Industrial Pollutants Tend to Increase Genetic Diversity: Evidence from Field-Grown European Scots Pine Populations

The effect of heavy metal and gaseous pollution on genetic make up due to selection and mortality was studied in eight European Scots pine (Pinus sylvestris L.) populations. Genetic structure of these populations was evaluated after 13 years of growth at two sites, one located in the vicinity of a copper smelter in Glogow (southern Poland) and another in a control area (Kornik, central Poland). Based on data from 10 enzymatic loci, studied by starch gel electrophoresis, the following genetic parameters were characterized: mean number of alleles and genotypes per locus, heterozygosity and genotype polymorphism index, genetic diversity among sites and genetic similarity according to Nei and Roychoudhury. Most of the parameters differed both between sites as well as between pairs of populations. Mean multilocus observed heterozygosity and genotype polymorphism indices were 8% and 6% lower respectively at the control site than in the polluted one. Populations from the site polluted by heavy metals demonstrate higher genetic diversity then those from the control. Genetic similarities showed differentiation of particular populations from both locations in response to industrial pollution. These results provide evidence that the general pattern of adaptation strategy of populations to pollution stress is connected with increasing genetic variation. The best isoenzymatic markers for monitoring changes in the genetic structure of Scots pine populations under the influence of industrial pollution are fluorescent esterase (FEST), glutamic-oxaloacetatic transaminase (GOT-A and GOT-B), alcohol dehydrogenase (ADH), malate dehydrogenase (MDH-A) and shikimate dehydrogenase (ShDH-A) loci.     

Microsatellite DNA Analysis of Wild Hops, Humulus lupulus L.

To study the relationships and genetic diversity among wild hops, Humulus lupulus, we analyzed 133 samples of wild hops collected from Europe, Asia and North America using polymorphism on 11 microsatellite loci. Although only three primers showed bands in Japanese hops, all other samples showed polymorphic bands at most loci. There were no duplicate genotypes among samples of European, Chinese and North American hops, and each individual hop could be distinguished completely. The phylogenetic tree constructed from DA distance with the UPGMA method showed a large cluster comprised of European hops, although Russian hops from the Caucasus and Altai regions were separate from the European cluster. Chinese and North American samples gave distinct clusters suggesting genetic differentiation. This study has indicated that hop microsatellite DNA is differentiated, and is dependent upon the origin in regions of Europe, Asia and North America.     

Population structure and genetic differentiation among the USDA common bean (Phaseolus vulgaris L.) core collection

Genetic diversity data were collected from a large population of common bean (Phaseolus vulgaris L.) landraces representing the United States Department of Agriculture core collection. The data were based on microsatellite data from all linkage groups. A procedure was developed to determine if we collected sufficient marker data to adequately estimated pairwise diversity. The diversity data were used to define populations using distance and model-based approaches. Genetic differentiation and genetic isolation by distance data were collected. Diversity was also compared for markers linked and unlinked to domestication loci. Using a model-based approach, the landraces were divided into the traditional Middle American and Andean gene pools. Diversity was greater for the Middle American gene pool. Six Middle American and three Andean subpopulations were defined, and the Middle American subpopulations exhibited strong geographic identity. Unlike other studies, seed size varied considerably with subpopulations, and a number of the subpopulations contained landraces from multiple common bean races. All of the subpopulations were highly differentiated, with the Middle American subpopulations showing the greatest differentiation. Genetic isolation by distance was observed among the Middle American and Andean subpopulations but not among subpopulations within a gene pool. Within each gene pool, diversity was lower for markers linked to domestication loci.     

A-genome cotton as a source of genetic variability for Upland cotton (<Emphasis Type="Italic">Gossypium hirsutum</Emphasis>)

Since Upland cotton (Gossypium hirsutum) is known to have relatively low levels of genetic diversity, a better understanding of variation and relationships among possible sources of novel genes would be valuable. Therefore, analysis of genetic variation of the genus Gossypium, especially the diploids, which are the putative donors of the A and D genomes for the commercially important allotetraploid cottons (AADD), G. hirsutum and G. barbadense, could provide important information about the feasibility of using these genetic resources for cotton improvement. The primary objective of this study was to analyze the genetic diversity in A-genome diploid cotton species, G. herbaceum (A1) and G.␣arboreum (A2) by using microsatellite markers. Forty-one A-genome germplasm accessions were evaluated with 32 microsatellite loci. Genetic similarities between A1 and A2 ranged from 0.62 to 0.86 with a mean of 0.70. Within each A-genome species similarities ranged from 0.80 to 0.97 with a mean of 0.89 for A1 and from 0.82 to 0.98 with a mean of 0.89 for A2. A UPGMA tree and principal coordinate analysis based on genetic similarity matrices showed distinct clusters consistent with the genomic groups.     

