Assessment of genetic diversity and population structure of Bergenia stracheyi (Saxifragaceae) in the Western Himalaya (India)

Genetic diversity and population structure in Bergenia stracheyi, a threatened medicinal herb in the Western Himalaya of India was analysed using directed amplification of minisatellite DNA (DAMD) and inter simple sequence repeats (ISSR) markers. A total of 41 accessions of B. stracheyi representing three populations (Khillenmarg –KLM, Jalori Pass-JLP and Rohtang-RTG) were considered in the present study. The cumulative data analysis for 26 (10 DAMD + 16 ISSR) markers revealed 87.1% polymorphism. The maximum inter-population genetic distance was found between KLM and JLP, whereas the minimum genetic distance was found between RTG and JLP populations. The analysis of molecular variance (AMOVA) revealed maximum percentage of variation among individuals within populations (75%) than among the populations (25%). Clustering pattern of the three sample populations in STRUCTURE and PCoA analyses showed high genetic variation at population level. The present study revealed that distribution patterns, high altitudinal ranges, high habitat specificity, relatively high gene flow, small and isolated population size have shaped the current population structure of B. stracheyi in the Western Himalayan region. DAMD and ISSR markers have provided significant insights into characterization of B. stracheyi populations, and facilitate selection of appropriate accessions for further utilization in conservation and bioprospecting programmes.     

Genetic variability and population structure of Bergenia ciliata (Saxifragaceae) in the Western Himalaya inferred from DAMD and ISSR markers

Genetic variability and population structure of Bergenia ciliata (Haw.) Sternb., commonly known as “Pashanbheda” (Stone-breaker), collected from the Western Himalayan region of India were estimated using two DNA fingerprinting methods viz., directed amplification of minisatellite DNA (DAMD) and inter simple sequence repeats (ISSR). The cumulative data analysis of DAMD and ISSR markers for 74 accessions from eight populations showed 86.1% polymorphism. Analysis of molecular variance (AMOVA) showed highest percentage of variation within individuals of populations (73.6%) and 21.7% among populations. STRUCTURE and PCoA analyses on the hierarchical partitioning of genetic diversity showed strong admixture of individuals among the eight assumed geographical populations of B. ciliata. The data suggests that high genetic flow is one of the major factors responsible for low genetic differentiation. Preservation of genetic diversity of B. ciliata is important, both to promote adaptability of the populations to changing environment as well as to preserve a large gene pool for future prospection. The present study using DAMD and ISSR markers, therefore, provide the means of rapid characterization of accessions within the populations, and thus enable the selection of appropriate accessions for further utilization in conservation and prospection programmes.     

舟山群岛四个养殖獐种群遗传多样性和遗传结构

基于ISSR分子标记技术,对来自舟山群岛4个獐(Hydropotes inermis)养殖种群的遗传多样性和遗传结构进行了分析.26条ISSR引物共扩增出286个可分析位点,多态位点百分比(PPL)为64.34％.獐物种水平上的Nei's遗传多样性指数(H)为0.210,Shannon's多态信息指数(Ⅰ)为0.318,各种群的H介于0.157-0.190之间,I在0.228-0.278之间,与已报道的ISSR标记在其它动物物种中的应用结果相比,其遗传多样性较为丰富.Structure软件分析结果显示,所有个体根据遗传信息的不同可以被分为4个组群,每个养殖场内的个体基本上都在各自独立的组群中,这与地理区域的划分相似.另外发现各养殖场獐种群间已表现出了较大的遗传分化(Gst=0.163).同时,为了解各种群间的遗传关系,计算了各种群间的Nei's遗传距离,结果显示舟山种群(ZS)和秀山种群(XS)之间的遗传距离最近,为0.045,而岱山种群(DS)和朱家尖种群(ZJJ)间的遗传距离最大,为0.066.基于以上结果,建议加强不同岛屿种群间的个体交流,特别是朱家尖种群(ZJJ)与其它种群间的交流.     

