Population genetic structure of Yushania niitakayamensis (Bambusoideae, Poaceae) in Taiwan

Yushania niitakayamensis is distributed in Taiwan, south-west China and northern Philippines. In Taiwan, the species occurs in the central mountain ranges from 1500 to 3500 m in altitude. Morphological variation, especially in terms of plant height, is large, with plants ranging from 10 cm to 5 m in height. The species appears to spread mainly by rhizomes and flowers rarely, leading to the prediction that most populations are comprised of a single or a few clonal genotypes and that the observed morphological variation is primarily due to phenotypic plasticity. The purpose of the present study was to investigate the genetic structure of this species on Mt Hohuan in central Taiwan. Ten plants from a single clone and ten plants of unknown genetic background were surveyed at one site in order to select RAPD primers useful for clone identification. Plants at a second site were collected at 1-m intervals across a 50-m transect through the population. Plants at one extreme (exposed portion) of the transect were approximately 15–30 cm in height, whereas plants up to 410 cm in height were found at the other shaded end of the transect. Comparison of amplification profiles for 12 primers revealed that in contrast to our predictions of genetic uniformity, many samples had reproducibly different RAPD amplification profiles, with the 51 samples representing 31 clones. These data imply that the clone size is relatively small, and the population is actually highly diverse genetically. The genetic variation in this population may be due to a higher frequency of sexual reproduction during the evolutionary history of the species and/or a high somatic mutation rate for RAPD loci in clones of Yushania.     

The spatial distribution of chloroplast DNA and allozyme polymorphisms within A population of Silene alba (Caryophyllaceae)

Genetic structure within a population of Silene alba was studied using a chloroplast DNA (cpDNA) and six allozyme polymorphisms. A 20 × 65 m area was sampled by constructing a 5 × 5 m grid and determining the genotype of the plant nearest to each grid node. Analysis of the spatial distribution of genotypes by Moran's I and join-counts showed a significant degree of association of like cpDNA haplotypes (I = 0.52, S.N.D. = 2.55) but a random or slightly repulsed distribution of allozyme genotypes. A second sample was taken by collecting all individuals from within a 1-m wide transect established along the perimeter of the grid. Genotype and allele frequencies were calculated by grouping individuals from arbitrary 3-m intervals along the transect, and analyzed by Wright's F statistics. The F_st value calculated for cpDNA (0.875) differed markedly from that based on all allozymes (0.027). Taken together, the results suggest that in this population gene flow in the maternally inherited cpDNA is limited by restricted seed dispersal, whereas gene flow in the nuclear DNA based allozymes is more pervasive owing to the added effects of pollen dispersal. The utility of cpDNA polymorphism for the study of fine-scale gene flow is discussed.     

Local-scale genetic structure in the peatmoss Sphagnum fuscum

Sphagnum (peatmoss) dominates huge areas of the Northern Hemisphere and acts as a significant carbon sink on a global scale, yet little is known about the genetic structure of Sphagnum populations. We investigated genetic structure within a population of the common peatmoss Sphagnum fuscum, to assess local patterns of genetic diversity and the spatial extent of clones. One hundred seventeen shoots were sampled from five transects in Fuglmyra, central Norway, and sequenced for three anonymous DNA regions. Five neighbourhood patches were marked along each transect, and from each patch, five stems were sampled for molecular analyses. Seventeen haplotypes could be distinguished and two major groups of haplotypes differed by 12 mutational steps. The two major haplotype groups differed significantly in microhabitat association along the distance to groundwater table and the pH gradients, indicating microhabitat differentiation. The haplotypes within these groups were all genetically similar, differing by one or two mutations. The most common haplotype occurred in four transects separated by 250-m distance. Most of the molecular variation in the population was found among transects, and within patches. Large dominating clones within each transect resulted in low variation explained by the among-patch-within-transect component of spatial structure. Mutation appears to account for a larger proportion of the population variation than recombination. Within the population, vegetative growth and asexual reproduction from gametophyte fragments dominate as the main reproductive mode.     

