Estimation of genetic distance and coefficient of gene diversity from single-probe multilocus DNA fingerprinting data

DNA fingerprinting exhibits multilocus genotypes of individuals, detected by the use of a single multilocus probe. Consequently, population data on DNA fingerprinting do not provide a complete characterization of the genetic variation in terms of allele-frequency distributions, since neither the number of loci nor the locus affiliation of alleles is directly observable. Yet DNA fingerprinting has been proved to be a cost-effective method of detecting hypervariable polymorphisms in several organisms, where the traditional loci fail to detect enough variation for microevolutionary studies. In the present paper we demonstrate that the above-mentioned features of DNA fingerprinting data do not cause any serious problem when they are used in evolutionary studies. Bias-corrected estimators of Nei's standard and minimum genetic distances are derived, and, by an application of this theory to data on seven short tandem repeat loci in three major human populations, it is shown that these modified measures of genetic distances based on DNA fingerprint patterns are quite close to Nei's distances based on locus-specific allele frequencies. Empirical as well as theoretical support of the adequacy of such genetic distances from DNA fingerprinting data is also discussed, and it indicates that the technical limitations of DNA fingerprinting should not deter the use of the method for short-term evolutionary studies.      

Forensic characteristic and population structure dissection of Shaanxi Han population in the light of diallelic deletion/insertion polymorphism data

The genetic polymorphisms of diallelic deletion/insertion polymorphic (DIP) loci in the Shaanxi Han population are still not clearly characterized. Herein, allele frequencies and forensic application efficiencies for 30 diallelic DIP loci were investigated in 506 unrelated healthy Han individuals from Chinese Shaanxi province. Based on population data of the same 30 diallelic DIP loci, the genetic differentiations, hierarchical clustering relationships and population architectures among Shaanxi Han and other 50 populations were further dissected through genetic and bioinformatics analyses. Results indicated that most of the 30 diallelic DIP loci were relatively high polymorphisms in the Shaanxi Han population; and there were the genetically intimate relationships between Shaanxi Han and the East Asian populations. In summary, this study provided significant insights into genetic background of Shaanxi Han population, and the multiplex amplification of these 30 diallelic DIP loci was appropriate for forensic individual identification and population genetic research in Shaanxi Han population.     

Genetic variation at allozyme and RAPD loci in sessile oak Quercus petraea (Matt.) Liebl.: the role of history and geography

The nuclear genetic variation within and among 21 populations of sessile oak was estimated at 31 RAPD loci in conjunction with previous estimates of variation at eight allozyme loci. The aim of the study was to assess the relative role of isolation-by-distance and postglacial history on patterns of nuclear variation. Because of its small effective population size and maternal transmission, the chloroplast genome is a good marker of population history. Both kinds of nuclear variation (RAPD and allozyme) were therefore compared, first, to the geographical distances among populations and, secondly, to chloroplast DNA restriction polymorphism in the same populations. Multiple Mantel tests were used for this purpose. Although RAPDs revealed less genetic diversity than allozymes, levels of genetic differentiation ( G _ST) were identical. The standard genetic distance calculated at all RAPD loci was correlated with geographical distances but not with the genetic distance calculated from chloroplast DNA data. Conversely, allozyme variation was correlated with chloroplast DNA variation, but not with geography. Possibly, divergent selection at two allozyme loci during the glacial period could explain this pattern. Because of its greater number of loci assayed, RAPDs probably provided a less biased picture of the relative role of geography and history.     

Molecular and genetic characterization of the allelic variants of Du215, Du281, Du323, and Du47G microsatellite loci in parthenogenetic lizard <Emphasis Type="Italic">Darevskia armeniaca</Emphasis> (Lacertidae)

A key issue in the study of unisexual (parthenogenetic) vertebrate species is the determination of their genetic and clonal diversity. In pursuing this aim, various markers of nuclear and mitochondrial genomes can be used. The most effective genetic markers include microsatellite DNA, characterized by high variability. The development and characterization of such markers is a necessary step in the genetic studies of parthenogenetic species. In the present study, using locus-specific PCR, for the first time, an analysis of allelic polymorphism of four microsatellite loci is performed in the populations of parthenogenetic species Darevskia armeniaca. In the studied populations, allelic variants of each locus are identified, and the nucleotide sequences of each allele are determined. It is demonstrated that allele differences are associated with the variation in the structure of microsatellite clusters and single nucleotide substitutions at fixed distances in flanking DNA regions. Structural allele variations form haplotype markers that are specific to each allele and are inherited from their parental bisexual species. It is established which of the parental alleles of each locus were inherited by the parthenogenetic species. The characteristics of the distribution and frequency of the alleles of microsatellite loci in the populations of D. armeniaca determining specific features of each population are obtained. The observed heterozygosity of the populations at the studied loci and the mutation rates in genome regions, as well as Nei’s genetic distances between the studied populations, are determined, and the phylogenetic relationships between them are established.     

