Within-population Genetic Structure Research Articles

Genomic and common garden data reveal significant genetic differentiation in the endangered San Fernando Valley spineflower Chorizanthe parryi var. fernandina

AbstractSan Fernando Valley spineflower (Chorizanthe parryi var. fernandina [S. Watson] Jeps.) (Polygonaceae) is an herbaceous annual plant, endemic to California, and until rediscovered in 1999 had been thought to be extinct for almost seven decades. Historically documented at 10 locations, it currently persists at 2, separated by approximately 27 km. State listed as endangered, a description of its genetic diversity and structure is of conservation interest. After determining a lack of variation in ploidy, we examined genetic variation from samples within both populations: a common garden study for potentially adaptive genetic variation in selected growth and phenological traits and analysis of single nucleotide polymorphisms identified through restriction-site associated DNA sequencing. Both measures indicated that this highly restricted taxon nevertheless harbors substantial levels of genetic diversity and has significant between- and within-population genetic structure. Combining approaches from population genomics and common garden studies provided more insight into the patterns and basis of genetic diversity than is typical for studies of non-model species. Although local adaptation was not specifically studied (i.e., via reciprocal transplant studies), the differences determined from these two independent lines of evidence indicate that mixing gene pools between populations is not recommended at this time. Further, with significant differences revealed among subpopulations, we caution against mixing genotypes across subpopulations for the most part, and without much more evidence that this would not pose a risk of outbreeding depression. The importance of supporting pollinator health and diversity is highlighted. With genetic diversity—particularly with an annual species—being dynamic, fluctuating with the usual processes and with contributions from the soil seedbank, we recommend periodic resampling to monitor genetic diversity and structure. Climate change is anticipated to contribute to this variability.

Stronger genetic differentiation among within-population genetic groups than among populations in Scots pine provides new insights into within-population genetic structuring

We investigated the presence of spatial genetic groups within forest tree populations and determined if the genetic divergence among these groups is greater than that between populations using Scots pine (Pinus sylvestris) as a model species. We genotyped 890 adult trees of Scots pine in six natural populations in Lithuania at 11 nuclear microsatellite loci. We used a Bayesian clustering approach to identify the within-population genetic groups within each of the six populations. We calculated the differentiation indexes among the genetic groups within each population and among the six populations by ignoring the genetic groups. The Bayesian clustering revealed 2 to 6 distinct genetic groups of varying size as the most likely genetic structures within populations. The genetic differentiation indexes among the genetic groups within populations were nearly tenfold greater (FST = 0.012–0.070) than those between the populations (FST = 0.003). We conclude on the existence of markedly stronger structuring of genetic variation within populations than between populations of Scots pine in large forest tracts of northern Europe. Such genetic structures serve as a contributing factor to large within population genetic diversity in northern conifers. We assume that within population mating in Scots pine is not completely random but rather is stratified into genetic clusters. Our study provides pioneering novel key insights into structuring of genetic variation within populations. Our findings have implications for examining within-population genetic diversity and genetic structure, conservation, and management of genetic resources.

Fine-scale genetic structure in the orchid Gymnadenia conopsea is not associated with local density of flowering plants.

Density-dependent pollinator visitation can lead to density-dependent mating patterns and within-population genetic structure. In Gymnadenia conopsea, individuals in low-density patches receive more self pollen than individuals in high-density patches, suggesting higher relatedness at low density. Ongoing fragmentation is also expected to cause more local matings, potentially leading to biparental inbreeding depression. To evaluate whether relatedness decreases with local density, we analyzed 1315 SNP loci in 113 individuals within two large populations. We quantified within-population genetic structure in one of the populations, recorded potential habitat barriers, and visualized gene flow using estimated effective migration surfaces (EEMS). We further estimated the magnitude of biparental inbreeding depression that would result from matings restricted to within 5 m. There was no significant relationship between local density and relatedness in any population. We detected significant fine-scale genetic structure consistent with isolation by distance, with positive kinship coefficients at distances below 10 m. Kinship coefficients were low, and predicted biparental inbreeding depression resulting from matings within the closest 5 m was a modest 1-3%. The EEMS suggested that rocks and bushes may act as barriers to gene flow within a population. The results suggest that increased self-pollen deposition in sparse patches does not necessarily cause higher selfing rates or that inbreeding depression results in low establishment success of inbred individuals. The modest relatedness suggests that biparental inbreeding depression is unlikely to be an immediate problem following fragmentation of large populations. The results further indicate that habitat structure may contribute to governing fine-scale genetic structure in G. conopsea.

