The population genetic structure of a large temperate pollinator species, Bombus pascuorum (Scopoli) (Hymenoptera: Apidae)

The genetic population structure of the bumble bee Bombus pascuorum was studied using six microsatellite loci and a partial sequence of the mitochondrial gene cytochrome b . Eighteen populations from central and northern Europe were included in the analysis. Observed levels of genetic variability and heterozygosity were high. Estimates of population differentiation based on F - and Φ-statistics revealed significant genetic differentiation among B. pascuorum populations and suggest that two partially isolated gene pools, separated by the Alps, do exist. The distribution of mtDNA haplotypes supports this view and presents direct evidence for gene flow across the Alps. Estimates of the number of migrants exchanged among populations north of the Alps suggest that historical events may have left a strong imprint on population structure.     

Genome and population dynamics under selection and neutrality: an example of S-allele diversity in wild cherry (Prunus avium L.)

Self-incompatibility, a common attribute of plant development, forms a classical paradigm of balancing selection in natural populations, in particular negative frequency-dependent selection. Under negative frequency-dependent selection population genetics theory predicts that the S-locus, being in command of self-incompatibility, keeps numerous alleles in equal frequencies demonstrating a wide allelic range. Moreover, while natural populations exhibit a higher within population genetic diversity, a reduction of population differentiation and increase of effective migration rate is expected in comparison to neutral loci. Allelic frequencies were investigated in terms of distribution and genetic structure at the gametophytic self-incompatibility locus in five wild cherry (Prunus avium L.) populations. Comparisons were also made between the differentiation at the S-locus and at the SSR loci. Theoretical expectations under balancing selection were congruent to the results observed. The S-locus showed broad multiplicity (16 S-alleles), high genetic diversity, and allelic isoplethy. Genetic structure at the self-incompatibility locus was almost four times lower than at 11 nSSR loci. Analysis of molecular variance revealed that only 5?% of the total genetic variation concerns differentiation among populations. In conclusion, the wealth of S-allelic diversity found in natural wild cherry populations in Greece is useful not only in advancing basic population genetics research of self-incompatibility systems in wild cherry but also in the development of breeding programs.     

Stability of genetic structure and effective population size inferred from temporal changes of microsatellite DNA polymorphisms in the land snail Helix aspersa (Gastropoda: Helicidae)

Temporal evolution of genetic variability may have far-reaching consequences for a diverse array of evolutionary processes. Within the polders of the Bay of Mont-Saint-Michel (France), populations of the land snail Helix aspersa are characterized by a metapopulation structure with occasional extinction processes resulting from farming practices. A temporal survey of genetic structure in H . aspersa was carried out using variability at four microsatellite loci, in ten populations sampled two years apart. Levels of within-population genetic variation, as measured by allelic richness, H _e or F _is , did not change over time and similar levels of population differentiation were demonstrated for both sampling years. The extent of genetic differentiation between temporal samples of the same population established (i) a stable structure for six populations, and (ii) substantial genetic changes for four populations. Using classical F -statistics and a maximum likelihood method, estimates of the effective population size ( N _e) illustrated a mixture of stable populations with high N _e, and unstable populations characterized by very small N _e estimates (of 5–11 individuals). Owing to human disturbances, intermittent gene flow and genetic drift are likely to be the predominant evolutionary processes shaping the observed genetic structure. However, the practice of multiple matings and sperm storage is likely to provide a reservoir of variability, minimizing the eroding genetic effects of population size reduction and increasing the effective population size.  © 2004 The Linnean Society of London, Biological Journal of the Linnean Society , 2004, 82 , 89–102.     

Microsatellites can be misleading: an empirical and simulation study

Abstract. It has been long recognized that highly polymorphic genetic markers can lead to underestimation of divergence between populations when migration is low. Microsatellite loci, which are characterized by extremely high mutation rates, are particularly likely to be affected. Here, we report genetic differentiation estimates in a contact zone between two chromosome races of the common shrew ( Sorex araneus ), based on 10 autosomal microsatellites, a newly developed Y-chromosome microsatellite, and mitochondrial DNA. These results are compared to previous data on proteins and karyotypes. Estimates of genetic differentiation based on F - and R -statistics are much lower for autosomal microsatellites than for all other genetic markers. We show by simulations that this discrepancy stems mainly from the high mutation rate of microsatellite markers for F -statististics and from deviations from a single-step mutation model for R -statistics. The sex-linked genetic markers show that all gene exchange between races is mediated by females. The absence of male-mediated gene flow most likely results from male hybrid sterility.     

