cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.ch200
title: Data from: Long-distance gene flow outweighs a century of local selection and prevents local adaptation in the Irish famine pathogen Phytophthora infestans

description: Sustainably managing plant resistance to epidemic pathogens implies
 controlling the genetic and demographic changes in pathogen populations
 faced with resistant hosts. Resistance management thus depends upon the
 dynamics of local adaptation, mainly driven by the balance between
 selection and gene flow. This dynamics is best investigated with
 populations from locally dominant hosts in islands with long histories of
 local selection. We used the unique case of the potato late blight
 pathosystem on Jersey, where a monoculture of potato cultivar ‘Jersey
 Royal’ has been in place for over a century. We also sampled populations
 from the coasts of Brittany and Normandy, as likely sources for gene flow.
 The isolation by distance pattern and the absence of genetic
 differentiation between Jersey and the closest French sites revealed gene
 flow at that spatial scale. Microsatellite allele frequencies revealed no
 evidence of recombination in the populations, but admixture of two
 genotypic clusters. No local adaptation in Jersey was detected from
 pathogenicity tests on Jersey Royal and on French cultivars. These data
 suggest that long-distance gene flow (~ 50/100 km) prevents local
 adaptation in Jersey despite a century of local selection by a single host
 cultivar and emphasize the need for regional rather than local management
 of resistance gene deployment.
description: GenepopData_Glais-et-alSSR data for isolatesPhenotypicData_Glais-et-alPathogenicity data for the isolates included in paper
DOI: 10.5061/dryad.gd0nc
title: Data from: How the length of genital parts affects copulation performance in a carabid beetle: implications for correlated genital evolution between the sexes

description: To identify factors leading to the correlated evolution of exaggerated
 male and female genitalia, we studied the effects of the variable
 dimensions of corresponding functional genital parts (male copulatory
 piece and female vaginal appendix) on copulatory performance in the
 polygamous carabid beetle Carabus (Ohomopterus) maiyasanus. We used mating
 pairs of individuals from two populations to increase the variances in
 genital dimensions and determined the copulation performance (insemination
 and spermatophore replacement, and copulation time) in single- and
 double-mating situations. In single mating, insemination success was not
 affected by genital dimensions, although the copulation time was
 significantly shorter when the male aedeagus was longer. In the
 double-mating experiment, insemination and replacement of spermatophores
 by the second male succeeded more frequently when the copulatory piece was
 shorter and the vaginal appendix was longer, and when the difference
 between the length of the copulatory piece and the vaginal appendix was
 smaller. Thus, a matching of the corresponding genital parts between the
 sexes increases the male's reproductive success in sperm competition,
 but elongation of the copulatory piece cannot be explained simply by the
 improvement in male reproductive success. We discuss possible factors for
 the elongation of genital parts in terms of sexual conflict and
 reproductive interference through interspecific copulation.
description: Beetle and experimental
 dataBody length and genital
 dimensions of Carabus maiyasanus beetles, and individual data for single
 and double mating experimentsData.xlsx
DOI: 10.5061/dryad.6p676
title: Data from: Influence of leaf trichomes on boundary layer conductance and gas-exchange characteristics in Metrosideros polymorpha (Myrtaceae)

description: The amount of trichomes on the leaves of Metrosideros polymorpha varies
 enormously, ranging from 0 to ca 150 g/m2 across environmental gradients
 on the island of Hawaii. Pubescent individuals are abundant in dry areas
 or on young lava flows, whereas glabrous individuals are abundant in wet
 areas or on developed soils. To understand the adaptive advantages of
 pubescent individuals in arid environments, we addressed the following
 questions: (1) whether leaf trichomes increase the boundary layer
 resistance to gas diffusion, which in turn reduces the transpiration rate
 and increases water-use efficiency (WUE); and (2) whether pubescent
 individuals have other associated leaf and shoot traits that have adaptive
 significance in arid environments. We made detailed ecophysiological
 measurements on M. polymorpha in three populations in habitats that varied
 in aridity. We found a large allocation of leaf mass to trichomes, up to
 33 percent at the arid site, but our analyses showed that trichomes had
 small effects (1–9%) on gas exchange and negligible effects on WUE,
 suggesting the trichomes may have roles beyond increasing WUE. However,
 pubescent individuals did have higher Rubisco amount and a lower leaf-to-
 sapwood area ratio, which are considered adaptive in arid environments.
 These results suggest that pubescent individuals of M. polymorpha are
 indeed adapted to arid environments with changes in a suite of traits. The
 adaptive significance of the enormous variation in amounts of trichomes
 remains unclear and may be related to functions other than increasing
 boundary layer resistance.
description: Leaf_dataThis excel data include leaf physiological and morphological data; and site climate data.
DOI: 10.5061/dryad.v82jf
title: Data from: Behavioral evidence for fruit odor discrimination and sympatric host races of Rhagoletis pomonella flies in the western United States