Within-population genetic diversity and population structure of Plasmodium knowlesi merozoite surface protein 1 gene from geographically distinct regions of Malaysia and Thailand

BackgroundThe C-terminal 42 kDa domain of Plasmodium knowlesi merozoite surface protein 1 (PkMSP1) is a potential asexual blood-stage vaccine candidate, however, only a limited number of clinical isolates have been analysed from Malaysia and no inter-country comparative diversity study has been conducted. In the present study, nucleotide diversity, haplotypes and natural selection levels of pkmsp1 in clinical samples from geographically distinct regions of Malaysia and Thailand were investigated. The overall population structure of the parasite from the region was determined.MethodsEleven full-length pkmsp1 sequences obtained from clinical isolates of Malaysia along with the H-strain were downloaded from the database for domain wise characterization of pkmsp1 gene. Additionally, 76 pkmsp-142 sequences from Thailand and Malaysia were downloaded from the database for intra and inter-population analysis. DnaSP 5.10 and MEGA 5.0 software were used to determine genetic diversity, polymorphism, haplotypes and natural selection. Genealogical relationships were determined using haplotype network tree in NETWORK software v5.0. Population genetic differentiation index (FST) of parasites were analysed using Arlequin v3.5.ResultsSequence analysis of 11 full-length pkmsp1 sequences along with the H-strain identified 477 (8.4%) polymorphic sites, of which 107 were singleton sites. The overall diversity observed in the full-length genes were high in comparison to its ortholog pvmsp1 and the 4 variable domains showed extensive size variations. The nucleotide diversity was low towards the pkmsp1-42 compared to the conserved domains. The 19 kDa domain was less diverse and completely conserved among isolates from Malaysian Borneo. The nucleotide diversity of isolates from Peninsular Malaysia and Thailand were higher than Malaysian Borneo. Network analysis of pkmsp1-42 haplotypes showed geographical clustering of the isolates from Malaysian Borneo and grouping of isolates from Peninsular Malaysia and Thailand. Population differentiation analysis indicated high FST values between parasite populations originating from Malaysian Borneo, Peninsular Malaysia and Thailand attributing to geographical distance. Moderate genetic differentiation was observed for parasite populations from Thailand and Peninsular Malaysia. Evidence of population expansion and purifying selection were observed in all conserved domains with strongest selection within the pkmsp1-42 domain.ConclusionsThis study is the first to report on inter country genetic diversity and population structure of P. knowlesi based on msp1. Strong evidence of negative selection was observed in the 42 kDa domain, indicating functional constrains. Geographical clustering of P. knowlesi and moderate to high genetic differentiation values between populations identified in this study highlights the importance of further evaluation using larger number of clinical samples from Southeast Asian countries.

Pollen-mediated gene flow and fine-scale spatial genetic structure in Olea europaea subsp. europaea var. sylvestris.

