香菇沪香F2菌株重要农艺性状在F2和F3代中的遗传规律

以香菇菌株沪香F2及其自交优良F2代菌株申香1504为实验材料,收集孢子单核体,对其交配型进行鉴定,然后通过单孢自交的方法,构建F2和F3代群体,并对孢子单核体、F2、F3代群体各阶段培养、出菇情况以及重要农艺性状进行详细统计分析,研究各性状表型分化的情况及遗传规律.结果 表明:2个亲本所获得的孢子单核体中A2...     

Linkage and heritability analysis of migraine symptom groupings: a comparison of three different clustering methods on twin data

Migraine is a painful disorder for which the etiology remains obscure. Diagnosis is largely based on International Headache Society criteria. However, no feature occurs in all patients who meet these criteria, and no single symptom is required for diagnosis. Consequently, this definition may not accurately reflect the phenotypic heterogeneity or genetic basis of the disorder. Such phenotypic uncertainty is typical for complex genetic disorders and has encouraged interest in multivariate statistical methods for classifying disease phenotypes. We applied three popular statistical phenotyping methods—latent class analysis, grade of membership and grade of membership “fuzzy” clustering (Fanny)—to migraine symptom data, and compared heritability and genome-wide linkage results obtained using each approach. Our results demonstrate that different methodologies produce different clustering structures and non-negligible differences in subsequent analyses. We therefore urge caution in the use of any single approach and suggest that multiple phenotyping methods be used.     

Assessing models for genetic prediction of complex traits: a comparison of visualization and quantitative methods

Background

In silico models have recently been created in order to predict which genetic variants are more likely to contribute to the risk of a complex trait given their functional characteristics. However, there has been no comprehensive review as to which type of predictive accuracy measures and data visualization techniques are most useful for assessing these models.

Methods

We assessed the performance of the models for predicting risk using various methodologies, some of which include: receiver operating characteristic (ROC) curves, histograms of classification probability, and the novel use of the quantile-quantile plot. These measures have variable interpretability depending on factors such as whether the dataset is balanced in terms of numbers of genetic variants classified as risk variants versus those that are not.

Results

We conclude that the area under the curve (AUC) is a suitable starting place, and for models with similar AUCs, violin plots are particularly useful for examining the distribution of the risk scores.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1616-z) contains supplementary material, which is available to authorized users.     

Genomic prediction based on data from three layer lines: a comparison between linear methods

Background

The prediction accuracy of several linear genomic prediction models, which have previously been used for within-line genomic prediction, was evaluated for multi-line genomic prediction.

Methods

Compared to a conventional BLUP (best linear unbiased prediction) model using pedigree data, we evaluated the following genomic prediction models: genome-enabled BLUP (GBLUP), ridge regression BLUP (RRBLUP), principal component analysis followed by ridge regression (RRPCA), BayesC and Bayesian stochastic search variable selection. Prediction accuracy was measured as the correlation between predicted breeding values and observed phenotypes divided by the square root of the heritability. The data used concerned laying hens with phenotypes for number of eggs in the first production period and known genotypes. The hens were from two closely-related brown layer lines (B1 and B2), and a third distantly-related white layer line (W1). Lines had 1004 to 1023 training animals and 238 to 240 validation animals. Training datasets consisted of animals of either single lines, or a combination of two or all three lines, and had 30 508 to 45 974 segregating single nucleotide polymorphisms.

Results

Genomic prediction models yielded 0.13 to 0.16 higher accuracies than pedigree-based BLUP. When excluding the line itself from the training dataset, genomic predictions were generally inaccurate. Use of multiple lines marginally improved prediction accuracy for B2 but did not affect or slightly decreased prediction accuracy for B1 and W1. Differences between models were generally small except for RRPCA which gave considerably higher accuracies for B2. Correlations between genomic predictions from different methods were higher than 0.96 for W1 and higher than 0.88 for B1 and B2. The greater differences between methods for B1 and B2 were probably due to the lower accuracy of predictions for B1 (~0.45) and B2 (~0.40) compared to W1 (~0.76).

