Genetic Variation and Differentiation of Larix decidua Populations in Swiss Alps (in English)

Genetic diversity within and among six subpopulations of Larix decidua Mill. from two altitudinal transects of Swiss Alps was investigated using 6 enzyme systems coding for 8 loci. Globally, the mean proportion of polymorphic loci was 22.9%, the average number of alleles per locus was 1.3, and the mean expected heterozygosity was 0.095. Only 5.8% of the genetic variation resided among populations. The mean genetic distance was 0.006. Several significant differences of gene frequencies were found between different age classes. Positive values of the species mean fixation index observed in this study suggested a considerable deficit of heterozygotes in the populations of L. decidua of Swiss Alps. At one of the sites (Arpette), the highest subpopulation in elevation gave the lowest level of genetic diversity (as evidenced by the lowest proportion of polymorphic loci and the lowest mean expected heterozygosity) and the largest value of genetic distance when compared to other subpopulations. The genetic differences between the highest subpopulation and the other ones suggest that the founder effect may be an important factor influencing genetic differentiation of L. decidua populations at Arpette transect.     

瑞士阿尔卑斯山欧洲落叶松居群的遗传变异和分化

应用等位酶分析技术,沿两个海拔梯度在瑞士阿尔卑斯山研究了欧洲落叶松（Larix decidua Mill.)居群内和居群间的遗传多态性,结果表明,多态性位点的比例为22.9%,平均每个位点的等位基因数为1.3,平均期望杂合度为0.095,遗传变异的5.8%存在于居群之间,平均遗传距离为0.006。几个有统计意义的基因频率差别在不同树龄类被发现,正在繁育系数值表明在瑞士阿尔卑斯山欧洲落叶松居群有相当的杂合体缺乏,在阿尔拜特（Ar-pette),海拔最高的亚居群与其他亚居群相比较显示最低的遗传多态性（如显示最低的我态性位点比例和最低的平均期望杂合度）和最大的遗传距离值,在最高亚居群和其他亚居群间的遗传差别暗示奠基效应可能是影响这个定样场所欧洲落叶松居群遗传分化的主要因素。     

Genetic variation and evolution of Polaskia chichipe (Cactaceae) under domestication in the Tehuacán Valley, central Mexico

Polaskia chichipe is a columnar cactus under artificial selection in central Mexico because of its edible fruits. Our study explored the effect of human manipulation on levels and distribution of genetic variation in wild, silviculturally managed and cultivated sympatric populations. Total genetic variation, estimated in nine populations with five microsatellite loci, was H(T) = 0.658 +/- 0.026 SE, which was mainly distributed within populations (H(S) = 0.646) with low differentiation among them (F(ST) = 0.015). Fixation index (F(IS)) in all populations was positive, indicating a deficit of heterozygous individuals with respect to Hardy-Weinberg expectations. When populations were pooled by management type, the highest expected heterozygosity (H(E) = 0.631 +/- 0.031 SE) and the lowest fixation index (F(IS) = 0.07) were observed in wild populations, followed by cultivated populations (H(E) = 0.56 +/- 0.03 SE, F(IS) = 0.14), whereas the lowest variation was found in silviculturally managed populations (H(E) = 0.51 +/- 0.05 SE, F(IS) = 0.17). Low differentiation among populations under different management types (F(ST) 0.005, P < 0.04) was observed. A pattern of migration among neighbouring populations, suggested from isolation by distance (r2 = 0.314, P < 0.01), may have contributed to homogenizing populations and counteracting the effects of artificial selection. P. chichipe, used and managed for at least 700 generations, shows morphological differentiation, changes in breeding system and seed germination patterns associated with human management, with only slight genetic differences detected by neutral markers.     

