Allele Size Variance Research Articles

Isolation and characterization of microsatellite markers for analysis of molecular variation in the medicinal plant Madagascar periwinkle ( Catharanthus roseus (L.) G. Don)

Catharanthus roseus (L.) G. Don, commonly known as Madagascar periwinkle, is a plant of great medicinal value. In this study microsatellite markers were developed and utilized for analysis of genetic diversity in C. roseus. In order to isolate microsatellite sequences, two small insert genomic libraries of C. roseus cv. Nirmal were constructed and screened with CA, CT, GC and GCG oligonucleotide repeats. Sixty-five microsatellite motifs were identified, from which 38 functional STMS primer pairs were designed and validated. Out of these, 24 STMS markers were used to evaluate the genetic polymorphism in 37 genotypes, which comprised of 32 accessions of C. roseus, a single accession each of two related species ( C. trichophyllus and C. pusillus) and one accession each of three related genera ( Vinca minor, Thevetia peruviana and Nerium indicum). The 24 STMS markers detected 26 loci with two markers amplifying more than one locus. A total of 124 alleles were amplified in the 37 genotypes ranging from 2 to 10 alleles with an average of 4.76 alleles per locus. The high average expected heterozygosity ( H E) value of 0.56 and observed heterozygosity ( H O) value of 0.52 established the efficiency of the STMS markers for discriminating the C. roseus genotypes. Nei and Li's similarity coefficients were calculated and a UPGMA-based dendrogram was constructed which clearly distinguished all genotypes except two pairs. Sequence analysis of the length variant alleles at three STMS loci revealed that the variation in the copy number of repeat motifs was the major source of length polymorphism within C. roseus. However, isolated point mutations and indels in the microsatellite flanking regions (MFRs) of homologus loci from other species also contributed to size homoplasy and allelic size variation. This study is the first report of microsatellite development and utilization in C. roseus, providing significant insights into its genome structure and organization.

Genetic differentiation of pink salmon Oncorhynchus gorbuscha Walbaum in the Asian part of the range

Genetic variation at 19 allozyme (including 11 polymorphic) and 10 microsatellite loci was examined in the population samples of odd- and even-broodline pink salmon from the southern part of Sakhalin Island, Southern Kuril Islands, and the northern coast of the Sea of Okhotsk. The estimates of relative interpopulation component of genetic variation over the allozyme loci, per broodline, were on average 0.43% (GST), while over the microsatellite loci it was 0.26% (the theta(ST) coefficient, F-statistics based on the allele frequency variance), and 0.90% (the rho(ST) coefficient, R-statistics based on the allele size variance). The values of interlinear component constituted 2.34, 0.31, and 1.05% of the total variation, respectively. Using the allozyme loci, statistically significant intralinear heterogeneity was demonstrated among the regions, as well as among the populations of Southern Sakhalin Island. Multivariate scaling based on the allozyme data demonstrated regional clustering of the sample groups, representing certain populations during the spawning run or in different years. Most of the microsatellite loci examined were found to be highly polymorphic (mean heterozygosity > 0.880). The estimates of interlinear, interregional, and interpopulation variation over these loci in terms of theta(ST) values were substantially lower than in terms of rho(ST) values. Regional genetic differentiation, mostly expressed at the allozyme loci among the populations from the northern and southern parts of the Sea of Okhotsk (i.e., between the Sakhalin and Kuril populations), was less expressed at the microsatellite loci. The differentiation between these regions observed can be considered as the evidence in favor of a large-scale isolation by distance characterizing Asian pink salmon. It is suggested that in pink salmon, low genetic differentiation at neutral microsatellite loci can be explained by extremely high heterozygosity,of the loci themselves, as well as by the migration gene exchange among the populations (the estimate of the genetic migration coefficient inferred from the "private" allele data constituted 2.6 to 3.4%), specifically, by the ancient migration exchange, which occurred during postglacial colonization and colonization of the range.

