Genetic Diversity and Tests of the Hybrid Origin of the Endangered Yellow Larkspur

Abstract: Delphinium luteum ( Ranunculaceae), an endangered larkspur, is restricted to two wild populations near Bodega Bay, California. The total number of individuals in these two populations is estimated to be <100. We used allozyme and random amplified polymorphic DNA ( RAPD) markers to (1) assess levels and patterns of genetic diversity in one wild population and two cultivated populations and (2) test the hypothesis that D. luteum is of hybrid origin between D. decorum and D. nudicaule . These data will be used to aid in developing a management plan to conserve the species. The wild population maintains high levels of genetic diversity. Genetic data indicate that both cultivated populations, especially the north Sonoma population, have several allozymes and RAPD markers not found in the wild population and could be used to establish new populations of D. luteum or to enhance the diversity and size of the wild population. The allozyme data did not reveal any fixed differences between D. decorum and D. nudicaule , although allele frequencies of the putative parental populations differed. At these loci, D. luteum resembled D. nudicaule more than D. decorum  . Many unique RAPD markers distinguish each of the three species. The diagnostic markers from populations of D. nudicaule and D. decorum were not additive in the putative hybrid, and these data indicate that D. luteum is not of recent hybrid origin. Conservation of the yellow larkspur should include strategies that use the cultivated populations of D. luteum , but hybridizing D. decorum and D. nudicaule to "recreate" D. luteum is not recommended.     

Application of random amplified polymorphic DNA (RAPD) markers to evaluate intraspecific genetic variation in red mullet (Mullus barbatus)

The random amplified polymorphic DNA (RAPD) technique was used to evaluate genetic affinities among eight red mullet (Mullus barbatus L., 1758) samples from the Mediterranean Sea. Twenty-nine random primers were used. Despite the variability which was found within samples, no specific RAPD marker for the discrimination of the populations was detected. The data analysis revealed that the genetic diversity among populations is positively related to their geographic distances. The results of this study indicate that the estimated intraspecific variation may be more␣pronounced with RAPD markers than with allozymes when the two approaches are applied on the same populations. Received: 7 November 1997 / Accepted: 30 May 1998     

Mode of larval development and genetic population structure inNodilittorina africana knysnaensis (Prosobranchia: Littorinidae)

We examined electrophoretic variation in the supralittoral gastropod,Nodilittorina africana knysnaensis, along the coast of South Africa in 1989. There was little allozyme variation in nine samples collected over 1 500 km for three highly polymorphic loci,Est, Gpi, andPgm, and Wahlund's effect was absent in the pooled sample. A gene diversity analysis showed that 98.1% of total genic diversity, on average, was contained within populations, and that only 1.9% was due to allozyme frequency differences among populations. Since the mode of larval development has not yet been described for this species, we suggest that the lack of strong allozyme frequency differences over long distances indicates thatN. a. knysnaensis has a planktonic mode of larval development.     

Interspecific variation in thermal denaturation of proteins in the congeneric musselsMytilus trossulus andM. galloprovincialis: evidence from the heat-shock response and protein ubiquitination

The genetic population structure of the precominant zooplankter, the copepod Calanus finmarchicus (Gunnerus), was examined to determine whether genetically distinct populations exist in the Gulf of Maine. C. finmarchicus was sampled in three regions of the Gulf of Maine (Great South Channel, spring 1989; northern Gulf of Maine, winter 1990; Great South Channel and Georges Bank, spring 1990). Copepods from seven locations in the Great South Channel, five in the northern Gulf of Maine and four on or near Georges Bank were assayed for allozyme variation and mitochondrial DNA variation of amplified 16S rRNA and cytochrome b genes. Restriction fragment length polymorphism (RFLP) analyses of both mitochondrial DNA genes revealed no variation among any of the individuals assayed. Analysis of five polymorphic allozyme loci revealed that genetic variation among the three geographic regions was low, and genetic identities were high between all locations (I>0.97). Most of the genetic variation was among locations regardless of region. Chi-square tests were used to examine genetic similarity between specific pairs of locations within and between regions. In the northern Gulf of Maine, genetic homogeneity occurred over larger spatial scales (hundreds of km) than in either the Great South Channel or Georges Bank (tens of km). Only copepods from the Bay of Fundy and Nova Scotian Shelf locations were genetically distinct from Wilkinson Basin copepods at two loci. Copepod populations from the northern locations may have been partially isolated or they may represent immigrant populations (e.g., from the Gulf of St. Lawrence). Several pairs of locations were genetically distinct at one or more loci in the two southern regions. Differences between locations in these regions may represent distinct populations advected into the areas at different times or from different sources (e.g., genetic variation may represent a mixture of genetically distinct northern and southern copepod populations). These results suggest extensive gene flow among populations of C. finmarchicus in the Gulf of Maine with some evidence of genetic population subdivision near the Gulf's northeastern and southern boundaries.     

