SOMATIC CELL INCOMPATIBILITY IN DIDYMIUM IRIDIS: LOCUS IDENTIFICATION AND FUNCTION

Somatic incompatibility in two strains of the myxomycete Didymium iridis is controlled by at least 13 loci: seven fusion loci and six clear-zone loci. Details on correlating loci of the Hon 1 strain with Pan 1 loci are given and a unified nomenclature, applicable to both strains, has been developed from data presented in this paper. Although fusion loci generally prevent fusion between different plasmodial incompatibility phenotypes, studies on individual loci have shown that a limited transient fusion may occasionally take place. Thus, the differences between the fusion and clear-zone loci are not as distinct as once thought. However, the 13 somatic incompatibility loci are still easily designated as either fusion or clear-zone loci, and no locus has thus far been found with true intermediate function. Studies on individual locus function are also discussed.     

Rate and directionality of mutations and effects of allele size constraints at anonymous, gene-associated, and disease-causing trinucleotide loci.

We studied the patterns of within- and between-population variation at 29 trinucleotide loci in a random sample of 200 healthy individuals from four diverse populations: Germans, Nigerians, Chinese, and New Guinea highlanders. The loci were grouped as disease-causing (seven loci with CAG repeats), gene-associated (seven loci with CAG/CCG repeats and eight loci with AAT repeats), or anonymous (seven loci with AAT repeats). We used heterozygosity and variance of allele size (expressed in units of repeat counts) as measures of within-population variability and GST (based on heterozygosity as well as on allele size variance) as the measure of genetic differentiation between populations. Our observations are: (1) locus type is the major significant factor for differences in within-population genetic variability; (2) the disease-causing CAG repeats (in the nondisease range of repeat counts) have the highest within-population variation, followed by the AAT-repeat anonymous loci, the AAT-repeat gene-associated loci, and the CAG/CTG-repeat gene-associated loci; (3) an imbalance index beta, the ratio of the estimates of the product of effective population size and mutation rate based on allele size variance and heterozygosity, is the largest for disease-causing loci, followed by AAT- and CAG/CCG-repeat gene-associated loci and AAT-repeat anonymous loci; (4) mean allele size correlates positively with allele size variance for AAT- and CAG/CCG-repeat gene-associated loci and negatively for anonymous loci; and (5) GST is highest for the disease-causing loci. These observations are explained by specific differences of rates and patterns of mutations in these four groups of trinucleotide loci, taking into consideration the effects of the past demographic history of the modern human population.     

Genetic variation in Australian Merino sheep

Variation at 22 gene loci was investigated in a flock of Australian Merino sheep using restriction fragment length polymorphism (RFLP) analysis. Polymorphism was observed at 20 loci, including loci for wool keratin, hormone and immunoglobulin light chain genes. Eleven loci yielded unambiguous genotypes suitable for population data analysis. Average heterozygosity, determined from these and two monomorphic loci, was estimated as 0.107 (SE = 0.024). Average heterozygosity excluding all monomorphic data was estimated as 0–377 (SE = 0.031), which is comparable with human RFLP heterozygosities for loci chosen in the same way that we selected sheep loci.     

种间转移扩增法筛选长爪沙鼠微卫星位点

目的筛选长爪沙鼠新的微卫星位点,为长爪沙鼠遗传分析提供遗传标记物。方法从GenBank中随机选取小鼠微卫星位点引物536对,用这些引物对长爪沙鼠基因组DNA扩增,将阳性目的条带进行序列分析,找出符合微卫星序列特征的短串联重复序列。结果 536对小鼠微卫星引物在长爪沙鼠基因组中扩增出了313个阳性条带,经序列分析,确定130个长爪沙鼠微卫星位点;其中完美型位点占80.77%(105/130),不完美型位点占19.23%(25/130),与小鼠同源性为24.3%(130/536)。将筛选出的微卫星位点在GenBank中注册,注册号从GU562694到GU562823。结论小鼠和沙鼠的微卫星位点具有较高的同源性,用小鼠的微卫星位点引物直接扩增长爪沙鼠基因组DNA可有效地筛选出长爪沙鼠微卫星位点。     

Organization and Evolution of the Mammalian Genome: I. Polymorphism of H-2 Linked Loci

