cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.1nq73
title: Data from: Landscape genetic inferences vary with sampling scenario for a pond breeding amphibian

description: A critical decision in landscape genetic studies is whether to use
 individuals or populations as the sampling unit. This decision affects the
 time and cost of sampling and may affect ecological inference. We analyzed
 334 Columbia spotted frogs at 8 microsatellite loci across 40 sites in
 northern Idaho to determine how inferences from landscape genetic analyses
 would vary with sampling design. At all sites, we compared a proportion
 available sampling scheme (PASS), in which all samples were used, to
 resampled datasets of 2-11 individuals. Additionally, we compared a
 population sampling scheme (PSS) to an individual sampling scheme (ISS) at
 18 sites with sufficient sample size. We applied an information theoretic
 approach with both restricted maximum likelihood and maximum likelihood
 estimation to evaluate competing landscape resistance hypotheses. We found
 that PSS supported a low-density forest model (0.87) and ISS supported
 this model as well as additional models when testing hypotheses of
 landcover types that create the greatest resistance to gene flow for
 Columbia spotted frogs. Increased sampling density and study extent, seen
 by comparing PSS to PASS, showed a change in model support from a model of
 only low-density forest to a model of only high-density forest. As number
 of individuals increased, model support converged at 7 individuals for ISS
 to PSS. ISS may be useful to increase study extent and sampling density,
 but may lack power to provide strong support for the correct model with
 microsatellite datasets. Our results highlight the importance of
 additional research on sampling design effects on landscape genetics
 inference.
description: RALUNoSibsMicrosatellite data for individualsRALUNoSibs_GPSPopulation locations.
DOI: 10.5061/dryad.8hq75j7
title: Data from: Selective logging intensity in an East African rain forest predicts reductions in ant diversity

description: As natural forest ecosystems increasingly face pressure from
 deforestation, it is ever more important to understand the impacts of
 habitat fragmentation and degradation on biodiversity. Most studies of
 anthropogenic change in the tropics come from Southeast Asia and South
 America, and impacts of habitat modification are often taxon-specific.
 Here we empirically assessed the impact of habitat fragmentation and
 recent (within 25 years) and historic (&gt;25 years ago) selective
 logging on the diversity of ants in the Kakamega rain forest in western
 Kenya, and asked whether these forms of degradation interact as multiple
 stressors. We found that the severity of recent selective logging was
 negatively related to overall species richness and abundance as well as
 the richness and abundance of forest specialists, but found no detrimental
 effect of past selective logging or habitat fragmentation on ant
 diversity, although habitat fragment size was correlated with estimated
 species richness. There was also no effect of any form of habitat
 degradation on the richness or abundance of open habitat specialists, even
 though these species often exploit niches created in disturbed
 environments. Ultimately, this study reveals the detrimental impact of
 even moderate forms of habitat degradation on insect biodiversity in the
 understudied African rain forests.
description: Ant Community
 Composition of selectively logged forest, Kakamega Forest,
 KenyaData originally
 collected in the field in Kakamega forest, Kenya. Ants were sampled via
 pitfall traps and winkler leaf litter sampling. Data represent species
 identity and occurrence data for all ant species sampled in Kakamega
 forest (.xlsx format)Ross et al.
 Biotropica_Dryad.xlsx
DOI: 10.6084/m9.figshare.24093751.v1
title: Genomic epidemiology sheds light on the emergence and spread of <i>Mycobacterium bovis</i> Eu2 Clonal Complex in Portugal

