cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.2fh81pd
title: Data from: ­Challenges of NGS in conservation management: insights from long-term monitoring of corridor effects on the genetic diversity of mouse lemurs in a fragmented landscape

description: Long-term genetic monitoring of populations is essential for efforts aimed
 at preserving genetic diversity of endangered species. Here, we employ a
 framework of long-term genetic monitoring to evaluate the effects of
 fragmentation and the effectiveness of the establishment of corridors in
 restoring population connectivity and genetic diversity of mouse lemurs
 Micocebus ganzhorni. To this end, we supplement estimates of neutral
 genetic diversity with the assessment of adaptive genetic variability of
 the MHC. In addition, we address the challenges of long-term genetic
 monitoring of functional diversity by comparing the genotyping performance
 and estimates of MHC variability generated by SSCP/Sanger-sequencing with
 those obtained by high throughput sequencing (NGS, Illumina), an issue
 that is particularly relevant when previous work serves as a baseline for
 planning management strategies that aim to ensure the viability of a
 population. We report that SSCP greatly underestimates individual
 diversity and that discrepancies in estimates of MHC diversity
 attributable to the comparisons of traditional and NGS genotyping
 techniques can influence the conclusions drawn from conservation
 management scenarios. Evidence of migration among fragments in Mandena
 suggests that mouse lemurs are robust to the process of fragmentation and
 that the effect of corridors is masked by ongoing gene flow. Nonetheless,
 results based on a larger number of shared private alleles at neutral loci
 between fragment pairs found after the establishment of corridors in
 Mandena suggest that gene flow is augmented as a result of enhanced
 connectivity. Our data points out that despite low effective population
 size, M. ganzhorni maintains high individual heterozygosity at neutral
 loci and at MHC II DRB gene and that selection plays a predominant role in
 maintaining MHC diversity. These findings highlight the importance of
 long-term genetic monitoring in order to disentangle between the processes
 of drift and selection maintaining adaptive genetic diversity in small
 populations.
description: EVA-2018-135-OA.R1_MHCIIDRB_1998-2016MHII DRB exon 2 genotypes of mouse lemurs caught in the littoral forests of Mandena during two sampling periods: 1998-2003 and 2012-2016. Data was generated using single-stranded conformation polymorphism (SSPC) and amplicon based NGS (Illumina) approach.EVA-2018-135-OA.R1_msats_1998-2016Microsatellite genotypes of mouse lemurs caught in the littoral forests of Mandena during two sampling periods: 1998-2003 and 2012-2016.
DOI: 10.5061/dryad.m02hm
title: Data from: Context-dependent seed dispersal by a scatter-hoarding corvid

description: 1. Corvids (crows, jays, magpies and nutcrackers) are important dispersers
 of large-seeded plants. Studies on captive or supplemented birds suggest
 that they flexibly adjust their scatter-hoarding behaviour to the context
 of social dynamics and relative seed availability. Because many
 corvid-dispersed trees show high annual variation in seed production,
 context-dependent foraging can have strong effects on natural corvid
 scatter-hoarding behaviour. 2. We investigated how seed availability and
 social dynamics affected scatter-hoarding in the island scrub jays
 (Aphelocoma insularis). We quantified rates of scatter-hoarding behaviour
 and territorial defence of 26 colour-marked birds over a three-year period
 with variable acorn crops. 3. We tested whether caching parameters were
 correlated with variation in annual seed production of oaks as predicted
 by the predator dispersal hypothesis, which states that caching rates and
 distances should vary with seed abundance in ways that benefit tree
 fitness. We also tested whether antagonistic interactions with
 conspecifics would affect scatter-hoarding adversely, as found in
 experimental studies. 4. Caching behaviour varied with acorn availability.
 Caching distances correlated positively with annual acorn crop size,
 increasing by as much as 40% between years. Caching rates declined over
 time in years with small acorn crops, but increased when crops were large.
 Acorn foraging and caching rates were also negatively correlated with
 rates of territorial aggression. Overall foraging rates, however, were not
 associated with aggression, suggesting that reduced dispersal rates were
 not simply due to time constraints. 5. Our field results support
 laboratory findings that caching rates and distances by scatter-hoarding
 corvids are context-dependent. Furthermore, our results are consistent
 with predictions of the predator dispersal hypothesis and suggest that
 large seed crops and social interactions among scatter-hoarders affect
 dispersal benefits for oaks and other masting tree species.
description: focal follow
 dataThis are summary data of
 focal follows of island scrub-jays, during which we recorded foraging
 events (frg), acorn foraging events (acorn), caching events (cac),
 aggressive displacements (dis), calculated their hourly rates (ffh, fah,
 fch, fdh), the Julian date (day), acorn counts per plot (count.y), study
 plot (plot), calendar week (week), and proportions of acorns
 cached.Pesendorfer_etal_ISSJ_focals.csvPesendorfer_etal_ISSJ_cachesCaching observations. Includes individual, plot, year, caching distance, acorn count on the plot, and calendar week.
DOI: 10.5061/dryad.nd58h
title: Data from: Evolving interactions between diazotrophic cyanobacterium and phage mediate nitrogen release and host competitive ability

