Random Amplified Polymorphic DNA Phenotypes Research Articles

RAPD마크를 이용한 한국 내 괭이밥속 식물의 유전적 다양성과 표현형 관계

RAPD마크를 이용한 한국 내 괭이밥속(Oxalis L.) 식물의 유전적 다양성과 표현형 관계를 평가하였다. 10개의 시발체로 125개의 밴드를 얻었으며 시발체당 12.5개였다. 이들 밴드 중 121개(96.8%)는 다형성을 나타내었으며 단지 4개만 단형성을 나타내었다. 6개 분류군에서 RAPD 표현형의 평균은 3.6개(선괭이밥, 괭이밥)에서 4.8개(붉은괭이밥)였다. 종간 변이에서 선괭이밥과 자주괭이밥이 가장 낮은 변이를 나타내었으며(28.8%), 붉은괭이밥이 가장 높은 변이를 나타내었다(38.4%). 분류군 내 대립유전자좌위는 평균 32.7%였다. 종 간 전체 유전적 다양도와 종내 유전적 다양도는 각각 0.362와 0.122였다. 종간 분화에 근거한 전체 변이의 몫(<TEX>$G_{ST}$</TEX>)은 0.663이였다. 이는 전체 변이의 66.3%는 종간에 있음을 나타낸다. NJ tree에서 선괭이밥과 붉은괭이밥의 분지군은 높은 지지도를 가지며 괭이밥과 자매군을 형성하였다. 염색체의 수와 RAPD의 표현형적 관계와 일치하지 않았다. We evaluated the phenetic relationships within six taxa of genus Oxalis L. in Korea with random amplified polymorphic DNA (RAPD) markers. Ten primers produced 125 bands for six taxa, and the mean number of bands per primer was 12.5. Across the six taxa, 121 (96.8%) bands were polymorphic, and only four were monomorphic. The mean number of RAPD phenotypes across the six taxa varied from 3.6 (O. stricta and O. corymbosa) to 4.8 (O. corniculata for. rubrifolia). In a simple measure of intraspecies variability according to the percentage of polymorphic bands, O. stricta and O. corymbosa exhibited the lowest variation (28.8%), and O. corniculata for. rubrifolia showed the highest (38.4%). A mean of 32.7% of the loci was polymorphic within taxa. The total interspecies genetic diversity (<TEX>$H_T$</TEX>) and intraspecies genetic diversity (<TEX>$H_S$</TEX>) was 0.362 and 0.122, respectively. On a per-locus basis, the proportion of total genetic variation due to differences among species (<TEX>$G_{ST}$</TEX>) was 0.663. This indicates that about 66.3% of the total variation was among species. The node of O. stricta and O. corniculata for. rubrifolia was strongly supported, with a high bootstrap value in the NJ tree and sistered with O. corniculata. According to RAPD analysis, the number of chromosomes was not congruent with a phenetic relationship.

Genetic diversity of Austrian pine (Pinus nigra Arnold) populations in Serbia revealed by RAPD

The ability of random amplified polymorphic DNA (RAPD) to distinguish among populations of Austrian pine from Serbia was evaluated. Ten arbitrary 10mer primers employed in the analysis produced 113 fragments of which 100 were polymorphic (88.5%). All populations had specific RAPD phenotypes. Certain rare and genotype specific bands were identified which could be effectively used to distinguish the populations. Polymorphism in RAPD markers among P. nigra population was high and sufficient to distinguish each of the populations. The results obtained suggest that RAPD markers are valuable for the genetic diversity estimation in Pinus nigra and for the study of the divergence among populations.

Extensive clonality of the endemic Calamagrostis pseudopurpurea Gerstl. ex O.R. Heine in central Germany revealed by RAPD markers

