Polymorphism of the <Emphasis Type="Italic">BoLA-DRB3</Emphasis> gene in the Mongolian,Kalmyk, and Yakut cattle breeds

Polymorphism of the BoLA-DRB3 gene was studied with the use of the PCR-RFLP technique in three cattle breeds (Mongolian, Kalmyk, and Yakut) representing the Bos taurus turano-mongolicus group. 35 BoLA-DRB3.2 alleles were detected in the Mongolian breed and 34 alleles in the Kalmyk breed. The frequencies of alleles in both populations are distributed rather evenly: the frequencies of the most widely represented alleles (*18, *20, and *28) in the Mongolian cattle varied from 7.75 to 8.45%. The most frequent alleles in the Kalmyk cattle were *28 (14.52%), *24 (7.26%), and *12 (6.45%). Only five alleles were identified in the Yakut cattle breed. The prevailing allele was *29 (77.3%); a relatively frequent allele was *1 (13.1%), and the remaining three alleles constituted only 9.6%. Such a low level of diversity of BoLA-DRB3 gene alleles was not observed earlier in any other cattle breed. The Mongolian and Kalmyk breeds showed a wide diversity of BoLA-DRB3 genotypes (56 and 51 genotypes, respectively) and a high level of expected heterozygosity (H _e = 0.953 and 0.946, respectively). Both breeds had a deficiency of heterozygotes (Mongolian cattle: H _o = 0.775, D = −0.187; Kalmyk cattle: H _o = 0.708, D = −0.252). A low level of genotypic diversity for the BoLA-DRB3 locus (only seven genotypes; the frequency for the genotype *29/*29 is 71.4%) and a very low level of observed heterozygosity (H _o = 0.12) were revealed in the Yakut breed. BoLA-DRB3.2 alleles associated with resistance to persistent lymphocytosis caused by the bovine leukemia virus (total frequencies 15.49 and 24.19%) and to various forms of mastitis (total frequencies 12.68 and 20.96%, respectively) were identified in the Mongolian and Kalmyk animals. In the Yakut breed, alleles associated with resistance to diseases are represented only by the BoLA-DRB3.2 allele *7 (1.2%). Thus, the Mongolian and Kalmyk cattle breeds are characterized by a wide diversity of alleles and genotypes for the BoLA-DRB3 gene. In contrast, the population of Yakut cattle from the Verkhoyanskii region of the Republic of Sakha has a poor diversity of alleles and genotypes for the BoLA-DRB3 gene and a very low level of heterozygosity, suggesting an unfavorable state of the population that is probably caused by inbreeding depression due to a long-term isolation and a small number of animals.     

中药黄芪植物分类及其区系地理分布研究

确认了中药黄芪的原植物有膜荚黄芪(Astragalus membranaceus (Fisch.) Bunge)、蒙古黄芪(A. mongholicus Bunge)和北蒙古黄芪(A. borealimongolicus Y. Z. Zhao)3种,其中北蒙古黄芪为一新种;确定了这三种植物的区系地理成分：膜荚黄芪为东亚北部—西伯利亚南部森林带的分布种,蒙古黄芪为华北森林草原带的分布种,北蒙古黄芪为蒙古高原北部草原带的分布种,3种黄芪存在着明显的地理替代分布格局。     

Genetic variability of tall junipers (Juniperus excelsa Bieb.) on the northern and southern boundaries of their natural distribution

The genetic structure, subdivision, and differentiation of six populations of tall junipers (Juniperus excelsa Bieb.) in the Crimean Mountains and one population in Lebanon were investigated using 18 polymorphic allozyme loci as genetic markers. A high level of genetic variability of J. excelsa was established at the northern and southern boundaries of their natural habitats. The mean values of the main indicators of genetic polymorphism were P₉₉ = 1.000, A = 3.167, H_E = 0.370, and H_O = 0.405. The subdivision and differentiation of populations were low (F_ST = 0.032, D_N = 0.026), indicating the similarity of their gene pools.     

