cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.nj2n99s
title: Data from: Understanding policing as a mechanism of cheater control in cooperating bacteria

description: Policing occurs in insect, animal and human societies, where it evolved as
 a mechanism maintaining cooperation. Recently, it has been suggested that
 policing might even be relevant in enforcing cooperation in much simpler
 organisms such as bacteria. Here, we used individual‐based modelling to
 develop an evolutionary concept for policing in bacteria, and identify the
 conditions under which it can be adaptive. We modelled interactions
 between cooperators, producing a beneficial public good, cheaters
 exploiting the public good without contributing to it, and public good
 producing policers that secrete a toxin to selectively target cheaters. We
 found that toxin‐mediated policing is favoured when (i) toxins are potent
 and durable, (ii) cheap to produce, (iii) cell and public good diffusion
 is intermediate, and (iv) toxins diffuse farther than the public good.
 While our simulations identify the parameter space where toxin‐mediated
 policing can evolve, we further found that policing decays when the
 genetic linkage between public good and toxin production breaks. This is
 because policing is itself a public good, offering protection to
 toxin‐resistant mutants that still produce public goods, yet no longer
 invest in toxins. Our work thus highlights that not only specific
 environmental conditions are required for toxin‐mediated policing to
 evolve, but also strong genetic linkage between the expression of public
 goods, toxins and toxin resistance is essential for this mechanism to
 remain evolutionarily stable in the long run.
description: Data used for generating
 the figuresThe Excel file contains
 all the individual entries used to plot the figures presented in the
 study. The file contains a description of all the parameters and
 abbreviations used in the file.2019_Wechsler_etal_JEB_rawdata_Dryad.xlsx
DOI: 10.5061/dryad.rt400df
title: Data from: The adaptive potential of plant populations in response to extreme climate events

description: The frequency and magnitude of extreme climate events are increasing with
 global change, yet we lack predictions and empirical evidence for the
 ability of wild populations to persist and adapt in response to these
 events. Here, we used Fisher’s Fundamental Theorem of Natural Selection to
 evaluate the adaptive potential of Lasthenia fremontii, an herbaceous
 winter annual that is endemic to seasonally flooded wetlands in
 California, to alternative flooding regimes that occur during El Niño
 Southern Oscillation (ENSO) events. The results indicate that populations
 may exhibit greater adaptive potential in response to dry years than wet
 years, and that the relative performance of populations will change across
 climate scenarios. More generally, our findings show that extreme climate
 events can substantially change the potential for populations to adapt to
 climate change by modulating the expression of standing genetic variation
 and mean fitness.
description: LfremontiiAdaptivePotentialThe zip file "L.fremontiiAdaptivePotential" contains the input data, outputs and SAS codes implemented to estimate the adaptive potential of L.fremontii in response to ENSO events. All associated climate data is also contained within this file (see README)
DOI: 10.5061/dryad.d0mv3dh
title: Data from: Behavioral responses of individual blue whales (Balaenoptera musculus) to mid-frequency military sonar

description: This study measured the degree of behavioral responses in blue whales
 (Balaenoptera musculus) to controlled noise exposure off the southern
 California coast. High-resolution movement and passive acoustic data were
 obtained from non-invasive archival tags (n=42) while surface positions
 were obtained with visual focal follows. Controlled exposure experiments
 (CEEs) were used to obtain direct behavioral measurements before, during,
 and after simulated and operational military mid-frequency active sonar
 (MFAS), pseudorandom noise (PRN), and controls (no noise exposure). For a
 subset of deep-foraging animals (n=21), active acoustic measurements of
 prey were obtained and used as contextual covariates in response analyses.
 To investigate potential behavioral changes within individuals as a
 function of controlled noise exposure conditions, two parallel analyses of
 time-series data for selected behavioral parameters (e.g., diving,
 horizontal movement, feeding) were conducted. This included expert scoring
 of responses according to a specified behavioral severity rating paradigm
 and quantitative change-point analyses using Mahalanobis distance
 statistics. Both methods identified clear changes in some conditions. More
 than 50% of blue whales in deep feeding states responded during CEEs,
 while no changes in behavior were identified in shallow-feeding blue
 whales. Overall, responses were generally brief, of low to moderate
 severity, and highly dependent on exposure context such as behavioral
 state, source-to-whale horizontal range, and prey availability. Response
 probability did not follow a simple dose-response model based on received
 exposure level. These results, in combination with additional analytical
 methods to investigate different aspects of potential responses within and
 among individuals, provide a comprehensive evaluation of how free-ranging
 blue whales responded to mid-frequency military sonar.
description: Blue whale individual
 CEE results_JEB for DryadExpert scoring and
 Mahalanobis distance figures as well as metadata syntheses of results are
 given for all 42 blue whale subjects
DOI: 10.5061/dryad.j5577d2
title: Data from: Selection for longer-lived sperm within ejaculate reduces reproductive ageing in offspring

