Genetic microstructure in two Spanish cat populations. II: gametic disequilibrium and spatial autocorrelation

In a previous publication, we described some aspects of the microgenetic structure of two Spanish cat populations (in Barcelona and Alicante). In the present study, the possible existence ofgametic disequilibrium and spatial genetic structure for these populations, at the coat colour pattern and length genes O, A, T D, L, S and W, was analyzed. There was little gametic disequilibrium between pairs of these loci, despite certain pairs that showed significant systematic gametic disequilibrium (a-d and O-S), which appears to show the action of natural selection on domestic cat populations. Nevertheless, we believe that the major cause of the small amount of gametic disequilibrium found was probably a combination of gene drift and gene flow. The results obtained here were clearly in disagreement with those of Hedrick (1985), who concluded that epistatic selection was the cause of the gametic disequilibrium that he found in cat populations. We also found that although Hardy-Weinberg equilibrium could not be demonstrated, the gametic disequilibrium statistics were not affected by this fact, adding credence to the estimates obtained. We found no genetic spatial structure inside the city of Barcelona, as shown by analysis of the spatial autocorrelation of the individual loci, and analysis of the coordinates of the two first axes of a multidimensional scale. However, some gametic disequilibrium statistics showed certain spatial patterns, which leads us to consider the possibility of several evolutionary processes acting upon some of Barcelona's cat colonies.     

Population Genetics of Euphydryas Butterflies. I. Genetic Variation and the Neutrality Hypothesis

Twenty-one populations of the checkerspot butterfly, Euphydryas editha, and ten populations of Euphydryas chalcedona were sampled for genetic variation at eight polymorphic enzyme loci. Both species possessed loci that were highly variable from population to population and loci that were virtually identical across all populations sampled. Our data indicate that the neutrality hypothesis is untenable for the loci studied, and therefore selection is indicated as the major factor responsible for producing these patterns. Thorough ecological work allowed gene flow to be ruled out (in almost all instances) as a factor maintaining similar gene frequencies across populations. The Lewontin-Krakauer test indicated magnitudes of heterogeneity among standardized variances of gene frequencies inconsistent with the neutrality hypothesis. The question of whether or not to correct this statistic for sample size is discussed. Observed equitability of gene frequencies of multiple allelic loci was found to be greater than that predicted under the neutrality hypothesis. Genetic differentiation persisting through two generations was found between the one pair of populations known to exchange significant numbers of individuals per generation. Two matrices of genetic distance between populations, based on the eight loci sampled, were found to be significantly correlated with a matrix of environmental distance, based on measures of fourteen environmental parameters. Correlations between gene frequencies and environmental parameters, results of multiple regression analysis, and results of principle component analysis showed strong patterns of association and of "explained" variation. The correlation analyses suggest which factors might be further investigated as proximate selective agents.     

重要昆虫病原真菌粉棒束孢种群的遗传分化

粉棒束孢是一种重要的昆虫病原真菌.运用ISSR分子标记研究了安徽省6个不同地理环境的粉棒束孢种群遗传异质性.结果表明:10个多态性引物多态位点百分率高达98.5％,但种群水平的多态位点差异较大,在59.6％ - 93.2％.基于Nei遗传异质性分析得出各种群间的遗传分化系数(Gst)为0.3365,基因流(Nm)为0.4931;各种群间的遗传分化低于种群内的遗传分化,表明安徽省粉棒束孢的遗传变异主要存在于种群内.根据各菌株间的遗传相似系数进行UPGMA聚类,结果表明,西山种群是单系的同质种群,其余5个种群皆为多系的异质种群,其中鹞落坪种群的异质性最高,琅琊山种群异质性最低.各种群之间的地理距离与遗传距离之间无相关关系.根据6个种群间的遗传距离进行UPGMA聚类,可将它们分成3个类群,分类的结果与各种群的地理环境相符,反映出环境的异质性对种群异质性的影响.     

Genetic diversity and hierarchical population structure of a rare autotetraploid plant,Aster kantoensis (Asteraceae)

We sampled 17 populations of a rare autotetraploid Aster kantoensis (Asteraceae) from three river systems located in central Japan, and studied them for allelic variation at 22 enzyme loci. There was no significant correlation between the actual population size and three genetic diversity parameters, suggesting that the effective population size was very small even for the large populations, i.e., even large populations may still have a high probability of being of recent origin and remain influenced by the founder effect. Compared to other autotetraploid species, the total genetic variation of A. kantoensis is small. The number of alleles and gene diversity of a population were not significantly different among the river systems, although the percentage of polymorphic loci was different. Genetic differentiation among river systems was larger than between populations within the river systems, thereby indicating that gene flow between river systems is small, especially between the Kinu River system and Tama or Sagami River systems.     

