Inter-simple sequence repeat (ISSR) diversity within Monarda fistulosa var. brevis (Lamiaceae) and divergence between var. brevis and var. fistulosa in West Virginia

Inter-simple sequence repeat (ISSR) banding patterns were used to examine genetic diversity within and among populations ofMonarda fistulosa var.brevis, a rare taxon restricted to several populations in limestone glades and barrens in eastern West Virginia and Virginia. More than 34% of the total ISSR diversity in var.brevis occurred among populations, which is high when compared to the few other rare species that have been examined for ISSR variation. Prior studies demonstrated that var.brevis is morphologically distinct from the more widespread var.fistulosa, and that the differences are maintained when the two varieties are grown together in a uniform environment. The present study utilizing ISSR markers indicated that the two varieties are distinct, though quite similar genetically, and this is concordant with prior investigations documenting their morphological and habitat differences. However, the ISSR results suggest that the two varieties have diverged relatively recently and/or there is a low level of gene flow between them.     

Population Genetic structure ofPotentilla fragariodes var.major (Rosaceae) in Korea

The genetic diversity and population structure of eighteenPotentilla fragariodes var.major (Rosaceae) populations in Korea were determined using genetic variations at 22 allozyme loci. The percent of polymorphic loci within the enzymes was 66.7%. Genetic diversity at the species level and at the population level was high (Hes = 0.203; Hep = 0.185, respectively), whereas the extent of the population divergence was relatively low (G_ST = 0.069). F_IS, a measure of the deviation from random mating within the 18 populations, was 0.075. An indirect estimate of the number of migrants per generation (Nm = 3.36) indicated that gene flow was high among Korean populations of the species. In addition, analysis of fixation indices revealed a slight heterozygote deficiency in some populations and at some loci. Wide geographic ranges, perennial herbaceous nature and the persistence of multiple generations are associated with the high level of genetic variation. AlthoughP. fragariodes var.major usually propagated by asexually-produced ramets, we could not rule out the possibility that sexual reproduction occurred at a low rate because each ramet may produce terminal flowers. Mean genetic identity between populations was 0.983. It is highly probable that directional movement toward genetic uniformity in a relatively homogeneous habitat operates among Korean populations ofP. fragariodes var.major.     

Conservation of genetic diversity in the endangered plant Eriogonum ovalifolium var. vineum (Polygonaceae)

The purpose of his research was to describethe organization of genetic variation in thefederally endangered plant taxon Eriogonumovalifolium var. vineum using allozymes. Such information can help prioritize sites andmanagement choices for capturing andmaintaining genetic variation and can reducethe number of populations necessary to committo conservation, thus reducing costs andconflicts with competing land uses. Information on genetic diversity patterns alsoprovides insight into evolutionary anddemographic history of a taxon which canprovide means to assess future risk of erosionof diversity. Similar to other Eriogonumovalifolium varieties, E. ovalifoliumvar. vineum is diverse atboth the taxon (proportion of polymorphic loci[P] = 0.55 and alleles per locus [A] =5.45 [SD = 2.5]) and population (P = 0.56 [SD =0.11] and A = 2.68 [SD = 0.35]) levels. Gene diversity (H _e) withinpopulations averaged 0.19 (SD = 0.03). Wefound some evidence for limited clonalreproduction within populations. Populationswere moderately differentiated from one another(_S = 0.14) and showed moderatedeviations from Hardy-Weinberg equilibriumwithin populations (f = 0.14 and F =0.19). Mean Nei's genetic distance (D)among all pairs of populations was 0.02. Populations with high levels of multiplemeasures of genetic diversity, high levels ofdifferentiation, and low levels of apparentinbreeding are suggested as conservationpriorities.     