Allozyme Variation and Phylogenetic Relationships in Picea jezoensis (Pinaceae) Populations of the Russian Far East

Genetic variation and differentiation of 12 populations of Picea jezoensis from the Russian Far East were studied using 20 allozyme loci. The mean number of alleles per locus was 2.63, the percent of polymorphic loci was 88.1%, the observed heterozygosity was 0.181, and the mean value of expected heterozygosity amounted to 0.189. The values of expected heterozygosity of the northern and central mainland populations were higher than in the southern part of the natural range. A significant bias of Hardy–Weinberg heterozygosity to equilibrium heterozygosity (H_eq) suggests that most of the mainland populations have recently experienced a severe expansion in population size while populations from Kamchatka Peninsula have undergone a reduction in population size. Unbiased Nei’s genetic distance values were low within and between the mainland and Sakhalin Island populations (D_N=0.008). The largest values (D_N=0.063) were found between the mainland/Sakhalin and Kamchatka Peninsula populations. Based on genetic distance, P. jezoensis and P. kamtschatkensis could be considered as distinct taxa, but P. ajanensis, P. microsperma, and P. komarovii do not warrant taxonomic recognition.     

Physiological genetics of the dominant gibberellin-nonresponsive maize dwarfs,Dwarf8 and Dwarf9

Maize (Zea mays L.) Dwarf8-1 (D8-1) is an andromonoecious dwarf mutant proposed to be involved in gibberellin (GA) reception (Fujioka et al. 1988b; Harberd and Freeling 1989). The mutant D8-1 is dominant and GA-nonresponsive (Phinney 1956). We show by map position and similarity of phenotype that five additional dwarf mutants are D8 alleles. We show by map position and similarity of phenotype that a second andromonoecious dwarf mutant, D9-1, defines a duplicate gene. Maize D9-1 and each dominant D8 allele specify a different plant stature, from very mild to very severe dwarfism. Plants of D9-1 and all dominant D8 alleles, except D8-1591, were GA-nonresponsive when treated with 7500 nmol GA₃. The behavior of the mild dwarf D8-1591 was unique in that a small but significant growth response was detected (37% for D8-1591 vs. 130% for the wild type) when treated with 7500 nmol GA₃. These results establish that all dwarf genotypes, except D8-1591, in one dose set a maximum limit on plant growth and block the normal response to GA. When treated with the GA-synthesis inhibitor paclobutrazol, plants of all dwarf genotypes and wild-type siblings were severely dwarfed. Plants of all dwarf genotypes treated with the GA-synthesis inhibitor paclobutrazol and GA₃ were returned to their normal dwarf phenotype. Dominant dwarfing, delayed flowering, increased tillering, and anther development in the ear are characteristic features of D9-1 and all D8 alleles. The GA-synthesis-deficient dwarfs also have these characteristic features. We discuss the function of the wild-type gene product in the context of the observed results.Abbreviations D8 Dwarf8 - D9 Dwarf9 - GA_(n) gibberellin A_(n) - GA₃ gibberellic acid - MNL Maize Genetics Cooperation Newsletter - NIL near-isogenic lines - RFLP restriction fragment length polymorphism - WT wild type This work was supported, in part, by a National Science Foundation Plant Postdoctoral Fellowship to R.G.W., by grants from NIH and ICI Seeds to M.F., the NSF Center for Plant Developmental Biology and the California Agriculture Experiment Station. Much of the work was done in the laboratory of Tim Helentjaris and was supported by a grant from Pioneer Hi-Bred Int'l. The generous gifts of the dominant dwarfing mutants from M.G. Neuffer and O.E. Nelson Jr. are gratefully acknowledged.     

Temporal and Spatial Allozyme Variation in the South American Cactophilic Drosophila antonietae (Diptera; Drosophilidae)

Drosophila antonietae is an endemic South American cactophilic species that uses Cereus hildmaniannus rotting cladodes as breeding sites. We assessed temporal and spatial intrapopulational allozyme variation of two natural populations. Our results suggest that environmental variation (rain precipitation) is probably influencing allozyme temporal variation. Moreover, it seems that D. antonietae does not have intrapopulation structure and has N _ev (variance effective size) 83 and N _ec (number of adult flies that colonize each rotting cladode) = 21. The deficiency of heterozygotes found must be due to null alleles, a temporal Wahlund effect, or selection against heterozygotes. Assortative mating and inbreeding are discarded. This is the first report on allozyme variation in D. antonietae. It gives some insight on intrapopulational genetics through space and time for this species. This is important to understand its general genetic variability and will be essential to future works on the natural history and evolution of this species.     

