cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.3bk3j9khq
title: Survival and density of New England cottontail and Eastern cottontail

description: Habitat quality regulates fitness and population density, making it a key
 driver of population size. Hence, increasing habitat quality is often a
 primary goal of species conservation. Yet assessments of fitness and
 density are difficult and costly to obtain. Therefore, species
 conservation often uses “best available science”, extending inferences
 across taxa, space or time, and inferring habitat quality from studies of
 habitat selection. However, there are scenarios where habitat selection is
 not reflective of habitat quality, and this can lead to maladaptive
 management strategies. The New England cottontail (Sylvilagus
 transitionalis) is an imperiled shrubland obligate lagomorph whose
 successful recovery hinges on creation of suitable habitat. Recovery of
 this species is also negatively impacted by the non-native eastern
 cottontail (Sylvilagus floridanus), which can competitively exclude New
 England cottontails from preferred habitat. Herein we evaluate habitat
 quality for adult and juvenile New England and eastern cottontails using
 survival and density as indicators. Our findings did not support selection
 following an ideal free distribution by New England cottontails. Instead
 selected resources, which are a target of habitat management, were
 associated with low survival and density and pointed to a complex tradeoff
 between density, survival, habitat, and the presence of eastern
 cottontails. Further, movement distance was inversely correlated with
 survival in both species, suggesting that habitat fragmentation limits the
 ability of cottontails to freely distribute based on habitat quality.
 While habitat did not directly regulate survival of juvenile cottontails,
 tick burden had a strong negative impact on juvenile cottontails in poor
 body condition. Given the complex interactions among New England
 cottontails, eastern cottontails, and habitat, directly assessing and
 accounting for factors that limit New England cottontail habitat quality
 in management plans is vital to their recovery. Our study demonstrates an
 example of management for possible ecological trap conditions via the
 application of incomplete knowledge.
description: Cottontails were live-trapped using box traps. Captured
 individuals were used to assess capture per unit effort as a measure of
 density and affixed with radio transmitters to determine factors
 influencing survival. Cottontails were tracked 1-3 times weekly and their
 locations were related to grid-based vegetation surveys of habitat across
 sites.
description: Missing values were filled with the mean.
DOI: 10.5061/dryad.m63xsj40t
title: Data from: Within-trio tests provide little support for post-copulatory selection on MHC haplotypes in a free-living population

description: Sexual selection has been proposed as a force that could maintain the
 diversity of major histocompatibility complex (MHC) genes in vertebrates.
 Potential selective mechanisms can be divided into pre-copulatory and
 post-copulatory, and in both cases the evidence for occurrence is mixed,
 especially in natural populations. In this study, we used a large number
 of parent-offspring trios that were diplotyped for MHC class II genes in a
 wild population of Soay sheep (Ovis aries) to examine whether there was
 within-trio post-copulatory selection on MHC genes at both the haplotype
 and diplotype levels. We found there was transmission ratio distortion of
 one the eight MHC class II haplotype (E) which was transmitted less than
 expected by fathers, and transmission ratio distortion of another
 haplotype (A) which was transmitted more than expected by chance to male
 offspring. However, in both cases these deviations were not significant
 after correction for multiple tests. In addition, we did not find any
 evidence of post-copulatory selection on diplotype level. These results
 imply given known parents, there is no strong post-copulatory selection on
 MHC genes in this population.
description: MHC diplotype of parent-offspring trios : MHC_trio.csv
 MHC diplotype of parent-offspring trios excluding repeated
 parental pairs : MHC_trio2.csv MHC divergence betweem
 each MHC diplotype (p-distance) : MHC_divergence.csv R
 script : simulation_post_copulatory.txt Readme
 file
DOI: 10.5061/dryad.fqz612jrh
title: The influence of nutrient enrichment on riverine food web function and stability

