cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.4p7gk
title: Data from: Genome-wide association study of Arabidopsis thaliana identifies determinants of natural variation in seed oil composition

description: The renewable source of highly reduced carbon provided by plant
 triacylglycerols (TAGs) fills an ever increasing demand for food,
 biodiesel, and industrial chemicals. Each of these uses requires different
 compositions of fatty acid proportions in seed oils. Identifying the genes
 responsible for variation in seed oil composition in nature provides
 targets for bioengineering fatty acid proportions optimized for various
 industrial and nutrition goals. Here, we characterized the seed oil
 composition of 391 world-wide, wild accessions of Arabidopsis thaliana,
 and performed a genome-wide association study (GWAS) of the 9 major fatty
 acids in the seed oil and 4 composite measures of the fatty acids. Four to
 19 regions of interest were associated with the seed oil composition
 traits. Thirty-four of the genes in these regions are involved in lipid
 metabolism or transport, with 14 specific to fatty acid synthesis or
 breakdown. Eight of the genes encode transcription factors. We have
 identified genes significantly associated with variation in fatty acid
 proportions that can be used as a resource across the Brassicaceae.
 Two-thirds of the regions identified contain candidate genes that have
 never been implicated in lipid metabolism and represent potential new
 targets for bioengineering.
description: TableS1List of the natural accessions of Arabidopsis thaliana used in this study with collection locations and accession identifiers supplied by The Arabidopsis Information Resource (TAIR).TableS2Association mapping results of the top 100 SNPs for each trait including P-values, negative log transformed P-values, FDR corrections, physical positions and ranking information.TableS3List of the regions of interest and the genes within them for each of the traits. Lipid genes are in bold and transcription factors are italicized.Fatty acid proportions for 391 Arabidopsis thaliana accessions.bio_FAprops.csvBox-Cox transformed fatty acid proportions for 391 Arabidopsis thaliana accessions.bioBC_FAs.csv
DOI: 10.5061/dryad.1252
title: Data from: Lineage diversification in a widespread species: roles for niche divergence and conservatism in the Common Kingsnake, Lampropeltis getula

description: Niche conservatism and niche divergence are both important ecological
 mechanisms associated with promoting allopatric speciation across
 geographic barriers. However, the potential for variable responses in
 widely distributed organisms has not been fully investigated. For
 allopatric sister lineages, three patterns for the interaction of
 ecological niche preference and geographic barriers are possible: i) niche
 conservatism at a physical barrier, ii) niche divergence at a physical
 barrier, and iii) niche divergence in the absence of a physical barrier.
 We test for the presence of these patterns in a transcontinentally
 distributed snake species, the Common Kingsnake (Lampropeltis getula), to
 determine the relative frequency of niche conservatism or divergence in a
 single species complex inhabiting multiple distinct niches. We infer the
 phylogeographic structure of the kingsnake using a rangewide dataset
 sampled for the mitochondrial gene cyt-b. We use coalescent simulation
 methods to test for the presence of structured lineage formation versus
 fragmentation of a widespread ancestor. Finally, we use statistical
 techniques for creating and evaluating ecological niche models to test for
 conservatism of ecological niche preferences. Significant geographic
 structure is present in the kingsnake, for which coalescent tests indicate
 structured population division. Surprisingly, we find evidence for all
 three patterns of conservatism and divergence. This suggests that
 ecological niche preferences may be labile on recent phylogenetic time
 scales, and that lineage formation in widespread species results from an
 interaction between inertial tendencies of niche conservatism and natural
 selection on populations in ecologically divergent habitats.
description: Information for
 kingsnake specimensClade designations,
 museum voucher numbers, GenBank accession numbers, general localities, and
 latitude/longitude data for kingsnake specimens in the molecular
 datasetPyron_Burbrink_Supporting_Information1.docPresence localities for kingsnakesLarger presence locality dataset, containing specimens from the molecular analysis as well as older museum records. Used to generate niche models for the separate lineages.Pyron_Burbrink_Supporting_Information2.csv
DOI: 10.5061/dryad.785sc4d
title: Data from: Marine protected areas enhance structural complexity but do not buffer the consequences of ocean warming for an overexploited precious coral