description: The recent shift of Rhagoletis pomonella (Diptera: Tephritidae) from its
 native host downy hawthorn, Crataegus mollis, to introduced domesticated
 apple, Malus domestica, in the eastern U.S. is a model for sympatric host
 race formation. However, the fly is also present in the western U.S.,
 where it may have been introduced via infested apples within the last 60
 years. In addition to apple, R. pomonella also infests two hawthorns in
 the West, one the native black hawthorn, C. douglasii, and the other the
 introduced English ornamental hawthorn, C. monogyna. Here, we test for
 behavioral evidence of host races in the western U.S. through flight
 tunnel assays of western R. pomonella flies to host fruit volatile blends.
 We report that western apple, black hawthorn, and ornamental hawthorn
 flies showed significantly increased levels of upwind directed flight to
 their respective natal compared to non-natal fruit volatile blends,
 consistent with host race status. We discuss the implications of the
 behavioral results for the origin(s) of western R. pomonella, including
 the possibility that western apple flies were not introduced, but may
 represent a recent shift from local hawthorn fly populations.
description: Figure
 S1Map
 of collecting sites in the states of Washington and Oregon for Rhagoletis
 pomonella flies behaviorally analyzed in the study.FigS1StudySiteLocations.pdfTable S1Relative percentages of chemical compounds comprising the synthetic fruit volatile blends used in the study to test Rhagoletis pomonella fly behavior.TableS1CompositionSyntheticFruitBlends.docxTable S2Behavioral responses of Rhagoletis pomonella flies from the western and eastern U.S. to synthetic host fruit volatile blends in flight tunnel assays.TableS2WesternPomonellaBehaviorData.xlsx
DOI: 10.5061/dryad.76m54
title: Data from: Evolutionary potential of the extrinsic incubation period of dengue virus in Aedes aegypti

description: Dengue fever is the most common arboviral disease worldwide. It is caused
 by dengue viruses (DENV) and the mosquito Aedes aegypti is its primary
 vector. One of the most powerful determinants of a mosquito's ability
 to transmit DENV is the length of the extrinsic incubation period (EIP),
 the time it takes for a virus to be transmitted by a mosquito after
 consuming an infected blood meal. Here, we repeatedly measured DENV load
 in the saliva of individual mosquitoes over their lifetime and used this
 in combination with a breeding design to determine the extent to which EIP
 might respond to the evolutionary forces of drift and selection. We
 demonstrated that genetic variation among mosquitoes contributes
 significantly to transmission potential and length of EIP. We reveal that
 shorter EIP is genetically correlated with reduced mosquito lifespan,
 highlighting negative life-history consequences for virus-infected
 mosquitoes. This work highlights the capacity for local genetic variation
 in mosquito populations to evolve and to dramatically affect the nature of
 human outbreaks. It also provides the impetus for isolating mosquito genes
 that determine EIP. More broadly, our dual experimental approach offers
 new opportunities for studying the evolutionary potential of transmission
 traits in other vector/pathogen systems.
description: YeetalEvolutiondataAug_2016Excel file containing all data. Separate experiments are on different tabs.
DOI: 10.5061/dryad.4142d
title: Data from: Life-history evolution and density-dependent growth in experimental populations of yeast