Molecular genotype identification of the Gallus gallus major histocompatibility complex

The chicken major histocompatibility complex (MHC) is commonly defined by serologic reactions of erythrocytes with antibodies specific to the highly polymorphic MHC class I (BF) and MHC class IV (BG) antigens. The microsatellite marker LEI0258 is known to be physically located within the MHC, between the BG and BF regions. DNA from various serologically defined MHC haplotypes was amplified by polymerase chain reaction with primers surrounding this marker. Twenty-six distinctive allele sizes were identified. Some serologically well-defined MHC haplotypes shared a common LEI0258 allele size but could be distinguished either by the addition of information from another nearby marker (MCW0371) or by small indels or single nucleotide polymorphism (SNP) differences between the alleles. The association between LEI0258 allele and serologically defined MHC haplotype was very consistent for the same haplotype from multiple sources. Sequence information for the region defined by LEI0258 was obtained for 51 different haplotypes. Two internal repeats whose lengths were 13 and 12 bp, respectively, are the primary basis for allelic variability. Allele size variation ranges from 182 to 552 bp. Four indels and five SNPs in the surrounding sequence provide additional means for distinguishing alleles. Typing with LEI0258 and MCW0371 will be useful in identifying MHC haplotypes in outbred populations of chickens particularly for the initial development of serological reagents.

Microsatellite diversity reveals the interplay of language and geography in shaping genetic differentiation of diverse Proto‐Australoid populations of west‐central India

Microsatellite diversity was analyzed in four Proto-Australoid tribes, including Indo-European (Marathi)-speaking Katkari, Pawara, Mahadeo-Koli, and Dravidian (Gondi)-speaking groups of Maharashtra, west-central India, to understand their genetic structure and to identify the congruence between language and gene pool. Allele frequency data at 15 short tandem repeat (STR) loci in studied tribes was compared with data of 22 Indo-European- and Dravidian-speaking caste and tribal populations using heterozygosity, allele size variance, analysis of molecular variance (AMOVA), G(ST) estimate, PC plot, and Mantel correlation test. Our results demonstrate that "Gondi" tribes comprising the Madia-Gond, a hunter-gatherer population, and the agriculturist Dheria-Gond harbor lower diversity than "Marathi" tribal groups, which are culturally and genetically distinct. Katkari, a hunter-gatherer tribe, showed greater diversity and the presence of a large number of unique alleles, genetically distinct from all others except the Pawara, supporting their old cultural links. The agriculturist Pawara tribe represents a splinter subgroup of the Bhil tribe and has experienced gene flow. The Mahadeo-Koli, an agriculturally oriented tribe, displayed significant heterozygote deficiency, attributable to the practice of high endogamy. The Proto-Australoid tribal populations were genetically differentiated from castes of similar morphology, suggesting different evolutionary mechanisms operating upon the populations. The populations showed genetic and linguistic similarity, barring a few groups with varied migratory histories. The microsatellite variation clearly demonstrates the interplay of sociocultural factors including linguistic, geographical contiguity, and microevolutionary processes in shaping the genetic diversity of populations in contemporary India. This study supports the ethno-historical relationships of Indian populations.

SSR allelic variation in almond (Prunus dulcis Mill.)

Sixteen SSR markers including eight EST-SSR and eight genomic SSRs were used for genetic diversity analysis of 23 Chinese and 15 international almond cultivars. EST- and genomic SSR markers previously reported in species of Prunus, mainly peach, proved to be useful for almond genetic analysis. DNA sequences of 117 alleles of six of the 16 SSR loci were analysed to reveal sequence variation among the 38 almond accessions. For the four SSR loci with AG/CT repeats, no insertions or deletions were observed in the flanking regions of the 98 alleles sequenced. Allelic size variation of these loci resulted exclusively from differences in the structures of repeat motifs, which involved interruptions or occurrences of new motif repeats in addition to varying number of AG/CT repeats. Some alleles had a high number of uninterrupted repeat motifs, indicating that SSR mutational patterns differ among alleles at a given SSR locus within the almond species. Allelic homoplasy was observed in the SSR loci because of base substitutions, interruptions or compound repeat motifs. Substitutions in the repeat regions were found at two SSR loci, suggesting that point mutations operate on SSRs and hinder the further SSR expansion by introducing repeat interruptions to stabilize SSR loci. Furthermore, it was shown that some potential point mutations in the flanking regions are linked with new SSR repeat motif variation in almond and peach.