Genetic and morphological divergence in island and mainland birds: Informing conservation priorities

Evolutionary processes can complicate conservation efforts for species with uncertain taxonomic classifications and discrete geographic populations. Discordant morphological and genetic patterns across the geographic range of species further calls for the identification of evolutionary significant units for conservation. Using island and mainland populations of a small Australian passerine (the superb fairy-wren, Malurus cyaneus), we examine the relationship between morphological and genetic divergence among two subspecies, M. c. ashbyi (Kangaroo Island, South Australia) and M. c. leggei (South Australia, mainland), using eight microsatellite markers. Island birds showed clear evidence for morphological divergence, with a larger body size and thinner bill compared to mainland birds. Two genetic clusters were found using Bayesian methods, comprising mainland and island regions. Estimates of recent migration rates between all sites were very low (<2%). Morphological and genetic differentiation between island and mainland sites correlated significantly, but not when controlling for isolation by distance. Genetic and morphological substructure was evident with three distinct genetic clusters in each region. Males, the highly sedentary sex, appeared to drive correlations between morphological and genetic differentiation. Our study provides evidence that the subspecies classification of M. cyaneus in island and mainland regions encapsulates two independently diverging populations that can be recognised in conservation planning.     

Genetic Survey of Chinese and Swedish Oilseed Rape (Brassica napus L.) by Simple Sequence Repeats (SSRs)

Eleven Chinese and twelve Swedish rapeseed (Brassica napus) genotypes were analysed by PCR with 41 microsatellite primers, generating a total of 50 loci. For these 50 loci, the number of alleles ranged from 1 to 14, and the average number of alleles per loci was 2.7. As an example of simple sequence repeat (SSR) scoring in Metaphor agarose gel, a single marker could distinguish 14 different DNA profiles. Based on cluster analysis (UPGMA), the dendrogram clearly distinguished three clusters, a cluster with exclusively Swedish genotypes, and two clusters with Chinese genotypes. The genetic diversity within the Chinese genotypes was broad compared to the genetic diversity within the Swedish material. The genetic similarity within the Swedish breeding lines ranged from 69.5 to 95.6%, while that of Chinese genotypes ranged from 57.1 to 81.6%. The results in this report will permit to establish a set of microsatellite primers that can be used for selecting appropriate parents for Brassica napus hybrids and for monitoring hybridity level.     

A forage grass and small grain legume plant collecting expedition in South East Poland, 1990

Summary The Plant Genetic Resources Unit (PGRU) of the Institute of Grassland and Environmental Research, Welsh Plant Breeding Station (IGER, WPBS), UK, and the Plant Genetic Resources Section of the Plant Breeding and Acclimatization Institute (PBAI), Poland, carried out a joint collecting expedition in Poland between 25 August and 7 September 1990. The expedition was unique in that it was the first time that vegetative sampling had been applied to the perennial forage grass and legume populations of south east Poland. The expedition focused on seminatural vegetation in agriculturally managed situations and detailed collection site data on management systems was obtained from landowners.Samples were collected from 62 sites. Vegetative collections of Lolium spp. (37 populations) and Trifolium spp. (56 populations), and seed collections of Festuca spp. (32 populations) were made by the IGER team (Table 2). The PBAI team made 59 separate seed collections, mainly of Leguminosae.The expedition covered four geographical subregions of south east Poland. (See Fig. 1). These were the Nizina Mazowiecka south of Warszawa, the Wyzyna Malopolska with the town of Kielce at its centre and the Beskidy Zachodnie and Beskidy Wschodnie regions of the Carpathian mountains.A diverse range of habitats was sampled covering a broad range of altitude agricultural management systems and ecological conditions. Polish agriculture is faced with the problems of a rapid orientation to a market economy and it is likely that the diverse range of habitats encoutered will be reduced as agricultural practices change. This will lead to genetic erosion of the unique forage grass and legume populations to be found in Poland.Abbreviations ECP/GR European Co-operative Programme on Crop Genetic Resources - IGER Institute of Grassland and Environmental Research - PBAI Plant Breeding and Acclimatization Institute - PGRU Plant Genetic Resources Unit - WPBS Welsh Plant Breeding Station     