瑞士阿尔卑斯山欧洲落叶松居群的遗传变异和分化

应用等位酶分析技术,沿两个海拔梯度在瑞士阿尔卑斯山研究了欧洲落叶松（Larix decidua Mill.)居群内和居群间的遗传多态性,结果表明,多态性位点的比例为22.9%,平均每个位点的等位基因数为1.3,平均期望杂合度为0.095,遗传变异的5.8%存在于居群之间,平均遗传距离为0.006。几个有统计意义的基因频率差别在不同树龄类被发现,正在繁育系数值表明在瑞士阿尔卑斯山欧洲落叶松居群有相当的杂合体缺乏,在阿尔拜特（Ar-pette),海拔最高的亚居群与其他亚居群相比较显示最低的遗传多态性（如显示最低的我态性位点比例和最低的平均期望杂合度）和最大的遗传距离值,在最高亚居群和其他亚居群间的遗传差别暗示奠基效应可能是影响这个定样场所欧洲落叶松居群遗传分化的主要因素。     

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.     

Sampling within the genome for measuring within-population diversity: trade-offs between markers

Experimental results of diversity estimates in a set of populations often exhibit contradictory patterns when different marker systems are used. Using simulations we identified potential causes for these discrepancies. These investigations aimed also to detect whether different sampling strategies of markers within the genome resulted in different estimates of the diversity at the whole genome level. The simulations consisted in generating a set of populations undergoing various evolutionary scenarios which differed by population size, migration rate and heterogeneity of gene flow. Population diversity was then computed for the whole genome and for subsets of loci corresponding to different marker techniques. Rank correlation between the two measures of diversity were investigated under different scenarios. We showed that the heterogeneity of genetic diversity either between loci (genomic heterogeneity, GH) or among populations (population heterogeneity, PH) varied greatly according to the evolutionary scenario considered. Furthermore, GH and PH were major determinants of the level of rank correlation between estimates of genetic diversities obtained using different kinds of markers. We found a strong positive relationship between the level of the correlation and PH, whatever the marker system. It was also shown that, when GH values were constantly low during generations, a reduced number of microsatellites was enough to predict the diversity of the whole genome, whereas when GH increased, more loci were needed to predict the diversity and amplified fragment length polymorphism markers would be more recommended in this case. Finally the results are discussed to recommend strategies for gene diversity surveys.     

八面山银杉林的遗传多样性和群体分化

采用水平淀粉凝胶电泳技术对分布于湖南八面山的濒危植物银杉(cathaya argyrophylla Chun etKuang)的遗传多样性和群体分化进行了初步研究。对13个酶系统25个等位酶位点的检测表明,该地区的银杉林群体遗传变异水平很低,多态位点比率 P=0.28,等位基因平均数 A=1.36,平均期望杂合度He=0.100;但3个小群体间存在着明显的遗传分化,基因分化系数高达G_ST=0.26,明显不同于其它裸子植物的报道。八面山银杉林低水平的遗传变异和明显的群体分化,一方面反映了银杉的古老性和残遗性,另一方面也说明在银杉的进化过程中可能发生了严重的遗传漂变,而且群体之间的基因流明显受阻。     

Genetic structure of the saxicole Pitcairnia geyskesii (Bromeliaceae) on inselbergs in French Guiana

South American inselbergs constitute singular and fragmented habitats in the tropical rain forest. Pitcairnia geyskesii is restricted to these habitats and exhibits both sexual and asexual reproduction. The genetic structure of populations on three inselbergs in French Guiana is examined by analysis of ten isozyme loci. All analyzed populations show high levels of genetic variation. On average, 63.3% of loci per population were polymorphic, with a mean number of 2.21 alleles per polymorphic locus, and mean observed and expected heterozygosities of 0.185 and 0.183, respectively. The analyses of genetic variability displayed at different levels (inselbergs, subpopulations, and mats) give different but complementary information. A significant multilocus disequilibrium was detected in one subpopulation, whereas none was observed within the whole populations sampled on the three inselbergs. Tests on spatial genetic structure indicate a patchy distribution of genotypes on two inselbergs. The data give some insights on the reproductive behavior of P. geyskesii. (1) Efficient sexual reproduction leads to seed recruitment at the level of the inselberg. (2) Both clonality and seed recruitment occur within mats. (3) Vegetative spread by fragmentation is involved in the establishment of new mats. There is substantial differentiation (F(ST) = 0.322) and low gene flow among inselbergs (Nm = 0.234). High genetic diversity within inselbergs appears as a consequence of the association of genet longevity induced by clonal replication and recruitment of new genets produced by sexual reproduction.     