Genotypic Diversity Within a Natural Coastal Bacterioplankton Population

The genomic diversity and relative importance of distinct genotypes within natural bacterial populations have remained largely unknown. Here, we analyze the diversity and annual dynamics of a group of coastal bacterioplankton (greater than 99% 16S ribosomal RNA identity to Vibrio splendidus). We show that this group consists of at least a thousand distinct genotypes, each occurring at extremely low environmental concentrations (on average less than one cell per milliliter). Overall, the genomes show extensive allelic diversity and size variation. Individual genotypes rarely recurred in samples, and allelic distribution did not show spatial or temporal substructure. Ecological considerations suggest that much genotypic and possibly phenotypic variation within natural populations should be considered neutral.

Genetic Variation at Nine Short Tandem Repeat Loci Among Islanders of the Eastern Adriatic Coast of Croatia

We have analyzed the extent of genetic variation at nine autosomal short tandem repeat loci (D3S1358, VWA, FGA, TH01, TPOX, CSF1PO, D5S818, D13S317, D7S820) among six populations from Croatia: five distributed in the islands of the eastern Adriatic coast and one from the mainland. The purpose is to investigate the usefulness of these loci in detecting regional genetic differentiation in the studied populations. Significant heterogeneity among the island and mainland populations is revealed in the distributions of allele frequencies; however, the absolute magnitude of the coefficient of gene differentiation is small but significant. The summary measures of genetic variation, namely, heterozygosity, number of alleles, and allele size variance, do not indicate reduced genetic variation in the island populations compared to the mainland population. In contrast to the two measures of genetic variation, allele size variance and within-locus heterozygosity, the imbalance index (beta) indicates evidence of recent expansion of population sizes in all islands and in the mainland. High mutation rates of the studied loci together with local drift effects are likely explanations for interisland genetic variation and the observed lack of reduced genetic diversity among the island populations.

Microsatellite Diversity in HbS Carrier and Normal Individuals of Tribal Populations of Malaria Infested Regions

Sickle cell gene is a variant form of beta globin developed in human genome as a protective mechanism to malaria. The frequency of HbS gene varies considerably with ethnic group and geographical location coinciding with distribution of malaria. Occurrence of sickle cell mutation is very high among different endogamous groups of Chattisgarh, Maharastra, and Jharkhand state with equally high incidence of malaria infection. Hardy-Weinberg test was performed to assess genetic equilibrium among HbS carriers and normal individual of Agharia, Pawra and Oraon communities of the three states. Genetic diversity in two groups across fifteen microsatellite markers was studied using three important parameters viz., number of alleles, allele size variance and heterozygosity. Significant departure from Hardy Weinberg equilibrium was observed only at TH01 (11p15.5) among the carriers, which could be due to association of the locus with beta globin gene (11p15.5). Allele diversity is observed to be very high in normal individuals at each locus (with additional rare alleles at FGA, Penta D and D21S11 loci) in comparison to sickle cell carriers. The difference in the heterozygosity level (~5%) between two groups was observed to be highest at two significant loci THOI and CSF1PO (5q33.3-34), thereby indicating maximum pressure of the malarial parasite at these loci, leading to increase in the number of repeat units, among the normal individuals. Perhaps high genetic diversity in the normal group is to add resistant allele against malaria. Our study clearly demonstrates that microsatellites, besides being hot spots for recombination has another important role in enabling the individual to adapt to the stressful environment of parasite.