description: We studied the evolution of the correlation between growth rate r and
 yield K in experimental lineages of the yeast Saccharomyces cerevisiae.
 First, we isolated a single clone every ~250 generations from each of
 eight populations selected in a glucose-limited medium for 5000
 generations at ~6.6 population doublings per day (20 clones per line × 8
 lines) and measured its growth rate and yield in a new, galactose-limited
 medium (with ~1.3 doubling per day). For most lines, r on galactose
 increased throughout the 5000 generations of selection on glucose while K
 on galactose declined. Next, we selected these 160 glucose-adapted clones
 in the galactose environment for ~120 generations and measured changes in
 r and K in galactose. In general, growth rate increased and yield
 declined, and clones that initially grew slowly on galactose improved more
 than did faster clones. We found a negative correlation between r and K
 among clones both within each line and across all clones. We provide
 evidence that this relationship is not heritable and is a negative
 environmental correlation rather than a genetic trade-off.
description: Jasmin_Zeyl_data_LifeHistorySaccharomycesLife-history traits data of clones isolated from experimental populations of Saccharomyces.
DOI: 10.5061/dryad.mb88mh2
title: Data from: Manipulation of parental nutritional condition reveals competition among family members

description: Parental care is thought to be costly, as it consumes time and energy.
 Such costs might be reduced in animal parents that raise their young on
 valuable food sources such as dung or carcasses, as parents are able to
 invest in self-maintenance by feeding from the same resource. However,
 this might lower the nutritional value for other family members and, as a
 consequence, food competition might arise. To promote our understanding of
 the outcome of such competition, we manipulated the necessity of parents
 to feed from the resource. Using a full factorial design, we paired
 food-deprived or well-fed males with food-deprived or well-fed females of
 burying beetles, which are known to raise their young on vertebrate
 cadavers. We found that food-deprived parents consumed more of the carrion
 than those that were well-fed and this had a negative impact on other
 family members. However, the outcome of the competition depended on the
 sex of the parents, with females suffering when males fed more and
 offspring suffering when females fed more. Thus, family life involves
 selfish elements, as both parents remove resources for the purpose of
 self-maintenance. However, females show altruistic aspects, as they appear
 to restrict their food consumption for the benefit of their offspring when
 paired with a food-deprived male. Interestingly, males extend their stay
 with the brood when having faced food scarcity prior to reproduction,
 presumably to replenish their energy reserves. Our study therefore reveals
 that breeding on shared resources can promote family living, but also
 results in competition.
description: Keppner et
 al_Data_DryadExcel file with three
 spreadsheets. The first spreadsheet contains data on male and female
 nutrional status, pronotum width, body mass at different time points,
 carcass mass at different time points, number of larvae raised, average
 larval weight, total brood mass, male care duration. The second
 spreadsheet contains the weight of each single larva of the first brood.
 The third spreadsheet contains the weight of each single larva of the
 second brood.
DOI: 10.5061/dryad.7ck38
title: Data from: Effects of beneficial mutations in pykF gene vary over time and across replicate populations in a long-term experiment with bacteria

