Microsatellites in the sand lizard (Lacerta agilis): description, variation, inheritance, and applicability

We developed microsatellite markers for the sand lizard (Lacerta agilis) to enable investigations of the genetic variability within and among populations with a heterogeneous spatial distribution in Sweden. The populations, which could not be characterized by variation in allozymes or mitochondrial DNA, had a substantial level of variability in microsatellite loci. However, the variability in Swedish populations was limited compared to a large, outbred Hungarian population. In the sand lizard, the number of (GT/CA)n repeats was approximately three times higher than that for (CT/GA)n. The number of repeats and the frequency of microsatellites were within the range reported for other species. Three of nine microsatellite loci showed alleles that could not be amplified, which is in agreement with recent reports describing microsatellite "null alleles" as a common occurrence. We discuss the caution which this calls for when calculating paternity probabilities and when estimating between-population allelic differentiation. A potential problem with different mutation rates for alleles within the same locus is discussed.     

Field trial to evaluate the immunogenicity of pseudorabies virus vaccines with deletions for glycoproteins G and E

This study is a geographically systematic genetic survey of the easternmost subspecies of chimpanzee, Pan troglodytes schweinfurthii. DNA was noninvasively collected in the form of shed hair from chimpanzees of known origin in Uganda, Rwanda, Tanzania, and Za?re. Two hundred sixty-two DNA sequences from hypervariable region 1 of which of the mitochondrial control region were generated. Eastern chimpanzees display levels of mitochondrial genetic variation which are low and which are similar to levels observed in humans (Homo sapiens). Also like humans, between 80% and 90% of the genetic variability within the eastern chimpanzees is apportioned within populations. Spatial autocorrelation analysis shows that genetic similarity between eastern chimpanzees decreases clinically with distance, in a pattern remarkably similar to one seen for humans separated by equivalent geographic distances. Eastern chimpanzee mismatch distributions (frequency distributions of pairwise genetic differences between individuals) are similar in shape to those for humans, implying similar population histories of recent demographic expansion. The overall pattern of genetic variability in eastern chimpanzees is consistent with the hypothesis that the subject has responded demographically to paleoclimatically driven changes in the distribution of eastern African forests during the recent Pleistocene.     

Extent of heterogeneity in mitochondrial DNA of European populations

Variation in the mitochondrial DNA (mtDNA) control region as detected by sequence-specific oligonucleotide (SSO) probes is described for 595 individuals from six European or European-derived populations. Estimates of diversity for mtDNA types exceed 0.91 in all populations, while 50% of the 158 types which were observed occur only once. Of 68 shared types, most occur rarely (< 3% of the total population); only one type occurs at a frequency greater than 10%, and it is present at comparable frequencies in all six populations (18-29%). An analysis of molecular variance (AMOVA) incorporating genetic distances between types shows that 100% of the variation present in the total sample is attributable to within-population diversity, while there are essentially no between-population differences. Another AMOVA was performed for the first hypervariable region SSO sites only, which included this sample plus an additional 537 SSO types from mine more European populations that were inferred from published mtDNA control region sequence data. Similar results were obtained, with over 99% of the variation overall attributable to within-population differences, and less than 1% of the variation attributable to between-population differences. The Saami were the most different from other populations, which had been observed in an earlier study of nucleotide sequence data. Overall, there is no statistically significant heterogeneity for European populations (p > 0.001), and these groups are virtually indistinguishable with respect to mtDNA SSO types. These results demonstrate the utility of mtDNA typing for forensic investigations.     

