High population differentiation and unusual haplotype structure in a shade-intolerant pioneer tree species, Zanthoxylum ailanthoides (Rutaceae) revealed by analysis of DNA polymorphism at four nuclear loci

Differences in demographic history, life-history traits, and breeding systems affect nucleotide variation patterns. It is expected that shade-intolerant pioneer tree species have different patterns of genetic polymorphism and population structure than climax species. We studied patterns of nucleotide polymorphism at four putative starch pathway loci (agpSA, agpSB, agpL, and GBSSI) in Zanthoxylum ailanthoides , a shade-intolerant pioneer tree species that occupies forest gaps in warm-temperate forests of East Asia. Genetic diversity was lower within each population than among populations, and differentiation among populations was high across the loci ( F _ST = 0.32–0.64), as expected from the insect-pollinated breeding system and the metapopulation structure of this pioneer species. Numbers of haplotypes were smaller than those expected from the observed numbers of segregating sites. Single haplotypes accounted for more than 47% of all the sampled genes at the respective loci. These variation patterns were incompatible with neutral predictions for populations of a finite island model. Complex population dynamics, such as bottleneck and/or admixture, in the history of this pioneer tree species might have resulted in the observed patterns of genetic variation and population structure, which are different from those of climax wind-pollinated tree species, such as conifers. In contrast to the other loci investigated in this study, agpL showed nearly no variation in Z. ailanthoides (one singleton only), but there was some extent of variation in a closely related species, Zanthoxylum schinifolium . This suggests possibly a recent selective sweep at or near the locus in Z. ailanthoides .     

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.     

Genetic structure of endangered Emmenopterys henryi Oliv. based on ISSR polymorphism and implications for its conservation

Inter-simple sequence repeat (ISSR) markers were used to determine the genetic variation and genetic differentiation of nine populations of Emmenopterys henryi Oliv., an endangered plant endemic to China. Relatively low genetic diversity was detected at population level (the percentage of polymorphic loci P=22.56%, the number of alleles per locus A=1.183+/-0.045, the effective number of alleles per locus A(E)=1.007+/-0.345, Nei's gene diversity h=0.071+/-0.017, Shannon information index I=0.104+/-0.025). However, the genetic diversity at species level was relatively high (P=56.05%; A=1.561+/-0.498, A(E)=1.325+/-0.371, h=0.191+/-0.199, I=0.287+/-0.284). Analysis of molecular variance showed that most of the ISSR variation (68.03%) in E. henryi occurred among populations. The estimated Nm from F (ST )was 0.235. It indicated that the fragmentation and isolation of populations might result from specific evolutionary history and anthropogenic activity. Consequently, genetic drift might play an important role in determining the genetic structure of E. henryi. Conservation strategies for this endangered species are proposed based on the genetic data.     

Genetic Variation of Microsatellite Loci in the Major Histocompatibility Complex (MHC) Region in the Southeast Asian House Mouse (<Emphasis Type="Italic">Mus musculus castaneus</Emphasis>)

Major histocompatibility complex (MHC) genes are the most polymorphic loci known for vertebrates. Here we employed five microsatellite loci closely linked to the MHC region in an attempt to study the amount of genetic variation in 19 populations of the southeast Asian house mouse (Mus musculus castaneus) in Taiwan. The overall polymorphism at the five loci was high (H_e = 0.713), and the level of polymorphism varied from locus to locus. Furthermore, in order to investigate if selection is operating on MHC genes in natural mouse populations, we compared the extent and pattern of genetic variation for the MHC-linked microsatellite loci (the MHC loci) with those for the microsatellite loci located outside the MHC region (the non-MHC loci). The number of alleles and the logarithm of variance in repeat number were significantly higher for the MHC loci than for the non-MHC loci, presumably reflecting linkage to a locus under balancing selection. Although three statistical tests used do not provide support for selection, their lack of support may be due to low statistical power of the tests, to weakness of selection, or to a profound effect of genetic drift reducing the signature of balancing selection. Our results also suggested that the populations in the central and the southwestern regions of Taiwan might be one part of a metapopulation structure.     