Genetic structure of Japanese Chattonella marina (Raphidophyceae) populations revealed using microsatellite markers

Chattonella marina var. antiqua and C. marina var. marina (Raphidophyceae) are red tide‐forming, harmful phytoplankton species. We investigated the genetic diversity and genetic relationship among the populations using microsatellite markers to identify putative sources of C. marina var. antiqua and C. marina var. marina in Japanese coastal populations. A positive correlation between genetic divergence and geographical distance (isolation by distance) was recognized for C. marina var. antiqua. The C. marina var. antiqua populations were established throughout a geological time scale, and genetic divergence had progressed in each population with gene flow depending on geographic distances. In contrast, isolation by distance was not observed for C. marina var. marina populations, and the genetic divergence among populations was extremely high. The Tokyo Bay population of C. marina var. marina, which was first recognized in 2008, had many private alleles but was related to the Kagoshima Bay population. The Tokyo Bay population may have been established by several invasions from the Kagoshima Bay population and other regions.     

Population variation and phylogeny in the endangered <Emphasis Type="BoldItalic">Chamaesyce skottsbergii</Emphasis> (Euphorbiaceae) based on RAPD and ITS analyses

Chamaesyce skottsbergii var. skottsbergii is federally listed as an endangered taxon, and is found in small and isolated populations restricted to calcareous soils in dry shrubland habitats on the Hawaiian islands of Oahu and Molokai. Concern over the genetic relationship among these disjunct populations arose as a result of threats to the habitat of the Oahu population. The populations were examined using random amplified polymorphic DNA (RAPD) markers and sequence analysis of the internal transcribed spacer (ITS) region of the rDNA cistron. Chamaesyce skottsbergii var. vaccinioides, a closely related variety found in several small populations on Molokai, was used for baseline comparison of the genetic divergence among populations. RAPD analysis demonstrated that variation within and among populations is the highest for any Hawaiian species examined. Polymorphism was greater than 95% within populations and was 99.4% at the species level. Similarly, measures of genetic similarity indicate that differentiation among these populations is higher than is known for some species. Both RAPD and ITS sequence analysis indicate that populations of C. skottsbergii var. skottsbergii on Oahu and Molokai are genetically distinct, and the extent of this genetic differentiation supports the recognition of these populations as distinct varieties. The Molokai population is in fact much more closely related to var. vaccinioides than to var. skottsbergii on Oahu, and thus should be recognized by the previously used variety name, C. skottsbergii var. audens. Further conservation measures for each of the varieties are addressed.     

A contribution to characterisation of genetic variation in some natural Polish populations of Elymus repens (L.) Gould and Elymus hispidus (Opiz) Melderis (Poaceae) as revealed by RAPD markers*

To determine the relative importance of clonal growth and sexual reproduction, the Randomly Amplified Polymorphic DNA (RAPD) method was used to study genetic diversity and clonal structure of six populations of Elymus repens and four populations of Elymus hispidus from Poland. These outbreeding species are virtually self‐sterile and form widely spreading and long‐lived rhizomes. Using 12 primers, a total of 150 unambiguous RAPD fragments were amplified and scored. Results of AMOVA showed no significant genetic distinction between morphologically distinguished varieties of E. repens and E. hispidus. E. repens had slightly higher intra‐specific genetic polymorphism than E. hispidus; the percentage of polymorphic bands per population ranged from 38 to 49 and from 19 to 38 respectively. Clonal diversity measured using the Simpson diversity index (D) indicated different contributions of clonal reproduction in particular populations of E. repens (D: 0.20–0.72). Populations of E. hispidus were dominated by one or a few clones, which were generally restricted to a single population (D: 0.00–0.22). RAPD revealed that most genetic diversity resided within populations of the two studied species, suggesting that, despite their clonal character, propagation by seeds contributes considerably to reproduction of E. repens and E. hispidus.     

Population Analysis of Licuala glabra Griff. var. glabra (Palmae) using RAPD Profiling

Random amplified polymorphic DNA (RAPD) profiling revealed geneticdiversity among three populations ofLicuala glabra var. glabra,an understorey palm growing in the dipterocarp forests of Terengganu,Malaysia. The Bukit Bauk population had individuals withoutaerial stems. The Bukit Besi individuals had stem heights to30 cm, while those of the Rasau Kerteh population had stemsup to 4 m in height. Southern blot analysis confirmed that anapparent monomorphic band generated by the primer OPU-17 amongthe three different populations corresponds to the same locus.Six primers were used to generate 87 RAPD bands that formed2-state character raw data for estimating genetic distancesusing the simple matching coefficient of similarity. The phenogramgenerated by UPGMA of the RAPD data grouped the individualsfrom the three populations under three clusters. This was inagreement with the morphological grouping. The infraspecificL. glabra var.selangorensis Becc. was grouped closer to theL. glabra var. glabra individuals than to the outgroupL. scortechiniiBecc. Principal component analysis supported the observationfrom the phenogram. The results show discrete genetic structuringin the populations studied and provide useful information forfuture conservation measures. Copyright 1999 Annals of BotanyCompany Licuala glabra Griff. var. glabra, RAPD, palm, AMOVA, population, genetic diversity, conservation.     

