Genetic diversity of Lavandula multifida L. (Lamiaceae) in Tunisia: implication for conservation

The genetic variation within and among eight Tunisian natural populations of Lavandula multifida L., from different bioclimatic zones was assessed using random amplified polymorphic DNA (RAPDs). Of a total of 97 generated bands from seven selected primers, 84 bands were polymorphic. The genetic diversity within a population was high and varied according to the populations (0.308 < H’ < 0.459) without relationships to altitudes or pluviothermic indices of sites. The genetic differentiation among populations was high (G_ST = 0.395 and Φ_ST = 0.318). All population pairs were significantly differentiated. Among populations, within ecological groups genetic structure was high (0.219); whilst among them it was low (Φ_CT = 0.049; P < 0.05). The correlation between Φ_ST and geographic distance matrices among pairs of populations was not significant, suggesting that genetic connectivity between populations has a stochastic component at all spatial scales. The neighbour‐joining cluster analysis showed that individuals from each population clustered together. UPGMA cluster analysis showed that population groupings are not strictly in accordance with bioclimates or geographic location. The genetic differentiation in L. multifida could have occurred at local scales because of genetic drift. Efforts should be made to protect all populations. The maintenance of substantial population size should be initiated via fencing and controlling collection to restore the regeneration of populations.     

Biscogniauxia mediterranea associated with cork oak (Quercus suber) in Tunisia: Relationships between phenotypic variation,genetic diversity and ecological factors

Biscogniauxia mediterranea is a xylariaceous ascomycete responsible for ‘charcoal disease’, the most frequent disease of cork oak in the Mediterranean basin. However, little is known regarding this fungus in North Africa. This is the first report on the morphological and genetic diversity of B. mediterranea populations in Tunisia.A total of forty-eight isolates from cork oak trees, corresponding to three different sites and three tree parts, were identified as B. mediterranea based on morphological and molecular diagnosis. Variability among the isolates was evaluated using morphological traits and microsatellite-primed PCR (MSP-PCR). B. mediterranea isolates showed high variability in culture, specifically in colony color. A high level of genetic diversity within populations and within tree parts was detected (H = 0.417, I = 0.605, and H = 0.415, I = 0.601 respectively). Significant genetic differentiation among populations (G_ST = 0.116 and Φ_ST = 0.137; p < 0.001) was determined. However, a low genetic differentiation among tree parts (G_ST = 0.066 and Φ_ST = 0.018; p = 0.07) was observed. Principal coordinate analysis showed that genetic divergence was partially related to the geographical origin. Cluster analysis based on morphological traits showed that the grouping of the isolates occurs independently of the geographic location and the tree part. The effective number of alleles (Ne), the Nei's gene diversity index (H), the Shannon's information index (I), the colony color and the presence of exudates were significantly correlated with the altitude and the rainfall. The number of alleles (Na), the percentage of polymorphic loci (PPL), the texture and the density of the mycelium were significantly correlated with the temperature. These results provide a deeper understanding of population genetics of B. mediterranea and its adaptation to environmental conditions which could help to develop control strategies against charcoal canker disease.     

Genetic diversity of nine faba bean (Vicia faba L.) populations revealed by isozyme markers

Seven isozyme systems (Sod, 6-Pgd, Me, Est, Skdh, Fdh and Gdh) representing nine loci were used to study the genetic diversity of nine faba bean populations. Seven loci revealed polymorphic bands and showed the same quaternary structure as that found in several species. They revealed a high number of phenotypes. Indeed, from 3 to 9 phenotypes per locus were investigated in this study. The percentage of polymorphic loci (P = 59.3 %) was higher than that mentioned in the autogamous species (P = 20.3 %) and less than the optimum (P=96 %) indicated for allogamous plants. Total genetic diversity (H _T) and within population genetic diversity (H _S) were estimated with the isozyme markers. The contribution of among population genetic diversity (D _ST) to total genetic diversity was 22%. Enzyme markers pointed out an average inbreeding level for whole population (F _IT) and within population (F _IS). Within population genetic diversity represents 78% of total diversity. Intra-population genetic diversity (H _S = 0.206) was ranged with the respect of allogamous species and was clearly higher than that of among population genetic diversity (D _ST = 0.057) indicating an out-crossing predominance in the studied populations. The expected heterozygosity was higher than that observed heterozygosity at the allogamous species was confirmed in this study. Although, the mean estimated gene flow was less than 1(Nm=0.814), the dendrogram based on Nei’s genetic distance of the 9 populations using UPGMA method showed some genetic drift between populations.     

