Random amplified polymorphic DNA diversity of marginal and central populations in Pinus contorta subsp. latifolia

Genome ◽  
2001 ◽  
Vol 44 (1) ◽  
pp. 13-22 ◽  
Author(s):  
Aron J Fazekas ◽  
Francis C Yeh
Keyword(s):  
Pinus Contorta ◽  
Random Amplified Polymorphic Dna ◽  
Single Locus ◽  
Population Subdivision ◽  
Founder Effects ◽  
Marginal Populations ◽  
Clear Trend ◽  
Wahlund Effect ◽  
Multilocus Associations ◽  
F Statistics

Fifteen populations of lodgepole pine (Pinus contorta subsp. latifolia) were surveyed for diversity across 52 random amplified polymorphic DNAs (RAPDs). The objective was to compare single-locus and multilocus structures in four marginal, three intermediate, and eight central populations. Single-locus estimates indicated average observed and expected heterozygosity to be 0.19 and 0.17, respectively. When these estimates were split into population categories, a clear trend of increasing diversity was detected in the direction of marginal to central populations. F-statistics indicated an excess of heterozygotes, with FIS ranging from -0.08 for marginal populations to -0.15 for central populations and averaging -0.12 over 15 populations. The estimates of FST decreased towards the margins of the species range, indicating increased population differentiation. Forty-nine of 52 RAPDs tested neutral in the Ewens-Watterson analysis. Multilocus analysis showed significant two-locus and high-order gametic disequilibria in all 15 populations. The most prominent components of the two-locus analysis were the variance of disequilibrium (VD, 46.2%) and the multilocus Wahlund effect (31.9%). This high value for VD indicated that founder effects could explain much of the observed multilocus associations. When analyzed by population categories, the VD showed a decreasing trend indicating that variation due to founder effects was more prominent in marginal populations. The two-locus Wahlund effect (WC) that is characteristic of strong population subdivision was highest in the central populations. This indicated significant levels of gene flow between populations with different allelic combinations.Key words: multilocus genetic structure, central and marginal populations, RAPD, Pinus contorta subsp. latifolia.

Genetic variability in the canker pathogen fungus, Gremmeniella abietina. 2. Fine-scale investigation of the population genetic structure

1997 ◽  
Vol 75 (9) ◽  
pp. 1460-1469 ◽  
Author(s):  
Xiao-Ru Wang ◽  
Alfred E. Szmidt ◽  
Richard A. Ennos ◽  
Per Hansson
Keyword(s):  
Genetic Variability ◽  
Population Genetic ◽  
Pinus Contorta ◽  
Random Amplified Polymorphic Dna ◽  
Sampling Site ◽  
Population Subdivision ◽  
Northern Sweden ◽  
Canker Pathogen ◽  
Total Genetic Diversity ◽  
Small Clusters

Genetic variation at 32 polymorphic random amplified polymorphic DNA loci was analysed in the ascomycete canker pathogen fungus Gremmeniella abietina (Lagerb.) Morelet collected from one plantation of Pinus contorta Dougl. ex Loud, in northern Sweden. The genetic variability maintained in the G. abietina population was high. Many different multilocus genotypes were found on each tree and in each sampling site within the plantation. The clonal fraction of the population was small, and identical genotypes were found either on the same tree or branch or on trees in the same sampling site. The finding of very few widely distributed clones suggests that the effective dispersal of asexual spores is limited to a few metres and resulted in small clusters of clones in local sites. Analysis of molecular variance revealed that 45.3% of the total variation was attributable to differences among isolates within trees, 22.5% to trees within sites and 32.3% to sampling sites differences. Allele frequencies at most of the loci varied significantly among the sampling sites and average total genetic diversity over the 32 loci was 0.27 indicating high population subdivision. The factors that could have contributed to the observed population structure were discussed. Key words: Gremmeniella abietina, genotype and clone distribution, population subdivision, RAPD.

