Allozyme variation of the pygmy wood mouse <Emphasis Type="Italic">Apodemus uralensis</Emphasis> (Rodenita,Muridae) in the ural region

Variation of 17 allozyme loci was examined in 530 Apodemus uralensis individuals caught in the Ural region from 2005 to 2007. In the populations examined, the mean value of the genetic differentiation index F _ST constituted 0.169. It was demonstrated that F _ST values for the samples obtained from the 1-km2 plot in different years, as well as for the samples trapped at a distance from 0.3 to 5 km during one year, could be remarkably higher than the mean value, pointing to their high, statistically significant differentiation. It seems likely that this differentiation was caused by spatial population subdivision, associated with the mice migrations, temporal change of the population structure, and the gene drift. Population of A. uralensis from radioactively contaminated zone displayed no specificities in the allozyme set and frequencies, which could basically distinguish these animals from the other Ural populations.     

F Statistics in Drosophila Buzzatii: Selection, Population Size and Inbreeding

Drosophila buzzatii is confined to reproducing in a well defined patchy environment consisting of rotting cactus cladodes which are ephemeral, permitting at most three generations. Flies emerging from such rots were used to estimate the additive genetic variance within rots and the genetic variance between rots for body size and also were electrophoresed to determine their genotypes at six polymorphic loci. F statistics were estimated from body size and allozyme data. The F(ST) derived from body size was significantly larger than the allozyme F(ST). It is proposed this is due to selective differentiation of body size. The allozyme F(ST) is used to estimate effective population size: 10 < N < 50. It is suggested that the regularly observed positive F(IS)'s could be due to partial sib mating, S. If so, the estimated lower bound is S = 0.258. Experiments are identified which could support or contradict these interpretations.     

Genetic variation in the acorn barnacle from allozymes to population genomics

Understanding the patterns of genetic variation within and among populations is a central problem in population and evolutionary genetics. We examine this question in the acorn barnacle, Semibalanus balanoides, in which the allozyme loci Mpi and Gpi have been implicated in balancing selection due to varying selective pressures at different spatial scales. We review the patterns of genetic variation at the Mpi locus, compare this to levels of population differentiation at mtDNA and microsatellites, and place these data in the context of genome-wide variation from high-throughput sequencing of population samples spanning the North Atlantic. Despite considerable geographic variation in the patterns of selection at the Mpi allozyme, this locus shows rather low levels of population differentiation at ecological and trans-oceanic scales (F(ST)?～?5%). Pooled population sequencing was performed on samples from Rhode Island (RI), Maine (ME), and Southwold, England (UK). Analysis of more than 650 million reads identified approximately 335,000 high-quality SNPs in 19 million base pairs of the S. balanoides genome. Much variation is shared across the Atlantic, but there are significant examples of strong population differentiation among samples from RI, ME, and UK. An F(ST) outlier screen of more than 22,000 contigs provided a genome-wide context for interpretation of earlier studies on allozymes, mtDNA, and microsatellites. F(ST) values for allozymes, mtDNA and microsatellites are close to the genome-wide average for random SNPs, with the exception of the trans-Atlantic F(ST) for mtDNA. The majority of F(ST) outliers were unique between individual pairs of populations, but some genes show shared patterns of excess differentiation. These data indicate that gene flow is high, that selection is strong on a subset of genes, and that a variety of genes are experiencing diversifying selection at large spatial scales. This survey of polymorphism in S. balanoides provides a number of genomic tools that promise to make this a powerful model for ecological genomics of the rocky intertidal.     

