PCR–restriction fragment length polymorphism (RFLP) analyses reveal both extensive clonality and local genetic differences in Candidaalbicans

Using a polymerase chain reaction–restriction fragment length polymorphism (PCR–RFLP) method to obtain genotypes for the diploid pathogenic yeast, Candidaalbicans, we analysed 204 C. albicans isolates from three populations of the Duke University community: two from clinical sources [one from patients infected with human immunodeficiency virus (HIV) and the other from patients without HIV infection], and the third from healthy student volunteers. The results indicated: (i) extensive evidence for clonality within and between populations of C. albicans; and (ii) greater genotypic and gene diversities in the nonclinical population than those derived from clinical specimens, regardless of HIV status. The two clinical populations were genetically more similar to each other than either was to the population consisting of isolates from healthy people. Within each population sample there was a general lack of heterozygotes, and random associations of alleles within and between loci were found in less than 50% of the loci or pairs of loci. These findings were consistent between the two sets of samples analysed: those including all isolates and those including only clone-corrected isolates. Possible mechanisms are presented to explain the observed patterns of genetic variation within and between C. albicans populations.     

Electrophoretic variability in natural populations of Drosophila melanogaster and Drosophila simulans

Genetic variation at 59 gene loci coding for enzymes (50) and larval proteins (9) has been studied in sympatric populations of Drosophila melanogaster and D. simulans from insular and continental origin. The average number of alleles per locus, the mean proportion of polymorphic loci and the mean heterozygosity are similar both within and between species. There are however some significant differences between D. simulans populations in the genotypic frequencies for four polymorphic loci.     

Genetic variation of ticks (Ixodes ricinus L.) in the Lithuanian and Norwegian populations

RAPD markers were used to measure the genetic diversity of 119 individuals of Ixodes ricinus collected from Lithuania and Norway. The samples were analysed within and also between the populations. We analysed 74 loci in each of 6 populations. Our results show high levels of diversity within the populations. The percentage of polymorphic loci of the six analysed populations: Birzai, Vilnius, Kretinga, Tjore, Kjosvik and Odderoya were 68.9%, 58.1%, 78.38%, 62.2%, 44.6% and 68.9%, respectively. The percentage of polymorphic loci in the Lithuanian populations was 93.2%, and in the Norwegian populations 81.08%. The genetic distance ranged from 0.019 to 0.079 within Norwegian populations and from 0.005 to 0.0967 within Lithuanian populations and between the countries from 0.022 to 0.146. The genetic variation of I. ricinus among Norwegian populations was lower than among Lithuanian populations. The highest part of genetic variation in I. ricinus ticks depends on variation within Kretinga (Lithuania) and Odderoya (Norway) populations situated in coastal areas where many migratory and sea birds are aggregated.     

Amplified fragment length polymorphism analysis to identify the genetic structure of the Gymnocypris przewalskii (Kessler, 1876) population from the Qinghai Basin, China

Amplified fragment length polymorphism (AFLP) was used to analyse the genetic structure of 45 individuals of Gymnocypris przewalskii (Kessler, 1876), an endangered and state‐protected rare fish species, from three areas [the Heima (HM), Buha (BH) and Shaliu rivers (SL), all draining into Qinghai Lake]. A total of 563 polymorphic loci were detected. The HM, BH and SL populations have 435, 433 and 391 loci, respectively ( Zhu and Wu, 1975 ), which account for 77.26%, 76.91% and 69.45% of the total number of polymorphic loci of each population, respectively. The Nei indices of genetic diversities (H) of the three populations were calculated to be 0.2869 (HM), 0.2884 (BH) and 0.2663 (SL), respectively. Their Shannon informative indices are 0.4244, 0.4251 and 0.3915, respectively. Research results show that the mean genetic distance between HM and BH is the smallest (0.0511), between BH and SL is the second shortest (0.0608), and between HM and SL is the largest (0.0713), with the mean genetic distance among the three populations being over 0.05. Data mentioned above indicate that the three populations have a certain genetic differentiation. The total genetic diversity (H_t = 0.3045) and the mean value of genetic diversity within the population (H_s = 0.2786) indicate that the variations have mainly come from within the population.     

