cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.01c53v5
title: Data from: Sex ratio variations among years and breeding systems in a facultatively parthenogenetic termite

description: Some species of termites evolved an outstanding reproductive strategy
 called asexual queen succession (AQS), in which the primary queen is
 replaced by multiple parthenogenetically produced daughters (neotenics)
 that mate with the primary king. When the primary king is eventually
 replaced, this time by sexually produced neotenic king(s), sex-asymmetric
 inbreeding occurs and the queen’s genome is more transmitted than that of
 the king, thereby increasing the reproductive value of female dispersers,
 and female-biased population sex ratio is expected. Yet, the life cycle,
 the breeding system dynamics and AQS modalities differ between AQS
 species, thereby modifying the relative genetic contribution of primary
 reproductives in the colony and thus also the equilibrium sex ratio. We
 estimated colonial and population sex ratio over two consecutive dispersal
 periods in a French Guiana population of Cavitermes tuberosus (Termitinae)
 in which the founding queen may be replaced only after colony maturity,
 some neotenic females may be sexually produced, and some female dispersers
 arise through parthenogenesis. Colonial sex ratio varied among colonies:
 primary-headed nests with higher within-nest relatedness produced more
 females than neotenic-headed nests with lower relatedness among
 individuals. Over the two dispersal periods, the population investment sex
 ratio fluctuated around 1:1, thereby confirming that AQS breeding system
 is not necessarily linked with female biased sex ratio. The balanced alate
 sex ratio, combined with the occurrence of sexually produced neotenic
 queens, is possibly the outcome of a queen-king conflict between the
 primary reproductives.
description: Genotypes of Cavitermes
 tuberosusMicrosatellite data of
 Cavitermes tuberosus at 17 loci. The nest of origin, developmental stage,
 sex, reproductive origin is given for each individual.Hellemans et al_Sex ratio in
 the termite Cavitermes
 tuberosus_Genotypes.xlsx
DOI: 10.5061/dryad.p2c0b
title: Data from: Microsatellite evidence for obligate autogamy, but abundant genetic variation in the herbaceous monocarp Lobelia inflata (Campanulaceae)

description: Although high levels of self-fertilization (&gt;85%) are not uncommon
 in nature, organisms reproducing entirely through selfing are extremely
 rare. Predominant selfers are expected to have low genetic diversity
 because genetic variation is distributed among rather than within
 lineages, and is readily lost through genetic drift. We examined genetic
 diversity at 22 microsatellite loci in 105 individuals from a population
 of the semelparous herb Lobelia inflata L., and found (1) no evidence of
 heterozygosity through outcrossing, yet (2) high rates of genetic
 polymorphism (2-4 alleles per locus). Furthermore, this genetic variation
 among lineages was associated with phenotypic traits (e.g. flower colour,
 size at first flower). Coupled with previous work characterizing the
 fitness consequences of reproductive timing, our results suggest that
 temporal genotype-by-environment interaction may maintain genetic
 variation and, because genetic variation occurs only among lineages, this
 simple system offers a unique opportunity for future tests of this
 mechanism.
description: Microsatellite and
 Phenological Data for Lobelia inflataThis dataset contains
 five spreadsheets. The first shows the growth conditions, initial size and
 phenological characters for the 811 S1 offspring of the field-sourced P1
 generation of experimental plants. This data was analyzed using the GLM
 and GLMM models shown in the paper. The second shows the pairwise
 comparisons between the eleven genetic lineages for each locus. When two
 lineages share the same allele at a given locus, this is listed as “1”,
 and if they differ, this is listed as “0”. The total (overall) pairwise
 similarity between lineages is shown at the bottom of the spreadsheet. The
 third shows summary data reporting the pairwise similarity data for all
 lineages. The fourth reports the environmental data used to plot Figures
 S1-S3. The fifth shows the genotypic data for each of the original P1
 individuals as analyzed by GENEPOP 4.2.Hughes and Simons 2015
 Data.xlsx
DOI: 10.5061/dryad.tt7p900
title: Data from: The impact of autotrophic versus heterotrophic nutritional pathways on colony health and wound recovery in corals