Temporal-method estimates of Ne from highly polymorphic loci

The temporal method is used widely to estimategenetic effective population size (N _e), a parameter of fundamental interestto studies of evolutionary and conservationbiology. The statistical properties oftemporal-method estimates have not beenexplored for highly polymorphic DNA markersthat often contain many alleles occurring invery low frequencies. We used a Monte Carlosimulation approach to assess accuracy andprecision of the temporal method whenimplemented with haplotypic/allelic data atmitochondrial (mt)DNA and nuclear-encodedmicrosatellite DNA loci. Estimates of N _e were between 2%–106% greater thantheir true values in 48 simulationsparameterized using different demographicscenarios, models of mutation, and samplesizes. Overestimation of N _e resultsfrom a bias in the approximation used by Waples(1989) to derive the relationship between theexpected temporal variance (F) and N _e when allele frequencies are very closeto 0 or 1. Our results show that one commonlyapplied solution to this problem, binning oflow-frequency alleles, results in a trade-offof accuracy and precision in some cases. Weshow that both chi-square and normalapproximations are appropriate for estimating95% confidence intervals of N _e andwe develop a power analysis based on thechi-square distribution to estimate samplesizes and allelic diversity required toevaluate specific hypotheses. For highlypolymorphic loci like mtDNA andmicrosatellites, the increased precisionafforded by the presence of rare allelesoutweighs the upward bias in temporal-methodestimates of N _e.     

Latitudinal variability of Drosophila melanogaster: Allozyme frequencies divergence between European and Afrotropical populations

Allelic frequencies at five polymorphic loci were determined in seven European and six Afrotropical populations of Drosophila melanogaster. African populations, which may be considered as ancestral for the species, showed a greater genetic diversity as measured by the number of alleles found. Within each geographic group (Europe or tropical Africa) genetic distances between local populations were very small (D=0.027). By contrast, the average distance between European and African populations (D=0.389) was more than 12 times bigger. It was previously known that various morphological or physiological differences, which probably reflect genetic adaptations to different environments, exist between these temperate and tropical populations. Data presented here suggest that the divergence in allozyme frequencies also reflects some selective mechanisms.     

Genetic diversity of Cryptomeria japonica using co-dominant DNA markers based on sequenced-tagged sites

 We have investigated the genetic diversity of 11 natural populations of C. japonica using 13 polymorphic STS markers. The average unbiased heterozygosities (H _e ), the average number of alleles per locus (N _a ) and the proportion of polymorphic loci (Pl) were 0.281, 1.93 and 76.92%, respectively. Coefficients of linkage disequilibrium were calculated, and no significant deviation was found except in four combinations – which might have occurred by chance alone. The fixation index (F _IS ) for 3 loci showed statistically significant values at the 1% level. The genetic differentiation between populations was only 0.047, and there were no clear geographical tendencies in the allele frequencies or the heterozygosities among populations. Consequently, the results from STS-based co-dominant DNA marker analysis were very similar to those from a previous allozyme study. However, the resolution of the technique is greater than allozyme analysis because many loci with high heterozygosities can be evaluated, and it is very simple. Therefore, the STS-based marker approach is very useful and convenient for population genetics and genome mapping of C. japonica. Received: 18 July 1998 / Accepted: 13 August 1998     

Genetic Diversity of the Carrion and Jungle Crows as Evidenced by RAPD–PCR Analysis

