Enzyme variability in the Drosophila willistoni group. VI. Levels of polymorphism and the physiological function of enzymes

We have studied allelic variation at 28 loci coding for soluble enzymes in three sibling species of Drosophila. The average proportion of polymorphic loci per population is 58% in D. willistoni, 71% in D. equinoxialis, and 60% in D. tropicalis. An individual of any one of these three species is heterozygous at 18–22% of its genes. The correlation between the amount of polymorphism at a given locus and the equilibrium constant of the reaction catalyzed by the corresponding enzyme is not significantly different from zero. We have separated enzymes into those involved in glucose metabolism (group I) and all other enzymes (group II). The genes coding for group II enzymes are about twice as polymorphic as those coding for group I enzymes.This investigation was supported by NSF grants GB 20694 and GB 30895.     

THE DETECTION OF GAMETIC DISEQUILIBRIUM BETWEEN ALLOZYME LOCI IN NATURAL POPULATIONS OF DROSOPHILA

The capacity of the usual tests (chi-square and related tests) to detect gametic disequilibrium between allozyme loci in natural populations of Drosophila has been investigated. We analyzed a large collection of previously reported gametic samples from natural populations involving a variety of loosely linked allozyme loci located along the O chromosome of Drosophila subobscura and the second chromosome of D. melanogaster. It is found that the statistical power of the individual tests to detect the sample disequilibria between allozyme loci is remarkably low, being the average (over pairs of loci) of power estimates close to 0.20 in both species. Moreover, the average minimum disequilibrium (D‘_min) that would be required to reject (90% probability) the hypothesis of gametic equilibrium is higher than 0.50 given the observed degree of polymorphism and sample sizes used. This means that statistically significant associations between allozyme loci would rarely be detected by single-sample tests even when much disequilibrium is present in natural populations of Drosophila. However, an alternative approach based on the analysis of disquilibrium for large sets of gametic samples, combining probabilities from single independent tests and assessing significance by a bootstrap procedure, reveals that most of the locus pairs within segment I and II of the O chromosome of D. subobscura and left arm of the second chromosome of D. melanogaster present significant nonrandom associations. Within these chromosomal sections, the observed average absolute value of disquilibrium (D‘) between loci is around 0.25 (under the more conservative estimation). Also, a positive relationship between the magnitude of disequilibrium and linkage was detected. These findings suggest that weak or moderate values of disequilibrium between loosely linked allozyme loci are more frequent in natural populations of Drosophila than is currently believed.     

Population Genetic Structure of Endemic and Endangered Yellow Catfish, Horabagrus brachysoma, Using Allozyme Markers

The allozyme variation and population genetic structure of Horabagrus brachysoma in three natural populations from the southern part of the Western Ghats region, India, were investigated by polyacrylamide gel electrophoresis. Variations at 14 loci from 14 enzyme systems were analyzed. The allozyme analysis revealed a high level of genetic variation in this species, with an average of observed alleles per locus of 2.357 and observed heterozygosity of 0.178. The positive value of the fixation index (FIS=0.507) implied a significant deficiency of heterozygosity at the population level. The highly significant probability (P<0.0001) for the overall loci suggested that the three sample sets were not part of the same gene pool.     

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     

Allozyme polymorphisms of maize populations from southwestern China

Maize (Zea mays L.) is one of the most-important food crops in southwestern China. The diversity of maize populations from southwestern China has been evaluated on the basis of agronomic and morphological data, but not on marker data. Our objectives were to evaluate the allozyme polymorphism of these populations, and group the populations on the basis of allozyme data. We analyzed 27 maize populations from southwestern China and two populations [BS13(S)C2 and Lancaster] from the USA for genetic variation at 18 allozyme loci. We found a total of 69 alleles at 18 allozyme loci with an average of 3.8 alleles per locus. Compared with inbreds, hybrids, and populations from the U.S. Corn Belt, the 27 Chinese populations had a significantly higher (p<0.01) number of allozyme alleles per locus. Maize populations from southwestern China have accumulated abundant genetic diversity, and might be valuable germplasm for broadening the genetic base of U.S. Corn Belt breeding germplasm. The analyses of allele-frequency distributions and the expected heterozygosity also reflected the differences between the Chinese and the U.S. germplasm. The Chinese populations might be valuable germplasm for complementing U.S. Corn Belt breeding germplasm. The analysis of gene diversity showed that 77% of the allozyme variation resided within populations and 23% between populations. This result suggested that breeders should identify one or a few Chinese populations with the best agronomic performance, and exploit the genetic variation within these selected populations. Cluster analysis classified the 29 populations into four main groups. Groupings based on allozyme data could be useful for classifying the populations into different heterotic groups and, consequently, exploiting them in hybrid breeding. Received: 12 October 2000 / Accepted: 13 March 2001     

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.     