description: For animals that harbor photosynthetic symbionts within their tissues,
 such as corals, the different relative contributions of autotrophy versus
 heterotrophy to organismal energetic requirements have direct impacts on
 fitness. This is especially true for facultatively symbiotic corals, where
 the balance between host-caught and symbiont-produced energy can be
 altered substantially to meet the variable demands of a shifting
 environment. In this study, we utilized a temperate coral-algal system
 (the northern star coral, Astrangia poculata, and its photosynthetic
 endosymiont, Symbiodinium psygmophilum) to explore the impacts of
 nutritional sourcing on the host’s health and ability to regenerate
 experimentally excised polyps. For fed and starved colonies, wound healing
 and total colony tissue cover were differentially impacted by heterotrophy
 versus autotrophy. There was an additive impact of positive nutritional
 and symbiotic states on a coral’s ability to initiate healing, but a
 greater influence of symbiont state on the recovery of lost tissue at the
 lesion site and complete polyp regeneration. On the other hand, regardless
 of symbiont state, fed corals maintained a higher overall colony tissue
 cover, which also enabled more active host behavior (polyp extension) and
 endosymbiont behavior (photosynthetic ability of Symbiondinium). Overall,
 we determined that the impact of nutritional state and symbiotic state
 varied between biological functions, suggesting a diversity in energetic
 sourcing for each of these processes.
description: Wound Surface
 AreaWound surface area based
 on symbiotic state (with regards to Symbiodinium psygmophilum) and
 nutritional state (fed or starved). Values represent wound surface area
 (mm2) at the beginning and end of experimentation. Proportional difference
 is calculated with respect to initial wound size (week 0) (.csv
 file)Burmester2018_NutritionHealing.csvHealing StageStage of healing (initiation and polyp formation) of Astrangia poculata colonies with regards to symbiont state (S. psygmophilum) as well as nutritional state (fed or starved) (.csv file)Burmester2018_HealingStage.csvPhotosynthetic EfficiencyPhotosynthetic efficiency (Fv/Fm) for symbiotic and aposymbiotic colonies of A. poculata under fed and starved conditions. PAR stands for photosynthetically active radiation. (.csv file)Burmester2018_Photosynthetic Efficiency.csvColony Surface AreaProportional change in total colony surface area for tissue cover for symbiotic and aposymbiotic colonies under fed and starved conditions.Burmester2018_ColonySurfaceArea.csvBurmester2018_PolypExtensionPolyp Extension Scores for symbiotic and aposymbiotic colonies of A. poculata across time under fed and starved conditions (.xlsx file)Chlorophyll DensityApproximated chlorophyll density (ug cm-2) as determined through red-green-blue (RGB) values for symbiotic and aposymbiotic colonies of A. poculata (.xlsx file)Burmester2018_ChlorophyllDensity.xlsx
DOI: 10.5061/dryad.2n8055g
title: Data from: Exploring mechanisms and origins of reduced dispersal in island Komodo dragons

description: Loss of dispersal typifies island biotas, but the selective processes
 driving this phenomenon remain contentious. This is because selection via,
 both indirect (e.g. relaxed selection or island syndromes) and direct
 (e.g. natural selection or spatial sorting) processes may be involved, and
 no study has yet convincingly distinguished between these alternatives.
 Here we combined observational and experimental analyses of an island
 lizard, the Komodo dragon (Varanus komodoensis, the world’s largest
 lizard), to provide evidence for the actions of multiple processes that
 could contribute to island dispersal loss. In the Komodo dragon,
 concordant results from telemetry, simulations, experimental
 translocations, mark-recapture and gene flow studies indicated that
 despite impressive physical and sensory capabilities for long distance
 movement, Komodo dragons exhibited near complete dispersal restriction:
 individuals rarely moved beyond the valleys they were born/captured in.
 Importantly, lizard site-fidelity was insensitive to common agents of
 dispersal evolution (i.e. indices of risk for inbreeding, kin and
 intraspecific competition and low habitat quality) that consequently
 reduced survival of resident individuals. We suggest that direct selection
 restricts movement capacity (e.g. via benefits of spatial philopatry and
 increased costs of dispersal) alongside use of dispersal-compensating
 traits (e.g. intraspecific niche partitioning) to constrain dispersal in
 island species.
description: Jessop_dataprovides data for estimates of daily movement, exploration and spatial mark-recapture data
DOI: 10.5061/dryad.f7p18
title: Data from: Diverse phenotypic and genetic responses to short-term selection in evolving Escherichia coli populations