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.     

Microsatellite variability of Sardinian pine martens, Martes martes

The pine marten, Martes martes, is a medium-sized terrestrial carnivore associated with woodland habitats of the western Palearctic region. The present distribution area of the species also includes six islands of the western Mediterranean basin. The origin of these insular populations and their taxonomic status are still debated; their molecular characterization appears relevant for conservation purposes. To describe the genetic variability of the pine martens from Sardinia we characterized 40 insular and 14 Italian individuals at seven nuclear microsatellite loci. The identification of private alleles and the calculated F(ST) value of 0.074 revealed some genetic differentiation between the two populations, which accounts for the high percentages of correct allocation (96.39-98.80%) scored by the genotype assignment test. The presence of two distinct clusters corresponding to Sardinia and mainland Italy was further confirmed by the multivariate Factorial Correspondence Analysis of individual genotypes. Moreover, the genome of the Sardinian individuals bore signs of past demographic fluctuations, i.e. the presence of the monomorphic locus Ma-4, a lower allelic richness and a lower number of private alleles, which may derive from the combination of drift, founder effects, and human overexploitation. Anyway, if such events ever affected the Sardinian population, this is likely to have happened in the past since, according to our microsatellite data, the present-day population does not show evidence of recent bottlenecks or inbreeding, the Wilcoxon sign-rank test and the F(IS) index being not statistically significant (both P > 0.05). Based on this genetic evidence, we advance hypotheses about the distinctiveness of the Sardinian population and its significance for taxonomy and conservation.     

Self-fertilization is the main sexual reproduction mechanism in native wine yeast populations

Saccharomyces cerevisiae is a model eukaryotic organism for classical genetics and genomics, and yet its ecology is still largely unknown. In this work, a population genetic analysis was performed on five yeast populations isolated from wine-making areas with different enological practices using simple sequence repeats and restriction fragment length polymorphism of mitochondrial DNA as molecular markers on 292 strains. In accordance with other studies, genome size estimation suggests that native S. cerevisiae strains are mainly homothallic and diploids. Analysis of mtDNA data showed that yeast populations from nonindustrial areas have 40% higher genetic diversity than populations isolated from industrial areas, demonstrating that industrial enological practices are likely to affect native yeast populations negatively by reducing its biodiversity. On the other hand, genetic differentiation analysis based on their microsatellite showed no correlation between genetic and geographic distance and a nonsignificant value when a Mantel test was applied. Finally, in the five populations studied, positive inbreeding ( F _is) values from 0.4 to 0.75, a low but significant level of linkage disequilibrium and a high number of multilocus genotypes were detected. These results strongly advocate that sexual reproduction is frequent enough to erase clonal signature in natural populations and that self-fertilization is the main mating system.     

Statistical properties of population differentiation estimators under stepwise mutation in a finite island model

Microsatellite loci mutate at an extremely high rate and are generally thought to evolve through a stepwise mutation model. Several differentiation statistics taking into account the particular mutation scheme of the microsatellite have been proposed. The most commonly used is R(ST) which is independent of the mutation rate under a generalized stepwise mutation model. F(ST) and R(ST) are commonly reported in the literature, but often differ widely. Here we compare their statistical performances using individual-based simulations of a finite island model. The simulations were run under different levels of gene flow, mutation rates, population number and sizes. In addition to the per locus statistical properties, we compare two ways of combining R(ST) over loci. Our simulations show that even under a strict stepwise mutation model, no statistic is best overall. All estimators suffer to different extents from large bias and variance. While R(ST) better reflects population differentiation in populations characterized by very low gene-exchange, F(ST) gives better estimates in cases of high levels of gene flow. The number of loci sampled (12, 24, or 96) has only a minor effect on the relative performance of the estimators under study. For all estimators there is a striking effect of the number of samples, with the differentiation estimates showing very odd distributions for two samples.     

