Biochemical genetic variation among populations of the greenshell mussel, Perna canaliculus, from New Zealand: preliminary findings

Seven polymorphic and four monomorphic allozyme loci were assayed from nine wild populations and one cultured population of the endemic New Zealand greenshell mussel, Perna canaliculus. Genetic variation was examined to determine the extent of intra-population subdivision and inter-population variability. Five of seven polymorphic loci exhibited significant heterozygote deficiencies compared to Hardy-Weinberg equilibrium. Population F-statistics indicated that significant genetic heterogeneity exists among populations, indicating that there is insufficient gene flow between geographically isolated populations to create panmixia. The observed genetic heterogeneity among populations is best explained by an isolation-by-distance model of gene flow, which is modified by localized hydrographic conditions. These preliminary findings are discussed in the context of the one previous survey of population genetic variation in P. canaliculus and how this information relates to the gene flow of the greenshell mussel in New Zealand, which is often mediated by human transport from the main collection site of Kaitaia to aquaculture sites throughout the country.     

Genetic divergence and a hybrid zone between Baltic and North Sea Mytilus populations (Mytilidae: Mollusca)

Populations of the common mussel ( Mytilus edulis ) from the North Sea area (Skakerrak-Kattegat) and those from the Baltic Sea are almost diagnostically differentiated at five out of 22 studied allozyme loci; at a further seven loci, alleles predominant or common in one area are nearly absent in the other. Genetic distance was estimated at 0.28; this is similar to the distances of these populations to the Mediterranean mussel M. galloprovincialis. The three mussel types obviously represent equal evolutionary divergence from one another, and should also be taxonomically equally separated; a semispecies rank within a more comprehensive M. edulis complex or superspecies is suggested. The age of the Baltic mussel type ( 'M. trossulus' ), as an independent evolutionary lineage, is probably far greater than that of the post-glacial Baltic Sea.
Allele frequencies change gradually and in parallel when entering from the Kattegat through the Sound into the Baltic. Only a slight Wahlund effect at the strongly diverged Gpi and Pgm loci was found in intermediate populations, indicating that extensive hybridization of the two taxa takes place in the area. However, strong interlocus genotypic associations suggest that selection against hybrids is intense in later generations; the c. 100 km wide hybrid zone is narrow relative to the dispersal distance. The genotypic structure of the Lap locus does not conform with those of the other loci studied in the hybrid zone; it cannot be viewed merely as a neutral marker of the process of hybridization.     

Genetic variation in cultivars of diploid ryegrass,Lolium perenne andL. multiflorum,at five enzyme systems

Summary Samples of approximately 100 plants from each of 22 populations ofLolium perenne representing 15 cultivars, and from 13 populations ofLolium multiflorum representing six cultivars were scored for iso-zyme variants in five enzyme systems, PGI, GOT, ACP, PGM and 6-PGD. From the individual banding patterns a genetic interpretation of the variation was formulated and population studies of the resulting six polymorphic enzyme loci were performed. No strong indications of partial selfing was found since at four of the six loci,Pgi 2, Got 3, Pgm 1 andPgd 1, the genotypic proportions were in correspondence with the Hardy-Weinberg expectations. This indicated, further, that the genetical interpretations of the banding patterns might be correct. Deviations from Hardy-Weinberg proportions forAcp 1 andGot 2 indicated presumably selection working on the linkage group including these loci. Gametic phase disequilibrium was observed betweenPgi 2 andPgd 1 for populations of one cultivar. These results were discussed in relation to the variation expected within a cultivar.     

Inheritance and linkage relationships of isozyme loci in cucumber (Cucumis sativus L.)

