cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.72s8g4j
title: Data from: Adaptive phenotypic plasticity for life-history and less fitness-related traits

description: Organisms are faced with variable environments and one of the most common
 solutions to cope with such variability is phenotypic plasticity, a
 modification of the phenotype to the environment. These modifications are
 commonly modelled in evolutionary theories as adaptive, influencing
 ecological and evolutionary processes. If plasticity is adaptive, we would
 predict that the closer to fitness a trait is, the less plastic it would
 be. To test this hypothesis, we conducted a meta-analysis of 213 studies
 and measured the plasticity of each reported trait as a coefficient of
 variation (CV). Traits were categorised as closer to fitness -
 life-history traits (LHt) including reproduction and survival
 related-traits, and farther from fitness - non-life-history traits (N-LHt)
 including traits related to development, metabolism and physiology,
 morphology and behaviour. Our results showed, unexpectedly, that although
 traits differed in their amounts of plasticity, trait plasticity was not
 related to its proximity to fitness. These findings were independent of
 taxonomic groups or environmental types assessed. We caution against
 general expectations that plasticity is adaptive, as assumed by many
 models of its evolution. More studies are needed that test the adaptive
 nature of plasticity, and additional theoretical explorations on adaptive
 and non-adaptive plasticity are encouraged.
description: Meta-analysis from
 articles reporting phenotypic plasticity between 1987 and
 2011Data clean and ordered
 including all the selected articles. We conducted a meta-analysis on
 studies reporting reaction norms in different trait types across
 environments and species. We performed this meta-analysis investigating 24
 years of research literature on phenotypic plasticity. We selected papers
 employing the keywords “life history & morphology & plasticity”
 between 1991-2006 from all databases in Web of Knowledge (WoK-ISI) and
 between 2007-2011 from Web of Science (ISI). We set out with 583 papers in
 total, including a few studies known to us that met the criteria published
 between 1987 and 2011. From this initial set, we extracted data from 213
 studies reporting reaction norms. Data extraction from each paper included
 information from all tables, text, and figures using the software Image J.
 Quantification of the reaction norms was achieved through the computation
 of the CV of the trait expression across environments. We computed 5,885
 coefficients of variation including 211 species exposed to at least two
 and at most 11 environment levels reporting phenotypic
 plasticity.Alldata_6.csv
DOI: 10.5061/dryad.450c2v7
title: Data from: Contemporary ancestor? Adaptive divergence from standing genetic variation in Pacific marine threespine stickleback

description: Background: Populations that have repeatedly colonized novel environments
 are useful for studying the role of ecology in adaptive divergence -
 particularly if some individuals persist in the ancestral habitat. Such
 "contemporary ancestors" can be used to demonstrate the effects
 of selection by comparing phenotypic and genetic divergence between the
 derived population and their extant ancestors. However, evolution and
 demography in these "contemporary ancestors" can complicate
 inferences about the source (standing genetic variation, de novo mutation)
 and pace of adaptive divergence. Marine threespine stickleback
 (Gasterosteus aculeatus) have colonized freshwater environments along the
 Pacific coast of North America, but have also persisted in the marine
 environment. To what extent are marine stickleback good proxies of the
 ancestral condition? Results: We sequenced &gt;5800 variant loci in
 over 250 marine stickleback from eight locations extending from Alaska to
 California, and phenotyped them for platedness and body shape. Pairwise
 FST varied from 0.02 to 0.18. Stickleback were divided into five genetic
 clusters, with a single cluster comprising stickleback from Washington to
 Alaska. Plate number, Eda, body shape, and candidate loci showed evidence
 of being under selection in the marine environment. Comparisons to a
 freshwater population demonstrated that candidate loci for freshwater
 adaptation varied depending on the choice of marine populations.
 Conclusions: Marine stickleback are structured into phenotypically and
 genetically distinct populations that have been evolving as freshwater
 stickleback evolved. This variation complicates their usefulness as
 proxies of the ancestors of freshwater populations. Lessons from
 stickleback may be applied to other "contemporary
 ancestor"-derived population studies.
description: Marine stickleback
 structure fileStacks output as a
 Structure file for the "marine sites" data
 setbatch_1.struAdegenet-recognized clusters structure fileStacks output as a Structure file, for Adegenet-recognized clustersadegenet_batch_1.struMarine-freshwater structure fileStacks output as a Structure file for the marine-freshwater data setmarinefw_batch_1.struMorphological data setAmira output with coordinates for 3D landmarks, used in MorphoJ analysis.landmark_summary_withAK.txtPlate counts and EdaBasic information on each fish, including standard length, sum of plates on left and right side, sex, Eda genotype, and which part of the study it was used in.plates.xlsx
DOI: 10.5061/dryad.474j412
title: Data from: Self-limiting population genetic control with sex-linked genome editors