description: Animal tuberculosis (TB) remains a serious concern for animal and human health. <i>Mycobacterium bovis</i> circulates in multi-host systems, dominated by the European 2 clonal complex (Eu2) in Iberia. In this work, we use genomic epidemiology to infer the emergence, spread, and spatiotemporal patterns of Eu2 in the official epidemiological risk area of animal TB in Portugal. Phylogenetic analysis of 144 <i>M. bovis</i> whole-genome sequences from cattle, wild boar, and red deer, representing the 2002–2021 period, distinguished three Eu2 clades that evolved independently. The major Eu2 clade underwent phylodynamic inferences to estimate the time and location of outbreaks, host transitions, and spatial diffusion as well. The origin of this Eu2 clade was attributed to the red deer population in the Castelo Branco district, near the border with Spain. Most host transitions were intraspecific (80%), while interspecific transmissions between wildlife species (wild boar-red deer), and between wild boar and cattle, were highly supported. Phylogeographic reconstruction evidenced that most transitions (82%) occur within municipalities, highlighting local transmission corridors. Our study indicates that <i>M. bovis</i> continues to spread at the cattle-wildlife interface within the animal TB hotspot area, possibly driven by the foraging behaviour of wild boar near agricultural lands. Red deer seems to be an important driver of TB within wildlife hosts, while the wild boar links the multi-host wildlife community and livestock. This work highlights the value of combining genomic epidemiology with phylodynamic inference to resolve host jumps and spatial patterns of <i>M. bovis</i>, providing real-time clues about points of intervention.
DOI: 10.5061/dryad.5j618
title: Data from: Patterns of species relatedness created by competitive exclusion depend on species niche differences: evidence from Iberian Atlantic grasslands

description: It is commonly assumed that closely related species share more similar
 niches than do distantly related species, thus limiting their ability to
 coexist and leading to patterns of phylogenetic over-dispersion. On the
 contrary, recent theoretical developments argue that competitive exclusion
 may lead to patterns of either over-dispersion, clustering or randomness,
 depending on the relative importance of niche differences and
 interspecific competitive ability differences. In this study, we utilized
 semi-natural grassland communities to test the hypothesis that the pattern
 of species relatedness generated by competitive exclusion depends on
 species niche differences. Instead of inferring processes from observed
 patterns, we experimentally manipulated grassland plots to test the
 effects of competitive exclusion. We compared grazed plots (in which
 grazing functioned as an equalizing mechanism and suppressed aboveground
 competition) with neighbouring plots experimentally excluded from grazing
 over the course of nine years (in which aboveground competition was not
 prevented). Weak niche differences between species allowed competitive
 exclusion to generate phylogenetic clustering, because phylogenetically
 structured plant canopy height and capacity for lateral spread conferred
 superior competitive ability to grasses that outcompeted species in all
 dicot branches. By contrast, moderate niche differences allowed
 competitive exclusion to result in a random pattern of phylogenetic
 species assembly, because species niche differences partially
 counterbalanced competitive exclusion by superior competitors in the grass
 family. We conclude that patterns of species relatedness created by
 competitive exclusion in Iberian Atlantic grasslands depend on species
 niche differences. Competitive exclusion may cause differential patterns
 of phylogenetic assembly.
description: Aralar_DatasetFine-scale floristic composition and soil descriptors in two grassland sites of Aralar Natural Park (northern Iberian Peninsula). Species functional traits. Phylogenetic trees of the two grassland sites.Archive.zip
DOI: 10.6084/m9.figshare.24047073
title: Emergence of a new designated clade 16 with significant antigenic drift in hemagglutinin gene of H9N2 subtype avian influenza virus in eastern China

description: H9N2 avian influenza viruses (AIVs) pose an increasing threat to the poultry industry worldwide and have pandemic potential. Vaccination has been principal prevention strategy to control H9N2 in China since 1998, but vaccine effectiveness is persistently challenged by the emergence of the genetic and/or antigenic variants. Here, we analysed the genetic and antigenic characteristics of H9N2 viruses in China, including 70 HA sequences of H9N2 isolates from poultry, 7358 from online databases during 2010–2020, and 15 from the early reference strains. Bayesian analyses based on hemagglutinin (HA) gene revealed that a new designated clade16 emerged in April 2012, and was prevalent and co-circulated with clade 15 since 2013 in China. Clade 16 viruses exhibited decreased cross-reactivity with those from clade 15. Antigenic Cartography analyses showed represent strains were classified into three antigenic groups named as Group1, Group2 and Group3, and most of the strains in Group 3 (15/17, 88.2%) were from Clade 16 while most of the strains in Group2 (26/29, 89.7%) were from Clade 15. The mean distance between Group 3 and Group 2 was 4.079 (95%CI 3.605–4.554), revealing that major switches to antigenic properties were observed over the emergence of clade 16. Genetic analysis indicated that 11 coevolving amino acid substitutions primarily at antigenic sites were associated with the antigenic differences between clade 15 and clade 16. These data highlight complexities of the genetic evolution and provide a framework for the genetic basis and antigenic characterization of emerging clade 16 of H9N2 subtype avian influenza virus.
DOI: 10.6084/m9.figshare.23540588.v2
title: Assessment and sero-diagnosis for coronaviruses with risk of human spillover