Allozyme and microsatellite loci provide discordant estimates of population differentiation in the endangered dusky grouper (Epinephelus marginatus) within the Mediterranean Sea

The dusky grouper, Epinephelus marginatus, inhabits coastal reefs in the Mediterranean Sea and Atlantic Ocean. A decline in the abundance of this long-lived protogynous hermaphrodite has led to its listing as an endangered species in the Mediterranean, and heightened management concerns regarding its genetic variability and population substructure. To address these concerns, we analysed genetic variation at seven microsatellite and 28 allozyme loci in dusky groupers sampled from seven areas (for microsatellites) and three areas (for allozymes) in the west-central Mediterranean. Levels of genetic variability were higher for microsatellites than for allozymes (mean H(E) = 0.78 and 0.07, respectively), but similar to those observed in other marine fishes with comparable markers. Both microsatellites and allozymes revealed significant genetic differentiation among all areas analysed with each class of marker, but the magnitude of differentiation revealed by allozymes over three locales (F(ST) = 0.214) was greater than that detected with microsatellites over seven areas, or over the three areas shared with the allozyme analysis (F(ST) = 0.018 and approximately 0, respectively). A large proportion of the allozyme differentiation was due to a single locus (ADA*) possibly influenced by selection, but allozyme differentiation over the three areas was still highly significant (F(ST) = 0.06, P < 0.0001), and the 95% confidence intervals for allozyme and microsatellite F(ST) did not overlap when this locus was excluded. There was no evidence of isolation by distance with either class of markers. Our results lead us to conclude that dusky groupers are not panmictic in the Mediterranean Sea and suggest that they should be managed on a local basis. However, more work is needed to elucidate genetic relationships among populations.     

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.     

松嫩平原中部地区羊草种群的遗传结构研究

松嫩平原中部地区的羊草,依其生长的微环境不同可分成灰绿色和黄绿色两种叶色类型的种群。移栽实验表明,这两类种群实际上是灰色和灰绿色两种类型的混生群体。采用淀粉凝胶电泳技术及等位酶分析方法测定了不同生境、不同分类种群的遗传结构,发现羊草种群遗传变异度很高;但是无论如何归属,这一草原区域上的羊草种群遗传分化程度很低(FST ≤ 0.034)。这可能与羊草为异花授粉、不同类型混生及种群间基因流强度大有关。     

Gene Flow in European Beech (Fagus sylvatica L.)

Three relatively isolated stands were used to study gene flow in European beech (Fagus sylvatica L.) in Northern Germany. Nine allozyme loci (Got-B, Idh-A, Lap-A, Mdh-B, Mdh-C, Mnr-A, 6-pgdh-A, Pgi-B and Pgm-A) were utilized for multilocus-genotyping adult trees and seeds. Expected heterozygosity (He) ranged from 0.325 to 0.351 for the three stands. F(ST) revealed that there was small differentiation among stands (mean F(ST) = 0.013). The indirect estimates of gene flow (Nm) based on the mean F(ST) were high and the average Nm was 19.14. External gene flow by pollen ranged from 0.7 to 1.2% inferred from new alleles in seed samples. Moreover, paternity analysis was used to assess effective pollen dispersal by inferring paternity of offspring. The weighted mean distances of pollen dispersal for these three stands were 36.8 and 37.1 m based on simple exclusion procedure and most-likely method, respectively. Two of the trees in one stand had rare allozyme alleles (Lap-A1 and Idh-A4, respectively), which were used to directly measure pollen movement away from those trees. The frequency of the rare Lap and Idh alleles in seeds declines as the distance from the source tree increases. The weighted mean distance of pollen dispersal with rare allele Lap-A1 or Idh-A4 was 26.3 m.     

High levels of genetic differentiation of Oryza officinalis Wall. ex Watt. from China

In order to determine the population genetic structure of wild rice (Oryza officinalis Wall. ex Watt.), an endangered tropical and subtropical species, allozyme diversity encoded by 24 loci was analyzed electrophoretically in 145 individuals of eight natural populations from Hainan, Guangxi, and Yunnan provinces, China. A fairly high genetic differentiation (F(ST) = 0.882 and mean I = 0.786) was found among the studied populations. Our results suggest that restricted gene flow may play a significant role in shaping such a population genetic structure. In addition, high genetic differentiation among populations within a geographically limited region may stem from a reduced population size and consequent genetic drift.     