Wild olive ( Olea europaea subsp. europaea var. sylvestris ) is important from an economic and ecological point of view. The effects of anthropogenic activities may lead to the genetic erosion of its genetic patrimony, which has high value for breeding programmes. In particular, the consequences of the introgression from cultivated stands are strongly dependent on the extent of gene flow and therefore this work aims at quantitatively describing contemporary gene flow patterns in wild olive natural populations. The studied wild population is located in an undisturbed forest, in southern Spain, considered one of the few extant hotspots of true oleaster diversity. A total of 225 potential father trees and seeds issued from five mother trees were genotyped by eight microsatellite markers. Levels of contemporary pollen flow, in terms of both pollen immigration rates and within-population dynamics, were measured through paternity analyses. Moreover, the extent of fine-scale spatial genetic structure (SGS) was studied to assess the relative importance of seed and pollen dispersal in shaping the spatial distribution of genetic variation. The results showed that the population under study is characterized by a high genetic diversity, a relatively high pollen immigration rate (0·57), an average within-population pollen dispersal of about 107 m and weak but significant SGS up to 40 m. The population is a mosaic of several intermingled genetic clusters that is likely to be generated by spatially restricted seed dispersal. Moreover, wild oleasters were found to be self-incompatible and preferential mating between some genotypes was revealed. Knowledge of the within-population genetic structure and gene flow dynamics will lead to identifying possible strategies aimed at limiting the effect of anthropogenic activities and improving breeding programmes for the conservation of olive tree forest genetic resources.

Nature and Extent of Genetic Diversity of Dengue Viruses Determined by 454 Pyrosequencing.

Dengue virus (DENV) populations are characteristically highly diverse. Regular lineage extinction and replacement is an important dynamic DENV feature, and most DENV lineage turnover events are associated with increased incidence of disease. The role of genetic diversity in DENV lineage extinctions is not understood. We investigated the nature and extent of genetic diversity in the envelope (E) gene of DENV serotype 1 representing different lineages histories. A region of the DENV genome spanning the E gene was amplified and sequenced by Roche/454 pyrosequencing. The pyrosequencing results identified distinct sub-populations (haplotypes) for each DENV-1 E gene. A phylogenetic tree was constructed with the consensus DENV-1 E gene nucleotide sequences, and the sequences of each constructed haplotype showed that the haplotypes segregated with the Sanger consensus sequence of the population from which they were drawn. Haplotypes determined through pyrosequencing identified a recombinant DENV genome that could not be identified through Sanger sequencing. Nucleotide level sequence diversities of DENV-1 populations determined from SNP analysis were very low, estimated from 0.009–0.01. There were also no stop codon, frameshift or non-frameshift mutations observed in the E genes of any lineage. No significant correlations between the accumulation of deleterious mutations or increasing genetic diversity and lineage extinction were observed (p>0.5). Although our hypothesis that accumulation of deleterious mutations over time led to the extinction and replacement of DENV lineages was ultimately not supported by the data, our data does highlight the significant technical issues that must be resolved in the way in which population diversity is measured for DENV and other viruses. The results provide an insight into the within-population genetic structure and diversity of DENV-1 populations.

Individual differences in migratory behavior shape population genetic structure and microhabitat choice in sympatric blackcaps (Sylvia atricapilla)

In migratory birds, traits such as orientation and distance are known to have a strong genetic background, and they often exhibit considerable within-population variation. How this variation relates to evolutionary responses to ongoing selection is unknown because the underlying mechanisms that translate environmental changes into population genetic changes are unclear. We show that within-population genetic structure in southern German blackcaps (Sylvia atricapilla) is related to individual differences in migratory behavior. Our 3-year study revealed a positive correlation between individual migratory origins, denoted via isotope (δ2H) values, and genetic distances. Genetic diversity and admixture differed not only across a recently established migratory polymorphism with NW- and SW-migrating birds but also across δ2H clusters within the same migratory route. Our results suggest assortment based on individual migratory origins which would facilitate evolutionary responses. We scrutinized arrival times and microhabitat choice as potential mechanisms mediating between individual variation in migratory behavior and assortment. We found significant support that microhabitat choice, rather than timing of arrival, is associated with individual variation in migratory origins. Moreover, examining genetic diversity across the migratory divide, we found migrants following the NW route to be genetically more distinct from each other compared with migrants following the traditional SW route. Our study suggests that migratory behavior shapes population genetic structure in blackcaps not only across the migratory divide but also on an individual level independent of the divide. Thus, within-population variation in migratory behavior might play an important role in translating environmental change into genetic change.