Isolation and characterization of microsatellite loci from the truffle‐like ectomycorrhizal fungi Rhizopogon occidentalis and Rhizopogon vulgaris

We have isolated and characterized five microsatellite loci from Rhizopogon occidentalis and six loci from Rhizopogon vulgaris (Boletales, Basidiomycota). Microsatellite variation was assessed using 32 R. occidentalis and 48 R. vulgaris individuals from four populations in California. The number of alleles across populations ranged from two to 10 for R. occidentalis and three to eight for R. vulgaris. Expected heterozygosity values within populations ranged from 0.00 to 0.85 for R. occidentalis and 0.00 to 0.75 for R. vulgaris. These are the first microsatellite loci isolated for R. occidentalis and R. vulgaris and will be useful in the examination of their population genetic structure.     

Analysis of genetic structure in soil populations of Rhizobium leguminosarum recovered from the USA and the UK

Although many studies have shown that animal-associated bacterial species exhibit linkage disequilibrium at chromosomal loci, recent studies indicate that both animal-associated and soil-borne bacterial species can display a nonclonal genetic structure in which alleles at chromosomal loci are in linkage equilibrium. To examine the situation in soil-borne species further, we compared genetic structure in two soil populations of Rhizobium leguminosarum bv. trifolii and two populations of R. leguminosarum bv. viciae from two sites in Oregon, with genetic structure in R. leguminosarum bv. viciae populations recovered from peas grown at a site in Washington, USA, and at a site in Norfolk, UK. A total of 234 chromosomal types (ET) were identified among 682 strains analysed for allelic variation at 13 enzyme-encoding chromosomal loci by multilocus enzyme electrophoresis (MLEE). Chi-square tests for heterogeneity of allele frequencies showed that the populations were not genetically uniform. A comparison of the genetic diversity within combined and individual populations confirmed that the Washington population was the primary cause of genetic differentiation between the populations. Each individual population exhibited linkage disequilibrium, with the magnitude of the disequilibrium being greatest in the Washington population and least in the UK population of R. leguminosarum bv. viciae. Linkage disequilibrium in the UK population was created between two clusters of 9 and 23 ETs, which, individually, were in linkage equilibrium. Strong linkage disequilibrium between the two major clusters of 8 and 12 ETs in the Washington population was caused by the low genetic diversity of the ETs within each cluster relative to the inter-cluster genetic distance. Because neither the magnitude of genetic diversity nor of linkage disequilibrium increased as hierarchical combinations of the six local populations were analysed, we conclude that the populations have not been isolated from each other for sufficient time, nor have they been exposed to enough selective pressure to develop unique multilocus genetic structure.     

Genetic structure and relationships of four populations of the stalk boring moth, Eldana saccharina

Twenty-seven protein coding loci were examined by means of horizontal starch gel electrophoresis in samples of larvae from four populations of the stalk borer Eldana saccharina Walker (Lepidoptera: Pyralidae) in Natal, South Africa. The populations were collected in two localities approximately 250 km apart. In each locality a sample was obtained from sugarcane and also from the locally most abundant indigenous host plant of this insect (Cyperuspapyrus L. in one locality and C. dives Delile - synonomous with C. immensus CB CI. - in the other). More than one allele was detected at eight of the loci in all four populations and at a further locus in three of the populations; the other 18 loci were monomorphic for the same allele in all populations. Average expected heterozygosity over the 27 loci was approximately 0.12 in all populations. Genetic distances among the populations were small, but were greater between the two populations from the indigenous hosts and the two from sugarcane than within either of these pairs of populations. Possible explanations of these results are discussed.     