Calamagrostis pseudopurpurea is one of only a few endemic species in Germany and is confined to the catchment area of the River Mulde in the states of Saxony and Saxony-Anhalt. We studied the genetic structure and seed viability across its entire distribution area. Patterns of random amplified polymorphic DNA (RAPD) variation were analysed using 183 individuals from 43 stands in order to assess the overall genetic structure and the extent of clonality. In addition, four related Calamagrostis species (C. canescens, C. epigejos, C. phragmitoides and C. villosa) were included in our study to consider the probable phylogenetic origin of C. pseudopurpurea. We detected two clearly different RAPD phenotypes of C. pseudopurpurea, each distributed along the river banks of two spatially isolated stream courses. Both phenotypes are present downstream of the confluence. Our results indicate that C. pseudopurpurea originates from two distinct periods of hybridisation between the same parental taxa, and that clonal propagation is most likely the main reproduction method. In line with its hybrid origin, embryos of sampled C. pseudopurpurea caryopses were found to be mostly degraded or unviable over several years. Calamagrostis pseudopurpurea is genetically closer to C. canescens and C. phragmitoides than it is to other studied species, but C. canescens and C. phragmitoides have not been proven to be direct parental taxa of C. pseudopurpurea. Calamagrostis pseudopurpurea should therefore still be treated as a separate species that needs special attention from a conservation point of view.

Genetic diversity of two Brazilian populations of the Pampas deer (Ozotoceros bezoarticus, Linnaeus 1758)

The Pampas deer (Ozotoceros bezoarticus) is one of the most endangered Neotropical cervid with populations that have been drastically reduced to small and isolated ones, mainly because of its habitat destruction. Random amplified polymorphic DNA (RAPD) markers were used to analyze population divergence and genetic variation within and between two populations corresponding to distinct subspecies. The RAPD markers displayed substantial genetic variation with all animals possessing unique RAPD phenotypes over 105 polymorphic bands produced by 15 primers. An analysis of molecular variance (AMOVA) and a neighbor-joining cluster analysis were performed to assess levels of differentiation between populations. No differentiation was recorded and about 96.0% (P<0.00001) of the total variance was attributable to variation within populations. This result is quite distinct from data obtained by the analysis of the mtDNA control region, and is discussed on the basis of genetic differences between the different markers and the male-biased dispersal patterns generally observed in the mammal species. The data presented herein are potentially useful for future taxonomic and genetic studies in this species, for the monitoring of the genetic variation observed within these populations, and for the development of management guidelines for its conservation.

Clonal diversity and structure of the invasive aquatic plant Eichhornia crassipes in China

The information on diversity and spatial distribution of clones of an invasive clonal plant is crucial for the understanding of its clonal structure and invasive history. In this paper, random amplified polymorphic DNA (RAPD) markers were used to explore the clonal diversity and clonal structure of Eichhornia crassipes (Mart.) Solms in natural populations, and their possible effects on the plant success as an invader are also discussed. Five populations covering the entire distribution area in China were studied, sampling 43 individuals per population at an interval of 1 m in a sampling plot. Twelve RAPD primers produced 69 reproducible bands, with 22 being polymorphic. Only five RAPD phenotypes (clones) were detected in these five populations, but each population consisted of at least three clones, contrary to the traditional expectations that E. crassipes populations should be monoclonal. The diversity of clones within populations is thought to be mainly resulted from multiple introductions by humans. The evenness of distribution of clones varied slightly and most clones were widespread, suggesting clonal growth is the predominant mode of regeneration in all the populations. A single clone dominated each population and this clone might be the first one introduced into China or the genotype with a higher phenotypic plasticity, which could survive and reproduce via clonal growth in various habitats. The clones in each population were highly intermixed, especially in river populations, suggesting this species has a guerilla clonal structure which can be facilitated by water current.

A preliminary examination of genetic diversity in the Indian false vampire bat Megaderma lyra

Habitat loss and fragmentation have serious consequences for species extinction as well as genetic diversity within a species. Random Amplified Polymorphic DNA (RAPD) analysis was employed to assess the genetic diversity within and between four natural populations of M. lyra. Our results suggest that the genetic diversity varied from 0.21 to 0.26 with a mean of 0.11 to 0.13 (± SD). The mean Gst value of 0.15 was obtained from all four populations and estimated average Nm (1.41) showing gene flow between the populations. AMOVA analysis showed 88.96% within and 11.04% among the studied populations. Cluster analyses of RAPD phenotypes showed that specimens were not grouped by geographical origin. The genetic diversity found in the M. lyra population may be explained by its breeding behaviors. Though preliminary, the results indicate that all four populations should be considered to maintain the genetic diversity.