Genetic Diversity Within and Among Lepidium draba Populations from Eastern Anatolia Based on RAPD Analysis

Genetic variation and structure of six natural populations of Lepidium draba L. from Eastern Anatolia were assessed using random amplified polymorphic DNA (RAPD) markers. For RAPD analysis, 12 primers generated 218 reproducible bands across the six populations analyzed, of which 73 bands (33.3%) were polymorphic. The mean Nei’s gene diversity value for all six populations was 0.1771. Shannon’s information index varied with population (0.2278–0.3082), averaging 0.2608. Analysis of molecular variance (AMOVA) showed that genetic diversity was greater within populations (58.66%) than among populations (30.68%). In addition, the variation between groups was 10.33%. The genetic differentiation among populations (G _ST) was 0.3210, indicating that most genetic diversity occurs within populations. Gene flow (Nm) was low, at only 0.5288.     

Development of Microsatellite Markers and Analysis of Genetic Diversity and Population Structure of Colletotrichum gloeosporioides from Ethiopia

Twenty three polymorphic microsatellite markers were developed for citrus plant pathogenic fungus, Colletotrichum gloeosporioides, and were used to analyze genetic diversity and population structure of 163 isolates from four different geographical regions of Ethiopia. These loci produced a total of 118 alleles with an average of 5.13 alleles per microsatellite marker. The polymorphic information content values ranged from 0.104 to 0.597 with an average of 0.371. The average observed heterozygosity across all loci varied from 0.046 to 0.058. The gene diversity among the loci ranged from 0.106 to 0.664. Unweighted Neighbor-joining and population structure analysis grouped these 163 isolates into three major groups. The clusters were not according to the geographic origin of the isolates. Analysis of molecular variance showed 85% of the total variation within populations and only 5% among populations. There was low genetic differentiation in the total populations (F_ST = 0.049) as evidenced by high level of gene flow estimate (N_m = 4.8 per generation) among populations. The results show that Ethiopian C. gloeosporioides populations are generally characterized by a low level of genetic diversity. The newly developed microsatellite markers were useful in analyzing the genetic diversity and population structure of the C. gloeosporioides populations. Information obtained from this study could be useful as a base to design strategies for better management of leaf and fruit spot disease of citrus in Ethiopia.     

Conservation genetics of the annual hemiparasitic plant <Emphasis Type="Italic">Melampyrum sylvaticum</Emphasis> (Orobanchaceae) in the UK and Scandinavia

Melampyrum sylvaticum is an endangered annual hemiparasitic plant that is found in only 19 small and isolated populations in the United Kingdom (UK). To evaluate the genetic consequences of this patchy distribution we compared levels of diversity, inbreeding and differentiation from ten populations from the UK with eight relatively large populations from Sweden and Norway where the species is more continuously distributed. We demonstrate that in both the UK and Scandinavia, the species is highly inbreeding (global F _IS = 0.899). Levels of population differentiation were high (F’_ST = 0.892) and significantly higher amongst UK populations (F’_ST = 0.949) than Scandinavian populations (F’_ST = 0.762; P < 0.01). The isolated populations in the UK have, on average, lower genetic diversity (allelic richness, proportion of loci that are polymorphic, gene diversity) than Scandinavian populations, and this diversity difference is associated with the smaller census size and population area of UK populations. From a conservation perspective, the naturally inbreeding nature of the species may buffer the species against immediate effects of inbreeding depression, but the markedly lower levels of genetic diversity in UK populations may represent a genetic constraint to evolutionary change. In addition, the high levels of population differentiation suggest that gene flow among populations will not be effective at replenishing lost variation. We thus recommend supporting in situ conservation management with ex situ populations and human-mediated seed dispersal among selected populations in the UK.     