RAPD–PCR analysis of the genetic diversity of the carrion crow (Corvus corone) and jungle crow (C. macrorhynchos) living in the continental parts of their species ranges and on some Russian and Japanese Far Eastern islands has been performed. Taxon-specific molecular markers have been found for each species. The genetic diversity of the carrion crow is considerably less than that of the jungle crow at the same genetic distance (P ₉₅ = 68.2%, D _N = 0.27 and P ₉₅ = 88.4%, D _N = 0.24, respectively). In both species, the genetic polymorphism of island samples is almost two times greater than that of continental samples (62 and 31.8%, respectively, for C. corone and 81.5 and 47.2%, respectively, for C. macrorhynchos). In addition, differences in genetic diversity between males and females (P ₉₅ = 55.1 and 72.1, respectively) has been found in the carrion crow but not in the jungle crow. The gene diversity of C. macrorhynchos is greater than that of C. corone: the mean numbers of alleles per locus are 2 and 1.81, effective numbers of alleles are 1.62 and 1.43, and the mean expected heterozygosities are 0.39 and 0.30, respectively. The phenograms and phylograms significantly segregate the clusters of the carrion and jungle crows. The clustering patterns of carrion crows corresponds to the intraspecies taxonomic and geographic differentiation: subspecies C. c. corone and C. c. orientalis living in the western and eastern parts of the species range, respectively, form different subclusters. The cluster of the jungle crow does not exhibit differentiation into subspecies C. m. mandshuricus and C. m. japonensis; molecular genetic differences between them are small.     

Allozyme comparison of three nemertean species of the genus Oerstedia (Nemertea: Monostilifera) from the Sea of Japan

Three species of hoplonemerteans, all very similar in external features (Oerstedia oculata, Oerstedia phoresiae, and Oerstedia zebra) were compared using 23 allozyme loci. The results of this study confirm the specific validity of O. phoresiae. At 20 of the 23 loci this species shares no common alleles with O. oculata (D = 2.718) and at 21 of the 23 loci O. phoresiae shares no common alleles with O. zebra (D = 2.730). Most likely O. zebra is a color variation of O. oculata, because these species are very similar in their allozyme markers (D = 0.000).     

Frequency of alleles conferring resistance to Bacillus thuringiensis maize in Louisiana populations of the southwestern corn borer

Transgenic maize [Zea mays L. (Poaceae)] expressing Bacillus thuringiensis proteins (Bt maize) has become the most important tool for managing stalk borers in maize in the USA. The current strategy for delaying the evolution of resistance in target insects for Bt maize is referred to as high dose/refuge strategy. A key requirement of the strategy is that initial resistance allele frequencies in field insect populations are low (e.g., <0.001). More than 200 iso‐line families of the southwestern corn borer, Diatraea grandiosella Dyar (Lepidoptera: Crambidae), a major target stalk borer pest of Bt maize, were developed from Louisiana populations and evaluated for Bt resistance using a modified F₂ screening method during 2005. No major resistance alleles were detected in these populations. The results showed that the expected Bt resistance allele frequency in the Louisiana populations was <0.0035 with 95% probability and a detection power of 83.9 ± 0.6%. The F₂ screen indicates that Bt resistance allele frequencies in D. grandiosella are low among the Louisiana populations and should meet the rare resistance allele requirement of the ‘high dose/refuge’ strategy.     

Analysis of Microsatellite DNA Polymorphisms in Rockfish Sebastes thompsoni and Application to Population Genetics Studies

Population differentiation and relationships among 6 natural rockfish populations collected from northern coastal seas around Japan were assayed using microsatellite DNA loci. Seven loci examined were polymorphic in all populations. The number of alleles per locus ranged from 6.7 to 9.3, and the average of observed and expected heterozygosity ranged from 0.63 to 0.68, and from 0.66 to 0.69, respectively. The observed genotype frequencies at each locus were almost in agreement with Hardy-Weinberg expectations with two exceptions (P < .05). The allele frequencies of 16 population pairs were significantly different (P < .05). Genetic distance (D _A ) between 6 populations ranged from 0.03 to 0.08. According to a neighbor-joining tree generated from the D _A values, the 6 populations fell into 3 clusters. These clusters were correlated with the geographical positions of each population; larval dispersions due to water current were also found to have an effect on these results. Received May 2, 2000; accepted July 17, 2000.     

Calculations of population differentiation based on GST and D: forget GST but not all of statistics!