Limited seed dispersal and microspatial population structure of an agamospermous grass of West African savannahs, Hyparrhenia diplandra (Poaceae)

We studied the microspatial population structure of the perennial tussock grass, Hyparrhenia diplandra (Poaceae), a facultative agamospermous species of West African savannahs. The microspatial population structure of H. diplandra was investigated by choosing two 100-m(2); quadrats at random from which all individuals were mapped. The genotype of every individual was determined using two highly polymorphic microsatellite loci. A chloroplast locus was also used to investigate the role of seed dispersal on the genetic structure of populations. The genetic diversity index (0.85) was high for a clonal species. Significant genetic differentiation over short distances was detected by F statistics, and spatial autocorrelation analyses within both quadrats showed significant isolation-by-distance patterns, both with the cytoplasmic locus and the nuclear loci. Some clones formed large patches (up to 5 m in diameter) whereas others were more scattered. However, the genetic differentiation between quadrats was much higher when studied with the cytoplasmic locus than with the nuclear loci, indicating that gene flow via pollen, but not seeds, may frequently occur between quadrats. The maintenance of genetic diversity in this facultative agamospermous species most likely results from several factors, such as low seed dispersal ability, nonnegligible gene flow through pollen, and selective pressures induced by regularly occurring fires in this ecosystem.     

Allozyme differentiation and genetic structure of the Lady's slipper (Cypripedium calceolus) island populations in north-east Poland

The population genetic structure in the rare and endangered perennial plant, Cypripedium calceolus , from north-east Poland was investigated. A total of 11 loci were analysed, of which five were polymorphic for the species and in every population. The 11 loci resolved gave a total of 19 alleles with the mean number of 1.73 alleles per locus. The proportion of polymorphic loci (P) was the same for the species and in every population, 45.5%. The average observed and expected heterozygosities for the total Lady's slipper data set were 0.156 and 0.184, respectively. The average expected heterozygosity for the populations under study ranged from 0.176 to 0.188 and did not differ significantly among populations. Genetic diversity within C. calceolus populations from the Biebrza Valley is relatively high compared with rare taxa and taxa with similar life histories. The genetic diversity among populations of C. calceolus studied ( F _ST = 0.016) is much smaller than the genetic diversity within populations. In the species studied, there was no significant correlation between genetic and geographical distances ( r = −0.73, Mantel test). This may indicate the relatively recent origin of the populations studied, or a high level of gene flow among populations. © 2002 The Linnean Society of London, Botanical Journal of the Linnean Society , 2002, 138 , 433–440.     

Concordance of genetic divergence among sockeye salmon populations at allozyme, nuclear DNA, and mitochondrial DNA markers

Abstract.— We examined genetic variation at 21 polymorphic allozyme loci, 15 nuclear DNA loci, and mitochondrial DNA in four spawning populations of sockeye salmon ( Oncorhynchus nerka ) from Cook Inlet, Alaska, to test for differences in the patterns of divergence among different types of markers. We were specifically interested in testing the suggestion that natural selection at allozyme loci compromises the effectiveness of these markers for describing the amount and patterns of gene flow among populations. We found concordance among markers in the amount of genetic variation within and among populations, with the striking exception of one allozyme locus ( sAH ), which exhibited more than three times the amount of among-population differentiation as other loci. A consideration of reports of discordance between allozymes and other loci indicates that these differences usually result from one or two exceptional loci. We conclude that it is important to examine many loci when estimating genetic differentiation to infer historical amounts of gene flow and patterns of genetic exchange among populations. It is less important whether those loci are allozymes or nuclear DNA markers.     