Summary Genetic analyses were conducted among 18 provisionary isozyme loci in Cucumis sativus L. Fourteen loci demonstrated simple Mendelian inheritance while observed variation at four loci (Gpi2, Gr2, Pgm3, Skdh2) was determined not to have a predictable genetic basis. Joint segregation analyses among the 14 genetically predictable polymorphic loci resulted in the assignment of 12 loci to four linkage groups. Linkage groups contain the following loci: (1) Gr1, Pgm1, Idh, Pgd1; (2) Pep-pap, Mdh2, Mdh3, Gpi1; (3) Pep-la, Per4; (4) Pgd2, G2dh. Mpi2 and Mdh1 segregated independently. Recombination fractions for linked loci ranged between 0.051 (Pgm1-Idh) to 0.385 (Pep-la-Per4). Some practical applications of isozyme marker loci for cucumer improvement are discussed.     

Random amplified polymorphic DNA analysis of Anopheles nuneztovari (Diptera: Culicidae) from Western and northeastern Colombia

Random amplified polymorphic DNA (RAPD) markers were used to analyze 119 DNA samples of three Colombian Anopheles nuneztovari populations to study genetic variation and structure. Genetic diversity, estimated from heterozygosity, averaged 0.34. Genetic flow was greater between the two populations located in Western Colombia (F ST: 0.035; Nm: 6.8) but lower between these two and the northeastern population (F ST: 0.08; Nm: 2.8). According to molecular variance analysis, the genetic distance between populations was significant (phi ST 0.1131, P < 0.001). The variation among individuals within populations (phi ST 0.8869, P < 0.001)was also significant, suggesting a greater degree of population subdivision, not considered in this study. Both the parameters evaluated and the genetic flow suggest that Colombian An. nuneztovari populations are co-specific.     

A method for distinguishing consanguinity and population substructure using multilocus genotype data

We use the patterns of homozygosity at multiple loci to distinguish between excess homozygosity caused by consanguineous mating and that due to undetected population subdivision (the Wahlund effect). Clarification of the underlying causes of excess homozygosity is of practical importance in explaining the occurrence of recessive genetic disorders and in forensic match probability calculations. We calculated a likelihood surface for two parameters: C, the proportion of the population practicing consanguinity, and theta, the genetic correlation due population subdivision. To illustrate the method, we applied it to multilocus genotypic data of two U.K. Asian populations, one practicing a high frequency of cousin marriage, and another in which caste endogamy was suspected. The method was able to successfully distinguish the different patterns of relatedness. The method also returned accurate estimates of C and theta using simulated data sets. We show how our method can be extended to allow for degrees of inbreeding closer than cousin unions, including selfing. With closer inbreeding, the relatedness of recent ancestors beyond the parents becomes an issue.     

Genetic variation and differentiation of Abies alba Mill. populations from Ukrainian Carpathians

Using electrophoretic analysis of 11 enzyme systems, we studied the genetic structure and differentiation of eight natural populations of silver fir Abies alba Mill. in the Ukrainian Carpathians. Of 24 isozyme loci identified, 66.8% proved to be polymorphic. The mean numbers of alleles and genotypes per locus in the populations were respectively 3.1 and 4.5. Each A. alba tree was on average heterozygous at 15.9% of genes. In six populations, the genotypic distribution for all of the loci examined corresponded to Hardy-Weinberg proportions. The populations studied had low levels of subdivision (F(ST) = 0.018; GST = 0.019) and differentiation. Nei's genetic distances between the A. alba populations in the region ranged from 0.002 to 0.009, being on average 0.006.     

Allozyme polymorphisms within and among open-pollinated and adapted exotic populations of maize

Summary Twelve U.S. Corn Belt open-pollinated and five adapted exotic populations of maize (Zea mays L.) were assayed for allozyme (allele) variation at 13 enzyme marker loci. Extensive allozyme variability was observed in all populations studied. No locus was monomorphic over all populations. Each of the lociIdh2, Got1, Mdh2, Pgd1, andPgd2 expressed two allozymes over all populations,Adh1, Acp1, Prx1, andEst1 each had three allozymes present,Est4, Glu1, andEnp1 had five allozymes, andAcp4 had six allozymes present. Significant deviations of genotypic frequencies were detected from Hardy-Weinberg equilibrium frequencies and 94% of average Fixation Index values indicated heterozygote deficiencies, which suggested that nonrandom mating and/or natural selection favoring homozygotes were possible factors affecting the maintenance or loss of genetic variability marked by these enzyme loci. Genetic distance and cluster analyses indicated that the observed genetic variability at the 13 enzyme loci was closely related to Dent and Flint types of maize.     