Population genetics and gene variation in screwworms (Diptera: Calliphoridae) from Brazil

Allozyme variation in New World screwworm,Cochliomyia hominivorax (Coquerel), populations from Brazil was examined. Variability was observed in 8 of 13 enzyme loci and the frequency of the most common allele was <0.95 for seven loci. Observed and expected heterozygosities were 0.159 and 0.165, respectively. Comparisons of the Brazilian populations with previously studied populations from Costa Rica resulted in Nei's genetic distances of between 0.000 and 0.006, with the greatest distance being between populations within Brazil. Comparisons with Mexican populations using only three loci resulted in genetic distances ≤0.031. Goodness-of-fit statistics for Hardy-Weinberg equilibrium and Wright'sF statistics indicated small deviations from expected equilibrium genotype frequencies and low levels of differentiation between populations within Brazil. Differentiation among screwworm populations from Brazil, Costa Rica, and Mexico was minimal.     

Unique pattern of <Emphasis Type="Italic">R-</Emphasis>gene variation within populations in Arabidopsis

An understanding of the variation pattern in disease resistance (R) genes is essential for its use in breeding programs aimed at neutralizing the threat of pathogens. Although the variation between populations is well known, there is little research about R-gene variation patterns within populations. Here, we investigate the polymorphism at three R-gene loci of 39 individual plants from nine populations of Arabidopsis thaliana. Our data suggest that alleles of each locus from individuals within a local population were either nearly identical, or highly diverse as ones between populations. The vast majority (92.5%) of within-population variation was shared globally, with high levels of allelic diversity (up to 11.7%) and abundant diverse-alleles. This unique pattern of within-population variation at R-loci suggests that individual plants within a population had the great potential to maintain a high level of globally-shared polymorphisms, and that the diversifying selection was the major force maintaining such polymorphisms. Consequently, the shared-polymorphism became recyclable for new R-genes, as the corresponding avirulence re-emerges in pathogen populations. Nucleotide sequence data reported are available in the GenBank databases under the accession numbers EF368054-EF368158.     

Genetic differentiation of theErigeron species (Asteraceae) in the Alps: A case of unusual allozymic uniformity

Allozyme variation was studied in all nine diploidErigeron species known from the Alps:E. alpinus, E. neglectus, E. polymorphus, E. candidus, E. uniflorus, E. atticus, E. gaudinii, E. acer, andE. angulosus. A total of 248 individuals from 24 natural populations was investigated using starch gel electrophoresis. Seven enzymes and 13 loci were assessed. Genetic variation within populations was low with the proportion of polymorphic loci ranging from 0.0–0.385, and average number of alleles per polymorphic locus from 2.0–2.5. In general, 70–100% of the genetic variation was attributed to between population differences. Mean genetic identities for pair-wise comparisons of populations averaged 0.893 within species, and 0.890 among species. Interspecific genetic variation of populations usually did not exceed intraspecific variation. It was concluded that theErigeron species from the Alps may have arisen by recent speciation probably during the epoches of glaciation. Morphological and ecological differences between species seem to be based on few gene loci.     

Genetic variation within and between populations of hermaphroditic <Emphasis Type="Italic">Bulinus truncatus</Emphasis> tetraploid freshwater snails of the Albertine Rift,East Africa

Genetic variability within and among Bulinus truncatus of the Albertine Rift freshwater bodies were assessed to investigate the degree of inbreeding and gene flow in the snail populations. The effect of ploidy on the genetic structuring of B. truncatus is also described. We characterized the genetic structure of seven B. truncatus populations from Lake Albert, Lake Kivu, and Katosho swamp in Tanzania using five polymorphic microsatellite loci. Genetic differentiation was quantified using pairwise FST values and Nei’s standard genetic distances. Different alleles were observed across all loci and genetic diversity was low although it varied greatly across populations; observed heterozygosity was, however, higher than the expected heterozygosity in three of the populations studied. Significant heterozygote deficiencies were observed coupled with significant linkage disequilibria in five populations for all the five loci examined in this study. We found significant genetic differentiation among the seven freshwater bodies; private alleles were observed across all loci indicating restricted or absence of gene flow between populations. Limited snail dispersal and the reproductive biology of B. truncatus are the major forces shaping the genetic variation observed. Low genetic variation within B. truncatus populations exposes them to a high parasite infection risk as predicted in the Red Queen hypothesis.     

