cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.v5978
title: Data from: Is biodiversity energy-limited or unbounded? A test in fossil and modern bivalves

description: The quantity of biomass in an ecosystem is constrained by energy
 availability. It is less clear, however, how energy availability
 constrains taxonomic and functional diversity. Competing models suggest
 biodiversity is either resource-limited or far from any bound. We test the
 hypothesis that functional diversity in marine bivalve communities is
 constrained by energy availability, measured as particulate organic carbon
 (POC) flux, in the modern oceans. We find that POC flux predicts the
 relative prevalence of ecological modes in both the Atlantic and Pacific
 oceans. Moreover, the associations of ecological modes with POC fluxes are
 similar between the Atlantic and Pacific despite being based on
 independent sets of species, indicating a direct causal relationship. We
 then use the relationship between POC flux and the prevalence of
 functional groups in the modern to test the hypothesis that the trend of
 increasing functional diversity in bivalves across the past 500 million
 years has occurred in response to increased POC flux. We find no evidence
 that the earliest appearing modes of life are preferentially associated
 with low POC environments or that the mean POC flux experienced by marine
 bivalves has increased across geological time. To reconcile the close
 association between ecological mode and POC flux in the modern oceans with
 the lack of evidence for increasing POC fluxes across time, we propose
 that POC flux has not increased substantially over time but, rather, the
 increase in bivalve functional diversity enabled bivalves to become more
 abundant, to occupy a broader range of environments, and to capture a
 greater fraction of the total POC flux. The results here suggest at
 geographic scale of oceans and through geologic time bivalve diversity was
 not bounded by food availability.
description: Pacific and Atlantic
 Marine Bivalve Range and SizesDataset of Pacific and
 Atlantic marine bivalve data gathered from published literature including
 biogeographic range (latitude, longitude, depth), body size, taxonomy, and
 an estimate of particulate organic carbon over the species geographic
 range.McClainetal_modern_bivalves.csvAtlantic Deep-Sea BivalvesBiogeographic and ecological data for deep-sea bivalves. Location data based on Allen (2008). Read McClain et al. (2011) for more details (doi: 10.1098/rspb.2011.2166)species2.csvEcological modes of fossil bivalve generaThis data set contains ecological modes of life assigned to fossil bivalve genera with stage-level resolution first and last appearance dates.bivalve_modes_dataset.csv
DOI: 10.5061/dryad.7s393
title: Data from: The genomics of incompatibility factors and sex determination in hybridizing species of Cottus (Pisces)

description: Cottus rhenanus and Cottus perifretum have formed hybrid lineages and
 narrow hybrid zones that can be best explained through the action of
 natural selection. However, the underlying selective forces as well as
 their genomic targets are not well understood. This study identifies
 genomic regions in the parental species that cause hybrid
 incompatibilities and tests whether these manifest in a sex-specific
 manner to learn about processes that affect natural hybridization in
 Cottus. Interspecific F2 crosses were analyzed for 255 markers for genetic
 mapping and to detect transmission distortion as a sign for genetic
 incompatibilities. The Cottus map consists of 24 linkage groups with a
 total length of 1575.4 cM. A male heterogametic (XY) sex determination
 region was found on different linkage groups in the two parental species.
 Genetic incompatibilities were incomplete, varied among individuals and
 populations and were not associated with the heterogametic sex. The
 variance between populations and individuals makes it unlikely that there
 are species-specific incompatibility loci that could affect the gene pool
 of natural hybrids in a simple and predictable way. Conserved synteny with
 sequenced fish genomes permits to genetically study the Cottus genome
 through the transfer of genomic information from the model fish species.
 Homology relationships of candidate genomic regions in Cottus indicate
 that sex determination is not based on the same genomic regions found in
 other fish species. This suggests a fast evolutionary turnover of the
 genetic basis of sex determination that, together with the small size of
 the heterogametic regions, may contribute to the absence of fitness
 effects related to the Haldane’s rule.
description: Table S1-Cheng et
 al.-HeredityLoci included in the
 consensus map for Cottus with locus name, segregating alleles that
 distinguished C.perifretum and C. rhenanus populations, the sequence from
 which the marker was developed and that was used for BLAST searches
 (variable position marked in square brackets).Table S4-Cheng et
 al.-HeredityGenotype data for QTL
 mapping of sex determination regions in Cottus as well as additional loci
 not included in the genetic map. Sex was coded as a binary character:
 male-0; female-1. Different types of crosses are separated in different
 sheets.SexQTL-Cheng et
 al.-Heredity.xlsx
DOI: 10.5061/dryad.6sf28
title: Data from: Indirect effects drive evolutionary responses to global change