Genetic structure of crown-of-thorns starfish (Acanthaster planci ) on the Great Barrier Reef, Australia: comparison of two sets of outbreak populations occurring ten years apart

Six populations of the crown-of-thorns starfish, Acanthaster planci, showing large increases in population size in 1994 to 1995, were examined by allozyme electrophoresis of 100 to 300 individuals collected from each population in November 1995 to February 1996. Analysis of nine loci, used to determine the structure of outbreak populations in the early-mid-1980s, demonstrated no significant differentiation among the 1996 outbreak populations in any age class (2 to 6 yr old). No significant variation was detected between age classes in any of the six populations. These data are consistent with the recent outbreak populations having been derived from one genetic source, and suggest no change in the source of recruits to these reefs between 1989/1990 to 1994/1995. In a multi-dimensional scaling analysis, the 1996 samples clustered with the eight 1986 outbreak populations in a small part of the genetic space spanned by the 1986 non-outbreak populations, suggesting that the outbreak populations were derived from the same genetic source in both 1986 and 1996. Statistically significant, but small, differences in gene frequencies detected between the 1986 and 1996 outbreak populations are thought to result from genetic drift, but are unlikely to provide a means of distinguishing sets of outbreak populations because of the large sample sizes required to detect the small shifts in gene frequency. Received: 21 March 1997 / Accepted: 2 April 1997     

Genetic variation in Symbiodinium isolates from giant clams based on random-amplified-polymorphic DNA (RAPD) patterns

We have compared the random-amplified-polymorphic DNA (RAPD) patterns of Symbiodinium isolates from seven species of giant clams to investigate the large genetic variation that we previously reported for this group of dinoflagellate symbionts using allozyme analysis. Comparisons of 163 RAPD characters by unweighted pair-group arithmetic-average cluster analysis (UPGMA) corroborate our previous findings that giant clams associate with a large number of genetically distinguishable algal symbionts, and that the isolates from a single Tridacna gigas individual form a group of closely related algae. However, the overall topology of the UPGMA tree constructed from RAPD data differs from that of the previous allozyme data, indicating that the combined data we have collected to date are insufficient to accurately infer phylogenetic affiliations between the isolates studied. Comparisons of our data set with those published for strains of Gymnodinium catenatum, a toxic dinoflagellate with a sexual life stage, shows that our isolates are even more diverse. Algal isolates from giant clams have a level of RAPD variation comparable to organisms that are able to undergo sexual recombination. This study demonstrates the sensitivity of the RAPD technique in detecting genetic diversity in this group of algae, and highlights the need for more comparative data for the major clades of Symbiodinium. Received: 24 August 1999 / Accepted: 8 March 2000     

11个猕猴桃品种间的遗传多样性分析

利用随机扩增多态性DNA标记(RAPD)技术对采自四川省猕猴桃科研基地的11个猕猴桃品种进行了遗传多样性分析.通过引物筛选,从15个RAPD引物中扩增出135条带,其中100条为多态带,占74.07%.UPGMA聚类分析结果揭示了各品种间的亲缘关系.RAPD标记说明猕猴桃品种间遗传距离与地理分布有一定关系,地理位置较近的材料能聚在一起.分子标记可用于猕猴桃种质资源的分类、鉴定及良种选育.图2表2参15     

Genetic structure of local populations and divergence between growth forms in a clonal invertebrate,the Caribbean octocoral Briareum asbestinum