description: Nutrient enrichment of rivers and lakes has been increasing rapidly over
 the past few decades, primarily because of agricultural intensification.
 Although nutrient enrichment is known to drive excessive algal and
 microbial growth, which can directly and indirectly change the ecological
 community composition, the resulting changes in food web emergent
 properties are poorly understood. We used ecological network analysis
 (ENA) to examine the emergent properties of 12 riverine food webs across a
 nutrient enrichment gradient in the Manawatu, New Zealand. We also derive
 Keystone Sensitivity Indices to explore whether nutrients change the
 trophic importance of species in a way that alters the resilience of the
 communities to further nutrient enrichment or floods. Nutrient enrichment
 resulted in communities composed of energy inefficient species with high
 community (excluding microbes) respiration. Community respiration was
 several times greater in enriched communities and this may drive hypoxic
 conditions even without concomitant changes in microbial respiration.
 Enriched communities exhibited weaker trophic cascades, which may yield
 greater robustness to energy flow loss. Interestingly, enriched
 communities were also more structurally and functionally affected by
 species sensitive to flow disturbance making these communities more
 vulnerable to floods.
DOI: 10.5061/dryad.ns1rn8pr8
title: Diverging functional strategies but high sensitivity to an extreme drought in tropical dry forests: supporting data

description: Extreme drought events have negative effects on forest diversity and
 functioning. Here, we presented a dataset of functional traits
 representing the hydraulic safety-efficiency trade-offs and investment in
 tissues of 338 tropical dry forest tree species, and long-term biomass
 demographic data, which support the main strategies of these species in
 response to an extreme dry event in Northern South America.
description: This dataset was assemble using 15 functional traits 524
 populations belonging to 338 species on TDF, and records of biomass
 demography for these species (growth and mortality of trees) measured
 between 2013 and 2017. In the middle of census periods, species
 experienced the strongest drought event of the last 36 years in Northern
 South America, “El Niño” Southern Oscillation 2015-2016. The data format
 is a RDS for upload in R-program using "readRDS" extension
 (ele_TDFdata.rds). The data consists of two sources. Firstly, a dataset
 with two-PCA trait scores, code of the individuals (1553), species (338),
 sampled plots (11), and the loadings for the 15 leaf and stem traits. This
 source is called "traits.data" into the RDS. Secondly, a dataset
 with standing biomass and biomass demographic changes of species (biomass
 gain by the growth of surviving and recruited trees, biomass loss by the
 mortality of trees). This source is called "biomass.data" into
 the RDS. For biomass.data, standing biomass values per species are in
 kg/ha and biomass demographic rates are in kg/ha/yr.
description: The R-scripts lines used the datasets are: 1.
 To charge data: ele_TDFdata &lt;-
 readRDS("~/DOWNLOAD.DIRECTORY/ele_TDFdata.rds") # Please change
 the download directory 2. To access traits
 data: ele_TDFdata$traits.data 3. To access biomass
 data:  ele_TDFdata$biomass.data
DOI: 10.5061/dryad.ghx3ffbmn
title: Evolution of bacterial cross-resistance to lytic phages and albicidin antibiotic

description: Due to concerns over the global increase of antibiotic-resistant bacteria,
 alternative antibacterial strategies, such as phage therapy, are
 increasingly being considered. However, evolution of bacterial resistance
 to new therapeutics is almost a certainty; indeed, it is possible that
 resistance to alternative treatments might result in an evolved trade-up
 such as enhanced antibiotic resistance. Here, we hypothesize that
 selection for Escherichia coli bacteria to resist phage T6, phage U115, or
 albicidin will result in a pleiotropic trade-up in the form of
 cross-resistance, because all three antibacterial agents interact with the
 Tsx porin. Selection imposed by any one of the antibacterials resulted in
 cross-resistance to all three of them, in 29 spontaneous bacterial mutants
 examined in this study. Furthermore, cross-resistance did not cause
 measurable fitness deficiencies under normal growth conditions for any of
 the bacterial mutants. A combination of whole-genome and targeted
 sequencing confirmed that mutants differed from wildtype E. coli via
 change(s) in the tsx gene. Our results indicate that evolution of
 cross-resistance occurs frequently in E. coli subjected to independent
 selection by phage T6, phage U115 or albicidin. This study cautions that
 deployment of new antibacterial therapies such as phage therapy, should be
 preceded by a thorough investigation of evolutionary consequences of the
 treatment, to avoid the potential for evolved trade-ups.
DOI: 10.5061/dryad.wdbrv15mz
title: Neural and social correlates of attitudinal brokerage: using the complete social networks of two entire villages