Partitioning and diversity of nuclear and organelle markers in native and introduced populations of Epipactis helleborine (Orchidaceae)

Variability of allozymes (1170 individuals, 47 populations) and chloroplast DNA (692 individuals, 29 populations) was examined in native European and introduced North American populations of Epipactis helleborine (Orchidaceae). At the species level, the percentage of allozyme loci that were polymorphic (P(99)) was 67%, with a mean of 2.11 alleles (A) per locus, and an expected heterozygosity (H(exp)) of 0.294. At the population level, mean P(99) = 56%, mean A = 1.81, and mean H(exp) = 0.231. Although field observations suggest that self-pollination occurs frequently, populations had a genetic structure consistent with Hardy-Weinberg expectations and random mating (mean F(IS) = 0.002). There was significant deviation from panmixia associated with population differentiation (mean F(ST) = 0.206). The distribution of two chloroplast haplotypes showed that 15 of the 29 populations were polymorphic. Using both nuclear and organelle F(ST) estimates, a pollen to seed flow ratio of 1.43?:?1 was calculated. This is very low compared with published estimates for other plant groups, consistent with the high dispersability of orchid seeds. Finally, there was no evidence for a genetic bottleneck associated with the introduction of E. helleborine to North America.     

Molecular and quantitative genetic differentiation across Europe in yellow dung flies

Relating geographic variation in quantitative traits to underlying population structure is crucial for understanding processes driving population differentiation, isolation and ultimately speciation. Our study represents a comprehensive population genetic survey of the yellow dung fly Scathophaga stercoraria, an important model organism for evolutionary and ecological studies, over a broad geographic scale across Europe (10 populations from the Swiss Alps to Iceland). We simultaneously assessed differentiation in five quantitative traits (body size, development time, growth rate, proportion of diapausing individuals and duration of diapause), to compare differentiation in neutral marker loci (F(ST)) to that of quantitative traits (Q(ST)). Despite long distances and uninhabitable areas between sampled populations, population structuring was very low but significant (F(ST) = 0.007, 13 microsatellite markers; F(ST) = 0.012, three allozyme markers; F(ST) = 0.007, markers combined). However, only two populations (Iceland and Sweden) showed significant allelic differentiation to all other populations. We estimated high levels of gene flow [effective number of migrants (Nm) = 6.2], there was no isolation by distance, and no indication of past genetic bottlenecks (i.e. founder events) and associated loss of genetic diversity in any northern or island population. In contrast to the low population structure, quantitative traits were strongly genetically differentiated among populations, following latitudinal clines, suggesting that selection is responsible for life history differentiation in yellow dung flies across Europe.     

Distinguishing adaptive from nonadaptive genetic differentiation: comparison of Q(ST) and F(ST) at two spatial scales

Genetic differentiation in 20 hierarchically sampled populations of wild barley was analyzed with quantitative traits, allozymes and Random Amplified Polymorphic DNAs (RAPDs), and compared for three marker types at two hierarchical levels. Regional subdivision for both molecular markers was much lower than for quantitative traits. For both allozymes and RAPDs, most loci exhibited minor or no regional differentiation, and the relatively high overall estimates of the latter were due to several loci with exceptionally high regional differentiation. The allozyme- and RAPD-specific patterns of differentiation were concordant in general with one another, but not with quantitative trait differentiation. Divergent selection on quantitative traits inferred from very high regional Q(ST) was in full agreement with our previous results obtained from a test of local adaptation and multilevel selection analysis. In contrast, most variation in allozyme and RAPD variation was neutral, although several allozyme loci and RAPD markers were exceptional in their levels of regional differentiation. However, it is not possible to answer the question whether these exceptional loci are directly involved in the response to selection pressure or merely linked to the selected loci. The fact that Q(ST) and F(ST) did not differ at the population scale, that is, within regions, but differed at the regional scale, for which local adaptation has been previously shown, implies that comparison of the level of subdivision in quantitative traits, as compared with molecular markers, is indicative of adaptive population differentiation only when sampling is carried out at the appropriate scale.     