Genetic diversity of Mexican brook lamprey <Emphasis Type="Italic">Lampetra (Tetrapleurodon) geminis</Emphasis> (Alvarez del Villar, 1966)

Lampreys are the only surviving representatives of the oldest known vertebrates. The Mexican lamprey L. geminis (nonparasitic), is particularly interesting, because it is an endemic, biogeographical relict, and a threatened species. RAPD markers were used to describe genetic diversity in L. geminis A total of 77 specimens were collected from five populations, three in the R'o Grande de Morelia-Cuitzeo basin and two in the R'o Duero-Lerma-Chapala basin, Mexico. Eighty-eight RAPD markers were obtained from eight primers. Genetic diversity within each population was estimated using Shannon's index (S), heterozygosity (H) and gene diversity (h). These estimates revealed significant variation within populations, although a variance homogeneity test (HOMOVA) showed no significant differences among populations or between basins. Nei genetic distance values indicate a low genetic differentiation among populations. Analysis of molecular variance (AMOVA) indicates that most of the genetic diversity occurs within populations (91.4%), but that a statistically significant amount is found among populations (P0.001). Principal coordinates and cluster analyses of RAPD phenotypes show that specimens are not grouped by geographical origin. The genetic diversity found within L. geminispopulations may be explained by its breeding system and an overlapping of generations. The scarce genetic differentiation among populations is likely to the low rate of DNA change that characterizes the lamprey group.     

濒危羊踯躅子代幼苗遗传多样性的SSR分析

利用本课题组此前开发的20对多态性较高的羊踯躅SSR引物,分析来自3个省份的4个羊踯躅野生幼苗自然居群(共64个株系)的遗传多样性和遗传结构,以期为羊踯躅保护提供科学依据。结果显示:(1)20对SSR引物共扩增出314个等位基因,每个SSR位点的平均等位基因数为15.700,多态信息含量PIC和有效等位基因数N_e的均值分别为0.850和4.457。(2)羊踯躅幼苗自然居群的基因多样性指数H和Shannon多样性指数I的均值分别为0.717和1.557,其中江西金溪(JX)居群的遗传多样性最丰富,浙江磐安(PA)的最低。(3)基于无限等位基因模型(IAM)分析发现,羊踯躅幼苗种群的基因流N_m和遗传分化系数F_(st)分别为1.372和0.155;AMOVA分析表明,羊踯躅幼苗种群的86.0%变异发生于居群内,仅有14%变异发生在居群间。(4)遗传距离法聚类NJ分析和Structure分析结果基本一致,分别聚为3大类和4大类。综合比较分析发现,羊踯躅幼苗种群中的各个遗传多样性相关的指标参数均低于成年自然居群,表明生境片段化已对羊踯躅的生存构成了极大的威胁。     

Inter-populational variation,but no-annual variation within populations,in terms of reproductive size and genetic structure in a monocarpic perennial herb,Cardiocrinum cordatum var. glehnii

Cardiocrinum cordatum var. glehnii (Liliaceae) is a monocarpic perennial herb living in temperate broad-leaved deciduous forests. In the present study we examined the sizes (basal diameter of the stem and flower numbers) of flowering individuals and genetic diversity using microsatellite loci of 23 populations of C. cordatum var. glehnii in Hokkaido, Japan, over 2 years (2009 and 2010). As a result, we found both the basal stem diameter and the number of flowers varied widely among the populations. However, although the sizes of flowering individuals differed among the populations, these were very stable in each population and in each year. In addition, for genetic diversity, the same trends (i.e. wide variation among the populations but non-annual variation) were detected.     