description: Zoonotic coronaviruses (CoVs) caused major human outbreaks in the last two decades. One of the biggest challenges during future CoV disease is ensuring rapid detection and diagnosis at the early phase of a zoonotic event, and active surveillance to the zoonotic high-risk CoVs appears the best way at the present time to provide early warnings. However, there is neither an evaluation of spillover potential nor diagnosis tools for the majority of CoVs. Here, we analyzed the viral traits, including population, genetic diversity, receptor and host species for all 40 alpha- and beta-CoV species, where the human-infecting CoVs are from. Our analysis proposed 20 high-risk CoV species, including 6 of which jumped to human, 3 with evidence of spillover but not to human and 11 without evidence of spillover yet, which prediction were further supported by an analysis of the history of CoV zoonosis. We also found three major zoonotic sources: multiple bat-origin CoV species, the rodent-origin sub-genus <i>Embecovirus</i> and the CoV species AlphaCoV1. Moreover, the <i>Rhinolophidae</i> and <i>Hipposideridae</i> bats harbour a significantly higher proportion of human-threatening CoV species, whereas camel, civet, swine and pangolin could be important intermediate hosts during CoV zoonotic transmission. Finally, we established quick and sensitive serologic tools for a list of proposed high-risk CoVs and validated the methods in serum cross-reaction assays using hyper-immune rabbit sera or clinical samples. By comprehensive risk assessment of the potential human-infecting CoVs, our work provides a theoretical or practical basis for future CoV disease preparedness.
DOI: 10.34740/kaggle/dsv/14635626
title: Peer-to-Peer Boliviano (BOB) Exchange Data
DOI: 10.5061/dryad.27vq2
title: Data from: Experimental demonstration of the benefits of somatic fusion and the consequences for allorecognition

description: Allorecognition, the ability to distinguish ‘self’ from ‘non-self’ based
 on allelic differences at allorecognition loci, is common in all domains
 of life. Allorecognition restricts the opportunities for social
 parasitism, and is therefore crucial for the evolution of cooperation.
 However, the maintenance of allorecognition diversity provides a paradox.
 If allorecognition is costly relative to cooperation, common alleles will
 be favored. Thus, the cost of allorecognition may reduce the genetic
 variation upon which allorecognition crucially relies, a prediction now
 known as ‘Crozier's paradox’. We establish the relative costs of
 allorecognition, and their consequences for the short-term evolution of
 recognition labels theoretically predicted by Crozier. We use fusion among
 colonies of the fungus Neurospora crassa, regulated by highly variable
 allorecognition genes, as an experimental model system. We demonstrate
 that fusion among colonies is mutually beneficial, relative to absence of
 fusion upon allorecognition. This benefit is due not only to absence of
 mutual antagonism, which occurs upon allorecognition, but also to an
 increase in colony size per se. We then experimentally demonstrate that
 the benefit of fusion selects against allorecognition diversity, as
 predicted by Crozier. We discuss what maintains allorecognition diversity.
description: Dataset Bastiaans et al.
 2015 Evolutiondataset Bastiaans et al. 2015
 Evolution.xlsx
DOI: 10.5061/dryad.994f813
title: Data from: Phylogeny matters: revisiting ‘a comparison of bats and rodents as reservoirs of zoonotic viruses’