description: 1. Global warming and overexploitation both threaten the integrity and
 resilience of marine ecosystems. Many calls have been made to at least
 partially offset climate change impacts through local conservation
 management. However, a mechanistic understanding of the interactions of
 multiple stressors is generally lacking for habitat-forming species;
 preventing the development of sound conservation strategies. 2. We
 examined the effectiveness of no-take marine protected areas (MPAs) at
 enhancing structural complexity and resilience to climate change on
 populations of an overexploited and long-lived octocoral. We used
 long-term data over eight populations, subjected to varying levels of
 disturbances, and Integral Projection Models to understand how the
 interaction between overfishing and mass-mortality events shapes the
 stochastic dynamics of the Mediterranean red coral Corallium rubrum. 3.
 MPAs largely reduced colony partial mortality (i.e. shrinkage), enhancing
 the structural complexity of coral populations. However, there were no
 significant differences in individual mortality or population growth rates
 between protected and exploited populations. In contrast, warming had
 detrimental consequences for the long-term viability of red coral
 populations, driving steady declines and potential local extinctions due
 to sharp effects in survival rates. Stochastic demographic models revealed
 only a weak compensatory effect of MPAs on the impacts of warming. 4.
 Policy implications. Our results suggest that marine protected areas
 (MPAs) are an effective local conservation tool for enhancing the
 structural complexity of red coral populations. However, MPAs may not be
 enough to ensure red coral’s persistence under future increases in thermal
 stress. Accordingly, conservation strategies aiming to ensure the
 persistence and functional role of red coral populations should include
 management actions at both local (well-enforced MPAs) and global scales
 (reductions in greenhouse gas emissions). Finally, this study unravels the
 divergent demographic consequences that can arise from multiple stressors
 and highlights the key role of demography in better understanding and
 predicting the consequences of combined impacts for vulnerable ecosystems.
description: Demographic data red
 coral Corallium rubrumDemographic data for
 eight red coral (Corallium rubrum) populations in the NW Mediterranean Sea
 (Spain and France). This dataset includes colony size-based estimates of
 annual survival, shrinkage and fecundity rates of red coral populations
 subjected to different disturbances (fishing and warming) and a growth
 model based in coral colonies from two populations.Demographic_data_red_coral_MPAs_Warming 22Nov.xlsx
DOI: 10.5061/dryad.52qh9
title: Data from: Urine is an important nitrogen source for plants irrespective of vegetation composition in an Arctic tundra: insights from a 15N-enriched urea tracer experiment

description: 1. Mammalian herbivores can strongly influence nitrogen (N) cycling and
 herbivore urine could be a central component of the N cycle in grazed
 ecosystems. Despite its potential role for ecosystem productivity and
 functioning, the fate of N derived from urine has rarely been investigated
 in grazed ecosystems. 2. This study explored the fate of 15N-enriched urea
 in tundra sites that have been either lightly or intensively grazed by
 reindeer for more than 50 years. We followed the fate of the 15N applied
 to the plant canopy, at 2 weeks and 1 year after tracer addition, in the
 different ecosystem N pools. 3. 15N-urea was rapidly incorporated in
 cryptogams and in aboveground parts of vascular plants, while the soil
 microbial pool and plant roots sequestered only a marginal proportion.
 Further, the litter layer constituted a large sink for the 15N-urea, at
 least in the short term, indicating a high biological activity in the
 litter layer and high immobilization in the first phases of organic matter
 decomposition. 4. Mosses and lichens still constituted the largest sink
 for the 15N-urea 1 year after tracer addition at both levels of grazing
 intensity demonstrating their large ability to capture and retain N from
 urine. Despite large fundamental differences in their traits, deciduous
 and evergreen shrubs were just as efficient as graminoids in taking up the
 15N-urea. The total recovery of 15N-urea was lower in the intensively
 grazed sites, suggesting that reindeer reduce ecosystem N retention. 5.
 Synthesis The rapid incorporation of the applied 15N-urea indicates that
 arctic plants can take advantage of a pulse of incoming N from urine. In
 addition, δ 15N values of all taxa in the heavily grazed sites converged
 towards the δ 15N values for urine, bringing further evidence that urine
 is an important N source for plants in grazed tundra ecosystems.
description: Complete
 datasetBiomass, N pool, 15N
 recovery and 15N enrichment for the different ecosystem N pools: Plants
 (aboveground + root), litter, microbial N and soil extractable N at the
 heavily and lightly grazed sitesDataset.xlsxPlant biomass and analysisPlant biomass, 15N natural abundance and 15N enrichment at the heavily and lightly grazed sitesSoil chemical analysisSoil extractable and microbial N, soil organic matter and moisture content, 15N natural abundance, 15N enrichment and % 15N recovery in the soil and microbial N pool at the heavily and lightly grazed sitesSoil microclimatesSoil moisture and temperatures at the heavily and lightly grazed sites
DOI: 10.5061/dryad.tb552
title: Data from: Sexual selection and population divergence I: the influence of socially flexible cuticular hydrocarbon expression in male field crickets (Teleogryllus oceanicus)