Allozyme variation in the three extant populations of the narrowly endemic cycad Dioon angustifolium Miq. (Zamiaceae) from North-eastern Mexico

BACKGROUND AND AIMS: Dioon angustifolium was considered within D. edule. Recent morphometric and allozyme studies on D. edule have shown that D. angustifolium has originated from geographic isolation and is therefore considered to be a separate species. This cycad is endemic to north-eastern Mexico and is known only from three populations in the Sierra Madre Oriental mountain chain. Its populations are small when compared with its southern relative D. edule. In this study, genetic variation was determined within and between populations of D. angustifolium and the genetic consequences of habitat fragmentation and isolation of populations of this species were assessed. METHODS: Allozyme electrophoresis of 14 presumptive loci was used. The data were analysed with statistical approximations for estimating genetic diversity, structure, gene flow and recent genetic bottlenecks. KEY RESULTS: Means and standard deviations of genetic diversity estimators were: number of alleles per locus (A = 1.67 +/- 0.23), percentage of polymorphic loci (P = 52.4 +/- 23 %) and expected heterozygosity (H(E) = 0.218 +/- 0.093). The genetic variation attributable to differences among populations was 16.7 %. Mean gene flow between paired populations was Nm = 1.55 +/- 0.67, which is similar to that reported for endemic plant species of narrow geographical distribution and species with gravity-dispersed seed. A recent bottleneck is detected in the populations studied. CONCLUSIONS: Dioon angustifolium presents high levels of genetic diversity compared with other cycad species, in spite of small population sizes. The recent bottleneck effect did not effectively reduce the genetic variation to the extent of eliminating these populations. The distribution of D. angustifolium appears to be the result of historical biogeographical effects related to the Pleistocene glaciations. It is recommended that this species be catalogued in the IUCN Red List of Threatened Species and conservation efforts be made to preserve it.     

Isozyme variation in roe deer in relation to their population history in Britain

The level of genetic variation in 245 roe deer (Cupreolus cupreolus L.), taken from 15 populations across Britain, was estimated by investigating electrophoretic polymorphism at 15 enzyme loci. The proportion of polymorphic loci and the average heterozygosity of roe deer in Britain were estimated as 13.3% and 3.2%, respectively. Allele frequencies at one locus suggested the existence of an east-west cline of an allelic variant in southern Britain which may have originated from an introduction of roe from continental Europe in the last century. These results are discussed in relation to the theoretical expectations for this species and the documented historical background of roe deer inBritain.     

中国沿海中部珊瑚菜居群等位酶变异及其遗传多样性

利用聚丙烯酰胺凝胶电泳方法,分析了我国沿海中部（江苏、山东和浙江）海滨沙滩珊瑚菜（Glehnia littoralis Fr.Schmidt ex Miq.)7个居群8种酶系统19个位点的等位基因遗传变异特征,结果表明居群内多态位点比率平均为82．4％,每一位点平均等位基因数为2．77,有效等位基因数为2．24,固定指数F的平均值为－0．091。珊瑚菜居群基因多样性80．9％产生于居群内,19．1％产生于居群间。居群间的遗传距离平均为0．317,遗传一致性为0．728,居群内维持着较高水平的遗传多样性。据此,对珊瑚菜的渐危机理进行了讨论。     

Allelic variation at (TAA)n microsatellite loci in a world collection of chickpea (Cicer arietinum L.) germplasm

A set of 12 randomly selected (TAA)_n microsatellite loci of the cultivated chickpea (Cicer arietinum L.) were screened in a worldwide sample comprising 72 landraces, four improved cultivars and two wild species of the primary gene pool (C. reticulatum and C. echinosperum) to determine the level and pattern of polymorphism in these populations. A single fragment was amplified from all the accessions with each of 12 sequence-tagged microsatellite site markers, except for one locus where no fragment was obtained from either of the two wild species. There was a high degree of intraspecific polymorphism at these microsatellite loci, although isozymes, conventional RFLPs and RAPDs show very little or no polymorphism. Overall, the repeat number at a locus (excluding null alleles) ranged from 7 to 42. The average number of alleles per locus was 14.1 and the average genetic diversity was 0.86. Based on the estimates obtained, 11 out of the 12 frequency distributions of alleles at the loci tested can be considered to be non-normal. A significant positive correlation between the average number of repeats (size of the locus) and the amount of variation was observed, indicating that replication slippage may be the molecular mechanism involved in generation of variability at the loci. A comparison between the infinite allele and stepwise mutation models revealed that for 11 out of the 12 loci the number of alleles observed fell in between the values predicted by the two models. Phylogenetic analysis of microsatellite polymorphism in C. arietinum showed no relationship between accession and geographic origin, which is compatible with the recent expansion of this crop throughout the world. Received: 18 September 1998 / Accepted: 2 December 1998     