description: To avoid polarization and maintain small-worldness in society, people who
 act as attitudinal brokers are critical. These people maintain social ties
 with people who have dissimilar and even incompatible attitudes. Based on
 resting-state functional magnetic resonance imaging (n=139) and the
 complete social networks from two Korean villages (n=1508), we
 investigated the individual-level neural capacity and social-level
 structural opportunity for attitudinal brokerage regarding gender role
 attitudes. First, using a connectome-based predictive model, we
 successfully identified the brain functional connectivity that predicts
 attitudinal diversity of respondents’ social network members. Brain
 regions that contributed most to the prediction included (1) mentalizing
 regions known to be recruited in reading and understanding others’ belief
 states; and (2) regions associated with moral judgments or information
 propagation. This result was corroborated by leave-one-out
 cross-validation, five-fold cross-validation, and external validation
 where the brain connectivity identified in one village was used to predict
 the attitudinal diversity in another independent village. Second, the
 association between functional connectivity and attitudinal diversity of
 social network members was contingent on a specific position in a social
 network, namely, the brokerage position where people have ties with two
 people who are not otherwise connected.
description: Please read readme.txt. Code to replicate the results are
 available at https://github.com/JunsolKim/neural-and-social-correlates-of-attitudinal-brokerage
DOI: 10.5061/dryad.xgxd254f7
title: Low genetic variability in Bemisia tabaci MEAM1 populations within farmscapes of Georgia, USA

description: Sweetpotato whitefly, Bemisia tabaci Gennadius, is a
 serious pest of many agricultural crops worldwide. Numerous studies have
 examined the genetic structure of whitefly populations separated by
 geographical barriers; however, very few have assessed the population
 structure of B. tabaci at a farmscape level. A farmscape
 in this study is defined as heterogenous habitat with crop and non-crop
 areas spanning about 8 square kilometers. To assess the roles of
 farmscapes as drivers of B. tabaci genetic variations,
 thirty-five populations of the sweetpotato whitefly were collected from
 crop and non-crop plant species from fifteen farmscapes. Using
 mitochondrial COI gene sequences (mtCOI) and six nuclear microsatellite
 markers, the genetic diversity and genetic differentiation among
 collected B. tabaci MEAM1 populations were examined.
 Haplotype analysis using mtCOI sequences revealed the presence of a
 single B. tabaci MEAM1 haplotype across farmscapes of
 Georgia. Results from microsatellite markers further showed no significant
 genetic structuring among populations that corresponded to plant species
 or farmscapes from which they were collected. Annual whitefly population
 explosions and subsequent dispersal might have facilitated the presence of
 a single panmictic B. tabaci population over all sampled
 farmscapes in this region.
DOI: 10.5061/dryad.k98sf7m4x
title: Competition for pollination and isolation from mates differentially impact four stages of pollination in a model grassland perennial

description: 1. Species that persist in small populations isolated by habitat
 destruction may experience reproductive failure. Self-incompatible plants
 face dual threats of mate-limitation and competition with co-flowering
 plants for pollination services. Such competition may lower pollinator
 visitation, increase heterospecific pollen transfer, and reduce the
 likelihood that a visit results in successful pollination. 2. To
 understand how isolation from mates and competition with co-flowering
 species contribute to reproductive failure in fragmented habitat, we
 conducted an observational study of a tallgrass prairie perennial,
 Echinacea angustifolia. We quantified the isolation of focal individuals
 from mates, characterized species richness and counted inflorescences
 within 1m radius, observed pollinator visitation, collected pollinators,
 quantified pollen loads on pollinators and on Echinacea stigmas, and
 measured pollination success. Throughout the season, we sampled 223 focal
 plants. 3. We present evidence that both co-flowering species and
 isolation from mates substantially limit reproduction in Echinacea. As the
 flowering season progressed, the probability of pollinator visitation to
 focal plants decreased and evidence for pollen-limited reproduction
 increased. Pollinators were most likely to visit Echinacea plants from
 low-richness floral neighbourhoods with close potential mates, or plants
 from high-richness neighbourhoods with distant potential mates. Frequent
 visitation only increased pollination success in the former case, likely
 because Echinacea in high-richness floral neighbourhoods received
 low-quality visits. 4. Synthesis: In Echinacea, reproduction was limited
 by isolation from potential mates and the richness of co-flowering
 species. These aspects of the floral neighbourhood influenced pollinator
 visitation and pollination success, although conditions that predicted
 high visitation did not always lead to high pollination success. These
 results reveal how habitat modification and destruction, which influence
 floral neighbourhood and isolation from conspecific mates, can
 differentially affect various stages of reproductive biology in
 self-incompatible plants. Our results suggest that prairie conservation
 and restoration efforts that promote patches of greater floral diversity
 may improve reproductive outcomes in fragmented habitats.
description: Please refer to the readMe.txt file for metadata and descriptions
 of all included files. 1. ff.csv<br> 2.
 bb.csv<br> 3. ppCon.csv<br> 4. ppHet.csv<br> 5.
 ssCon.csv<br> 6. ssHet.csv<br> 7. rr.csv<br> 8.
 pollinatorCommunity.R<br> 9.
 pollinatorVisitationAnalysis.R<br> 10.
 pollenOnPollinatorsAnalysis.R<br> 11.
 pollenOnStylesAnalysis.R<br> 12.
 stylePersistenceAnalysis.R<br> 13. supplementalFigures.R<br>
DOI: 10.5061/dryad.n8pk0p2th
title: Supplemental data for article: DNA content variation and SNP diversity within a single population of asexual snails

