Measures of gene flow in the Columbian ground squirrel

From analyses of published data and a review of the literature, I studied indirect and direct measures of gene flow among populations of Columbian ground squirrels, Spermophilus columbianus. New analyses were used to examine an allozyme data set (seven polymorphic loci) that had been collected by Zammuto and Millar (1985a) from six populations of ground squirrels that were spread over 183 km. G-tests indicated significant variation in allele frequencies among populations, but F-statistics revealed relatively little population differentiation (average F _ST=0.026). F _ST values were used to estimate rates of gene flow indirectly and indicated fairly high rates of gene flow (average N _e m=13.5). Recorded dispersal distances of individual ground squirrels were fairly short (most<4 km, maximum recorded distance was 8.5 km), and the minimum distance between populations used to create the allozyme data set was about 25 km. Thus, direct dispersal among the populations in the allozyme data set was highly unlikely. Small genetically effective populations may have experienced high rates of migration over short distances (about 43% of adults in local populations were immigrants), however, resulting in homogeneous allele frequencies over the geographic range. This explanation provides an alternative to invoking gene flow in the recent past to explain discrepancies between dispersal distances in the field and homogenization of allele frequencies over large ranges, Mammalian species that have virtually complete dispersal of subadult males from the natal area might be expected to exhibit relatively high rates of gene flow, regardless of actual dispersal distances. Genetically effective populations may be much smaller than more extensive ecological populations and experience higher rates of gene flow.     

Multilocus structure in Pinus contorta Dougl.

We studied isozyme variation at 21 loci in 66 populations from three subspecies of Pinus contorta Dougl.; 35 in spp. latifolia, 20 in spp contorta and 11 in spp. murrayana. The objectives were to assess gametic disequilibria and multilocus structure. There was considerable differentiation of allele frequencies at 19 polymorphic loci across the 66 populations and within the subspecies. Allele frequencies at many loci correlated with geographic variables. Genetic variability varied considerably among populations within subspecies but the subspecies means were similar. The mean number of polymorphic loci and the mean heterozygosity over 19 polymorphic loci were, respectively, 13 and 0.194 in latifolia, 12 and 0.196 in murrayana, and 12 and 0.180 in contorta. The mean heterozygosity correlated with longitude and altitude across the 66 populations and with latitude in latifolia. Gametic disequilibria were evident in 40 populations; 29 in latifolia, eight in murrayana and three in contorta. Gametic disequilibria correlated with latitude across the 66 populations and with longitude in latifolia. The single-locus F _ST averaged 0.0339 in latifolia, 0.0567 in murrayana, and 0.0764 in contorta. The multilocus F _STM was 0.1227 in latifolia, 0.2926 in murrayana, and 0.3328 in contorta. Multilocus Wahlund and founder effects, migration patterns, and natural selection, probably played significant roles in generating and maintaining the multilocus genetic structure in P. contorta in general and the subspecies latifolia in particular.     

珊瑚菜居群遗传多样性的SRAP分析

利用SRAP对伞形科单种属珊瑚菜7个野生居群和1个栽培居群进行了研究。结果表明:共筛选出8个引物组合,在珊瑚菜8个居群中共扩增出168条条带,其中多态性条带为118条,多态性比率为70.23%;平均每对引物扩增的多态性条带为14.75。各居群之间珊瑚菜遗传相似性系数范围为0.8306~0.9836,遗传距离范围为0.0165~0.1856。聚类分析表明,以相似性系数大于0.8并结合地理分布来看,所研究的野生珊瑚菜居群可以大体分为3类,辽宁大连的野生居群为一类,山东威海—山东青岛的居群为一类,而山东日照—广州深圳之间的为一类。     

Genetic structure of natural populations of the red-spotted newt,Notophthalmus viridescens

Genetic variation is described at 15 loci in 2 neotenic and 12 nonneotenic populations of red-spotted newts. Though high levels of genetic similarity (I=0.990) were found among all populations, allele frequencies at six of the eight most polymorphic loci show significant heterogeneity across populations. Change in allele frequencies at two of these loci (Pep-2 and Ldh-1) is significantly correlated with latitude. Interspecific homologies are established for newt peptidases based on substrate specificities and lactate dehydrogenases based on tissue distribution, thermal stability, and kinetic properties. Nonneotenic populations are highly variable (H=0.157) and neotenic populations are only slightly, but significantly, less variable (H=0.120). The high levels of heterozygosity detected in nonneotenic populations may result from large effective population size and/or environmental heterogeneity. The unexpectedly high heterozygosity values obtained for the neotenic populations may indicate adult dispersal or the presence of some previously undetected red efts at these localities. In any case, a major change in life history has apparently had little effect on the genetic structure of these populations.This research was supported by grants from the Blakeslee Fund of Smith College.     