description: Diseases emerging from wildlife have been the source of many major human
 outbreaks. Predicting key sources of these outbreaks requires an
 understanding of the factors that explain pathogen diversity in reservoir
 species. Comparative methods are powerful tools for understanding
 variation in pathogen diversity and rely on correcting for phylogenetic
 relatedness among reservoir species. We reanalyzed a previously published
 dataset, examining the relative effects of species’ traits on patterns of
 viral diversity in bats and rodents. We expanded on prior work by using
 more highly resolved phylogenies for bats and rodents and incorporating a
 phylogenetically controlled principal components analysis. For rodents,
 sympatry and torpor use were important predictors of viral richness and,
 as previously reported, phylogeny had minimal impact in models. For bats,
 in contrast to prior work, we find that phylogeny does have an effect in
 models. Patterns of viral diversity in bats were related to geographic
 distribution (i.e., latitude and range size) and life history (i.e.,
 lifespan, body size, and birthing frequency). However, the effects of
 these predictors were marginal relative to citation count, emphasizing
 that the ability to accurately assess reservoir status largely depends on
 sampling effort and highlighting the need for additional data in future
 comparative studies.
description: RCode for
 Analyses_R2Condensed version of R
 code used to implement analyses outlined in the main
 text.RCode
 for Analyses.txt
DOI: 10.15468/dl.ty6hyd
title: Occurrence Download

description: A dataset containing 39 species occurrences available in GBIF matching the query:
{
 "and" : [
 "CoordinateUncertaintyInMeters 0.0-5000.0",
 "TaxonKey is Cullen corylifolium"
 ]
}

 The dataset includes 39 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001209-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.5040n
title: Data from: Rate maximization and hyperbolic discounting in human experiential intertemporal decision making

description: Decisions between differently timed outcomes are a well-studied topic in
 as diverse academic disciplines as economics, psychology, and behavioral
 ecology. Humans and other animals have been shown to make these
 intertemporal choices by hyperbolically devaluing rewards as a function of
 their delays (‘delay discounting’), thus often deemed to behave
 myopically. In behavioral ecology, however, intertemporal choices are
 assumed to meet optimization principles, that is, the maximization of
 energy or reward rate. Thus far it is unclear how different approaches
 assuming these two currencies, reward devaluation and reward rate
 maximization, could be reconciled. Here we investigated the degree at
 which humans (N = 81) discount reward value and maximize reward rate when
 making intertemporal decisions. We found that both hyperbolic discounting
 and rate maximization well approximated the choices made in a range of
 different intertemporal choice design conditions. Notably, rate
 maximization rules provided even better fits to the choice data than
 hyperbolic discounting models in all conditions. Interestingly, in
 contrast to previous findings, rate maximization was universally observed
 in all choice frames, and not confined to foraging settings. Moreover,
 rate maximization correlated with the degree of hyperbolic discounting in
 all conditions. This finding is in line with the possibility that
 evolution has favored hyperbolic discounting because it subserves reward
 rate maximization by allowing for flexible adjustment of preference for
 smaller, sooner or larger, later rewards. Thus, rate maximization may be a
 universal principle that has shaped intertemporal decision making in
 general and across a wide range of choice problems.
description: Demographic and
 discounting data of participantsIn the xlsx file the
 demographic data (i.e., gender and age) of our 81 participants are
 included. Moreover, we included the larger-later option choice proportion
 for each of the 6 blocks of both tasks (i.e., self-control design and
 patch design) along with the respective earnings. Then, we list the
 computed hyperbolic log-k values for the two tasks (as well as for the two
 tasks collapsed) and for the Kirby task. Then we included the computed
 Long Term maximization Rate (LTR) for the two tasks (considering both all
 choices and only the last 5) and the Akaike Information Criterion for both
 the LTR and the hyperbolic models for both task designs.Finally, we
 included the performance at the time production task at each of the four
 delay conditions and the scores at the Barrat Impulsiveness Scale
 subscales and at the Quick Delay Questionnaire
 subscales.Seinstra_data.xlsx
DOI: 10.5061/dryad.3fc8m7c
title: Data from: Artificial selection on reproductive timing in hatchery salmon drives a phenological shift and potential maladaptation to climate change