description: The fitness effects of mutations can depend on the genetic backgrounds in
 which they occur and thereby influence future opportunities for evolving
 populations. In particular, mutations that fix in a population might
 change the selective benefit of subsequent mutations, giving rise to
 historical contingency. We examine these effects by focusing on mutations
 in a key metabolic gene, pykF, that arose independently early in the
 history of 12 Escherichia coli populations during a long-term evolution
 experiment. Eight different evolved nonsynonymous mutations conferred
 similar fitness benefits of ~10% when transferred into the ancestor, and
 these benefits were greater than the one conferred by a deletion mutation.
 By contrast, the same mutations had highly variable fitness effects,
 ranging from about 0 to 25%, in evolved clones isolated from the
 populations at 20,000 generations. Two mutations that were moved into
 these evolved clones conferred similar fitness effects in a given clone,
 but different effects between the clones, indicating epistatic
 interactions between the evolved pykF alleles and the other mutations that
 had accumulated in each evolved clone. We also measured the fitness
 effects of six evolved pykF alleles in the same populations in which they
 had fixed, but at seven time points between 0 and 50,000 generations.
 Variation in fitness effects was high at intermediate time points, and
 declined to a low level at 50,000 generations, when the mean fitness
 effect was lowest. Our results demonstrate the importance of genetic
 context in determining the fitness effects of different beneficial
 mutations even within the same gene.
description: PykF fitness effects:
 ancestor and 20KColony counts of
 competitions measuring the effect of pykF mutations in the ancestral
 strain (REL606) and in the 20,000 generation evolved strains each mutation
 was found in.pykF_anc-20k_data.txtPykF fitness analysis: ancestor and 20KR script to analyze and plot pykF fitness effects in ancestor and 20,000 generation evolved strainspykF_anc-ev_epistasis.RPykF allele transfer fitness effectsResults of fitness competitions measuring the effect of pykF alleles transferred across different 20,000 generation evolved strains.pykF_ev_allele_transfer.txtpykF allele transfer analysisR script to analyze and plot fitness of pykF mutations across different 20,000 generation evolved strainspykF_ev_allele_transfer.RPykF time-series fitness effectsResults of competitions to measure the effect of six of the evolved pykF mutations at up to six time points along their evolutionary trajectorypykF_time_series_data.txtPykF time-series analysisR script analyzing and plotting effect of pykF mutations at steps along evolutionary trajectoriespykF_time_series_epistasis.R
DOI: 10.5061/dryad.vv0gg
title: Data from: Estimating genotyping errors from genotype and reconstructed pedigree data

description: 1. Genotyping errors are rules rather than exceptions in reality, and are
 found in virtually all but very small datasets. These errors, even when
 occurring at an extremely low rate, can derail many genetic analyses such
 as parentage/sibship assignments and linkage/association studies. 2.
 Nonetheless, few robust and accurate methods are available for estimating
 the rate of occurrence of genotyping errors and for identifying individual
 erroneous genotypes at a locus. Methods based on duplicate genotyping are
 expensive, and estimate genotype inconsistency rather than error rate at a
 locus. Methods based on Hardy-Weinberg equilibrium tests have low
 robustness and low power, and apply only to those particular errors that
 cause excessive homozygosity. Methods based on pedigrees are powerful,
 robust and accurate. However, they rely on known and complete pedigrees
 that are unfortunately rarely available from natural populations in the
 wild. 3. I proposed a maximum likelihood method to reconstruct pedigrees
 from genotype data with errors occurring at a roughly estimated (presumed)
 rate. In this paper, I describe how to use the method and inferred
 pedigree in estimating allelic dropout (or null allele) rate and false
 allele rate jointly at each marker locus, in identifying the erroneous
 genotypes, and in inferring the most likely genotypes at each locus of
 each individual. I examine the power, accuracy and robustness of the
 method by extensive simulations, and demonstrate the usefulness of the
 method by analysing three empirical datasets. 4. It is concluded that,
 both pedigrees and the rates of genotyping errors at each locus can be
 reliably estimated from the same genotype data by the same likelihood
 method, when marker information is sufficient and some sampled individuals
 are first-degree relatives. The erroneous genotypes are however inferred
 conservatively, and are reliably detected only when they occur in large
 families and/or at highly polymorphic loci. Estimation of genotyping error
 rates per locus and identification of erroneous genotypes of each
 individual at each locus should be routinely conducted to assess and
 improve data quality, to highlight markers for optimization of genotyping
 protocols or for replacement, and to enable the integration of genotyping
 errors in a robust statistical analysis.
description: 3 real datasets for
 Colony analysis of mistyping ratesThis zipped file
 contains three real datasets in the format of Colony input files. In each
 input file, the assumed dropout and false allele rates of each marker can
 be modified manually before running Colony analysis.ColonyInputFiles.zip
DOI: 10.5061/dryad.bb67v
title: Data from: Evidence for facilitation among avian army-ant attendants: specialization and species associations across elevations