Localization of the Po2 locus in the S, Phi, Hal, H, Po2, Pgd linkage group in pigs

The localization of the Po2 locus controlling a polymorphic serum postalbumin was studied in 41 families of the Czech Landrace breed. The haplotypes involving six closely linked loci (S, Phi, Hal, H, Po2, Pgd) were determined for each family member. The crossovers observed between the H, Po2 and Pgd loci indicated that Po2 is located between H and Pgd. The Po2 locus appears to be closer to H [theta = 0.54% (0.06%-1.92%)] than to Pgd [theta = 4.02% (1.67%-7.96%)]. A strong Ha-Po2S association (r = 0.96, P less than 0.001) and H-PO2 linkage disequilibrium (D = 0.2218, P less than 0.01, D/DMax = 0.98) were found.     

Population genetic analysis of the genes APOE, APOB(3'VNTR) and ACE in some black and Amerindian communities from Colombia

A population genetic study was carried out with the APOE, APOB and ACE loci in 17 Colombian human populations. Ten of them were Amerindian communities coming from the northeastern part of Colombia, Pacific region, Eastern Plains and Amazonia. Six were black populations from Providence Island, Caribbean and Pacific coasts. Finally, the Mestizo population of Bogota was studied as well. The APOE and ACE loci were in Hardy-Weinberg equilibrium, whereas the APOB locus was not studied in all populations. The genetic heterogeneity was substantially greater among the Amerindian populations (G(ST) = 0.059) than in the Afrocolombian populations (G(ST) = 0.009). Also the gene flow population pair estimates were so much higher among the Afrocolombian populations (Nm = 49.08 +/- 43.07) than among Amerindian populations (Nm = 9.66 +/- 18.04). Different phylogenetic and multivariant analyses showed that the Amerindian populations analyzed were clustered in three different arrays: one constituted by the Colombian northeastern and Pacific populations, the second one by the two Amazon populations (Coreguaje and Nukak) and the last one by the Yuco (the unique Caribbe-speaking population among those studied). The latter population was highly divergent from a genetic point of view from the remainder Amerindian populations studied. By using the Mantel test, the existence of a positive and significant correlation between the genetic and geographical distances found among Amerindian populations was demonstrated. This fact was not observed among the Afrocolombian populations. Nevertheless, an isolation-by-distance Slatkin analysis test did not show a significant clear structure of this special pattern among the Indian tribes studied.     

Patterns of differentiation and hybridization in North American wolflike canids, revealed by analysis of microsatellite loci

Genetic divergence and gene flow among closely related populations are difficult to measure because mutation rates of most nuclear loci are so low that new mutations have not had sufficient time to appear and become fixed. Microsatellite loci are repeat arrays of simple sequences that have high mutation rates and are abundant in the eukaryotic genome. Large population samples can be screened for variation by using the polymerase chain reaction and polyacrylamide gel electrophoresis to separate alleles. We analyzed 10 microsatellite loci to quantify genetic differentiation and hybridization in three species of North American wolflike canids. We expected to find a pattern of genetic differentiation by distance to exist among wolflike canid populations, because of the finite dispersal distances of individuals. Moreover, we predicted that, because wolflike canids are highly mobile, hybrid zones may be more extensive and show substantial changes in allele frequency, relative to nonhybridizing populations. We demonstrate that wolves and coyotes do not show a pattern of genetic differentiation by distance. Genetic subdivision in coyotes, as measured by theta and Gst, is not significantly different from zero, reflecting persistent gene flow among newly established populations. However, gray wolves show significant subdivision that may be either due to drift in past Ice Age refugia populations or a result of other causes. Finally, in areas where gray wolves and coyotes hybridize, allele frequencies of gray wolves are affected, but those of coyotes are not. Past hybridization between the two species in the south-central United States may account for the origin of the red wolf.      