Population genetic structure of the cyclic snowshoe hare (Lepus americanus) in southwestern Yukon,Canada

Spatial population structure has important ecological and evolutionary consequences. Little is known about the population structure of snowshoe hares (Lepus americanus), despite their ecological importance in North American boreal forests. We used seven variable microsatellite DNA loci to determine the spatial genetic structure of snowshoe hares near Kluane Lake, Yukon during a cyclic population peak. We sampled 317 hares at 12 sites separated by distances ranging from 3 to 140 km, and used 46 additional samples from Alaska and Montana. The level of genetic variation was high (13.4 alleles/locus, 0.67 expected heterozygosity) and the distribution of alleles and genotypes was not homogeneous across the sites. The degree of differentiation was low among Yukon sites (FST = 0.015) and between Yukon and Alaska (FST = 0.012), but the Montana site was highly differentiated (FST = 0.20). A weak pattern of isolation by distance was found over the Yukon study area, with an indication that local genetic drift may be important in shaping the regional genetic structure. Landscape barriers expected to influence gene flow did not consistently affect genetic structure, although there was evidence for a partial barrier effect of Kluane Lake. The high level of inferred gene flow confirms that snowshoe hare dispersal is widespread, successful and equal between the sexes. A stepping-stone model of gene flow, potentially influenced by the synchronous density cycle, appears to best explain the observed genetic structure. Our results suggest that despite their dramatic fluctuations in density, snowshoe hares in the northern boreal forest have a large evolutionary effective population size and are not strongly subdivided by either physical or social barriers to gene flow.     

Microsatellite analysis of genetic diversity and population genetic structure of a wild rice (<Emphasis Type="Italic">Oryza rufipogon</Emphasis> Griff.) in China

Genetic diversity and population genetic structure of natural Oryza rufipogon populations in China were studied based on ten microsatellite loci. For a total of 237 individuals of 12 populations collected from four regions, a moderate to high level of genetic diversity was observed at population levels with the number of alleles per locus ( A) ranging from 2 to 18 (average 10.6), and polymorphic loci ( P) from 40.0% to 100% (average 83.3%). The observed heterozygosity ( H(O)) varied from 0.163 to 0.550 with the mean of 0.332, and the expected heterozygosity ( H(E)) from 0.164 to 0.648 with the mean of 0.413. The level of genetic diversity for Guangxi was the highest. These results are in good agreement with previous allozyme and RAPD studies. However, it was unexpected that high genetic differentiation among populations was found ( R(ST) = 0.5199, theta = 0.491), suggesting that about one-half of the genetic variation existed between the populations. Differentiation (pairwise theta) was positively correlated with geographical distance ( r = 0.464), as expected under the isolation by distance model. The habitat destruction and degradation throughout the geographic range of O. rufipogon may be the main factor attributed to high genetic differentiation among populations of O. rufipogon in China.     

Genetic Diversity Among Turkish Native Chickens, Denizli and Gerze, Estimated by Microsatellite Markers

The genetic diversity of the Turkish native chicken breeds Denizli and Gerze was evaluated with 10 microsatellite markers. We genotyped a total of 125 individuals from five subpopulations. Among loci, the mean number of alleles was 7.5, expected heterozygosity (H (e)) was 0.665, PIC value was 0.610, and Wright's fixation index was 0.301. H (e) was higher in the Denizli breed (0.656) than in the Gerze breed (0.475). The PIC values were 0.599 and 0.426 for Denizli and Gerze, respectively. A phylogenetic tree was constructed using genetic distance and the neighbor-joining method. Its topology reflects the general pattern of genetic differentiation among the Denizli and Gerze breeds. The present study suggests that Denizli and Gerze subpopulations have a rich genetic diversity. The information about Denizli and Gerze breeds estimated by microsatellite analysis may also be useful as an initial guide in defining objectives for designing future investigations of genetic variation and developing conservation strategies.     