Genetic diversity at electrophoretic loci in the house fly,Musca domestica L.

Vertical polyacrylamide gel electrophoresis was used to separate enzyme proteins at 73 putative loci in natural house fly populations sampled in central Iowa. Thirty-nine of the loci were polymorphic (53%). The mean effective number of alleles per polymorphic locus was 1.93 and 1.47 alleles among 68 scored loci. Observed and expected heterozygosities at 34 house fly loci were 0.1628 and 0.1834, respectively. No statistically significant differentiation was detected among nine central Iowa fly populations in 1989 or among nine Iowa and three Minnesota populations in 1990. Journal Paper No. J-14125 of the Iowa Agriculture and Home Economics Experiment Station, Ames. Project No. 2949.     

Genetic diversity of common carp from two largest Chinese lakes and the Yangtze River revealed by microsatellite markers

Six polymorphic microsatellites (eight loci) were used to study the genetic diversity and population structure of common carp from Dongting Lake (DTC), Poyang Lake (PYC), and the Yangtze River (YZC) in China. The gene diversity was high among populations with values close to 1. The number of alleles per locus ranged from 2 to 11, and the average number of alleles among 3 populations ranged from 6.5 to 7.9. The mean observed (H _O) and expected (H _E) heterozygosity ranged from 0.4888 to 0.5162 and from 0.7679 to 0.7708, respectively. Significant deviations from Hardy–Weinberg Equilibrium expectation were found at majority of the loci and in all three populations in which heterozygote deficits were apparent. The analysis of molecular variance (AMOVA) indicated that the percent of variance among populations and within populations were 3.03 and 96.97, respectively. The Fst values between populations indicated that there were significant genetic differentiations for the common carp populations from the Yangtze River and two largest Chinese freshwater lakes. The factors that may result in genetic divergence and significant reduction of the observed heterozygosity were discussed.     

Allozyme genotype-environment relationships in natural populations of Drosophila buzzatii

Allozyme frequency data from natural populations of Drosophila buzzatii were analyzed for genotype-environment relationships. Allele frequency and heterozygosity at six loci polymorphic throughout eastern Australia and a number of environmental factors (both means and variabilities) were examined by a variety of multivariate techniques. Significant genotype-environment associations were found for five of the six loci, and after correcting for geographic location significant associations remained for Est-2 and Adh-1 gene frequencies and heterozygosities and for Pgm gene frequencies. The results are discussed in relation to selection and gene flow and provide the basis for laboratory studies to disentangle confounded effects of (1) environmental means and environmental variabilities and (2) allele frequency and heterozygosity, and thus to further test for and determine the nature of any natural selection at particular allozyme loci.This work was supported by a grant from the Australian Research Grants Committee to J. S. F. B.     

Isozyme variation in Desmodium nudiflorum

Five populations of Desmodium nudiflorum were assayed for genetic variability in eight enzyme systems encoding thirteen genetic loci. The proportion of polymorphic loci for the species as a whole is 46.2% while the proportion of polymorphic loci within populations averages 13.5%. Average individual heterozygosity is 2.3%. D. nudiflorum shows significant differences in gene frequencies between populations, and genotypic frequencies within populations conform to Hardy-Weinberg expectations.     

Isolation and characterization of polymorphic nuclear microsatellite loci in <Emphasis Type="Italic">Taxus baccata</Emphasis> L.