MICROGEOGRAPHIC GENETIC STRUCTURE OF MORPHOLOGICAL AND LIFE HISTORY TRAITS IN A NATURAL POPULATION OF IMPATIENS CAPENSIS

To investigate the microgeographic spatial structure of genetic variation for quantitative traits in a natural population of Impatiens capensis, we performed a common-garden greenhouse experiment. Seedlings were collected at 10-m intervals from a 40 times 40-m permanent grid in a natural population and grown to maturity in a greenhouse. From these parents, 3 self-fertilized seed families per grid point were then grown in a randomized design in the greenhouse and scored for a variety of morphological and life-history traits. Virtually all of the traits displayed significant variation among families, and many were significantly heterogeneous among grid points, indicating microgeographic genetic differentiation on a fine spatial scale. Overall morphological divergence, measured as Mahalanobis distances between grid points, increased with geographical distance. In general, spatial autocorrelation coefficients of grid point character means were positive at 11–20 m and negative beyond 40 m, although power for significance testing was low. The first factor in a principal component analysis of grid point means was positively loaded on height-related traits and negatively loaded on total reproduction at 50 days, accounting for 31% of the variation. This factor displayed significant positive spatial autocorrelation at 11–20 m and negative autocorrelation at >40 m. The remaining factors showed no detectable spatial structuring among grid points. These differences in spatial pattern among characters suggest that forces other than drift may have influenced the genetic structure of the population. There was no evidence for density-dependent selection; seedling density was not significantly correlated with the grid point mean of any trait.     

Clonal distribution,fertility and sex ratios of the moss Plagiomnium affine (Bland.) T.Kop. in forests of contrasting age

Abstract

Six populations of the clonal forest floor moss Plagiomnium affine from forests of different age were screened for genetic variation at 23 allozyme loci, of which nine were polymorphic. Samples consisting of two adjacent unconnected shoots were taken at regular intervals along one transect from each population. A total of 602 shoots was analysed. Almost 80% of the shoots were sterile (i.e. not expressing male or female gender). Sex remained unknown for only 10% of shoots after identification of genets based on electrophoretic data. We identified a mean number of 3.7 fertile clones per population. The mean length of clones along transects in each population ranged between 2 and 3 m. The size distribution within populations was bimodal, with a few dominant clones and a varying number of much smaller clones. The overall sex ratio was slightly female biased at the ramet level, but balanced at the genet level. Forest age was negatively correlated with percentage of sterile shoots and positively correlated with frequency of sporophytes. In both cases correlations were significant only if population 1, which was subject to extreme soil disturbance by badgers, was excluded. We conclude that the effective population size is larger, and the susceptibility to genetic drift is lower, in old forests.     

Genetic diversity and differentiation between the two remaining populations of the critically endangered Mediterranean monk seal

The Mediterranean monk seal Monachus monachus , is a critically-endangered species of which only two populations, separated by c . 4000 km, remain: the eastern Mediterranean (150–300 individuals) and the Atlantic/western Sahara populations (100–130 individuals). We measured current levels of nuclear genetic variation at 24 microsatellite loci in 12 seals from the eastern Mediterranean and 98 seals from the western Sahara population and assessed differences between them. In both populations, genetic variation was found to be low, with mean allelic richness for the loci polymorphic in the species of 2.09 and 1.96, respectively. For most loci, the observed allele frequency distributions in both populations were discontinuous and the size ranges similar. The eastern Mediterranean population had 14 private alleles and the western Sahara had 18, but with a much larger sample size. Highly significant differences in allele frequencies between the two populations were found for 14 out of 17 loci. F _ST between the two populations was 0.578 and the estimated number of migrants per generation was 0.046, both clearly indicating substantial genetic differentiation. From a conservation perspective, these results suggest that each population may act as a source for introducing additional genetic variation into the other population.     

Fine spatial structure of allozyme genotypes in isolated population of pedunculate oak Quercus robur L. (Fagaceae)

The extent and spatial pattern of genetic variation at polymorphic allozyme loci in a population of pedunculate oak Quercus robur from the Bashkir Transural region was investigated using autocorrelation analysis. In the plantation examined, statistically significant local concentration of most of the alleles in two-dimensional space was identified. The measures for protection of this small population located outside of the western border of the species range, in the mountain--steppe habitat, and characterized by specific gene pool, are suggested.     