New polymorphic microsatellite loci in two fish species: bluefin killifish (Lucania goodei) and yellow bullhead (Ameiurus natalis)

We identified four new polymorphic microsatellite loci in bluefin killifish (Lucania goodei) and five loci in yellow bullheads (Ameiurus natalis). We screened 400 killifish from 20 populations and 180 bullheads from nine populations, finding a high degree of polymorphism (nine to 54 alleles per locus; average expected heterozygosity 0.678–0.976). We found no evidence for linkage disequilibrium. Three of the loci found in bluefin killifish show heterozygote deficiency; the other loci do not deviate from Hardy–Weinberg expectations.     

Allozyme variation of Cyclobalanopsis championii (Fagaceae), a narrowly distributed species in southern Taiwan

Allozyme genetic variability in five natural populations of Cyclobalanopsis championii (Fagaceae) in Taiwan was investigated using 12 loci from 9 enzyme systems. The average values of parameters describing within-population variation, expected heterozygosity (He = 0.151), the percentage of polymorphic loci per individual (P = 50%), the average number of alleles per locus (A = 1.7), effective number of alleles per locus (Ae = 1.25), and the average number of alleles per polymorphic loci (AP = 2.2) are comparable to those of other long-lived woody plants. The overall fixation index (Fis = 0.208) indicates a significant deficiency of heterozygotes at the population level. Allelic frequency deviation from Hardy-Weinberg equilibrium was found for different loci in different populations. An exact test for population differentiation using the Tools for Population Genetic Analyses program also indicates that allelic frequencies among populations are significantly different (P < .001). Among-population variation, Gst, accounted for 9.2% of the total heterozygosity. The population at Shouchia and the southernmost population Nanjenshan had higher inbreeding coefficients (0.177 and 0.153, respectively) than did the northern populations. Genetic drift is supported by the observations of the variance components of linkage disequilibrium and a large proportion of loci in Nanjenshan and Shouchia that show pairwise locus disequilibrium. We believe continuous genetic drift in the southern populations will increase genetic divergence among populations of C. championii in Taiwan. Significant correlation was found between elevation and expected heterozygosity. We therefore inferred that temperature is the most important ecological factor to influence the genetic diversity of C. championii.     

A microsatellite-based genetic linkage map for channel catfish, Ictalurus punctatus

Microsatellite loci were identified in channel catfish gene sequences or random clones from a small insert genomic DNA library. Outbred populations of channel catfish contained an average of eight alleles per locus and an average heterozygosity of 0.70. A genetic linkage map of the channel catfish genome (N = 29) was constructed from two reference families. A total of 293 microsatellite loci were polymorphic in one or both families, with an average of 171 informative meioses per locus. Nineteen type I loci, 243 type II loci, and one EST were placed in 32 multipoint linkage groups covering 1958 cM. Nine more type II loci were contained in three two-point linkage groups covering 24.5 cM. Twenty-two type II loci remained unlinked. Multipoint linkage groups ranged in size from 11.9 to 110.5 cM with an average intermarker distance of 8.7 cM. Seven microsatellite loci were closely linked with the sex-determining locus. The microsatellite loci and genetic linkage map will increase the efficiency of selective breeding programs for channel catfish.     

Patterns and levels of genetic differentiation in North American populations of the Alaskan wheatgrass complex

Levels and distribution of genetic variation were assessed using six allozymes in 27 populations of Alaskan wheatgrass (Elymus alaskanus) from different locations in Canada, USA, Greenland and Russia to obtain information on the genetic structure of these populations. The enzyme systems were ACO, DIA, GPI, MDH, PGM and SKD. Allozyme variation at the species level was high, with 64.3% (Ps) of the loci being polymorphic, an average number of alleles per locus of 1.9 (As), and an average genetic diversity of 0.17 (Hes). Differentiation was found in the populations studied, with the following findings: (1) statistically significant differences were found in allele frequencies among populations for every polymorphic locus (P < 0.001); (2) 63% of the total allozyme variation at polymorphic loci was partitioned among populations (GST = 0.63); (3) relatively low mean genetic distances between the populations were obtained (mean D = 0.029); (4) the genetic structure of Russian populations are clearly distinct from the other populations, the cluster and principal component analyses revealed the same genetic patterns of relationships among populations. This study also indicates that E. alaskanus contains different levels of allozyme variation in its populations. Furthermore, some banding patterns at the loci Aco-1, Aco-2, Gpi-2, Mdh-1, Skd-1, Skd-2 can be used as markers to identify individual populations.     

