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


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.
    Full-text · Article · Jan 2016 · South African Journal of Botany
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    • "In addition, a distance matrix based on Nei–Li distances (Nei and Li 1979) was used to estimate a neighbor-joining phenogram (NJ, Saitou and Nei 1987) in PAUP* version 4.0b10 (Swofford 2002). Bootstrap support was estimated based on 10,000 replicates using the NJ algorithm. "
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    ABSTRACT: Quercus ilex L. (holm oak) is a wind-pollinated, sclerophyllous tree that copes with the environmental variability of the Mediterranean climate and that displays flexible ecophysiological adaptability in relation to hydric and thermic stresses. The holm oak dominates Mediterranean woodlands on both acidic and calcareous soils and has been exposed to management (dehesas) for thousands of years. Both protected areas and glacial refugia are supposed to preserve a substantial fraction of the genetic diversity of Iberian species. Genetic diversity was examined for 68 populations sampled throughout Spain using ptDNA SNPs, ptDNA microsatellites, and primarily nuclear AFLPs. Protected populations did not significantly differ from nonprotected populations by any of the measures of levels of genetic diversity. The three-level hierarchical AMOVA indicated that a low number of protected populations harbor most of the species' genetic diversity. In addition , we found no evidence from either ptDNA or AFLP variation to support that populations from putative glacial refugia are divergent genetic groups as expected during isolation. Outcrossing, anemophilous long-distance pollen dispersal, acorn transport by animals, tree reliance, and habitat availability in Spain probably played a primarily role in homogenizing allele frequency among populations. This result leads us to suggest that extensive gene flow has been prevalent across Spanish populations. We conclude that glacial refugia have not been essential to maintain the neutral genetic makeup of Q. ilex. Nevertheless, conservation of the holm oak in protected areas ensures protection of the species' genetic diversity , the most widespread woodland ecosystem in Iberia and indirectly the four iconic, endangered animal species (black stork, cinereous vulture, Iberian lynx, western imperial eagle).
    Full-text · Article · Nov 2015 · Tree Genetics & Genomes
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    • "To estimate the net nucleotide divergence, d, we assumed that the ancestral coalescence time was similar to the present one and estimated h p from the available samples. Then, h p /2 was subtracted from the average divergence d xy (Nei and Li, 1979). Among the available samples, we used the five largest samples (all with size greater than 15 individuals), including two samples from the Southern Hemisphere (PAT and KER, AM905187–AM905211), two samples of M. edulis from Sweden (AY723897–AY723917) and Nova Scotia (AF241951–AF24195157, AY130016–AY130023, AY723881–AY723887, AY723889, AY723890) and a sample of M. trossulus (AY130061–AY130067, AF242027–AF242029, AF242031– AF242035). "

    Full-text · Dataset · Oct 2015
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