Genetic diversity of Typha latifolia (Typhaceae) and the impact of pollutants examined with tandem-repetitive DNA probes

Genetic diversity at variable-number-tandem-repeat (VNTR) loci was examined in the common cattail, Typha latifolia (Typhaceae), using three synthetic DNA probes composed of tandemly repeated “core” sequences (GACA, GATA, and GCAC). The principal objectives of this investigation were to determine whether: (1) the previously reported almost complete lack of polymorphism at allozyme loci in this species was indicative of a reduced amount of genetic diversity at VNTR loci as well; (2) VNTR markers were informative about possible clonal propagation; and (3) significant differences in genetic structure of sampling sites were associated with differences in environmental levels of pollutants at those sites. Previously, widespread sampling across the eastern United States, surveying across ten allozyme loci, has detected only two genotypes, involving a difference at a single locus, among 104 populations. In this study, the amount of genetic diversity detected at VNTR loci: (1) among ramets (N = 40; 40 genotypes detected) collected at ∼8-km intervals along a 320-km transect; (2) among ramets (N = 220; 117 genotypes detected) from five study sites separated by 50–3000 m; and (3) even among ramets within each study site [N = 44 per site; from 13 to 34 genotypes detected per site (270 m²)] exceeds that previously found in those more geographically widespread allozyme surveys. Among the 260 ramets analyzed here, the mean number of bands scored per individual was 48.61 (SD = 2.80). Mean genetic similarity among ramets collected along the 320-km transect was 0.91, which was within the range of mean genetic similarity within the five study sites (range: 0.89–0.95). Among the five study sites, 61% of the samples analyzed appeared to be clonal ramets, with up to 12 clones detected for 44 ramets sampled within a site. Clones grew intermingled and ranged up to 39 m in extent. Permutation tests of genetic similarity revealed significant genetic differentiation between each of the five study sites. Consistent with the previous allozyme studies, T. latifolia was characterized by extremely low genetic variation relative to levels of polymorphism detected at VNTR loci in other plant species. Estimated heterozygosity among ramets along the 320-km transect ranged from 0.11 to 0.13, while that within the five study sites ranged from 0.05 to 0.12. Estimates of F_st (0.32–0.41) also indicated considerable genetic subdivision among these stands. Significantly higher genetic diversity was detected at the two study sites that chemistry and toxicity data indicate to be the most severely impacted by pollutants. Although this correlation does not establish cause and effect, the results of this study indicate that the analysis of genetic diversity at VNTR loci may be a useful tool for monitoring anthropogenic-induced changes in the genetic structure of natural populations of plants.     

Clonal dispersal and spatial mixing in populations of the plant pathogenic fungus, Sclerotinia sclerotiorum

Two thousand seven hundred and forty-seven isolates of Sclerotinia sclerotiorum were sampled from four field populations of canola in western Canada. Each field was sampled in a grid of 128 50-m 50-m quadrats plus four intensive quadrats each sampled in a diagonal transect. Sampling was done at two phases of the disease cycle: (1) from ascospore inoculum on petals and (2) from disease lesions in stems. A total of 594 unique genotypes was identified by DNA fingerprinting. In each field, a small group of clones represented the majority of the sample, with a large group of clones or genotypes sampled once or twice. Clone frequencies were compared by χ² tests. The difference in profiles of clone frequencies for the two fields sampled in 1991 was not significant, but in 1992 the difference in profiles was marginally significant, indicating some local population substructure. The difference in profiles of clone frequencies for petals and lesions was not significant in each of the two fields sampled in 1991. In each of the two fields sampled in 1992, however, the difference was highly significant, consistent either with selection for some clones or with waves of immigration during the disease cycle. Nine of the 30 most frequently sampled clones from this study were previously recovered in a macrogeographical sample from western Canada in 1990. For spatial analyses, randomization tests indicated no significant spatial aggregation of either clones on petals or clones from lesions. Also, isolates of a clone on petals were not closer to isolates of the same clone from lesions than could be predicted by chance. Both observations suggest spatial mixing of ascospore inoculum from resident or immigrant sources.     