Random amplified polymorphic DNA markers reveal low genetic variation and a single dominant genotype in Eichhornia crassipes populations throughout China

SummaryGenetic variation within and between 34 populations of Eichhornia crassipes (water hyacinth) in China was surveyed using random amplified polymorphic DNA (RAPD) markers. A total of 1009 individuals were analysed, for which 12 RAPD primers amplified 69 reproducible bands, with 22 (32%) being polymorphic. The percentage of polymorphic loci (p) within a population ranged from 4.4% to 17.4%, and the mean Nei's gene diversity (He) was 0.046 ± 0.0145, indicating a low genetic diversity of E. crassipes in China. Each population contained at least four RAPD phenotypes (genotypes), and the same particular genotype was invariably dominant in all the populations sampled. The mean proportion of distinguishable genotypes was 0.29. Analysis of molecular variance revealed a large proportion of genetic variation (83.9%) residing within populations and a slightly larger proportion (88.1%) within localities, indicating a low genetic differentiation of E. crassipes populations, both locally and regionally. Human‐mediated dispersal, vigorous clonal growth, and a generally low level of sexual reproduction were thought to be responsible for such a pattern of genetic structure.

Fine-scale Clonal Structure and Diversity within Patches of a Clone-forming Dioecious Shrub, Ilex leucoclada (Aquifoliaceae)

The mode of reproduction (sexual vs. asexual) is likely to have important effects on genetic variation and its spatial distribution within plant populations. An investigation was undertaken of fine-scale clonal structure and diversity within patches of Ilex leucoclada (a clone-forming dioecious shrub). Six patches were selected in a 1-ha plot previously established in an old-growth beech forest. Two of the selected patches were composed predominantly of stems with male flowers (male patch), and two contained stems with predominantly female flowers (female patch). The remaining two patches contained stems with male flowers and stems with female flowers in more or less equal proportions (mixed patch). Different genets were distinguished using random amplified polymorphic DNA (RAPD) markers. One hundred and fifty-six genets with different RAPD phenotypes were identified among 1928 stems from the six patches. Among the six patches, the male patches had the lowest clonal diversity, and the mixed patches had the highest. Distribution maps of the genets showed that they extended downhill, reflecting natural layering that occurred when stems were pressed to the ground by heavy snow. In every patch, there were a few large genets with many stems and many small genets with a few stems. The differences in clonal diversity among patches may be due to differences in seedling recruitment frequencies. The skewed distribution of genet size (defined as the number of stems per genet) within patches may be due to differences in the timing of germination, or age (with early-establishing genets having clear advantages for acquiring resources) and/or intraspecific competition.

Variation in aggressiveness and genetic diversity of grape phylloxera in Southern France

&lt;p style="text-align: justify;"&gt;The aphid relative &lt;em&gt;Daktulosphaira vitifoliae&lt;/em&gt; (Fitch) (&lt;em&gt;Homoptera : Phylloxeridae&lt;/em&gt;) feeds on the leaves and roots of grapevine (&lt;em&gt;Vitis&lt;/em&gt; spp.). The insect was introduced into France from North America around 140 years ago and caused severe damage until control of the root-infesting form was initiated by grafting European cultivars onto resistant rootstocks. The objective of our research was to analyze both the variation in pathogenicity and the genetic diversity of the insect in southern France. Twenty samples of phylloxera were collected from leaf galls throughout the region. Their aggressiveness was monitored by measuring the reduction in root dry mass of artificially inoculated potted plants. One trial was performed with three rootstocks (41B, 3309C and 140R) and another with the highly susceptible &lt;em&gt;Vitis vinifera&lt;/em&gt; cv. Carignan. No evidence for preference was shown, but aggressiveness varied widely among phylloxera samples, especially in the Carignan trial. Genetic diversity was assessed using 30 Random Amplified Polymorphic DNA (RAPD) markers obtained with 15 primers. Wide diversity was found and all samples corresponded to distinct RAPD phenotypes. The genetic structure of phylloxera population in Southern France was not showed to be influenced either by the location or by the host.&lt;/p&gt;

Marker-Assisted Selection for Resistance to Black Shank Disease in Tobacco.