To test the hypothesis that the H-2 polymorphism is adaptive, the degree of polymorphism of loci linked to the H-2 complex on chromosome 17 of the house mouse was compared to the degree of polymorphism of loci located on other chromosomes. Published theoretical analyses show that polymorphisms subject to natural selection usually reduce the polymorphism of linked neutral loci. The first test of the hypothesis was based on data obtained from a survey of the polymorphism of 12 isozyme-encoding loci in wild house mice from Europe, North Africa and South America. Results of this test showed that, on the average, H-2-linked loci were as polymorphic as loci located on other chromosomes. In fact, the data suggested that H-2 linked loci might be more polymorphic than other loci. To test this hypothesis more rigorously, data for the 12 isozyme-encoding loci were augmented with data from published surveys of the polymorphisms of 59 loci in house mice from Europe and North America. Results of these tests showed that polymorphic loci linked to the H-2 complex tended to be more, rather than less, polymorphic than loci located on other chromosomes. The cluster of highly polymorphic loci seems to be related to linkage of these loci to the highly polymorphic H-2 complex, but the way in which the influence is exerted could not be readily explained.     

Comparing geographical genetic differentiation between candidate and noncandidate loci for adaptation strengthens support for parallel ecological divergence in the marine snail Littorina saxatilis

The Galician sympatric ecotypes of Littorina saxatilis have been proposed as a model system for studying parallel ecological speciation. Such a model system makes a clear prediction: candidate loci (for divergent adaptation) should present a higher level of geographical differentiation than noncandidate (neutral) loci. We used 2356 amplified fragment length polymorphisms (AFLPs) and four microsatellite loci to identify candidate loci for ecological adaptation using the F _ST outlier method. Three per cent of the studied AFLP loci were identified as candidate loci associated with adaptation, after multitest adjustments, thus contributing to ecotype differentiation (candidate loci were not detected within ecotypes). Candidate and noncandidate loci were analysed separately at four different F _ST partitions: differences between ecotypes (overall and local), differences between localities and micro-geographical differences within ecotypes. The magnitude of F _ST differed between candidate and noncandidate loci for all partitions except in the case of microgeographical differentiation within ecotypes, and the microsatellites (putatively neutral) showed an identical pattern to noncandidate loci. Thus, variation in candidate loci is determined partially independent by divergent natural selection (in addition to stochastic forces) at each locality, while noncandidate loci are exclusively driven by stochastic forces. These results support the evolutionary history described for these particular populations, considered to be a clear example of incomplete sympatric ecological speciation.     

Protein polymorphism and genic variation in a population of the loach Cobitis delicata

Hemoglobin, non-enzymatic and enzymatic muscle proteins of the loach Cobitis delicata were examined electrophoretically. Eleven proteins were shown to be under control by 20 loci. Only two loci were defined as polymorphic and 14 loci were completely monomorphic. Estimated average heterozygosity over all 20 loci was 0.011 in the loach population.     

Novel microsatellite DNA loci for Bombus terrestris (Linnaeus, 1758)

We present details and characteristics of 123 novel polymorphic microsatellite DNA loci for Bombus terrestris. Thirty-four of these loci have been tested in nine other Bombus species and 25 of them showed polymorphisms in at least one species. These microsatellite DNA loci together with the already established 60 loci will be useful for characterizing wild and managed populations of B. terrestris and other Bombus species as well as for detailed genetic studies in including mapping studies and genome annotations.     

Autosomal and sex-linked microsatellite loci in the green oak leaf roller Tortrix viridana L. (Lepidoptera, Tortricidae)

Eight microsatellite markers were developed for the lepidopteran species Tortrix viridana using an enrichment protocol. The loci were highly variable with number of alleles ranging from four to 38. Six of the eight loci were in Hardy-Weinberg equilibrium. The other two were linked to the Z-chromosome. Values of observed heterozygosity ranged for the autosomal loci from 0.510 to 0.957. All loci will be useful to study dispersal and the autosomal loci, as well for phylogeographical studies.     

Isolation and characterization of nine microsatellite loci from the pike-perch, Sander lucioperca (Linnaeus, 1758)

In order to facilitate studies on the genetic structure of wild populations as well as to monitor genetic changes in cultured stocks, nine polymorphic microsatellite loci were isolated from pike-perch (Sander lucioperca). Single loci allele numbers varied between two (loci MSL-3 and MSL-7) and six (loci MSL-1 and MSL-2), and observed heterozygosities ranged from 0.36 (locus MSL-2) to 1.00 (locus MSL-9) in a test panel of 25 individuals. Only one pair of loci (MSL-5 and MSL-8) displayed significant linkage disequilibrium after sequential Bonferroni corrections. Hardy-Weinberg tests revealed significant excesses of heterozygotes at three loci (MSL-1, MSL-7, and MSL-9).     

