Nei M, Tajima F, Tateno Y.. Accuracy of estimated phylogenetic trees from molecular data. II. Gene frequency data. J Mol Evol 19: 153-170

Journal of Molecular Evolution (Impact Factor: 1.68). 02/1983; 19(2):153-70. DOI: 10.1007/BF02300753
Source: PubMed


The accuracies and efficiencies of three different methods of making phylogenetic trees from gene frequency data were examined by using computer simulation. The methods examined are UPGMA, Farris' (1972) method, and Tateno et al.'s (1982) modified Farris method. In the computer simulation eight species (or populations) were assumed to evolve according to a given model tree, and the evolutionary changes of allele frequencies were followed by using the infinite-allele model. At the end of the simulated evolution five genetic distance measures (Nei's standard and minimum distances, Rogers' distance, Cavalli-Sforza's f theta, and the modified Cavalli-Sforza distance) were computed for all pairs of species, and the distance matrix obtained for each distance measure was used for reconstructing a phylogenetic tree. The phylogenetic tree obtained was then compared with the model tree. The results obtained indicate that in all tree-making methods examined the accuracies of both the topology and branch lengths of a reconstructed tree (rooted tree) are very low when the number of loci used is less than 20 but gradually increase with increasing number of loci. When the expected number of gene substitutions (M) for the shortest branch is 0.1 or more per locus and 30 or more loci are used, the topological error as measured by the distortion index (dT) is not great, but the probability of obtaining the correct topology (P) is less than 0.5 even with 60 loci. When M is as small as 0.004, P is substantially lower. In obtaining a good topology (small dT and high P) UPGMA and the modified Farris method generally show a better performance than the Farris method. The poor performance of the Farris method is observed even when Rogers' distance which obeys the triangle inequality is used. The main reason for this seems to be that the Farris method often gives overestimates of branch lengths. For estimating the expected branch lengths of the true tree UPGMA shows the best performance. For this purpose Nei's standard distance gives a better result than the others because of its linear relationship with the number of gene substitutions. Rogers' or Cavalli-Sforza's distance gives a phylogenetic tree in which the parts near the root are condensed and the other parts are elongated. It is recommended that more than 30 loci, including both polymorphic and monomorphic loci, be used for making phylogenetic trees. The conclusions from this study seem to apply also to data on nucleotide differences obtained by the restriction enzyme techniques.