description: Debates about how coevolution of sexual traits and preferences might
 promote evolutionary diversification have permeated speciation research
 for over a century. Recent work demonstrates that the expression of such
 traits can be sensitive to variation in the social environment. Here we
 examined social flexibility in a sexually selected male trait – cuticular
 hydrocarbon (CHC) profiles – in the field cricket Teleogryllus oceanicus
 and tested whether population genetic divergence predicts the extent or
 direction of social flexibility in allopatric populations. We manipulated
 male crickets’ social environments during rearing and then characterised
 CHC profiles. CHC signatures varied considerably across populations and
 also in response to the social environment, but our prediction that
 increased social flexibility would be selected in more recently founded
 populations exposed to fluctuating demographic environments was
 unsupported. Furthermore, models examining the influence of drift and
 selection failed to support a role of sexual selection in driving
 population divergence in CHC profiles. Variation in social environments
 might alter the dynamics of sexual selection, but our results align with
 theoretical predictions that the role social flexibility plays in
 modulating evolutionary divergence depends critically on whether responses
 to variation in the social environment are homogeneous across populations,
 or whether gene-by-social-environment interactions occur.
description: Pascoal et al.
 (cuticular hydrocarbon data)Pascoal et al.
 (microsatellite data)Pascoal et al. (song
 data)
DOI: 10.5061/dryad.mn159hq6
title: Data from: Generalized linear mixed models for mapping multiple quantitative trait loci

description: Many biological traits are discretely distributed in phenotype but
 continuously distributed in genetics because they are controlled by
 multiple genes and environmental variants. Due to the quantitative nature
 of the genetic background, these multiple genes are called quantitative
 trait loci (QTL). When the QTL effects are treated as random, they can be
 estimated in a single generalized linear mixed model (GLMM), even if the
 number of QTL may be larger than the sample size. The GLMM in its original
 form cannot be applied to QTL mapping for discrete traits if there are
 missing genotypes. We examined two alternative missing genotype-handling
 methods: the expectation method and the overdispersion method. Simulation
 studies show that the two methods are efficient for multiple QTL mapping
 (MQM) under the GLMM framework. The overdispersion method showed slight
 advantages over the expectation method in terms of smaller mean-squared
 errors of the estimated QTL effects. The two methods of GLMM were applied
 to MQM for the female fertility trait of wheat. Multiple QTL were detected
 to control the variation of the number of seeded spikelets.
description: Data and Programs
 HDY-11-OR0427RThis folder contains
 many files related to the manuscript number HDY-11-OR0427R. In the
 Simulation folder, there are two datasets (binary and binomial) and two
 SAS programs used to analyze these data. In the Wheat folder, there is a
 dataset collected from a wheat QTL mapping experiment (Dou et al. 2009)
 and a SAS program that analyzes this dataset. The wheat data can also be
 downloaded from the original publication's journal website
 (Supplemental Material).
DOI: 10.5061/dryad.r1f52
title: Data from: Genetic mapping of horizontal stripes in Lake Victoria cichlid fishes: benefits and pitfalls of using of dense linkage mapping in non-model organisms