description: Males produce numerous sperm in a single ejaculate that greatly outnumber
 their potential egg targets. Recent studies found that phenotypic and
 genotypic variation among sperm in a single ejaculate of a male affects
 the fitness and performance of the resulting offspring. Specifically,
 within-ejaculate sperm selection for sperm longevity increased the
 performance of the resulting offspring in several key life-history traits
 in early-life. Because increased early-life reproductive performance often
 correlates with rapid ageing, it is possible that within-ejaculate sperm
 selection increases early-life fitness at the cost of accelerated
 senescence. Alternatively, within-ejaculate sperm selection could improve
 offspring quality throughout the life cycle, including reduced
 age-specific deterioration. We tested the two alternative hypotheses in an
 experimental setup using zebrafish Danio rerio. We found that
 within-ejaculate sperm selection for sperm longevity reduced age-specific
 deterioration of fecundity and offspring survival but had no effect on
 fertilization success in males. Remarkably, we found an opposing effect of
 within-ejaculate sperm selection on female fecundity, where selection for
 sperm longevity resulted in increased early-life performance followed by a
 slow decline, while females sired by unselected sperm started low but
 increased their fecundity with age. Intriguingly, within-ejaculate sperm
 selection also reduced the age-specific decline in fertilization success
 in females, suggesting that selection for sperm longevity improves at
 least some aspects of female reproductive ageing. These results
 demonstrate that within-ejaculate variation in sperm phenotype contributes
 to individual variation in animal life histories in the two sexes and may
 have important implications for assisted fertilization programs in
 livestock and humans.
description: Evolution Letters
 GAlavioon dataRaw data for all
 analyses presented in the paper.
DOI: 10.5061/dryad.p6m4jm3
title: Data from: The pursuit strategy of predatory bluefish

description: A predator's ability to capture prey depends critically on how it
 coordinates its approach in response to a prey's motion. Flying
 insects, bats, and raptors are capable of capturing prey with a strategy
 known as parallel navigation, which allows a predator to move directly
 toward the anticipated point of interception. It is unclear if predators
 using other modes of locomotion are capable of employing this strategy
 when pursuing evasive prey. Using kinematic measurements and mathematical
 modeling, we tested whether bluefish (Pomatomus saltatrix) pursue prey
 fish (Fundulus heteroclitus) with parallel navigation. We found that the
 directional changes of bluefish were not consistent with this strategy,
 but rather were predicted by a strategy known as deviated pursuit.
 Although deviated pursuit requires few sensory cues and relatively modest
 motor coordination, a comparison of mathematical models suggested
 negligible differences in path length from parallel navigation, largely
 due to the acceleration exhibited by bluefish near the end of a pursuit.
 Therefore, the strategy of bluefish is unlike flying predators, but offers
 comparable performance with potentially more robust control that may be
 well-suited to the visual system and habitat of fishes. These findings
 offer a foundation for understanding the sensing and locomotor control of
 predatory fishes.
description: Kinematic
 dataKinematic data for all
 experimentspooled
 data.zipPredator-preyCatalog of videos recording during experiments.Analysis codeMatlab code used to perform analysis.ana_whitney.zip
DOI: 10.5061/dryad.56b1t40
title: Data from: Opsin genes of select treeshrews resolve ancestral character states within Scandentia