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    • "Genetic affinities among collections were examined with an unrooted neighbor-joining (NJ) analysis of Nei's D A distance (Nei et al. 1983) bootstrapped over all loci (10,000 replications) using POPTREE2 (Takezaki et al. 2010). Genetic relationships among locations were assessed with a Principal Coordinate Analysis (PCoA) of pairwise F ST values generated by FSTAT, using GenAlEx (v.6.41; "
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    ABSTRACT: Stocking programs have been used extensively to mitigate declines in anadromous fishes, but these programs can have long-term unintended genetic consequences. Stocking can homogenize population structure, impede local adaptation, and hinder the use of genetic stock identification as a fishery management tool. Using 12 microsatellite loci, we evaluate the spatiotemporal genetic structure of 16 anadromous alewife (Alosa pseudoharengus) populations in Maine, USA, to determine whether inter-basin stocking practices have influenced population structure and the genetic diversity of the species in this region. Although, no pre-supplementation samples exist, comparative analyses of stocked and non-stocked populations show that stock transfers have influenced alewife population genetic structure. Genetic isolation by distance (IBD) was non-significant among stocked populations, but significant among non-stocked populations. However, two populations, Dresden Mills and Sewell Pond, appear to have resisted genetic homogenization despite stocking. Non-significant genic and genetic differentiations were broadly distributed among alewife populations. Hierarchical AMOVA indicated highly significant differentiation among temporal replicates within populations, and Bayesian clustering analysis revealed weak population structure. A significant correlation was observed between stocking (time and events) and pairwise \({\text{F}}_{\text{ST}}^{{\prime }}\) among alewife collections, and an analysis of IBD residuals showed a significant decline in the amount of genetic differentiation among populations as the extent of stocking activity increased. These findings call for an increased awareness of evolutionary processes and genetic consequences of restoration activities such as inter-basin stock transfers by fisheries management and conservation practitioners.
    Conservation Genetics 10/2015; 16(5). DOI:10.1007/s10592-015-0733-1 · 2.19 Impact Factor
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    • "The genotyping results were employed to perform a cluster analysis using the PowerMarker software (Liu and Muse, 2005). Nei's genetic distance (Nei et al., 1983) was used, and the support values for the degree of confidence at the nodes of the dendrogram were analyzed by bootstrap re-sampling 1000 times. Phylip 3.69 software (Felsenstein, 1997) was employed to construct the consensus tree and TreeView32 (Page, 1996) to visualize it. "
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    ABSTRACT: Melon has undergone an intense process of selection and crossbreeding, resulting in many landraces distributed all over Europe, Africa and Asia. Due to this huge variability, the systematic position of this taxon has been reviewed many times in the last two decades. The goal of this article is to compare the phenotypic characterization achieved by seed features with the molecular analysis on melon genotypes. A set of 124 accessions of Cucumis melo has been selected for molecular and morpho-colourimetric analyses plus an additional selection of accessions of Cucumis sativus, Citrullus lanatus and Citrullus colocynthis used to highlight seed morphology distances among genus and species. Genotyping was performed on the basis of 211 polymorphic SNPs and was executed using the iPLEX® Gold MassARRAY Sequenom technology. A total of 137 parameters were specifically designed to evaluate seed colour, size, shape and texture. Both molecular and seed morpho-colourimetrical analyses confirm the existence of two melon subspecies while an intermediate group has also been found. A non random allelic distribution in SNPs located in specific genomic regions suggests that some of these regions may account for a part of the observed variation in seed size. Six major groups of varieties can be discriminated on the basis on seed traits.
    Scientia Horticulturae 08/2015; 192:441-452. DOI:10.1016/j.scienta.2015.06.006 · 1.37 Impact Factor
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    • "Different prioritization methods were utilized through measuring the breed contribution to aggregate genetic diversity (contributions to the between-breed and to the within-breed diversity) as in the following: a) According to Ollivier and Foulley method (Ollivier and Foulley, 2005), the contribution to between-breed diversity (CB) was computed by estimation of Weitzman values (Weitzman, 1993) based on the Nei's genetic distance (Nei et al., 1983) with WEITZPRO (Derban et al., 2002). Within breed contributions to diversity (CW) were calculated using the average values of within-breed expected heterozygosity as in the formula: H k = 1-H(S/k) / H(S), where H k is the contribution to within-breed diversity (CW) of breed k, H(S) is the average internal heterozygosity of the whole set S and H(S/k) the average internal heterozygosity of the set excluding breed k. "
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    DESCRIPTION: Genetic diversity is essential in optimizing both conservation and utilization strategies for animal genetic resources. Local poultry breeds make up most of the world’s poultry genetic diversity, and are still very important in developing countries where they represent up to 95 percent of the total poultry population. Local Egyptian poultry breeds are highly adapted to harsh environmental conditions and thought to constitute genetic reservoirs. For instance, Fayoumi chicken breed can be seen as a unique breed from the viewpoint of disease resistance and Sinai chicken strain possesses superiority in heat tolerance. The development and increased focus on more efficient selection programmes have accelerated genetic improvement in a number of breeds. As a result, highly productive breeds have replaced local ones across the world. Moreover, intensive selection caused narrowing of genetic base and inbreeding which is associated with declines in both population fitness and disease resistance. This development has led to growing concerns about the erosion of genetic resources, as the genetic diversity of low productive local breeds is likely to contribute to current or future traits of interest and they are considered essential for maintaining future breeding options. The first problem for conservation is the lack of information, so the identification and genetic characterization of all breeds particularly local ones has high priority in the FAO global strategy. Information of poultry genetic resources is considered a useful model for studying conservation of genetic diversity in wild animal species. Therefore in this study, I evaluated the genetic diversity of Egyptian chickens and pigeons in order to apply this information for conservation purpose by using two different strategies. The first strategy (in chapter 2) was maximization of genetic diversity based on neutral microsatellites genetic markers while the second strategy (in chapter 3) was genetic improvement by low selective pressure based on functional gene polymorphisms. For the first strategy, I evaluated the genetic structure, breeds diversity and the breed contribution to aggregate genetic diversity as important criteria for their conservation by utilizing three different prioritization methods in order to set the priorities for conservation of Egyptian chickens and pigeons based on neutral genetic markers (microsatellites). For chickens, the six studied Egyptian populations showed a moderate level for both within-population (MNA = 4.9; HE = 0.595) and between-population (FST = 0.082) genetic diversity and were clustered into four clusters by STRUCTURE. Fayoumi, Dandarawy and El-Salam populations were assigned independently into their respective clusters while the remaining three populations (Baladi, Sinai and Golden Montazah) were clustered together forming admixed mosaic cluster. Regarding breed contribution to aggregate genetic diversity, Dandarawy breed contributed the most and ranked the first, while Fayoumi breed contributed negatively to aggregate genetic diversity and ranked the last. For pigeons, the six studied Egyptian populations showed moderate within-population (MNA = 4.10; HE = 0.584) and high between-population (FST = 0.211) genetic diversity. The Egyptian in addition to Japanese racing pigeon populations were clustered into six clusters. Krezly, Safi, Romani, Ablaq and Japanese racing populations were assigned independently into their respective clusters while the remaining two populations (Asfer Weraq and Zagel) appeared as a mosaic clusters. Zagel breed contributed the most and ranked the first, while Asfer Weraq ranked the last in the contribution for aggregated genetic diversity. For the second strategy, I focused on the genes which might be related with effective utilisation of the poultry genetic resources. The polymorphisms of functional genes might be used as genetic markers for selection of high performance pigeons. For instance, the Lactate dehydrogenase gene family is involved in aerobic and anaerobic metabolism; therefore it determines muscle endurance, recovery and aerobic capacity. I found that the long allele (600bp) of Lactate dehydrogenase-A (LDH-A) gene showed significantly higher frequencies than short one (595bp) in the homing than non-homing in both Japanese and Egyptian pigeons and it might be useful for conservation and sustainable utilisation through improvement of local population’s performance. Also for wildlife, basic understanding of LDH-A genotype and homing ability might be useful for studying of wild migrating birds. Consideration of neutral genetic diversity and functional genes diversity in addition to breed merits and threat status, enabled us to balance the trade-offs between conserving genetic diversity as insurance against future uncertainties and current sustainable utilization.
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