Individual variation in microsatellite mutation rate in barn swallows

The hypermutable nature of some microsatellite loci implies realistic possibilities for the large-scale detection of germline mutations by pedigree analysis. We have developed a model system for mutation analysis by the characterisation of patterns of mutation at three hypervariable microsatellites (two tetranucleotide and one pentanucleotide repeat loci) in barn swallows, all three markers having mutation rates at the percentage level. Here, we study how the mutation rate varies between individual birds of a Spanish population of barn swallows. A total of 53 mutations were identified from 2920 germline transmissions in 90 families with a total of 694 offspring. Mutations were not randomly distributed among individuals ( P=0.020). Attempts to correlate mutation rate with allele size, degree of inbreeding, immunocompetence and male age only revealed a strong effect of allele size. The mean mutation rate differed between colonies of breeding swallows which was probably due to a corresponding variation in allele size between colonies. There was no difference in the mean mutation rate between the Spanish and an Italian population. These results corroborate earlier findings, at the population level, of an allele size effect on the microsatellite mutation rate.

Genetic signatures of pre-expansion bottleneck in the Choctaw population of Oklahoma.

Previous research showed that the Choctaw Indians of Oklahoma exhibit considerable linkage disequilibria (LD) in a number of regions of the genome that has allowed genetic fine mapping for potential susceptibility genes for the autoimmune connective tissue disease scleroderma, or systemic sclerosis (SSc). In principle, such enhanced background LD in the Choctaws could be caused by population bottleneck event(s) followed by recent population expansion. This investigation utilizes genome-scan data on 175 dinucleotide loci from 76 Choctaw individuals to seek genetic evidence of the demographic history of the Choctaw Nation. Of the 175 loci examined, 105 are in Hardy-Weinberg equilibrium. The average unbiased homozygosity over the 105 loci for the Choctaws (29.3%) is significantly higher than that in the European descent group (20.9%); and when adjusted for sample-size differences, the Choctaw also exhibit a significantly smaller number of segregating alleles (6.65 vs. 8.14) at these loci. Both of these observations are consistent with the trend expected in an isolated population. Comparison of the allele size variance and gene diversity yields an imbalance index (lnbeta) of 0.811 in the Choctaw. Of the 105 loci examined, 93 exhibit excess expected homozygosity in comparison to the expectations of a stepwise mutation model in a population of constant size. Taken together, these observations are consistent with a signature of the recent population size expansion of the Choctaws, preceded by bottleneck event(s).

Microsatellite analysis reveals a progressive widening of the genetic basis in the elite durum wheat germplasm.

It has been argued that the level of genetic diversity in the modern durum wheat ( Triticum turgidum L. var. durum) elite germplasm may have declined due to the high selection pressure applied in breeding programs. In this study, 58 accessions covering a wide spectrum of genetic diversity of the cultivated durum wheat gene pool were characterized with 70 microsatellite loci (or simple sequence repeats, SSRs). On average, SSRs detected 5.6 different allelic variants per locus, with a mean diversity index (DI) equal to 0.56, thus revealing a diversity content comparable to those previously observed with SSRs in other small-grain cereal gene pools. The mean genetic similarity value was equal to 0.44. A highly diagnostic SSR set has been identified. A high variation in allele size was detected among SSR loci, suggesting a different suitability of these loci for estimating genetic diversity. The B genome was characterized by an overall polymorphism significantly higher than that of the A genome. Genetic diversity is organised in well-distinct sub-groups identified by the corresponding foundation-genotypes. A large portion (92.7%) of the molecular variation detected within the group of 45 modern cvs was accounted for by SSR alleles tracing back to ten foundation-genotypes; among those, the most recent CIMMYT-derived founders were genetically distant from the old Mediterranean ones. On the other hand, rare alleles were abundant, suggesting that a large number of genetic introgressions contributed to the foundation of the well-diversified germplasm herein considered. The profiles of recently released varieties indicate that the level of genetic diversity present in the modern durum wheat germplasm has actually increased over time.