Genetic differentiation within and between isolated Algerian subpopulations of Barbary macaques (Macaca sylvanus): evidence from microsatellites

This study of wild-living Algerian Barbary macaques ( Macaca sylvanus ) was designed to examine genetic variability in subpopulations isolated in residual forest patches, in an attempt to obtain data on the effects of habitat fragmentation. The wild population of this species (estimated at a maximum of 15 000) is vulnerable and this study therefore has direct relevance for conservation measures. Data from five microsatellite loci were analysed for 159 individuals from nine different groups living in four isolates in Algeria. Genetic polymorphism was found to be relatively high (4–12 alleles per locus) compared with other genetic markers used in previous studies of this species; mean expected heterozygosity was 65%. The four isolates are all genetically distinct ( F _ST = 0; P < 0.001). Indeed, the results suggest that dispersal is limited even between some social groups within a single isolate. Genetic distances based on models not assuming stepwise mutation ( F _ST and chord distance) gave very similar results and are highly correlated with geographical distances within one isolate but not between isolates. This may indicate that isolation by distance exerts a significant influence within an isolate but that genetic drift prevails between the four isolates. After allowing for variation in sample size, we found no evidence of reduced allelic diversity within small isolates that may have been separated for 250 years or more. The surviving population of Algerian Barbary macaques taken as a whole still shows marked variability in microsatellite alleles, but maintenance of genetic variability over the long term will surely require effective protection of all isolates.     

Low microsatellite variation in laboratory gerbrils

The Mongolian gerbil has become a model organism of increasing importance for the understanding of aging, epilepsy, the process of domestication or sociobiological questions. We report the development and characterization of the first nine polymorphic dinucleotide repeat loci in this species. Average observed heterozygosity and allele number of laboratory animals measured 0.136 (SE = +/-0.065) and 1.78 (SE = +/-0.278) compared to 0.761 (SE = +/-0.025) and 9.2 (SE = +/-0.57) found for a reference group of wild gerbils. The extreme low genetic variation observed in laboratory animals is caused by several severe population size bottlenecks due to the initial founder event and the later establishment of subpopulations. Reduced levels of allelic polymorphism in experimental animals hamper genetic mapping or parental studies. Therefore experiments relying on kinship analyses have to be carried out on wild animals. Estimates of genetic identity and parental exclusion were calculated as Pid = 2.8 x 10(-12) and Pex > 0.999 in wild gerbils. Laboratory gerbil strains show the expected high degree of genetic similarity. However, significant allele frequency differences (P < .001) between American and European gerbils at some microsatellite loci may still allow discrimination between breeding lines.     

Biogeography and degree of endemicity of fluorescent Pseudomonas strains in soil

Fluorescent Pseudomonas strains were isolated from 38 undisturbed pristine soil samples from 10 sites on four continents. A total of 248 isolates were confirmed as Pseudomonas sensu stricto by fluorescent pigment production and group-specific 16S ribosomal DNA (rDNA) primers. These isolates were analyzed by three molecular typing methods with different levels of resolution: 16S rDNA restriction analysis (ARDRA), 16S-23S rDNA intergenic spacer-restriction fragment length polymorphism (ITS-RFLP) analysis, and repetitive extragenic palindromic PCR genomic fingerprinting with a BOX primer set (BOX-PCR). All isolates showed very similar ARDRA patterns, as expected. Some ITS-RFLP types were also found at every geographic scale, although some ITS-RFLP types were unique to the site of origin, indicating weak endemicity at this level of resolution. Using a similarity value of 0.8 or more after cluster analysis of BOX-PCR fingerprinting patterns to define the same genotypes, we identified 85 unique fluorescent Pseudomonas genotypes in our collection. There were no overlapping genotypes between sites as well as continental regions, indicating strict site endemism. The genetic distance between isolates as determined by degree of dissimilarity in BOX-PCR patterns was meaningfully correlated to the geographic distance between the isolates' sites of origin. Also, a significant positive spatial autocorrelation of the distribution of the genotypes was observed among distances of <197 km, and significant negative autocorrelation was observed between regions. Hence, strong endemicity of fluorescent Pseudomonas genotypes was observed, suggesting that these heterotrophic soil bacteria are not globally mixed.     