Although the genetic structure of many populations of marine organisms show little deviation from panmixia, in those marine species with limited larval dispersal, patterns of microgeographic genetic differentiation may be common. The octocoral Briareum asbestinum should show local population differentiation because colonies reproduce asexually by fragmentation, most matings occur between colonies in very close proximity, and the sexually produced larvae and sperm appear to disperse only short distances. Variability in secondary chemistry of individual B. asbestinum colonies from different populations in close proximity also suggests local population differentiation. We determined the genetic composition of local populations by surveying allozyme variation of three shallow and two deep populations within a 300 m² area at San Salvador Island, Bahamas and at a site 161 km away on Little San Salvador, Bahamas in July 1990. As B. asbestinum occurs as either an erect branching form or an encrusting mat often at the same sites, we sampled both morphs to examine the extent of genetic exchange between them. Five of 21 loci were polymorphic and most populations showed a deficit of heterozygotes. Allele frequencies differed significantly between morphs at each site where they occurred together. The mean genetic distance (D=0.065) between morphs is consistent with the interpretation that the two morphs are genetically isolated. Despite the close spatial proximity of the San Salvador populations, both the branching and encrusting morphs showed significant genetic heterogeneity among neighboring populations. Similarly, pooled allelic frequencies for samples collected from the islands of San Salvador and Little San Salvador differed significantly at 1 locus for the branching morph and at 3 out of 5 loci for the encrusting morph.     

朱■的随机扩增多态DNA分析与种内亲缘关系研究

利用随机扩增多态ＤＮＡ技术对朱（Ｎｉｐｐｏｎｉａｎｉｐｐｏｎ）８个个体进行了随机扩增多态ＤＮＡ分析．用２０个１０ｂｐ的随机引物对每只朱的基因组ＤＮＡ进行扩增,共得到１６８个扩增片段,其中共有片段为１０２个．根据聚类分析所得到的树状图确定了８只朱的亲缘关系,这为进一步构建全部朱个体的谱系关系图打下了基础,有利于制定更有效的朱保护计划     

朱鹮的随机扩增多态DNA分析与种内亲缘关系研究

利用随机扩增多态DNA技术对朱鹮 ( Nipponia nippon ) 8个个体进行了随机扩增多态DNA分析. 用20个10bp的随机引物对每只朱鹮的基因组DNA进行扩增,共得到168个扩增片段,其中共有片段为102个. 根据聚类分析所得到的树状图确定了8只朱鹮的亲缘关系,这为进一步构建全部朱鹮个体的谱系关系图打下了基础,有利于制定更有效的朱鹮保护计划.     

基于RAPD技术检测不同烃链长度咪唑基离子液体对日本三角涡虫的遗传毒性

RAPD标记通常用于遗传作图、分类和系统发育研究,该技术也可用于检测DNA损伤或突变。本研究利用RAPD技术检测了4种不同烃链长度的咪唑基离子液体对日本三角涡虫(Dugesia japonica)的遗传毒性。在20条随机引物中共筛选出11条用于RAPD扩增,其中对照组共扩增出65条带。与对照组相比,离子液体处理组的RAPD图谱变化表现在条带亮度增强或减弱以及新带的出现和正常带的消失。各处理组多态性带及变异带的总数随离子液体烃链碳原子数增加而增加,而基因组模板稳定性则随离子液体烃链长度增加而降低,这说明咪唑基离子液体对涡虫有遗传毒性,且随着离子液体烃链长度增加其对涡虫的遗传毒性增强。同时研究结果也证明RAPD分析是一种检测环境污染物对动物DNA损伤的灵敏方法。     

Isozyme, ISSR and RAPD profiling of genotypes in marvel grass (Dichanthium annulatum)

Genetic analysis of 30 accessions of marvel grass (Dichanthium annulatum Forsk.), a tropical range grass collected from grasslands and open fields of drier regions, was carried out with the objectives of identifying unique materials that could be used in developing the core germplasm for such regions as well as to explore gene (s) for drought tolerance. Five inter-simple sequence repeat (ISSR) primers [(CA)4, (AGAC), (GACA) 4; 27 random amplified polymorphic DNA (RAPD) and four enzyme systems were employed in the present study. In total, ISSR yielded 61 (52 polymorphic), RAPD 269 (253 polymorphic) and enzyme 55 isozymes (44 polymorphic) bands. The average polymorphic information content (PIC) and marker index (MI) across all polymorphic bands of 3 markers systems ranged from 0.419 to 0.480 and 4.34 to 5.25 respectively Dendrogram analysis revealed three main clusters with all three markers. Four enzymes namely esterase (EST), polyphenoloxidase (PPO), peroxidase (PRX) and superoxide dismutase (SOD) revealed 55 alleles from a total of 16 enzyme-coding loci. Of these, 14 loci and 44 alleles were polymorphic. The mean number of alleles per locus was 3.43. Mean heterozygosity observed among the polymorphic loci ranged from 0.406 (SOD) to 0.836 (EST) and accession wise from 0.679 (1G3108) to 0.743 (IGKMD-10). Though there was intermixing of few accessions of one agro-climatic region to another largely groupings of accessions were with their regions of collections. Bootstrap analysis at 1000 iterations also showed large numbers of nodes (11 to 17) having strong clustering (> 50 bootstrap values) in all three marker systems. The accessions of the arid and drier regions forming one cluster are assigned as distinct core collection of Dichanthium and can be targeted for isolation of gene (s) for drought tolerance. Variations in isozyme allele numbers and high PIC (0.48) and MI (4.98) as observed with ISSR markers indicated their usefulness for germplasm characterization.     