Comparison of population genetic structures of common wild rice (Oryza rufipogon Griff.), as revealed by analyses of quantitative traits, allozymes, and RFLPs

We investigated genetic diversity among and within natural populations of Asian common wild rice, Oryza rufipogon, from three different classes of data: quantitative traits, allozymes, and restriction fragment length polymorphisms (RFLPs). The seven populations examined showed polymorphism to varying degrees. The amount of intrapopulation variability appeared to be influenced not only by breeding system but also by the evolutionary history of each population. Interpopulation differentiation was clear, but different classes of data elucidated different patterns. Quantitative traits revealed ecotype differentiation into perennial and annual types of population, whereas allozyme and RFLP analyses revealed geographical differentiation among populations. These results suggest that the diversity patterns shown by quantitative trait analysis reflect mainly the occurrence of adaptive differentiation in response to habitat conditions and that those shown by allozyme and RFLP analyses reflect mainly the effect of isolation by distance. Population differentiation parameters (F(ST)) were highly variable among loci in allozymes as well as in RFLPs.     

Evidence for contrasting modes of selection at interacting globin genes in the European rabbit (Oryctolagus cuniculus)

In hybrid zones between genetically differentiated populations, variation in locus-specific rates of introgression may reflect adaptation to different environments or adaptation to different genetic backgrounds. The European rabbit, Oryctolagus cuniculus, is well-suited to studies of such hybrid zone dynamics because it is composed of two genetically divergent subspecies that hybridize in a zone of secondary contact in central Iberia. A species-wide survey of allozyme variation revealed a broad range of locus-specific divergence levels (F(ST) ranged from 0 to 0.54, mean F(ST)=0.16). Interestingly, the two loci that fell at opposite ends of the distribution of F(ST) values, haemoglobin alpha-chain (HBA) and haemoglobin beta-chain (HBB), encode interacting subunits of the haemoglobin protein. The contrasting patterns of spatial variation at these two loci could not be reconciled under a neutral model of population structure. The HBA gene exhibited higher-than-expected levels of population differentiation, consistent with a history of spatially varying selection. The HBB gene exhibited lower-than-expected levels of population differentiation, consistent with some form of spatially uniform selection. Patterns of linkage disequilibrium and allele frequency variation do not appear to fit any simple model of two-locus epistatic selection.     

Microsatellite DNA analyses support an east-west phylogeographic split of American alligator populations

We examined the population genetic structure of American alligators (Alligator mississippiensis) sampled from 12 localities across the southeastern United States. The primary goal of this study was to determine the extent of population differentiation among alligators from four Florida lakes using eight microsatellite loci and compare the results to additional sites located at varying distances from them. Analyses of population structure revealed little differentiation (F(ST)=0.039; Rho=0.012) among the four Florida lakes, Apopka, Griffin, Orange and Woodruff, which are all located in the St. John&'s River watershed in north-central Florida. Further, there was little differentiation among these samples and samples collected from the Everglades National Park (F(ST)=0.044; Rho=0.009) and south Georgia (F(ST)=0.045; Rho=0.032). Therefore, these six samples were pooled together as a "FL/sGA group." Similarly, samples collected in the western extent of the range, Anahuac National Wildlife Refuge in Texas and Salvador Wildlife Management Area, Marsh Island Wildlife Refuge and Rockefeller Wildlife Refuge in Louisiana, also lacked population structure (F(ST)=0.024; R(ST)=0.040). These four populations were pooled into the "TX/LA group." Comparisons of these two groups with samples taken from the Santee Coastal Reserve in South Carolina and Mobile, Alabama yielded three to four times more differentiation among groups (F(ST)=0.131; Rho=0.187). These and other analyses support the hypothesis of an east-west phylogeographic split in American alligator populations and are consistent with studies of many freshwater fish and aquatic and terrestrial turtles distributed throughout this same geographic region.     