Biochemical genetic variation among populations of the greenshell mussel, Perna canaliculus, from New Zealand: preliminary findings

Seven polymorphic and four monomorphic allozyme loci were assayed from nine wild populations and one cultured population of the endemic New Zealand greenshell mussel, Perna canaliculus. Genetic variation was examined to determine the extent of intra-population subdivision and inter-population variability. Five of seven polymorphic loci exhibited significant heterozygote deficiencies compared to Hardy-Weinberg equilibrium. Population F-statistics indicated that significant genetic heterogeneity exists among populations, indicating that there is insufficient gene flow between geographically isolated populations to create panmixia. The observed genetic heterogeneity among populations is best explained by an isolation-by-distance model of gene flow, which is modified by localized hydrographic conditions. These preliminary findings are discussed in the context of the one previous survey of population genetic variation in P. canaliculus and how this information relates to the gene flow of the greenshell mussel in New Zealand, which is often mediated by human transport from the main collection site of Kaitaia to aquaculture sites throughout the country.     

Genetic Variation and Differentiation of Larix decidua Populations in Swiss Alps (in English)

Genetic diversity within and among six subpopulations of Larix decidua Mill. from two altitudinal transects of Swiss Alps was investigated using 6 enzyme systems coding for 8 loci. Globally, the mean proportion of polymorphic loci was 22.9%, the average number of alleles per locus was 1.3, and the mean expected heterozygosity was 0.095. Only 5.8% of the genetic variation resided among populations. The mean genetic distance was 0.006. Several significant differences of gene frequencies were found between different age classes. Positive values of the species mean fixation index observed in this study suggested a considerable deficit of heterozygotes in the populations of L. decidua of Swiss Alps. At one of the sites (Arpette), the highest subpopulation in elevation gave the lowest level of genetic diversity (as evidenced by the lowest proportion of polymorphic loci and the lowest mean expected heterozygosity) and the largest value of genetic distance when compared to other subpopulations. The genetic differences between the highest subpopulation and the other ones suggest that the founder effect may be an important factor influencing genetic differentiation of L. decidua populations at Arpette transect.     

Genetic population structure in olive fly Bactrocera oleae (Gmelin): gene flow and patterns of geographic differentiation

Four wild Spanish populations of Bactrocera oleae (Gmelin) (Dipt., Tephritidae) were studied by gel electrophoresis, in order to find out their population genetic structure and the relative importance of gene flow in that structure. A great amount of genetic variability was observed. In terms of the pattern of the genetic variability in our populations, the most noticeable characteristics were the similarity of the configuration of allelic frequencies from locality to locality, the existence of exceptions and quantitative differences within that similarity, and the heterogeneity among the variable loci. Gene flow estimated from Wright's method gave a value of Nm = 8.9. However, the F _ST statistic in three of the loci ranged from 0.0451 to 0.0620 indicating a substantial degree of differentiation among populations (P < 0.001). The present observations seem to support the hypothesis that although gene flow could be high ( Nm = 8.9), 'natural' selection, probably due to agricultural practices, may be the major factor responsible for the pattern of the genetic variability observed in B. oleae .     

Genetic diversity within and among 11 juvenile populations of green alder (Alnus crispa) in Canada

Germinated seeds from 11 populations of green alder [ Alnus crispa (Ait.) Pursh] sampled in four Canadian provinces were analysed for electrophoretically demonstrable diversity of 10 enzymes encoded by 15 structural loci. Of these, nine were polymorphic, and on average, 52% of the loci per population were polymorphic. Assuming a diploid model of expression, average level of expected heterozygosity was 0.11 with nearly all populations in Hardy-Weinberg equilibrium for the set of polymorphic loci analysed. No significant inbreeding and associated subpopulation structuring were noted. Rates of gene flow appeared high within and among populations. Although little divergence was observed among populations, genetic and geographical distances between populations were related. Discriminant and cluster analyses revealed a pattern of genetic variation associated with geography. Populations from northern Quebec were poorly differentiated, whereas western populations from Alberta exhibited a larger degree of genetic differentiation. Introgresive hybridization with the sympatric species Alnus sinuata (Regel) Rydberg and partial isolation in the West are suggested as an explanation for this larger differentiation. The occurrence and significance of rare alleles is discussed in relation to the importance of geographical distance in the process of population differentiation in this species.     