description: Treeshrews are small, squirrel-like mammals in the order Scandentia, which
 is nested together with Primates and Dermoptera in the superordinal group
 Euarchonta. They are often described as living fossils, and researchers
 have long turned to treeshrews as a model or ecological analogue for
 ancestral primates. A comparative study of colour vision-encoding genes
 within Scandentia found a derived amino acid substitution in the
 long-wavelength sensitive opsin gene (OPN1LW) of the Bornean smooth-tailed
 treeshrew (Dendrogale melanura). The opsin, by inference, is red-shifted
 by ca. 6 nm with an inferred peak sensitivity of 561 nm. It is tempting to
 view this trait as a novel visual adaptation; however, the genetic and
 functional diversity of visual pigments in treeshrews is unresolved
 outside of Borneo. Here we report gene sequences from the northern
 smooth-tailed treeshrew (Dendrogale murina) and the Mindanao treeshrew
 (Tupaia everetti, the senior synonym of Urogale everetti). We found that
 the opsin genes are under purifying selection and that D. murina shares
 the same substitution as its congener, a result that distinguishes
 Dendrogale from other treeshrews, including T. everetti. We discuss the
 implications of opsin functional variation in light of limited knowledge
 about the visual ecology of smooth-tailed treeshrews.
description: KY825132Tupaia everetti voucher DMP298 short wavelength sensitive opsin (OPN1SW) gene, partial cdsKY825133Tupaia everetti voucher DMP322 short wavelength sensitive opsin (OPN1SW) gene, partial cdsKY825134Tupaia everetti voucher DMP298 long wavelength sensitive opsin (OPN1LW) gene, partial cdsKY825135Tupaia everetti voucher DMP322 long wavelength sensitive opsin (OPN1LW) gene, partial cdsTreeshrew OPN1SW alignment for PAMLOPN1SW alignment used for PAML analysisTreeshrew OPN1LW alignment for PAMLOPN1LW alignment for PAML analysis
DOI: 10.5061/dryad.k7t33tg
title: Data from: Multiple parapatric pollinators have radiated across a continental fig tree displaying clinal genetic variation

description: The ways that plant-feeding insects have diversified is central to our
 understanding of terrestrial ecosystems. Obligate nursery pollination
 mutualisms provide highly relevant model systems of how plants and their
 insect associates have diversified and the over 800 species of fig trees
 (Ficus) allow comparative studies. Fig trees can have one or more
 pollinating fig wasp species (Agaonidae) that breed within their figs, but
 factors influencing their number remain to be established. In some widely
 distributed fig trees, the plants form populations isolated by large
 swathes of sea, and the different populations are pollinated by different
 wasp species. Other Ficus species with continuous distributions may
 present genetic signatures of isolation by distance, suggesting more
 limited pollinator dispersal, which may also facilitate pollinator
 speciation. We tested the hypothesis that Ficus hirta, a species for which
 preliminary data showed genetic isolation by distance, would support
 numerous pollinator species across its range. Our results show that across
 its range Ficus hirta displays clinal genetic variation and is pollinated
 by nine parapatric species of Valisia. This is the highest number of
 pollinators reported to date for any Ficus species and it is the first
 demonstration of the occurrence of parapatric pollinator species on a fig
 host displaying continuous genetic structure. Future comparative studies
 across Ficus species should be able to establish the plant traits that
 have driven the evolution of pollinator dispersal behaviour, pollinator
 speciation and host plant spatial genetic structure.
description: upload data of
 MEC-18-1245.R1Metadata associated with
 Yu et al. Molecular Ecology
DOI: 10.5281/zenodo.18350492
title: KEYS_BRAND7_50F_4_23C_0k_EDLC_single
DOI: 10.5281/zenodo.18350493
title: KEYS_BRAND7_50F_4_23C_0k_EDLC_single
DOI: 10.5061/dryad.bh8m7v8
title: Data from: Do genomics and sex predict migration in a partially migratory salmonid fish, Oncorhynchus mykiss?