Population structure of a parasitic plant and its perennial host

Characterization of host and parasite population genetic structure and estimation of gene flow among populations are essential for the understanding of parasite local adaptation and coevolutionary interactions between hosts and parasites. We examined two aspects of population structure in a parasitic plant, the greater dodder (Cuscuta europaea) and its host plant, the stinging nettle (Urtica dioica), using allozyme data from 12 host and eight parasite populations. First, we examined whether hosts exposed to parasitism in the past contain higher levels of genetic variation. Second, we examined whether host and parasite populations differ in terms of population structure and if their population structures are correlated. There was no evidence that host populations differed in terms of gene diversity or heterozygosity according to their history of parasitism. Host populations were genetically more differentiated (F(ST) = 0.032) than parasite populations (F(ST) = 0.009). Based on these F(ST) values, gene flow was high for both host and parasite. Such high levels of gene flow could counteract selection for local adaptation of the parasite. We found no significant correlation between geographic and genetic distance (estimated as pairwise F(ST)), either for the host or for the parasite. Furthermore, host and parasite genetic distance matrices were uncorrelated, suggesting that sites with genetically similar host populations are unlikely to have genetically similar parasite populations.     

If FST does not measure neutral genetic differentiation,then comparing it with QST is misleading. Or is it?

The comparison between neutral genetic differentiation (F(ST) ) and quantitative genetic differentiation (Q(ST) ) is commonly used to test for signatures of selection in population divergence. However, there is an ongoing discussion about what F(ST) actually measures, even resulting in some alternative metrics to express neutral genetic differentiation. If there is a problem with F(ST) , this could have repercussions for its comparison with Q(ST) as well. We show that as the mutation rate of the neutral marker increases, F(ST) decreases: a higher within-population heterozygosity (He) yields a lower F(ST) value. However, the same is true for Q(ST) : a higher mutation rate for the underlying QTL also results in a lower Q(ST) estimate. The effect of mutation rate is equivalent in Q(ST) and F(ST) . Hence, the comparison between Q(ST) and F(ST) remains valid, if one uses neutral markers whose mutation rates are not too high compared to those of quantitative traits. Usage of highly variable neutral markers such as hypervariable microsatellites can lead to serious biases and the incorrect inference that divergent selection has acted on populations. Much of the discussion on F(ST) seems to stem from the misunderstanding that it measures the differentiation of populations, whereas it actually measures the fixation of alleles. In their capacity as measures of population differentiation, Hedrick's G'(ST) and Jost's D reach their maximum value of 1 when populations do not share alleles even when there remains variation within populations, which invalidates them for comparisons with Q(ST) .     

Evidence for fine-scale genetic structure and estuarine colonisation in a potential high gene flow marine goby (Pomatoschistus minutus)

Marine fish seem to experience evolutionary processes that are expected to produce genetically homogeneous populations. We have assessed genetic diversity and differentiation in 15 samples of the sand goby Pomatoschistus minutus (Pallas, 1770) (Gobiidae, Teleostei) from four major habitats within the Southern Bight of the North Sea, using seven microsatellite and 13 allozyme loci. Despite its high dispersal potential, microsatellite loci revealed a moderate level of differentiation (overall F(ST)=0.026; overall R(ST)=0.058). Both hierarchical analysis of molecular variance and multivariate analysis revealed significant differentiation (P<0.01) between estuarine, coastal and marine samples with microsatellites, but not with allozymes. Comparison among the different estimators of differentiation (F(ST) and R(ST)) pointed to possible historical events and contemporary habitat fragmentation. Samples were assigned to two breeding units in the estuary and coastal region. Despite this classification, there were indications of a complex and dynamic spatiotemporal structure, which is, most likely, determined by historical events and local oceanic currents.     