Patterns of selection and allele diversity of class I and class II major histocompatibility loci across the species range of sockeye salmon (Oncorhynchus nerka)

The major histocompatibility complex (MHC), an important component of the vertebrate immune system, provides an important suite of genes to examine the role of genetic diversity at non‐neutral loci for population persistence. We contrasted patterns of diversity at the two classical MHC loci in sockeye salmon (Oncorhynchus nerka), MHC class I (UBA) and MHC class II (DAB), and neutral microsatellite loci across 70 populations spanning the species range from Washington State to Japan. There was no correlation in allelic richness or heterozygosity between MHC loci or between MHC loci and microsatellites. The two unlinked MHC loci may be responding to different selective pressures; the distribution of F_ST values for the two loci was uncorrelated, and evidence for both balancing and directional selection on alleles and lineages of DAB and UBA was observed in populations throughout the species range but rarely on both loci within a population. These results suggest that fluctuating selection has resulted in the divergence of MHC loci in contemporary populations.     

RAPD analysis reveals low genetic variability in the endangered light-footed clapper rail

Numbers of light-footed clapper rails Rallus longirostris levipes, an endangered bird inhabiting southern California salt marshes, have substantially declined from historic levels. RAPD (randomly amplified polymorphic DNA) analysis was employed to assess the genetic variability within and among four of the largest remaining light-footed clapper rail populations. A single, larger population of the endangered Yuma clapper rail Rallus longirostris yumanensis was used for comparison. A total of 325 RAPD primers were tested on DNA from a subset of five clapper rails composed of a single representative for each of the four light-footed clapper rail populations and a representative for the single Yuma clapper rail population. Of the 1338 amplified bands (loci) surveyed in these five representative birds, approximately 1% were polymorphic, indicating the level of differentiation across all loci is quite low. Nine primers yielding these 16 polymorphic bands were used to analyse 48 individuals from five populations. Five of these bands were polymorphic in both subspecies, six were polymorphic only within the light-footed clapper rails, and five were polymorphic only within the Yuma clapper rail samples. Considering the few bands that were polymorphic among the light-footed clapper rail populations, a surprisingly high level of population differentiation (G_ST= 0.28) was found. This is in accord with the results of AMOVA analyses which show that a fairly high percentage of the limited variability among the rails is due to either differences between subspecies or differences between the light-footed rail populations. Because inbreeding depression is suspected and overall genetic distances between populations are low, movement of light-footed clapper rails from larger populations into smaller ones might be considered as a management strategy. Employing RAPDs as one of a series of assays is useful in revealing the population structure of genetically depauperate species.     

GENETIC DIVERSITY AND POPULATION STRUCTURE IN TRADESCANTIA HIRSUTICAULIS (COMMELINACEAE)

Tradescantia hirsuticaulis, the hairy-stemmed spiderwort, is an insect-pollinated perennial plant species found primarily on rock outcrops in Georgia, South Carolina, and Alabama. Although populations of T. hirsuticaulis are rare and scattered, local populations are frequently large. Levels of genetic variation were assessed for 13 populations representing the species' range in these three states. Despite the disjunct distribution of this habitat specialist and apparent lack of specialized seed and pollen dispersal mechanisms, exceptionally high levels of genetic variation are maintained within the species, with a moderate level of variation (18%) found among populations. Twenty-nine of the 33 loci resolved (88%) were polymorphic within the species; the mean number of loci polymorphic within populations was 54%. The mean number of alleles per polymorphic locus was 3.24 across all populations and averaged 2.37 within populations. Genetic diversity was 0.206 for the species, whereas mean population genetic diversity was 0.157, both much higher than the average for other short-lived herbaceous perennials. Estimated levels of gene flow were moderate (Nm = 0.95), and a significant association between geographic distance and genetic distance between populations was found (r = 0.68; P < 0.0001). Habitat destruction is the major threat to this genetically diverse species. Since gene flow among its highly dispersed populations is limited, diminution or extinction of local populations could jeopardize the long-term evolutionary potential of this species.     