description: Beneficial mutations fuel adaptation by altering phenotypes that enhance
 the fit of organisms to their environment. However, the phenotypic effects
 of mutations often depend on ecological context, making the distribution
 of effects across multiple environments essential to understanding the
 true nature of beneficial mutations. Studies that address both the genetic
 basis and ecological consequences of adaptive mutations remain rare. Here,
 we characterize the direct and pleiotropic fitness effects of a collection
 of 21 first-step beneficial mutants derived from naïve and adapted
 genotypes used in a long-term experimental evolution of Escherichia coli.
 Whole-genome sequencing was able to identify the majority of beneficial
 mutations. In contrast to previous studies, we find diverse fitness
 effects of mutations selected in a simple environment and few cases of
 genetic parallelism. The pleiotropic effects of these mutations were
 predominantly positive but some mutants were highly antagonistic in
 alternative environments. Further, the fitness effects of mutations
 derived from the adapted genotypes were dramatically reduced in nearly all
 environments. These findings suggest that many beneficial variants are
 accessible from a single point on the fitness landscape, and the fixation
 of alternative beneficial mutations may have dramatic consequences for
 niche breadth reduction via metabolic erosion.
description: Supplementary Dataset 1:
 Data summary of alternative fitness metricsSummary of raw cell
 counts for the reference strain (Nai, Naf) and the mutant (Nbi, Nbf) at
 the beginning and end of each competition, along with calculations of
 growth rate difference between the two strains (Δrab), number of
 generations elapsed by the reference strain (G), selection coefficients
 (s), and Malthusian fitness (w). Raw cell counts at the end of the
 competition are multiplied by 106 to account for three days of 1:100
 dilution and growth, but selection coefficients and Malthusian fitness are
 not corrected for the marker effect, as was the case for the Malthusian
 fitness data presented in the main text.SupplementaryDataset1.xlsxSupplementaryDataset2: Summary of mutation identification and filteringSummary of all putative mutations derived from REL606 and REL1206 that were identified by breseq prior to manual filtration. Mutations that passed our manual filtration criteria are highlighted using bolded text and the justification for discarding all of the remaining mutations is presented in each respective row.SupplementaryDataset2.xlsx
DOI: 10.5061/dryad.hd45h
title: Data from: Dynamics of molecular evolution in RNA virus populations depend on sudden versus gradual environmental change

description: Understanding the dynamics of molecular adaptation is a fundamental goal
 of evolutionary biology. While adaptation to constant environments has
 been well characterized, the effects of environmental complexity remain
 seldom studied. One simple but understudied factor is the rate of
 environmental change. Here we used experimental evolution with RNA viruses
 to investigate whether evolutionary dynamics varied based on the rate of
 environmental turnover. We used whole-genome next-generation sequencing to
 characterize evolutionary dynamics in virus populations adapting to a
 sudden versus gradual shift onto a novel host cell type. In support of
 theoretical models, we found that when populations evolved in response to
 a sudden environmental change, mutations of large beneficial effect tended
 to fix early, followed by mutations of smaller beneficial effect; as
 predicted, this pattern broke down in response to a gradual environmental
 change. Early mutational steps were highly parallel across replicate
 populations in both treatments. The fixation of single mutations was less
 common than sweeps of associated “cohorts” of mutations, and this pattern
 intensified when the environment changed gradually. Additionally, clonal
 interference appeared stronger in response to a gradual change. Our
 results suggest that the rate of environmental change is an important
 determinant of evolutionary dynamics in asexual populations.
description: allele frequencies in
 virus populations over timeThis data set describes
 the frequencies of mutant alleles relative to the ancestral genome in
 Sindbis virus populations over the course of an evolution experiment.
 Virus populations were sampled at 8 time points, labeled in the table by
 experimental passage number. All virus samples were prepared and sequenced
 in duplicate. The table reports frequencies for mutant alleles that were
 detected in both technical replicates at a frequency &gt;0.01. For these
 frequencies, the mean of the two technical replicates is reported. Alleles
 are named by the position of the nucleotide in the genome and the base
 detected. Raw sequencing data used to generate this table is in the
 process of being deposited in SRA.allele_frequency_trajectories.csv
DOI: 10.5061/dryad.g5rq3
title: Data from: Correlated evolution of male and female reproductive traits drive a cascading effect of reinforcement in Drosophila yakuba