Genetic diversity in populations of Dalbulus maidis (DeLong and Wolcott) (Hemiptera: Cicadellidae) from distant localities in Brazil assessed by RAPD-PCR markers

Populations of Dalbulus maidis (DeLong and Wolcott) from the northeastern and central-southern regions of Brazil differ morphologically, suggesting that they could be genetically isolated. Here we used the random amplified polymorphic DNA (RAPD)-polymerase chain reaction (PCR) technique to estimate genetic structuring of this leafhopper species among five geographically distant localities across those regions and to estimate gene flow between populations. Ten specimens were sampled per population and genotyped with RAPD markers generated from amplification with nine oligonucleotides. The percentage of polymorphic loci was 78% in relation to the total number of amplified loci, and genetic similarity either between or within populations was higher than 0.72. Cluster analysis grouped specimens from the northeastern population (Mossoró/RN) into a single group, whereas central-southern specimens were not grouped in relation to their places of origin. Overall, the genetic subdivision index (Fst) was low (or= 0.192 and Nm 相似文献   

Genetic differentiation in the Agave deserti (Agavaceae) complex of the Sonoran desert

The Agave deserti complex, comprising A. deserti, A. cerulata and A. subsimplex, represents a group of species and subspecies with a near allopatric distribution and clear differences in morphology. Genetic differentiation and taxonomic status with respect to spatial distribution of 14 populations of the complex were analyzed in an effort to understand the evolution and speciation process within the genus. Allelic frequencies, levels of genetic variation, expected heterozygosity (H(S)), proportion of polymorphic loci (P), and genetic differentiation (theta and Nei's genetic distance) were estimated using 41 putative RAPD loci. All three species show high levels of genetic variation (H(S)=0.12-0.29, P=63.4-95.1), and low genetic differentiation between populations and species (theta populations=0.14+/-0.02 (SE); G(st)=0.11+/-0.02). Accordingly, gene flow among populations was estimated as high by three different methods (N(m)=2.91-6.14). Nei's genetic distances between the three species were low compared to the values obtained from other Agavaceae, and there was no clear correlation with taxonomic divisions. In a UPGMA analysis, A. subsimplex and A. cerulata formed exclusive monospecific clusters, whereas the A. deserti populations appear in more than one cluster together with other species. The results were consistent with a pattern of genetic isolation by distance.     

Diversity and genetic structure of the Mexican endemic epiphyte Tillandsia achyrostachys E. Morr. ex Baker var. achyrostachys (Bromeliaceae)

BACKGROUND AND AIMS: The monoecious, bird-pollinated epiphytic Tillandsia achyrostachys E. Morr. ex Baker var. achyrostachys is an endemic bromeliad of the tropical dry forests of Mexico with clonal growth. In the Sierra de Huautla Natural Reserve this species shows a host preference for Bursera copallifera (Sessé & Moc ex. DC) Bullock. As a result of deforestation in the study area, B. copallifera has become a rare tree species in the remaining forest patches. This human-induced disturbance has directly affected the population densities of T. achyrostachys. In this study the genetic consequences of habitat fragmentation were assessed by comparing the genetic diversity, gene flow and genetic differentiation in six populations of T. achyrostachys in the Sierra de Huautla Natural Reserve, Mexico. METHODS: Allozyme electrophoresis of sixteen loci (eleven polymorphic and five monomorphic) were used. The data were analysed with standard statistical approximations for obtaining diversity, genetic structure and gene flow. KEY RESULTS: Genetic diversity and allelic richness were: HE = 0.21 +/- 0.02, A = 1.86 +/- 0.08, respectively. F-statistics revealed a deficiency of heterozygous plants in all populations (Fit = 0.65 +/- 0.02 and Fis = 0.43 +/- 0.06). Significant genetic differentiation between populations was detected (Fst = 0.39 +/- 0.07). Average gene flow between pairs of populations was relatively low and had high variation (Nm = 0.46 +/- 0.21), which denotes a pattern of isolation by distance. The genetic structure of populations of T. achyrostachys suggests that habitat fragmentation has reduced allelic richness and genetic diversity, and increased significant genetic differentiation (by approx. 40 %) between populations. CONCLUSIONS: The F-statistic values (>0) and the level of gene flow found suggest that habitat fragmentation has broken up the former population structure. In this context, it is proposed that the host trees of T. achyrostachys should be considered as a conservation priority, since they represent the limiting factor to bromeliad population growth and connectivity.     

