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81.
Genetic analysis of unusual complex-heterozygous genotypes in populations ofO. grandiflora from Alabama (USA) has shown that these strains are composed of a typicalgrandiflora (B) complex and an altered B complex (designated as BA) which probably contains genetic elements derived from an A genotype such as the beta complex ofO. biennis group 1. Analysis of the meiotic configurations of artificial hybrids between the new strains and a series of complexes of known segmental arrangement allowed determination of the arrangements of the unknown complexes. These data are evidence for origin of the altered B complexes. 相似文献
82.
speed‐ne: Software to simulate and estimate genetic effective population size (Ne) from linkage disequilibrium observed in single samples 下载免费PDF全文
Matthew B. Hamilton Maria Tartakovsky Amy Battocletti 《Molecular ecology resources》2018,18(3):714-728
The genetic effective population size, Ne, can be estimated from the average gametic disequilibrium () between pairs of loci, but such estimates require evaluation of assumptions and currently have few methods to estimate confidence intervals. speed‐ne is a suite of matlab computer code functions to estimate from with a graphical user interface and a rich set of outputs that aid in understanding data patterns and comparing multiple estimators. speed‐ne includes functions to either generate or input simulated genotype data to facilitate comparative studies of estimators under various population genetic scenarios. speed‐ne was validated with data simulated under both time‐forward and time‐backward coalescent models of genetic drift. Three classes of estimators were compared with simulated data to examine several general questions: what are the impacts of microsatellite null alleles on , how should missing data be treated, and does disequilibrium contributed by reduced recombination among some loci in a sample impact . Estimators differed greatly in precision in the scenarios examined, and a widely employed estimator exhibited the largest variances among replicate data sets. speed‐ne implements several jackknife approaches to estimate confidence intervals, and simulated data showed that jackknifing over loci and jackknifing over individuals provided ~95% confidence interval coverage for some estimators and should be useful for empirical studies. speed‐ne provides an open‐source extensible tool for estimation of from empirical genotype data and to conduct simulations of both microsatellite and single nucleotide polymorphism (SNP) data types to develop expectations and to compare estimators. 相似文献
83.
Quantitative genetic theory predicts that variation due to rare alleles at many loci will generate a transient acceleration in the response to directional selection. We have tested this prediction by constructing experimental lines ofDrosophila melanogaster that carry positively selected ethanol resistance alleles at low frequencies, and then subjecting the lines to directional selection for ethanol resistance. Approximately 468,000 files were subjected to artificial selection over 30 generations. The predicted non-linear selection responses were observed in all experimental lines and replicates, on three genetic backgrounds. In contrast, un-selected controls and lines carrying random alleles at low frequencies on the same genetic backgrounds exhibited linear selection responses. These results demonstrate that non-linearities due to rare alleles are detectable and repeatable, provided that experiments are done on a sufficiently large scale. The results suggest that it may be possible to test for rare-alleles as a component of naturally occurring genetic variation by careful examination of selection response curves. 相似文献
84.
Highly efficient de novo mutant identification in a Sorghum bicolor TILLING population using the ComSeq approach 下载免费PDF全文
Habte Nida Shula Blum Dina Zielinski Dhruv A. Srivastava Rivka Elbaum Zhanguo Xin Yaniv Erlich Eyal Fridman Noam Shental 《The Plant journal : for cell and molecular biology》2016,86(4):349-359
Screening large populations for carriers of known or de novo rare single nucleotide polymorphisms (SNPs) is required both in Targeting induced local lesions in genomes (TILLING) experiments in plants and in screening of human populations. We previously suggested an approach that combines the mathematical field of compressed sensing with next‐generation sequencing to allow such large‐scale screening. Based on pooled measurements, this method identifies multiple carriers of heterozygous or homozygous rare alleles while using only a small fraction of resources. Its rigorous mathematical foundations allow scalable and robust detection, and provide error correction and resilience to experimental noise. Here we present a large‐scale experimental demonstration of our computational approach, in which we targeted a TILLING population of 1024 Sorghum bicolor lines to detect carriers of de novo SNPs whose frequency was less than 0.1%, using only 48 pools. Subsequent validation confirmed that all detected lines were indeed carriers of the predicted mutations. This novel approach provides a highly cost‐effective and robust tool for biologists and breeders to allow identification of novel alleles and subsequent functional analysis. 相似文献
85.
