Nei M, Li WH. Mathematical model for studying genetic variation in terms of restriction endonucleases. PNAS USA 76: 5269-5273

Proceedings of the National Academy of Sciences (Impact Factor: 9.67). 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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    • "Genotypic data were subjected to analyses with various measures of genetic diversity within and among genotypes using FSTAT version 2.9.3 and GenAlex software version 6.5 (Goudet, 2001; Peakall and Smouse, 2012). Genetic diversity parameters such as total number of alleles per locus, number of effective alleles per locus, Shannon's Information Index, and gene diversity were determined using the protocol of Nei and Li (1979). Other genetic parameters such as differentiation, gene flow and polymorphic information content (PIC) were estimated using GenAlex software. "
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    ABSTRACT: Genetic diversity assessment of 48 Tanzanian sweetpotato genotypes was conducted using nine polymorphic simple sequence repeat markers to determine genetic relationship and select unique parents which could be used for future breeding. Genetic diversity parameters, cluster analysis, and analysis of molecular variance were calculated to determine genetic diversity and relationships. Results showed that the SSR markers used had the mean PIC of 0.78, allelic richness per locus ranged from 4–17 with a mean of 10.0 and the number of effective alleles varied from 2.2–6.1 with a mean value 3.5. The un-weighted pair group method with arithmetic mean allocated the germplasm collection into three major genetic clusters. The greatest genetic distance was identified between the genotypes sourced from Kagera, Temeke, Mkuranga and Kisarawe areas of Tanzania. The study identified genetically unrelated and complementary sweetpotato genotypes such as Ex-Ramadhani, Kibakuli, Mkombozi,Mjomba mkwe, Ex-Halima-3 and Kabuchenji which are recommended for future breeding programmes.
    South African Journal of Botany 01/2016; 102:40-45. DOI:10.1016/j.sajb.2015.08.001 · 0.98 Impact Factor
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    • "The Dice coefficients were employed by using Simqual subprogram in similarity routine of software NTSYS-pc version 2.2 (Exeter Software, Setauket, NY, U.S.A.) software package. The estimation of genetic similarity (F) were calculated by following the method described elsewhere [11]. The resultant similarity matrix data was employed to construct a dendrogram by using Sequential Agglomerative Hierarchical Nesting (SAHN) based on unweighted pair-group method with an arithmetic average (UPGMA) to infer genetic relationships and phylogeny among cultivars. "
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    ABSTRACT: Salinity stress is the major constraint in rice production. Selection for salinity tolerance genotypes of rice based on phenotypic performance alone is less reliable and will delay in progress in breeding. Recent advent of molecular markers, microsatellites or simple sequence repeats (SSRs) were used to find out salt tolerant rice genotypes. In this study three selected SSR markers viz. RM336, RM510 and RM3412 were used to screen the germplasm for salt tolerance. For genotyping rice germplasm, DNA was extracted from leaf samples using CTAB mini-prep method. The number of allele per locus was 10, with an average number of 10 per locus. The average gene diversity of overall SSR loci for the 25 genotypes was 0.8693, ranging from 0.8608 to 0.8768. The PIC values for 3 SSR markers varied from 0.8456 (RM336) to 0.8645 (RM510) with an average PIC of 0.8556. Unweighted Pair Group Method of Arithmetic Means (UPGMA) dendrogram, constructed from Nei's genetic distance produced three distinct clusters of 25 rice genotypes which is very much similar to Principal Component Analysis (PCA). It can be concluded that Jamai naru, Kajol shail, Hogla, Khak shail, Tal mugur, BINA dhan8 were salt tolerant compared to FL 478 because they showed a lower similarity value with FL 478. Marker RM510 showed the highest level of diversity due to high PIC value. This scientific information could be used for selection of suitable parents and development of salt tolerant rice varieties as well.
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    • "These groups of populations are highlighted in Figure 1. More specifically, the following statistics were estimated using SPADS 1.0 (Dellicour & Mardulyn, 2014): (1) nucleotide diversity p (Nei & Li, 1979) within groups and over the entire range of each species , (2) phylogeographic signal within-species ranges as measured by N ST –G ST (Pons & Petit, 1996), separately for each locus, and (3) AMOVA (hierarchical analysis of molecular variance, Excoffier, Smouse & Quattro, 1992) Φ-statistics to evaluate population structure (with two hierarchical levels: populations, i.e. sampling sites, and groups of populations as shown in Fig. 1 "
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    ABSTRACT: We characterised the phylogeographic patterns displayed by five species of bumblebees with largely overlapping ranges in Eurasia, but different levels of range fragmentation, range size and food specialization. Genetic variation across the range of each species was explored by using sequence variation of a total of 368 specimens at one mitochondrial and two nuclear DNA fragments (total of ~2380 bp). Comparing patterns of genetic variation across species allowed us to investigate whether diet specialization, relative range size and/or fragmentation, impact phylogeographic patterns in bumblebees. As expected, stronger fragmentations of the species range are associated with a stronger overall geographic differentiation. Furthermore, diet specialization appears to increase population structure at the landscape level, presumably due to the less widespread and more heterogeneously distributed food resources. Conversely, no clear association was highlighted between diet specialization or overall range size and genetic diversity. Surprisingly, the two generalist and co-distributed species investigated, B. pratorum and B. hortorum, displayed widely divergent patterns in terms of genetic diversity and population structure. We suggest these differences are best explained by contrasting responses to past climate changes, possibly involving different glacial refuges. Overall, our results are compatible with a combined impact of two interacting parameters on intraspecific genetic variation: environment disturbances (presumably related to past climate changes) and features specific to the organism, such as diet specialization. They thus further highlight the challenge of dissociating both parameters in phylogeographic studies.
    Biological Journal of the Linnean Society 08/2015; DOI:10.1111/bij.12636 · 2.26 Impact Factor
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