Global genetic variation at nine short tandem repeat loci and implications on forensic genetics

We have studied genetic variation at nine autosomal short tandem repeat loci in 20 globally distributed human populations defined by geographic and ethnic origins, viz., African, Caucasian, Asian, Native American and Oceanic. The purpose of this study is to evaluate the utility and applicability of these nine loci in forensic analysis in worldwide populations. The levels of genetic variation measured by number of alleles, allele size variance and heterozygosity are high in all populations irrespective of their effective sizes. Single- as well as multi-locus genotype frequencies are in conformity with the assumptions of Hardy-Weinberg equilibrium. Further, alleles across the entire set of nine loci are mutually independent in all populations. Gene diversity analysis shows that pooling of population data by major geographic groupings does not introduce substructure effects beyond the levels recommended by the National Research Council, validating the establishment of population databases based on major geographic and ethnic groupings. A network tree based on genetic distances further supports this assertion, in which populations of common ancestry cluster together. With respect to the power of discrimination and exclusion probabilities, even the relatively reduced levels of genetic variation at these nine STR loci in smaller and isolated populations provide an exclusionary power over 99%. However, in paternity testing with unknown genotype of the mother, the power of exclusion could fall below 80% in some isolated populations, and in such cases use of additional loci supplementing the battery of the nine loci is recommended.

Allelic variation of a Beauveria bassiana (Ascomycota: Hypocreales) minisatellite is independent of host range and geographic origin.

The minisatellite locus, BbMin1, was isolated from a partial Beauveria bassiana genomic library that consisted of poly(GA) flanked inserts. Polymerase chain reaction (PCR) of the BbMin1 repeat demonstrated allele size variation among 95 B. bassiana isolates. Amplification was also observed from single isolates of Beauveria amorpha, Beauveria brongniartii, and Beauveria caledonica. Eight alleles were identified at the haploid locus, where repeat number fluctuated between one and fourteen. AMOVA and theta (Fst) indicated that fixation of repeat number has not occurred within pathogenic ecotypes or geographically isolated samples of B. bassiana. Selective neutrality of allele size, the rate of BbMin1 mutation, and the age of the species may contribute to host and geographic independence of the marker. Presence of alleles with a large number of repeat units may be attributed to the rare occurrence of somatic recombination or DNA replication error. The molecular genetic marker was useful for the identification of genetic types of B. bassiana and related species.

The polymorphic CAG repeat in the androgen receptor gene in Jewish Israeli women with endometrial carcinoma.

Endometrial carcinoma is considered a hormonal-dependent tumor; estrogen induces endometrial cellular proliferation, whereas progestins display an antiproliferative effect on endometrial tissue. The role that androgen and its receptor (androgen receptor [AR]) play in the pathogenesis of endometrial carcinoma is less clear. Although androgen has an in vitro inhibitory effect on endometrial cell proliferation, up to 75% of endometrial carcinoma express AR somatically. A polymorphic CAG repeat within exon 1 of the AR encodes for a polyglutamine tract, with length range of 8 to 33 repeats, which is inversely correlated with the transcriptional activity of the AR. To gain insight into the role of AR in endometrial carcinoma, the authors analyzed the polymorphic CAG repeat in 79 Jewish Israeli patients with endometrial carcinoma as compared with 44 healthy Jewish women serving as controls. Analysis was conducted using germline DNA as template and using polymerase chain reaction primers flanking the CAG repeat with subsequent fluorescent determination of allele sizes. Allele size range of the longer of the two alleles in the patients was 11-33 (mean, 19.8 +/- 2.7) and in the controls 10-22 (mean, 17.9 +/- 1.9), a statistically significant difference (P < 0.01). Allele size variation within the patient group did not correlate with disease stage, grade, reproductive history, or age at diagnosis. The authors conclude that AR-CAG repeat length differs in Jewish patients with endometrial carcinoma as compared with healthy individuals in Israel, and this finding increases the possibility that the AR is involved in the predisposition to this neoplasm.