Seven polymorphic nuclear microsatellite markers for Taxus baccata L. (English yew) were developed using an enriched-library method. An additional polymorphic SSR was obtained by testing eight primer pairs from the congeneric species Taxus sumatrana. Mendelian inheritance for the seven Taxus baccata SSRs was proved by genotyping 17 individuals and 124 megagametophytes (conifer seed haploid tissue). A total of 96 individuals from 5 different populations (10–26 samples per population) were used to estimate genetic diversity parameters. High levels of genetic diversity, with values ranging from 0.533 to 0.929 (6–28 alleles per SSR) were found. No linkage disequilibrium between pairs of loci was detected. All loci but one showed significant departures from Hardy–Weinberg equilibrium. Excess of homozygosity was probably due to high inbreeding in English yew populations, an outcome of low effective population size and/or fragmented distribution. Highly polymorphic SSRs will be used to conduct population genetic studies at different geographical scales and to monitor gene flow.     

Genetic Variation and Population Structure of Oriental Migratory Locust, Locusta migratoria manilensis, in China by Allozyme, SSRP-PCR, and AFLP Markers

Allozyme analysis, microsatellite primer PCR (SSRP-PCR), and amplified fragment length polymorphism (AFLP) techniques were used to assess genetic diversity and population structure of the Chinese oriental migratory locust, Locusta migratoria manilensis. A total of 299 PCR markers (67 SSRPs and 232 AFLPs) were detected in eight populations, of which 98.7% were polymorphic markers. The proportion of polymorphic loci (95.5–98.8%) by SSRP+AFLP markers indicated no significant differences between populations, and all populations exhibited a similar level of variability; results of the allozyme analysis demonstrated that 19 loci gave rise to a lower level of polymorphism (55.6–66.7%). The genetic distances between the populations were relatively low. Shannon’s index and Nei’s gene diversity showed low differentiation among the populations. Allozyme analysis, however, reflected greater similarity and smaller differentiation between the populations than those shown by SSRP and AFLP markers. Neighbor-joining dendrograms derived from both the allozyme and SSRP+AFLP markers showed that the genetic distances among Chinese oriental migratory locust populations were not greatly influenced by geographic distance and breeding habitats.     

Genetic Variability of Iris setosa

Genetic variability of Iris setosa Pall. ex Link. was studied by the RAPD method. Plants from three different habitats were compared by 135 loci revealed with eight arbitrary primers. The three plant accessions all exhibited a high level of polymorphism, and each was characterized by different frequencies of polymorphic fragments, which probably reflected the geographic isolation of the analyzed populations. The average level of polymorphism detected was 35%.     

Phylogenetic signals from point mutations and polymorphic Alu

Allelic frequency data derived from five polymorphic Alu insertion loci and five point mutation polymorphic loci were compared to determine their ability to infer phylogenetic relationships among human populations. While point mutation polymorphisms inferred a monophyletic Caucasian clade that is corroborated by other studies, these data failed to support the generally accepted monophyly of Orientals with native Americans. In addition, there is less statistical bootstrap support for the maximum-likelihood tree derived from the point mutation polymorphisms as compared to those generated from either the Alu insertion data or the combined Alu insertion+point mutation data. The Alu data and the combined Alu insertion+point mutation data inferred a monophyletic relationship among the Oriental and native American populations. The Alu insertion data and the combined Alu insertion+point mutation data also displayed two separate, well defined, tight clusters of the Caucasian and the Oriental+native American populations which was not inferred from the point mutation data. These findings indicate greater phylogenetic information contained in Alu insertion frequencies than in allelic frequencies derived from point-mutations. This revised version was published online in July 2006 with corrections to the Cover Date.     

Allozyme Variation in a Threatened Freshwater Fish, Spotted Murrel (Channa punctatus) in a South Indian River System

Samples of the spotted murrel (Channa punctatus) were collected from three rivers of Tamil Nadu and Kerala. The allozyme variation of C. punctatus was investigated by polyacrylamide gel electrophoresis. Eighteen enzymes were detected, but only 10 (EST, PGM, G3PDH, G6PDH, SOD, GPI, ODH, GDH, XDH, and CK) showed consistent phenotypic variations. Allele frequencies were estimated at the 18 polymorphic loci representing 10 enzymes. Two rare alleles, EST-4*C and G6PDH-2*C, were noted in the Tamirabarani and Kallada populations but were absent in the Siruvani population. The allele frequencies of the Tamirabarani and Kallada populations were similar, except for a few loci. Among the three populations, the maximum genetic distance (0.026) and FST (0.203) were found between the geographically distant Siruvani and Kallada populations. Overall the study showed that among the three populations, the Tamirabarani and Kallada have similar genetic structures.     