Geographic variation in Loligo forbesi in the Northeast Atlantic Ocean: analysis of morphometric data and tests of causal hypotheses

Geographic variation in the squid Loligo forbesi was investigated using multivariate analysis of morphometric and meristic characters in samples of squid taken from 13 localities in the Northeast Atlantic Ocean. Two character sets, body morphometrics and beak morphometrics, indicated similar patterns of variation, with squid from the Azores differing markedly from those on the continental shelf. No consistent pattern was apparent in meristic data. Partial Mantel tests indicated that similarity matrices for morphological data were significantly correlated with distance matrices for (a) geographic proximity, (b) whether the capture site was on the continental shelf or the Azorean bank, and (c) (beak data only) average seasurface temperature at site of capture. Partial Mantel tests on allozyme data for the same individuals support hypothesis (b). The results suggest that L. forbesi in the Azores may reasonably be regarded as a distinct stock, differing significantly from L. forbesi on the continental shelf.     

Fitness in the Endangered Gila Topminnow

The Gila topminnow (Poeciliopsis o. occidentalis) is a small, live-bearing, endangered fish extant in a maximum of nine locales in four separate watersheds in the United States. To determine if these populations differed in their fitness, we obtained samples from the four watersheds and examined them for four fitness correlates: survival, growth rate, fecundity, and bilateral asymmetry. Earlier research found that one population, Sharp Spring, had higher allozyme heterozygosity than the other three and had higher survival, growth rate, and fecundity and lower bilateral asymmetry than a sample from one of the other populations with no polymorphic allozyme loci, Monkey Spring. We also verified that Sharp Spring fish were polymorphic for the same allozyme loci whereas the Monkey Spring population was not. We did not, however, find positive associations of allozyme heterozygosity with the four fitness correlates for the four samples. Because the earlier study had much lower survival, it is likely that the differences resulted from differential response of the two populations to a stressful laboratory environment. Whether this unknown stress occurs in natural environments or its effect is predictive of other stresses remains unresolved. As a result, we concur with suggestions in the draft recovery plan that topminnows from nearby sources be used for reintroductions and that the Sharp Spring stock not be used outside the upper Santa Cruz River drainage.     

Genetic Variation and Outcrossing Rate in Relation to Population Size in Gentiana pneumonanthe L

The amount of genetic variation in the rare perennial herb Gentiana pneumonanthe L. was determined to explore its relation to population size. Differences in isozyme variation between maternal plants and their offspring were used to investigate the relationship between population size and outcrossing rate. In 25 populations in The Netherlands, differing in size from 1 to more than 50,000 flowering individuals, 16 allozyme loci were analyzed on leaves of maternal plants and offspring grown in a greenhouse. Population size was significantly positively correlated with the proportion of polymorphic loci, but only marginally with heterozygosity and the mean effective number of alleles. Most of the studied populations were characterized by a complete absence of rare alleles, and F -statistics suggest relatively high levels of genetic differentiation among populations and thus a low level of gene flow. Leaf samples (maternal) were mostly in Hardy-Weinberg equilibrium, while several offspring samples showed an excess of homozygotes, which suggests selection favoring heterozygotes. Because most small populations consist only of adult survivors from formerly larger populations, this may partly explain the absence of a clear relationship between genetic variation of the maternal plants and population size. A significant positive correlation was found between the level of cross-fertilization and population size. From these results, we conclude that, to some degree, small populations have a reduced level of genetic variation, while their present isolation in nature reserves has resulted in a very limited interpopulational gene flow level. At present a higher level of inbreeding in small populations contributes to a further loss of genetic variation and may also result in reduced offspring fitness.     