G _ST‐values and its relatives (F_ST) belong to the most used parameters to define genetic differences between populations. Originally, they were developed for allozymes with very low number of alleles. Using highly polymorphic microsatellite markers it was often puzzling that G_ST‐values were very low but statistically significant. In their papers, Jost (2008) and Hedrick (2005) explained that G_ST‐values do not show genetic differentiation, and Jost suggested calculating D‐values instead. Theoretical mathematical considerations are often difficult to follow; therefore, we chose an applied approach comparing two artificial populations with different number of alleles at equal frequencies and known genetic divergence. Our results show that even for more than one allele per population G_ST‐values do not calculate population differentiation correctly; in contrast, D‐values do reflect the genetic differentiation indicating that data based on G_ST‐values need to be re‐evaluated. In our approach, statistical evaluations remained similar. We provide information about the impact of different sample sizes on D‐values in relation to number of alleles and genetic divergence.     

Genetic polymorphism of Siberian spruce (Picea obovata Ledeb.) in Middle Siberia

Based on the analysis of 22 loci controlling allozyme variation of MDH, SKDH, 6-PGD, IDH, PEPCA, GOT, FDH, LAP, PGI, PGM, SOD, and GDH, the data on within-and among-population variation for nine cenopopulations of Siberian spruce (Picea obovata Ledeb.) located along the Yenisei mieridian, from 65°50′ NL to 52°14′NL, were obtained. It was demonstrated that 86.36% of the loci, tested in the species analyzed, were polymorphic. The mean number of alleles per locus was 2.91, and the observed and expected heterozygosity constituted 0.161 and 0.168, respectively. More than 97% of total variation occurred within the populations, while the proportion of the among-population variation constituted only 2.3% (F _st =0.0230). Genetic distance (D _N) between the populations examined varied from 0.0019 to 0.0115, averaging at 0.0051. It was shown that in the part of the Siberian spruce range examined there was no close association between the level of the genetic differentiation of the populations and the geographic distance between them. It seems likely, that this finding can be associated with the fact that Siberian spruce, growing on this territory, is the intrazonal species, i.e., it is not attached to a certain forest zone, and its distribution is mostly determined by local ecological conditions.     

Electrophoretic and heat-stability polymorphism at the phosphoglucomutase (Pgm) locus in natural populations of Drosophila melanogaster

Genetic polymorphism for electrophoretic and heat-sensitive alleles is known at the phosphoglucomutase (Pgm) locus in Drosophila melanogaster. Analysis of the distribution of electrophoretic and thermosensitive (ts) alleles was carried out in natural populations from Canada and West Africa and compared with already known data on Italian populations [Trippa, G., Loverre, A., and Catamo, A. (1976). Nature 260:42]. The data show the existence of five common alleles, Pgm ^1.00,tr, Pgm ^1,00,ts, Pgm ^0.70,ts, Pgm ^1.20,ts, and Pgm ^1.50,tr, and two rare alleles, Pgm ^0.55,ts and Pgm ^1.20,tr. The most frequent allele is always Pgm ^1.00,tr; the second most common allele is always of the ts type. The cumulated frequencies of ts alleles in the populations varies between 11 and 32%. The heat stability polymorphism is present in all populations examined and shows again the uniform geographic pattern that has been found for electrophoretic variation at this locus.This research was partially supported by an operating grant (to G.R.C.) from the Canadian National Science and Engineering Research Council (NSERC).     

Estimation and adjustment of microsatellite null alleles in nonequilibrium populations

Nonamplified (null) alleles are a common feature of microsatellite genotyping and can bias estimates of allele and genotype frequencies, thereby hindering population genetic analyses. The frequency of microsatellite null alleles in diploid populations can be estimated for populations that are in Hardy–Weinberg equilibrium. However, many microsatellite data sets are from nonequilibrium populations, often with known inbreeding coefficients (F) or fixation indices (F_IS or F_ST). Here, we propose a novel null allele estimator that can be used to estimate the null allele frequency and adjust visible allele frequencies in populations for which independent estimates of F, F_IS or F_ST are available. The algorithm is currently available as an Excel macro that can be downloaded at no cost from http://www.microchecker.hull.ac.uk/ and will be incorporated into the software micro ‐checker .     