description: Interactions between nitrogen-fixing (i.e. diazotrophic) cyanobacteria and
 their viruses, cyanophages, can have large-scale ecosystem effects. These
 effects are mediated by temporal alterations in nutrient availability in
 aquatic systems owing to the release of nitrogen and carbon sources from
 cells lysed by phages, as well as by ecologically important changes in the
 diversity and fitness of cyanobacterial populations that evolve in the
 presence of phages. However, ecological and evolutionary feedbacks between
 phages and nitrogen-fixing cyanobacteria are still relative poorly
 understood. Here, we used an experimental evolution approach to test the
 effect of interactions between a common filamentous, nitrogen-fixing
 cyanobacterium (Nodularia sp.) and its phage on cellular nitrogen release
 and host properties. Ecological, community-level effects of phage-mediated
 nitrogen release were tested with a phytoplankton bioassay. We found that
 cyanobacterial nitrogen release increased significantly as a result of
 viral lysis, which was associated with enhanced growth of phytoplankton
 species in cell-free filtrates compared with phage-resistant host controls
 in which lysis and subsequent nutrient release did not occur after phage
 exposure. We also observed an ecologically important change among
 phage-evolved cyanobacteria with phage-resistant phenotypes, a
 short-filamentous morphotype with reduced buoyancy compared with the
 ancestral long-filamentous morphotype. Reduced buoyancy might decrease the
 ability of these morphotypes to compete for light compared with longer,
 more buoyant filaments. Together, these findings demonstrate the potential
 of cyanobacteria–phage interactions to affect ecosystem biogeochemical
 cycles and planktonic community dynamics.
description: Nodularia and phage
 counts from 4 day experiment4_day_exp_Nodularia_and_phage_counts.xlsxPhytoplankton cell counts from filtrate experimentFiltrate_experiment_phytoplankton_cell_counts.xlsxFilament length data for phage susceptible and phage resistant Nodularia isolatesFilament_length.xlsx
DOI: 10.5061/dryad.hv6gf
title: Data from: The spatial dynamics of predators and the benefits and costs of sharing information