Genetic differences and similarities in the introduced population of European beaver (Castor fiber L., 1785) in the Kirov and Novosibirsk regions of Russia

Potential factors were analyzed that affected the formation of gene pools of two introduced beaver populations founded in the 1940s-1950s by releasing beavers from Voronezh oblast and Belarus into rivers of the Kirov and Novosibirsk oblasts. The populations from these two regions were shown to differ in four allozyme loci (Ahd-2, Gpi, Es-5, and Dia-2). Within Kirov oblast, the samples from three tributaries of the Vyatka River differed in three other loci (Ck-1, Gp-9, and Trf). It is suggested that these features of the allele distribution at these loci are explained by the history of the introduced populations, hybridization between beavers from Voronezh oblast and Belarus, and founder effect during the subsequent artificial and spontaneous migration. Generally, genetic differences between the populations in all studied loci were very small: D = 0.02 between populations from different regions and D = 0.01 between populations from the tributaries of third-order rivers of the Kirov oblast. At the same time, disequilibrium was detected for ten polymorphic loci in the combined sample from the populations of Kirov oblast, which indicates the existence of interpopulation heterogeneity at the level of local populations of fourth- and fifth-order rivers. The unexpected finding of a genetic similarity between one studied individual of Tuvinian beaver subspecies (Castor fiber tuvinicus) and C. f. orientoeuropeas was recorded.     

Genetic structure of populations of the domestic cat in Catalonia (Spain) and upper midwestern USA: A microgeographic and macrogeographic study

The genetic structure of natural populations of the domestic cat was examined at the microgeographic level (in the Spanish city of Barcelona) and the macrogeographic level (in Catalonia in Spain, and in upper midwestern USA) using frequency data for seven monogenic morphological traits. At the microgeographic level in the city of Barcelona there was no evidence for nonrandom mating within colonies, and estimates of between-colony gene flow were quite high. At the macrogeographic level, the populations from Catalonia and upper midwestern USA differed in two major respects: (i) The Catalan populations were in reasonably good agreement with expectations of Hardy-Weinberg equilibrium while the North American populations showed some evidence of the Wahlund effect (overall heterozygote deficiency indicating population substructuring). (ii) In the Catalan populations, approximately fifty per cent of the genetic differentiation between populations could be explained by geographical separation while in North America only four per cent of the total differentiation was attributable to geographical distance.     

Microgeographic genetic variation in the apple maggot rhagoletis pomonella

We examined electrophoretic variability at five enzyme loci in the apple maggot fly, Rhagoletis pomonella, on a microgeographic scale. Treating flies from individual hawthorn trees as separate populations, we estimated F(ST) values from allele frequencies. The results indicate that there is significant allele frequency heterogeneity among fly populations over a small spatial scale at some loci but not at others. This variation among loci in degree of differentiation is itself statistically significant, casting doubt on the role of genetic drift in maintaining the heterogeneity. There is also heterogeneity between years in flies from a given tree. These data provide a baseline with which future work on genetic differentiation among apple maggot populations associated with different species of host plants may be compared.     

Island isolation and habitat heterogeneity correlate with DNA variation in a marine snail (Littorina saxatilis)

The null assumption of molecular variation is that most of it is neutral to natural selection. This is in contrast to variation in morphological traits that we generally assume is maintained by selection, and therefore often by selection coupled to environmental heterogeneity in time and space. Examples of molecular variation that vary over habitat-shifts, particularly in allozymes, show that the relative impact of non-neutral variation as compared to neutral variation might be substantial in some systems. To assess the importance of habitat-generated variation in relation to variation generated by random processes in nuclear DNA markers at small spatial scales, we compared the effects of island isolation and habitat heterogeneity on genetic substructuring in a rocky shore snail ( Littorina saxatilis ). This species has a restricted migration among islands owing to the lack of free-floating larvae. Earlier studies show that allozymes vary extensively as a consequence of isolation by water barriers among islands, but also as a consequence of divergent selection among different microhabitats within islands. In the DNA markers we observed genetic differentiation owing to island isolation at three of nine loci. In addition, variation at three loci correlated with habitat type, but the correlation for two of the loci was weak. Overall, isolation contributed slightly more to the genetic variation among populations than did habitat-related factors but the difference was small. It is concluded that both island isolation, which interrupts gene flow, and a heterogeneous habitat cause genetic substructuring at the DNA level in L. saxatilis in the studied area, and thus in this species we need to be somewhat concerned about habitat heterogeneity also at DNA loci.  © 2004 The Linnean Society of London, Biological Journal of the Linnean Society , 2004, 82 , 377–384.     