Population genetic studies of leafhopper (Empoasca) species

Seven populations of the genus Empoasca Walsh 1864 (Homoptera, Typhlocybinae) collected from six different host-plants were electrophoretically analyzed for thirteen enzyme loci. By using both the allozymes and the morphological characters of the male genitalia we found that these populations consisted of only two Empoasca species; E. decedens and E. decipiens. The use of allozymes proved to be the faster and more efficient method for discrimination; nine out of thirteen enzyme loci were diagnostic. E. decedens was found to be the most abundant species in all populations studied. There are no genetic differences between E. decedens populations associated with different host-plants. The total genetic variability was mainly organized within E. decedens populations, explaining more than 95% of the total variability.     

Microsatellite DNA Population Structure and Stock Identification of Steelhead Trout (<Emphasis Type="BoldItalic">Oncorhynchus mykiss</Emphasis>) in the Nass and Skeena Rivers in Northern British Columbia

Population structure and the application to genetic stock identification for steelhead (Oncorhynchus mykiss) in the Nass and Skeena Rivers in northern British Columbia was examined using microsatellite markers. Variation at 8 microsatellite loci (Oki200, Omy77, Ots1, Ots3, Ssa85, Ots100, Ots103, and Ots108) was surveyed for approximately 930 steelhead from 7 populations in the Skeena River drainage and 850 steelhead from 10 populations in the Nass River drainage, as well as 1550 steelhead from test fisheries near the mouth of each river. Differentiation among populations within rivers accounted for about 1.9 times the variation observed among years within populations, with differences between drainages less than variation among populations within drainages. In the Nass River, winter-run populations formed a distinct group from the summer-run populations. Winter-run populations were not assessed in the Skeena River watershed. Simulated mixed-stock samples suggested that variation at the 8 microsatellite loci surveyed should provide relatively accurate and precise estimates of stock composition for fishery management applications within drainages. In the Skeena River drainage in 1998, Babine River (27%) and Bulkley drainage populations (31%) comprised the main components of the returns. For the Nass River in 1998 steelhead returning to Bell-Irving River were estimated to have comprised 39% of the fish sampled in the test fishery, with another 27% of the returns estimated to be derived from Cranberry River. The survey of microsatellite variation did not reveal enough differentiation between Nass River and Skeena River populations to be applied confidently in estimation of stock composition in marine fisheries at this time. Received January 14, 2000; accepted July 13, 2000.     

RAPD analysis of genetic diversity and population genetic structure of Stipa krylovii reshov. in Inner Mongolia steppe

Random amplified polymorphic DNA (RAPD) analysis was used to characterize the genetic diversity and population genetic structure of Stipa krylovii populations in Inner Mongolia steppe of North China. Thirteen 10-bp oligonucleotide primers, which generated 237 RAPD bands, were used to analyze 90 plants of five populations from three regions, meadow steppe, typical steppe and desert steppe, from the east to the west. The genetic diversity of Stipa krylovii that was revealed by observed number of alleles (na), expected number of alleles (ne), Nei’s diversity index (h), Shannon’s diversity index (H), amplificated loci, polymorphic loci and the percentage of polymorphic loci (PPB) increased from the east to the west. The Pearson’s correlation analysis between genetic diversity parameters and ecological parameters indicated that the genetic diversity of Stipa krylovii was associated with precipitation and cumulative temperature variations along the longitude (humidity were calculated by precipitation and cumulative temperature). Dendrogram based on Jaccard’s genetic distance showed that the individuals from the same population formed a single subgroup. Although most variation (56.85%) was within populations, there was high genetic differentiation among populations of Stipa krylovii, high differentiation within and between regions by AMOVA analysis. Either Nei’s unbiased genetic distance (G _ST) or gene flow (Nm) among pairwise populations was not correlated with geographical distance by Mantel’s test (P > 0.05), suggesting that there was no consistency with the isolation by distance model in these populations. Natural selection may have played a role in affecting the genetic diversity and population structure, but habitat destruction and degradation in northem grassland in China may be the main factor responsible for high genetic differentiation among populations, within and among regions. The text was submitted by the authors in English.     