Within-Population Genetic Structure in Beech (Fagus sylvatica L.) Stands Characterized by Different Disturbance Histories: Does Forest Management Simplify Population Substructure?

The fine-scale assessment of both spatially and non-spatially distributed genetic variation is crucial to preserve forest genetic resources through appropriate forest management. Cryptic within-population genetic structure may be more common than previously thought in forest tree populations, which has strong implications for the potential of forests to adapt to environmental change. The present study was aimed at comparing within-population genetic structure in European beech (Fagus sylvatica L.) plots experiencing different disturbance levels. Five plot pairs made up by disturbed and undisturbed plots having the same biogeographic history were sampled throughout Europe. Overall, 1298 individuals were analyzed using four highly polymorphic nuclear microsatellite markers (SSRs). Bayesian clustering within plots identified 3 to 11 genetic clusters (within-plot θ ST ranged from 0.025 to 0.124). The proportion of within-population genetic variation due to genetic substructuring (F CluPlot = 0.067) was higher than the differentiation among the 10 plots (F PlotTot = 0.045). Focusing on the comparison between managed and unmanaged plots, disturbance mostly explains differences in the complexity of within-population genetic structure, determining a reduction of the number of genetic clusters present in a standardized area. Our results show that: i) genetic substructuring needs to be investigated when studying the within-population genetic structure in forest tree populations, and ii) indices describing subtle characteristics of the within-population genetic structure are good candidates for providing early signals of the consequences of forest management, and of disturbance events in general.

Within-population genetic structure differs between two sympatric sister-species of ectomycorrhizal fungi, Rhizopogon vinicolor and R. vesiculosus

Using spatial autocorrelation analysis, we examined the within-population genetic structure of Rhizopogon vinicolor and R. vesiculosus, two hypogeous ectomycorrhizal (EM) species that are sympatric sister taxa known to differ in their clonal structure. We collected 121 sporocarps and 482 tuberculate EM of both species from a 20 ha forest stand dominated by Douglas-fir (Pseudotsuga menziesii). Field collections were identified to species with restriction fragment length polymorphism analysis of the nuclear ribosomal internal transcribed spacer. Five and six microsatellite markers were used to characterize the genetic diversity of EM and sporocarp samples from R. vesiculosus and R. vinicolor respectively. After correcting for genet structure, spatial autocorrelation analyses of the EM samples were used to test the null hypothesis that multilocus genotypes characterized from each species were randomly distributed within the study area. We detected positive and statistically significant fine-scale genetic structure up to 120 m within the R. vesiculosus sample. In contrast, no spatial genetic structure was evident for R. vinicolor, indicating that the genotypes characterized for this species were randomly distributed throughout the study area. Differences in statistical power or the nuclear count of basidiospores are unlikely agents of the genetic patterns observed. Our results suggest that differences in reproductive output or competitive ability may act individually or in combination to create clusters of similar genotypes for R. vesiculosus throughout the study area.

Mixed but not admixed: a spatial analysis of genetic variation of an invasive ascidian on natural and artificial substrates

Following the introduction to a new area (pre-border dispersal), post-border processes determine the success in the establishment of non-indigenous species (NIS). However, little is known on how these post-border processes shape the genetic composition of NIS at regional scales. Here, we analyse genetic variation in introduced populations along impacted coastlines to infer demographic and kinship dynamics at the post-border stage. We used as a model system the ascidian species Microcosmus squamiger that has been introduced worldwide. This species can colonize and grow fast on man-made artificial structures, impacting activities such as mariculture. However, it can also establish itself on natural substrates, thus altering natural communities and becoming an ecological problem. We genotyped 302 individuals from eight populations established on natural and artificial substrates in the north-western Mediterranean Sea, using six microsatellite loci. We then compared the resulting genotypes with those found within the native range of the species. We found high levels of genetic diversity and allelic richness in all populations, with an overall deficit of heterozygotes. Autocorrelation analyses showed that there was no within-population genetic structure (at a scale of tens of metres); likewise, no significant differentiation in pairwise comparisons between populations (tens of kilometres apart) and no isolation-by-distance pattern was found. The results suggest that M. squamiger has a natural capacity for high dispersal from one patch of hard substrate to another and no differences whatsoever could be substantiated between natural and artificial substrates. Interestingly, two groups of genetically differentiated individuals were detected that were associated with the two ancestral source areas of the worldwide expansion of the species. Individual assignment tests showed the coexistence of individuals of these two clusters in all populations but with little interbreeding among them as the frequency of admixed individuals was only 15 %. The mechanism responsible for maintaining these genetic pools unmixed is unknown, but it does not appear to compromise post-border colonization of introduced populations.