Population genetic structure of banana corm weevil Cosmopolites sordidus (Germar) in India

The population genetic structure of Cosmopolites sordidus (Germar), an economically important pest of bananas, was studied using the sequence data of the internal transcribed rDNA (ITS1+ITS2) and the mitochondrial ‘COI-tRNA^Leu-COII’ region from seventy nine individuals collected from six sampling locations in India. The ITS data revealed 70% within population variation and non-significant genetic differentiation estimates suggesting lack of phylogeographic sub-structuring. 49% within population variation and highly significant genetic differentiation values were obtained with the mitochondrial data. The Mantel test revealed lack of correlation between genetic and geographic distance with both the markers. Demographic expansion of the populations was confirmed by the star shaped haplotype networks, demographic tests and mismatch distribution curves using both the markers. Molecular diversity indices show a high haplotype diversity (Hd) but low nucleotide diversity (π) suggesting that the populations are closely related. Considering the low self-dispersal ability of the weevils, these results suggest that the range expansion of this banana pest in India has taken place mainly through transport of infested corms and plant material resulting in the weevils forming localised populations which are not genetically distinct from each other. The high gene diversity (Hd) has enabled the weevils to adapt to varying environmental conditions which could explain the range expansion of this pest in India. The observed discrepancy in the genetic differentiation estimates using these two markers can be attributed to the evolutionary dynamics of the nuclear and mitochondrial genomes.     

Analysis of the genetic structure of Rhodiola rosea (Crassulaceae) using inter-simple sequence repeat (ISSR) polymorphisms

The genetic diversity and differentiation of eleven R. rosea populations from different parts of its wide area of occurrence were studied by ISSR markers. Using eight primers, 252 DNA fragments were generated, and 243 of those DNA fragments were found to be polymorphic, indicating a high genetic variability at the species level (P = 96.4%, h = 0.176, SI = 0.291). Relatively low levels of diversity were determined at the population level (P 30.6-59.1%, h 0.088-0.165, SI 0.137-0.257). AMOVA analysis revealed that the majority of the genetic variation was within populations (65.42%), and the variance among populations was 34.58%. Cluster analysis revealed two groups of R. rosea populations; these groups likely represent distinct evolutionary lines in the species, which are different in genetic structure, evolutionary history and chorological migration routes.     

Inter-simple sequence repeat (ISSR) analysis of genetic variation of Chondrus crispus populations from North Atlantic

ISSR analysis was used to investigate genetic variations of 184 haploid and diploid samples from nine North Atlantic Chondrus crispus Stackhouse populations and one outgroup Yellow Sea Chondrus ocellatus Holmes population. Twenty-two of 50 primers were selected and 163 loci were scored for genetic diversity analysis. Genetic diversity varied among populations, percentage of polymorphic bands (PPB) ranged from 27.0 to 55.8%, H (Nei's genetic diversity) ranged from 0.11 to 0.20 and I (Shannon's information index) ranged from 0.16 to 0.30. Estimators PPB, H and I had similar values in intra-population genetic diversity, regardless of calculation methods. Analysis of molecular variance (AMOVA) apportioned inter-population and intra-population variations for C. crispus, showing more genetic variance (56.5%) occurred in intra-population, and 43.5% variation among nine populations. The Mantel test suggested that genetic differentiation between nine C. crispus populations was closely related with geographic distances (R = 0.78, P = 0.002). Results suggest that, on larger distance scale (ca. >1000 km), ISSR analysis is useful for determining genetic differentiations of C. crispus populations including morphologically inseparable haploid and diploid individuals.     