Absence of population genetic differentiation in the New Zealand greenshell mussel Perna canaliculus (Gmelin 1791) as assessed by allozyme variation

Genetic variation in the endemic New Zealand greenshell mussel, Perna canaliculus (Gmelin 1791), was examined using starch-gel electrophoresis at seven protein-coding loci (Idh; Acon-1; Acon-2; Gpd; Pgi; Pgm; Pgd) in 35 populations (N=1038 mussels). For all loci and all populations, Fisher's exact tests indicated highly significant departures from Hardy-Weinberg equilibrium (HWE), but this overall result was caused by significant heterozygote deficiencies at only two loci (Pgm and Pgd), and in only three northern populations (Kuaotunu, Te Haumi and Days Bay). Allelic and genotypic differentiation between population pairs at individual loci and across all loci were nonsignificant, and genotypic disequilibrium at each locus pair was also nonsignificant for all populations. Genetic variation in all populations was high (mean heterozygosity, 0.210+/-0.113), while Nei's D among populations was very low (0.002+/-0.002). Low population subdivision (θ=-0.001+/-0.002) and high levels of gene flow (Nm(p)=10.18; Nm(θ)=infinity) also indicated that the single panmictic unit model best explains population genetic homogeneity in P. canaliculus over a north-south distance >2000 km. Lack of genetic subdivision in this species is discussed in light of two previous allozyme studies, with differing results: one suggested that a north-south division exists between greenshell mussel stocks, and the other suggested that population structure in this species can be explained through isolation by distance model modified by local hydrology.     

Molecular polymorphism: How much is there and why is there so much?

The evidence for genetic variation can be traced to Mendel's experiments: The discovery of the laws of heredity was made possible by the expression of segregating alleles. Since that time, the study of genetic variation in natural populations has been characterized by a gradual discovery of ever-increasing amounts of genetic variation. In the early decades of this century geneticists thought that an individual is homozygous at most gene loci and that individuals of the same species are genetically almost identical. Recent discoveries suggest that, at least in outcrossing organisms, the DNA sequences inherited one from each parent are likely to be different for nearly every gene locus in every individual; ie, that every individual may be heterozygous at most, if not all, gene loci. But the efforts to obtain precise estimates of genetic variation have been thwarted for various reasons.     

Enzyme Variability in the DROSOPHILA WILLISTONI Group. IV. Genic Variation in Natural Populations of DROSOPHILA WILLISTONI

We describe allelic variation at 28 gene loci in natural populations of D. willistoni. Seventy samples were studied from localities extending from Mexico and Florida, through Central America, the West Indies, and tropical South America, down to South Brazil. At least several hundred, and often several thousand, genomes were sampled for each locus. We have discovered a great deal of genetic variation. On the average, 58% loci are polymorphic in a given population. (A locus is considered polymorphic when the frequency of the most common allele is no greater than 0.95). An individual fly is heterozygous, on the average, at 18.4% loci.-Concerning the pattern of the variation, the most remarkable finding is the similarity of the configuration of allelic frequencies from locality to locality throughout the distribution of the species. Our observations support the conclusion that balancing natural selection is the major factor responsible for the considerable genetic variation observed in D. willistoni.     

Electrophoretic variation in six populations of brown trout (Salmo trutta L.)