基于ISSR的豚草和三裂叶豚草遗传多样性研究

[目的]研究不同地理种群的豚草和三裂叶豚草的遗传多样性水平和遗传结构。[方法]应用筛选的13条ISSR引物对8个豚草居群和7个三裂叶豚草居群共240个样品进行分子标记。[结果]8个豚草居群128个样品,共扩增出304条带,多态性位点比率为98.68%;Shannon''s信息指数为0.6716,Nei''s基因多样性指数为0.4788。7个三裂叶豚草居群112个样品,共扩增出266条带,多态性位点比率为95.86%;Shannon''s信息指数为0.6593,Nei''s基因多样性指数为0.4670。豚草和三裂叶豚草各居群遗传距离较近。[结论]豚草和三裂叶豚草在居群间具有一定的遗传稳定性;居群内具有丰富的遗传多样性。豚草和三裂叶豚草遗传变异主要来源于居群内部。豚草各居群遗传距离和地理距离有显著相关性,三裂叶豚草各居群遗传距离和地理距离无显著相关性。     

Genetic structure of Halotydeus destructor and Penthaleus major populations in Victoria (Acari: Penthaleidae)

The redlegged earth mite (Halotydeus destructor) and the blue oat mite (Penthaleus major) are major pests of pastures and crops in southern Australia. Reproductive modes, migration rates and levels of differentiation between populations were investigated using allozyme electrophoresis. Collections were made throughout Victoria and a sample was also obtained from Western Australia. Three enzyme loci were polymorphic in H. destructor (Mdh-1, Mdh-2 and Idh). Genotype frequencies of these loci did not differ between phenotypic males and females, providing no evidence for haplodiploidy. Allele frequencies were in Hardy-Weinberg equilibrium, indicating that H. destructor is diploid and sexual. This was confirmed via crosses between males and females. Allele frequencies differed between Victorian sites, although F statistics indicated little differentiation over all loci. A sample from Western Australia did not differ in allele frequencies from the Victorian sites. Four polymorphic loci were found in P. major (Mdh-1, Mdh-2, Idh and Gpi). Only a few multilocus genotypes occurred in a sample, indicating that P. major is parthenogenic. No male P. major were found in this study. A number of colour morphs were also identified and a genetic association between genital plate colour and clonal type was found in one population of P. major. Two different body colour morphs were associated with different clonal types.     

Isolation and characterization of microsatellite loci in the Amami rabbit (Pentalagus furnessi)

We report on the isolation and characterization of eight polymorphic and five monomorphic microsatellites in the Amami rabbit (Pentalagus furnessi). Microsatellite polymorphism was determined using 25 individuals. There were 2–11 alleles for each polymorphic locus with heterozygosity ranging between 0.08 and 0.76. Linkage disequilibrium was not suggested between any pairs among the eight polymorphic loci. We suggest that these primers be used in future studies to monitor population size, determine dispersal patterns, and genetic diversity within and between populations of this and related species.     

Genetic diversity and morphological differentiation in Liatris helleri (Asteraceae), a threatened plant species

Liatris helleri (Asteraceae) is an insect-pollinated herbaceous perennial endemic to several high-elevation sites in the Blue Ridge Mountains of North Carolina. Allozymes were used to describe the genetic diversity and population structure in nine populations of this rare, federally listed species. Differences in leaf morphology were also examined for greenhouse-grown plants representing several populations. The proportion of the total genetic diversity found among populations, as indicated by the allozyme data, was 16%. Higher levels of population differentiation were found for differences in leaf shape; population of origin accounted for 37% of the variation in maximum leaf width, while families within populations accounted for 7%. In contrast to many endemic species, L. helleri maintains fairly high levels of genetic diversity. For the species, the percent polymorphic loci was 87.5, the average number of alleles at variable loci was 3.00 and the gene diversity was 0.276. Mean population values were percent polymorphic loci =58.4, mean number of alleles per polymorphic locus =2.59 and gene diversity =0.219. The estimated gene flow was low (Nm=0.85–1.32) and a relatively high correlation (r=0.55; p<0.005) was found between linear geographic and genetic distance. This suggests that the populations are partially isolated by distance, despite the limited range (<60 km) of the species. We recommend that population distinetiveness be maintained in restoration efforts.     