description: Anthropogenic environmental changes pose significant threats to plant and
 animal populations. These changes also may affect the evolution of natural
 populations either directly or indirectly by altering the outcome of
 species interactions that are important drivers of evolution. This latter
 indirect pathway may be especially important for evolutionary responses to
 elevated atmospheric CO2 concentrations (eCO2), which appear to have
 minimal direct effects on plant evolution but have large effects on
 interspecific interactions, such as competition. We manipulated
 competitive and CO2 environments of experimental Arabidopsis thaliana
 populations to test whether eCO2 alters evolutionary trajectories
 indirectly by altering selection imposed by competitors. We found that
 interspecific competition increased selection on growth traits, reduced
 heritabilities, and altered genetic covariances between traits and that
 the magnitude of these effects depended upon the CO2 environment. Although
 eCO2 had minimal direct effects on evolutionary processes, eCO2 typically
 reduced the strength of selection imposed by competitors and, therefore,
 relaxed selection on plant traits when competitors were present. Our
 results indicate that global changes may affect plant evolution indirectly
 by altering competitive interactions and underscore the importance of
 conducting research in natural communities when attempting to predict
 population responses to global change.
description: Lau et al. 2014 data for
 phenotypic analysesThis csv file provides
 both the raw data on plant phenotypes and standardized trait values used
 in the analyses presented in the main text of Lau et al.
 2014.Lau et
 al. 2014 data for phenotypic selection
 analysis.csvLau et al. data for
 phenotypic selection analyses standardized across
 treatmentsThis dataset includes
 the raw phenotypic values, but also trait values that are standardized
 based on the mean trait values of all individuals included in the
 experiment (averaged across all CO2 x competition treatments). Results
 from these analyses are presented in Supporting Information (Tables S1-S5)
 in Lau et al. 2014.
DOI: 10.5061/dryad.962dt
title: Data from: Colonization history, host distribution, anthropogenic influence and landscape features shape populations of white pine blister rust, an invasive alien tree pathogen

description: White pine blister rust is caused by the fungal pathogen Cronartium
 ribicola J.C. Fisch (Basidiomycota, Pucciniales). This invasive alien
 pathogen was introduced into North America at the beginning of the 20th
 century on pine seedlings imported from Europe and has caused serious
 economic and ecological impacts. In this study, we applied a population
 and landscape genetics approach to understand the patterns of introduction
 and colonization as well as population structure and migration of C.
 ribicola. We characterized 1,292 samples of C. ribicola from 66 geographic
 locations in North America using single nucleotide polymorphisms (SNPs)
 and evaluated the effect of landscape features, host distribution, and
 colonization history on the structure of these pathogen populations. We
 identified eastern and western genetic populations in North America that
 are strongly differentiated. Genetic diversity is two to five times higher
 in eastern populations than in western ones, which can be explained by the
 repeated accidental introductions of the pathogen into northeastern North
 America compared with a single documented introduction into western North
 America. These distinct genetic populations are maintained by a barrier to
 gene flow that corresponds to a region where host connectivity is
 interrupted. Furthermore, additional cryptic spatial differentiation was
 identified in western populations. This differentiation corresponds to
 landscape features, such as mountain ranges, and also to host
 connectivity. We also detected genetic differentiation between the
 pathogen populations in natural stands and plantations, an indication that
 anthropogenic movement of this pathogen still takes place. These results
 highlight the importance of monitoring this invasive alien tree pathogen
 to prevent admixture of eastern and western populations where different
 pathogen races occur.
description: Cronartium ribicola SNP
 genalex SNPsAn excel spreadsheet
 containing genotypes of 1292 Cronartium ribicola individuals genotyped at
 31 SNPs using sequenom. The data are arranged for processing in Genalex
 http://biology-assets.anu.edu.au/GenAlEx/Welcome.htmlDryad_Genalex.xlsxCronartium ribicola ArlequinCronartium ribicola Arlequin file comprising genotypes at 31 SNP loci for 1292 individuals sampled across 66 populations in North America and separated into eastern and western regions for AMOVA analysesCR_1292_region.arp
DOI: 10.5061/dryad.dg4hq
title: Data from: Detecting short spatial scale local adaptation and epistatic selection in climate-related candidate genes in European beech (Fagus sylvatica) populations

