broader interorbital region, and proportionally
 shorter temporal region. Most strikingly, Abdalodon has a lengthy diastema
 between the canines and postcanines on both the maxilla and the dentary.
 Charassognathus has a short diastema between the upper canine and
 postcanines, but not the lowers, and diastemata are absent from the tooth
 rows of Procynosuchus. Phylogenetic analysis recovers Abdalodon as the
 sister-taxon of Charassognathus, forming a clade (Charassognathidae fam.
 nov.) at the base of Cynodontia. These taxa represent a previously
 unrecognized radiation of small-bodied Permian cynodonts. Despite their
 small size, the holotypes of Abdalodon and Charassognathus probably
 represent adults and indicate that early evolution of cynodonts may have
 occurred at small body size, explaining the poor Permian fossil record of
 the group.
description: Abdalodon
 matrixTNT-formatted character
 matrix for parsimony analysis of early cynodont
 therapsids
DOI: 10.5281/zenodo.18385912
title: Visentin et al. - Datasets

description: The archive contains datasets with the data from Visentin et al. "Lactoplantibacillus plantarum enhances grain filling process under nitrogen deficiency conditions in the presence of rice blast/brown spot in organic rice cropping systems"
DOI: 10.5281/zenodo.18385913
title: Visentin et al. - Datasets

description: The archive contains datasets with the data from Visentin et al. "Lactoplantibacillus plantarum enhances grain filling process under nitrogen deficiency conditions in the presence of rice blast/brown spot in organic rice cropping systems"
DOI: 10.5061/dryad.30rf6
title: Data from: Conservation under uncertainty: optimal network protection strategies for worst-case disturbance events

description: 1. Conservation goals are ideally set after a thorough understanding of
 potential threats; however, predicting future spatial patterns of threats,
 such as disturbance, remains challenging. Here, we develop a novel
 extension of network fortification-interdiction models (NFIM) that deals
 with uncertainty in future spatial patterns of disturbance by optimally
 selecting sites that will best mitigate a worst-case scenario for a given
 magnitude of disturbance. 2. This approach uses information on
 between-patch movement probabilities and patch-specific survival, which
 can be estimated from mark-recapture data, to optimize life expectancy.
 Optimization occurs in three interrelated stages: protection, followed by
 disturbance, and then assessment. 3. We applied the modeling approach to
 two mark-recapture data sets: Roseate terns Sterna dougallii in the
 northeastern United States and the Everglade snail kite Rostrhamus
 sociabilis plumbeus in Florida. We contrasted the results to a more
 conventional approach of protecting sites that maximize connectivity (by
 minimizing the distances among protected sites) and a bi-objective model
 that maximizes connectivity and the number of individuals under
 protection. 4. Protecting sites that best mitigate future worst-case
 disturbance scenarios consistently resulted in higher predicted life
 expectancies than protecting patches that minimize dispersal distance.
 Predicted life expectancy was similar between NFIM and the biobjective
 model for the small roseate tern network, yet, the NFIM predicted higher
 life expectancy than any of the scenarios in the bi-objective model in the
 snail kite network. 5. Synthesis and applications. This application of
 interdiction models prescribed a combination of patches for protection
 that results in the least possible decrease in life expectancy. Our
 analyses of the snail kite and roseate tern networks suggest that managing
 to protect these prescribed patches by the network fortification
 interdiction model (i.e. protecting against the worst-case disturbance
 scenario) is more beneficial than managing patches that minimize dispersal
 distance or maximize the number of individuals under protection if the
 conservation goal is to ensure the long term persistence of a species.
description: snail_kite_data.rtfdTransition probabilities for adult Everglade snail kites used for optimization model.
DOI: 10.5061/dryad.48kc1
title: Data from: Stacking the odds: light pollution may shift the balance in an ancient predator-prey arms race