Analysis of the genetic diversity and relationships among and within species of Hippophae (Elaeagnaceae) based on RAPD markers

RAPD markers were used to assess the genetic diversity and inter- and intra-specific relationships of the genus Hippophae L. and to study the correlation between genetic distances and geographic distances among populations of H. rhamnoides ssp. sinensis. The results analyzed by the percentage of polymorphic loci and Shannon information index indicated that a high level of genetic diversity existed both among and within species of the genus Hippophae. In the UPGMA dendrogram, the species or subspecies were clustered into two main groups but not strictly grouped according to sect. Hippophae and sect. Gyantsensis Lian. The multiple regression analysis and Mantel test both indicated a significant correlation between genetic distance and altitude distance among populations of H. rhamnoides ssp. sinensis, and the cluster analysis suggested that the genetic variation among populations of H. rhamnoides ssp. sinensis was linked to their monophyletic origin. Moreover, some degree of genetic differentiation was found among samples collected at different times.     

在韩国境内Potentilla fragarioides var .sprengeliana的遗传多样性和种群结构(英文)

根据 2 2个等位酶位点遗传变异 ,探讨了韩国境内委陵菜 (PotentillafragarioidesL .var.sprengeliana)的遗传多样性和种群结构。酶位点的多态位点百分比为 5 9 1%。种和种群水平上的遗传多样性比较高 ,分别为Hes=0 .2 10 ,Hep=0 .199;而种群的分化水平则相对较低 (GST=0 .0 74)。 19个种群中随机交配的偏差为FIS=0 .331。每代迁移数的间接估计 (Nm=3.15 )表明该种在韩国的种群间基因流较高。另外 ,固定指数分析显示在一些种群和位点有轻微的杂合子缺乏。种群间平均遗传一致度为 0 985。这些韩国委陵菜种群存在于较为均一的生境 ,这很有可能是造成其种群遗传一致性较高的原因。     

Patterns of Genetic Diversity and Population Structure of the Clonal Herb,Potentilla fragarioides var. sprengeliana (Rosaceae) in Korea

The genetic diversity and population structure of Potentilla fragarioides var. sprengeliana(Rosaceae) in Korea were investigated using genetic variation at 22 allozyme loci. The percent of polymorphic loci within the enzymes was 59.1%. The genetic diversity at the species level and at the population level was high (Hes=0.210; Hep=0.199, respectively), whereas the extent of the population divergence was relatively low (GST=0.074). FIS, a measure of the deviation from random mating within the 19 populations, was 0.331. An indirect estimate of the number of migrants per generation (Nm=3.15) indicates that gene flow is high among Korean populations of the species. In addition, analysis of fixation indices revealed a slight heterozygote deficiency in some populations and at some loci. The mean genetic identity between populations was 0.985. It is highly probable that the trend of genetic uniformity in a relatively homogeneous habitat is thought to be operated among Korean populations of P. fragarioides var.sprengeliana.     

Genetic Diversity and Population Differentiation of Liaoning Weedy Rice Detected by RAPD and SSR Markers

Weedy rice refers to populations of usually annual Oryza species that diminish farmer income through reduction of grain yield and lowered commodity value at harvest. The genetic diversity and population genetic structure of weedy rice in Liaoning Province were studied by RAPD and SSR markers. The results indicate that the level of genetic diversity of Liaoning weedy rice is very low, with polymorphic loci being only 3.70% (RAPDs) and 47.62% (SSRs). On the other hand, high genetic differentiation was found among populations, in particular between two regions (Shenyang and Dandong), with Fst values of 0.746 (RAPDs) and 0.656 (SSRs), suggesting that more than two thirds of the genetic variation resides among regions. Combined with our investigations of cultural traditions, the low level of genetic diversity in Liaoning Province is attributed to its narrow genetic background enhanced by exchanges of cultivar seeds, whereas the high genetic differentiation between the two regions is most likely the result of different founding parents and gene flow from local rice varieties to weedy rice. The rice cultivars in the two regions are all local varieties and are different genetically. A comparison of the two marker systems demonstrates that SSR is more informative and powerful in terms of the assessment of genetic variability, although both RAPD and SSR provide useful genetic information on weedy rice.     