Fine spatial structure of allozyme genotypes in isolated population of pedunculate oak <Emphasis Type="Italic">Quercus robur</Emphasis> L. (Fagaceae)

The extent and spatial pattern of genetic variation at polymorphic allozyme loci in a population of pedunculate oak Quercus robur from the Bashkir Transural region was investigated using autocorrelation analysis. In the plantation examined, statistically significant local concentration of most of the alleles in two-dimensional space was identified. The measures for protection of this small population located outside of the western border of the species range, in the mountain-steppe habitat, and characterized by specific gene pool, are suggested.     

Recombination and genetic differentiation in the mycorrhizal fungus Cenococcum geophilum Fr

Population genetic analyses of the mycorrhizal fungus Cenococcum geophilum were conducted to test for a clonal or recombining population structure. Multilocus genotypes based on polymorphisms in 9 loci, identified in this study by PCR-SSCP techniques, were obtained for two populations. Genotypic variation occurred on a fine scale because unique genotypes were identified at most every transect point, and in some cases occurred even within one soil sample (equivalent to about a 500 mL volume). The largest genet observed occurred over a 30 meter transect space. The two population genetic methods employed to distinguish between clonality and recombination, (1) Index of Association; and (2) "Parsimony Tree Length Permutation Test" (PTLPT), could not reject the null hypothesis of recombination in either population. Wright's Fst, as estimated by theta, was used to examine gene flow between the two populations based on allele frequencies. Two of the nine loci had theta values that were not significantly different from what one would expect for the null hypothesis of panmixia. However, the other seven loci were consistent with reduced gene flow. The theta value for the Fisher combined probability (combining all 9 loci) was significant and indicated that there was genetic differentiation between these two populations.     

Microsite differentiation in a Mediterranean oak savanna

Abstract. Microscale variation of vegetation was studied in a Mediterranean oak savanna dominated by annual plants at Neve Ya'ar Experimental Station, in the lower Galilee of Israel. Species presence/absence data were recorded in 20 cm x 20 cm quadrats on a 500-quadrat transect. These data were ordinated with Detrended Correspondence Analysis. Soil nitrate, phosphorous, potassium, pH, soil moisture and salinity were determined at 2-m intervals on the 100-m transect, at monthly intervals from November 1981 to April 1982. Litter cover and canopy shade were surveyed in October 1981 and April 1982. A sharp rise in available nitrate occurred in November, following the first winter rains. Patterns in herbaceous vegetation, as expressed by sample ordination scores, correlated best with litter cover in October. This suggested that vegetation pattern in this community may be strongly influenced by environmental conditions at the time of seedling germination and establishment.     

云南红豆杉天然群体内同工酶遗传变异的研究

采用水平淀粉凝胶电泳技术,对分布于金沙江流域的云南红豆杉天然群体的10种酶系统同工酶的遗传变异进行了研究。在谱带遗传分析的基础上确定了15个酶基因座及其等位基因。其中有14个酶基因座属多态,只有一个单态基因座（ME－3）。14个多态基因座中,4个基因座遗传变异小,对该天然群体的遗传变异贡献不大,其余10个基因座遗传变异丰富,对该天然群体的遗传变异贡献大。该天然群体具有明显丰富的遗传变异性,多态基因座比率P=0.933,等位基因平均数A=2.90,平均期望杂合度He=0.290。紫杉醇含量与群体遗传变异有着密切的关系。 Abstract：Genetic variation of ten isoenzymes was studied within population of Taxus yun nanensis Cheng et L. K. Fu in the Jinsha River Valley using the method of hor izo ntal starch gel electrophoresis.On the basis of banding analysis,eight enzyme sy stems , presumablly coded by fifteen isoenzyme loci and their alleles were score d , and fourteen were polymorphic with only one monomorphic locus（ME－3）. Amon g them , four polymorphic loci with inevident genetic variation made little cont ribution to genetic variation of this population and other ten polymorphic loci with evident genetic variation made great contribution to genetic variation of this population . Isoenzyme data indicated high level of genetic variability in this population with P=0.933,A=2.90,He=0.290 . The taxol content had close r elation to genetic variation of population.     