Conclusions

Multi-line genomic prediction did not affect or slightly improved prediction accuracy for closely-related lines. For distantly-related lines, multi-line genomic prediction yielded similar or slightly lower accuracies than single-line genomic prediction. Bayesian variable selection and GBLUP generally gave similar accuracies. Overall, RRPCA yielded the greatest accuracies for two lines, suggesting that using PCA helps to alleviate the “n ≪ p” problem in genomic prediction.

Electronic supplementary material

The online version of this article (doi:10.1186/s12711-014-0057-5) contains supplementary material, which is available to authorized users.     

Estimating mass change of migrant songbirds during stopover: comparison of three different methods

ABSTRACT Stopover‐site quality has often been assessed using changes in the body mass of migrants estimated from individuals recaptured on subsequent days or using regression methods. We compared estimates of mass change using these two techniques to estimates of mass change determined from birds recaptured on the same day. Using spring and fall banding data collected on Appledore Island, Maine, from 1990–2007, we examined body mass changes of the five most common species. Over this period, 18,954 individuals of these five species were captured and banded, with 11.6% of birds recaptured at least 1 d after initial capture and 3.1% recaptured on the same day. Using both regression and same‐day recapture methods, all five species had positive hourly mass gains during fall migration; results were mixed for the subsequent‐day analysis method. Trends were less consistent during spring migration. Using all three methods of estimating mass change, Red‐eyed Vireos (Vireo olivaceus) lost mass, American Redstarts (Setophaga ruticilla) and Northern Waterthrushes (Parkesia noveboracensis) gained mass, and results for Yellow‐bellied Flycatchers (Empidonax flaviventris), and Black‐and‐white Warblers (Mniotilta varia) varied with method. We found similar trends in mass change using the same‐day recapture and regression methods. However, we found lower mean mass gain for most species using the same‐day recapture method, suggesting that there may be a short‐term capture and handling effect. Our results provide additional support for the use of regression models to compare changes in mass of migrating songbirds at stopover sites.     

Testing the prediction from sexual selection of a positive genetic correlation between human mate preferences and corresponding traits

Sexual selection can cause evolution in traits that affect mating success, and it has thus been implicated in the evolution of human physical and behavioural traits that influence attractiveness. We use a large sample of identical and nonidentical female twins to test the prediction from mate choice models that a trait under sexual selection will be positively genetically correlated with preference for that trait. Six of the eight preferences we investigated, i.e. height, hair colour, intelligence, creativity, exciting personality, and religiosity, exhibited significant positive genetic correlations with the corresponding traits, while the personality measures ‘easy going’ and ‘kind and understanding’ exhibited no phenotypic or genetic correlation between preference and trait. The positive results provide important evidence consistent with the involvement of sexual selection in the evolution of these human traits.     

A simple method for estimating recombination percentages and linkage intensities from F2 data: examples from Triticum monococcum and other self-fertilizing diploid plant species

Summary We offer an alternative approach to the extensively used maximum likelihood and product methods for calculating recombination values and linkage intensities from F₂ data. This new method which we designate as the square root approach is simpler than the ones in current use in that it obviates the need for formulae and tables. It can be applied to autosomal F₂ data from F₁'s heterozygous in both the coupling and repulsion phases. It has greater applicability than the product method in that it can be used in all cases involving 2-, 3-, 4-, 6- and 9-class segregations regardless whether gene interaction occurs or not, provided the double recessive and other specific phenotypes are each determined by one particular genotype. The proposed method is based on the same well established genetic facts as the other two approaches. Percent recombinant gametes and therefore percent recombination are calculated by deriving the square root of the proportion of the F₂ population that expresses the double recessive or equivalent phenotype. The recombination values obtained by our method are compared with those derived by product method for 17 crosses in 7 different species and were found to be insignificantly different from the latter. The advantages and disadvantages of the square root method compared with the two most used ones are discussed.     

The evolution of alternative reproductive strategies: fitness differential, heritability, and genetic correlation between the sexes

Paternity analyses using molecular markers have become standard in studies of mating systems, parentage, and kinship. In systems where individuals exhibit alternative mating strategies, molecular analyses have been productively used to estimate the reproductive success of each behavioral type and hence the fitness consequences to each individual. Here we review the fitness results in a system of five alternative mating strategies present in one population of side-blotched lizards (Uta stansburiana). Males in this population adopt one of three behavioral strategies that differ in their degree of territoriality and mate guarding. In contrast, females adopt one of two strategies that differ in offspring quantity and quality. We use paternity analyses to estimate the fitness of each morph, the heritability of reproductive strategy, and the correlation in strategy between the sexes and discuss the implications of our findings for the evolution and maintenance of reproductive polymorphism in this and other systems.     