Patterns of differentiation in a colour polymorphism and in neutral markers reveal rapid genetic changes in natural damselfly populations

The existence and mode of selection operating on heritable adaptive traits can be inferred by comparing population differentiation in neutral genetic variation between populations (often using F(ST) values) with the corresponding estimates for adaptive traits. Such comparisons indicate if selection acts in a diversifying way between populations, in which case differentiation in selected traits is expected to exceed differentiation in neutral markers [F(ST )(selected) > F(ST )(neutral)], or if negative frequency-dependent selection maintains genetic polymorphisms and pulls populations towards a common stable equilibrium [F(ST) (selected) < F(ST) (neutral)]. Here, we compared F(ST) values for putatively neutral data (obtained using amplified fragment length polymorphism) with estimates of differentiation in morph frequencies in the colour-polymorphic damselfly Ischnura elegans. We found that in the first year (2000), population differentiation in morph frequencies was significantly greater than differentiation in neutral loci, while in 2002 (only 2 years and 2 generations later), population differentiation in morph frequencies had decreased to a level significantly lower than differentiation in neutral loci. Genetic drift as an explanation for population differentiation in morph frequencies could thus be rejected in both years. These results indicate that the type and/or strength of selection on morph frequencies in this system can change substantially between years. We suggest that an approach to a common equilibrium morph frequency across all populations, driven by negative frequency-dependent selection, is the cause of these temporal changes. We conclude that inferences about selection obtained by comparing F(ST) values from neutral and adaptive genetic variation are most useful when spatial and temporal data are available from several populations and time points and when such information is combined with other ecological sources of data.     

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.     

Pattern of genetic differentiation in the Maculinea alcon species group (Lepidoptera, Lycaenidae) in Central Europe

The taxonomic status of Alcon Blues living in Central and Western Europe (conventionally: Maculinea alcon and Maculinea rebeli ) is quite confused. Some authors distinguish them as separate species of the M. alcon species group, while others consider them as subspecies or simply ecological forms. Our aim was to study the pattern of genetic differentiation among several populations of these taxa with reference to their taxonomic position. Imagoes were collected from 27 localities in Central Europe between 1999 and 2003. Samples originated from four regions: northern Hungary, central Hungary, Romania: Transylvania and Slovenia. Enzyme polymorphism was analysed using polyacrylamide gel electrophoresis. In all samples 16 enzyme loci were studied. In the analysis of the data, F -statistics was computed and the total genetic variation was partitioned into within and between population components. Nei's genetic distances were calculated and UPGMA dendrogram was constructed on the basis of the distance matrix. Hierarchical F -statistics and amova was computed to study the pattern of genetic differentiation among the samples. Principal component analysis (PCA) was also carried out using the allele frequencies of the samples. The results of all analyses indicated a high level of differentiation among the samples. The differences among the samples collected in different years from the same population accounted for a considerable amount of the between sample variation. The distribution of the between sample variation did not exhibit a species pattern. The results of amova and PCA indicated that the geographic pattern was slightly more expressed in the between sample variation compared with the species pattern of it. These results seem to contradict with the conventional taxonomical subdivision.     

Population genetic structure of the sidespot barb,Barbus neefi,from the north-eastern escarpment,South Africa

Allozyme analysis was used to determine patterns of genetic variation within and between populations of Barbus neefi. The products of 29 loci were analysed, with 17 loci being monomorphic in all populations. The genetic variability estimates compared well with values reported in the literature. The percentage of polymorphic loci (0.95 criterion) ranged from 0–20.69% and average expected heterozygosity from 0.004–0.069. Headstream populations generally revealed lower genetic variability than populations in low lying areas, which emphasizes the importance of conserving headstream populations. Fixed allele mobility differences were observed at the MPI-1 protein coding locus between the Selons River population and the other populations. The measures of genetic differentiation as assessed by F-statistics, the effective number of migrants per generation and Nei's unbiased genetic distance consistently separated the Selons River population from the rest. Nevertheless, these estimates all fell within the range considered for conspecific populations. There was also a clear genetic division between populations from north and south of the Olifants River. The three populations from the Dorps, Spekboom and Blyde Rivers (Limpopo River system) and the population from the Crocodile River (Incomati River system) showed negligible genetic differentiation. Human-assisted transfer of populations may be responsible for this close similarity.     