Biogeography and Degree of Endemicity of Fluorescent Pseudomonas Strains in Soil

Fluorescent Pseudomonas strains were isolated from 38 undisturbed pristine soil samples from 10 sites on four continents. A total of 248 isolates were confirmed as Pseudomonas sensu stricto by fluorescent pigment production and group-specific 16S ribosomal DNA (rDNA) primers. These isolates were analyzed by three molecular typing methods with different levels of resolution: 16S rDNA restriction analysis (ARDRA), 16S-23S rDNA intergenic spacer-restriction fragment length polymorphism (ITS-RFLP) analysis, and repetitive extragenic palindromic PCR genomic fingerprinting with a BOX primer set (BOX-PCR). All isolates showed very similar ARDRA patterns, as expected. Some ITS-RFLP types were also found at every geographic scale, although some ITS-RFLP types were unique to the site of origin, indicating weak endemicity at this level of resolution. Using a similarity value of 0.8 or more after cluster analysis of BOX-PCR fingerprinting patterns to define the same genotypes, we identified 85 unique fluorescent Pseudomonas genotypes in our collection. There were no overlapping genotypes between sites as well as continental regions, indicating strict site endemism. The genetic distance between isolates as determined by degree of dissimilarity in BOX-PCR patterns was meaningfully correlated to the geographic distance between the isolates' sites of origin. Also, a significant positive spatial autocorrelation of the distribution of the genotypes was observed among distances of <197 km, and significant negative autocorrelation was observed between regions. Hence, strong endemicity of fluorescent Pseudomonas genotypes was observed, suggesting that these heterotrophic soil bacteria are not globally mixed.     

Population genetic structure and differentiation of Anthoxanthum alpinum in the subalpine-alpine ecocline of Swiss Alps

Allozyme variation in 6 enzyme systems coding 10 loci was estimated for 18 subpopulations of Anthoxanthum alpinum from three altitudinal transects in two localities of the Swiss Alps. Mean proportions of polymorphic loci (95% criterion), average number of alleles per locus, and mean expected heterozygosity were 64.9%, 2.37 and 0. 252, respectively. Mean genetic distance among populations was 0.011, and 79% of the genetic variation resided within populations. Based on allozyme analysis, marginal subpopulations appeared to have similar level of genetic variability to central subpopulations. Relatively high genetic differentiation, low gene flow values and small neighbourhood sizes suggested that inbreeding followed by genetic drift was possible causes of lowgenetic variability in Arpette A. alpinum populations.     

Characterization of genetic diversity and population structure in wheat using array based SNP markers

Genetic diversity is crucial for successful adaptation and sustained improvement in crops. India is bestowed with diverse agro-climatic conditions which makes it rich in wheat germplasm adapted to various niches. Germplasm repository consists of local landraces, trait specific genetic stocks including introgressions from wild relatives, exotic collections, released varieties, and improved germplasm. Characterization of genetic diversity is done using morpho-physiological characters as well as by analyzing variations at DNA level. However, there are not many reports on array based high throughput SNP markers having characteristics of genome wide coverage employed in Indian spring wheat germplasm. Amongst wheat SNP arrays, 35K Axiom Wheat Breeder’s Array has the highest SNP polymorphism efficiency suitable for genetic mapping and genetic diversity characterization. Therefore, genotyping was done using 35K in 483 wheat genotypes resulting in 14,650 quality filtered SNPs, that were distributed across the B (~?50%), A (~?39%), and D (~?10%) genomes. The total genetic distance coverage was 4477.85 cM with 3.27 SNP/cM and 0.49 cM/SNP as average marker density and average inter-marker distance, respectively. The PIC ranged from 0.09 to 0.38 with an average of 0.29 across genomes. Population structure and Principal Coordinate Analysis resulted in two subpopulations (SP1 and SP2). The analysis of molecular variance revealed the genetic variation of 2% among and 98% within subpopulations indicating high gene flow between SP1 and SP2. The subpopulation SP2 showed high level of genetic diversity based on genetic diversity indices viz. Shannon’s information index (I)?=?0.648, expected heterozygosity (He)?=?0.456 and unbiased expected heterozygosity (uHe)?=?0.456. To the best of our knowledge, this study is the first to include the largest set of Indian wheat genotypes studied exclusively for genetic diversity. These findings may serve as a potential source for the identification of uncharacterized QTL/gene using genome wide association studies and marker assisted selection in wheat breeding programs.