Bulked segregant (BSA) and random amplified polymorphic DNA (RAPD) analyses were used to identify markers linked to the dominant black shank resistance gene, Ph, from flue-cured tobacco (Nicotiana tabacum) cv. Coker 371-Gold. Sixty RAPD markers, 54 in coupling and 6 in repulsion phase linkage to Ph, were identified in a K 326-derived BC1F1 (K 326-BC1F1) doubled haploid (DH) population. Thirty RAPD markers, 26 in coupling and 4 in repulsion phase linkage to Ph, were used to screen 149 K 326-BC2F1 haploid plants. Complete linkage between the 26 coupling phase markers and Ph was confirmed by screening 149 K 326-BC2F1 DH lines produced from the haploid plants in black shank nurseries. RAPD markers OPZ-5770 in coupling and OPZ-7370 in repulsion phase linkage were used to select plants homozygous for the Ph gene for further backcrossing to the widely grown flue-cured cultivar K 326. Black shank disease nursery evaluation of 11 K 326-BC4S1 lines and their testcross hybrids to a susceptible tester confirmed linkage between Ph and OPZ-5770. The results demonstrated the efficiency of marker-assisted selection for Ph using a RAPD marker linked in coupling and repulsion. Complete linkage between 26 RAPD markers and the Ph gene was confirmed in the K 326-BC5 generation, and RAPD phenotypes were stable across generations and ploidy levels. These RAPD markers are useful in marker-assisted selection for Ph, an important black shank resistance gene in tobacco.

Estimating dispersal and gene flow in the neotropical freshwater turtle Hydromedusa maximiliani (Chelidae) by combining ecological and genetic methods

Hydromedusa maximiliani is a vulnerable neotropical freshwater turtle endemic to mountainous regions of the Atlantic rainforest in southeastern Brazil. Random amplified polymorphic DNA (RAPD) was used to estimate the gene flow and dispersal for individuals inhabiting rivers and streams within a drainage. Nine primers generated 27 scoreable bands, of which 9 (33%) were polymorphic and produced 12 RAPD phenotypes. The gene flow estimates (Nm) among turtles inhabiting different rivers and streams were variable, ranging from 0.09 to 3.00 (mean: 0.60). For some loci, the rates of gene flow could offset population differentiation (Nm > 1), whereas for others random genetic drift could result in population divergence (Nm < 1). Since the genetic variation of this turtle seems to be structured according to the natural hierarchical system of rivers and streams within drainages, management programs involving translocations between different regions across the geographical range of H. maximiliani should be viewed with caution.

Partitioning of molecular variation at local spatial scales in the vulnerable neotropical freshwater turtle, Hydromedusa maximiliani (Testudines, Chelidae): implications for the conservation of aquatic organisms in natural hierarchical systems

Hydromedusa maximiliani is a vulnerable freshwater turtle endemic to mountainous regions of the Atlantic rainforest in southeastern Brazil. Random amplified polymorphic DNA (RAPD) were surveyed with the purpose of assessing the genetic structure and determining the partitioning of molecular variation in H. maximiliani across the natural spatial hierarchical scale of its habitat. The goal of the study was to integrate ecological data with estimates of molecular genetics diversity to develop strategies for the conservation of this freshwater turtle. Specimens were sampled from rivers and streams across three drainages. Nine of the 80 primers used generated 27 scoreable bands of which 10 (37%) were polymorphic and produced 16 RAPD phenotypes. Significant heterogeneity was found in the distribution of RAPD molecular phenotypes across the three drainages. Analysis of molecular variance for molecular phenotypes showed that the heterogeneity had a spatial structure since a significant amount (22%) of the total variance was attributable to variation among rivers and streams. Since the genetic variation of this turtle seems to be structured according to the natural hierarchical system of rivers and streams within drainages, it is suggested that local populations should be considered as separate management units.

Genetic diversity and structure of natural populations of Plathymenia reticulata (Mimosoideae), a tropical tree from the Brazilian Cerrado.

Plathymenia reticulata is a tropical tree native to the Brazilian Cerrado, one of the most important and endangered ecosystems in Brazil. This species presents high-quality wood and potential for recovery of degraded areas. Despite its importance, almost nothing is known about its genetic or ecological features. Random amplified polymorphic DNA (RAPD) markers were used to investigate the genetic diversity and structure of six natural populations of P. reticulata. DNAs from 117 adult individuals were amplified with 10 random primers and Shannon's index and amova were used to evaluate the levels of genetic diversity within and among populations. Through 72 markers, 70.8% of which were polymorphic, it was possible to obtain 117 unique RAPD phenotypes. The levels of genetic variability found in the six populations of P. reticulata were considerable and most of the genetic variation was found between individuals within populations, although pairwise PH(ST) values indicated significant divergence between populations. The among-population component accounted for, respectively, 12.3% and 16% of the genetic variation, according to amova and Shannon's index. These results were compared with other genetic studies on plant species and such a level of differentiation among populations corresponds to that which has usually been observed for outcrossing plants. The importance of maintenance of the P. reticulata populations and implications of the analysis of adult individuals, considering the longevity of this species and the relatively recent Cerrado fragmentation, are discussed.