Low genetic diversity and significant structuring in the endangered Mentha cervina populations and its implications for conservation

Eighteen populations of the endangered aromatic and medicinal plant Mentha cervina (Lamiaceae) were sampled across its natural range, in the western half of the Iberian Peninsula, and inter-simple sequence repeats (ISSRs) markers were used to assess genetic diversity and population structure. M. cervina populations exhibited a relatively low genetic diversity (percentage of polymorphic loci PPB = 14.2–58.3%, Nei's genetic diversity H_e = 0.135–0.205, Shannon's information index I = 0.08 − 0.33). However, the genetic diversity at species level was relatively high (PPB = 98.3%; H_e = 0.325; I = 0.23). The results of the analysis of molecular variance indicated very structured populations, with 50% of the variance within populations, 44% among populations and 6% between regions defined by hydrographic basins, in line with the gene differentiation coefficient (G_ST = 0.532). A Mantel test did not find significant correlation between genetic and geographic distance matrices (r = 0.064), indicating that isolation by distance is not shaping the present genetic structure. The levels and patterns of genetic diversity in M. cervina populations were assumed to result largely from a combination of evolutionary history and its unique biological traits, such as breeding system, low capacity of dispersion, small effective size and habitat fragmentation. The high genetic differentiation among populations indicates the necessity of conserving the maximum possible number of populations. The results also provide information to select sites for ex situ conservation. Optimal harvesting strategies, cultivation and tissue culture should also be developed as soon as possible to guarantee sustainable use of the species under study.     

Non-Mendelian segregation influences the infection biology and genetic structure of the African tree pathogen Ceratocystis albifundus

The African fungal tree pathogen, Ceratocystis albifundus, undergoes uni-directional mating type switching, giving rise to either self-fertile or self-sterile progeny. Self-sterile isolates lack the MAT1-2-1 gene and have reduced fitness such as slower growth and reduced pathogenicity, relative to self-fertile isolates. While it has been hypothesized that there is a 1:1 ratio of self-fertile to self-sterile ascospore progeny in relatives of C. albifundus, some studies have reported a significant bias in this ratio. This could be due to the fact that either fewer self-sterile ascospores are produced or that self-sterile ascospores have low viability. We quantified the percentage of self-sterile and self-fertile ascospores from ascospore masses in C. albifundus using real-time PCR. Primers were designed to distinguish between spores that contained the MAT1-2-1 gene and those where this gene had been deleted. A significant bias towards the self-fertile mating type was observed in all single ascospore masses taken from sexual structures produced in haploid-selfed cultures. The same result was observed from a disease outbreak situation in an intensively managed field of cultivated native trees, and this was coupled with very low population diversity in the pathogen. This was in contrast to the results obtained from ascospore masses taken from the crosses performed under laboratory conditions or ascomata on native trees in a non-disease situation, where either self-fertile or self-sterile ascospores were dominant. The results suggest that reproductive strategies play a significant role in the infection biology and genetic structure of C. albifundus populations.     

Variation and genetic structure of Melipona quadrifasciata Lepeletier (Hymenoptera, Apidae) populations based on ISSR pattern

For a study of diversity and genetic structuring in Melipona quadrifasciata, 61 colonies were collected in eight locations in the state of Minas Gerais, Brazil. By means of PCR analysis, 119 ISSR bands were obtained, 80 (68%) being polymorphic. H_e and H _B were 0.20 and 0.16, respectively. Two large groups were obtained by the UPGMA method, one formed by individuals from Januária, Urucuia, Rio Vermelho and Caeté and the other by individuals from São João Del Rei, Barbacena, Ressaquinha and Cristiano Otoni. The Φst and θ^B values were 0.65 and 0.58, respectively, thereby indicating high population structuring. UPGMA grouping did not reveal genetic structuring of M. quadrifasciata in function of the tergite stripe pattern. The significant correlation between dissimilarity values and geographic distances (r = 0.3998; p < 0.05) implies possible geographic isolation. The genetic differentiation in population grouping was probably the result of an interruption in gene flow, brought about by geographic barriers between mutually close geographical locations. Our results also demonstrate the potential of ISSR markers in the study of Melipona quadrifasciata population structuring, possibly applicable to the studies of other bee species.     