Allozyme differentiation of populations of the dogwhelk Nucella lapillus, (L.): the relative effects of geographic distance and variation in chromosome number

Geographic patterns of genie differentiation were compared with differentiation between karyotypes in the intertidal snail Nucella lapillus. Samples from 24 sites covering the species range in Europe and North America were analysed for allozyme variation at 16 soluble enzyme loci. Two homokaryotypes have been identified with diploid numbers 2n = 26 and 2n= 36 (variation is Robertsonian and hybrids have intermediate chromosome numbers) and samples were classified (on the basis of published data) according to karyotype. Group 1 consisted of samples from three English Channel populations of higher chromosome number (on average 2n > 32) and Group 2 consisted of the remaining 21 samples (presumed to be 2n= 26). Karyotype variation accounts for roughly the same amount of the absolute allozyme variance as geographic variation (46.3 °, and 53.7°, respectively). Yet the patterns of differentiation seen between karyotypes and with geographic separation are very different. In samples classified as 2n= 26 (Group 2), while there is a significant amount of heterogeneity (F_ST per locus averaged 0.128 for 10 polymorphic loci), allozyme variation occurs independently at different loci so mean genetic identity (Nei) is high: 0.972. There is only a slight decline in genetic identity with distance (genetic identity averaged 0.965 for amphi-atlantic comparisons) indicating that passive transport of juveniles or adults may contribute significantly to gene flow. Conversely, allozyme variation between karyotypes was concordant. High chromosome number populations possessed a suite of alleles at four allozyme loci (Esl-3, Lap-2, Mdh-1 and Pep-2) which were absent or rare in Group 2 samples resulting in high F_ST values for these loci (from 0.294 to 0.472) when karyotypic classes were combined. Consequently the mean genetic identity between these Robertsonian races is low, 0.856, and falls within the range more usually associated with congeneric comparisons than with con-specific comparisons. The mechanisms maintaining this genie difference are unclear. However the distribution of the karyotypes and physiological and morphological differences (in shell shape) between them strongly suggest that karyotypic variation in Nucella is adaptive.     

Isolation and characterization of polymorphic microsatellites in Iris ensata (Iridaceae)

• Premise of the study: Microsatellite primers were developed in Iris ensata (Iridaceae) to provide polymorphic markers for further studies into population genetics. • Methods and Results: Thirteen polymorphic microsatellite loci were isolated from I. ensata. These loci were successfully amplified in two natural populations of I. ensata from eastern China (Longwangshan, Zhejiang Province) and northeastern China (Jinchuan, Jilin Province). There was no significant linkage disequilibrium found for any pair of loci. These loci contained between two and 12 alleles per locus across all 48 individuals of I. ensata. The number of alleles per locus varied from two to 10 at the population level and the observed and expected heterozygosities ranged from 0.167 to 0.958 and from 0.284 to 0.853, respectively. • Conclusions: These loci showed high levels of polymorphism and could be used to study the population genetic structure, genetic relationships, and phylogeography of I. ensata.     

Isolation and characterization of microsatellite loci in the beaver (Castor canadensis)

We have isolated and characterized 10 microsatellite loci in the beaver (Castor canadensis). Sixty individuals from southern and central Illinois were screened at each locus. All loci exhibited moderate levels of polymorphism, ranging from five to 13 alleles per locus with average heterozygosity ranging from 0.317 to 0.867. Locus Cca5 deviated significantly from HWE (P < 0.001). The locus pair Cca4/Cca5 was shown to be in linkage disequilibrium in southern Illinois, but not in the central Illinois population. The remaining eight loci will be useful in investigations of mating and kinship patterns in beaver populations in Illinois.     

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 30 new microsatellite markers,developed from enriched genomic DNA library of zoysiagrass Zoysia japonica Steud.

The present study reports the development of 30 polymorphic microsatellite markers for zoysiagrass Zoysia japonica Steud. The 30 markers produced a total of 125 alleles with an average of 4.2 alleles per locus. Values for observed and expected heterozygosities ranged from 0.10 to 0.95 and from 0.15 to 0.81, respectively. At significance threshold (P < 0.05), 11 loci deviated from Hardy–Weinberg equilibrium, whereas significant linkage disequilibrium values were observed between 16 pairs of loci. These markers may provide information needed to select genetically diverse parents for developing breeding and mapping populations of zoysiagrass.     