Trans‐Atlantic dispersal and phylogeography of Cerastium arcticum (Caryophyllaceae) inferred from RAPD and SCAR markers

Cerastium arcticum is an autogamous pioneer species with a distribution limited to the North Atlantic region. It has been suggested that such species must have survived in ice-free refugia on both sides of the Atlantic throughout the last, or even several, of the Pleistocene glaciations, because they lack special adaptations for long-distance dispersal. To address the possibility for recent trans-Atlantic dispersal of C. arcticum, we analyzed random amplified polymorphic DNA (RAPD) and sequence characterized amplified region (SCAR) differentiation among 26 populations of this high-polyploid species. Three SCAR markers were obtained that verified the main patterns identified in the RAPD analysis. Eighty-four multilocus RAPD phenotypes were observed in the 126 plants analyzed, based on 35 polymorphic markers. Multivariate analyses and analyses of molecular variance (AMOVAs) identified two highly divergent groups of populations: one arctic group (western and eastern Greenland, and the archipelagos of Svalbard and Franz Josef Land) and one nonarctic group (southern and northern Norway, and Iceland), indicating that C. arcticum is composed of two lineages with different evolutionary histories. However, there was little geographic structuring within each lineage, in spite of the fact that both lineages are disjunctly distributed across the Atlantic. Occurrence of very similar, in some cases even identical RAPD multilocus phenotypes on both sides of the Atlantic in this autogamous allopolyploid is most probably caused by postglacial dispersal. The present geographic distribution of C. arcticum may thus have been established after trans-Atlantic expansion from two Weichselian refugia, one for each evolutionary lineage. Unexpectedly, the level of intrapopulational variation increased towards the north. This may reflect that interpopulational migration is most extensive in the treeless arctic environment, where the species has a more continuous distribution than in the more southerly areas.

Reciprocal hybrid formation ofSpartinain San Francisco Bay

Diversity in the tRNALEU1 intron of the chloroplast genome of Spartina was used to study hybridization of native California cordgrass, Spartina foliosa, with S. alterniflora, introduced to San Francisco Bay approximately 25 years ago. We sequenced 544 bases of the tRNALEU1 intron and found three polymorphic sites, a pyrimidine transition at site 126 and transversions at sites 382 and 430. Spartina from outside of San Francisco Bay, where hybridization between these species is impossible, gave cpDNA genotypes of the parental species. S. foliosa had a single chloroplast haplotype, CCT, and this was unique to California cordgrass. S. alterniflora from the native range along the Atlantic coast of North America had three chloroplast haplotypes, CAT, TAA, and TAT. Hybrids were discriminated by random amplified polymorphic DNA (RAPD) phenotypes developed in a previous study. We found one hybrid that contained a cpDNA haplotype unknown in either parental species (TCT). The most significant finding was that hybridization proceeds in both directions, assuming maternal inheritance of cpDNA; 26 of the 36 hybrid Spartina plants from San Francisco Bay contained the S. foliosa haplotype, nine contained haplotypes of the invading S. alterniflora, and one had the cpDNA of unknown origin. Furthermore, cpDNA of both parental species was distributed throughout the broad range of RAPD phenotypes, suggesting ongoing contributions to the hybrid swarm from both. The preponderance of S. foliosa cpDNA has entered the hybrid swarm indirectly, we propose, from F1s that backcross to S. foliosa. Flowering of the native precedes by several weeks that of the invading species, with little overlap between the two. Thus, F1 hybrids would be rare and sired by the last S. foliosa pollen upon the first S. alterniflora stigmas. The native species produces little pollen and this has low viability. An intermediate flowering time of hybrids as well as pollen that is more vigourous and abundant than that of the native species would predispose F1s to high fitness in a vast sea of native ovules. Thus, spread of hybrids to other S. foliosa marshes could be an even greater threat to the native species than introductions of alien S. alterniflora.