description: Selection against maladaptive hybridization can drive the evolution of
 reproductive isolation in a process called reinforcement. While the
 importance of reinforcement in evolution has been historically debated,
 many examples now exist. Despite these examples, we typically lack a
 detailed understanding of the mechanisms limiting the spread of reinforced
 phenotypes throughout a species' range. Here we address this issue in
 the fruit fly Drosophila yakuba, a species that hybridizes with its sister
 species D. santomea and is undergoing reinforcement in a well-defined
 hybrid zone on the island of São Tomé. Within this region, female D.
 yakuba show increased postmating-prezygotic (gametic) isolation towards D.
 santomea when compared with females from allopatric populations. We use a
 combination of natural collections, fertility assays, and experimental
 evolution to understand why reinforced gametic isolation in D. yakuba is
 confined to this hybrid zone. We show that, among other traits, D. yakuba
 males from sympatric populations sire fewer progeny than allopatric males
 when mated to allopatric D. yakuba females. Our results provide a novel
 example of reinforcement acting on a postmating-prezygotic trait in males,
 resulting in a cascade of reproductive isolation among conspecific
 populations.
description: R script for analyzing
 Sao Tome transect dataThis R script contains
 the code used when analyzing the "data_saotome_transect.csv"
 data table. This is the primary script used to analyze fertility of D.
 yakuba along the transect on Sao Tome.script1_transect_SaoTome.RR script used to analyze Bioko transect dataThis R script contains code used to analyze fertility along the Bioko transect.script2_transect_Bioko.RR script used to analyze experimental evolution studyThis R script contains code used to analyze fertility at the beginning and end of the experimental evolution component of our study.script3_experiment.Rdata_saotome_transectThis file contains data associated with the Sao Tome transect, including details regarding fertility of all the lines collected along this transect.data_bioko_transectData table containing fertility for lines assayed along the transect on the island of Bioko.data_exp_evolutionTable containing fertility data for the experimental populations used in the 'kill-the-hybrids' experimental evolution component of our study.data_exp_evol_means_controlsTable containing fertility data for the control populations used to compare with the experimentally evolved populations.
DOI: 10.5061/dryad.p31vn
title: Data from: Intraspecific competition and inbreeding depression: increased competitive effort by inbred males is costly to outbred opponents

description: A recent theoretical model suggests that intraspecific competition is an
 important determinant of the severity of inbreeding depression. The reason
 for this is that intraspecific competition is density dependent, leading
 to a stronger negative effect on inbred individuals if they are weaker
 competitors than outbred ones. In support of this prediction, previous
 empirical work shows that inbred individuals are weaker competitors than
 outbred ones and that intraspecific competition often exacerbates
 inbreeding depression. Here, we report an experiment on the burying beetle
 Nicrophorus vespilloides, in which we recorded the outcome of competition
 over a small vertebrate carcass between an inbred or outbred male resident
 caring for a brood and a size-matched inbred or outbred male intruder. We
 found that inbred males were more successful as intruders in taking over a
 carcass from a male resident and were injured more frequently as either
 residents or intruders. Furthermore, inbred males gained less mass during
 the breeding attempt and had a shorter adult life span than outbred males.
 Finally, successful resident males reared a substantially smaller brood
 comprised of lighter larvae when the intruder was inbred than when it was
 outbred. Our results shows that inbred males increased their competitive
 effort, thus contradicting previous work suggesting that inbred males are
 weaker competitors. Furthermore, our results shows that inbred intruders
 impose a greater cost to resident males, suggesting that outbred
 individuals can suffer fitness costs as a result of competition with
 inbred ones.
description: Data for the effects of
 inbreeding on competitive effort in Nicrophorus
 vespilloidesRichardson&Smiseth.csv
DOI: 10.5061/dryad.hb558
title: Data from: Dispersal ability and habitat requirements determine landscape-level genetic patterns in desert aquatic insects