description: Detecting signatures of selection in tree populations threatened by
 climate change is currently a major research priority. Here, we
 investigated the signature of local adaptation over a short spatial scale
 using 96 European beech (Fagus sylvatica L.) individuals originating from
 two pairs of populations on the northern and southern slopes of Mont
 Ventoux (south-eastern France). We performed both single and multilocus
 analysis of selection based on 53 climate-related candidate genes
 containing 546 SNPs. FST outlier methods at the SNP level revealed a weak
 signal of selection, with three marginally significant outliers in the
 northern populations. At the gene level, considering haplotypes as
 alleles, two additional marginally significant outliers were detected, one
 on each slope. To account for the uncertainty of haplotype inference, we
 averaged the Bayes factors over many possible phase reconstructions.
 Epistatic selection offers a realistic multilocus model of selection in
 natural populations. Here, we used a test suggested by Ohta based on the
 decomposition of the variance of linkage disequilibrium. Overall
 populations, 0.23% of the SNP pairs (haplotypes) showed evidence of
 epistatic selection, with nearly 80% of them being within genes. One of
 the between gene epistatic selection signals arose between an FST outlier
 and a nonsynonymous mutation in a drought response gene. Additionally, we
 identified haplotypes containing selectively advantageous allele
 combinations which were unique to high or low elevations and northern or
 southern populations. Several haplotypes contained nonsynonymous mutations
 situated in genes with known functional importance for adaptation to
 climatic factors.
description: Csillery_Lalague_etal_rawSNPdataThis file includes the raw SNP data (with a rate of 24.6% missing data)Csillery_Lalague_etal_imputedSNPdataThis file includes the imputed SNP data (with a rate of 12.1% missing data instead of 24.6% after using PHASE software)Csillery_Lalague_etal_phasedSNPdataThis file includes the phased SNP data (with a rate of 12.4% missing data instead of 24.6% after using PHASE software)
DOI: 10.15482/usda.adc/29619260
title: Data from: Investigating the Benefits of Integrating Rainbow Trout (<i>Oncorhynchus mykiss</i>) and Lettuce (<i>Lactuca sativa</i>) Cultivation in California

description: Global food production, both aquatic and terrestrial, is rife with sustainability issues. Aquaculture is a rapidly growing industry that is on track to surpass wild-caught fishery production by 2030. The integration of aquaculture and agriculture systems could help to reduce some of their respective and shared environmental issues. Integrated Aquaculture–Agriculture (IAA) has been shown to provide a variety of benefits to both aquaculture and agriculture including increased system water use efficiency (WUE), a reduction in fertilizer use, and increases in total farm yield and resilience. This study was performed to examine the potential for rainbow trout aquaculture effluent to improve the yield, nutrient composition, and WUE of lettuce, as well as act as a partial fertilizer replacement. We used four irrigation treatments throughout the experiment: city water, aquaculture effluent, city water with added organic fertilizer, and aquaculture effluent with added organic fertilizer. Throughout the trial, there were some issues of herbivory in the growing plot, but overall, the lettuce receiving city water with organic fertilizer (30. ± 3.4 g/plant) showed significantly higher fresh biomass than effluent treatments (18 ± 1.4 g/plant and 17 ± 2.9 g/plant) at the end of the trial. We did not detect any significant differences among treatments in the macro- and micronutrients of the lettuce shoots and roots. However, the WUE of effluent treatments (4.4 ± 0.030 kg/m<sup>3</sup> and 1.0 ± 0.070 kg/m<sup>3</sup>) was greater than that of organic fertilizer (0.28 ± 0.050 kg/m<sup>3</sup>) and control treatments (0.23 ± 0.040 kg/m<sup>3</sup>). The results indicate that adopting IAA in California could improve statewide WUE and conserve water for sustainable agricultural production.<br>This data submission contains the data collected and used to calculate the results of the above paper. This consists of data on nutrient analysis, biomass, and water use efficiency.
DOI: 10.15482/usda.adc/29619260.v1
title: Data from: Investigating the Benefits of Integrating Rainbow Trout (<i>Oncorhynchus mykiss</i>) and Lettuce (<i>Lactuca sativa</i>) Cultivation in California