description: In male heterogametic species the Y chromosome is transmitted solely from
 fathers to sons, and is selected for based only on its impacts on male
 fitness. This fact can be exploited to develop efficient pest control
 strategies that use Y-linked editors to disrupt the fitness of female
 descendants. With simple population genetic and dynamic models we show
 that Y-linked editors can be substantially more efficient than other
 self-limiting strategies and, while not as efficient as gene drive
 approaches, are expected to have less impact on non-target populations
 with which there is some gene flow. Efficiency can be further augmented by
 simultaneously releasing an autosomal X-shredder construct, in either the
 same or different males. Y-linked editors may be attractive option to
 consider when efficient control of a species is desired in some locales
 but not others.
description: YLEcodeForDryadMathematic code used to generate the figures and numbers in the paper
DOI: 10.5061/dryad.3s58201
title: Data from: Chemically-mediated sexual signals restrict hybrid speciation in a flea beetle

description: The evolution of reproductive isolation following hybridization is a major
 obstacle that may limit the prevalence of hybrid speciation among specific
 groups of organisms. Here we use a flea beetle system to offer a
 behavioral hypothesis for why there are so few examples of homoploid
 hybrid speciation among insects. Specifically, we examined cuticular
 hydrocarbon (CHC) mating signals and mate choice decisions of Altica
 fragariae and A. viridicyanea to test whether the signals produced by
 hybrids cause prezygotic reproductive isolation. Although hybrids of A.
 fragariae and A. viridicyanea had unique CHC profiles as compared to the
 parental species, mate choice trials indicated that these differences were
 insufficient to prevent gene flow between hybrids and parental species. We
 found that mate choice decisions and CHC signals were not correlated.
 Considering the ubiquity of CHC signaling molecules in insects, we propose
 that decoupling of CHC signals and mate choice may be a general mechanism
 limiting hybrid speciation in insects.
description: Table
 S1Table S1. Composition of
 the cuticular hydrocarbons (CHCs) of the 14 genetic lines of Altica.
 Relative peak areas (% total peak area), mean ± SD. “tr”, trace; “\”, not
 detected in all of them. Altica fragariae (AF), A. viridicyanea (AV), F1
 hybrids (AV♀×AF♂), F2 hybrids (F1♀×F1♂), backcross BC1 (AV♀×F1♂),
 backcross BC2 (AF♀×F1♂), and backcross BC3 (F1♀×AF♂).Figure
 S1Figure S1 Discriminant
 analysis of the cuticular hydrocarbons of A. viridicyanea (AV) and
 backcross BC1 (AV♀×F1♂).Fig
 S1.tifFigure
 S2Figure S2 Discriminant
 analysis of the cuticular hydrocarbons of two backcrosses BC2 (AF♀×F1♂)
 and BC3 (F1♀×AF♂).Fig
 S2.tifFigure
 S3Figure S3 Discriminant
 analysis of relative amounts of cuticular hydrocarbons of 14 Altica from
 seven genetic lines. Altica fragariae (AF), A. viridicyanea (AV), F1
 hybrids (AV♀×AF♂), F2 hybrids (F1♀×F1♂), backcross BC1 (AV♀×F1♂),
 backcross BC2 (AF♀×F1♂), and backcross BC3 (F1♀×AF♂).Fig
 S3.tif
DOI: 10.5061/dryad.1fp7830
title: Data from: How to quantify (the response to) sexual selection on traits