Genetic diversity of the narrow endemic Allium aaseae (Alliaceae)

Low levels of genetic variability are common for a number of geographically restricted plants: these data are consistent with theoretical expectations that small populations should be genetically depauperate. However, in some species, high levels of variability have been found in rare species. Allium aaseae is a rare, narrow endemic in the foothills of the Boise Front of southwestern Idaho. Genetic variation in the rare endemic A. aaseae, and nearby populations of the more common species, A. simillimum, was examined with randomly amplified polymorphic DNA (RAPD) data. Eight populations of A. aaseae and six populations of A. simillimum (three near the range of A. aaseae, and three distant populations) of 25 individuals each were examined for this analysis. Genetic diversity as determined with RAPD markers of both species examined in this study is largely found within and not among populations. Levels of genetic diversity are high, especially for a narrow endemic species such as A. aaseae. Proportion of RAPD loci polymorphic was high in both species, although slightly higher in the more common A. simillimum. Because these higher levels of genetic variability run counter to theory, alternative explanations beyond population size must be invoked to explain the levels of genetic diversity found in this study. Possible explanations are (1) A. aaseae is only recently derived from A. simillimum, (2) hybridization between A. aaseae and A. simillimum is occurring, (3) multiple origins of A. aaseae, (4) populations of A. simillimum included in the analysis are all A. aaseae, (5) A. aaseae and A. simillimum are conspecific, and (6) an artifact of RAPD data.     

Impact of geographical isolation on genetic differentiation in insular and mainland populations of Weigela coraeensis (Caprifoliaceae) on Honshu and the Izu Islands

Aim To provide insights into genetic differentiation between insular endemic Weigela coraeensis var. fragrans and its progenitor variety W. coraeensis var. coraeensis, the population genetic structure of both varieties was examined, and factors promoting genetic differentiation between the two taxa were explored. Location The natural range of W. coraeensis (sensu lato) throughout mainland Japan (Honshu) and the Izu Islands. Methods The analysis included 349 and 504 individuals across the mainland (Honshu) and the Izu Islands, respectively, using 10 allozyme and 10 microsatellite loci. The population genetic structure of W. coraeensis was assessed by analysing genetic diversity indices for each population, genetic differentiation among populations, model‐based Bayesian clustering or distance‐based clustering, and bottleneck tests. Results The level of genetic diversity in each of the populations on the Izu Islands was negatively correlated with geographical distance between each island and the mainland. The populations on the mainland and on the Izu Islands were genetically differentiated to a certain extent; however, the microsatellite analyses suggested that gene flow also occurred between the mainland and the islands, and among individual islands. These microsatellite analyses also suggested recent bottlenecks in several populations in both areas. Main conclusions The decrease in genetic diversity throughout the Izu Islands, which correlated with distance to the mainland, Honshu, may be the result of a repeated founder effect occurring at a series of inter‐island colonizations from north to south. The stepping stone‐like configuration of the islands may have played a role in the dispersal of the species. Geographical isolation by sea would effectively result in genetic differentiation of W. coraeensis between mainland Honshu and the Izu Islands, although some gene flow may still occur between Honshu and the northern Izu Islands. The differentiation process of the endemic plants on the Izu Islands is anagenetic but not completed, and the study of these plants will provide insightful knowledge concerning the evolution of insular endemics.     

Population genetic study in the Balearic endemic plant species Digitalis minor (Scrophulariaceae) using RAPD markers