Multilocus structure in the Pinus contorta – Pinus banksiana complex

2007 ◽  
Vol 85 (8) ◽  
pp. 774-784 ◽  
Author(s):  
Rong-Cai Yang ◽  
Francis C. Yeh ◽  
Terrance Z. Ye
Keyword(s):  
Population Structure ◽  
Pinus Banksiana ◽  
Pinus Contorta ◽  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Natural Hybridization ◽  
Gene Pools ◽  
Different Populations ◽  
Multilocus Associations ◽  
Gametic Disequilibria

Natural hybridization between lodgepole pine ( Pinus contorta Dougl. ex Loud.) and jack pine ( Pinus banksiana Lamb.) in western Canada provides a distinct opportunity to infer evolutionary and demographic determinants of nonrandom associations of the alleles at different loci occurring in this Pinus contorta – Pinus banksiana complex (PCBC). Here, we investigated multilocus associations among and within 40 PCBC populations sampled from central and northwestern Alberta, using 39 random amplified polymorphic DNA (RAPD) markers. For each of the 40 PCBC populations, we examined distributions of 741 pairs of linkage (gametic) disequilibria (LD) between the 39 RAPDs and measured the “average” multilocus associations using the summary statistics that allow for packaging of individual LD in each population. We then partitioned the variance of LD in the total population to assess the causes of multilocus population structure. The results showed that (i) LD were more prominent in hybrid populations than in parental populations; (ii) multilocus Wahlund effect was a much more important determinant of population structure than its single-locus counterpart, particularly in hybrid populations; and (iii) considerable mutlilocus associations across the populations within each taxa group was due to the presence of different multilocus haplotypes in different populations. Such results are best explained by the fact that PCBC populations are geographically and ecologically marginal and are produced at the balance between mixing of two distinct gene pools creating new recombinants and selection in favor of parental gametes, but against the recombinants.

Genetic variability among and within closely spaced populations of lodgepole pine

1984 ◽  
Vol 26 (2) ◽  
pp. 177-184 ◽  
Author(s):  
Peggy Knowles
Keyword(s):  
Genetic Variability ◽  
Pinus Contorta ◽  
Lodgepole Pine ◽  
Elevational Gradient ◽  
Front Range ◽  
Genetic Composition ◽  
Genetic Pattern ◽  
Breeding Groups ◽  
Slight Deficiency ◽  
F Statistics

The genetic composition of Pinus contorta var. latifolia as determined by isozyme analysis was assessed and examined at two hierarchical levels; within closely spaced populations and within adjacent subpopulations. Four populations of lodgepole pine consisting of 125 trees each were sampled along an elevational gradient spanning a distance of approximately 2 km in the Front Range of the Rocky Mountains in Colorado. Each population was further divided into five subpopulations. Four isozymes were electrophoretically resolved from needle tissue removed from each tree. Statistics characterizing the genetic structure were calculated including measures of genetic variability, tests of allelic heterogeneity, and F statistics. The results indicate that lodgepole pine has a relatively low level of genetic variation with 44% of its loci polymorphic, an average of 1.33 alleles per locus, heterozygous at 13.5% of their loci, and a polymorphic index of 0.144. Slightly less than 1% of the observed genetic variability resided among the four populations with the remainder residing among the individuals within populations. A slight deficiency of heterozygotes was indicated by the F statistics analysis. Allelic distributions at the subpopulation level indicated that clustering was evident although not a predominant characteristic of the genetic pattern. It is suggested that inbreeding and (or) the pooling of individuals from different breeding groups are likely phenomena contributing to the genetic pattern in lodgepole pine over microgeographical distances.Key words: genetic variability, lodgepole pine, Pinus contorta var. latifolia, isozyme.

scholarly journals Populational genetic structure of free-living maned wolves (Chrysocyon brachyurus) determined by proteic markers

2004 ◽  
Vol 64 (3b) ◽  
pp. 639-644 ◽  
Author(s):  
P. S. R. De Mattos ◽  
M. A. Del Lama ◽  
R. H. Toppa ◽  
A. R. Arno Rudi Schwantes
Keyword(s):  
Total Sample ◽  
Electrophoretic Analysis ◽  
Genetic Distances ◽  
Population Subdivision ◽  
Plasma Samples ◽  
Free Living ◽  
Paulo State ◽  
Genotype Frequencies ◽  
Chrysocyon Brachyurus ◽  
F Statistics