description: Predators of all kinds, be they lions hunting in the Serengeti or
 fishermen searching for their catch, display various collective
 strategies. A common strategy is to share information about the location
 of prey. However, depending on the spatial characteristics and mobility of
 predators and prey, information sharing can either improve or hinder
 individual success. Here, our goal is to investigate the interacting
 effects of space and information sharing on predation efficiency,
 represented by the expected rate at which prey are found and consumed. We
 derive a feeding functional response that accounts for both
 spatio-temporal heterogeneity and communication, and validate this
 mathematical analysis with a computational agent-based model. This
 agent-based model has an explicit yet minimal representation of space, as
 well as information sharing about the location of prey. The analytical
 model simplifies predator behavior into a few discrete states and one
 essential trade-off, between the individual benefit of acquiring
 information and the cost of creating spatial and temporal correlation
 between predators. Despite the absence of an explicit spatial dimension in
 these equations, they quantitatively predict the predator consumption
 rates measured in the agent-based simulations across the explored
 parameter space. Together, the mathematical analysis and agent-based
 simulations identify the conditions for when there is a benefit to sharing
 information, and also when there is a cost.
description: Agent-Based Model
 dataSimulation data for
 figures in the article.Foundation-upload.zip
DOI: 10.5061/dryad.b1039
title: Data from: Mimicry among unequally defended prey should be mutualistic when predators sample optimally

description: Understanding the conditions under which moderately defended prey evolve
 to resemble better-defended prey and whether this mimicry is parasitic
 (quasi-Batesian) or mutualistic (Müllerian) is central to our
 understanding of warning signals. Models of predator learning generally
 predict quasi-Batesian relationships. However, predators’ attack decisions
 are based not only on learning alone but also on the potential future
 rewards. We identify the optimal sampling strategy of predators capable of
 classifying prey into different profitability categories and contrast the
 implications of these rules for mimicry evolution with a classical
 Pavlovian model based on conditioning. In both cases, the presence of
 moderately unprofitable mimics causes an increase in overall consumption.
 However, in the case of the optimal sampling strategy, this increase in
 consumption is typically outweighed by the increase in overall density of
 prey sharing the model appearance (a dilution effect), causing a decrease
 in mortality. It suggests that if predators forage efficiently to maximize
 their long-term payoff, genuine quasi-Batesian mimicry should be rare,
 which may explain the scarcity of evidence for it in nature. Nevertheless,
 we show that when moderately defended mimics are profitable to attack by
 hungry predators, then they can be parasitic on their models, just as
 classical Batesian mimics are.
description: R CodeR code to determine the
 optimal sampling strategy for unfamiliar prey belonging potentially to
 three different profitability classes. Simulations conducted to draw the
 graphs in the AmNat article.DPEAnalysisFigures.R
DOI: 10.5061/dryad.r3645
title: Data from: Asymptotic allometry and transition to the canopy in Abies balsamea

description: There is a lack of consensus in theoretical and empirical literature on
 whether height-diameter (H:D) relationships of canopy trees are
 asymptotic. To investigate H:D allometry, particularly in the transition
 to the canopy, we focus on shade-tolerant Abies balsamea, across steep
 physical gradients associated with elevation, and correlated
 biotically-generated gradients of stem density, canopy height and canopy
 species composition. We addressed these questions: A. What is the relation
 between H:D allometric form and emergence into the canopy? B. Is H:D
 allometry asymptotic? C. What aspects of the H:D relationship are most
 sensitive to environmental conditions? Using maximum likelihood, we
 compared the performance of alternative H:D forms (linear, power function,
 non-sigmoid-asymptotic and sigmoid-asymptotic), incorporating elevation
 and local canopy height as covariates. A. balsamea H:D allometric form was
 clearly sigmoid-asymptotic, by a wide AIC margin, across all gradients, to
 an asymptote slightly above canopy height. The commonly used power
 function had essentially no empirical support (Δ AIC &gt; &gt;
 10). Canopy height decreased with elevation, but with much variation, so
 elevation was a poor predictor of the asymptote. Across environmental
 gradients, H:D allometries overlapped for trees far below the canopy, but
 diverged strongly for trees approaching different canopy heights. Changes
 in resource allocation and modification of growth form that could generate
 asymptotic H:D allometries are consistent with known physical forces and
 diverse research findings in tree developmental biology and physiology.
 Synthesis. The H:D asymptote and its tight relation to canopy height,
 unapparent in aggregated H:D data, became clear only when canopy height
 and elevation were included explicitly in allometric models. Asymptotic
 H:D allometries may be the norm, though often undetected, in unmanaged
 forests without recent catastrophic disturbance. Appropriate asymptotic
 H:D models may reduce error in forest carbon and biomass estimation and
 promote theoretical and empirical integration in the ecology and evolution
 of tree allometry.
description: Abies balsamea
 height:diameter allometry dataAbies_bals_allom_data_Peart.csv
DOI: 10.5061/dryad.ng07t
title: Data from: Metabolite profile of a mouse model of Charcot-Marie-Tooth type 2D neuropathy: implications for disease mechanisms and interventions