description: Global food production, both aquatic and terrestrial, is rife with sustainability issues. Aquaculture is a rapidly growing industry that is on track to surpass wild-caught fishery production by 2030. The integration of aquaculture and agriculture systems could help to reduce some of their respective and shared environmental issues. Integrated Aquaculture–Agriculture (IAA) has been shown to provide a variety of benefits to both aquaculture and agriculture including increased system water use efficiency (WUE), a reduction in fertilizer use, and increases in total farm yield and resilience. This study was performed to examine the potential for rainbow trout aquaculture effluent to improve the yield, nutrient composition, and WUE of lettuce, as well as act as a partial fertilizer replacement. We used four irrigation treatments throughout the experiment: city water, aquaculture effluent, city water with added organic fertilizer, and aquaculture effluent with added organic fertilizer. Throughout the trial, there were some issues of herbivory in the growing plot, but overall, the lettuce receiving city water with organic fertilizer (30. ± 3.4 g/plant) showed significantly higher fresh biomass than effluent treatments (18 ± 1.4 g/plant and 17 ± 2.9 g/plant) at the end of the trial. We did not detect any significant differences among treatments in the macro- and micronutrients of the lettuce shoots and roots. However, the WUE of effluent treatments (4.4 ± 0.030 kg/m<sup>3</sup> and 1.0 ± 0.070 kg/m<sup>3</sup>) was greater than that of organic fertilizer (0.28 ± 0.050 kg/m<sup>3</sup>) and control treatments (0.23 ± 0.040 kg/m<sup>3</sup>). The results indicate that adopting IAA in California could improve statewide WUE and conserve water for sustainable agricultural production.<br>This data submission contains the data collected and used to calculate the results of the above paper. This consists of data on nutrient analysis, biomass, and water use efficiency.
DOI: 10.5061/dryad.2533p
title: Data from: Evolution of Drosophila resistance against different pathogens and infection routes entails no detectable maintenance costs

description: Pathogens exert a strong selective pressure on hosts, entailing host
 adaptation to infection. This adaptation often affects negatively other
 fitness-related traits. Such trade-offs may underlie the maintenance of
 genetic diversity for pathogen resistance. Trade-offs can be tested with
 experimental evolution of host populations adapting to parasites, using
 two approaches: (1) measuring changes in immunocompetence in
 relaxed-selection lines and (2) comparing life-history traits of evolved
 and control lines in pathogen-free environments. Here, we used both
 approaches to examine trade-offs in Drosophila melanogaster populations
 evolving for over 30 generations under infection with Drosophila C Virus
 or the bacterium Pseudomonas entomophila, the latter through different
 routes. We find that resistance is maintained after up to 30 generations
 of relaxed selection. Moreover, no differences in several classical
 life-history traits between control and evolved populations were found in
 pathogen-free environments, even under stresses such as desiccation,
 nutrient limitation, and high densities. Hence, we did not detect any
 maintenance costs associated with resistance to pathogens. We hypothesize
 that extremely high selection pressures commonly used lead to the
 disproportionate expression of costs relative to their actual occurrence
 in natural systems. Still, the maintenance of genetic variation for
 pathogen resistance calls for an explanation.
description: Figure1B_RelaxedSelectionFigure1C_LastGenFigure2A_ReproductionFigure2B_DevTimeFigure3A_StarvationFigure3B_DessicationFigure4A_FoodSurvivalFigure4B_FoodDtimeFigure4C_CompetitionFigureS1_ReproInfection
DOI: 10.5061/dryad.8jn67
title: Data from: Physiological plasticity and local adaptation to elevated pCO2 in calcareous algae: an ontogenetic and geographic approach