A power analysis of microsatellite-based statistics for inferring past population growth.

We present results concerning the power to detect past population growth using three microsatellite-based statistics available in the current literature: (1) that based on between-locus variability, (2) that based on the shape of allele size distribution, and (3) that based on the imbalance between variance and heterozygosity at a locus. The analysis is based on the single-step stepwise mutation model. The power of the statistics is evaluated for constant, as well as variable, mutation rates across loci. The latter case is important, since it is a standard procedure to pool data collected at a number of loci, and mutation rates at microsatellite loci are known to be different. Our analysis indicates that the statistic based on the imbalance between allele size variance and heterozygosity at a locus has the highest power for detection of population growth, particularly when mutation rates vary across loci.

Microsatellite variation and recombination rate in the human genome.

Background (purifying) selection on deleterious mutations is expected to remove linked neutral mutations from a population, resulting in a positive correlation between recombination rate and levels of neutral genetic variation, even for markers with high mutation rates. We tested this prediction of the background selection model by comparing recombination rate and levels of microsatellite polymorphism in humans. Published data for 28 unrelated Europeans were used to estimate microsatellite polymorphism (number of alleles, heterozygosity, and variance in allele size) for loci throughout the genome. Recombination rates were estimated from comparisons of genetic and physical maps. First, we analyzed 61 loci from chromosome 22, using the complete sequence of this chromosome to provide exact physical locations. These 61 microsatellites showed no correlation between levels of variation and recombination rate. We then used radiation-hybrid and cytogenetic maps to calculate recombination rates throughout the genome. Recombination rates varied by more than one order of magnitude, and most chromosomes showed significant suppression of recombination near the centromere. Genome-wide analyses provided no evidence for a strong positive correlation between recombination rate and polymorphism, although analyses of loci with at least 20 repeats suggested a weak positive correlation. Comparisons of microsatellites in lowest-recombination and highest-recombination regions also revealed no difference in levels of polymorphism. Together, these results indicate that background selection is not a major determinant of microsatellite variation in humans.

Molecular characterization and population study of an X chromosome homolog of the Y-linked microsatellite DYS391.

A novel microsatellite homologous to DYS391, a (GATA)(n) short tandem repeat on the human Y chromosome, was identified and characterized in the present work. Employing somatic cell hybrid and deletion panels in a PCR-based approach, we found out that the new microsatellite is located in Xp21.2-22.3, while its Y counterpart mapped to Yq11.21. This X-linked locus (provisionally called DXYS391) and its Y homolog constitute one more example of similarity outside the pseudoautosomal regions between the two human sex chromosomes. Sequencing data showed high levels of homology in the flanking regions of DXYS391 and DYS391 that differ primarily by the presence of a (GACA)(3) motif in the Y locus. Both loci were detected in chimpanzee DNA, suggesting that a putative transposition from the X to the Y occurred before the human/chimpanzee split. The allele frequencies of DYS391 and DXYS391 were investigated, respectively, in 271 Y and 337 X chromosomes from distinct human populations worldwide. DYS391 consistently displayed greater among-population component of the variance of the allele frequencies than DXYS391, as expected due to the three-times lower effective population size of Y chromosomes relative to the X. The intra-population diversity of DYS391, measured by Nei's locus diversity as well as by allele size variance, was lowest in Amerindians, while very low diversity of DXYS391 was seen in Africans. Since our African data are based on a small sample, further studies will be necessary to evaluate better this observation.