description: The genetic dissection of naturally occurring phenotypes sheds light on
 many fundamental and longstanding questions in speciation and adaptation
 and is a central research topic in evolutionary biology. Until recently,
 forward-genetic approaches were virtually impossible to apply to non-model
 organisms, but the development of next-generation sequencing techniques
 eases this difficulty. Here, we use the ddRAD-seq method to map a color
 trait with a known adaptive function in cichlid fishes, well-known
 textbook examples for rapid rates of speciation and astonishing phenotypic
 diversification. A suite of phenotypic key-innovations are related to
 speciation and adaptation in cichlids, among which body coloration
 features prominently. The focal trait of the present study, horizontal
 stripes, evolved in parallel in several cichlid radiations and is
 associated with piscivorous foraging behavior. We conducted interspecific
 crosses between Haplochromis sauvagei and H. nyererei, and constructed a
 linkage map with 867 SNP markers distributed on 22 linkage groups and
 total size of 1130.63cM. Lateral stripes are inherited as a Mendelian
 trait and map to a single genomic interval that harbors a paralog of a
 gene with known function in stripe patterning. Dorsolateral and midlateral
 stripes were always co-inherited and are thus under the same genetic
 control. Additionally, we directly quantify the genotyping error rates in
 RAD markers and offer guidelines for identifying and dealing with errors.
 Uncritical marker selection was found to severely impact linkage map
 construction. Fortunately, by applying appropriate quality control steps,
 a genotyping accuracy of &gt;99.9% can be reached, thus allowing for
 efficient linkage-mapping of evolutionarily relevant traits.
description: Henning et al Mol Ecol
 PhenotypesPhenotypes of the 171 F2
 individuals: "0" and "1" indicate absence and presence
 of horizontal stripes, respectively.Henning et al Mol Ecol
 genotypesGenotypes of 183
 individuals (2 parents, 10 F1s and 171 F2s) in JoinMap format. 1517
 markers, as exported by the "genotypes" module of the program
 Stacks, are reported.Henning et al Mol Ecol
 Linkage MapLinkage map including
 the final set of 867 markers obtained after the quality-filtering steps
 described in the manuscript.
DOI: 10.5061/dryad.d63t5
title: Data from: Diversification of R2R3-MYB transcription factors in the tomato family Solanaceae

description: MYB transcription factors play an important role in regulating key plant
 developmental processes involving defense, cell shape, pigmentation, and
 root formation. Within this gene family, sequences containing an R2R3 MYB
 domain are the most abundant type and exhibit a wide diversity of
 functions. In this study, we identify 559 R2R3 MYB genes using whole
 genome data from four species of Solanaceae and reconstruct their
 evolutionary relationships. We compare the Solanaceae R2R3 MYBs to the
 well-characterized Arabidopsis thaliana sequences to estimate functional
 diversity and to identify gains and losses of MYB clades in the
 Solanaceae. We identify numerous R2R3 MYBs that do not appear closely
 related to Arabidopsis MYBs, and thus may represent clades of genes that
 have been lost along the Arabidopsis lineage or gained after the
 divergence of Rosid and Asterid lineages. Despite differences in the
 distribution of R2R3 MYBs across functional subgroups and species, the
 overall size of the R2R3 subfamily has changed relatively little over the
 roughly 50 million-year history of Solanaceae. We added our information
 regarding R2R3 MYBs in Solanaceae to other data and performed a
 meta-analysis to trace the evolution of subfamily size across land plants.
 The results reveal many shifts in the number of R2R3 genes, including a 54
 % increase along the angiosperm stem lineage. The variation in R2R3
 subfamily size across land plants is weakly positively correlated with
 genome size and strongly positively correlated with total number of genes.
 The retention of such a large number of R2R3 copies over long evolutionary
 time periods suggests that they have acquired new functions and been
 maintained by selection. Discovering the nature of this functional
 diversity will require integrating forward and reverse genetic approaches
 on an -omics scale.
description: DryadTwo amino acid
 alignments (ClustaX and Mafft), a PAL2NAL translated nucleotide alignment
 based upon the ClustalX amino acid alignment and a nucleotide tree and
 amino acid (ClustalX alignment) tree.
DOI: 10.5061/dryad.n5q05
title: Data from: Very low levels of direct additive genetic variance in fitness and fitness components in a red squirrel population