Electrophoretic analysis of presumptive twenty gene loci products was conducted in hemolisates and plasma samples of twenty-eight maned wolves (Chrysocyon brachyurus) from an area in northeastern São Paulo State, Brazil. The area sampled was divided into three sub-areas, with the Mogi-Guaçu and Pardo rivers regarded as barriers to the gene flow. The polymorphism degree and heterozygosity level (intralocus and average) estimated in this study were similar to those detected by other authors for maned wolves and other species of wild free-living canids. The samples of each sub-area and the total sample exhibited genotype frequencies consistent with the genetic equilibrium model. The values of the F-statistics evidenced absence of inbreeding and population subdivision and, consequently, low genetic distances were found among the samples of each area.

THE ORGANIZATION OF GENETIC VARIABILITY IN CENTRAL AND MARGINAL POPULATIONS OF LODGEPOLE PINE PINUS CONTORTA spp. LATIFOLIA

1979 ◽  
Vol 21 (4) ◽  
pp. 487-503 ◽  
Author(s):  
F. C. Yeh ◽  
C. Layton
Keyword(s):  
Genetic Variability ◽  
Pinus Contorta ◽  
Gene Diversity ◽  
Lodgepole Pine ◽  
Clinal Variation ◽  
Marginal Populations ◽  
Variation Patterns ◽  
Mutation Theory ◽  
Neutral Mutation Theory ◽  
Made In

A survey was conducted of genetic variation at 25 loci in extracts of individual megagametophytes of lodgepole pine. Collections were made in nine widely separated localities representing four marginal, two intermediate and three central populations. Single populations of lodgepole pine were, on the average, polymorphic at 58.67% of their loci, and had 1.90 alleles per locus. Both expected and observed heterozygosity averaged 0.16. There was a definite trend towards decreased genetic variability at the margins. The measures of gene diversity for the 25 loci showed a 4% but significant effect of interpopulation differentiation; 96% of the total gene diversity resided within populations. Estimated outcrossing rates [Formula: see text] for the nine populations ranged between 0.92–1.29. Comparisons among populations with different levels of outcrossing revealed no clear relationship between [Formula: see text] and amount of genetic variability. The overall pattern of genetic differentiation agrees with expectations based on the neutral mutation theory. However, two loci demonstrated conspicuous clinal variation patterns which may be incompatible with this stochastic model.

scholarly journals A Comparison of Isozyme and Quantitative Genetic Variation in Pinus contorta ssp. latifolia by FST

Genetics ◽  
1996 ◽  
Vol 142 (3) ◽  
pp. 1045-1052 ◽  
Author(s):  
Rong-Cai Yang ◽  
Francis C Yeh ◽  
Alvin D Yanchuk
Keyword(s):  
Specific Gravity ◽  
Population Differentiation ◽  
Regional Differences ◽  
Pinus Contorta ◽  
Continuous Distribution ◽  
Branch Length ◽  
Stem Diameter ◽  
Stem Height ◽  
Branch Angle ◽  
F Statistics

Abstract We employed F-statistics to analyze quantitative and isozyme variation among five populations of Pinus contorta ssp. latifolia, a wind-pollinated outcrossing conifer with wide and continuous distribution in west North America. Estimates of population differentiation (FST) for six quantitative traits were compared with the overall estimate of the differentiation (FST∗) from 19 isozymes that tested neutral to examine whether similar evolutionary processes were involved in morphological and isozyme differentiation. While the FST estimates for specific gravity, stem diameter, stem height and branch length were significantly greater than the FST∗ estimate, as judged from the 95% confidence intervals by bootstrapping, the FST estimates for branch angle and branch diameter were indistinguishable from the FST∗ estimate. Differentiation in stem height and stem diameter might reflect the inherent adaptation of the populations for rapid growth to escape suppression by neighboring plants during establishment and to regional differences in photoperiod, precipitation and temperature. In contrast, divergences in wood specific gravity and branch length might be correlated responses to population differentiation in stem growth. Possible bias in the estimation of FST due to Hardy-Weinberg disequilibrium (FIS ≠ 0), linkage disequilibrium, maternal effects and nonadditive genetic effects was discussed with special reference to P. contorta ssp. latifolia.

