Accuracy of estimated phylogenetic trees from molecular data. II. Gene frequency data.

Journal of Molecular Evolution (Impact Factor: 1.86). 02/1983; 19(2):153-70.
Source: PubMed

ABSTRACT 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.

  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Wild pear (Pyrus pyraster (L.) Burgsd.) is pear species growing naturally in Lithuania and is related to cultivated pear (Pyrus communis L.). In some cases, plants identified as P. pyraster represent various stages of hybridization between original P. pyraster and P. communis. Therefore a boundary between cultivated pear, naturalized plants and wild pear is ambiguous. There is limited information on genetic variation and structure of P. pyraster population. The aim of our study was to characterize morphological traits and microsatellite loci of pear originally collected from different localities of Lithuania as naturally growing specimens, presently grown in germplasm collection at the Institute of Horticulture Lithuanian, Research Centre for Agriculture and Forestry (IH LRCAF), and establish capacity of the markers to assess genetic structure of the pear population and suitability for species specific identification. Assessment of thirteen morphological parameters revealed high variation among Pyrus accessions. Morphological differences among the accessions were quantitative rather than qualitative. Characterization of 9 polymorphic microsatellite loci of 84 pear accessions identified 152 polymorphic alleles. The allele number per locus ranged from 12 to 20. The most polymorphic microsatellite loci were EMPc106, EMPc117, NB109a and CH02c11. High genetic polymorphism was demonstrated by genetic relationship and heterozygosity analysis among accessions. Lower Ho than He values indicated possible occurrence of self fertilisation in naturally growing pears.It was shown that morphological variability of Pyrus accessions weakly reflects genetic variation among them. The results of the molecular marker analysis of the accessions of free growing pear collection provided information about genetic background of local pear population that would be useful for restoration and maintaining of genetic diversity of forests.
    Baltic Forestry 01/2013; 19(1):13-21. · 0.30 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: The genome-wide discovery and high-throughput genotyping of SNPs in chickpea natural germplasm lines is indispensable to extrapolate their natural allelic diversity, domestication and linkage disequilibrium (LD) patterns leading to the genetic enhancement of this vital legume crop. We discovered 44844 high-quality SNPs by sequencing of 93 diverse cultivated desi, kabuli and wild chickpea accessions using reference genome- and de novo-based GBS (genotyping-by-sequencing) assays that were physically mapped across eight chromosomes of desi and kabuli. Of these, 22546 SNPs were structurally annotated in different coding and non-coding sequence components of genes. Genes with 3296 non-synonymous and 269 regulatory SNPs could functionally differentiate accessions based on their contrasting agronomic traits. A high experimental validation success rate (92%) and reproducibility (100%) along with strong sensitivity (93-96%) and specificity (99%) of GBS-based SNPs was observed. This infers the robustness of GBS as a high-throughput assay for rapid large-scale mining and genotyping of genome-wide SNPs in chickpea with sub-optimal use of resources. With 23798 genome-wide SNPs, a relatively high intra-specific polymorphic potential (49.5%) and broader molecular diversity (13-89%)/functional allelic diversity (18-77%) was apparent among 93 chickpea accessions, suggesting their tremendous applicability in rapid selection of desirable diverse accessions/inter-specific hybrids in chickpea crossbred varietal improvement program. The genome-wide SNPs revealed complex admixed domestication pattern, extensive LD estimates (0.54-0.68) and extended LD decay (400-500 kb) in a structured population inclusive of 93 accessions. These findings reflect the utility of our identified SNPs for subsequent genome-wide association study (GWAS) and selective sweep-based domestication trait dissection analysis to identify potential genomic loci (gene-associated targets) specifically regulating importan
    Frontiers in Plant Science 03/2015; DOI:10.3389/fpls.2015.00162 · 3.64 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Detecting quantity trait locus (QTLs) and elite alleles that are associated with grain-filling rate (GFR) in rice is essential for promoting the utilization of hybrid japonica rice and improving rice yield. Ninety-five varieties including 58 landraces and 37 elite varieties from the core germplasm collection were genotyped with 263 simple sequence repeat (SSR) markers. The GFR of the 95 varieties was evaluated at five stages, 7, 14, 21, 28 and 35 days after flowering (DAF) both in 2011 and 2012. We found abundant phenotypic and genetic diversity in the studied population. A population structure analysis identified seven subpopulations. A linkage disequilibrium (LD) analysis indicated that the levels of LD ranged from 60.3 cM to 84.8 cM and artificial selection had enhanced the LD. A time-course association analysis detected 31 marker-GFR associations involving 24 SSR markers located on chromosomes 1, 2, 3, 4, 5, 6, 8, 9, 11 and 12 of rice at five stages. The elite alleles for high GFR at each stage were detected. Fifteen excellent parental combinations were predicted, and the best parental combination 'Nannongjing62401×Laolaihong' could theoretically increase 4.086 mg grain-1 d-1 at the five stages. Our results demonstrate that the time-course association mapping for GFR in rice could detect elite alleles at different filling stages and that these elite alleles could be used to improve the GFR via pyramiding breeding.
    PLoS ONE 01/2015; 10(3):e0119959. DOI:10.1371/journal.pone.0119959 · 3.53 Impact Factor