Genetic structure of the subtidal red alga Delisea pulchra

We used random amplified polymorphic DNA (RAPDs) to examine small-scale spatial genetic structure in the red alga Delisea pulchra (Greville) Montagne at two locations near Sydney, Australia. We examined genetic structure among plants at four spatial scales ranging from 2 km apart down to <50 cm apart between locations, among sites within locations, among quadrats within sites, and among plants within quadrats. Haploid stages of D. pulchra were absent from the populations studied, suggesting that they are maintained through asexual reproduction of diploid plants. Consistent with this, we found that 19 RAPD phenotypes scored in this study had multiple individuals, indicating the presence of clones in these populations. However, there were no RAPD phenotypes common to two locations separated by only 2 km. Analysis of molecular variance revealed that strong genetic differences occurred between plants from these two locations, with 46.3% of the total genetic variation occurring at this scale, most probably reflecting limited gene flow. Within each location, <25% of the genetic variation was attributable to differences among sites or quadrats, indicating gene flow at those smaller scales. Most of the variation within each location occurred at the smallest spatial scale, among plants within 0.25 m2 quadrats. Nonetheless, some pairwise genetic distances (φST) between sites or quadrats within locations were large, indicating some genetic divergence on smaller scales. Genetic distance was independent of spatial distance within both locations, suggesting that fine-scale differences within locations were most probably caused by variation in fine-scale patterns of water movement or fine-scale natural selection. We assessed the impact of one potential selective agent, grazing sea urchins, on the fine-scale genetic structure of D. pulchra. There was no evidence that grazing by sea urchins affected the genetic structure of D. pulchra. In combination with demographic data, our results indicated that local populations of D. pulchra within locations were relatively open and that fine-scale genetic structure was probably constrained by gene flow. At the larger scale however, strong genetic differentiation indicated little gene flow between locations and restricted dispersal of spores.

Virulence and Molecular Polymorphism in International Collections of the Wheat Leaf Rust Fungus Puccinia triticina

ABSTRACT Collections of Puccinia triticina, the wheat leaf rust fungus, were obtained from Great Britain, Slovakia, Israel, Germany, Australia, Italy, Spain, Hungary, South Africa, Uruguay, New Zealand, Brazil, Pakistan, Nepal, and eastern and western Canada. All single-uredinial isolates derived from the collections were tested for virulence polymorphism on 22 Thatcher wheat lines that are near-isogenic for leaf rust resistance genes. Based on virulence phenotype, selected isolates were also tested for randomly amplified polymorphic DNA (RAPD) using 11 primers. The national collections were placed into 11 groups based on previously established epidemiological zones. Among the 131 single-uredinial isolates, 105 virulence phenotypes and 82 RAPD phenotypes were described. In a modified analysis of variance, 26% of the virulence variation was due to differences in isolates between groups, with the remainder attributable to differences within groups. Of the RAPD variation, 36% was due to differences in isolates between groups. Clustering based on the average virulence distance (simple distance coefficient) within and between groups resulted in eight groups that differed significantly. Collections from Australia-New Zealand, Spain, Italy, and Britain did not differ significantly for virulence. Clustering of RAPD marker differences (1 - Dice coefficient) distinguished nine groups that differed significantly. Collections from Spain and Italy did not differ significantly for RAPD variation, neither did collections from western Canada and South America. Groups of isolates distinguished by avirulent/virulent infection types to wheat lines with resistance genes Lr1, Lr2a, Lr2c, and Lr3 also differed significantly for RAPD distance, showing a general relationship between virulence and RAPD phenotype. The results indicated that on a worldwide level collections of P. triticina differ for virulence and molecular backgrounds.

Random amplified polymorphic DNA analysis of southern brown bandicoot (Isoodon obesulus) populations in Western Australia reveals genetic differentiation related to environmental variables.