description: Natural selection operates via fitness components like mating success,
 fecundity and longevity, which can be understood as intermediaries in the
 causal process linking traits to fitness. Sexual selection occurs when
 traits influence mating or fertilisation success, which, in turn,
 influences fitness. We show how to quantify both these steps in a single
 path analysis, leading to better estimates of the strength of sexual
 selection. Our model controls for confounding variables, such as body size
 or condition, when estimating the relationship between mating and
 reproductive success. Correspondingly, we define the Bateman gradient and
 the Jones index using partial rather than simple regressions, which better
 captures how they are commonly interpreted. The model can be applied both
 to purely phenotypic data and to quantitative genetic parameters estimated
 using information on relatedness. The phenotypic approach breaks down
 selection differentials into a sexually selected and a ‘remainder’
 component. The quantitative genetic approach decomposes the estimated
 evolutionary response to selection analogously. We apply our method to
 analyse sexual selection in male dusky pipefish, Syngnathus floridae, and
 in two simulated datasets. We highlight conceptual and statistical
 limitations of previous path-based approaches, which can lead to
 substantial misestimation of sexual selection.
description: FatSexyFecund-DataData for the worked example 'Fat, sexy and fecund' from the main text (see also the associated R code)FatSexyFecund-CodeR code for the worked example 'Fat, sexy and fecund' from the main text (see also the associated data file)Pipefish-DataData for the worked example 'Size selection in male pipefish' from the main text (see also the associated R code). Many thanks to Kenyon Mobley and Adam Jones for generously sharing this data (see main text for references to the original publications).Pipefish-CodeR code for the worked example 'Size selection in male pipefish' from the main text (see also the associated data file)CheatingVsCaring-RelTraitDataTrait data for the worked example 'Cheating vs caring' from the Supporting Information (see also the associated pedigree data and R code)CheatingVsCaring-PedigreePedigree data for the worked example 'Cheating vs caring' from the Supporting Information (see also the associated trait data and R code)CheatingVsCaring-CodeR code for the worked example 'Cheating vs caring' from the Supporting Information (see also the associated pedigree and trait data files). The code for estimating additive genetic (co)variances requires the commercial package ASReml-R. The rest of the code requires only freely available packages.
DOI: 10.5281/zenodo.18388954
title: DATASET FOR EVALUATING CULTURAL TRANSMISSION PROCESSES FROM MESOLITHIC GEOMETRIC PROJECTILE MODELS USING EXPERIMENTAL PROTOCOLS

description: The dataset contains four TPS files (TC trapezoid, TC triangle, CG G1, and CG G2) with the coordinates of 260 geometric microliths from an experimental project. These microliths were fabricated using two learning models (linear transmission chain and constant group). The dataset also includes the R code used for the morphometric analyses. The data allows for an evaluation of the similarities and differences in morphometric variation depending on each learning model.
DOI: 10.5281/zenodo.18388955
title: DATASET FOR EVALUATING CULTURAL TRANSMISSION PROCESSES FROM MESOLITHIC GEOMETRIC PROJECTILE MODELS USING EXPERIMENTAL PROTOCOLS

description: The dataset contains four TPS files (TC trapezoid, TC triangle, CG G1, and CG G2) with the coordinates of 260 geometric microliths from an experimental project. These microliths were fabricated using two learning models (linear transmission chain and constant group). The dataset also includes the R code used for the morphometric analyses. The data allows for an evaluation of the similarities and differences in morphometric variation depending on each learning model.
DOI: 10.5061/dryad.m7d9414
title: Data from: Contrasting fine-root production, survival and soil CO2 efflux in pine and poplar plantations