description: Species occupying the same geographic range can exhibit remarkably
 different population structures across the landscape, ranging from highly
 diversified to panmictic. Given limitations on collecting population-level
 data for large numbers of species, ecologists seek to identify proximate
 organismal traits—such as dispersal ability, habitat preference and life
 history—that are strong predictors of realized population structure. We
 examined how dispersal ability and habitat structure affect the regional
 balance of gene flow and genetic drift within three aquatic insects that
 represent the range of dispersal abilities and habitat requirements
 observed in desert stream insect communities. For each species, we tested
 for linear relationships between genetic distances and geographic
 distances using Euclidean and landscape-based metrics of resistance. We
 found that the moderate-disperser Mesocapnia arizonensis (Plecoptera:
 Capniidae) has a strong isolation-by-distance pattern, suggesting
 migration–drift equilibrium. By contrast, population structure in the
 flightless Abedus herberti (Hemiptera: Belostomatidae) is influenced by
 genetic drift, while gene flow is the dominant force in the strong-flying
 Boreonectes aequinoctialis (Coleoptera: Dytiscidae). The best-fitting
 landscape model for M. arizonensis was based on Euclidean distance.
 Analyses also identified a strong spatial scale-dependence, where
 landscape genetic methods only performed well for species that were
 intermediate in dispersal ability. Our results highlight the fact that
 when either gene flow or genetic drift dominates in shaping population
 structure, no detectable relationship between genetic and geographic
 distances is expected at certain spatial scales. This study provides
 insight into how gene flow and drift interact at the regional scale for
 these insects as well as the organisms that share similar habitats and
 dispersal abilities.
description: Microsatellite genotype
 data for 3 aquatic insect speciesThe data set includes 3
 text files, one for each of three aquatic insect species. Each is a
 GENEPOP input file. Loci are microsatellite markers. The order of the
 populations in each file is the same as in the
 manuscript.Insect_Genotype_Data.zipThree-Species-LandGen_Data for R analysis_ABHEThree-Species-LandGen_Data for R analysis_MLPE_MEAR_GR1Three-Species-LandGen_Data for R analysis_MLPE_MEAR_GR2Three-Species-LandGen_Data for R analysis_STAEStats in R_MLPE_VanStrien_ABHER scripts for running MLPE on Abedus herberti msat data.Stats in R_MLPE_VanStrien_MEARR scripts for running MLPE on Mesocapnia arizonensis msat data.Stats in R_MLPE_VanStrien_STAER scripts for running MLPE on Boreonectes aequinoctialis msat data.
DOI: 10.5061/dryad.60659
title: Data from: Heterogeneous genomic differentiation in marine threespine sticklebacks: adaptation along an environmental gradient

description: Evolutionary divergence among populations occupying ecologically distinct
 environments can occur even in the face of on-going gene flow. However,
 the genetic underpinnings, as well as the scale and magnitude at which
 this differentiation occurs in marine habitats are not well understood. We
 investigated the patterns and degree of genomic heterogeneity in
 threespine sticklebacks (Gasterosteus aculeatus) by assessing genetic
 variability in 20 nongenic and 20 genic (associated with genes important
 for freshwater adaptation) microsatellite loci in samples collected from
 38 locations spanning the entire Baltic Sea coast to the North Sea
 boundary. Population divergence (FST ≈ 0.026) and structuring (five
 genetic clusters) was significantly more pronounced in the genic as
 compared to nongenic markers (FST ≈ 0.008; no genetic clusters). Patterns
 of divergence in the genic markers—45% of which were identified as
 outliers—correlated with local differences in salinity. Yet, a strong
 positive correlation between divergence in genic and nongenic markers, and
 their association with environmental factors suggests that adaptive
 divergence is reducing gene flow across the genome. Apart from providing a
 clear demonstration of heterogeneous genomic patterns of differentiation
 in a marine species, the results are indicative of adaptive population
 structuring across the relatively young Baltic Sea in spite of ample
 opportunities for gene flow.
description: dryadGenotypes in genepop
 3-digit format, from microsatellites described in Peichel et al. 2001 (The
 genetic architecture of divergence between threespine stickleback species.
 Nature,414, 901-905) and Shimada et al. (A high incidence of selection on
 physiologically important genes in the three-spined stickleback,
 Gasterosteus aculeatus. Molecular Biology and Evolution, 28, 181-193).
 Population codes are as follows in Table 1.