Microsatellite diversity and population genetic structure of Squalidus argentatus (Cyprinidae) on the Island of Hainan and mainland China

Squalidus argentatus is a small-sized cyprinid fish and widely distributed in mainland China. A total of nine polymorphic microsatellite markers were employed to study 216 individuals collected from nine populations. The average number of alleles among nine populations was 8.0 with a range from 6.5 to 9.7. The mean observed (H_O) and expected (H_E) heterozygosity ranged from 0.56 to 0.68 and from 0.74 to 0.86, respectively. The analysis of molecular variance (AMOVA) showed that most genetic variation was maintained within individual component, rather than shaped according to geographical regions. Small but highly significant values of pairwise F_ST values were detected among nine populations. The genetic homoplasy and overfishing are supposed to be major factors responsible for the current genetic structure. This study can be not only helpful for sustainable management of genetic resources, but also valuable to demonstrate genetically how freshwater species is vulnerable to human activity.     

Isozyme analysis of genetic variability and population structure of Lactuca L. germplasm

Isozymes were used to investigate the genetic variability, population structure, and relationships of Lactuca germplasm. The isozyme systems revealed 16 putative loci of a total of 31 alleles. Out of these 16 loci, 11 were polymorphic. The average values of expected heterozygosity (H_e), observed heterozygosity (H_o), mean number of alleles per locus (A) and effective number of alleles per locus (A_e) were 0.2227, 0.266, 1.3005 and 1.369, respectively. The average fixation indices were lower than zero for most of the accessions studied, indicating an excess of heterozygotes. Genetic differentiation among accessions (F_ST) exhibited that 51.3% of the isozyme variation was recorded among accessions, and 48.7% of the genetic variation resided within accessions. The average values of total heterozygosity (H_T) and intra-accessional genetic diversity (H_S) were 0.352 and 0.171, respectively. Moreover, the inter-accessional genetic diversity (D_ST) ranged from 0 to 0.424 with an average of 0.18. Cluster analysis revealed that L. sativa cultivars were distributed throughout different Lactuca species. Thereby, isozymes results confirms the hypothesis of the polyphyletic origin of L. sativa. This high level of genetic variation proved that isozymes are efficient for polymorphism analysis of Lactuca germplasm.     

Rhizobium laguerreae is the main nitrogen-fixing symbiont of cultivated lentil (Lens culinaris) in Morocco

Genetic diversity and population structure of 268 Lens culinaris symbiotic rhizobia collected from 40 cultivated fields in the main lentil production regions in Morocco were estimated. Three chromosomal housekeeping genes (recA, glnII and atpD) and one common symbiotic gene (nodC) were sequenced and analyzed in order to identify the local symbionts of lentil. The molecular phylogeny of the concatenated housekeeping genes clustered more than 95% of the isolates in one main clade together with Rhizobium laguerreae species. R. laguerreae represents the main symbiont of cultivated lentil in Morocco and, for the first time, a large sample of individuals is obtained for this species. There is a significant and high genetic differentiation of bacterial populations among the four regions for their symbiotic gene, and much lower for their housekeeping genes. The reasons why R. laguerreae is so frequently recovered in our study is discussed.     

Genetic diversity and population genetic structure of six dromedary camel (camelus dromedarius) populations in Saudi Arabia

Camels are an integral and essential component of the Saudi Arabian heritage. The genetic diversity and population genetic structure of dromedary camels are poorly documented in Saudi Arabia so this study was carried out to investigate the genetic diversity of both local and exotic camel breeds. The genetic diversity was evaluated within and among camel populations using 21 microsatellite loci. Hair and blood samples were collected from 296 unrelated animals representing 4 different local breeds, namely Majaheem (MG), Maghateer (MJ), Sofr (SO), and Shaul (SH), and two exotic breeds namely Sawahli (SL) and Somali (SU). Nineteen out of 21 microsatellite loci generated multi-locus fingerprints for the studied camel individuals, with an average of 13.3 alleles per locus. Based on the genetic analyses, the camels were divided into two groups: one contained the Saudi indigenous populations (MG, MJ, SH and SO) and the other contained the non-Saudi ones (SU and SL). There was very little gene flow occurring between the two groups. The African origin of SU and SL breeds may explain their close genetic relationship. It is anticipated that the genetic diversity assessment is important to preserve local camel genetic resources and develop future breeding programs to improve camel productivity.     