Phylogenetic analysis of globally distributed Mycosphaerella graminicola populations based on three DNA sequence loci

DNA sequence data from three nuclear loci were collected from 384 isolates representing fourteen globally distributed populations of the plant pathogenic fungus Mycosphaerella graminicola. Gene genealogies were constructed for the actin and beta-tubulin loci as well as for the previously characterized RFLP locus STS2. The STS2 and beta-tubulin loci showed greater potential for phylogenetic studies than the actin locus. Greater sequence diversity was found in the "Old World" populations (Middle East and Europe) than in the "New World" populations (North and South America and Australia). The gene trees were rooted using homologous DNA sequences of Septoria passerinii, the closest known relative to M. graminicola, as well as coalescent rooting. Based on the rooted trees, a tentative phylogenetic history of these populations was inferred. The Middle East appears to be the most likely center of origin, while European populations are more ancient than New World populations. A test for neutrality indicated that the intron in the actin locus could be under selection, while the other two sequence loci were neutral.     

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.     

Population differentiation and nuclear gene flow in the Dominican anole (Anolis oculatus)

Allele frequency data from nuclear microsatellite loci were used to investigate patterns of nuclear gene flow and population structure in the morphologically variable Dominican anole (Anolis oculatus). All six loci used proved to be highly polymorphic, with an average of 18.8 alleles per locus. Test for Hardy-Weinberg equilibrium revealed small numbers of heterozygote deficiencies at single loci in single populations and consistent patterns of increasingly significant heterozygote deficiency in global tests across populations and loci. No significant relationship between FST and patristic distances estimated from mitochondrial DNA sequences was detected and estimates of FIS were significantly higher in females than in males, indicating that gene flow may be sex-biased and mediated mainly by male migration. A highly significant correlation between linearized FST and loge (geographical distance) indicates that geographical proximity is a significant factor in the genetic structure of A. oculatus populations. However, levels of gene flow between morphologically differentiated parapatric populations are frequently seen to be relatively high. This supports the hypothesis of natural selection being the driving force behind the development and maintenance of morphological variation and shows that adaptive differentiation may be maintained despite the homogenizing influence of gene flow. Generally, the morphologically variable populations of A. oculatus are seen to be poor candidates for in situ speciation, but an exceptional case on the west coast of Dominica indicates that isolation resulting from vicariant events may lead to rapid differentiation at both mitochondrial and nuclear loci. This provides a possible mechanism for anole speciation on other Caribbean islands.     

Loss of genetic diversity and fitness in Common Toad (Bufo bufo) populations isolated by inimical habitat

Measures of genetic diversity (including heterozygosity), survival and developmental homeostasis were found to be significantly lower in small, urban populations of the Common Toad (Bufo bufo) than in larger, rural populations of the same region. The autecology and genetic analysis of this relatively sedentary species suggested that the causal mechanism was genetic drift, arising from barriers to migration created by urban development. The pre-metamorphic survival of larvae cultured in identical conditions increased positively with the mean number of alleles at a locus and the percentage of polymorphic loci. Observed heterozygosity in urban garden and rural populations was correlated inversely with the number of observed physical abnormalities (used as a measure of developmental homeostasis) in the developing tadpoles. Genetic distances between town sites of mean 2.2 km separation were significantly higher than those between rural sites of mean 37 km separation. Genetic data were based on allozyme analysis of 27 loci in 8 urban and 4 rural populations. A subset of these sites (3 urban, 2 rural) were also assessed at 3 minisatellite loci and a positive correlation found between the average number of alleles per locus detected by the two methods. Estimates of Nei's 1972 genetic distance, derived separately from the DNA and protein data, were not, however, correlated. The reduction in genetic diversity and fitness observed in these urban toads provides an example of the effect on population persistence that longer term depletion in numbers and habitat fragmentation can have in the wider environment.     

Allele polymorphism of micro- and minisatellite loci in populations of different regions of Ukraine

The results of molecular-genetic analysis of 12 mini- and microsatellite loci in populations of different regions of Ukraine (Kiev, Kremenchug, L'vov, Lugansk, and in Crimea tatars) were presented. Allele frequencies for each locus were determined and genetic distances between analyzed populations were calculated. The results of the analysis were applied for investigation of genetic heterogeneity and biological history of populations from different regions of Ukraine.     

Local scale population genetic structure of Entomophthora muscae epidemics

Isolates of the entomopathogenic fungus Entomophthora muscae were obtained from houseflies sampled at five stables on Zealand during an epidemic in fall 2005. DNA fingerprints were generated from single conidia from 40 E. muscae isolates using the PCR-based method of Inter-Simple Sequence Repeats (ISSR). This resulted in fingerprint patterns consisting of about 50 fragments, of which, 14 were polymorphic. From the polymorphic loci we estimated the reproductive mode, genetic differentiation and gene diversity of E. muscae populations using the statistics of index of association, Weir & Cockerhams theta and Nei's analysis of gene diversity in subdivided populations. Our results revealed no significant differences in allele frequencies among the five populations. The index of association test rejected the null hypothesis of random mating, but the test for paired locus compatibility showed weak or no linkage between loci indicating recombination or homoplasy in the dataset. From this study we cannot exclude the possibility that the population genetic structure underlying E. muscae epidemics could be panmictic consisting of several lineages with a high level of reciprocal migration.     