Random amplified polymorphic DNA (RAPD) markers were used to analyse genetic variation within and between populations of Isoodon obesulus in Western Australia. Genetically controlled geographical variation in body size associated with habitat type and rainfall exists in this species, raising the question of whether local conditions may influence gene flow in I. obesulus. The RAPD markers displayed substantial genetic variation, with all animals possessing unique RAPD phenotypes over 39 polymorphic bands produced by three primers. Significant geographical subdivision was apparent (PhiST = 0.208) with southwest locations being divergent from all others, despite there being no physical barriers to gene flow. The pattern of subdivision was unrelated to physical distance between the locations, but was related to both annual rainfall and habitat type. Therefore, the most reasonable explanation for this pattern of subdivision appears to be that gene flow is restricted by selection against migrants between local populations with substantially different habitat type or rainfall. Restriction of gene flow through selection against migrants is rarely investigated, and the results of this study suggest that the importance of this process in the formation of population structure may be underestimated.

Population Structure of Puccinia recondita in Western Europe During 1995, as Assessed by Variability in Pathogenicity and Molecular Markers

The population structure of Puccinia recondita f. sp. tritici (Prt) in western Europe was examined by assessing variability in pathogenicity and in randomly amplified polymorphic DNA (RAPD) among 61 single uredinial isolates. The isolates were chosen to represent pathotypes detected in a previous survey of pathogenic variability in the fungus in western Europe in 1995. Thirty-five pathotypes were identified by assessing infection types produced by the 61 isolates on 24 differential lines, each with a single gene for resistance to Prt. In contrast, only 18 RAPD phenotypes were identified by scoring 19 polymorphic RAPD bands generated with eight RAPD primers. When analysed by cluster and bootstrap analyses, the pathogenicity and RAPD results revealed little evidence for robust distinct clusters among the isolates. Multiple isolates of several pathotypes collected from widely separated locations such as Belgium, Germany, France, Italy and Switzerland had the same RAPD phenotype, providing evidence of clonal migration over considerable distances in western Europe. Some variability (one or two band differences) was observed in RAPD phenotype within several pathotypes, indicating the possible occurrence of genetic changes independent of pathogenicity, and/or the independent development of pathotypes with different genetic backgrounds. Two groups of isolates identified in the 1995 survey, differentiated by pathogenicity for genes Lr3a, Lr3bg, Lr3ka and Lr30, were not distinguished by RAPD phenotype, indicating that the groups probably do not constitute separate lineages within the pathogen population. Little correlation was apparent between the polymorphisms observed in pathogenicity and RAPD phenotypes. The similarity in the genetic backgrounds of the isolates, as assessed by RAPD markers, suggest that the observed differences in pathogenicity may have arisen by selection for specific virulences corresponding to genes for resistance in wheat cultivars grown in the region. Three isolates of pathotype 3, restricted in its distribution to southern France during 1995, were distinct from all other isolates in RAPD phenotype. Circumstantial evidence suggests that this pathotype originated from northern Africa, and that it belongs to a group of leaf rust pathogens specialized to durum wheats.

Nuclear DNA diversity, population differentiation, and phylogenetic relationships in the California closed-cone pines based on RAPD and allozyme markers

We studied nuclear gene diversity and population differentiation using 91-98 randomly amplified polymorphic DNA (RAPD) loci in the California closed-cone pines knobcone (Pinus attenuata Lemm.), bishop (P. muricata D. Don), and Monterey (P. radiata D. Don) pines. A total of 384 trees from 13 populations were analyzed for RAPDs and another sample of 242 trees from 12 of these 13 populations were analyzed at 32-36 allozyme loci, using a published data set. Twenty-eight of 30 (93%) comigrating RAPD fragments tested were found to be homologous by Southern hybridization in all three species. Using an enriched mitochondrial DNA (mtDNA) preparation and a chloroplast DNA (cpDNA) library as probes, two fragments of cpDNA origin, and one of mtDNA origin present among RAPD profiles were excluded from analysis of nuclear gene diversity. RAPD markers revealed moderately higher intrapopulation gene diversity and substantially higher total genetic diversity and population differentiation than did allozyme markers for each species. We performed a simulation study using allozyme data, which showed that the dominant and biallelic nature of RAPD markers could explain the differences observed in differentiation parameters, but not in gene diversity; RAPD phenotypes appear to represent more underlying gene diversity than do allozyme phenotypes. Results of joint phylogenetic analyses of both the RAPD and allozyme markers strongly supported a common ancestor for P. radiata and P. attenuata pines, and south-to-north migration histories for all three species.Key words: allozymes, dominance, gene diversity, Pinus attenuata, Pinus muricata, Pinus radiata, phylogeny, RAPDs.