Analysis of genetic diversity and population structure within the Icelandic cattle breed using molecular markers

The Icelandic cattle breed is believed to have been brought to Iceland from Norway around 1100 years ago. Since then it is thought to have been almost completely isolated and to have gone through large fluctuations in population size. Here molecular markers were used to assess the breed's genetic diversity and the current within-population genetic structure using a randomly selected unbiased sample from the population as verified by calculations of the coefficient of relationship (R). Measures of genetic diversity suggest that there is considerable diversity within the breed despite long-term isolation and the effective population size is high considering the isolation and the breeding system used in recent years. No evidence of recent bottlenecks was found and analysis of population structure suggests that the population is uniform in structure.

Microspatial population genetic structure of the Mediterranean shrub Fumana thymifolia

Fumana thymifolia (Cistaceae) is an insect-pollinated, gravity-dispersed evergreen shrub, which is a common component of fire-prone Mediterranean shrubland ecosystems. Despite the availability of basic knowledge on its ecology, little is known of its breeding system and no information is available on its population genetic structure. We explored the within-population genetic structure of this species using amplified fragment length polymorphism (AFLP) molecular markers and related this to predictions based on its breeding system, pollen and seed dispersal. Existing information on the reproductive ecology of F. thymifolia was supplemented by artificial pollination experiments. We determined that self-fertilisation can occur in F. thymifolia but results in reduced fruit set. Significant genetic structuring was detected within the population, a likely consequence of localised seed dispersal in combination with a mixed mating system. In a study site covering approximately 0.5 ha, amova revealed that approximately 9% of genetic variability was distributed among population subsamples. Significant spatial genetic structure was detected, with kinship coefficients being significantly elevated above the null expectation in the first six distance classes (maximum 5 m), and a value of Sp of up to 0.0342, comparable with species having similar ecological characteristics. Weak isolation by distance at the plot scale was detected, suggesting that insect-mediated pollen flow is non-random, despite being more extensive than seed dispersal. Fumana thymifolia provides a promising model for the investigation of both short- and long-term population dynamics in relation to fire frequency within this plant community.

Effects of population succession on demographic and genetic processes: predictions and tests in the daylily Hemerocallis thunbergii (Liliaceae)

Spatial genetic structure within plant populations is influenced by variation in demographic processes through space and time, including a population's successional status. To determine how demographic structure and fine-scale genetic structure (FSGS) change with stages in a population's successional history, we studied Hemerocallis thunbergii (Liliaceae), a nocturnal flowering and hawkmoth-pollinated herbaceous perennial with rapid population turnover dynamics. We examined nine populations assigned to three successive stages of population succession: expansion, maturation, and senescence. We developed stage-specific expectations for within-population demographic and genetic structure, and then for each population quantified the spatial aggregation of individuals and genotypes using spatial autocorrelation methods (nonaccumulative O-ring and kinship statistics, respectively), and at the landscape level measured inbreeding and genetic structure using Wright's F-statistics. Analyses using the O-ring statistic revealed significant aggregation of individuals at short spatial scales in expanding and senescing populations, in particular, which may reflect restricted seed dispersal around maternal individuals combined with relatively low local population densities at these stages. Significant FSGS was found for three of four expanding, no mature, and only one senescing population, a pattern generally consistent with expectations of successional processes. Although allozyme genetic diversity was high within populations (mean %P = 78.9 and H(E) = 0.281), landscape-level differentiation among sites was also high (F(ST) = 0.166) and all populations exhibited a significant deficit of heterozygotes relative to Hardy-Weinberg expectations (range F = 0.201-0.424, mean F(IS) = 0.321). Within populations, F was not correlated with the degree of FSGS, thus suggesting inbreeding due primarily to selfing as opposed to mating among close relatives in spatially structured populations. Our results demonstrate considerable variation in the spatial distribution of individuals and patterns and magnitude of FSGS in H. thunbergii populations across the landscape. This variation is generally consistent with succession-stage-specific differences in ecological processes operating within these populations.