Microsatellite DNA analysis of northern pike (Esox lucius L.) populations: insights into the genetic structure and demographic history of a genetically depauperate species

The northern pike Esox lucius L. is a freshwater fish exhibiting pronounced population subdivision and low genetic variability. However, there is limited knowledge on phylogeographical patterns within the species, and it is not known whether the low genetic variability reflects primarily current low effective population sizes or historical bottlenecks. We analysed six microsatellite loci in ten populations from Europe and North America. Genetic variation was low, with the average number of alleles within populations ranging from 2.3 to 4.0 per locus. Genetic differentiation among populations was high (overall θ_ST = 0.51; overall ρ_ST = 0.50). Multidimensional scaling analysis of genetic distances between populations and spatial analysis of molecular variance suggested a single phylogeographical race within the sampled populations from northern Europe, whereas North American and southern European populations were highly distinct. A population from Ireland was monomorphic at all loci, presumably reflecting founder events associated with introduction of the species to the island in the sixteenth century. Bayesian analysis of demographic parameters showed differences in θ (a product of effective population size and mutation rate) among populations from large and small water bodies, but the relative differences in θ were smaller than expected, which could reflect population subdivision within the larger water bodies. Finally, the analyses showed drastic population declines on a time scale of several thousand years within European populations, which we ascribe to either glacial bottlenecks or postglacial founder events.  © 2005 The Linnean Society of London, Biological Journal of the Linnean Society , 2005, 84 , 91–101.     

Diversity of some gene frequencies in European and Asian populations. VI. Geographic patterns of PGM and ACP

Genetic variation at the phosphoglucomutase-1 (PGM) and acid phosphatase (ACP) loci, in 160 and 120 European and Asian populations, respectively, is described by spatial autocorrelation statistics and directional variograms. Short-distance patterns of gene frequencies correspond to those predicted by models of isolation by distance, but long-range differentiation of populations is observed as well. A possible role of climatic selection in maintaining the PGM polymorphism is supported by the north-south orientation of the gradient for that locus, but not by biochemical evidence. By and large, the observed patterns of gene frequencies seem to reflect a combination of demographic processes, subdivision and isolation of local populations among them.     

Breeding structure of Glossina pallidipes populations evaluated by mitochondrial variation

Mitochondrial DNA diversity was studied at four loci in six natural populations of the tsetse fly Glossina pallidipes from Zimbabwe, Mozambique, Kenya, and Ethiopia. Single-locus diversity varied from 0.39 at 12S to 0.65 at COII. A total of 32 haplotypes was found with a mean of 6.4 +/- 2.9 per locus. To study breeding structure, diversity at two loci, COII and 16S2, was evaluated in 18 populations sampled from an area of approximately 1,611,000 km2 and in three laboratory cultures. Twenty-six haplotypes were detected at the two loci and mean haplotype diversity over all natural populations was 0.63. A high degree of population subdivision was detected within and among the Ethiopian and Kenya populations. The Zimbabwe and Zambia populations showed much less variation and differentiation than the northern populations. A population in Mozambique showed high levels of haplotype variation and affinities closest to populations in eastern Kenya, some 1700 km to the north. Analysis of variance of haplotype frequencies showed that 51.5% of the total lay within populations, 13% among populations within five nested groups, and 35.5% among the five groups. Wright's FST was 0.485, Nei's GST was 0.33, and Weir and Cunningham's theta = 0.45. Ecological data show that G. pallidipes is highly vagile. The large amount of genetic differentiation may be explained by genetic drift that occurred in scattered, relict populations during the rinderpest panzootic of the late 19th and early 20th centuries.     