description: To project how ocean acidification will impact biological communities in
 the future, it is critical to understand the potential for local
 adaptation and the physiological plasticity of marine organisms throughout
 their entire life cycle, as some stages may be more vulnerable than
 others. Coralline algae are ecosystem engineers that play significant
 functional roles in oceans worldwide, and are considered vulnerable to
 ocean acidification. Using different stages of coralline algae, we tested
 the hypothesis that populations living in environments with higher
 environmental variability and exposed to higher levels of pCO2 would be
 less affected by high pCO2 than populations from a more stable environment
 experiencing lower levels of pCO2. Our results show that spores are less
 sensitive to elevated pCO2 than adults. Spore growth and mortality were
 not affected by pCO2 level, however elevated pCO2 negatively impacted the
 physiology and growth rates of adults, with stronger effects in
 populations that experienced both lower levels of pCO2 and lower
 variability in carbonate chemistry, suggesting local adaptation.
 Differences in physiological plasticity and the potential for adaptation
 could have important implications for the ecological and evolutionary
 responses of coralline algae to future environmental changes.
description: Physiology_Corallina
 AdultsData set includes net
 photosynthesis, gross photosynthesis and respiration of Corallina
 vancouveriensis from four different sites in California and exposed to two
 different pCO2 levels.Physiology_Corallina.xlsxPigments Corallina AdultsData set includes pigment content of Corallina vancouveriensis from four different sites in California and exposed to two different pCO2 levels.pigments-2.xlsRelative Growth Rate Corallina AdultsData set includes relative growth rate of Corallina vancouveriensis from four different sites in California and exposed to two different pCO2 levels.Relative_growth_rate-2.xlsMortaility_Corallina_SporesData set includes mortality of spores Corallina vancouveriensis from four different sites in California and exposed to two different pCO2 levels.sporemortality_allsites.xlsxGrowth Corallina SporesData set includes growth of Corallina vancouveriensis from four different sites in California and exposed to two different pCO2 levels.Spore size for Dryad.xlsx
DOI: 10.5061/dryad.n571m
title: Data from: Taxonomic challenges in freshwater fishes: a mismatch between morphology and DNA barcoding in fish of the north-eastern part of the Congo basin

description: This study evaluates the utility of DNA barcoding to traditional
 morphology-based species identifications for the fish fauna of the
 north-eastern Congo basin. We compared DNA sequences (COI) of 821 samples
 from 206 morphologically identified species. Best match, best close match
 and all species barcoding analyses resulted in a rather low identification
 success of 87.5%, 84.5% and 64.1%, respectively. The ratio
 ‘nearest-neighbour distance/maximum intraspecific divergence’ was lower
 than 1 for 26.1% of the samples, indicating possible taxonomic problems.
 In ten genera, belonging to six families, the number of species inferred
 from mtDNA data exceeded the number of species identified using
 morphological features; and in four cases indications of possible synonymy
 were detected. Finally, the DNA barcodes confirmed previously known
 identification problems within certain genera of the Clariidae, Cyprinidae
 and Mormyridae. Our results underscore the large number of taxonomic
 problems lingering in the taxonomy of the fish fauna of the Congo basin
 and illustrate why DNA barcodes will contribute to future efforts to
 compile a reliable taxonomic inventory of the Congo basin fish fauna.
 Therefore, the obtained barcodes were deposited in the reference barcode
 library of the Barcode of Life Initiative.
description: COI barcodes of fish
 from the Congo basin_MER-15-0105Microsoft Excel Comma
 Separated Values file with COI barcodes of fish captured in the
 north-eastern Congo basin, more specifically in the main channel of the
 Middle and Upper Congo River, the Lomami, the Lobaye, the Itimbiri, the
 Aruwimi, the Ituri, the Epulu, the Maiko and the Loboya rivers. &gt;Unique
 sequence number [organism=organism name] River Nucleotide
 alignmentNeighbour Joining tree
 COI barcodes of fish from the Congo basin_MER-15-0105Neighbour Joining tree
 based on COI barcodes of fish captured in the north-eastern Congo basin,
 more specifically in the main channel of the Middle and Upper Congo River,
 the Lomami, the Lobaye, the Itimbiri, the Aruwimi, the Ituri, the Epulu,
 the Maiko and the Loboya rivers (Democratic Republic of the Congo). Branch
 lengths are shown; 100 bootstrap replications were used; tree was produced
 in MEGA 6.06.