description: Mixed-species assemblages can involve positive and negative interactions,
 but uncertainty about high-value patchy resources can increase the value
 of information sharing among heterospecific co-foragers. I sampled species
 composition of bird-flocks attending army-ant raids in three adjacent
 elevation zones in Costa Rica, across multiple years, to test for positive
 and negative associations among raid-attending bird species. My goal was
 to test whether the most frequent and specialized raid-attending species
 showed evidence of facilitating or excluding other bird species. I
 quantified elevational variation in avian community composition at raids,
 then asked whether species composition was associated with variation in
 flock characteristics (flock size and species richness). I identified the
 most frequent raid-attending species (those that attended raids most
 frequently relative to their mist-net capture rates), and bird species
 that performed specialized army ant-following behavior (bivouac-checking,
 which allows birds to memorize and track mobile army-ant colonies). There
 was significant turnover of bird species among zones (including the
 frequent and specialized attendants); patterns of species overlap
 suggested a gradual transition from a Pacific-slope to an Atlantic-slope
 raid-attending bird fauna. Raid-attendance frequency was positively
 correlated with bivouac-checking behavior. With few exceptions, the most
 frequent raid-attending bird species, and the bivouac-checking species,
 also participated in the most species-rich flocks. High
 species-gregariousness suggests many of the frequently attending and/or
 bivouac-checking species functioned as core flock members. However, some
 bird species pairs were significantly negatively associated at raids.
 Despite species turnover, per-flock numbers of birds at raids did not
 differ among geographic zones, but flocks on the Pacific-slope were
 heavier because larger bodied bird species attended raids. Previous
 studies showed that the size (biomass) of bird-flocks corresponds to the
 amount of food the birds kleptoparasitize from ant raids, and the heavier
 Pacific-slope bird-flocks could have greater negative kleptoparasitic
 impacts.
description: 29mar17 dryad AA bird
 flock dataSpreadsheet listing all
 bird flocks sampled and analyzed in the study, giving dates, locations,
 bird species, and numbers of individuals.
DOI: 10.5061/dryad.5qr6t
title: Data from: First molecular characterization of Echinococcus granulosus (sensu stricto) genotype 1 among cattle in Sudan

description: Background: Echinococcus granulosus sensu lato (s.l.) is the causative
 agent of cystic echinococcosis (CE), which is a cosmopolitan zoonotic
 parasitic disease infecting humans and a wide range of mammalian species
 including cattle. Currently, little information is available on the
 genetic diversity of Echinococcus species among livestock in Sudan. In the
 present study, fifty (n = 50) hydatid cysts were collected from cattle
 carcasses (one cyst sample per animal) at Al-kadarou slaughterhouse,
 Khartoum North, Sudan. DNA was extracted from protoscolices and the
 germinal layer of each cyst and subsequently amplified by PCR targeting
 the mitochondrial NADH dehydrogenase subunit 1 (NADH-1) gene. The
 amplified PCR products were purified and subjected to direct sequencing
 for subsequent construction of phylogenetic tree and net work analysis.
 Results: The phylogenetic tree revealed the presence of Echinococcus
 canadenesis genotype 6 (G6) in 44 cysts (88.0%), Echinococcus ortleppi
 genotype 5 (G5) in 4 cysts (8.0%) and Echinococcus granulosus sensu
 stricto (s.s) genotype 1 (G1) in 2 cysts (4.0%). The phylogenetic network
 analysis revealed genetic variation among the different
 haplotypes/genotypes. This report has provided, for the first time, an
 insight of the role of cattle in the transmission of the zoonotic G1
 echinococosis. Conclusions: The results of the study illustrate that
 Sudanese breeds of cattle may play an important role in the transmission
 dynamics and the epidemiology of cystic echinococcosis in Sudan. This
 study reports the first molecular identification of E. granulosus s.s. in
 cattle in Central Sudan.
description: Median Joining
 NetworkNW.pptxNADH1 gene alignmentNADH1.fas
DOI: 10.25345/c5cn6zc7n
title: MassIVE MSV000100597 - Analyses of Individual Singly-Charged Ions using a High-Field Orbitrap Analyzer
title: Raw data for ultralong transients (&gt; 20 s) measurements corresponding to single particle Orbitrap-based CDMS analysis [dataset license: CC0 1.0 Universal (CC0 1.0)].