Low Levels of Genetic Diversity within Populations of Hosta clausa (Liliaceae)

Abstract Genetic diversity of Korean populations in Hosta clausa was investigated using starch gel electrophoresis. Hosta clausa is widespread, grows only along streamsides, and has both sexual and asexual reproduction. Populations of the species are small and isolated. Thirty-two percent of the loci examined were polymorphic, and mean genetic diversity within populations (He_p=0.082) was lower than mean estimates for species with very similar life history characteristics (0.131), particularly for its congener H. yingeri (0.250). The mean number of multilocus genotypes per population was 8.7, and genotypic diversity index (D_G) was 0.84. Significant differences in allele frequencies among populations were found in all seven polymorphic loci (P < 0.001). About one-fifth of the total allozyme variation was among populations (G_ST=0.192). Indirect estimate of the number of migrants per generation (Nm=0.48, calculated from mean G_ST) and nine private alleles found indicate that gene movement among populations was low. The low levels of genetic diversity within populations and the relatively high levels of genetic diversity among populations suggest that strong moist habitat preferences, clonal reproduction, low level of gene flow among populations, genetic drift, and historical events may have played roles in the genetic structuring of the species.     

Genetic diversity of Astragalus nitidiflorus, a critically endangered endemic of SE Spain,and implications for its conservation

Inter-simple sequence repeats (ISSR) markers were used to assess the genetic diversity and population structure in five populations of Astragalus nitidiflorus, a critically endangered species endemic to southeast Spain. Eight primers amplified 78 bands with 40 (51.3%) being polymorphic. Statistical results indicated a low genetic diversity at the population and species level, with percentages of polymorphic bands (PPB) ranging from 28.2 to 37.2% (an average of 31.8%), and means of gene diversity (H_E) of 0.129 and 0.171 respectively. The Shannon’s index (SI) ranged from 0.160 to 0.214 at the population level and was 0.260 at the species level. A low level of genetic differentiation among populations was detected, based on the Shannon’s information index (0.297), the coefficient of genetic differentiation between populations (G_ST = 0.2418) and AMOVA analysis (Φ_ST = 0.255). The estimated gene flow (Nm) was 0.789. The high genetic connectivity found among populations of A. nitidiflorus is an evidence of a recent habitat fragmentation. In addition, a bottleneck event in the past has been revealed, with a subsequent reduction of population size and a loss of genetic variation. Based on these results, the conservation strategy of A. nitidiflorus was proposed.     

Genetic structure in peripheral Western European populations of the endangered species Cochlearia pyrenaica (Brassicaceae)

Cochlearia pyrenaica is one of the most endangered plant species in Europe, listed in many European and regional conservation policy documents (e.g. Spain, France, Belgium, Switzerland). To study its genetic structure, define its conservation units and propose a management strategy for this species, amplified fragment length polymorphism markers were used to analyse the genetic diversity within and between five representative populations of the species distribution in Western Europe (Cantabrian Range, North of Spain; Pyrenees, France; Wallonia, Belgium). Low levels of genetic diversity were revealed by the population percentage of polymorphic bands (PPB?=?36.56%), average within-population diversity (H _S?=?0.0990) and genetic diversity within populations (H _pop?=?0.1541), although high levels were reported at species level (PPB?=?81.16%; total genetic diversity for the species, H _T?=?0.0990; and genetic diversity within whole species, H _sp?=?0.2515). The coefficient of genetic differentiation among populations (G _ST) was 0.3869. The analysis of Shannon diversity index in population and for the total data set partitioned (38.72%) and AMOVA (53%) detected a high level of interpopulation diversity, in broad agreement with the result of genetic differentiation analysis. NeighborNet network and principal coordinate analyses clustered the populations in three major groups congruent with geographical regions. Bayesian clustering also confirmed these three distinct genetic clusters. The level of gene flow (Nm) was estimated as 0.3961 individuals per generation among populations, with the genetic identity (I) and genetic distance (D) among populations ranging from 0.8679 to 0.9651 and from 0.0355 to 0.1417, respectively. Therefore, the low levels of genetic variation and high divergence of regional gene pools indicate that there is a need to protect each disjunct region of Western Europe.     