Extracting aquatic mites from stream substrates: a comparison of three methods

Aquatic mites (Hydrachnida, Oribatida, Halacaroidea) are diverse, and can reach high densities in the substrates of streams and rivers. Although they are a ubiquitous component of these habitats, their small size means that they are often overlooked. Using substrate samples from streams in tropical Queensland, I compared the thoroughness and time-based efficiency of three methods of extraction: sorting live samples without magnification (live-picking); exhaustive sorting of preserved samples using a dissecting microscope (microscope-picking); and kerosene-flotation of preserved samples followed by sorting with a dissecting microscope (kero-float). Live-picked samples yielded significantly fewer individuals and species than other methods, and were biased towards larger species. Oribatids and halacarids were not found when live-picking was used. Live-picking and kero-float methods provided similar numbers of mites per minute of sampling effort, whereas microscope-picking had a lower efficiency than kero-float. A combination of live-picking and kerosene-floatation is recommended for thorough surveys of stream acarofauna.     

Importance of species interactions to community heritability: a genetic basis to trophic-level interactions

Recent community genetics studies have shown that specific genotypes of a host plant support distinct arthropod communities. Building upon these findings, we examined the hypothesis that a trophic community consisting of cottonwood trees, a galling herbivore and avian predators could also be related to the genetics of the host tree. We found genetic correlations among phytochemistry of individual tree genotypes, the density of a galling herbivore, and the intensity of avian predation on these herbivores. We detected significant broad-sense heritability of these interactions that range from H      = 0.70 to 0.83. The genetic basis of these interactions tended to increase across trophic levels suggesting that small genetic changes in the cottonwood phenotype could have major consequences at higher trophic levels affecting species interactions and energy flow. These findings show a heritable basis to trophic-level interactions indicating that there is a significant genetic basis to community composition and energy flow that is predictable by plant genotype. Our data clearly link plant genetics to patterns of avian foraging and show that species interactions are important components of community heritability and ecosystem processes. Overall, these data support the hypothesis that evolution of plant traits can alter trophic-level interactions and community composition.     

Estimating repertoire size in a songbird: a comparison of three techniques

Many animals produce multiple types of breeding vocalizations that, together, constitute a vocal repertoire. In some species, the size of an individual’s repertoire is important because it correlates with brain size, territory size or social behaviour. Quantifying repertoire size is challenging because the long recordings needed to sample a repertoire comprehensively are difficult to obtain and analyse. The most basic quantification technique is simple enumeration, where one counts unique vocalization types until no new types are detected. Alternative techniques estimate repertoire size from subsamples, but these techniques are useful only if they are accurate. Using 12 years of acoustic data from a population of rufous-and-white wrens in Costa Rica, we used simple enumeration to measure the repertoire size for 40 males. We then compared these to the estimates generated by three estimation techniques: curve fitting, capture–recapture and a new technique based on the coupon collector’s problem. To understand how sampling effort affects the accuracy and precision of estimates, we applied each technique to six different-sized subsets of data per male. When averaged across subset sizes, the capture–recapture and coupon collector techniques showed the highest accuracy, whereas the curve fitting technique underestimated repertoire size. Precision (the average absolute difference between the estimated and true repertoire size) was significantly better for the capture–recapture technique than the coupon collector and curve fitting techniques. Both accuracy and precision improved as subset size increased. We conclude that capture–recapture is the best technique for estimating the sizes of small repertoires.     