Mitochondrial DNA variation in Koryaks and Itel'men: population replacement in the Okhotsk Sea-Bering Sea region during the Neolithic

In this study, we analyzed the mitochondrial DNA (mtDNA) variation in 202 individuals representing one Itel'men and three Koryak populations from different parts of the Kamchatka peninsula. All mtDNAs were subjected to high resolution restriction (RFLP) analysis and control region (CR) sequencing, and the resulting data were combined with those available for other Siberian and east Asian populations and subjected to statistical and phylogenetic analysis. Together, the Koryaks and Itel'men were found to have mtDNAs belonging to three (A, C, and D) of the four major haplotype groups (haplogroups) observed in Siberian and Native American populations (A-D). In addition, they exhibited mtDNAs belonging to haplogroups G, Y, and Z, which were formerly called "Other" mtDNAs. While Kamchatka harbored the highest frequencies of haplogroup G mtDNAs, which were widely distributed in eastern Siberian and adjacent east Asian populations, the distribution of haplogroup Y was restricted within a relatively small area and pointed to the lower Amur River-Sakhalin Island region as its place of origin. In contrast, the pattern of distribution and the origin of haplogroup Z mtDNAs remained unclear. Furthermore, phylogenetic and statistical analyses showed that Koryaks and Itel'men had stronger genetic affinities with eastern Siberian/east Asian populations than to those of the north Pacific Rim. These results were consistent with colonization events associated with the relatively recent immigration to Kamchatka of new tribes from the Siberian mainland region, although remnants of ancient Beringian populations were still evident in the Koryak and Itel'men gene pools.     

Invasion genetics of the Mediterranean fruit fly: variation in multiple nuclear introns

Biological invasions generally start from low initial population sizes, leading to reduced genetic variation in nuclear and especially mitochondrial DNA. Consequently, genetic approaches for the study of invasion history and population structure are difficult. An extreme example is the Mediterranean fruit fly, Ceratitis capitata (Medfly), for which successive invasions during this century have resulted in a loss of 60% of ancestral genetic variation in isozymes and 75% of variation in mitochondrial DNA. Using Medflies as an example, we present a new approach to invasion genetics that measures DNA sequence variation within introns from multiple nuclear loci. These loci are so variable that even relatively recently founded Medfly populations within California and Hawaii retain ample genetic diversity. Invading populations have only lost 35% of the ancestral genetic variation. Intron variation will allow high-resolution genetic characterization of invading populations in both natural and managed systems, although non-equilibrium methods of analysis may be necessary if the genetic diversity represents sorting ancestral polymorphism.     

Genetic differentiation in Fomitopsis pinicola (Schwarts: Fr.) Karst studied by means of arbitrary primed-PCR

Genetic variation within and among one Finnish and three Swedish populations of Fomitopsis pinicola (Schwarts: Fr.) Karst. were studied by amplifying DNA from haploid isolates originating from single spore cultures using two arbitrary primers. Analysis offspring from single fruit bodies revealed only three pairs of codominant alleles among 42 variable genetic markers, the remaining 38 segregated independently. Genetic similarity was measured in terms of Euclidean distance. Individuals in the Finnish population tended to form a distinct cluster in the principal component analysis. Variation within and among populations/regions was partitioned by Analysis of Molecular Variance-AMOVA. Within population variation accounted for 91.6% of the total genetic variation. The remaining 7.68% was accounted for by variation between the Finnish population and each of the three Swedish ones. Variation among the Swedish populations accounted for only 0.72% of the total variation. Wright's Fst was 0.17 for all four populations and 0.13 for the three Swedish populations. These relatively low values indicate that there is gene flow among all populations or that they are derived from a common ancestral population. The observed pattern of genetic variation is probably the result of effective spore dispersal and the continuous distribution of this common early successional species.     

Patterns of prehistoric human mobility in polynesia indicated by mtDNA from the Pacific rat

Human settlement of Polynesia was a major event in world prehistory. Despite the vastness of the distances covered, research suggests that prehistoric Polynesian populations maintained spheres of continuing interaction for at least some period of time in some regions. A low level of genetic variation in ancestral Polynesian populations, genetic admixture (both prehistoric and post-European contact), and severe population crashes resulting from introduction of European diseases make it difficult to trace prehistoric human mobility in the region by using only human genetic and morphological markers. We focus instead on an animal that accompanied the ancestral Polynesians on their voyages. DNA phylogenies derived from mitochondrial control-region sequences of Pacific rats (Rattus exulans) from east Polynesia are presented. A range of specific hypotheses regarding the degree of interaction within Polynesia are tested. These include the issues of multiple contacts between central east Polynesia and the geographically distinct archipelagos of New Zealand and Hawaii. Results are inconsistent with models of Pacific settlement involving substantial isolation after colonization and confirm the value of genetic studies on commensal species for elucidating the history of human settlement.     