description: Charcot-Marie-Tooth disease encompasses a genetically heterogeneous class
 of heritable polyneuropathies that result in axonal degeneration in the
 peripheral nervous system. Charcot-Marie-Tooth type 2D neuropathy (CMT2D)
 is caused by dominant mutations in glycyl tRNA synthetase (GARS).
 Mutations in the mouse Gars gene result in a genetically and
 phenotypically valid animal model of CMT2D. How mutations in GARS lead to
 peripheral neuropathy remains controversial. To identify putative disease
 mechanisms, we compared metabolites isolated from the spinal cord of Gars
 mutant mice and their littermate controls. A profile of altered
 metabolites that distinguish the affected and unaffected tissue was
 determined. Ascorbic acid was decreased fourfold in the spinal cord of
 CMT2D mice, but was not altered in serum. Carnitine and its derivatives
 were also significantly reduced in spinal cord tissue of mutant mice,
 whereas glycine was elevated. Dietary supplementation with
 acetyl-L-carnitine improved gross motor performance of CMT2D mice, but
 neither acetyl-L-carnitine nor glycine supplementation altered the
 parameters directly assessing neuropathy. Other metabolite changes
 suggestive of liver and kidney dysfunction in the CMT2D mice were
 validated using clinical blood chemistry. These effects were not secondary
 to the neuromuscular phenotype, as determined by comparison with another,
 genetically unrelated mouse strain with similar neuromuscular dysfunction.
 However, these changes do not seem to be causative or consistent
 metabolites of CMT2D, because they were not observed in a second mouse
 Gars allele or in serum samples from CMT2D patients. Therefore, the
 metabolite 'fingerprint' we have identified for CMT2D improves
 our understanding of cellular biochemical changes associated with GARS
 mutations, but identification of efficacious treatment strategies and
 elucidation of the disease mechanism will require additional studies.
description: GARS Study Raw
 DataRaw data for Metabolic
 derangements in the GARS+/- transgenic mouse
DOI: 10.5061/dryad.ff6d4
title: Data from: Refuge or predation risk? Alternate ways to perceive hiker disturbance based on maternal state of female caribou

description: Human presence in natural environments is often a source of stress that is
 perceived by large ungulates as an increased risk of predation.
 Alternatively, disturbance induced by hikers creates a relatively
 predator-free space that may serve as a refuge. We measured the behavioral
 responses of female caribou to disturbance associated with the presence of
 hikers during summer in the Gaspésie National Park. We used those data to
 determine whether caribou responded negatively to human activity (i.e.,
 the predation risk hypothesis) or whether human activity resulted in a
 decrease in the magnitude of perceived risk (i.e., the refuge hypothesis).
 Female caribou with a calf spent nearly half of their time feeding,
 regardless of the presence of a trail or the number of hikers. They also
 decreased their vigilance near trails when the number of hikers increased.
 Conversely, lone females fed less frequently and almost doubled the time
 invested in vigilance under the same circumstances. However, both groups
 of females moved away from trails during the day, especially in the
 presence of hikers. We demonstrated that risk avoidance was specific to
 the maternal state of the individual. Lactating females accommodated the
 presence of hikers to increase time spent foraging and nutritional intake,
 providing support for the refuge hypothesis. Alternatively, lone females
 with lower energetic requirements and no maternal investment in a
 vulnerable calf appeared less tolerant to risk, consistent with the
 predation risk hypothesis. Synthesis and applications: Hikers influenced
 the vigilance–feeding trade-off in caribou, underlining the importance of
 appropriate management of linear structures and human activities,
 especially across the critical habitat of endangered species. Even if some
 individuals seemed to benefit from human presence, this behavioral
 adaptation was not sufficient to reduce annual calf mortality associated
 with predation.
description: Focal observation for
 lone femalesNumber of seconds and
 proportion of time spent in a given behaviour during focal observations
 for lone females (without a calf).focal_withoutcalf.csvFocal observation for females with a calfNumber of seconds and proportion of time spent in a given behaviour during focal observations for females accompanied by a calf.focal_withcalf.csvSpace use data for lone femalesData used in figure 2, i.e. frequency distribution of distances to a trail for telemetry locations for lone females (without a calf).f0datagraph_spaceuse.csvSpace use data for females with a calfData used in figure 2, i.e. frequency distribution of distances to a trail for telemetry locations for suited females (accompanied by a calf).f1datagraph_spaceuse.csv
DOI: 10.5061/dryad.d05h5
title: Data from: Shaping communicative colour signals over evolutionary time