Biochemical genetics of Fundulus heteroclitus (L.). I. Temporal and spatial variation in gene frequencies of Ldh-B,Mdh-A,Gpi-B,and Pgm-A

Natural populations of Fundulus heteroclitus show extensive spatial variation in gene frequencies at four unlinked polymorphic loci. Large clinal changes in gene frequencies were found for Ldh-B, Mdh-A, and Gpi-B, whereas the spatial variation for the Pgm-B locus was small. Since the geographical area over which these clines are found is characterized by a steep thermal gradient, the clines in gene frequency are correlated with a directional change in mean water temperature. Maximum gene diversity of these four loci was correlated with annual fluctuations in water temperature. Temporal stability of the allelic frequencies was established for a 2–4 year period.This work was supported by NSF Grants GB37548 and DEB 76-19877 and by a grant from the National Geographic Society. A. R. P. is an NIH trainee supported by a training grant (No. HD00139) to the Department of Biology.This is contribution No. 960 of the Department of Biology, Johns Hopkins University.     

Microsatellite Variation in Two Populations of Free-Ranging Yellow Baboons (Papio hamadryas cynocephalus)

We investigated genetic variation at six microsatellite (simple sequence repeat) loci in yellow baboons (Papio hamadryas cynocephalus) at two localities: the Tana River Primate Reserve in eastern Kenya and Mikumi National Park, central Tanzania. The six loci (D1S158, D2S144, D4S243, D5S1466, D16S508, and D17S804) were all originally cloned from and characterized in the human genome. These microsatellites are polymorphic in both baboon populations, with the average heterozygosity across loci equal to 0.731 in the Tana River sample and 0.787 in the Mikumi sample. The genetic differentiation between the two populations is substantial. Kolmogornov–Smirnov tests indicate that five of the six loci are significantly different in allele frequencies in the two populations. The mean F _ST across loci is 0.069, and Shriver's measure of genetic distance, which was developed for microsatellite loci (Shriver et al., 1995), is 0.255. This genetic distance is larger than corresponding distances among human populations residing in different continents. We conclude that (a) the arrays of alleles present at these six microsatellite loci in two geographically separated populations of yellow baboons are quite similar, but (b) the two populations exhibit significant differences in allele frequencies. This study illustrates the potential value of human microsatellite loci for analyses of population genetic structure in baboons and suggests that this approach will be useful in studies of other Old World monkeys.     

Genetic and clonal diversity in Korean populations ofVitex rotundifolia (Verbenaceae)

Vitex rotundifolia L.f. is a woody perennial and has sexual and asexual modes of reproduction. Allozyme study was conducted on 550 plants in 13 Korean populations. The levels of genetic variability and divergence within and among populations, respectively, are considerably lower and higher than the mean values for woody plants with similar life history tralts. Mean percentage of polymorphic loci (P _P), mean number of alleles per locus (A _P), and mean genetic diversity (He _P) within populations ofV. rotundifolia were: 16.7%, 1.21, and 0.047. On average, about 79% of the total variation inV. rotundifolia was common to all populations (meanG _ST=0.208). In addition, significant differences in allele frequencies among populations were found in all polymorphic loci examined (P<0.001). On the other hand, levels of genotypic diversity within and among populations were moderate. About 44% (18/41) of multilocus genotypes were “local genotypes” (genotypes occurring in only one population), whereas only one “widespread genotype” (genotypes occurring in more than 75% of the populations) were detected. The mean number of multilocus genotypes per population (G) and mean genotypic diversity index (D _G) were 8.4 and 0.74, respectively. Most common multilocus genotypes found in populations were homozygous for five polymorphic loci. The abundance of ramets of these genets is responsible for the low levels of expected heterozygosity within populations. The results indicate that clonal reproduction may act as an enhancer of genetic drift by reducing effective size of local populations ofV. rotundifolia.