Evaluation of genetic diversity and relationships within an on-farm collection of Perilla frutescens (L.) Britt. using microsatellite markers

The present study demonstrates utilization of 11 microsatellite markers to explore genetic diversity held in Perilla frutescens (L.) Britt. landrace accessions growing on farms in different parts of Korea and Japan and to assess their genetic relationships. All microsatellite loci were polymorphic and produced a total of 96 alleles ranging from 4 to 20, with an average of 8.7 alleles per locus. Of the 96 alleles found, a total of 15 unique landrace-specific alleles were observed at 9 different loci. The locus GBPFM203 provided the highest number of alleles (20), of which five were unique and each specific to a particular landrace accession. The occurrence of unique, accession-specific alleles presented molecular evidence for the generation of new alleles within on-farm collection of Perilla. The mean values of observed (H _O) and expected heterozygosity (H _E) were 0.39 and 0.68, respectively, indicating a considerable amount of polymorphism within this collection. A genetic distance-based phylogeny grouped the two Perilla varieties, var. frutescens and var. crispa (Thunb.) Decne into two distinct groups. Accessions belonging to var. frutescens could also be divided into two subgroups at a close genetic distance (GD = 0.432). The overall clustering pattern did not strictly follow the grouping of accessions according to their geographic origins. These observations are indicative of extensive germplasm exchange among farms from different geographical regions. The genetic similarity observed among the Perilla landraces may be useful for future Perilla crop variety identification, conservation, and improvement programs.     

The genetic structure of coastal giant salamanders (Dicamptodon tenebrosus) in a managed forest

The salamander, Dicamptodon tenebrosus, is threatened by habitat loss and fragmentation associated with forest harvest activities. We used three microsatellite loci and 38 amplified fragment length polymorphisms (AFLPs) to quantify population structure and indirectly evaluate the impacts of forest harvesting on this species. We sampled two old growth sites, three second growth sites and three recently clearcut sites in British Columbia, Canada. Microsatellite allelic richness and the percentage of polymorphic AFLPs were positively correlated with the age of forest stands. Similarly, heterozygosity estimated from both marker types was positively correlated with stand age. Population subdivision (F_st) estimated among forested sites using microsatellite and AFLP markers was 0.033 and 0.095, respectively. Lower genetic variation and heterozygosity in recent clearcuts suggest that clearcut logging may be associated with local population declines. Our genetic findings are consistent with previous studies that report lower salamander densities in recently clearcut sites.     

Genetic diversity of westerwold ryegrass landraces collected in Northwest Spain

Sixteen landraces of westerwold ryegrass (Lolium multiflorum Lam. var. westerwoldicum Wittm.) collected in Northwest Spain were evaluated at three locations: Mabegondo (La Corun~a), Puebla de Brollo´n (Lugo) and Salcedo (Pontevedra). Populations showed a high variability for morphologic, agronomic and isoenzimatic traits. Principal component analysis was carried out to identify clusters of morphologic and agronomic homogeneous behaviour. A hierarchical clustering method on the first five components was used to separate the different groups. A partition into four clusters was chosen (71% of variance explained). Each cluster was described by the means of the different traits and compared with the other clusters. Landraces were screened for allozyme diversity at nine loci. Population genetic statistics were higher than those previously reported for other outbreeding species (mean number of alleles = 3.59 and mean expected heterozygosity = 0.510). Genetic diversity was mainly explained by the within population component. The between population differentiation only accounted for 8% of the whole diversity. The use of these genetic resources is discussed.     