scholarly journals Genetic Diversity and Pathogenic Variation of Colletotrichum lindemuthianum in the Three Centers of Diversity of Its Host, Phaseolus vulgaris

1997 ◽  
Vol 87 (8) ◽  
pp. 807-813 ◽  
Author(s):  
D. Sicard ◽  
Y. Michalakis ◽  
M. Dron ◽  
C. Neema
Keyword(s):  
Genetic Diversity ◽  
Phaseolus Vulgaris ◽  
Common Bean ◽  
Random Amplified Polymorphic Dna ◽  
Geographic Origin ◽  
Colletotrichum Lindemuthianum ◽  
Population Subdivision ◽  
Gene Pools ◽  
Internal Transcribed Spacer Region ◽  
Mexican Strains

Population subdivision of Colletotrichum lindemuthianum, the causal agent of anthracnose, was studied in three regions located in three centers of diversity of its host, Phaseolus vulgaris. Random amplified polymorphic DNA (RAPD) markers, restriction endonuclease analysis of the amplified ribosomal internal transcribed spacer region, and virulence on a set of 12 cultivars were used to assess the genetic diversity of C. lindemuthianum strains isolated in Mexican, Ecuadorian, and Argentinean wild common bean populations. The three regions were significantly differentiated for molecular markers. For these markers, Mexico was the most polymorphic and the most distant from Ecuador and Argentina. The majority of the RAPD alleles present in Ecuador and Argentina were found in Mexico, suggesting that Andean populations have been derived from the Mesoamerican center. Pathogenicity tests on a set of 12 cultivars showed that all but one of the Mexican strains were virulent exclusively on Mesoamerican cultivars. Argentinean strains were virulent preferentially on southern Andes cultivars, and the Ecuadorian strains, except for one strain, were avirulent on all cultivars. These results suggest an adaptation of strains on cultivars of the same geographic origin. Thus, based on molecular and virulence markers, C. lindemuthianum strains isolated from wild common bean populations were divided into three groups corresponding to host gene pools.

scholarly journals Genetic Variation and Differentiation at Microsatellite Loci in Drosophila simulans: Evidence for Founder Effects in New World Populations

Genetics ◽  
1998 ◽  
Vol 150 (2) ◽  
pp. 777-790 ◽  
Author(s):  
Steven D Irvin ◽  
Kris A Wetterstrand ◽  
Carolyn M Hutter ◽  
Charles F Aquadro
Keyword(s):  
Microsatellite Loci ◽  
New World ◽  
Allozyme Variation ◽  
Drosophila Simulans ◽  
Population Subdivision ◽  
South American ◽  
Founder Effects ◽  
Closely Related Species ◽  
Similar Survey ◽  
North And South

Abstract Drosophila simulans isofemale lines from Africa, South America, and two locations in North America were surveyed for variation at 16 microsatellite loci on the X, second, and third chromosomes, and 18 microsatellites, which are unmapped. D. simulans is thought to have colonized New World habitats only relatively recently (within the last few hundred years). Consistent with a founder effect occurring as colonizers moved into these New World habitats, we find less microsatellite variability in North and South American D. simulans populations than for an African population. Population subdivision as measured at microsatellites is moderate when averaged across all loci (FST = 0.136), but contrasts sharply with previous studies of allozyme variation, which have showed significantly less differentiation in D. simulans than in D. melanogaster. There are substantially fewer private alleles observed in New World populations of D. simulans than seen in a similar survey of D. melanogaster. In addition to possible differences in population size during their evolutionary histories, varying colonization histories or other demographic events may be necessary to explain discrepancies in the patterns of variation observed at various genetic markers between these closely related species.

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