Genetic relationships among Japanese, northern Han, Hui, Uygur, Kazakh, Greek, Saudi Arabian, and Italian populations based on allelic frequencies at four VNTR (D1S80, D4S43, COL2A1, D17S5) and one STR (ACTBP2) loci

The genetic polymorphism at four variable number of tandem repeats (D1S80, D4S43, COL2A1, D17S5) and one short tandem repeat (ACTBP2) loci was assessed by polymerase chain reaction analysis of genomic DNA obtained from blood samples of eight human populations (Japanese, Northern Han, Hui, Uygur, Kazakh, Saudi Arabian, Greek, Italian). Allele frequencies at all loci were in the Hardy-Weinberg equilibrium for each population. With the exception of ACTBP2, the allelic distribution patterns for these loci revealed a marked genetic divergence among the eight populations. A dendrogram constructed by the neighbor-joining method based on the allele frequencies of the five loci suggested that the five Asian populations (Japanese, Northern Han, Hui, Uygur, and Kazakh) formed one cluster, whereas the two European populations and one West Asian population (Italian, Greek, and Saudi Arabian) formed another. The genetic relationship among these populations may have been greatly influenced by admixture as a result of the migration of individuals along the Silk Road throughout history.     

Major histocompatibility complex variation associated with juvenile survival and parasite resistance in a large unmanaged ungulate population

Antagonistic coevolution between hosts and parasites has been proposed as a mechanism maintaining genetic diversity in both host and parasite populations. In particular, the high levels of genetic diversity widely observed at the major histocompatibility complex (MHC) of vertebrate hosts are consistent with the hypothesis of parasite-driven balancing selection acting to maintain MHC genetic diversity. To date, however, empirical evidence in support of this hypothesis, especially from natural populations, has been lacking. A large unmanaged population of Soay sheep (Ovis aries L.) is used to investigate associations between MHC variation, juvenile survival, and parasite resistance. We show in an unmanaged, nonhuman population that allelic variation within the MHC is significantly associated with differences in both juvenile survival and resistance to intestinal nematodes. Certain MHC alleles are associated with low survivorship probabilities and high levels of parasitism or vice versa. We conclude that parasites are likely to play a major role in the maintenance of MHC diversity in this population.     

Heteroplasmy, length and sequence variation in the mtDNA control regions of three percid fish species (Perca fluviatilis, Acerina cernua, Stizostedion lucioperca)

The nucleotide sequence of the control region and flanking tRNA genes of perch (Perca fluviatilis) mtDNA was determined. The organization of this region is similar to that of other vertebrates. A tandem array of 10-bp repeats, associated with length variation and heteroplasmy was observed in the 5' end. While the location of the array corresponds to that reported in other species, the length of the repeated unit is shorter than previously observed for tandem repeats in this region. The repeated sequence was highly similar to the Mt5 element which has been shown to specifically bind a putative D-loop DNA termination protein. Of 149 perch analyzed, 74% showed length variation heteroplasmy. Single-cell PCR on oocytes suggested that the high level of heteroplasmy is passively maintained by maternal transmission. The array was also observed in the two other percid species, ruffe (Acerina cernua) and zander (Stizostedion lucioperca). The array and the associated length variation heteroplasmy are therefore likely to be general features of percid mtDNAs. Among the perch repeats, the mutation pattern is consistent with unidirectional slippage, and statistical analyses supported the notion that the various haplotypes are associated with different levels of heteroplasmy. The variation in array length among and within species is ascribed to differences in predicted stability of secondary structures made between repeat units.     