description: Many evolutionary forces can shape the evolution of communicative signals,
 and the long-term impact of each force may depend on relative timing and
 magnitude. We use a phylogenetic analysis to infer the history of blue
 belly patches of Sceloporus lizards, and a detailed spectrophotometric
 analysis of four species to explore the specific forces shaping
 evolutionary change. We find that the ancestor of Sceloporus had blue
 patches. We then focus on four species; the first evolutionary shift
 (captured by comparison of S. merriami and S. siniferus) represents an
 ancient loss of the belly patch by S. siniferus, and the second
 evolutionary shift, bounded by S. undulatus and S. virgatus, represents a
 more recent loss of blue belly patch by S. virgatus. Conspicuousness
 measurements suggest that the species with the recent loss (S. virgatus)
 is the least conspicuous. Results for two other species (S. siniferus and
 S. merriami) suggest that over longer periods of evolutionary time, new
 signal colours have arisen which minimize absolute contrast with the
 habitat while maximizing conspicuousness to a lizard receiver.
 Specifically, males of the species representing an ancient loss of blue
 patch (S. siniferus) are more conspicuous than are females in the UV,
 whereas S. merriami males have evolved a green element that makes their
 belly patches highly sexually dimorphic but no more conspicuous than the
 white bellies of S. merriami females. Thus, our results suggest that
 natural selection may act more immediately to reduce conspicuousness,
 whereas sexual selection may have a more complex impact on communicative
 signals through the introduction of new colours.
description: Data for Ossip-Drahos et
 al. 2016Mean spectrophotometric
 measures and Just-noticeable-differences estimated for bellies of males
 and females of four species of Sceloporus lizards.4SpAOK.xlsx
DOI: 10.5061/dryad.299h8
title: Data from: Effect of oceanographic barriers and overfishing on the population genetic structure of the European spiny lobster (Palinurus elephas)

description: Defining population structure and genetic diversity levels is of the
 utmost importance for developing efficient conservation strategies.
 Overfishing has caused mean annual catches of the European spiny lobster
 (Palinurus elephas) to decrease alarmingly along its distribution area. In
 this context, there is a need for comprehensive studies to evaluate the
 genetic health of the exploited populations. The present work is based on
 a set of 10 nuclear markers amplified in 331 individuals from 10 different
 localities covering most of P. elephas distribution area. Samples from
 Atlantic and Mediterranean basins showed small but significant
 differences, indicating that P. elephas populations do not behave as a
 single panmictic unit but form two partially-overlapping groups. Despite
 intense overfishing, our dataset did not recover a recent bottleneck
 signal, and showed a large and stable historical effective size instead.
 This result could be accounted for by specific life history traits
 (reproduction and longevity) and the limitations of molecular markers in
 covering very recent timescales for non temporal samples. Our study
 emphasizes the necessity of integrating information on effective
 population sizes and life history parameters when evaluating population
 connectivity levels from genetic data.
description: Data_P.elephas