The Distribution of Mutant Alleles in a Subdivided Population

The results are presented from a simulation study of the spatial distribution of mutant alleles in a subdivided population. Statistical measures of the spatial pattern are defined in such a way that the same quantities could be measured in a geographic survey of allele frequencies in natural populations. Two types of quantities are discussed in this paper: (1) the occupancy distribution provides information on the presence or absence of the mutant in different numbers of demes; and (2) the conditional frequency distribution provides information about the extent of local differentiation when the mutant is present in different numbers of demes. Properties of these distributions are found for different types of natural selection acting on the mutant. Some results are presented for the same statistical measures based on samples of individuals from a fraction of the total number of demes. The simulation results for intermediate levels of the migration rates are compared with analytic results obtained on the limits of high and low migration rates. The main conclusion is that these measures of the spatial distribution of mutants in a subdivided population have simple properties that could provide a new perspective on data from natural populations.     

Genetic Drift in a Cline

A model is developed of genetic drift in a cline maintained by spatially varying natural selection and local dispersal of individuals. The model is analyzed by an approximation scheme which is valid for weak selection and small migration rates. The results, which are based on numerical iterations of the approximate equations, are that the cline is less steep than predicted on the basis of the deterministic theory but that for weak selection the correlation between random fluctuations in neighboring colonies is approximately the same as in models of migration and drift in the absence of selection.     

Protection of mice from whole-body gamma radiation by deuteration of drinking water

Drinking water made available to mice was changed from ordinary tap water to tap water containing 30 atom% D2O when the animals were 6 to 8 weeks old. Twelve days later, the deuterated mice and an approximately equal number of nondeuterated control mice were subjected to whole-body gamma radiation from a 60Co source. All mice received ordinary tap water after the irradiation. Postirradiation mortality was significantly less in deuterated than in nondeuterated animals. These results may have practical implications for radiotherapy of human malignant tumors.     

Disequilibrium mapping of a quantitative-trait locus in an expanding population.

Linkage disequilibrium (LD) mapping can be successful if there is strong nonrandom association between marker alleles and an allele affecting a trait of interest. The principles of LD mapping of dichotomous traits are well understood, but less is known about LD mapping of a quantitative-trait locus (QTL). It is shown in this report that selective genotyping can increase the power to detect and map a rare allele of large effect at a QTL. Two statistical tests of the association between an allele and a quantitative character are proposed. These tests are approximately independent, so information from them can be combined. Analytic theory is developed to show that these two tests are effective in detecting the presence of a low-frequency allele with a relatively large effect on the character when the QTL is either already a candidate locus or closely linked to a marker locus that is in strong LD with the QTL. The latter situation is expected in a rapidly growing population in which the allele of large effect was present initially in one copy. Therefore, the proposed tests are useful under the same conditions as those for successful LD mapping of a dichotomous trait or disease. Simulations show that, for detection of the presence of a QTL, these tests are more powerful than a simple t-test. The tests also provide a basis for defining a measure of association, gamma, between a low-frequency allele at a putative QTL and a low-frequency allele at a marker locus.     

Trigilletine and tricordatine: Two new bisbenzylisoquinoline alkaloids from Triclisia species

Trigilletine and tricordatine, two new alkaloids from Ghanian menispermaceous species, have structures Ib and Ic, respectively and are examples of phenolic isotrilobine-type (Ia) alkaloids from higher plants.     

Inference of Microbial Recombination Rates from Metagenomic Data

Metagenomic sequencing projects from environments dominated by a small number of species produce genome-wide population samples. We present a two-site composite likelihood estimator of the scaled recombination rate, ρ = 2N_ec, that operates on metagenomic assemblies in which each sequenced fragment derives from a different individual. This new estimator properly accounts for sequencing error, as quantified by per-base quality scores, and missing data, as inferred from the placement of reads in a metagenomic assembly. We apply our estimator to data from a sludge metagenome project to demonstrate how this method will elucidate the rates of exchange of genetic material in natural microbial populations. Surprisingly, for a fixed amount of sequencing, this estimator has lower variance than similar methods that operate on more traditional population genetic samples of comparable size. In addition, we can infer variation in recombination rate across the genome because metagenomic projects sample genetic diversity genome-wide, not just at particular loci. The method itself makes no assumption specific to microbial populations, opening the door for application to any mixed population sample where the number of individuals sampled is much greater than the number of fragments sequenced.