Spatiotemporal allozyme divergence caused by aridity stress in a natural population of wild wheat, Triticum dicoccoides, at the Ammiad microsite, Israel

Spatiotemporal diversity at 35 allozyme loci was assayed over 6 years in 1,207 individuals of wild emmer wheat (Triticum dicoccoides)from a microgeographic microsite, Ammiad, north Israel. This analysis used new methods and two additional sample sets (1988 and 1993) and previous allozymic data (1984–1987). This microsite includes four major habitats (North-facing slope, Valley, Ridge, and Karst) that show topographic and ecological heterogeneity. Significant temporal and spatial variations in allele frequencies and levels of genetic diversity were detected in the four subpopulations. Significant associations were observed among allele frequencies and gene diversities at different loci, indicating that many allele frequencies change over time in the same or opposite directions. Multiple regression analysis showed that variation in soil-water content and rainfall distribution in the growing season significantly affected 10 allele frequencies, numbers of alleles at 8 loci, and gene diversity at 4 loci. Random genetic drift and hitchhiking models may not explain such locus-specific spatiotemporal divergence and strong allelic correlation or locus correlation as well as the functional importance of allozymes. Natural ecological selection, presumably through water stress, might be an important force adaptively directing spatiotemporal allozyme diversity and divergence in wild emmer wheat at the Ammiad microsite. Received: 3 July 2000 / Accepted: 1August 2000     

Intra‐ and interpopulation genetic differentiation and gene flow in a group of isolated populations of Bradybaena fruticum (O. F. Müller, 1774) in South Poland

Intra‐ and interpopulation variation was studied, by means of cellulose acetate allozyme electrophoresis, on 16 populations of helicoid snail Bradybaena fruticum (O. F. Müller, 1774) in South Poland. Four enzyme systems, coded by seven loci, were analysed. Calculated with Fisher's technique and Ohta's D‐statistics, four cases of linkage disequilibrium were detected, reflecting population subdivision. The mean number of alleles per locus equalled 2.16 and the mean expected heterozygosity was 0.287. Exact multipopulation and multilocus tests for Hardy–Weinberg equilibrium indicated a statistically significant homozygote excess in all the loci and all populations but three. Each population, however, was at Hardy–Weinberg equilibrium for most loci, though the values of f (F_IS) were usually high. Homozygote excess was ascribed partly to inbreeding and partly to Wahlund's effect (spatial subdivision of population; at least two cohorts of adult, reproducing snails), disrupting selection in this polymorphic species not excluded. F‐statistics showed relatively low values of θ (F_ST ; mean for all loci = 0.224) and those of Nm usually below 1 (mean 0.866). Pairwise values of either θ or Cavalli‐Sforza and Edwards arc distance were statistically significantly associated with geographic distances. Contrary to this, no geographic pattern of interpopulation differences was detected by correspondence analysis on allele frequencies, non‐linear multidimensional scaling, UPGMA clustering or neighbour‐joining trees constructed on θ and Cavalli‐Sforza and Edwards arc distance. Accordingly, some most distant populations were more similar to one another than the close ones.     

Regional Differentiation in Genetic Components for the American Beech, Fagus grandifolia Ehrh., in Relation to Geological History and Mode of Reproduction

Fagus grandifolia , were investigated throughout its geographical range, using allozyme polymorphisms. A total of 1,131 trees from 21 populations were examined for 32 alleles of 10 polymorphic and two monomorphic loci in eight enzyme systems. The mean expected heterozygosity was 0.186, which indicates a relatively high genetic diversity within the populations. The levels of population differentiation were high, as revealed by genetic parameters, i.e., G _ST =0.168 and F _ST =0.167. The results of principal component analysis on allele frequencies clearly revealed unique regional patterns of differentiation in genetic components among populations “with” and “without” vegetative regeneration by root suckers. The American beech populations consist of two genetically distinct clusters, one from the Gulf-coastal plain, eastern coastal plain, Piedmont Plateau and Ozark Plateau; and the other from the remaining northern glaciated territories. Populations from the Blue Ridge and Great Smoky Mountains turned out to belong to the latter cluster, which is also characterized by extensive regeneration via root suckers. The consequences of regional differentiation in genetic components are discussed in relation to the postglacial spread from refugia to the current geographic distributions and the mode of reproduction. Received 8 August 2000/ Accepted in revised form 29 May 2001