description: Tree root activity, including fine-root production, turnover and metabolic
 activity are significant components of forest productivity and nutrient
 cycling. Differences in root activity among forest types are not well
 known. A 3-year study was undertaken in red pine (Pinus resinosa Ait.) and
 hybrid poplar (Populus tristis X P. balsamifera cv `Tristis no. 1')
 plantations to compare belowground root dynamics. We measured fine-root
 production, mortality and standing crop, as well as soil CO2 efflux. Pine
 fine-root production was only 2.9% of that of poplar during three years;
 85 pine roots were observed in minirhizotron tubes compared with 4088
 poplar roots. Live-root density oscillated seasonally for both species
 with late winter minimum and autumn maximum. Poplar reached constant
 maximum live-root length within the first growing season, but pine
 continued to increase observed fine-root length for three growing seasons.
 Within the first 100 days following initial appearance, 22% of the pine
 roots disappeared and 38% of the poplar roots disappeared. Median
 fine-root longevity of pine was 291 days compared with 149 days for poplar
 roots. Fine-root longevity increased with depth in the soil, and was
 greater for roots with initial diameter &gt;0.5 mm. The probability of
 poplar root death from late February to May was more than three times that
 in any other season, regardless of root age. Despite the greater poplar
 root production and live-root length, fine-root biomass and soil CO2
 efflux was greater in pine. Greater metabolic activity in the pine stand
 may be due to greater fine-root biomass or greater heterotrophic
 respiration.
description: Fine-root production,
 mortality and standing cropThe worksheet titled
 "ProdMortCrop" includes average species fine-root production,
 mortality and standing crop by date. The worksheet titled "Info"
 includes data column descriptions.ProdMortCrop.xlsfine-root lifespanThe worksheet titled "Survival" includes lifespan for individual roots appearing in a specific frame of minirhizotron tubes. Each root includes appearance date, disappearance date (except censored), depth, appearance length and appearance diameter information. The worksheet titled "Info" includes data column descriptions.SURVIVAL.XLSMSU ROOTS outputIndividual root observations including root depth, length and diameter over more than two years. The "Tristis0996" worksheet includes data for hybrid poplar (Populus tristis X P. balsamifera cv. ‘Tristis no. 1’). The "PINE1196" worksheet includes data for pine (Pinus resinosa). The "Info" worksheet includes data column descriptions.Soil respirationThe data in the "RS.wk1" worksheet includes soil respiration collected at each minirhizotron tube during root observation sessions. The "mean" worksheet includes averages and standard errors of the four measurement locations presented in "RS.wk1".RSOIL.xls
DOI: 10.5061/dryad.n1804pf
title: Data from: Fencing solves human‐wildlife conflict locally but shifts problems elsewhere: a case study using functional connectivity modelling of the African elephant

description: 1. Fencing is one of the commonest methods for mitigating human-wildlife
 conflicts. At the same time, fencing is considered to be of one of the
 most pressing emerging threats to conservation globally. Although fences
 act as barriers and eventually can cause population isolation and
 fragmentation, it is challenging to quantitatively predict the possible
 consequences fences have for wildlife. 2. Here, we model how fencing
 designed to mitigate human-elephant conflict (HEC) on the Borderlands
 between Kenya and Tanzania will affect functional connectivity and
 movement corridors for African elephants. Specifically, we (1) model
 functional landscape connectivity integrating natural and anthropogenic
 factors; (2) predict seasonal movement corridors used by elephants in
 non-protected areas; and (3) evaluate whether fencing in one area can
 potentially intensify human-wildlife conflicts elsewhere. 3. We used GPS
 movement and remote sensing data to develop monthly step-selection
 functions to model functional connectivity. For future scenarios, we used
 a currently ongoing fencing project designed for human-elephant conflict
 mitigation within the study area. We modelled movement corridors using
 least-cost path and circuit theory methods, evaluated their predictive
 power and quantified connectivity changes resulting from the planned
 fencing. 4. Our results suggest that fencing will not cause landscape
 fragmentation and will not change functional landscape connectivity
 dramatically. However, fencing will lead to a loss of connectivity locally
 and will increase the potential for HEC in new areas. We estimated that
 wetlands important for movement corridors will be more intensively used by
 the elephants, which may also cause problems of overgrazing. Seasonal
 analysis highlighted an increasing usage of non-protected lands in the dry
 season and equal importance of the pinch point wetlands for preserving
 overall function connectivity. 5. Synthesis and applications. Fencing is a
 solution to small-scale HEC problems, but will not solve the issue at a
 broader scale. Moreover, our results highlight that it may intensify the
 conflicts and overuse of habitat patches in other areas, thereby negating
 any conservation benefits. If fencing is employed on a broader scale, then
 it is imperative that corridors are integrated within the protected area
 network to ensure local connectivity of affected species.
description: Movement corridors
 (current and future scenario)Predictive current flow
 surfaces for current and future fencing scenarios. Th surfaces were
 modeled based on step-selection functions resistance surfaces and using
 Linkage Mapper ArcGIS 10.5.1monthly_ssf_circ_corr_500_fence100.rarCorridors animationAnimation for the monthly predicted movement corridors (current and future fencing scenarios)Media S1. Corridors animation.mp4
DOI: 10.5061/dryad.p9m57n7
title: Data from: High-density cultivation of microalgae continuously fed with unfiltered water from a recirculating aquaculture system