大连地区岛屿与大陆藜（Chenopodium album L.）种群遗传多样性的ISSR分析

采用ISSR分子标记对分布于大连市周边的4个藜的天然种群100个个体进行了遗传多样性及遗传结构的研究。13个引物共检测了157个位点,多态位点比率为67.52%,Shannon信息指数在物种水平上为0.332 9。根据G_ST值,藜遗传变异有40.03%发生在种群间。遗传距离分析表明,DT种群与MLN种群遗传一致度最高,遗传距离与地理距离之间没有相关性。     

Spatial Genetic Structure of Campanula sabatia, a Threatened Narrow Endemic Species of the Mediterranean Basin

Campanula sabatia is endemic to NW Italy (Liguria) and it was included in the European Red list of endangered species due to the heavy human pressure on its habitat. AFLP markers were used to detect the genetic diversity within and among ten populations (totalling 83 individuals) representing the range of the species. In spite of the limited distribution of this endemic taxon, high levels in percentage of polymorphic bands (PPB), gene diversity (H _S and H _T) and Shannon??s information index (I) were detected both at population (PPB?=?60?%, H _S?=?0.1853, I?=?0.2836) and at species level (PPB?=?100?%, H _T?=?0.2415, I?=?0.3871). The coefficient of genetic differentiation among population (G??_ST) was 0.1935, while the level of gene flow (N?? _m) was estimated to be 2.0832. AMOVA analysis identified a genetic variation within populations of 83?% of the total. Bayesian clustering methods assigned individuals to two geographical groups partly found within the same population, probably due to a high rate of genetic exchange among its populations. Conservation measures are suggested on the basis of the genetic diversity detected to ensure an effective protection for this endemic species.     

Genetic diversity of the endangered Chinese endemic plant Monimopetalum chinense revealed by amplified fragment length polymorphism (AFLP)

Monimopetalum chinense Rehd. is an endangered woody vine endemic to eastern China. Using amplified fragment length polymorphism (AFLP) markers, we examined levels of genetic variation within and among eleven populations located across the species’ distribution. Although modest levels of heterozygosity were detected, other measures of genetic diversity registered relatively high levels of variability, both at the species level (P = 91.0%, H_E = 0.232, I_S = 0.365) and at the population level (P = 53.0%, H_E = 0.155, I_S = 0.239). Populations also exhibited high levels of genetic differentiation (Nei’s genetic diversity analysis, G_ST = 0.330), corresponding to isolation-by-distance and hierarchical population structure. These results indicate that, despite low levels of gene flow, populations of M. chinense still harbor substantial amounts of genetic diversity. Management plans for the species should include measures that ensure genetic diversity remains high within and among extant populations.     

Population genetic structure of Tunisian <Emphasis Type="Italic">Hypericum humifusum</Emphasis> assessed by RAPD markers

The genetic variation within and among seven Tunisian natural Hypericum humifusum L. populations belonging to three bioclimatic zones (sub-humid, upper semi-arid, and lower semi-arid) was assessed using random amplified polymorphic DNA markers. Eight selected primers produced a total of 166 bands, of which 153 were polymorphic. The genetic diversity within a population, based on Shannon’s index and percentage of polymorphic loci, was relatively high. The level of variation among populations did not differ significantly. However, the variation among populations grouped according to their bioclimates was significant.     

Genetic diversity and relationship of endangered plant Magnolia officinalis (Magnoliaceae) assessed with ISSR polymorphisms

Twenty-eight populations of the rare medicinal plant Magnolia officinalis (Magnoliaceae) were sampled across its natural range, and inter-simple sequence repeats (ISSRs) markers were used to assess the genetic variation within and among populations. Twelve primer combinations produced a total of 137 unambiguous bands of which 114 (83.2%) were polymorphic. M. officinalis exhibited a relatively low genetic diversity at population level (the percentage of polymorphic loci PPB = 49.8%, Nei’s genetic diversity H = 0.194, Shannon’s information index I = 0.286). However, the genetic diversity at species level was relatively high (PPB = 83.2%; H = 0.342; I = 0.496). The coefficient of gene differentiation (G_ST, 42.8%) and the results of analysis of molecular variance (AMVOA) indicated that genetic differentiation occurred mainly within populations. The estimated gene flow (Nm) from G_ST was 0.669. It indicated that the fragmentation and isolation of populations might result from specific evolutionary history and anthropogenic activity. Genetic drift played a more important role than gene flow in the current population genetic structure of M. officinalis. Conservation strategies for this rare species are proposed based on the genetic data.     