Identification and population genetic comparison of three ascidian species based on mtDNA sequences

Ascidians are sessile marine chordate invertebrates found along seashores worldwide and are typically regarded as invasive organisms. Knowledge concerning their global genetic structure and subsequent invasive potential is limited. Here, we identified three ascidians—Ciona robusta, Ciona savignyi, and Styela clava from the northeast region of China using morphological characteristics and mitochondrial cytochrome c oxidase subunit I (cox1) as genetic marker. We additionally used phylogenetics to aid in the identification of these three species. The results of a population genetic analysis showed that among the three species, the level of haplotype diversity was particularly high within C. savignyi, and nucleotide diversity varied moderately. We divided the three species separately into native and invasive populations using 170 cox1 sequences from global resources to explore population genetic structure and invasive potential. Although in the network analysis Ciona spp. formed haplogroups of native and invasive populations, some haplotypes were still shared. We found that the haplotypes did not cluster within the network of S. clava. Our AMOVA results also showed that Ciona spp. had a weak genetic structure, and less genetic differentiation was present in S. clava. These data suggest that there are extensive incursions of these three ascidians into different geographical regions. Global comparisons of ascidian populations will help in the understanding of their population genetic structure and invasive potential, hence providing important insights regarding conservation as well as management.     

MHC evolution in three salmonid species: a comparison between class II alpha and beta genes

The genes of the major histocompatibility complex (MHC) are amongst the most variable in vertebrates and represent some of the best candidates to study processes of adaptive evolution. However, despite the number of studies available, most of the information on the structure and function of these genes come from studies in mammals and birds in which the MHC class I and II genes are tightly linked and class II alpha exhibits low variability in many cases. Teleost fishes are among the most primitive vertebrates with MHC and represent good organisms for the study of MHC evolution because their class I and class II loci are not physically linked, allowing for independent evolution of both classes of genes. We have compared the diversity and molecular mechanisms of evolution of classical MH class II α and class II β loci in farm populations of three salmonid species: Oncorhynchus kisutch, Oncorhynchus mykiss and Salmo salar. We found single classical class II loci and high polymorphism at both class II α and β genes in the three species. Mechanisms of evolution were common for both class II genes, with recombination and point mutation involved in generating diversity and positive selection acting on the peptide-binding residues. These results suggest that the maintenance of variability at the class IIα gene could be a mechanism to increase diversity in the MHC class II in salmonids in order to compensate for the expression of one single classical locus and to respond to a wider array of parasites.     

Estimating seed dispersal distance: A comparison of methods using animal movement and plant genetic data on two primate‐dispersed Neotropical plant species

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Screening and genetic counseling for beta-thalassemia trait in a population unselected for interest: comparison of three counseling methods

We have assessed the effects of screening and genetic counseling for beta-thalassemia trait on knowledge, attitudes, and behavior in a prospective, controlled study of randomly selected adult members of a health maintenance organization. We report here that knowledge of manifestations and of inheritance of thalassemia, previously reported to be high immediately after counseling, were well maintained at 2 and 10 months following counseling. There was no detectable impairment of self-concept. Marital adjustment improved, and sexual activity increased significantly. Mood, assessed immediately before and after counseling, showed no undesirable changes. A patient-structured counseling method, designed to minimize negative psychological effects via discussion of feelings, was not superior to conventional and programmed methods, described in our previous reports, in terms of learning or attitude change.     

Heritable variation and genetic correlation of quantitative traits within and between ecotypes of Avena barbata

We examined heritable variation for quantitative traits within and between naturally occurring mesic and xeric ecotypes of the slender wild oat (Avena barbata), and in 188 recombinant inbred lines derived from a cross between the ecotypes. We measured a suite of seedling and adult traits in the greenhouse, as well as performance-related traits in field sites native to the two ecotypes. Although the ecotypes were genetically diverged for most traits, few traits showed significant heritable variation within either ecotype. In contrast, considerable heritable variation was released in the recombinant progeny of the cross, and transgressive segregation was apparent in all traits. Heritabilities were substantially greater in the greenhouse than in the field, and this was associated with an increase in environmental variance in the field, rather than a decrease in genetic variance. Strong genetic correlations were evident among the recombinants, such that 22 measured traits could be well represented by only seven underlying factors, which accounted for 80% of the total variation. The primary axis of variation in the greenhouse described a trade-off between vegetative and reproductive allocation, mediated by the date of first flowering, and fitness was strongly correlated with this trade-off. Other factors in the greenhouse described variation in size and in seedling traits. Lack of correlation among these factors represents the release of multivariate trait variation through recombination. In the field, a separate axis of variation in overall performance was found for each year/site combination. Performance was significantly correlated across field environments, but not significantly correlated between greenhouse and field.