description: A trait must genetically correlate with fitness in order to evolve in
 response to natural selection, but theory suggests that strong directional
 selection should erode additive genetic variance in fitness and limit
 future evolutionary potential. Balancing selection has been proposed as a
 mechanism that could maintain genetic variance if fitness components trade
 off with one another and has been invoked to account for empirical
 observations of higher levels of additive genetic variance in fitness
 components than would be expected from mutation–selection balance. Here,
 we used a long-term study of an individually marked population of North
 American red squirrels (Tamiasciurus hudsonicus) to look for evidence of
 (1) additive genetic variance in lifetime reproductive success and (2)
 fitness trade-offs between fitness components, such as male and female
 fitness or fitness in high- and low-resource environments. “Animal model”
 analyses of a multigenerational pedigree revealed modest maternal effects
 on fitness, but very low levels of additive genetic variance in lifetime
 reproductive success overall as well as fitness measures within each sex
 and environment. It therefore appears that there are very low levels of
 direct genetic variance in fitness and fitness components in red squirrels
 to facilitate contemporary adaptation in this population.
description: Kluane Red Squirrel
 PedigreeThis pedigree spans from
 1987 to 2011 and consists of both maternal and paternal links. The
 paternal genetic links start in 2003.Pedigree_dryadcopy.xlsxARS phenotype dataARS_dryadcopy.xlsxLRS phenotype dataLRS_fordryad.xlsx
DOI: 10.5061/dryad.16mp4
title: Data from: Strong and stable geographic differentiation of swamp buffalo maternal and paternal lineages indicates domestication in the China/Indochina border region

description: The swamp type of the Asian water buffalo is assumed to have been
 domesticated by about 4000 years BP, following the introduction of rice
 cultivation. Previous localizations of the domestication site were based
 on mitochondrial DNA (mtDNA) variation within China, accounting only for
 the maternal lineage. We carried out a comprehensive sampling of China,
 Taiwan, Vietnam, Laos, Thailand, Nepal and Bangladesh and sequenced the
 mtDNA Cytochrome b gene and control region and the Y-chromosomal ZFY, SRY
 and DBY sequences. Swamp buffalo has a higher diversity of both maternal
 and paternal lineages than river buffalo, with also a remarkable contrast
 between a weak phylogeographic structure of river buffalo and a strong
 geographic differentiation of swamp buffalo. The highest diversity of the
 swamp buffalo maternal lineages was found in South China and North
 Indochina on both banks of the Mekong River, while the highest diversity
 in paternal lineages was in the China-Indochina border region. We propose
 that domestication in this region was later followed by introgressive
 capture of wild cows west of the Mekong. Migration to the north followed
 the Yangtze valley as well as a more eastern route, but also involved
 translocations of both cows and bulls over large distances with a minor
 influence of river buffaloes in recent decades. Bayesian analyses of
 various migration models also supported domestication in the
 China-Indochina border region. Coalescence analysis yielded consistent
 estimates for the expansion of the major swamp buffalo haplogroups with a
 credibility interval of 900 to 3,900 years BP. The spatial differentiation
 of mtDNA and Y-chromosomal haplotype distributions indicates a lack of
 gene flow between established populations that is unprecedented in
 livestock.
description: Data files used in the
 paperA zip file including
 data sets and input files for various analysis methods.2014-03-31
 Dryad.zipinput file for skyline
 plot anlaysisThis is an example input
 file for skyline plot ananlysisSA1.xmlmtDNA Haplotype Sequence AlignmentSwamp type and river type haplotype alignments. These data were used to generate Fig.S1.sequenceAlignment.zip