Tracing the geographic origin of the cosmopolitan parthenogenetic insect pest Liposcelis bostrychophila (Psocoptera: Liposcelididae)

The randomly amplified polymorphic DNA technique was used to trace the geographic origin of Liposcelis bostrychophila Badonnel populations in Australia from unknown geographic sources internationally. Haplotype (or clonal) diversity was high, with 474 unique haplotypes found from 616 individuals genotyped. Gene diversity estimates (0.10-0.28) and percent polymorphic loci (38.1-88.1%) were moderate to high for most populations. This resulted in genetic distance estimates that ranged from 0.04 to 0.26 and were significantly different for most pairwise population combinations. G ST values for all populations were also moderate (0.04-0.54) and again were significantly different for most pairwise population comparisons. Analysis of molecular variance revealed that the majority of variation was apportioned among individuals within populations regardless of the level at which they were grouped. Gene flow (Nm) was mostly low for all pairwise populations comparisons with an average Nm=1.8. A non-significant negative correlation between genetic distance and geographic distance was found for worldwide populations. In contrast, within Australian populations a significant positive correlation between genetic distance and geographic distance was detected. Genetic relationships explored using unweighted pair group method analysis and non-metric multidimensional scaling indicated a mixed pattern of genetic similarities among all populations. Multiple introductions, from a wide range of international source populations, have obscured the ability to accurately determine the geographic origin of L. bostrychophila in Australia.     

High level of genetic differentiation of Juniperus phoenicea (Cupressaceae) in the Mediterranean region: geographic implications

Fourteen natural populations of Juniperus phoenicea L. from the quite entire species range have been compared using isoenzyme polymorphism. Among 17 loci, 5 (Got1, 6Pgd3, Pgi2, Pgm2 and Shdh2) appeared to be differentiated sufficiently to provide useful information for discrimination between the subspecies phoenicea and turbinata (Guss.) Nyman. Two distinct groups of populations were detected using the Nei’s genetic distance unweighted pair group method with arithmetic mean (UPGMA) and discrimination analyses, one including the inland populations of the eastern Iberian Peninsula and southern France (subsp. phoenicea), and the second from the Mediterranean and Atlantic shores, and from the Atlas mountains in Africa (subsp. turbinata). The high level of differences confirms a long period of isolation, probably during the whole Pleistocene. The population from the Aegean Sea shore differed from the other Mediterranean shore plus Atlas mountain population. It also suggests spatial isolation between them, at least during the last Glaciation.     

Occurrence of Theanine in Camellia Japonica and Camellia sasanqua Seedlings

Three additional structural gene loci (Acp, EstB-1 and Pgm, encoding the enzymes acid phosphatase, esterase B and phosphoglucomutase, respectively) were identified in commercial and research-maintained lines (155) of Agaricus bisporus. The addition of these new marker loci effectively increases the total number of biochemical loci now available in A. bisporus by 60%. Allozyme variability at all eight structural gene loci (Aat, Acp, Adh, EstB-1, Gpt, Pep-1, Pep-2 and Pgm) was used to classify the lines into only 37 genotypic classes out of more than 3 million possible. A recalculated UPGM (unweighted pair-group method) cluster analysis, based on coefficients of similarity for all lines examined, is presented. The limited genetic diversity in this germplasm collection, as evidenced by linkage disequilibrium between loci and a lack of fit to Hardy-Weinberg expectations, commercially remains untapped.