description: Water from recirculating aquaculture systems (RAS) has been shown to be a
 suitable growth medium for microalgae and their cultivation can,
 therefore, be used to reduce RAS emissions. However, while efficient
 wastewater treatment is possible, the nutrient content of RAS water limits
 attainable microalgae biomass densities to 1–2 g l−1 at best, which
 requires frequent harvesting of microalgae. We have taken advantage of the
 constant evaporation of water from an open thin-layer photobioreactor
 (200 l volume, 18 m2 illuminated surface, artificial supply of CO2) to
 continuously add water from RAS to a microalgae culture and thereby
 provide nutrients for continued growth while evaporating all water. To
 test for a possible inhibitory effect of RAS water on microalgae growth,
 components of mineral medium were omitted stepwise in subsequent
 cultivations and replaced by RAS water as the only source of nutrients.
 This approach showed that microalgae can be grown successfully for up to
 three weeks in RAS water without additional nutrients and that high
 (20 g l−1) biomass densities can be attained. While growth in wastewater
 did not reach productivities measured in mineral medium, analysis of
 growth data suggested that this reduction was not due to an inhibitory
 effect of the RAS water but due to an insufficient supply rate of
 nutrients, even though RAS water contained up to 158 mg l−1 NO3-N. It is,
 therefore, concluded that this method can be used to fully treat the
 wastewater discharge of a RAS. Furthermore, because both water evaporation
 from and microalgae growth in the photobioreactor correlated positively
 with each other due to their shared dependency on solar radiation, supply
 of nutrients continuously adjusts to changes in demand. It is estimated
 that the area of a photobioreactor required to treat all emissions of a
 RAS requires approximately 6.5 times the area of the latter.
description: Raw data for cultivation
 no. 1Run140514.csvRaw data of cultivation no. 2Run140708.csvRaw data for cultivation no. 3Run140722.csvRaw data for cultivation no. 4Run140814.csvRaw data for cultivation no. 5Run140902.csvRaw data of cultivation no. 6Run140619.csvRaw data for cultivation no. 7Run150624.csvRaw data for cultivation no. 8Run150817.csvRaw data for cultivation no. 9Run150909.csvLocal sunrise and sunset datasunrise2014.csvR script to make all raw data ready for analysisThe script requires the raw data in csv format and data on sunrise/sunset times. The script truncates the data correctly, removes false values, renames variables and saves all data as all.Data.RData1_prepare_data.RR script to carry out statistical analyses and produce figuresThis r script opens the file all.Data.RData (produced via the script 1_prepare_data.R) and conducts all statistical analyses and figures.2_analyse_data.R
DOI: 10.5061/dryad.2r984j6
title: Data from: Insights on decomposition process of c-C4F8 and c-C4F8/N2 mixture as substitutes for SF6

description: In recent years, many scholars have carried out studies on c-C4F8 and its
 gas mixture and found it has potential to be used as an
 environment-friendly insulating medium to replace SF6 in medium-voltage
 equipment. In this paper, the c-C4F8 and c-C4F8/N2 gas mixture models were
 built to study its decomposition process by the combination of reactive
 molecular dynamics method and density functional theory. The yield of the
 main decomposition products, the reaction pathways and enthalpy under
 different temperatures were explored. It was found that the decomposition
 of c-C4F8/N2 mainly produces CF2, F, CF3, CF, C, CF4 and C2F4. c-C4F8 can
 decompose to C2F4 by absorbing 43.28 kcal/mol, which is the main
 decomposition path and this process easily occurs under high temperature.
 There is a dynamic equilibrium process among the various produced
 radicals, which ensures the insulation performance of system to a certain
 extent. The decomposition performance of c-C4F8/N2 mixture is better than
 that of pure c-C4F8 at the same temperature. Relevant results provide
 guidance for engineering application of the c-C4F8/N2 gas mixture.
description: C4F8ReaxFF results of pure
 c-C4F8 system.C4F8/N2ReaxFF results of c-C4F8/N2 system.withN2.xlsxReaxFF-MD force field fileReaxFF force file.ff