The genetic relationship between the Finns and the Finnish Saami (Lapps): analysis of nuclear DNA and mtDNA

The genetic relationships between two Finno-Ugric-speaking populations, the Finns and the Finnish Saami (Lapps), were studied by using PCR for six nuclear-DNA marker loci, mitochondrial restriction-site polymorphism, and sequence variation of a 360-bp segment of the mitochondrial control region. The allele frequencies of each of the nuclear-DNA marker loci and the frequencies of mtDNA restriction haplotypes were significantly different between the populations. The Saami showed exceptionally low variation in their mtDNA restriction sites. The 9-bp deletion common in East Asian populations was not observed, nor did the haplotype data fit into the haplogroup categorization of Torroni et al. The average number of nucleotide substitutions from the mtDNA haplotype data indicated that the Finnish Saami may be closer to the Finns than to the other reference populations, whereas nuclear DNA suggested that the Finns are more closely related to the European reference populations than to the Finnish Saami. The similarity of the Finns to the other Europeans was even more pronounced according to the sequence data. We were unable to distinguish between the Finns and either the Swiss or Sardinian reference populations, whereas the Finnish Saami clearly stood apart. The Finnish Saami are distinct from other Circumarctic populations, although two of the lineages found among the Saami showed closer relationship to the Circumarctic than to the European lineages. The sequence data indicated an exceptionally high divergence for the Saami mtDNA control lineages. The distribution of the pairwise nucleotide differences in the Saami suggested that this population has not experienced an expansion similar to what was indicated for the Finns and the reference populations.     

Microsatellite variability and genetic distances

We analyze the within- and between-population dynamics of the distribution of the number of repeats at multiple microsatellite DNA loci subject to stepwise mutation. Analytical expressions for moments up to the fourth order within a locus and the variance of between-locus variance at mutation-drift equilibrium have been obtained. These statistics may be used to test the appropriateness of the one-step mutation model and to detect between-locus variation in the mutation rate. Published data are compatible with the one-step mutation model, although they do not reject the two-step model. Using both multinomial sampling and diffusion approximations for the analysis of the genetic distance introduced by Goldstein et al. [Goldstein, D. B., Linares, A. R., Cavalli-Sforza, L. L. & Feldman, M. W. (1995) Proc. Natl. Acad. Sci. USA 92, 6723-6727], we show that this distance follows a chi 2 distribution with degrees of freedom equal to the number of loci when there is no variation in mutation rates among the loci. In the presence of such variation, the variance of the distance is obtained. We conclude that the number of microsatellite loci required for the construction of phylogenetic trees with reliable branch lengths may be several hundred. Also, mutations that change repeat scores by several units, even though extremely rare, may dramatically influence estimates of population parameters.     

Multigene family of ribosomal DNA in Drosophila melanogaster reveals contrasting patterns of homogenization for IGS and ITS spacer regions. A possible mechanism to resolve this paradox

The multigene family of rDNA in Drosophila reveals high levels of within-species homogeneity and between-species diversity. This pattern of mutation distribution is known as concerted evolution and is considered to be due to a variety of genomic mechanisms of turnover (e.g., unequal crossing over and gene conversion) that underpin the process of molecular drive. The dynamics of spread of mutant repeats through a gene family, and ultimately through a sexual population, depends on the differences in rates of turnover within and between chromosomes. Our extensive molecular analysis of the intergenic spacer (IGS) and internal transcribed spacer (ITS) spacer regions within repetitive rDNA units, drawn from the same individuals in 10 natural populations of Drosophila melanogaster collected along a latitudinal cline on the east coast of Australia, indicates a relatively fast rate of X-Y and X-X interchromosomal exchanges of IGS length variants in agreement with a multilineage model of homogenization. In contrast, an X chromosome-restricted 24-bp deletion in the ITS spacers is indicative of the absence of X-Y chromosome exchanges for this region that is part of the same repetitive rDNA units. Hence, a single lineage model of homogenization, coupled to drift and/or selection, seems to be responsible for ITS concerted evolution. A single-stranded exchange mechanism is proposed to resolve this paradox, based on the role of the IGS region in meiotic pairing between X and Y chromosomes in D. melanogaster.     