     

Optimal sampling strategies for capture of genetic diversity differ between core and peripheral populations of <Emphasis Type="Italic">Picea sitchensis</Emphasis> (Bong.) Carr

In previous studies we reported that while core populations of Sitka spruce [Picea sitchensis (Bong.) Carr] have little within-population genetic structure, peripheral populations are strongly spatially structured at distances up to 500 m. Here we explore the implications of this difference in structure on ex situ gene conservation collections and estimates of genetic diversity from research collections. We test the effects of varying the number of individuals sampled and the total area they are sampled across on capture of neutral genetic variation in collections from core, continuous versus peripheral, disjunct populations. Bivariate response surface analysis of genetic marker data for eight sequence tagged site loci from core and peripheral populations suggest that a population sample from 150 trees covering at least 225 ha would be adequate for capturing 95% of the genetic diversity (as measured by allelic richness or expected heterozygosity) in core populations. However, a larger sample of 180 individuals from an area of at least 324 ha is needed in peripheral populations to capture the same proportion of standing variation because of stronger within-population spatial genetic structure. Standard population sampling protocols for estimating among and within-population genetic diversity would significantly underestimate the within-population allelic richness and expected heterozygosity of peripheral but not core populations, potentially leading to poor representation of genetic variation in peripheral populations as well as erroneous conclusions about their genetic impoverishment.     

Genetic differentiation in Eurasian populations of the postfire ascomycete Daldinia loculata

The genetic population structure of the postfire ascomycete Daldinia loculata was studied to test for differentiation on a continental scale. Ninety-six samples of spore families, each comprising mycelia from six to 10 spores originating from single perithecia, were sampled from one Russian and six Fennoscandian forest sites. Allelic distribution was assayed for six nuclear gene loci by restriction enzyme analyses of polymerase chain reaction (PCR)-amplified gene fragments. In addition, the full sequence of the gene fragment was analysed for a subset of haploid single-ascospore isolates in a multiallelic approach. A third data set was generated by using arbitrary-primed PCR with the core sequence of the phage M13 as primer. Although there was a reduction in heterozygosity in the total population from what would have been expected at random mating, the levels of genetic differentiation among the Eurasian subpopulations of D. loculata were low. All subpopulations were found to be in Hardy-Weinberg equilibrium and gametic equilibrium was observed between all investigated nuclear gene loci. The results obtained by the different markers were consistent; we confirmed low levels of genetic differentiation among the Eurasian subpopulations of D. loculata. The differentiation did not increase with distance; the Russian subpopulation, sampled more than 7000 km from the Fennoscandian subpopulations, was only moderately differentiated from the others (FST = 0.00-0.14). In contrast, one of the Swedish populations was the most highly differentiated from the others, with FST and GST values of 0.10-0.16. The results suggest that D. loculata consists of a long-lived background Eurasian population of latent mycelia in nonburned forests, established by sexual ascospores dispersed from scattered burned forest sites. Local differentiation is probably due to founder effects of populations in areas with low fire frequency. A tentative life cycle of D. loculata is presented.     

A genetic mosaic in the fruiting stage of Armillaria gallica

The basidiome stage of Armillaria gallica can be a genetic mosaic. Ten cells isolated from a single basidiome in 1986 produced nine different genotypes when analyzed for variation at six nuclear loci. Four additional basidiomes collected in 1986 produced mosaic patterns when analyzed for variation at a single nuclear (PCR-RFLP) locus. One basidiome collected in 1993 was not a genetic mosaic because 15 cells isolated from it produced only one genotype when analyzed for six nuclear loci. Two hundred seventy-four samples collected in the field between 1981 and 1998 were analyzed for variation at the PCR-RFLP locus. Samples collected prior to 1988 produced patterns consistent with the existence of mosaicism, but samples collected after 1988 showed no evidence of mosaicism. Genetic mosaicism represents a novel mechanism for partitioning genotypes among the cells of a basidiomycete and has interesting implications for the biology of A. gallica.     