Among-locus variation in Fst: fish, allozymes and the Lewontin-Krakauer test revisited.

Variation among loci in the distribution of allele frequencies among subpopulations is well known; how to tell when the variation exceeds that expected when all loci are subject to uniform evolutionary processes is not well known. If locus-specific effects are important, the ability to detect those effects should vary with the level of gene flow. Populations with low gene flow should exhibit greater variation among loci in Fst than populations with high gene flow, because gene flow acts to homogenize allele frequencies among subpopulations. Here I use Lewontin and Krakauer's k statistic to describe the variance among allozyme loci in 102 published data sets from fishes. As originally proposed, k > 2 was considered evidence that the variation in Fst among loci is greater than expected from neutral evolution. Although that interpretation is invalid, large differences in k in different populations suggest that locus-specific forces may be important in shaping genetic diversity. In these data, k is not greater for populations with expected low levels of gene flow than for populations with expected high levels of gene flow. There is thus no evidence that locus-specific forces are of general importance in shaping the distribution of allele frequencies at enzyme loci among populations of fishes.     

Estimates of gene flow, genetic substructure and population heterogeneity in bracken (Pteridium aquilinum)

Bracken [ Pteridium aquilinum (L.) Kuhn] is a cosmopolitan species and is a noxious weed in many areas. Because of its abundance, particularly in Britain, bracken affords an ideal system for investigating various aspects of population genetics and evolution. High mobility of dispersal units (spores) suggests that rates of gene flow among distant populations should be high. Gene flow is a major evolutionary force that influences the genetic structure of populations. To examine the effects of gene flow on population heterogeneity and population substructuring in bracken, starch gel electrophoresis of enzymes was used to provide the necessary genetic database. Allele frequency data at 21 loci were obtained for seven British populations, one Majorcan and one from the eastern United States. A model was employed to estimate the amount of gene flow ( Nm ) at several levels. Gene flow among British populations was extremely high ( Nm = 36.51), one of the highest estimates reported for plants. Among eight European populations gene flow was lower (but still considered high) at Nm = 2.47. Trans-Atlantic gene flow was low ( Nm = 0.0926).
F -statistics were used to assess population heterogeneity and substructuring. The data indicate that, compared with other species, there is very little genetic differentiation among British populations of bracken. Indeed, it appears that the whole island is behaving as a single randommating population. This result is consistent with high levels of gene flow. Only one population (on the Isle of Arran) showed statistically significant genetic substructuring. Habitat heterogeneity on the island and age structure are hypothesized as possible causes of this result.
The data reported here support previous studies demonstrating that bracken is genetically polymorphic and is an outcrossing species.     

Genetic differentiation in red‐bellied piranha populations (Pygocentrus nattereri,Kner, 1858) from the Solimões‐Amazonas River

Red‐bellied piranhas (Pygocentrus nattereri) are widely caught with different intensities throughout the region of Solimões‐Amazonas River by local fishermen. Thus, the management of this resource is performed in the absence of any information on its genetic stock. P. nattereri is a voracious predator and widely distributed in the Neotropical region, and it is found in other regions of American continent. However, information about genetic variability and structure of wild populations of red‐bellied piranha is unavailable. Here, we describe the levels of genetic diversity and genetic structure of red‐bellied piranha populations collected at different locations of Solimões‐Amazonas River system. We collected 234 red‐bellied piranhas and analyzed throughout eight microsatellite markers. We identified high genetic diversity within populations, although the populations of lakes ANA, ARA, and MAR have shown some decrease in their genetic variability, indicating overfishing at these communities. Was identified the existence of two biological populations when the analysis was taken altogether at the lakes of Solimões‐Amazonas River system, with significant genetic differentiation between them. The red‐bellied piranha populations presented limited gene flow between two groups of populations, which were explained by geographical distance between these lakes. However, high level of gene flow was observed between the lakes within of the biological populations. We have identified high divergence between the Catalão subpopulation and all other subpopulations. We suggest the creation of sustainable reserve for lakes near the city of Manaus to better manage and protect this species, whose populations suffer from both extractive and sport fishing.