Genetic differentiation of pedunculate oak Quercus robur L. in the European part of Russia based on RAPD markers

Using randomly amplified polymorphic DNA markers (RAPD), genetic variation and differentiation in four populations of pedunculate oak Quercus robur L. were examined. The populations occupy a large part of the Quercus robur range in the European Russia (Voronezh and Novgorod oblasts; Republics of Mordovia and Bashkortostan). With each of six random primers (A02, A09, A17, B01, B08, B11), 96 DNA samples were analyzed by PCR. In all, 48 putative polymorphic RAPD loci were detected. We failed to reveal population-specific DNA fragments for any primer although the frequencies of 14 fragments were significantly different among populations. The oak populations studied exhibited high variability: 73-90% of genes were polymorphic and the effective allele number was about 1.4. The total genetic variation varied from 0.202 (Vor) to 0.245 (Nov), which corresponded to the estimates for populations of this species from Central and Western Europe. The populations examined showed low among-population differentiation (GST = 0.098); gene flow Nem was 4.61. The proportion of among-population variation of the RAPD loci studied accounted for 7% of the total variability; more than 93% of the total variability was explained by individual and within--population variation.     

Genetic variation of Avicennia marina (Forsk.) Vierh. (Avicenniaceae) in Vietnam revealed by microsatellite and AFLP markers

Genetic variation of Avicennia marina in the costal area of Vietnam was examined using microsatellite and AFLP markers. By using five microsatellite loci a total of 21 alleles were detected. The average number of alleles per locus per population ranged from 1.667 to 3.000. The observed heterozygosity varied from 0.180 to 0.263, with an average of 0.210 indicating relatively low level of genetic variation comparing to the previous studies on A. marina in the worldwide range. The expected heterozygosity was larger than the observed heterozygosity leading to positive inbreeding coefficients in all the six populations. Highly significant departures from Hardy-Weinberg Equilibrium were detected in four populations. AFLP analysis revealed a total of 386 loci, of which 232 (60.1%) were polymorphic. In congruent with microsatellite markers relatively low levels of genetic variation were detected at both gene and nucleotide levels (H = 0.086; pi = 0.0054). Reduced level of genetic variation was found in the central population, and in the southern populations. Both microsatellite and AFLP markers revealed large genetic differentiation (F(ST) = 0.262 and 0.338, respectively) indicating strong genetic structure among regional populations. Pairwise genetic distance by AFLP showed two populations in the north and the other two in the south are closely related each other.     

Genetic variation of oaks (<Emphasis Type="Italic">Quercus</Emphasis> spp.) in Switzerland. 3. Lack of impact of postglacial recolonization history on nuclear gene loci

Quercus petraea, Quercus pubescens and Quercus robur are closely related and interfertile white oaks native to Switzerland. The three species are known to share identical cpDNA haplotypes, which are indicative of the postglacial recolonization history of populations. Only two haplotypes are common in Switzerland. We compared variation of cpDNA and of isozymes in 28 oak populations from Switzerland in order to assess the impact of the postglacial population history on current genetic structures of nuclear controlled isozyme gene loci. Species delineation was based on Principal Component Analysis of leaf morphological traits. The species status of populations was reflected at isozyme gene loci, but differentiation between populations with different cpDNA haplotypes and hence different recolonization history was very low at enzyme gene loci for all species. Thus, glacial and postglacial population history was not reflected at nuclear gene loci on the temporal and spatial scale covered by the present study. Extensive gene flow through pollen among populations is likely to have blurred a previously existing genetic differentiation at biparentally inherited gene loci that possibly evolved in the different glacial refugia of the above mentioned cpDNA haplotypes.     