Starch gel electrophoretic studies of 16 enzymes encoded by 34 Loci were performed on six brown trout populations. One new polymorphism is described at the Pmi-2 locus. Breeding data were analysed for both single and joint segregation of six loci: Aat-1, Cpk-1, G3p-2, Mdh-2, Mdh-3, and Pmi-2. All the loci are shown to segregate in simple mendelian ratios and one nonrandom joint segregation was observed. The polymorphism level, heterozygosities, and genetic distances were estimated and compared with those reported in other studies on brown trout and closely related salmonid species. The polymorphism level (25%) and average heterozygosity (9%) were high. Significant genetic distances were observed, but the average degree of differentiation between populations appeared to be small (9% of the total heterozygosity).     

An analysis of selection on a colour polymorphism in the northern leopard frog

In this study, we investigated the role of selection in the maintenance of a dorsal colour polymorphism in natural populations of the northern leopard frog, Rana pipiens. We determined genetic structure both spatially and temporally from a suite of putatively neutral molecular markers and tested whether or not the colour locus exhibited patterns of genetic variation that differed from those of the neutral loci. Spatial genetic structure at the colour locus was indistinguishable from structure at neutral loci [95% confidence intervals of F(ST) (neutral) = (0.07, 0.35), F(ST) (colour locus) = 0.114]. In the temporal analysis, we found that the variance among populations in the change in allele frequency at the colour locus (equal to 0.004) lies within the 95% confidence intervals for the variance among populations in changes in allele frequencies at neutral loci. In light of our inability to show evidence for the selective maintenance of the colour polymorphism, we used computer simulations to infer the power of our spatial and temporal techniques to detect selection. The computer simulations showed that although the strength of selection (s) would need to be relatively strong to have been detected by the temporal approach (s = 0.1-0.4, depending on the model tested), the spatial analysis would have detected all but weak selection (s = 0.01-0.04, depending on the model tested). This study illustrates the importance of using a locus comparison approach to detect evidence for selective maintenance before conducting studies to measure the selective mechanisms maintaining a polymorphism.     

Population genetic structure of the African elephant in Uganda based on variation at mitochondrial and nuclear loci: evidence for male-biased gene flow

A drastic decline has occurred in the size of the Uganda elephant population in the last 40 years, exacerbated by two main factors; an increase in the size of the human population and poaching for ivory. One of the attendant consequences of such a decline is a reduction in the amount of genetic diversity in the surviving populations due to increased effects of random genetic drift. Information about the amount of genetic variation within and between the remaining populations is vital for their future conservation and management. The genetic structure of the African elephant in Uganda was examined using nucleotide variation of mitochondrial control region sequences and four nuclear microsatellite loci in 72 individuals from three localities. Eleven mitochondrial DNA (mtDNA) haplotypes were observed, nine of which were geographically localized. We found significant genetic differentiation between the three populations at the mitochondrial locus while three out of the four microsatellite loci differentiated KV and QE, one locus differentiated KV and MF and no loci differentiated MF and QE. Expected heterozygosity at the four loci varied between 0.51 and 0.84 while nucleotide diversity at the mitochondrial locus was 1.4%. Incongruent patterns of genetic variation within and between populations were revealed by the two genetic systems, and we have explained these in terms of the differences in the effective population sizes of the two genomes and male-biased gene flow between populations.     

Genetic consequences of a single-founder population bottleneck in Trifolium amoenum (Fabaceae)

We investigated the genetic consequences of a single-founder bottleneck in a population of showy Indian clover (Trifolium amoenum), a species presumed to be extinct until rediscovered near Occidental, California, in 1993. Electrophoretic variation was evaluated in the bottlenecked population and in a larger population (Dillon Beach) discovered during the course of this study, as well as in populations of two closely related species, T. albopurpureum var. dichotomum and T. macraei. We found a surprisingly high amount of polymorphism in the single-founder T. amoenum population from Occidental (15% of loci polymorphic; an average of 1.1 alleles per locus). However, this represents a 53% reduction in number of polymorphic loci and a 20% reduction in average number of alleles per locus compared to three Trifolium populations with putatively similar mating systems (the Dillon Beach T. amoenum population and both populations of T. albopurpureum var. dichotomum). Expanding the genetic base of the Occidental T. amoenum population is a priority due to concerns about loss of evolutionary potential and the possibility of deleterious effects associated with inbreeding. However, using seed from the Dillon Beach T. amoenum population may not be beneficial due to distinct, presumably adaptive differences between plants from the two populations and concerns about outbreeding depression.     