Digitalis minor (Scrophulariaceae) is a cardenolide-producing plant endemic to the eastern Balearic Islands (Mallorca, Menorca, and Cabrera) that occurs in two morphologically distinct varieties: D. minor var. minor (pubescent) and D. minor var. palaui (glabrous). Levels and patterns of genetic diversity in 162 individuals from 17 D. minor populations across the entire geographic range were assessed using random amplified polymorphic DNA (RAPD) markers. Comigrating RAPD fragments tested were found to be homologous by Southern hybridization in both var. minor and var. palaui. To avoid bias in parameter estimation, analyses of population genetic structure were restricted to those RAPD bands that fulfilled the 3/N criterion (observed frequencies were less than 1 - [3/N] in each population) either among or within each island. Analyses of molecular variance (AMOVAs) with distances among individuals corrected for the dominant nature of RAPD (genotypic analysis) showed low values (1.57-17.55%) of between-population variability, indicating a relatively restricted population differentiation as expected for an outcrossing species such as D. minor. Nested AMOVAs demonstrated, however, a not significant partitioning of genetic diversity among Mallorca, Menorca, and Cabrera islands. Estimates of the Wright, Weir, and Cockerham and the Lynch and Milligan F(ST) from null allele frequencies corroborated AMOVA partitioning and provided evidence for population differentiation in D. minor. Our RAPD data did not show significant differences between pubescent and glabrous populations of D. minor, suggesting a failure to find a correlation between the RAPD loci and this morphological trait.     

Conservation Genetics of Mexican Beech, Fagus grandifoliavar. mexicana

Fagus grandifolia var. mexicana(Fagaceae) is a Mexican endemic tree, currently threatened with extinction. In order to assess the level and structure of genetic variation in four remaining populations, leaf samples were analysed using random amplified polymorphic DNA (RAPD) and cpDNA PCR-RFLP markers. A sample of the more widespread congener, F. grandifoliavar. grandifolia from the USA was also analysed for comparison. Thirty-three polymorphic RAPD bands were produced using 18 10-mer primers. AMOVA of RAPD data indicated significant (P < 0.002) population differentiation, with 15.6% of variation recorded between Mexican populations. PCR-RFLP analysis enabled three cpDNA haplotypes to be identified, denoted types A, B, and C. Types A and B were each restricted to an individual Mexican population, whereas Type C was fixed for two Mexican populations, and the population from the USA. Within-population genetic variation, quantified as percentage polymorphic bands, Shannon's Diversity Index and Nei's gene diversity measure, was found to be lower in Mexican populations than in that from the USA, and was positively related to population size. These results suggest that an unexpectedly high degree of genetic variation exists within Mexican beech, and this variation should be considered in developing the conservation strategy that is urgently required if extinction of this taxon is to be prevented.     

Genetic diversity in wild diploid wheats Triticum monococcum var. boeoticum and T. urartu (Poaceae)

Summary The genetic diversity of two wild diploid wheat species, Triticum monococcum var. boeoticum and T. urartu, was assessed using starch gel electrophoresis. Genetic diversity is uniformly low in both species. Number of alleles per locus was very low with a mean of 1.22 for T. monococcum var. boeoticum and 1.19 in T. urartu. Percentage of polymorphic loci was also low, with a mean of 19.71 for T. monococcum var. boeoticum and a mean of 18.35 for T. urartu. Mean gene diversity was low with a mean of 0.052 in populations of T. monococcum var. boeoticum and a mean of 0.040 in populations of T. urartu. Genetic affinities of the species and of populations were computed using Nei's identity index (NI). Overall genetic affinities of the two species are NI=0.697. The genetic affinities of different populations of a species are uniformly high with NIs ranging from 0.894 to 1.000 in T. monococcum var. boeoticum and from 0.898 to 1.000 in T. urartu.Research supported by the California Agricultural Experiment Station and the International Board of Plant Genetic Resources     

Genetic diversity of the endangered Chinese endemic herb Primulina tabacum (Gesneriaceae) revealed by amplified fragment length polymorphism (AFLP)

Primulina tabacum Hance, is a critically endangered perennial endemic to limestone area in South China. Genetic variability within and among four extant populations of this species was assessed using AFLP markers. We expected a low genetic diversity level of this narrowly distributed species, but our results revealed that a high level of genetic diversity remains, both at population level (55.5% of markers polymorphic, H _E = 0.220, I _S = 0.321), and at species level (P = 85.6% of markers polymorphic, H _E = 0.339, I _S = 0.495), probably resulting from its refugial history and/or breeding system. High levels of genetic differentiation among populations was apparent based on Nei’s genetic diversity analysis (G _st=0.350). The restricted gene flow between populations is a potential reason for the high genetic differentiation. The population genetic diversity of P. tabacum revealed here has clear implications for conservation and management. To maintain present levels of genetic diversity, in situ conservation of all populations is necessary.