Drift,selection and adaptive variation in small populations of a threatened rattlesnake

An important goal of conservation genetics is to determine if the viability of small populations is reduced by a loss of adaptive variation due to genetic drift. Here, we assessed the impact of drift and selection on direct measures of adaptive variation (toxin loci encoding venom proteins) in the eastern massasauga rattlesnake (Sistrurus catenatus), a threatened reptile that exists in small isolated populations. We estimated levels of individual polymorphism in 46 toxin loci and 1,467 control loci across 12 populations of this species, and compared the results with patterns of selection on the same loci following speciation of S. catenatus and its closest relative, the western massasauga (S. tergeminus). Multiple lines of evidence suggest that both drift and selection have had observable impacts on standing adaptive variation. In support of drift effects, we found little evidence for selection on toxin variation within populations and a significant positive relationship between current levels of adaptive variation and long‐ and short‐term estimates of effective population size. However, we also observed levels of directional selection on toxin loci among populations that are broadly similar to patterns predicted from interspecific selection analyses that pre‐date the effects of recent drift, and that functional variation in these loci persists despite small short‐term effective sizes. This suggests that much of the adaptive variation present in populations may represent an example of “drift debt,” a nonequilibrium state where present‐day levels of variation overestimate the amount of functional genetic diversity present in future populations.     

GENETIC DIFFERENTIATION AND HYBRIDIZATION BETWEEN CAREX GYNODYNAMA AND C. MENDOCINENSIS (CYPERACEAE) IN CALIFORNIA

Patterns of variation within and between Carex gynodynama and C. mendocinensis were investigated by studying allozyme and chromosome variation in natural populations and structural variation using herbarium specimens. Multivariate analyses of structural data demonstrated that C. gynodynama is clearly distinct from C. mendocinensis, and that sterile specimens similar to C. mendocinensis are intermediate between that species and C. gynodynama. The mean genetic distance between the two species, based on allozyme phenotypes at 17 enzyme-coding loci, was 0.22 ± 0.12. The sterile putative hybrids had the expected heterozygous pattern at three enzyme-coding loci at which the parental species were fixed for different alleles. Chromosome numbers are reported for the first time for both species and their putative hybrid. Carex mendocinensis had a different number in each of the three populations examined with n = 28, n = 29, or n = 30. Chromosome counts from one population of C. gynodynama revealed five plants with n = 25 and one with n = 26. Putative hybrids from this population exhibited irregular pairing at meiosis with 2n = ca. 55–57. Patterns of allozyme variation also suggest that C. mendocinensis has an outcrossing or mixed mating system but that C. gynodynama is an inbreeding species. Carex gynodynama exhibited very little variation in structure, habitat, or at the enzyme-coding loci examined, suggesting that it may have experienced a genetic bottleneck relatively recently. Carex mendocinensis had higher levels of variation both within and between populations at enzyme-coding loci and in structural features. This pattern of variation and a geographic distribution centered in serpentine areas of the Klamath–Siskiyou region, with disjunct smaller populations in serpentine areas farther south, suggest that C. mendocinensis once may have been a more widespread species.     

Characterization of microsatellite markers for Couch's spadefoot toad (Scaphiopus couchii) and cross‐amplification in other species of the family Scaphiopodidae

I developed 12 di‐ and tetranucleotide microsatellite loci for Couch's spadefoot toad (Scaphiopus couchii). These loci have 3–37 alleles per locus and observed heterozygosities ranging from 0.157 to 0.941 among 85 individuals from four populations. Global and within‐population exact tests do not reveal departure from Hardy–Weinberg expectations and all loci pairs are in linkage equilibrium. These independent markers will be useful for studies of population structure and kinship in this commonly studied amphibian. Additionally, several of these loci may be applicable for studies of other North American toads of the family Scaphiopodidae.