奶牛和肉牛6个STR基因座遗传多态性研究

利用PCR技术和复合电泳银染技术检测奶牛和肉牛BM2113、BM1862、BMc701、BM2934、TGLA122、BM720等6个STR基因座的多态性分布,并计算该6个基因座的基因频率(P_i)、个体鉴别力(DP)、杂合度(H)、多态信息含量(PIC)、和非父排除概率(PE)。结果显示:6个STR基因座的基因型分布符合Hardy-Weinberg平衡,奶牛中6个STR基因座中BM2113基因座的DP、H和PIC最高,TGLA122基因座的PE最高。6个STR基因座的累积个体鉴别力(CDP)为0.99997,累积非父排除能力(CPE)为0.98827。肉牛中6个STR基因座中BM1862基因座的DP、H、PIC、PE都是最高,6个STR基因座的累积个体鉴别力(CDP)为0.99999,累积非父排除能力(CPE)为0.99578。结果表明,6个STR基因座可用于牛的遗传连锁分析、个体识别和亲子鉴定等研究领域。     

The variance of sample heterozygosity

The variance of sample heterozygosity, averaged over several loci, is studied in a variety of situations. The variance depends on the sampling implicit in the mating system as well as on that explicit in the loci scored and individuals sampled. There are also effects of allelic distributions over loci and of linkage or linkage disequilibrium between pairs of loci. Results are obtained for populations in drift and mutation balance, for infinite populations undergoing mixed self and random mating, and for finite monoecious populations with or without selfing. For unlinked loci in drift/mutation balance, variances appear to be lessened more by increasing the number of loci scored than by increasing the number of individuals sampled. For infinite populations under the mixed self and random mating system, however, the reverse is true. Methods for estimating the variance of sample heterozygosity are discussed, with attention being paid to unbalanced data where not all loci are scored in all individuals.     

A Genetic Linkage Map of the Mouse Using Restriction Landmark Genomic Scanning (Rlgs)

We have developed a multiplex method of genome analysis, restriction landmark genomic scanning (RLGS) that has been used to construct genetic maps in mice. Restriction landmarks are end-labeled restriction fragments of genomic DNA that are separated by using high resolution, two-dimensional gel electrophoresis identifying as many as two thousand landmark loci in a single gel. Variation for several hundred of these loci has been identified between laboratory strains and between these strains and Mus spretus. The segregation of more than 1100 RLGS loci has been analyxed in recombinant inbred (RI) strains and in two separate interspecific genetic crosses. Genetic maps have been derived that link 1045 RLGS loci to reference loci on all of the autosomes and the X chromosome of the mouse genome. The RLGS method can be applied to genome analysis in many different organisms to identify genomic loci because it used end-labeling of restriction landmarks rather than probe hybridization. Different combinations of restriction enzymes yield different sets of RLGS loci providing expanded power for genetic mapping.     

DNA variants of the MHC show location-specific convergence between sheep, goat and cattle

Interspecific convergent evolution in sheep, goat and cattle was analysed with the help of orthologous microsatellite markers. Six of the loci are located in the major histocompatibility complex (MHC) region and three on different chromosomes. Samples from at least 60 animals per autochthonous breed of the three species were collected in central and southeast Anatolia (Turkey) as well as Baden-Württemberg (Germany). Allelic diversity, heterozygosity, population differentiation and genetic distances were calculated. The loci were polymorphic in all species and breeds. Apart from MSDRB, the loci linked to the MHC were similarly polymorphic as compared to the other loci. Allele numbers in the Turkish sheep and in the cattle breeds were higher than in the other breeds. The predominant occurrence of distinct allele lengths per locus differed depending on the species. For the three geographic locations, the genetic distances between species based on the MHC loci were significantly closer in comparison with distances based on quasi-neutral loci. This indicates convergent evolution of the MHC loci between sheep, goat and cattle caused by effects of location and demonstrates an approach for quantifying influences of adaptation on genetic variability.     

Protein Polymorphisms, Segregation in Genetic Crosses and Genetic Distances among Fishes of the Genus Xiphophorus (Poeciliidae)

The products of 49 protein-coding loci were examined by starch gel electrophoresis for populational variation in six species of Xiphophorus fishes and/or segregation in intra- and interspecific backcross and intercross hybrids. Electrophoretic variation was observed for 29 of the 35 locus products in a survey of 42 population samples. The highest frequency of polymorphic loci observed in noninbred populations was 0.143. After ten or more generations of inbreeding, all loci studied were monomorphic. Inbred strains generally exhibited the commonest electrophoretic alleles of the population from which they were derived. An assessment of genetic distances among Xiphophorus populations reflected classical systematic relationships and suggested incipient subspeciation between X. maculatus from different drainages as well as several species groups. Thirty-three loci were analyzed with respect to segregation in hybrids. The goodness of fit of segregations to Mendelian expectations at all loci analyzed (except loci in linkage group I) is interpreted as evidence for high genetic compatibility of the genomes of Xiphophorus species. It is anticipated that these data will result in a rapid expansion of the assignment of protein-coding loci to linkage groups in these lower vertebrate species.     