description: Partial migration is a common phenomenon wherein populations include
 migratory and resident individuals. Whether an individual migrates or not
 has important ecological and management implications, particularly within
 protected populations. Within partially migratory populations of O.
 mykiss, migration is highly correlated with a specific genomic region, but
 it is unclear how well this region predicts migration at the individual
 level. Here, we relate sex and life history genotype, determined using
 &gt;400 SNPs on the migratory-linked genomic region, to life history
 expression of marked juvenile O. mykiss from two tributaries to the South
 Fork Eel River, northern California. Most resident fish were
 resident-genotypes (57% resident, 37% heterozygous, 6% migratory genotype)
 and male (78%). Most migratory fish were female (62%), but were a mixture
 of genotypes (30% resident, 45% heterozygous, 25% migratory genotype). Sex
 was more strongly correlated with life history expression than genotype,
 but the best-supported model included both. Resident genotypes regularly
 migrated, highlighting the importance of conserving the full suite of life
 history and genetic diversity in partially migratory populations.
description: lifehistoryfishData table with all fish that were assigned a life history ecotype.tableS1Table S1 in the manuscript. Summary of genotype data, used to make figures in the code.genotype_phenotype_analysesCode including major data analyses and figures
DOI: 10.5061/dryad.4gg142s
title: Data from: Pre-infection effects of nectar secondary compounds on a bumble bee gut pathogen

description: Bumble bee pollinators can be exposed to pathogens when foraging on
 flowers previously visited by infected individuals. Infectious cells may
 be deposited in floral nectar, providing a site for pathogens to interact
 with nectar secondary compounds prior to infecting bees. Some nectar
 secondary compounds can reduce pathogen counts in infected bumble bees,
 but we know less about how exposure to these compounds directly affects
 pathogens prior to being ingested by their host. We exposed the
 trypanosomatid gut pathogen, Crithidia bombi (Trypanosomatida:
 Trypanosomatidae), to six different compounds found in nectar (aucubin,
 catalpol, nicotine, thymol, anabasine, and citric acid) for one hour prior
 to ingestion by Bombus impatiens (Hymenoptera: Apidae) workers that were
 then reared for one week on a control diet. All of these compounds except
 citric acid reduce pathogen levels when consumed in hosts after infection,
 and citric acid is a common preservative found in citrus fruits and some
 honeys. We found that both citric acid and aucubin reduced Crithidia cell
 counts compared to controls. However, catalpol, nicotine, thymol, and
 anabasine did not have significant effects on Crithidia levels. These
 results suggest that Crithidia exposure in some floral nectars may reduce
 cell viability, resulting in a lower risk to visiting pollinators, but
 this effect may not be widespread across all flowering species
description: Michaud_et_al_scriptR script for all analysesZip file with all CSV data filesThis zip folder contains all of the CSV data files and associated README file.Dryad-pre-ingestion.zip
DOI: 10.5061/dryad.6d8p7j1
title: Data from: Beta diversity and oligarchic dominance in the tropical Forests of Southern Costa Rica

description: Recent studies have reported a consistent pattern of strong dominance of a
 small subset of tree species in Neotropical forests. These species have
 been called ‘hyperdominant’ at large geographical scales and ‘oligarchs’
 at regional-landscape scales when being abundant and frequent. Forest
 community assembly is shaped by environmental factors and stochastic
 processes, but so far the contribution of oligarchic species to the
 variation of community composition (i.e. beta diversity) remains poorly
 known. To that end, we established 20 1-ha plots, i.e. 5 sites with 4
 forest types (ridge, slope and ravine primary forest, and secondary
 forest) per site, in humid lowland tropical forests of southwestern Costa
 Rica to (1) investigate how community composition responds to differences
 in topography, successional stage and distance among plots for different
 groups of species (all, oligarch, common and rare/very rare species) and
 (2) identify oligarch species characterizing changes in community
 composition among forest types. From a total of 485 species of trees,
 lianas and palms recorded in this study only 27 species (i.e. 6%) were
 nominated as oligarch species. Oligarch species accounted for 37% of all
 recorded individuals and were present in at least half of the plots. Plant
 community composition significantly differed among forest types, thus
 contributing to beta diversity at the landscape-scale. Oligarch species
 was the component best explained by geographical and topographic
 variables, allowing a confident characterization of the beta diversity
 among tropical lowland forest stands.
description: READMEDescription of the tree
 abundance data file (.xlsx)tree_abundance_data_GolfoDulce_BITR-18-091R2Abundance (individuals per hectare) of tree and palm species in the Golfo Dulce region, Costa Rica
DOI: 10.5061/dryad.c8c83nr
title: Data from: Future temperature and salinity do not exert selection pressure on cyst germination of a toxic phytoplankton species