广西石灰岩地区蜈蚣蕨居群的遗传多样性研究

采用等位酶分析方法 ,研究了广西石灰岩地区蜈蚣蕨居群的遗传多样性 ,分析了其空间变化趋势。检测了 8个酶系统 ,1 5个酶位点。分析结果表明 :广西石灰岩地区蜈蚣蕨居群遗传多样性程度较高 ,每个位点的等位基因平均数为 1 .6 7,多态位点为 5 7.78% ,平均期望杂合度为 0 .2 4 9。蜈蚣蕨居群的遗传组成在居群间有一定的差异 ,但差异的程度并不与空间距离成正比     

EFFECTS OF POPULATION BOTTLENECKS ON GENETIC DIVERSITY AS MEASURED BY ALLOZYME ELECTROPHORESIS

Low levels of allozyme heterozygosity in populations are often attributed to previous population bottlenecks; however, few experiments have examined the relationship between heterozygosity and bottlenecks under natural conditions. The composition and number of founders of 55 experimental populations of the eastern mosquitofish (Gambusia holbrooki), maintained under simulated field conditions, were manipulated to examine the effects of bottlenecks on three components of allozyme diversity. Correlations between observed and expected values of allozyme heterozygosity, proportions of polymorphic loci, and numbers of alleles per locus were 0.423, 0.602, and 0.772, respectively. The numbers of polymorphic loci and of alleles per locus were more sensitive indicators of differences in genetic diversity between the pre-bottleneck and post-bottleneck populations than was multiple-locus heterozygosity. In many populations, single- and multiple-locus heterozygosity actually increased as a result of the founder event. The weak relationship between a population's heterozygosity and the number and composition of its founders resulted from an increase in the variance of heterozygosity due to drift of allele frequencies. There was little evidence that selection influenced the loss of allozyme variation. When it is not possible to estimate heterozygosity at a large number of polymorphic loci, allozyme surveys attempting to detect founder events and other types of bottlenecks should focus on levels of locus polymorphism and allelic diversity rather than on heterozygosity.     

Allozyme variation in cork oak (Quercus suber L.): the role of phylogeography and genetic introgression by other Mediterranean oak species and human activities

 Genetic variation in the cork oak (Quercus suber L.) was investigated using 11 loci from seven enzyme systems in 40 populations sampled over the entire distribution of this species in the western Mediterranean Basin. Mean heterozygosity values over the polymorphic loci (Ho=0.283), the percentage of polymorphic populations (M=0.76), and the total genetic diversity (Ht=0.31) from which 11% was accounted for among-population variation, are among the highest recorded in oak species. In contrast to previous results in holm oak (Q. ilex L.), another evergreen species in the same area, cork oak possessed a smaller allele pool and a lower average number of alleles per locus and per population (A=2.0). More particularly, very few low-frequency alleles were observed in cork oak except for eight populations in which allozyme polymorphism at locus Pgi 1, diagnostic between both species, indicates that these low-frequency alleles are introgressed from holm oak. On the basis of the genetic distance estimated from allozyme frequencies, 32 of the 40 cork oak populations studied were classified into two very distinct sets which also corresponded to distinct geographic areas. One set gathered together the 18 populations from the Iberian peninsula and two adjacent areas in France, i.e. the centre of origin of cork oak, according to paleobotanical data. This set was characterized by a larger allele pool, a higher within-population genetic diversity and a lower differentiation between populations than was observed in the other set, which comprised the populations from North Africa, Sicily, Sardinia, Corsica, continental Italy and the region of Provence (southeastern France). In these more southern and eastern disjunct areas, cork oak migration from Iberia may have occurred at different periods since the end of the Tertiary. The possible effect of human activity on cork oak genetic structure, i.e. the selection of good-quality cork, acorn over-use for animal food, and even human nutrition, is discussed. Received: 3 March 1998 / Accepted: 19 March 1998     

Cloning and characterization of novel microsatellite DNA markers for the grass rockfish,Sebastes rastrelliger,and cross‐species amplification in 10 related Sebastes spp

Here we report development and characterization of seven polymorphic loci derived from grass rockfish (Sebastes rastrelliger) genomic DNA phagemid libraries enriched for microsatellite motifs. Within grass rockfish, average allelic diversity was 11.3 alleles per locus and average heterozygosity was 0.73. The seven loci also were surveyed in 10 related species of Sebastes, where allelic diversity ranged from highly polymorphic to monomorphic. Deviations from Hardy–Weinberg were nonsignificant in all but one species/locus combination suggesting low occurrence of null alleles. Significant linkage disequilibrium was detected among three loci, but these events were limited to a single species in each case.     

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。