Immunoglobulin allotypes (GM and KM) in Basques from Spain: approach to the origin of the Basque population

GM and KM immunoglobulin (Ig) allotypes have been tested in 310 autochthonous Basques from the three subpopulations of Vizcaya, Guipúzcoa, and Alava, Spain. They are compared with allotypes occurring in autochthonous French Basques, some Pyrenean subpopulations in France, and European populations. The analysis suggests that the Basque subpopulations show noticeable genetic distances between them and with other European populations. The genetic similarity between Basques and European populations is greater in the Basques from France than in the Basques from Spain. The genetic distances between Basque subpopulations in Spain fit well with the different historical levels of the spatial implantation of the Basque language. Guipúzcoa, the Basque province with the highest number of Basque-speaking people, shows the most genetic distinctiveness. The main underlying cause of this spatial genetic pattern seems to be admixture with surrounding populations. Our results do not support the hypothesis that Basques are a relict population of ancient Europeans. They might be a consequence of the colonization of the Basque area by a long-distance migrating group, probably a small Neolithic North Caucasian population that introduced agriculture in the region. They experienced early, rapid demographic growth, and they did not breed with the few hunter-gatherers wandering throughout the area. The North Caucasian migrants could have admixed with North Asian groups dating from many centuries before. Furthermore, Basques present polymorphic frequencies of a common African haplotype, suggesting that they have not been completely isolated from populations of Africa. However, another focus of the African haplotype has been detected in Central Asia, and the Basque frequencies alternatively might be due to North Asian groups.     

Genetic polymorphism of the 3' VNTR region of the human dopaminergic function gene DAT1 (human dopamine transporter gene) in the Mongolian population

The hypervariable region of the dopamine transporter gene (DAT1) was amplified from samples in the Mongolian population. This region includes a variable number of tandem repeats of a 40-bp core unit in the 3' untranslated region of DAT1. Vandenbergh et al. (1992) reported variability in the number of repeats of this 3' flanking region ranging from 3 to 11 times in white and black populations. We examined polymorphism at the DAT1 locus in 78 native Mongolian subjects. We found alleles with 7 to 13 repeats, which is different from the findings of Vandenbergh et al. (1992). The allele distribution of the Mongolian population is similar to that in the Japanese population, reported previously by Nakatome et al. (1995). Chi-square analysis showed a significant lack of homogeneity between our findings in Mongolian subjects and those reported previously in white and black populations. The DAT1 locus was estimated to have a heterozygosity index of 14.1%, and the polymorphic information content was calculated to be 0.16.     

Variation in the sequence of a mitochondrial NADH dehydrogenase I gene fragment among six natural populations of Schistosoma japonicum from China

The present study investigated the level of genetic variation among Schistosoma japonicum populations of different geographical origins from mainland China. Polymerase chain reaction-based methods were employed to determine the sequence for a subunit of the mitochondrial NADH dehydrogenase I gene for populations from Zhejiang, Anhui, Jiangxi, Hunan, Hubei and Sichuan. No variation was detectable in the NADH dehydrogenase I sequence within populations from Zhejiang and Hubei, whereas sequence variation of 0.2% was detected within populations from Anhui, Jiangxi, Hunan and Sichuan. Pairwise comparison of the sequences representing the six different populations revealed genetic differences ranging from 0 to 0.6%.     

Different patterns of variation at the X- and Y-chromosome-linked microsatellite loci DXYS156X and DXYS156Y in human populations

We compared the global pattern of variation at two homologous microsatellites mapping to the long arm of the X chromosome (DXYS156X) and to the short arm of the Y chromosome (DXYS156Y) in humans. A single pair of oligonucleotide primers amplifies these two nonallelic loci, each of which contains polymorphism in the number of pentanucleotide units. We observed 11 alleles in a sample of 2290 X chromosomes and 2006 Y chromosomes from 50 populations representing 6 major geographic regions. The overlapping size range of the X- and Y-chromosome alleles indicated a more complex distribution of alleles at these two loci than previously reported. Contrasting patterns of X-chromosome-linked and Y-chromosome-linked variation were reflected in statistically significant differences in genetic diversity values among geographic regions and between X and Y chromosomes. Higher levels of diversity characterized the DXYS156X locus in Africa (0.799 +/- 0.004) and the DXYS156Y locus in East Asia (0.700 +/- 0.006) compared with populations from other regions. These different patterns of variation can be explained by a combination of processes at both the molecular and population levels, including variable mutation rates, different effective population sizes, and genetic drift.     