Comparing the genetic structure of codling moth Cydia pomonella (L.) from Greece and France: long distance gene-flow in a sedentary pest species

Codling moth Cydia pomonella L. (Lepidoptera: Tortricidae) is the most important insect pest of apple production in Europe. Despite the economic importance of this pest, there is not information about the genetic structure of its population in Greece and the patterns of gene-flow which might affect the success of control programs. In this study, we analysed nine samples from apple, pear and walnut from various regions of mainland Greece using 11 microsatellite loci. Six samples from the aforementioned hosts from southern France were also examined for comparison. Bayesian clustering and genetic distance analyses separated the codling moth samples in two genetic clusters. The first cluster consisted mainly of the individuals from Greece, and the second of those from France, although admixture and miss-classified individuals were also observed. The low genetic differentiation among samples within each country was also revealed by F(ST) statistics (0.009 among Greek samples and 0.0150 among French samples compared to 0.050 global value among all samples and 0.032 the mean of the pair-wise values between the two countries). These F(ST) values suggest little structuring at large geographical scales in agreement with previous published studies. The host species and local factors (climatic conditions, topography, pest control programs) did not affect the genetic structure of codling moth populations within each country. The results are discussed in relation to human-made activities that promote gene-flow even at large geographic distances. Possible factors for the genetic differentiation between the two genetic clusters are also discussed.     

Allozyme variation of the pygmy wood mouse Sylvaemus uralensis (Rodentia, Muridae) and estimation of the divergence of its chromosome forms

The genetic divergence between the eastern European, southern European, and Asian chromosome forms of the pygmy wood mouse Sylvaemus uralensis, whose karyotypes differ from one another in the amount of pericentromeric heterochromatin, has been reevaluated using allozyme analysis. In general, Asian S. uralensis living in eastern Kazakhstan, eastern Turkmenistan (the Kugitang Ridge), and Uzbekistan are more monomorphic than European populations of this species. However, the allozyme differences between all chromosome forms of the pygmy wood mouse is comparable with the interpopulation differences within each form and are an order of magnitude smaller than those between "good" species of the genus Sylvaemus. Thus, the chromosome forms of S. uralensis cannot be considered to be separate species. The concept of races as large population groups that have not diverged enough to regard them as species but differ from one another in some genetic characters is used to describe the differentiation of S. uralensis forms more adequately. The currently available evidence suggests the existence of two S. uralensis races, the Asian and the European ones, and two chromosome forms (eastern and western) of the European race. The possible historical factors that have determined the formation of the races of the pygmy wood mouse are considered. According to the most plausible hypothesis, the shift and fragmentation of the broad-leaved forest zone during the most recent glacial period (late Pleistocene) were the crucial factors of the formation of these races, because they resulted in a prolonged isolation of the European and Asian population groups of S. uralensis from each other.     

Variability of allozyme and cpSSR markers in the populations of Siberian spruce

The variability of 21 allozyme and three microsatellite loci of chloroplast DNA (cpDNA) was studied in the populations of Siberian spruce (Picea obovata Ledeb.) from Irkutsk oblast, Magadan oblast, Buryatia, and Mongolia. It was demonstrated that the highest level of genetic diversity among the examined populations at both allozyme and microsatellite loci was observed in the Tulyushka population from Irkutsk oblast. The lowest level of genetic diversity was observed in marginal isolated populations of Bogd Uul and Magadan. In the relict spruce population from Olkhon Island, differing from the other populations in the lowest allelic diversity of both types of markers, no expected decline of expected heterozygosity and haplotype diversity was observed. In this population, the variability parameters mentioned were close to the population mean. The obtained intrapopulation and intraspecific variability parameters of allozyme and microsatellite loci of chloroplast DNA and the data on the population differentiation at these loci indicate that the given markers can be used for the analysis of the population structure of Siberian spruce.