The influences of habitat, landscape structure and climate on local distribution patterns of the nuthatch (Sitta europaea L.)

The nuthatch, Sitta europaea L., is a small (23 g), cavity-nesting woodland bird which, since the 1970s, has been expanding its range in Britain. However, within this range, the species is notably scarce in an area of eastern England. This gap in the species distribution could arise for several reasons including habitat quality, local landscape structure, regional landscape structure and climate. Field surveys and logistic models of breeding nuthatch presence/absence were used to investigate the relative influences of habitat quality, landscape structure and climate on the prevalence of nuthatches in eastern England. Field surveys of woods in the study area indicated that habitat quality was sufficient to support a nuthatch population. A model of habitat occupancy in relation to local landscape structure, developed in the Netherlands, was applied to the study area. The number of breeding pairs predicted for the study area by the model was lower than expected from habitat area alone, suggesting an additional effect of isolation. However, observed numbers were even lower than those predicted by the model. To evaluate the possible roles of climate and large-scale landscape structure on distribution, presence/absence data of breeding nuthatches at the 10-km grid square scale were related to variables describing climate and the amount and dispersion of broadleaved woodland. While climate in the study area appeared suitable, models including landscape variables suggested that the study area as a whole was unlikely to support nuthatches. Although suitable habitat was available, woodland in the study area appeared to be too isolated from surrounding nuthatch populations for colonisation to be successful. This situation may change if current increases in both national and regional populations continue, thus increasing the number of potential colonists reaching the study area. Received: 3 November 1997 / 22 January 1998     

Population genetic structure of the noxious weed Amaranthus retroflexus in Central Europe

Genetic variation was assessed in a range of populations of Amaranthus retroflexus using isoenzyme analysis. Population genetic diversity was measured by evaluating patterns of variation at six putatively neutral isoenzyme loci (comprising 24 putative alleles) within and among 20 populations of A. retroflexus collected in different habitats: ruderal habitats, cereal fields and hop gardens. Amaranthus retroflexus is a noxious weed of North American origin that infests various crops. Overall, A. retroflexus displayed moderate levels of genetic diversity in comparison with other herbaceous plants. The percentage of polymorphic loci was 50.0%, with mean values of 2.01, 0.142 and 0.227 for the average number of alleles per polymorphic locus (A), observed heterozygosity (H_o) and expected heterozygosity (H_e), respectively. A discrepancy between observed and expected heterozygosity and significant differences from H-W expectation indicate that there is an excess of homozygotes in many populations. As a result, there is strong evidence of inbreeding within populations (F_IS = 0.382) and significant population differentiation (F_ST = 0.270). Even though the species is partly autogamous, inbreeding does not lead to strong inbreeding depression resulting from self-pollination, as inbreeding has no effect on the success of the species in today's countryside. Moreover, allele frequencies detected in agricultural habitats (i.e., cereal fields and hop gardens) differed from those detected in populations collected from ruderal habitats, which is probably caused by systematic application of herbicides in agricultural ecosystems.     

Spatial genetic structure in natural populations of the overexploited tree Eremanthus erythropappus (DC.) macleish (Asteraceae)

Management and genetic conservation plans require knowledge of spatial genetic structure (SGS) to ensure the long-term maintenance of genetic variability in natural populations. This study uses spatial statistical analyses to assess the SGS in nine locations with diverse landscape characteristics where Eremanthus erythropappus occurs at varying densities. This species, commonly known as candeia, is widely distributed throughout Minas Gerais State, Brazil, and its wood has high economic value due to its natural durability and production of oil containing the active ingredient alpha-bisabolol. The species has undergone intense exploitation without adequate management planning. Our analyses were based on polymorphism at nine inter-simple sequence repeat (ISSR) loci. We observed SGS in five of the nine populations. The data indicate different degrees of SGS in the populations, which supports the premise that conservation plans and seed collection strategies should be informed by genetics studies.     