Multiple-scaled spatial genetic structures of <Emphasis Type="Italic">Fraxinus mandshurica</Emphasis> over a riparian–mountain landscape in Northeast China

Landscape genetics increasingly focuses on the way in which landscape features cause the fragmentation of lineages of terrestrial organisms. However, landscape features can also provide functional connectivity or corridors, enhancing the dispersal of plant populations, particularly the case in riparian habitat. Unfortunately, recent research in tree genetics has paid little attention to this role. To examine the possible effects of landscape connectivity on the current population genetic distribution of Fraxinus mandshurica and to provide insights into conserving the local genetic diversity for this endangered tree species, we used nine nuclear microsatellite loci to examine the spatial genetic structure of F. mandshurica at multiple-scales over a riparian–mountain landscape in Northeast China. F-statistics indicated that the magnitude of among-population genetic differentiation was significantly higher between the riparian and mountain habitats than within the riparian habitat. Spatial analysis of molecular variance and principal coordinate analysis consistently revealed that this species exhibited a clear landscape genetic structure between the riparian and mountain habitats, despite no significant isolation by distance pattern being identified by the Mantel test. Spatial autocorrelation analysis further demonstrated significant, positive fine-scale spatial genetic structure among individuals over short distances (<80 m) in each mountain population. Conversely, no spatial genetic structures were identified within and among the riparian populations. Overall, the results suggest that seed dispersal is very low among mountain populations; however seed transport is probably enhanced by a secondary phase of hydrochory (water-dispersal) among riparian populations during flooding. Despite this, there was no significant accumulation of genetic diversity in downstream populations along the main channel. This result suggests that hydrochory is not sufficient to produce a clear unidirectional gene flow along the water course, although it may impede the development of spatial genetic structuring within and among riparian populations.     

Comparison of population structure in Ohio's late archaic and late prehistoric periods

Previous studies of population structure among prehistoric groups in the Ohio valley region have shown that hunting-gathering populations exhibited a different structure than horticultural populations. Among both Late Archaic hunter-gatherers and Late Prehistoric horticulturists, covariance structures for cranial metrics were found to be homogenous within the populations, but the Late Archaic subpopulations showed little differentiation while the Late Prehistoric subpopulations exhibited a marked differentiation. Biodistance based on cranial discrete trait frequency showed similar patterns, but in the Late Archaic discrete trait distance was associated significantly with the geographical distance separating populations. The present investigation is an extension of the previous studies increasing the Late Prehistoric sample (n = 8 samples and n = 341 individuals) and using the Harpending-Ward model, modified for use with multivariate quantitative data, to estimate the effects of differential gene flow and the amount of differentiation within populations. Results of the present analyses indicate that differentiation among subpopulations, measured by minimum F(ST), was greater in the Late Prehistoric compared to the Late Archaic period. However, for both periods the minimum F(ST) is comparable to values found for historic native populations of the northeast woodlands. Analysis of differential gene flow in the Late Archaic period indicates that geographically peripheral populations were affected more by external gene flow than more central populations. Late Prehistoric populations exhibit a very complex pattern of differential gene flow. We discuss the latter pattern in terms of proposed culture change in the Late Prehistoric period of Ohio.     

The population genetics of clonal and partially clonal diploids

The consequences of variable rates of clonal reproduction on the population genetics of neutral markers are explored in diploid organisms within a subdivided population (island model). We use both analytical and stochastic simulation approaches. High rates of clonal reproduction will positively affect heterozygosity. As a consequence, nearly twice as many alleles per locus can be maintained and population differentiation estimated as F(ST) value is strongly decreased in purely clonal populations as compared to purely sexual ones. With increasing clonal reproduction, effective population size first slowly increases and then points toward extreme values when the reproductive system tends toward strict clonality. This reflects the fact that polymorphism is protected within individuals due to fixed heterozygosity. Contrarily, genotypic diversity smoothly decreases with increasing rates of clonal reproduction. Asexual populations thus maintain higher genetic diversity at each single locus but a lower number of different genotypes. Mixed clonal/sexual reproduction is nearly indistinguishable from strict sexual reproduction as long as the proportion of clonal reproduction is not strongly predominant for all quantities investigated, except for genotypic diversities (both at individual loci and over multiple loci).     