An estimate of the amount of genetic variation in the common mussel Mytilus edulis

Allozyme variation in a population of the common mussel Mytilus edulis in Mumbles, South Wales, has been studied by starch gel electrophoresis. On the basis of data obtained for 34 loci, we estimate the proportion of loci polymorphic to be 30%. Using only the 29 loci for which individual genotypes can be accurately typed, the average heterozygosity is estimated to be 9.5 +/- 3.6%. The calculated expected average heterozygosity based on Hardy-Weinberg expectations is identical with the observed value. Allele frequency data at six polymorphic loci are given for several other British populations. There is no significant geographic heterogeneity. The results are discussed in relation to genetic adaptive strategies and are shown to be inconsistent with the predictions of the neutral hypothesis.     

High Genetic Variability of Esterase Loci in Natural Populations of Parus major, P. caeruleus, and P. ater

In Parus major, P. caeruleus, and P. ater the genetic variation of 16 isozyme loci was determined. The focus was on esterases that show high phenotypic variation in natural populations of these species. The degree of heterozygosity of the "non-esterase" loci was 0.029 +/- 0.008 (P. major); 0.023 +/- 0.012 (P. caeruleus), and 0.034 +/- 0.034 (P. ater). Including the esterase loci with up to six alleles per locus the overall degree of heterozygosity increased to 0.130 +/- 0.056 (P. major); 0.143 +/- 0.067 (P. caeruleus), and 0.194 +/- 0.090 (P. ater). We explain the high level of variability of esterases by gene amplification and subsequent selection for high allelic heterogeneity. Substrate specificity of loci is assumed to allow for multiple resistance against various toxic components. Large allelic valiation of esterases, therefore, increases the fitness of Parus species and allows for utilizing new food resources.     

Cross-species amplification from crop soybean Glycine max provides informative microsatellite markers for the study of inbreeding wild relatives.

The development of microsatellite markers through transfer of primers from related species (cross-species amplification) remains a little-explored alternative to the de novo method in plants. In this study of 100 microsatellite loci from Glycine max, we examined two aspects of primer transfer. First, we tested if source locus properties can predict primer transfer and polymorphism in Glycine cyrtoloba and Glycine clandestina. We transferred 23 primers to G. cyrtoloba and 42 to G. clandestina, with 19 loci polymorphic within G. clandestina. However, we could not predict transfer or polymorphism from the source locus properties. Second, we evaluated the subset of 11 polymorphic loci for study in G. clandestina populations representing two local morphotypes. All loci were informative within populations (population mean He +/- SE = 0.58 +/- 0.04). We directly sequenced 28 alleles at 4 representative loci. The allelic patterns and sequencing results established that 8 of 11 loci were typical microsatellites, confirming the utility of primer transfer as an alternative to de novo development. Additionally, we found that morphotypic differentiation between populations was paralleled by changes in polymorphism level at six loci and size homoplasy at one locus. We interpret these patterns as being a product of selfing in G. clandestina. Our results demonstrate the value of allele sequence knowledge for the most effective use of microsatellites.     

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.     

Microsatellite Polymorphism in Natural Populations of the Wild Plant Arabidopsis Thaliana

Variation in repeat number at 20 microsatellite loci of Arabidopsis thaliana was studied in a worldwide sample of 42 ecotypes to investigate the pattern and level of polymorphism in repetitive sequences in natural plant populations. There is a substantial amount of variation at microsatellite loci despite the selfing nature of this plant species. The average gene diversity was 0.794 and the average number of alleles per locus was 10.6. The distribution of alleles was centered around the mean of repeat number at most loci, but could not be regarded as normal. There was a significantly positive correlation between the number of repeats and the amount of variation. For most loci, the observed number of alleles was between the expected values of the infinite allele and stepwise mutation models. The two models were rejected by the sign test. Linkage disequilibrium was detected in 12.1% of the pairwise comparisons between loci. In phylogenetic tree, there was no association between ecotype and geographic origin. This result is consistent with the recent expansion of A. thaliana throughout the world.