Genetic structure of black abalone (Haliotis cracherodii) populations in the California islands and central California coast: Impacts of larval dispersal and decimation from withering syndrome

The genetic structure of black abalone populations in the southern California Islands and central California coast was investigated by protein electrophoresis. Detailed sampling of San Nicolas Island (SN) permitted investigation of microgeographic genetic differentiation among local geomorphological features. In addition, temporal genetic differentiation was assessed by comparing juveniles and adults at three islands, San Miguel (SM), Santa Cruz (SC) and San Nicolas (SN). Mainland and island locations were genetically differentiated based on allele frequency differences and the presence of private alleles in some island populations. Although microgeographic genetic structure among sites on SN was weak and not statistically significant, heterozygosity varied among sites, with diversity decreasing from west to east. In addition, investigation among cohorts showed that adults were genetically differentiated among island locations, whereas no differences among juveniles were detected. Genetic differentiation between adult and juvenile abalones was detected at SC but not SM or SN. These data are generally consistent with local recruitment augmented by relatively more gene flow among island populations than among island and mainland populations, and possible selection acting on immigrant recruits.     

Population structure and genetic diversity of metamorphic and paedomorphic populations of the tiger salamander,Ambystoma tigrinum

Genetic relationships, population subdivision and genetic diversity were estimated from mtDNA and allozyme data for two subspecies of tiger salamander, one of which is obligately metamorphic and the other polymorphic for paedomorphosis (larval reproduction). Far greater genetic differentiation exists between subspecies than within subspecies, suggesting that the subspecies have evolved in allopatry. Values of F_st calculated from both mtDNA and allozymes were greater than 0.400 for each subspecies. Significant population subdivision was detected even on a microgeographic scale. This extensive population subdivision indicates that populations can respond to extremely localized selection pressures. In the case of paedomorphosis, populations in permanent water should evolve paedomorphosis as long as the appropriate genes exist. For both mtDNA and allozymes, comparisons of population structure within the polymorphic subspecies and between polymorphic and metamorphic subspecies reveal no discernible effects of paedomorphosis. However, a comparison of paedomorphic and metamorphic populations of the polymorphic subspecies showed significantly higher mtDNA diversity in paedomorphic populations. The discrepancy between the allozyme and mtDNA results may be due to the lower effective population size of mtDNA compared to autosomal genes.     

Genetic and allelopathic differences between populations of daisy fleabane Erigeron annuus (L.) Pers. (Asteraceae) from disturbed and stable habitats

The interactions between invasive plants and their habitats may vary at different phases of the invasion process and depend on the phenotypic plasticity or local adaptations of each species. In this study, we investigated whether habitat changes during the invasion process are related to variations in the physiological traits (allelopathic properties) and genetic differentiation of daisy fleabane (Erigeron annuus (L.) Pers.). E. annuus is a winter annual invasive species that originated in North America and is now distributed throughout Europe. Genetic and genotypic diversity analyses were performed for 37 populations of E. annuus based on inter simple sequence repeat (ISSR) polymorphisms. In total, 684 plants were analyzed; 342 were from stable habitats and 342 were from disturbed habitats. The genetic differences among the populations from the different habitats were studied using a Bayesian cluster analysis and an analysis of molecular variance (AMOVA) and by calculating the genetic and genotypic diversity parameters. A germination test using the juglone index was employed to examine the potential allelopathic properties of the plants from the different habitats. Bayesian cluster analysis, AMOVA and allelopathic effects evaluation revealed differences in the allelopathic potential and genetic structure of the E. annuus populations from the disturbed and stable habitats. This differentiation of populations could be associated with founder effects or with different selection pressures among habitats.