三种笛鲷的野生群体和养殖群体遗传多样性的微卫星分析

摘要：利用微卫星标记技术,采用10对微卫星引物对南海海域红鳍笛鲷、星点笛鲷、紫红笛鲷3种笛鲷鱼的野生种群（HYE、XYE、ZYE）和养殖种群（HYA、XYA、ZYA）进行了遗传多样性分析。10对微卫星引物在6个群体中共检测到78个等位基因,每个位点的等位基因数目在1~8个之间。6个群体的观测杂合度(Ho)为0.2500~1.0000,平均观测杂合度为：ZYE(0.9550)> ZYA(0.8900),HYE(0.8950)> HYA(0.8400),XYE(0.8450)>XYA(0.8100) ;平均多态信息含量(PIC) 为0.3648~0.7964,各野生群体均大于养殖群体;三种笛鲷鱼的野生群体和养殖群体遗传距离HYE与HYA,XYE与XYA,ZYE与ZYA分别为0.1029,0.0371,0.0135,基因分化系数分别为0.0371,0.0211,0.0352。群体遗传结构分析结果表明：红鳍笛鲷、星点笛鲷和紫红笛鲷的遗传多样性较丰富,养殖群体的遗传多样性较野生群体均有一定程度的降低,野生群体和养殖群体分化较弱。     

Microsatellite variability within and among local landrace populations of tea, Camellia sinensis (L.) O. Kuntze, in Kyoto, Japan

Genetic variability within and among eight landrace populations of tea (Camellia sinensis (L.) O. Kuntze) located in southern Kyoto, Japan, was surveyed with six microsatellite markers. The average number of alleles per locus was 3.83 to 4.67 for landrace populations, whereas the corresponding value among modern cultivars and breeding lines was 6.63. Expected heterozygosity values averaged over loci within landrace populations ranged from 0.498 to 0.723. A similar level of variation, 0.682, was observed for cultivars and breeding lines. High fixation index values (0.177–0.417) for each population are consistent with biparental inbreeding within the population. Genetic differentiation among local populations was extremely low with F _ST = 0.062, although AMOVA revealed significant differentiation among landrace populations. We propose that these populations share a common ancestral gene pool and that some degree of artificial selection within each population has been performed by local farmers. Neighbor-joining analysis revealed that genetic relationships among populations reflect geographical location of populations. This might result from more frequent genetic exchange by nearby farmers.     

Influence of forest fragmentation on an endangered large-bodied lemur in northwestern Madagascar

Madagascar’s diverse and mostly endemic fauna and flora suffer from recent landscape changes that are primarily caused by high levels of human activities. The loss and fragmentation of forest habitats are well known consequences of human activities. In this study, we investigate the effects of forest fragmentation on presence, abundance and genetic diversity in a larger-bodied lemur species, Lepilemur edwardsi, in northwestern Madagascar. In addition, we characterized the genetic differentiation among populations and demographic changes. We found L. edwardsi at only 13 (76.5%) of 17 visited sites, 11 of which were situated in the Ankarafantsika National Park (ANP). We captured between two and 17 individuals per site. We sequenced the mtDNA d-loop of all samples and genotyped 14 microsatellite loci in two exemplary populations for demographic analyses. A negative influence on forest fragmentation could be detected, since the fragments had a lower genetic diversity than sites in the ANP. Genetic differentiation between populations ranged from low to high but was almost always significant. A typical pattern of isolation-by-distance could not be detected and the data could rather be interpreted as results of random genetic drift. The data furthermore revealed signals of a demographic collapse of about two orders of magnitude in the two exemplary sites. This decline probably started during the last few hundred years of intensified human disturbances and population growth. Given the results of this study, urgent conservation actions are needed and should concentrate on an effective protection of the few remaining populations in order to ensure the long-term survival of L. edwardsi.     

The American mink in Europe: Status, impacts, and control

We examine the distribution of American mink Mustela vison in 28 European countries, and we review the impacts of this invasive species and the efforts made so far in controlling it. Our study reveals that, although mink farms are mostly concentrated in northern countries, mink are widely distributed across Europe, and that in some countries mink are apparently declining, although in most cases the causes are unknown. Countries for which the impact of mink on native species has been studied show that mink can have a significant effect on ground-nesting birds, rodents, amphibians and mustelids. The overall economic impact of feral mink seems to be relatively small but can be significant in specific regions. Recently, a number of eradication and local control projects have been carried out throughout Europe, indicating that these actions could be effective to protect native species. A consistent body of knowledge is starting to accumulate on issues concerning the American mink as an invasive alien species, but, as this review highlights, for most European countries there is currently a limited knowledge about its distribution or impacts. Taking all these observations together, we present some of the actions that have recently emerged as effective for dealing with this species and discuss which considerations may further encourage competent European authorities to take action to prevent and mitigate impacts of American mink.     