Genetic population structure of the southern oyster drillStramonita (=Thais)haemostoma

Nine collections in the southeastern USA of the thaidid molluscStramonita haemastoma, comprising 963 individuals, were made between June 1988 and November 1989, and examined for allozyme variation at 18 electrophoretically-detected loci. Two genetically-differentiated groups were identified and are referred to ascanaliculata-like andfloridana-like snails, based on previously-described subspecies ofS. haemastoma. The two groups were differentiated genetically at a level that is characteristic of congeneric species in other molluscan taxa. The two groups maintained their genetic differences in areas of sympatry, although rare hybrid individuals occurred (about 1.2% of the total set). Shell and radular characters showed little variation within or between the two groups. Within each group, allozyme allele frequencies showed little geographic variation across distances as great as 1 500 km. This result is consistent with the suggestion that species with planktonic larvae (such asS. haemastoma) should have higher rates of gene flow than related brooding species.     

Genetic population structure of the seagrass Thalassodendron ciliatum in sandy and rocky habitats in southern Mozambique

The genetic diversity of the dioecious seagrass Thalassodendron ciliatum in six populations in southern Mozambique was studied by means of random amplified polymorphic DNA (RAPD). Samples were taken from sandy and rocky habitats over a span of 880 km. Analysis of molecular variance (AMOVA) showed that most of the genetic variability (71.6% of total genetic variation) was observed within populations. There were also significant genetic differences among populations within each habitat (sandy and rocky). We did not find any significant overall genetic difference between sandy versus rocky populations, indicating that the morphological differences between plants from these two habitats are not maintained by reproductive isolation. There was no significant correlation between geographical and genetic distance, which is discussed in the light of current patterns along the coast. All sampled populations consisted of several genetically distinct individuals, indicating that sexual reproduction is widespread.     

Genetic Variation for Morphological and Allozyme Variation in Relation to Population Size in Clarkia dudleyana, an Endemic Annual

Abstract: The maintenance of genetic variation within populations is expected to allow species to respond to evolutionary challenges such as selection and environmental stress. Larger populations are generally expected to maintain larger amounts of genetic variation. Although several studies have found a positive relationship between population size and levels of genetic variation for molecular markers such as allozymes, few comparisons have been made between molecular measures of variation and genetic variation that is likely to be ecologically important. Most ecologically important traits require quantitative genetic analyses. I examined the relationship between levels of genetic variation and population size for both allozymes and morphological traits in a California endemic annual plant, Clarkia dudleyana . Levels of genetic variation for allozymes did not show a significant positive relationship with population size. The level of genetic variance for all of the 18 morphological traits exhibited no significant relationship with population size. Further, allozyme heterozygosities were not related to levels of quantitative genetic variation. These results indicate that levels of allozyme variability do not predict levels of genetic variation for morphological traits in C. dudleyana , suggesting that molecular measures of variation, in general, differ from quantitative genetic measures. These results imply that conservation genetic studies should generally focus on aspects other than measuring levels of genetic variation found within populations.     

与甘蔗抗黑穗病基因连锁的RAPD标记筛选

为了寻找与由黑粉菌(Ustilago sictaminea Syd．)引起的甘蔗黑穗病抗病基因连锁的分子标记，从而借助分子标记辅助选择(MAS)手段提高抗病育种效率，用甘蔗抗病亲本Co1001为母本，用感病亲本Ya71-374为父本，配置杂交组合创制抗病性分离群体为材料，采用人工接种新植蔗，田问种植方法鉴定分离个体新植和宿根的抗病性，借助RAPD和集群分离分析法(BSA)，筛选出一个与抗病基因连锁的多态性片段，并在抗、感池中的个体和池外部分个体上得到验证，该片段大小约520bp．对该片段的进一步克隆、测序和转换研究还在进行中，研究结果为抗病育种的MAS奠定了基础．图2表3参12     

中国茸鹿品种(品系)的随机扩增多态DNA(RAPD)研究

采用随机扩增多态ＤＮＡ技术研究了５个茸鹿品种（品系）７５个个体的遗传变异关系。在所使用的４１个引物中,有４０个引物扩增出多态谱带,共检测到３９５条扩增片段,其中２５９条（６５．６％）出现变异,用Ｓｈａｋｎｎｏｎ指数计算了５个品种（品系）的遗传变异及其遗传变异在群体内和群体间的分布。利用Ｎｅｉ氏片段共享度计算了７５个个体间的遗传距离,用ＵＰＧＭＡ聚类法构建了７５个个体的系统发育树状图,反映５个茸鹿品