description: A growing body of research suggests that many clonal populations maintain
 genetic diversity even without occasional sexual reproduction. The purpose
 of our study was to document variation in SNP diversity, DNA content, and
 pathogen susceptibility in clonal lineages of the New Zealand freshwater
 snail, Potamopyrgus antipodarum. We studied snails that
 were collected from multiple field sites around a single lake
 (Lake Alexandrina), as well as isofemale clonal lineages that had been
 isolated and maintained in the laboratory. We used the KASP method to
 genotype our samples at 46 nuclear SNP sites, and we used flow cytometry
 to estimate DNA content. We found high levels of SNP diversity, both in
 our field samples and in our clonal laboratory lines. We also found
 evidence of high variation in DNA content among clones, even among clones
 with identical genotypes across all SNP sites. Controlled pathogen
 exposures of the laboratory populations revealed variation in
 susceptibility among distinct clonal genotypes, which was independent of
 DNA content. Taken together, these results show high levels of diversity
 among asexual snails, especially for DNA content, and they suggest rapid
 genome evolution in asexuals.
description: Nuclear DNA content was measured via flow cytometry. Genomic DNA
 was extracted with a DNEasy Blood and Tissue kit. SNP genotyping was
 performed using the KASP method.
description: Some values for the SNP genotypes are missing. Data are in .csv
 and Word format.
DOI: 10.5061/dryad.stqjq2c29
title: Seasonal time constraints shape life history, physiology and behaviour independently, and decouple a behavioural syndrome in a damselfly

description: The integration of traits into 'syndromes' has been suggested as
 a useful framework to advance insights in trait responses to environmental
 stressors. Yet, how stressors shape the consistency (‘repeatability’) of
 traits and their covariation at the individual level remains debated. We
 studied how seasonal time constraints shape trait repeatability and
 integration of life-history, behavioural, and physiological traits along a
 fast-slow continuum, using the ‘pace-of-life syndrome’ as a framework. We
 manipulated the photoperiod during the larval development of the damselfly
 Ischnura elegans, generating a time-relaxed early, a control, and a
 time-constrained late group. The photoperiod treatment did not seem to
 affect the voltinism of the larvae. As predicted, late-period larvae
 accelerated development and growth, yet this acceleration was no longer
 detectable for growth and metabolic rate during the final instar, possibly
 due to costs of the initial life-history acceleration. This warrants
 caution when inferring a species’ pace-of-life based on a specific
 developmental stage. The late-period larvae were as predicted more active
 (only during the later stages of the final instar) and bolder than the
 control larvae, but not different from the early-period larvae. Most
 studies on time constraints only compared late and control animals,
 thereby potentially wrongly concluding adaptive responses to time
 constraints. Activity, boldness, and body mass were repeatable, while
 growth and metabolic rates were not. Notably, repeatabilities did not
 change under time constraints. There was no support for an overall trait
 integration in a pace-of-life syndrome, yet activity and boldness covaried
 positively as expected. Importantly, this ‘behavioural syndrome’ was
 decoupled in the late-period larvae, which might be adaptive to enhance
 energy acquisition to fuel the accelerated development rate. Our results
 suggest that besides the predicted plastic acceleration of life-history,
 plastic changes in behavioural trait integration may also be an important
 but overlooked adaptive aspect of responding to time constraints.
description: Variable names (column names) are self explanaroty.
 Note that the dataset is longitudinally structured (based on on
 the most repeated measurement, i.e. body mass [measured 4
 times]).
DOI: 10.5061/dryad.5dv41ns55
title: VNS and seizure outcomes in pediatric refractory epilepsy: Systematic review and meta-analysis