阿尔卑斯山高山-亚高山过渡区高山黄花茅的群体遗传结构和分化研究

应用等位酶分析,在瑞士阿尔卑斯山的阿尔拜特(Arpette)和拜阿尔普(Belalp),沿三个不同的海拔梯度,研究了高山黄花茅3个自然居群的遗传变异和分化。研究结果表明,平均的多态性位点比例为64．9％,每个位点平均等位基因数为2．37,平均期望杂合性为0．252。亚居群间平均的遗传距离为0．011,发现79％的遗传变异存在于居群内。基于等位酶分析,边缘亚居群与中心亚居群似乎有类似的遗传变异性。相对比较高的遗传分化、低的亚居群间基因流和小的邻居大小值暗示,近交和随后的遗传漂变可能是导致阿尔拜特黄花茅居群遗传变异性较低的主要原因。     

Genetic diversity of north-east Asian cattle based on microsatellite data

In order to assess the genetic variability and population structure of north-east Asian cattle, 13 microsatellite loci were analysed for a total of 200 individuals including Korean, Chinese, Japanese Black and European Holstein cattle. Observed and expected heterozygosity, two estimators (F(ST) and G(ST)) of gene differentiation, and Nei's DA distance were evaluated. Based on expected mean heterozygosity, the lowest genetic diversity was exhibited in Japanese Black cattle (H(E)=0.471), and the highest in Chinese cattle (H(E)=0.744). Korean cattle revealed a relatively high degree of genetic diversity (H(E)=0.728). Average proportion of genetic variation because of interpopulation subdivision among north-east Asian cattle varied between 10.9 and 9.9%, depending on the estimator used. N-J tree based on Nei's DA genetic distance showed that Korean and Chinese cattle are closely related, whereas Japanese Black cattle are clearly distinct from the other two populations, forming a north-east Asian outgroup.     

Genetic variation at enzyme loci in North Atlantic minke whales,Balaenoptera acutorostrata

Electrophoretic variation within and between North Atlantic minke whale samples(Balaenoptera acutorostrata) from West Greenland, Iceland, and Norway was investigated. In the West Greenland samples, 28 enzyme systems were examined, representing 36 loci, of which 6 were found to be polymorphic. In Icelandic and Norwegian samples, 22 enzyme systems were examined, representing 29 loci, of which 6 and 5 were found to be polymorphic, respectively. The average heterozygosity was 0.058 (SE=0.024) in samples from West Greenland, 0.074 (SE=0.028) in samples from Iceland, and 0.054 (SE=0.023) in samples from Norway. No significant deviations from the expected Hardy—Weinberg genotypic frequencies, within samples taken from the same area, were found. Significant differences in allele frequencies were observed, however, between samples from the three different areas. The average Nei's genetic distance was 0.014 and the averageF _st value was 0.126. The genetic differences between the samples from the different areas indicate that those from West Greenland, Iceland, and Norway represented different breeding populations.     

Genetic variation at allozyme and RAPD markers in Pinus longaeva (Pinaceae) of the White Mountains, California

We compared genetic diversity estimated from allozymes and from random amplified polymorphic DNA (RAPDs) in a sample of 210 Great Basin bristlecone pines (Pinus longaeva Bailey) from three groves in the White Mountains, California, USA. The White Mountains are the most westerly extension of bristlecone pine and home to the oldest known living trees. We assayed two forks of each tree to determine whether they originated from multiple seed caches of the Clark's nutcracker. Despite the limited and fragmented distribution of bristlecone pine, its level of genetic diversity was comparable to that of other pines, but lower than that reported for eastern populations of Great Basin bristlecone pine. Twenty-six of 36 allozymes were polymorphic (p(95) = 38.9%; p = 63.0%), with observed heterozygosity (H(o)) of 0.122 and expected heterozygosity (H(e)) of 0.134. The proportion of the total variation among populations (G(ST)) was only 0.011. The high proportion of trees with multiple stems was not due to germination in seed caches; only six of 210 forked trees had multiple allozyme genotypes. Of the 42 RAPD loci scored, 27 were monomorphic. Genetic diversity for RAPDs was nearly the same as that for allozymes (p(95) = 34.1%, H(e) = 0.130). However, the estimates of diversity and differentiation were much higher (H(e) = 0.321, G(ST) = 0.039) after excluding monomorphic loci.