Variation in the genetic structure and reproductive biology of holm oak populations

Five polymorphic enzymatic loci were studied in 30 populations of Quercus ilex distributed from Crete to North Africa. A high within-population genetic diversity was found for each locus studied. Most of the alleles were common to all the populations, indicating that the holm oak corresponds to a single genetic entity. Observation of breeding system characteristics showed that the holm oak is monoecious, wind-pollinated, and likely to possess genetic autoincompatibility. Furthermore, studies of flowering phenology in a single population showed that the period of flowering varied notably among trees. An average of 29% of the trees showed inter-annual variation in flowering time. The male, female or vegetative investment also varied widely among trees from one year to another. This results in a diversification of pollen source received by a given tree each year, and also from one year to another.     

Multi-scale genetic analysis of Uniola paniculata (Poaceae): a coastal species with a linear, fragmented distribution

Geographic and fine-scale population genetic structures of Uniola paniculata, the dominant coastal dune grass in the southeastern USA, were examined. The linear, naturally fragmented distribution of this native perennial was hypothesized to lead to high genetic structure and lower genetic diversity at the margin of the species range. The extensive ramet production and low seed germination of this species were also expected to cause populations to be dominated by a few large clones. At 20 sites throughout the range of the species, leaf tissue was collected from 48 individuals. Clonal structure was examined using leaf tissue collected from an additional 60 individuals, each in four patches at two sites. Starch gel electrophoresis was used to resolve 27 allozyme loci. The results indicated that Uniola had greater genetic structure (G(ST) = 0.304) than most other outcrossing species, indicating moderate barriers to gene flow. There was a weak but significant positive relationship between genetic distance and geographic distance, supporting an isolation-by-distance model of gene flow. There were no obvious disjunctions between regions. Genetic diversity (H(e)) was relatively uniform throughout most of the range of the species but was lower in all western Gulf of Mexico populations. Clonal diversity varied both within and among sites, but clones were often small, suggesting that sexual reproduction and recruitment from seeds are important factors maintaining genetic diversity.     

Genetic Characteristics of Western North Pacific Sei Whales, Balaenoptera borealis, as Revealed by Microsatellites

Genetic characteristics of sei whales, Balaenoptera borealis, inhabiting the western North Pacific were analyzed at 17 microsatellite loci in a total of 89 whales obtained from the area between 37°N–45°N and 147°E–166°E in 2002 (N = 39) and 2003 (N = 50). All the loci analyzed were polymorphic over the samples, some of the loci had more than 10 alleles, indicating a high level of genetic variation within samples. No significant deviation from the expected Hardy–Weinberg genotypic proportion was observed at the 17 loci in the samples. No evidence of genetic heterogeneity in allele frequencies was observed between sexes within samples as well as between the two temporally different samples, indicating a single population of sei whales inhabiting the western North Pacific. We finally tested and demonstrated that the population appeared not to suffer from genetic bottleneck as a result of population decline from past commercial whaling.     

Genetic diversity in Chihuahuan Desert populations of creosotebush (Zygophyllaceae: Larrea tridentata)

We examined isozyme variation in the dominant Chihuahuan Desert shrub, Larrea tridentata (creosotebush), to determine the genetic variation within and among populations, the biogeographic relationships of populations, and the potential inbreeding in the species. We surveyed 17 populations consisting of 20 to 50 individuals per population along a 1600-km north-south transect across the Chihuahuan Desert. The southernmost population was near Villa Hidalgo, Mexico, and the northernmost near Isleta Pueblo, New Mexico. All 12 isozyme loci examined were polymorphic (H(t) = 0.416), with up to nine alleles per locus. Despite high levels of variation, we detected moderate inbreeding in L. tridentata populations. Most variation was found within rather than among populations (G(ST) = 0.118). Furthermore, recently established populations in the northern limits of the Chihuahuan Desert did not show decreased levels of genetic variation (H(o) = 0.336). A significant correlation was found between pairwise genetic and geographic distances (r = 0.305). Larrea tridentata showed and continues to show a massive range expansion into the arid and semi-arid regions of the American Southwest, but as shown by the high genetic variation, this expansion took place as a wave, rather than a series of founder events.