description: This data provides supplemental information for the systematic review and
 Meta-analysis. Supplemental tables report the detailed serach strategy
 (Supplementary Table 1), details of included studies
 (Supplementary Table 2), list of excluded studies (Supplementary
 Table 3), 50% Responder Rate in children with
 Lennox-Gastaut syndrome after VNS insertion (Supplementary
 Table 4), 50% Responder Rate in children with Dravet
 syndrome after VNS insertion (Supplementary Table 5), VNS
 settings and other seizure outcomes reported in the included studies
 (Supplementary Table 6) and Studies reporting a formal Quality of
 life (QOL) assessment in children post VNS implantation (Supplementary
 Table 7). Supplemental figure 1 (S1) shows the PRISMA flowchart for this
 systematic review.  Supplemental Figure
 2 (S2): Determinants of Seizure Outcomes. Multivariable
 regression showed 50%-RR at last reported follow-up to increase with
 increasing age of onset of seizures and decrease with the number of ASMs
 tried before VNS implantation (A). Higher 50%-RR 1-year after VNS
 implantation was seen in patients with shorter duration of epilepsy and
 fewer number of ASM trials (B). Decline in 50%-RR at 1 and 2 year
 follow-up in studies with a higher proportion of males (C). Proportion of
 seizure free patients at last reported follow-up also decreases with a
 greater number of ASM trials before VNS implantation (D). [50%-RR: 50%
 Responder Rate, ASM: Anti-seizure Medication, VNS: Vagus Nerve Stimulator;
 Bubbles represent individual effect size for studies, lines represent
 ordinary least squares regression models, and the shading represents 95%
 confidence regions. Supplemental figure 3 (S3): Forest plots for
 proportion of seizure free patients. Forest plots for proportion
 of patients with 50% responder rate at 6 months (B), 1 year (C) and 2
 years (D) follow-up summarizing the pooled effect estimate and
 heterogeneity.  Supplemental figure
 4 (S4): Forest plots for proportion of seizure free
 patients. Forest plots for proportion of seizure free patients at
 6 months (B), 1 year (C) and 2 years (D) follow-up summarizing the pooled
 effect estimate and heterogeneity.
description: Data was extracted from 101 included studies in the systematic
 review.
DOI: 10.5061/dryad.866t1g1ph
title: Meta analysis data and fitness-related trait values

description: Crop-wild gene flow may alter the fitness performance of the recipient
 i.e. crop-wild hybrids, then potentially impact wild populations,
 especially for the gene flow carrying selective advantage crop alleles.
 Given the continuous crop-wild gene flow since crop domestication and the
 occasionally stressful environments, the extant wild populations of most
 crops are still "wild". This paradox hints some mechanisms may
 mitigate the effects of crop-wild gene flow but never been examined. We
 used wild rice (O. rufipogon) and transgenic (Bt/CpTI) rice as a crop-wild
 gene flow model and established cultivated, wild and hybrid rice
 populations (O. rufipogon × O. sativa) under four levels of insect (Chilo
 suppressalis) pressure. Then, we measured the fitness performance of the
 plants. The fitness performance of all plants varied with the insect
 pressure level; wild plants displayed over- or equal-compensatory
 responses to insect damage, whereas hybrids exhibited under-compensatory
 responses, showing wild plants have higher insect-tolerance. The high
 tolerance results in better performance of wild rice under stressful
 conditions, while transgenes expressed a beneficial effect on plant
 performance only under certain levels of insect pressure. Hybrid advantage
 is remarkable. Transgenes and hybrid advantage may increase hybrid
 fitness, but such effect is reduced by tolerance under stressful
 environments. Synthesis. These results suggest that high tolerance to
 environmental stress is a mechanism mitigating the impacts of crop gene
 flow on wild plants by weakening hybrid fitness performance.