description: The timing of breeding migration and reproduction links generations and
 substantially influences individual fitness. In salmonid fishes, such
 phenological events (seasonal return to fresh water and spawning) vary
 among populations but are consistent among years, indicating local
 adaptation in these traits to prevailing environmental conditions.
 Changing reproductive phenology has been observed in many populations of
 salmonids, and is sometimes attributed to adaptive responses to climate
 change. The sockeye salmon spawning in the Cedar River near Seattle,
 Washington have displayed dramatic changes in spawning timing over the
 past 50 years, trending later through the early 1990s, and becoming
 earlier since then. We explored the patterns and drivers of these changes
 using generalized linear models and mathematical simulations to identify
 possible environmental correlates of the changes, and test the alternative
 hypothesis that hatchery propagation caused inadvertent selection on
 timing. The trend toward later spawning prior to 1993 was partially
 explained by environmental changes, but the advance in spawning since was
 not. Instead, since its initiation in 1991 the hatchery has, on average,
 selected for earlier spawning, and, depending on trait heritability, could
 have advanced spawning by 1-3 weeks over this period. We estimated
 heritability of spawning date to be high (h2 ~ 0.8; 95% CI: 0.5-1.1), so
 the upper end of this range is not improbable, though at lower
 heritabilities a smaller effect would be expected. The lower reproductive
 success of early spawners and relatively low survival of early emerging
 juveniles observed in recent years suggest that artificial and natural
 selection are acting in opposite directions. The fitness costs of early
 spawning may be exacerbated by future warming, thus artificially advanced
 phenology could reduce the population’s productivity. Such artificial
 selection is known in many salmon hatcheries, so there are broad
 consequences for the productivity of wild populations comingled with
 hatchery produced fish.
description: Cedar River sockeye
 salmon annual phenology, abundance and environmental data
 1965-2016Observations of
 abundance, migration timing, environmental covariates of timing, and
 hatchery egg take data for 1965-2016. Data are observed for passage of the
 Ballard Locks, arrival at the Baker River and occupancy of the Cedar
 River. The heritability tab includes data used for estimating the
 heritability of spawning date for Cedar River sockeye salmon. These data
 are mean spawning dates of parent and offspring by release groups and
 years.Tillotson et Al_Dryad
 Submission.xlsx
DOI: 10.5281/zenodo.18383498
title: EEG Attention Dataset

description: This study’s EEG experiment was divided into five groups, each corresponding to a different auditory stimulation condition: classical music, alpha-wave music, singing bowl music, natural environmental sounds, and a no-music control group. Each group included three participants, for a total of fifteen participants. To ensure de-identification, participants are labeled only as P1–P15.


Each participant’s EEG data consists of three parts:


Meditation EEG: EEG recordings collected during deep meditation and resting state.


RSVP EEG with music background (pre-test): EEG recordings collected while participants performed the RSVP task under their assigned auditory condition.


RSVP EEG without music background (post-test): EEG recordings collected while participants performed the RSVP task without auditory stimulation.


All EEG data are stored in .csv files, with each file containing:


Time series


EEG signals from each electrode site, covering the theta–gamma frequency bands


This dataset structure supports subsequent EEG feature extraction, analysis of attentional performance, and comparative studies across conditions.
DOI: 10.5281/zenodo.18384428
title: EEG Attention Dataset

description: This study’s EEG experiment was divided into five groups, each corresponding to a different auditory stimulation condition: classical music, alpha-wave music, singing bowl music, natural environmental sounds, and a no-music control group. Each group included three participants, for a total of fifteen participants. To ensure de-identification, participants are labeled only as P1–P15.


Each participant’s EEG data consists of three parts:


Meditation EEG: EEG recordings collected during deep meditation and resting state.


RSVP EEG with music background (pre-test): EEG recordings collected while participants performed the RSVP task under their assigned auditory condition.


RSVP EEG without music background (post-test): EEG recordings collected while participants performed the RSVP task without auditory stimulation.


All EEG data are stored in .csv files, with each file containing:


Time series


EEG signals from each electrode site, covering the theta–gamma frequency bands


This dataset structure supports subsequent EEG feature extraction, analysis of attentional performance, and comparative studies across conditions.
DOI: 10.15468/dl.szfndz
title: Occurrence Download

description: A dataset containing 153 species occurrences available in GBIF matching the query:
{
 "and" : [
 "CoordinateUncertaintyInMeters 0.0-5000.0",
 "TaxonKey is Cuscuta reflexa"
 ]
}

 The dataset includes 153 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001210-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.