Genetic diversity within and among populations of the endangered and endemic species Primula merrilliana in China

Primula merrilliana Schltr. is an endangered and narrowly-distributed endemic species of southern Anhui Province in China. In this study, the level of genetic variation and the pattern of genetic structure in six natural populations of P. merrilliana were assessed by using ISSR (inter-simple sequence repeats) markers. Based on ten primers, 137 clear and reproducible DNA fragments were generated, of which 109 were polymorphic. The statistical results indicated that there was a relatively low genetic diversity within populations, and a high genetic differentiation among populations (G_ST = 0.53, Φ_ST = 0.49). The level of population genetic diversity was correlated to habitat type and the gene flow (N_m) was low with only 0.45. The unexpected genetic structure of P. merrilliana may be explained by limited gene flow that was caused by habitat fragmentation and limited seeds and pollen dispersal ability, self-compatible breeding system and biennial life form.     

Genetic diversity analysis of Hepatacodium miconioides at different altitude in Tiantai Mountain, Zhejiang Province, China and its relationship with environmental factors

The genetic diversity within and among populations of Hepatacodium miconioides collected at three different altitudes in Tiantai Mountain, Zhejiang Province and its relationships to environmental factors were analyzed by random amplified polymorphic DNA (RAPD) technique. Amplification using 12 random primers of 60 plants and 122 repetitive loci were produced. The percentage of polymorphic loci of three populations ranged from 18.85% to 23.77% with an average of 21.86%, indicating the relatively low genetic diversity of H. miconioides. The average Shannon index of phenotypic diversity (0.1329) and Nei index (0.0925) within populations were relatively low. A distinct genetic differentiation existed among populations of H. miconioides in spite of the relatively small geographical distribution. The average genetic diversity within populations of H. miconioides accounted for 33.58% of the total genetic diversity while the genetic diversity among populations accounted for 66.42% as estimated by the Shannon index of phenotypic diversity, The genetic differentiation among populations of H. miconioides was 0.6546, as estimated by Nei index. The gene flow estimated from G _ST was only 0.2656 and it indicated that gene flow among populations of H. miconioides was relatively low. The mean value of the genetic identity among populations of H. miconioides was 0.7126 and the average of genetic distance of H. miconioides was 0.3412. The genetic identity between populations at the elevation of 990 m and at the elevation of 780 m was the highest. The genetic identity between population at the elevation 500 m and other two populations was relatively low. The correlation analysis showed that the genetic diversity within populations was significantly related with the soil total nitrogen.     

Population structure and genetic diversity of Stipa grandis P. Smirn,a dominant species in the typical steppe of northern China

Random amplified polymorphic DNA (RAPD) markers were used to characterize genetic heterogeneity within and among five populations of Stipa grandis in the Xilingol Plateau. Estimates of the percentage of polymorphic bands, Shannon's diversity information index and Nei's gene diversity index were comparatively high in the five populations, and the Population GSM was found to have the highest genetic diversity among all populations. An analysis of molecular variance indicated that the majority of variation existed within populations (74.12%), and that there was significant differentiation among populations (Φ_ST = 25.88%, P < 0.001). Genetic distance (Φ_ST) ranged from 0.198 to 0.310 and the differentiation between pair-wise populations was significant when individual pairs of populations were compared. Based on the Φ_ST values, gene flow (Nm) was estimated and was found to vary from 0.556 to 1.013 between pair-wise populations and 0.7412 among populations. The results of UPGMA cluster analysis and nonmetric multi-dimensional scaling analysis indicated that most variation occurred within populations and that genetic differentiation had happened between populations. These findings are important for a better understanding of the adaptive strategy of S. grandis in northern China and will be useful for conservation managers to work out an effective strategy to protect this important species.     