Evolutionary inferences from DNA variation at the 6-phosphogluconate dehydrogenase locus in natural populations of drosophila: selection and geographic differentiation

Several allozyme-coding genes in Drosophila melanogaster show patterns suggesting that polymorphisms at these loci are targets of balancing selection. An important question is whether these genes have similar distributions of underlying DNA sequence variation which would indicate similar evolutionary processes occurring in this class of loci. One such locus, 6-phosphogluconate dehydrogenase (Pgd), has previously been shown to exhibit clinal variation for Fast/Slow electromorph variation in the United States and Australia, unusually large electromorph frequency differences between the United States and Africa, and other patterns indicative of selection. We measured four-cutter DNA restriction site and allozyme variation at Pgd among 142 D. melanogaster X chromosomes collected from several geographic regions including North Carolina, California, and Zimbabwe (Africa). We also sequenced a representative sample of 13 D. melanogaster Pgd genes collected in North Carolina and a single copy of Pgd from the sibling species, Drosophila simulans. While some population genetic models predict excess DNA polymorphism in genes which are targets of balancing selection, the D. melanogaster samples from the United States had significantly reduced levels of DNA polymorphism and extraordinarily high levels of linkage disequilibrium, providing evidence of hitchhiking effects of advantageous mutants at Pgd or at linked sites. Therefore, while selection has probably influenced the distribution of DNA variation at Pgd, the precise nature of these selective events remains obscure. Since the Pgd region appears to have low rates of crossing over, the reduced level of variation at this locus supports the idea that recombination rates are important determinants of levels of DNA polymorphism in natural populations. Furthermore, while patterns of allozyme variation are very similar at Pgd and Adh, the DNA data show that the evolutionary histories of these genes are dramatically different. We observed extensive differences in the amount and distribution of variation in D. melanogaster Pgd samples from the United States and Zimbabwe which cannot be explained by differential selection on the Fast/Slow polymorphism in these two geographic regions. Thus, genetic drift among partially isolated populations has also been an important factor in determining the distribution of variation at Pgd in D. melanogaster. Finally, we assayed four-cutter variation at Pgd in a sample of 19 D. simulans X chromosomes and observed reduced levels of DNA variability and high levels of linkage disequilibrium. These patterns are consistent with predictions of some hitchhiking models.     

Racial variability in the UDP-glucuronosyltransferase 1 (UGT1A1) promoter: a balanced polymorphism for regulation of bilirubin metabolism?

A polymorphism in the promoter of the UDP-glucuronosyltransferase 1 (UGT1A1) gene has been shown to cause Gilbert syndrome, a benign form of unconjugated bilirubinemia. Promoters containing seven thymine adenine (ta) repeats have been found to be less active than the wild-type six repeats, and the serum bilirubin levels of persons homozygous or even heterozygous for seven repeats have been found to be higher than those with the wild-type six repeats. We have now examined the genotypes in persons of Asian, African, and Caucasian ancestry. Although within the Caucasian ethnic group there is a strong correlation between promoter repeat number and bilirubin level, between ethnic groups we found that this relationship to be inverse. Among people of African ancestry there are, in addition to those with six and seven repeats, also persons who have five or eight repeats. Using a reporter gene we show that there is an inverse relationship between the number of ta repeats and the activity of the promoter through the range of 5-8 ta repeats. An incidental finding was a polymorphism at nucleotide -106, tightly linked to the (ta)5 haplotype. Serum bilirubin levels are influenced by many factors, both genetic and environmental. We suggest that the unstable UGT1A1 polymorphism may serve to "fine-tune" the plasma bilirubin level within population groups, maintaining it at a high enough level to provide protection against oxidative damage, but at a level that is sufficiently low to prevent kernicterus in infants.