Genetic variability in Irish populations of the invasive zebra mussel, Dreissena polymorpha: discordant estimates of population differentiation from allozymes and microsatellites

1. The recent arrival and explosive spread of the zebra mussel, Dreissena polymorpha (Pallas), in Ireland provided a rare opportunity to study the population genetics of an invasive species.
2. Eight polymorphic allozyme loci ( ACO-1, ACO-2 , EST-D, GPI, IDH-2, MDH, OPDH and PGM ) were used to investigate genetic diversity and population structure in five Irish populations, and the results were compared with those from a previous microsatellite study on the same samples.
3. The mean number of alleles per locus (2.7 ± 0.1) was similar to the mean for the same loci in European populations, suggesting that Irish founder populations were large and/or multiple colonization events took place after foundation. A deficiency of heterozygotes was observed in all populations, but was uneven across loci.
4. Pairwise comparisons, using Fisher's exact tests and F _ST values, revealed significant genetic differentiation among populations. The overall multilocus F _ST estimate was 0.118 ± 0.045, which contrasted with an estimate of 0.015 ± 0.007 from five microsatellite loci on the same samples in a previous study.
5. Assuming that microsatellites can be used as a neutral baseline, the discordant results from allozymes and microsatellites suggest that selection may be acting on some allozyme loci, specifically ACO-1, ACO-2 , IDH-2 and MDH, which contributed most to the significant differentiation between samples.     

Analysis of Alu-polymorphism in Buryat populations]

Polymorphism of three populations of the Buryat Republic and a population from Aginskii Buryat Autonomous okrug of Chita oblast was examined using a set of five autosomal Alu insertions at the ACE, PLAT, PV92, APOA1, and F13B loci. The allele frequency distribution patterns revealed in Buryat populations were typical to other Asian populations. Buryats were characterized by relatively low level of intrapopulation diversity (0.369 in the pooled population sample). Analysis of autosomal Alu insertions suggests the uniformity of the Buryat gene pool. The coefficient of genetic differentiation in the four populations studied was 0.8%.     

Genetic Variation and Differentiation among Populations of Chum Salmon Oncorhynchus ketaWalbaum from Southern Russian Far East

Allozyme variation of populations of chum salmon Oncorhynchus ketafrom southern Russian Far East was examined. Of 55 loci screened, 31 were polymorphic. Within-population variation accounted for most of the allele diversity; F _STaveraged over loci was 0.052. Linkage disequilibrium was found in less than 5% of locus pairs in the chum population examined. Analysis of within- and among-population variance components of linkage disequilibrium using D-statistics (Ohta, 1982) showed that most genetic variation was distributed among populations.     

Microsatellites and the Genetics of Highly Selfing Populations in the Freshwater Snail Bulinus Truncatus

Hermaphrodite tropical freshwater snails provide a good opportunity to study the effects of mating system and genetic drift on population genetic structure because they are self-fertile and they occupy transient patchily distributed habitats (ponds). Up to now the lack of detectable allozyme polymorphism prevented any intrapopulation studies. In this paper, we examine the consequences of selfing and bottlenecks on genetic polymorphism using microsatellite markers in 14 natural populations (under a hierarchical sampling design) of the hermaphrodite freshwater snail Bulinus truncatus. These population genetics data allowed us to discuss the currently available mutation models for microsatellite sequences. Microsatellite markers revealed an unexpectedly high levels of genetic variation with <=41 alleles for one locus and gene diversity of 0.20-0.75 among populations. The values of any estimator of F(is) indicate high selfing rates in all populations. Linkage disequilibria observed at all loci for some populations may also indicate high levels of inbreeding. The large extent of genetic differentiation measured by F(st), R(st) or by a test for homogeneity between genic distributions is explained by both selfing and bottlenecks. Despite a limited gene flow, migration events could be detected when comparing different populations within ponds.     

Utility of EST-derived SSRs as population genetics markers in a beetle

Microsatellite, or simple sequence repeat (SSR), loci can be identified by mining expressed sequence tag (EST) databases, and where these are available, marker development time and expense can be decreased considerably over conventional strategies of probing the entire genome. However, it is unclear whether they provide information on population structure similar to that generated by anonymous genomic SSRs. We performed comparative population genetic analyses between EST-derived SSRs (EST-SSRs) and anonymous SSRs developed from genomic DNA for the same set of populations of the insect Diabrotica virgifera, a beetle in the family Chrysomelidae. Compared with noncoding, nontranscribed regions, EST-SSRs were generally less polymorphic but had reduced occurrence of null alleles and greater cross-species amplification. Neutrality tests suggested the loci were not under positive selection. Across all populations and all loci, the genomic and EST-SSRs performed similarly in estimating genetic diversity, F(IS), F(ST), population assignment and exclusion tests, and detection of distinct populations. These findings, therefore, indicate that the EST-SSRs examined can be used with confidence in future genetic studies of Diabrotica populations and suggest that EST libraries can be added as a valuable source of markers for population genetics studies in insects and other animals.