Contrasting patterns of selection between MHC I and II across populations of Humboldt and Magellanic penguins 下载免费PDF全文
Nicole Sallaberry‐Pincheira Daniel González‐Acuña Pamela Padilla Gisele P. M. Dantas Guillermo Luna‐Jorquera Esteban Frere Armando Valdés‐Velásquez Juliana A. Vianna 《Ecology and evolution》2016,6(20):7498-7510
The evolutionary and adaptive potential of populations or species facing an emerging infectious disease depends on their genetic diversity in genes, such as the major histocompatibility complex (MHC). In birds, MHC class I deals predominantly with intracellular infections (e.g., viruses) and MHC class II with extracellular infections (e.g., bacteria). Therefore, patterns of MHC I and II diversity may differ between species and across populations of species depending on the relative effect of local and global environmental selective pressures, genetic drift, and gene flow. We hypothesize that high gene flow among populations of Humboldt and Magellanic penguins limits local adaptation in MHC I and MHC II, and signatures of selection differ between markers, locations, and species. We evaluated the MHC I and II diversity using 454 next‐generation sequencing of 100 Humboldt and 75 Magellanic penguins from seven different breeding colonies. Higher genetic diversity was observed in MHC I than MHC II for both species, explained by more than one MHC I loci identified. Large population sizes, high gene flow, and/or similar selection pressures maintain diversity but limit local adaptation in MHC I. A pattern of isolation by distance was observed for MHC II for Humboldt penguin suggesting local adaptation, mainly on the northernmost studied locality. Furthermore, trans‐species alleles were found due to a recent speciation for the genus or convergent evolution. High MHC I and MHC II gene diversity described is extremely advantageous for the long‐term survival of the species. 相似文献
86.
The essential oils of certain Mentha species and chemotypes have proportions of (?)-menthone and (+)-isomenthone which differ but show a high degree of heritability in clonal propagation. Oil from an F2 individual (69–296), selected from numerous 4n M. longifolia (4n = 48) × M. crispa (2n = 48) hybrids for high isomenthone content, had 41.3% isomenthone; the associated but seldom observed alcohols, 1.6% isomenthol, 10.3% neoiso-menthol; and 13% of their esters; in contrast to 8% menthone with 0.1% menthol, 5.0% neo-menthol, and 1.7% esters. Self-pollination of strain 69–296 gave a 3:1 ratio of high isomenthone: high menthone. Crosses with a true breeding high menthone plant having 80% menthone and 3.2% isomenthone gave a 1:1 ratio of the parental phenotypes by GLC analyses and herbage odor. This and data from high isomenthone and high menthone crosses with tester strains lead us to postulate the involvement of a single locus having multiple alleles with true breeding menthone having the genotype Ps Ps, true breeding isomenthone Pr Pr, 69–296 Pr Ps, and high pulegone pp. The Pr allele is not completely dominant over the Ps allele in 69–296 as about 18% of the total ketone derived from pulegone is menthone. Both are dominant over the recessive allele p that largely prevents menthone development. The quantitative amounts of the two isomers are believed to be controlled by the six combinations of the three alleles in a diploid species with graded effects obtained in the more complex genotypes possible in double diploid and octoploid species. 69–296 has (?)-piperitone even though (+)-piperitone is believed to be the common isomer in Mentha. 相似文献
87.
R. C. Griffiths 《Journal of mathematical biology》1991,29(8):763-777
This paper studies aspects of the distribution of non-mutant ancestors of a sample of gametes in a two-locus infinitely-many-alleles model. The ancestral process of two gametes is considered in detail. Included are algorithms for calculating the probability that the oldest allele is from the first locus, and the expected age of the oldest allele. Extensions to an r-locus model in the cases of complete linkage and independence are also studied. 相似文献
88.
Jork Meyer Annette Kohnen Walter Durka Johannes Wstemeyer Niels Blaum Eva Rossmanith Roland Brandl 《Mammalian Biology》2009,74(6):478-487
Dispersal greatly determines genetic structure of populations, although it is influenced by landscape heterogeneity, quality of the matrix, resource distribution and local population densities and dynamics. To get insights into some of those processes we analysed the genetic structure of the hairy-footed gerbil Gerbillurus paeba (Rodentia, Murinae, Gerbillinae) in the southern Kalahari (South Africa). Samples were taken from 20 populations covering an area of about 2200 km2. Genetic data were related to landscape characters and population dynamics. We used newly developed microsatellites and found at all loci some indication for the presence of null alleles. However, null alleles seem to have little influence on the general results of our analyses. Altogether we found even nearby populations of G. paeba to be significantly differentiated, although assignment tests revealed 24% of individuals as immigrants. Genetic structure was independent of landscape heterogeneities at all spatial scales. Autocorrelation analyses (range 50–90 km) revealed significant genetic structure within populations on distances <3 km. We found some indication for female-biased dispersal. Our study suggests that dispersing individuals have little influence on the long-term genetic structure and that drift is the major cause of genetic diversity. The observed genetic pattern likely derives from strong population fluctuations of G. paeba. The landscape structure has little influence on the genetic differentiation between populations. 相似文献
89.
90.
Populations of mice established outdoors as well as indoors have been investigated at 24 loci using starch gel electrophoresis. Two reproductively isolated groups are recognized, one of which is referable to a house mouse subspecies, Mus musculus brevirostris, and the other to a different species, Mus spretus, contrary to the view of Schwarz and Schwarz that only one species of Mus is present in the Mediterranean Basin. The genetic distance between these two groups is larger than between any pair of investigated subspecies of M. musculus. M. m. brevirostris is biochemically almost indistinguishable from M. m. domesticus. On the other hand, M. spretus exhibits several allelic variants unknown or at most very infrequent in M. musculus, as for instance at the lactate dehydrogenase B-chain locus.This work was supported by research grants from the Centre National de la Recherche Scientifique (E.R.A. No. 261) and the Ecole Pratique des Hautes Etudes. 相似文献