Restriction fragment variation in the nuclear and chloroplast genomes of cultivated and wild Sorghum bicolor

Summary Fifty-six accessions of cultivated and wild sorghum were surveyed for genetic diversity using 50 low-copy-number nuclear DNA sequence probes to detect restriction fragment length polymorphisms (RFLPs). These probes revealed greater genetic diversity in wild sorghum than in cultivated sorghum, including a larger number of alleles per locus and a greater portion of polymorphic loci in wild sorghum. In comparison to previously published isozyme analyses of the same accessions, RFLP analysis reveals a greater number of alleles per locus. Furthermore, many RFLP alleles have frequencies between 0.25–0.75, while the vast majority of isozyme alleles are either rare (< 0.25) or near fixation (> 0.75). Correlations between genetic and geographic distances among the accessions were stronger when calculated with RFLP than with isozyme data. Systematic relationships revealed by nuclear and chloroplast restriction site analysis indicate that cultivated sorghum is derived from the wild ssp. arundinaceum. The portion of the wild gene pool most genetically similar to the cultivars is from central-northeastern Africa. Previous published data also suggested that this is most likely the principal area of domestication of sorghum. Introgression between wild and cultivated sorghum was inferred from disconcordant relationships shown by nuclear and chloroplast DNA markers. Introgression apparently occurs infrequently enough that the crop and its wild relatives maintain distinct genetic constitutions.     

A genome scan to detect candidate regions influenced by local natural selection in human populations

As human populations dispersed throughout the world, they were subjected to new selective forces, which must have led to local adaptation via natural selection and hence altered patterns of genetic variation. Yet, there are very few examples known in which such local selection has clearly influenced human genetic variation. A potential approach for detecting local selection is to screen random loci across the genome; those loci that exhibit unusually large genetic distances between human populations are then potential markers of genomic regions under local selection. We investigated this approach by genotyping 332 short tandem repeat (STR) loci in Africans and Europeans and calculating the genetic differentiation for each locus. Patterns of genetic diversity at these loci were consistent with greater variation in Africa and with local selection operating on populations as they moved out of Africa. For 11 loci exhibiting the largest genetic differences, we genotyped an additional STR locus located nearby; the genetic distances for these nearby loci were significantly larger than average. These genomic regions therefore reproducibly exhibit larger genetic distances between populations than the "average" genomic region, consistent with local selection. Our results demonstrate that genome scans are a promising means of identifying candidate regions that have been subjected to local selection.     

Conservation genetics of endangeredBrasenia schreberi based on RAPD and AFLP markers

Brasenia schreberi J.F. Gmelin is a declared endangered species found in the lakes and ponds of South Korea. For planning its conservation strategy, we examined the genetic diversity within and among six populations, using randomly amplified polymorphic DNA (RAPD) and amplified fragment length polymorphism (AFLP). Polymorphisms were more frequently detected per loci with AFLP (69.3%) than RAPD (36.8%). High genetic diversity was recognized within populations: polymorphic loci (PPL) values ranged from 36.3% in the CJM population to 74.5% in the GGT population, with a mean value of 47.8% based on AFLP markers. Great genetic differentiation (θ^B) was detected among the six populations (0.670 on RAPD and 0.196 on AFLP), and we calculated a low rate of gene flow (N_em), i.e., 0.116 on RAPD and 0.977 on AFLP. Furthermore, a Mantel test revealed that no correlation existed between genetic distances and geographical distances among the six local populations, based on RAPD or AFLP markers. These results are attributed to a number of factors, including an insufficient length of time for genetic diversity to be reduced following a natural decline in population size and isolation, adaptation of the genetic system to small population conditions, and a restricted gene flow rate. Based on both its genetic diversity and population structure, we suggest that a strategy for conserving and restoringB. schreberi must focus on maintaining historical processes, such as high levels of outbreeding, while monitoring increased gene flow among populations. This is because a reduction in genetic diversity as a result of genetic drift is undesirable.     