Population dynamics coded in DNA: genetic traces of the expansion of modern humans

It has been proposed that modern humans evolved from a small ancestral population, which appeared several hundred thousand years ago in Africa. Descendants of the founder group migrated to Europe and then to Asia, not mixing with the pre-existing local populations but replacing them. Two demographic elements are present in this “out of Africa” hypothesis: numerical growth of the modern humans and their migration into Eurasia. Did these processes leave an imprint in our DNA? To address this question, we use the classical Fisher–Wright–Moran model of population genetics, assuming variable population size and two models of mutation: the infinite-sites model and the stepwise-mutation model. We use the coalescence theory, which amounts to tracing the common ancestors of contemporary genes. We obtain mathematical formulae expressing the distribution of alleles given the time changes of population size . In the framework of the infinite-sites model, simulations indicate that the pattern of past population size change leaves its signature on the pattern of DNA polymorphism. Application of the theory to the published mitochondrial DNA sequences indicates that the current mitochondrial DNA sequence variation is not inconsistent with the logistic growth of the modern human population. In the framework of the stepwise-mutation model, we demonstrate that population bottleneck followed by growth in size causes an imbalance between allele-size variance and heterozygosity. We analyze a set of data on tetranucleotide repeats which reveals the existence of this imbalance. The pattern of imbalance is consistent with the bottleneck being most ancient in Africans, most recent in Asians and intermediate in Europeans. These findings are consistent with the “out of Africa” hypothesis, although by no means do they constitute its proof.

Population substructure and isolation by distance in three continental regions.

Isolation by distance and divergence from a shared population history are two sources of population substructure. Isolation by distance erases population history as populations approach migration-drift equilibrium, while diverging populations descended from a single ancestral population will accumulate genetic differences with time. Here I investigate how much of the worldwide genetic diversity from Jorde et al.'s ([1997] Proc. Natl. Acad. Sci. USA 94:3100-3103) 60 tetranucleotide short tandem repeat (STR) data can be explained by isolation by distance. I use Slatkin's measure of population substructure, R(ST), principal components analyses, and Mantel tests to investigate the pattern of genetic diversity at both the intercontinental and intracontinental levels. Geographic distance accounts for almost 60% of world-wide interpopulation genetic relationships. Within continents, the correlations are less, although not significantly so because of wide confidence intervals. These results suggest that populations have not reached migration-drift equilibrium and that there is information in STR data to reconstruct population history. The level of population substructure worldwide is consistent with previous observations, but at the intracontinental level substructure is less. When one examines diversity against distance from the centroid, one sees excess heterozygosity in Africa, a pattern also noted by Stoneking et al. ([1998] Genome Research 7:1061-1071). A larger effective population size in Africa could explain the excess diversity. Greater gene flow in Africa is an unlikely explanation because the African R(ST) value is slightly larger than the Asian and European R(ST)s, pointing to less gene flow and greater substructure among African populations. Furthermore, there are differences in patterns between heterozygosity and allele size variance. Heterozygosity has a higher correlation with distance from the centroid than does allele size variance, and this may reflect demographic history. Kimmel et al. ([1998] Genetics 148:1921-1930) have shown that after a population expansion heterozygosity returns to equilibrium more quickly than does allele size variance. The contrasting patterns between heterozygosity and allele size variance may reflect different times after an expansion. However, simulations and further work need to be done to more thoroughly investigate the possibility that these data reflect population expansions.

Genetic Interpretation of Broad-Scale Microsatellite Polymorphism in Odd-Year Pink Salmon

Abstract We examined genetic variation at five microsatellite loci in 12 odd-year populations and one even-year population of pink salmon Oncorhynchus gorbuscha from six geographic regions of North America. The degree of polymorphism varied widely among loci. The total number of alleles in the odd-year samples varied from 4 (Oneμ3) to 53 (Ssa85). A probability test revealed significant heterogeneity in allele frequencies among all odd-year samples and among pooled odd-year samples from six regions. We compared estimates of a standard index of population structure (θ) based on variance in allele frequency with a new index suggested for microsatellites (ρST) based on variance in allele size. Our results suggest is a better estimator of intralineage (odd-year × odd-year) population structure, whereas is best suited for estimating interlineage (odd-year × even-year) population structure. The difference in performance of and for estimating intralineage and interlineage population structure suggests high migrat...