From genetic diversity and structure to conservation: Genetic signature of recent population declines in three mouse lemur species (Microcebus spp.)

The exceptional biodiversity of Madagascar is threatened by anthropogenic landscape changes that took place during the 2000 years of human colonization. This study focuses on the influence of geographic distance and forest fragmentation on genetic diversity and population differentiation of three rare, nocturnal, arboreal lemur species in northwestern Madagascar. Historic declines in population sizes as a consequence of forest fragmentation are quantified and dated. Eighteen sites were visited, and a total of 205 Microcebus ravelobensis, 45 M. bongolavensis and 78 M. danfossi were genotyped with eight microsatellite loci. Genetic differentiation among the sites, as measured by F_ST, ranged from 0.01 to 0.19. These values were significant in almost all cases and indicated genetic structure in the samples. Isolation-by-distance was detected in one species and a STRUCTURE analysis indicated that fragmentation further promoted genetic differentiation. Bayesian methods revealed that populations from all three species underwent a major demographic collapse of around two orders of magnitude. This decrease probably began after the arrival of humans, most likely within the last 500 years. This result suggests that anthropogenic changes may have been limited during the first 1500 years of human colonization in all three ranges. Two of the study species (M. danfossi, M. bongolavensis) lack effectively protected areas in their ranges. Consequently, quick conservation actions are now needed in order to secure the remaining genetic diversity of these species.     

江西青岚湖五种淡水蚌遗传多样性的微卫星DNA分析

利用北美Epioblasma capsaeformis（蚌科）和中欧Margaritifera margaritifera L.（珍珠蚌科）两种淡水双壳类的20对微卫星引物对江西青岚湖五种淡水蚌群体进行了PCR扩增，筛选出8对多态性较高的引物，并用这8个微卫星座位分别对三角帆蚌、褶纹冠蚌、洞穴丽蚌、射线裂脊蚌和中国尖嵴蚌五种蚌类群体进行了遗传多样性分析。结果表明：不同蚌类群体的平均等位基因数为2.8750～4.000，平均观测杂合度（HO）为0.4417～0.6333，平均期望杂合度（HE）为0.4430～0.5706，平均多态信息含量（PIC）为0.368～0.498，五个群体表现出较高的遗传多样性。有多个座位在不同蚌类群体中偏离哈代－温伯格平衡。五种蚌类群体间的遗传距离在0.6228与1.4724之间，三角帆蚌和褶纹冠蚌之间的遗传距离最大，射线裂脊蚌和洞穴丽蚌之间的遗传距离最小。     

Genetic diversity and population structure of Guinea yams and their wild relatives in South and South West Ethiopia as revealed by microsatellite markers

Genetic diversity and population structure of Guinea yams and their wild relatives collected from south and south west Ethiopia were assessed using microsatellite markers. The total number of alleles amplified for the 7 loci studied was found to be 60, with an average of 8.6 alleles per locus. The average expected heterozygosity for the entire population was found to be 64 % indicating that Guinea yams and their wild relatives in the study area display a high level of genetic diversity. Using allelic richness as a measure of genetic diversity the wild forms exhibited greater allelic diversity than the cultigens. Contrary to what is expected in vegetatively propagated crops, none of the seven loci studied showed a significant excess of heterozygotes. In all the comparisons made, a low mean F_ST (but significant) has been observed, indicating that the majority of microsatellite diversity in the populations under study was found within rather than between populations.     

Genetic consequences of animal translocations: A case study using the field cricket, Gryllus campestris L.