Patterns and levels of genetic differentiation in North American populations of the Alaskan wheatgrass complex

Levels and distribution of genetic variation were assessed using six allozymes in 27 populations of Alaskan wheatgrass (Elymus alaskanus) from different locations in Canada, USA, Greenland and Russia to obtain information on the genetic structure of these populations. The enzyme systems were ACO, DIA, GPI, MDH, PGM and SKD. Allozyme variation at the species level was high, with 64.3% (Ps) of the loci being polymorphic, an average number of alleles per locus of 1.9 (As), and an average genetic diversity of 0.17 (Hes). Differentiation was found in the populations studied, with the following findings: (1) statistically significant differences were found in allele frequencies among populations for every polymorphic locus (P < 0.001); (2) 63% of the total allozyme variation at polymorphic loci was partitioned among populations (GST = 0.63); (3) relatively low mean genetic distances between the populations were obtained (mean D = 0.029); (4) the genetic structure of Russian populations are clearly distinct from the other populations, the cluster and principal component analyses revealed the same genetic patterns of relationships among populations. This study also indicates that E. alaskanus contains different levels of allozyme variation in its populations. Furthermore, some banding patterns at the loci Aco-1, Aco-2, Gpi-2, Mdh-1, Skd-1, Skd-2 can be used as markers to identify individual populations.     

Correlation between genetic distances based on single loci and on skeletal morphology in inbred mice

Genetic and morphometric distances between 12 inbred strains of mice ranging from closely related substrains to a sub-species were estimated using published data on single locus polymorphisms, and on the basis of up to 44 measurements on seven different bones, respectively. Simulation was also used to investigate sampling effects for the single loci. There were strong and statistically highly significant correlations among all measures of genetic distance ranging from 0.58 for the comparison of single loci with the logarithm of the Mahalanobis distance based on 24 measurements on four bones, to 0.72 for estimates of genetic distance based on single loci and the morphology of the mandible. These findings are in sharp contrast with those of Wayne & O'Brien (1986) who claimed that 'structural gene and morphometric variation of mandible traits are uncoupled between mouse strains'. Their failure to find such a correlation is probably because their sample of inbred strains included only a single pair of closely related substrains, and no substrains separated for less than 40 years, and because they failed to correct for non-linearity between morphometric and single-locus measurement scales. Simulations and regression analysis suggested that genetic distances could be estimated with approximately equal precision using morphological data on bone measurements or about 10 cladistically informative single loci, which would usually involve sampling about 50 loci. Data based on single-gene markers is usually more informative than morphometric data for studying the similarity of independently-derived strains. However, similarities among closely related populations such as sublines of an inbred strain can usually be studied more efficiently using morphometry.     

濒危灌木长叶红砂遗传多样性的RAPD分析

应用RAPD分子标记对濒危灌木长叶红砂(Reaumuria trigyna)种群遗传多样性进行了分析.应用18条随机引物对长叶红砂5个种群的95个个体进行扩增,检测到118个位点,其中多态位点105个.结果表明:长叶红砂种群的多态位点比率(P)为88.98%,显示出长叶红砂种群存在较高的遗传多样性.Shannon多样性指数(0.4966)、Nei基因多样性指数(0.3303)和基因分化系数(Gst=0.1425)的分析结果显示,长叶红砂种群遗传变异大多存在于种群内,种群间的遗传分化占14.25%.聚类分析表明,长叶红砂种群遗传距离与地理距离之间无直接相关关系.遗传多样性水平与物种特性和所处不同群落有关,濒危植物并不一定表现为遗传变异水平的降低.     

Genetic affinities of Jewish populations.

Genetic relations between various Jewish (J) and non-Jewish (NJ) populations were assessed using two sets of data. The first set contained 12 pairs of matched J and NJ populations from Europe, the Middle East, and North Africa, for which 10 common polymorphic genetic systems (13 loci) were available. The second set included 22 polymorphic genetic systems (26 loci) with various numbers of populations (ranging from 21 to 51) for each system. Therefore, each system was studied separately. Nei's standard genetic distance (D) matrices obtained for these two sets of data were tested against design matrices specifying hypotheses concerning the affiliations of the tested populations. The tests against single designs were carried out by means of Mantel tests. Our results consistently show lower distances among J populations than with their NJ neighbors, most simply explained by the common origin of the former. Yet, there is evidence also of genetic similarity between J and corresponding NJ populations, suggesting reciprocal gene flow between these populations or convergent selection in a common environment. The results of our study also indicate that stochastic factors are likely to have played a role in masking the descent relationships of the J populations.