description: 1. Artificial night-lighting threatens to disrupt strongly conserved
 light-dependent processes in animals and may have cascading effects on
 ecosystems as species interactions become altered. Insectivorous bats and
 their prey have been involved in a nocturnal, coevolutionary arms race for
 millions of years. Lights may interfere with anti-bat defensive behaviours
 in moths, and disrupt a complex and globally ubiquitous interaction
 between bats and insects, ultimately leading to detrimental consequences
 for ecosystems on a global scale. 2. We combined experimental and
 mathematical approaches to determine effects of light pollution on a
 free-living bat–insect community. We compared prey selection by Cape
 serotine bats Neoromicia capensis in naturally unlit and artificially lit
 conditions using a manipulative field experiment, and developed a
 probabilistic model based on a suite of prey-selection factors to explain
 differences in observed diet. 3. Moth consumption by N. capensis was low
 under unlit conditions (mean percentage volume ± SD: 5.91 ± 6.25%), while
 moth consumption increased six-fold (mean percentage volume ± SD: 35.42 ±
 17.90%) under lit conditions despite a decrease in relative moth
 abundance. Predictive prey-selection models which included high-efficacy
 estimates for eared-moth defensive behaviour found most support given diet
 data for bats in unlit conditions. Conversely, models which estimated
 eared-moth defensive behaviour as absent or low, found more support given
 diet data for bats in lit conditions. Our models therefore suggest the
 increase in moth consumption was a result of light-induced, decreased
 eared-moth defensive behaviour. 4. Policy implications. In the current
 context of unyielding growth in global light pollution, we predict that
 specialist moth-eating bats and eared-moths will face ever-increasing
 challenges to survival through increased resource competition and
 predation risk, respectively. Lights should be developed to be less
 attractive to moths, with the goal of reducing effects on moth behaviour.
 Unfortunately, market preference for broad-spectrum lighting and possible
 effects on other taxa make development of moth-friendly lighting
 improbable. Mitigation should therefore focus on the reduction of
 temporal, spatial, and luminance redundancy in outdoor lighting.
 Restriction of light inside nature reserves and urban greenbelts can serve
 as dark refugia for moth-eating bats and moths, and may become important
 for their persistence.
description: Diet and morphological
 data for individual batsThis data file contains
 the following data for each individual bat: identification number; bat
 sex; experimental condition; weight; forearm length; the number of faecal
 pellets collected and analysed; percentage volume diet composition for
 each individual bat.JPEminnaar_individual_bat_diet_data.csv
DOI: 10.5061/dryad.2tn1rf9
title: Data from: Are pulp consumers effective seed dispersers? Tests with a large-seeded tropical relict tree

description: Several plant species in the Neotropics bear large, fleshy fruits that
 suggest adaptation to endozoochorous seed dispersal by large vertebrates.
 Many of these plants, however, occur in areas where large vertebrates are
 no longer present, consequently, their seeds are dispersed by pulp
 consumers; small vertebrates that only ingest the pulp reward because they
 are uncapable of swallowing the fruits whole. Few studies have examined
 the role of these pulp consumers on the regeneration of
 large-fruited/seeded plants. Here, we assessed seed disperser
 effectiveness (SDE) and context-dependence in SDE of pulp consumers of
 Pouteria splendens, a large-seeded tree, considered a tropical relict in
 Mediterranean Chile. We found that P. splendens fruits are consumed by six
 species of non-flying vertebrates; four of which act as dispersers with
 very low effectiveness. Low SDE resulted from the quantitative, rather
 than the qualitative component, specifically from low frugivore visitation
 rates. Most seeds remained under P. splendens trees, either from being
 dispersed there or because they were not dispersed at all. However, both
 emergence and establishment probabilities were higher under conspecific
 plants than in other habitats, suggesting no negative density-dependent
 effects on P. splendens recruitment. Although the absence of more
 effective dispersers does not seem to affect local recruitment
 probabilities, it results in the absence of long-distance dispersal
 services, further isolating the remnant P. splendens populations. Finally,
 although pulp consumers are dispersers of P. splendens with very low
 effectiveness, the key functional role of these species is to remove the
 fleshy pulp from the seed as its presence significantly reduces
 germination probability.
description: Seedling
 emergenceSeedling emergence in
 experimental stations set up in three habitats (Under Pouteria, open
 interspaces, and dry riverbeds) during 2015 and 2016Seedling_emergence.csvTotal number of visits and dispersed seeds per disperserTotal number of visits of each of the six frugivores that consume P. splendens, and total number of seeds dispersed during 2638 hours of video monitoring.visits_dispersed.csvTotal number of visits and dispersed seeds during 2015Total number of visits of each of the six frugivores that consume P. splendens, and total number of seeds dispersed during 2015 (473 h of video monitoring)visits_dispersed_2015.csvTotal number of visits and dispersed seeds during 2016Total number of visits of each of the six frugivores that consume P. splendens, and total number of seeds dispersed during 2016 (2165 hours of video monitoring)visits_dispersed_2016.csv