Linkage relationships and haplotype polymorphism among cichlid Mhc class II B loci.

The species flocks of cichlid fishes in the Great East African Lakes are paradigms of adaptive radiation and hence, of great interest to evolutionary biologists. Phylogenetic studies of these fishes have, however, been hampered by the lack of suitable polymorphic markers. The genes of the major histocompatibility complex hold the promise to provide, through their extensive polymorphism, a large number of such markers, but their use has been hampered by the complexity of the genetic system and the lack of definition of the individual loci. In this study we take the first substantial step to alleviate this problem. Using a combination of methods, including the typing of single sperm cells, gyno- or androgenetic individuals, and haploid embryos, as well as sequencing of class II B restriction fragments isolated from gels for Southern blots, we identify the previously characterized homology groups as distinct loci. At least 17 polymorphic class II B loci, all of which are presumably transcribed, have been found among the different species studied. Most of these loci are shared across the various cichlid species and genera. The number of loci per haplotype varies from individual to individual, ranging from 1 to 13. A total of 21 distinct haplotypes differing in the number of loci they carry has thus far been identified. All the polymorphic loci are part of the same cluster in which, however, distances between at least some of the loci (as indicated by recombination frequencies) are relatively large. Both the individual loci and the haplotypes can now be used to study phylogenetic relationships among the members of the species flocks and the mode in which speciation occurs during adaptive radiation.     

Microsatellite loci for the field cricket,Gryllus bimaculatus and their cross‐utility in other species of Orthoptera

We have isolated 16 microsatellite loci in the field cricket, Gryllus bimaculatus. Nine loci were found to be polymorphic in G. bimaculatus and the number of alleles varied from seven to 14. All 16 loci were tested for amplification in nine other species. In the five species tested belonging to the same subfamily (Gryllinae), a minimum of nine loci amplified. These loci will be used to determine paternity as part of a study to investigate the genetic benefits of polyandry.     

Factors affecting polymorphism at microsatellite loci in bread wheat [<Emphasis Type="Italic">Triticum aestivum</Emphasis> (L.) Thell]: effects of mutation processes and physical distance from the centromere

The effects of factors known to influence the level of polymorphism at microsatellite loci were studied using 99 markers and seven lines of bread wheat. Mutational factors as well as indirect selective events shape diversity at these loci. Theory predicts that the selection of favorable alleles should reduce polymorphism at neutral neighboring loci in genomic areas with low recombination rates. In wheat, local recombination rate is positively correlated with physical distance from the centromere. Seventy four loci among the 99 used could be physically located on the chromosome. We studied how the following affected the diversity among a set of inbred lines: the length of the alleles, the motif (CA versus CT), the structure of the loci (perfect versus imperfect) and the chromosomal position of the loci. For each locus, we determined whether the polymorphism observed at a locus was compatible with the Stepwise Mutation Model (SMM) or the Two-Phase Model (TPM). Both the mutation rate and the compatibility with the SMM or the TPM were shown to be variable between loci. Wheat microsatellite loci were found to be more variable when segregating alleles were perfect and had long motifs (composed of many repetitions). Diversity observed at 19 loci was not compatible with the SMM. Loci located in distal regions, with presumably high recombination rates, had longer allele sizes and were more polymorphic than loci located in proximal regions. We conclude that both mutation factors and indirect selective events vary according to the local recombination rate and therefore jointly influence the level of polymorphism at microsatellite loci in wheat.Communicated by J. Dvorak     

Beyond MHC: signals of elevated selection pressure on Atlantic salmon (Salmo salar) immune‐relevant loci

Using Atlantic salmon (Salmo salar) as a model system, we investigated whether 18 microsatellites tightly linked to immune‐relevant genes have experienced different selection pressures than 76 loci with no obvious association with immune function. Immune‐relevant loci were identified as outliers by two outlier tests significantly more often than nonimmune linked loci (22% vs. 1.6%). In addition, the allele frequencies of immune relevant markers were more often correlated with latitude and temperature. Combined, these results support the hypothesis that immune‐relevant loci more frequently exhibit footprints of selection than other loci. They also indicate that the correlation between immune‐relevant loci and latitude may be due to temperature‐induced differences in pathogen‐driven selection or some other environmental factor correlated with latitude.