description: Environmental conditions regulate the germination of phytoplankton resting
 stages. While some factors lead to synchronous germination, others
 stimulate germination of only a small fraction of the resting stages. This
 suggests that habitat filters may act on the germination level and thus
 affect selection of blooming strains. Benthic “seed banks” of the toxic
 dinoflagellate Alexandria ostenfeldii from the Baltic Sea are genetically
 and phenotypically diverse, indicating a high potential for adaptation by
 selection on standing genetic variation. Here, we experimentally tested
 the role of climate‐related salinity and temperature as selection filters
 during germination and subsequent establishment of A. ostenfeldii strains.
 A representative resting cyst population was isolated from sediment
 samples, and germination and reciprocal transplantation experiments were
 carried out, including four treatments: Average present day germination
 conditions and three potential future conditions: high temperature, low
 salinity, and high temperature in combination with low salinity. We found
 that the final germination success of A. ostenfeldii resting cysts was
 unaffected by temperature and salinity in the range tested. A high
 germination success of more than 80% in all treatments indicates that
 strains are not selected by temperature and salinity during germination,
 but selection becomes more important shortly after germination, in the
 vegetative stage of the life cycle. Moreover, strains were not adapted to
 germination conditions. Instead, highly plastic responses occurred after
 transplantation and significantly higher growth rates were observed at
 higher temperature. High variability of strain‐specific responses has
 probably masked the overall effect of the treatments, highlighting the
 importance of testing the effect of environmental factors on many strains.
 It is likely that A. ostenfeldii populations can persist in the future,
 because suitable strains, which are able to germinate and grow well at
 potential future climate conditions, are part of the highly diverse cyst
 population.
description: DataZipped files and a
 README file, containing variable descriptions and
 explanations.
DOI: 10.5061/dryad.7nt676d
title: Data from: Co-inheritance of sea age at maturity and iteroparity in the Atlantic salmon vgll3 genomic region

description: Co-inheritance in life history traits may result in unpredictable
 evolutionary trajectories if not accounted for in life-history models.
 Iteroparity (the reproductive strategy of reproducing more than once) in
 Atlantic salmon (Salmo salar) is a fitness trait with substantial
 variation within and among populations. In the Teno River in northern
 Europe, iteroparous individuals constitute an important component of many
 populations and have experienced a sharp increase in abundance in the last
 20 years, partly overlapping with a general decrease in age structure. The
 physiological basis of iteroparity bears similarities to that of age at
 first maturity, another life history trait with substantial fitness
 effects in salmon. Sea age at maturity in Atlantic salmon is controlled by
 a major locus around the vgll3 gene, and we used this opportunity
 demonstrate that these two traits are co-inherited around this genome
 region. The odds ratio of survival until second reproduction was up to 2.4
 (1.8-3.5 90% CI) times higher for fish with the early-maturing vgll3
 genotype (EE) compared to fish with the late-maturing genotype (LL). The L
 allele was dominant in individuals remaining only one year at sea before
 maturation, but the dominance was reversed, with the E allele being
 dominant in individuals maturing after two or more years at sea. Post hoc
 analysis indicated that iteroparous fish with the EE genotype had
 accelerated growth prior to first reproduction compared to first-time
 spawners, across all age groups, while this effect was not detected in
 fish with the LL genotype. These results broaden the functional link
 around the vgll3 genome region and help us understand constraints in the
 evolution of life history variation in salmon. Our results further
 highlight the need to account for genetic correlations between fitness
 traits when predicting demographic changes in changing environments.
description: Aykanat_et_al_2019_DryadR code and associated objects to replicate main results presented in Aykanat et al, 2019, Co-inheritance of sea age at maturity and iteroparity in the Atlantic salmon vgll3 genomic region, (DOI: 10.1111/jeb.13418) (More details are given in the R code.)