Animal relocations have become a common tool in nature conservation, but the genetic consequences of such projects have rarely been studied in insects. As both natural and artificial formation of new populations may lead to genetic drift (founder effect), decreased genetic diversity and increased rates of inbreeding, genetic analyses can provide valuable information to evaluate the success of a relocation project. The field cricket (Gryllus campestris) has been subjected to reintroduction and translocation projects in England and northern Germany. Here, we present a microsatellite study on the population genetics of one recently established population of this species in comparison with several older populations and some recently colonized sites. Our results show that the translocation did not result in a significant loss of genetic diversity, when compared to source and other natural populations suggesting that translocation of a high number of nymphs from different subpopulations may be a suitable method to decrease the loss of genetic diversity and reduce the risk of inbreeding. Furthermore, the translocation had no negative effect on the source population, which reached a new maximum population size in 2006. An assignment test showed that individuals from the translocated population (F4 generation) were still assigned to the source populations, whereas two young subpopulations that originated by natural colonization from the central population about ten years ago already formed separate genetic clusters. As the strong fragmentation of G. campestris populations in northern Germany hampers natural colonization of newly created potential habitats, translocation projects seem to be an appropriate method to preserve this species.     

Analysis of genetic diversity in the endangered tropical tree species <Emphasis Type="Italic">Hagenia abyssinica</Emphasis> using ISSR markers

Genetic diversity within and among 12 populations of the dioecious tropical tree species Hagenia abyssinica (Bruce) J.F. Gmel. in Ethiopia was examined with eight inter simple sequence repeat (ISSR) primers. A total of 104 clearly scorable bands were generated, among which 84 (81%) were polymorphic. Jaccard similarity coefficient was calculated for pairwise comparisons among all 120 individuals and ranged from 0.30 to 0.88 while average within-population similarity ranged from 0.53 to 0.66. Within-population variability was estimated as percentage polymorphic loci (ranging from 52% to 87%), Shannon’s information index (0.30–0.50) and Nei’s genetic diversity (0.21–0.35). The highest variability values were obtained for one recently planted population and for one wild population growing in an undisturbed primary forest area. Significant overall differentiation among populations was detected by both Shannon’s information index (0.26) and G _ST (0.25). Relatedness among samples was estimated with a principal coordinate analysis, and relatedness among populations was estimated with a cluster analysis (UPGMA). A Mantel test indicated a significant association between genetic and geographic distances, and an autocorrelation analysis showed significant evidence of gene flow over distances up to 30 km. This study is the first of its kind for H. abyssinica, which has decreased recently in Ethiopia and now must be regarded as an endangered species. Both within-population and between-population diversity estimates are typical of outcrossing, longlived and late successional species, suggesting that recent anthropogenic disturbances have not yet had much impact on population genetic parameters. DNA marker data can, however, be used to identify the most suitable sites for in situ conservation and for collection of material for establishment of genebanks and plant improvement programs.     

Genetic and phenotypic diversity and random association of DNA markers of isolates of the fungal plant pathogen Sclerotinia sclerotiorum from soil on a fine geographic scale

Sclerotia of the soil-borne plant pathogen Sclerotinia sclerotiorum were collected from 1 m² area of the top 1.27 cm layer of soil in an alfalfa field in southeastern Washington state of the US. Out of 272 sclerotia collected, 40 were randomly selected and analyzed for genetic diversity in terms of microsatellite loci, mycelial compatibility groups (MCGs) and phenotypic diversity using five phenotypic traits (fungicide sensitivity, oxalic acid production, growth rate, colony color and virulence). Sixteen microsatellite haplotypes and 15 MCGs were found among the 40 isolates. The isolates showed three colony colors (beige, dark and white) on Difco PDA and exhibited significant differences in growth rate, oxalic acid production, and sensitivity to three fungicides, benomyl, fluazinam and iprodione. However, these isolates did not show differences in their ability to colonize detached pea leaves. No apparent relationship among the neutral genetic markers and the phenotypic traits was detected. Two of the haplotypes accounted 40% of the isolates, suggesting isolates of these haplotypes might be better adapted to the environmental conditions in this alfalfa field. Several lines of evidence indicated high levels of genetic diversity and potential outcrossing within the population of S. sclerotiorum: 1) high likelihood of five genetic populations based on Bayesian probability and the presence of admixed isolates; 2) random association of alleles in every pair-wise linkage disequilibrium test among eight independent microsatellite loci; 3) discordances between microsatellite haplotypes and MCGs and 4) lack of correspondence among the genetic markers and phenotypic traits. Multilocus Index of Association test suggested that outcrossing occurs only within interbreeding subpopulations of S. sclerotiorum.