Nei, M. and Li, W. H.. Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc Natl Acad Sci USA. 76: 5269-5273

Proceedings of the National Academy of Sciences (Impact Factor: 9.81). 11/1979; 76(10):5269-73. DOI: 10.1073/pnas.76.10.5269
Source: PubMed

ABSTRACT A mathematical model for the evolutionary change of restriction sites in mitochondrial DNA is developed. Formulas based on this model are presented for estimating the number of nucleotide substitutions between two populations or species. To express the degree of polymorphism in a population at the nucleotide level, a measure called "nucleotide diversity" is proposed.

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    • "estimated at intra-population level (Nei and Li, 1979). Principal coordinate analysis (PCoA) and the Mantel Z-statistic between DAMD and ISSR datasets were carried out using the program GenAlEx ver. "
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    ABSTRACT: Genetic variability and population structure of Bergenia ciliata (Haw.) Sternb., commonly known as “Pashanbheda” (Stone-breaker), collected from the Western Himalayan region of India were estimated using two DNA fingerprinting methods viz., directed amplification of minisatellite DNA (DAMD) and inter simple sequence repeats (ISSR). The cumulative data analysis of DAMD and ISSR markers for 74 accessions from eight populations showed 86.1% polymorphism. Analysis of molecular variance (AMOVA) showed highest percentage of variation within individuals of populations (73.6%) and 21.7% among populations. STRUCTURE and PCoA analyses on the hierarchical partitioning of genetic diversity showed strong admixture of individuals among the eight assumed geographical populations of B. ciliata. The data suggests that high genetic flow is one of the major factors responsible for low genetic differentiation. Preservation of genetic diversity of B. ciliata is important, both to promote adaptability of the populations to changing environment as well as to preserve a large gene pool for future prospection. The present study using DAMD and ISSR markers, therefore, provide the means of rapid characterization of accessions within the populations, and thus enable the selection of appropriate accessions for further utilization in conservation and prospection programmes.
    Biochemical Systematics and Ecology 06/2015; 60:165-170. DOI:10.1016/j.bse.2015.04.018 · 1.17 Impact Factor
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    • "base pair alignment of mtCR was arranged for 179 individuals of C. temensis, in which there were 32 variable positions (21 parsimony informative; nucleotide diversity, p, on a per site basis, of 0.01334), and which exhibited 26 unique sequences among individuals (haplotypes, including gaps). Nei and Li's (1979) estimator of diversity (p,) at localities for which we had more than one sample ranged from 0 to 0.109, Watterson's (1975) estimator of diversity (h) ranged from 0 to 0.0119, and haplotype diversity ranged from 0 to 0.83 (Table 1). Statistics of neutrality or demographic change (Tajima's D and Fu's Fs) were marginally significant for a few localities, but not after correction for multiple tests. "
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    • "We used three mitochondrial (total 2.8 kb) and seven singlecopy nuclear gene fragments (total 3.5 kb). These genes [length, nucleotide diversity (π) (Nei & Li, 1979) and Watterson estimator (θ) (Watterson, 1975) considering only one sequence per species] are: the mitochondrial rRNA genes 12S (975 bp, "
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    ABSTRACT: AimThe evolutionary speed hypothesis is a mechanistic explanation for the latitudinal biodiversity gradient. The recently extended integrated evolutionary speed hypothesis (IESH) proposes that temperature, water availability, population size and spatial heterogeneity influence the rate of molecular evolution which, in turn, affects diversification. However, the evidence for some of the associations predicted by the IESH is not conclusive, and in some cases is contradictory.LocationThe Neotropics.Methods Using a comparative Bayesian method we tested the following predictions of the IESH: the association between the rate of molecular evolution and temperature (and elevation and latitude, as proxies), water availability (using precipitation and relative humidity as proxies), productivity and rate of diversification. We also accounted for the potential confounding effects of body size and UVB radiation. We tested these predictions separately in mitochondrial and nuclear genes.ResultsSubstitution rates of mitochondrial and nuclear genes were positively associated with temperature and negatively with elevation, while only the mitochondrial coding gene rate was associated with UVB radiation. However, when controlling for temperature, the association between substitution rate and elevation and UVB radiation disappeared, while a negative association with precipitation emerged. Moreover, diversification events were positively correlated with the rate of molecular evolution but only in mitochondrial genes.Main conclusionsOur results support two key predictions of the IESH. They highlight the important association between rate of molecular evolution and temperature within a recently diverged group and also confirm the positive association between molecular evolution and diversification rate, although only in mitochondrial genes. However, the lack of association between diversification and temperature and the low effect size of the relationship between substitution rates and diversification in mitochondrial genes emphasize the important role other factors, such as time, spatial heterogeneity and population size might have in the origin and maintenance of the latitudinal biodiversity gradient.
    06/2015; 24(7). DOI:10.1111/geb.12318
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