Comparison of the extent of genetic variation of Vallisneria natans and its sympatric congener V. spinulosa in lakes of the middle-lower reaches of the Yangtze River

Vallisneria natans and Vallisneria spinulosa are two morphologically very similar and sympatrically dominant submerged macrophytes in lakes of the middle-lower reaches of the Yangtze River. Genetic variation was compared based on a total of 196 individuals from six V. natans populations and 201 individuals from seven V. spinulosa populations. Using eight ISSR primers, a total of 139 and 129 DNA fragments were generated with 121 being polymorphic in V. natans and 99 in V. spinulosa. The two species maintained higher genetic variation both at the species and population levels in comparison with other aquatic macrophytes. A higher level of genetic diversity among populations was found in V. natans than in V. spinulosa: the percentage of polymorphic loci (PPL) in V. natans was 52-62% vs. 38-47% in V. spinulosa; gene diversity (H) was 0.21 in V. natans vs. 0.17 in V. spinulosa.Both an analysis of molecular variance (AMOVA) and F-estimation (F_ST) showed that most of the total genetic variation resided within populations of both species (AMOVA: 85% and 80%; F_ST: 0.132 and 0.202), indicating low genetic differentiation between populations. Principal coordinates analysis (PCA) indicated evident gene flow between populations of both species. The outcrossing reproductive mode and pervasive gene flow might have played important roles in maintaining high genetic diversity and in shaping low population differentiation of the two Vallisneria species, while the extent of clonal growth might account for the different levels of population divergence between them.     

Low genetic differentiation among widely separated populations of the pearl oyster Pinctada fucata as revealed by AFLP

Genetic variation within and among five populations of the pearl oyster Pinctada fucata, from China (Daya Bay, Sanya Bay and Beibu Bay), Japan (Mie Prefecture) and Australia (Port Stephens) was studied using AFLP. Three primer pairs generated 184 loci among which 91.8-97.3% is polymorphic. An overall genetic diversity of 0.38 among populations and an average of 0.37 within populations (ranging from 0.35 in Japanese population to 0.39 in Beibu Bay population) were observed. Genetic differentiation among the five populations is low but significant as indicated by pairwise G_ST (0.0079-0.0404). AMOVA further shows that differentiation is significant among the five populations but is not significant at a broader geographical scale, among the three groups of Chinese, Japanese and Australian populations or among the two groups of Australian and north Pacific populations. The low level of genetic differentiation indicated that P. fucata populations in the west Pacific are genetically linked. Among the five populations, the Australian one is more differentiated from the others, based on both pairwise AMOVA and G_ST analyses, and is genetically isolated by distance as indicated by Mantel test. However, genetic differences among the three Chinese populations are not correlated with the geographic distances, suggesting that Hainan Island and Leizhou Peninsula may act as barriers blocking gene flow.     

Population genetic structure of wild daffodils (Narcissus pseudonarcissus L.) at different spatial scales

We studied the population genetic and clonal structure of the endangered long-lived perennial plant Narcissus pseudonarcissus using random amplified polymorphic markers. Estimates for mean gene diversity within 15 populations of N. pseudonarcissus of three neighbouring geographical regions were high in comparison to other long-lived perennials (H _eN = 0.33). The genetic diversity of the two smallest populations (<200 plants) was significantly reduced, indicating loss of genetic variability due to drift. The analysis of the population genetic structure revealed a significant genetic differentiation both between regions (Φ_ST = 0.06) and between populations within regions (Φ_ST = 0.20). However, there was incomplete correspondence between geographical regions and the population genetic structure. In order to preserve the overall genetic variation in wild populations of N. pseudonarcissus, management measures should thus aim to protect many populations in each region. The spatial genetic structure within populations of N. pseudonarcissus was in agreement with an isolation by distance model indicating limited gene flow due to pollinator behaviour and restricted seed dispersal. The very restricted spatial extent of clonal growth (<5 cm) and the high level of clonal diversity indicate that clonal growth in N. pseudonarcissus is not an important mode of propagation and that management measures should favour sexual reproduction in order to avoid further reductions in the size and number of populations.