Optimal sampling strategies for capture of genetic diversity differ between core and peripheral populations of Picea sitchensis (Bong.) Carr

In previous studies we reported that while core populations of Sitka spruce [Picea sitchensis (Bong.) Carr] have little within-population genetic structure, peripheral populations are strongly spatially structured at distances up to 500 m. Here we explore the implications of this difference in structure on ex situ gene conservation collections and estimates of genetic diversity from research collections. We test the effects of varying the number of individuals sampled and the total area they are sampled across on capture of neutral genetic variation in collections from core, continuous versus peripheral, disjunct populations. Bivariate response surface analysis of genetic marker data for eight sequence tagged site loci from core and peripheral populations suggest that a population sample from 150 trees covering at least 225 ha would be adequate for capturing 95% of the genetic diversity (as measured by allelic richness or expected heterozygosity) in core populations. However, a larger sample of 180 individuals from an area of at least 324 ha is needed in peripheral populations to capture the same proportion of standing variation because of stronger within-population spatial genetic structure. Standard population sampling protocols for estimating among and within-population genetic diversity would significantly underestimate the within-population allelic richness and expected heterozygosity of peripheral but not core populations, potentially leading to poor representation of genetic variation in peripheral populations as well as erroneous conclusions about their genetic impoverishment.

Within‐population genetic structure and clonal diversity of a threatened endemic metallophyte, Viola calaminaria (Violaceae)

We studied the within-population genetic structure and the clonality extent of Viola calaminaria, a rare endemic species of calamine soils, by means of RAPD markers in two populations (one recent and one ancient) with expected harsh and heterogeneous heavy-metal stress. At a very local scale (0.2-3 m), clonal propagation was detected in both populations, but the levels of clonal diversity were high (number of genets/number of ramets sampled = 0.9 [recent] and 0.76 [ancient]) and the maximal observed extension of the clones was 0.4 m. This indicated that clonality is not, for the species, an important mode of propagation and that clonal growth cannot be interpreted as a strategy for propagating or perpetuating adapted genotypes under harsh ecological constraints. Spatial autocorrelations revealed a significant (P < 0.001) negative value of correlogram slope in the two populations even when a single individual per clone was considered (i.e., analysis at the genet level). We conclude that spatial genetic structure at a very local scale reflects limited gene flow due to restricted seed dispersal rather than variation in clonal pattern in response to environmental heterogeneity. At a larger scale (2-30 m), spatial autocorrelations revealed a positive (P < 0.001) correlation at < 3 m and a random pattern at larger distances for the two populations. This suggested a patchy distribution of the genetically linked individuals associated with a disrupted pattern at a longer distance probably due to gene flow by pollen dispersal and a seed bank effect. The implications for the conservation of V. calaminaria are discussed.

Spatial analysis of within-population microsatellite variability reveals restricted gene flow in the Pacific golden chanterelle (Cantharellus formosus)

We examined the within-population genetic structure of the Pacific golden chanterelle (Cantharellus formosus) in a 50 y old forest stand dominated by Douglas-fir (Pseudotsuga menziesii) and western hemlock (Tsuga heterophylla) with spatial autocorrelation analysis. We tested the null hypothesis that multilocus genotypes possessed by chanterelle genets were randomly distributed within the study area. Fruit bodies from 203 C. formosus genets were collected from a 50 ha study plot. One hundred six unique multilocus genotypes were identified after scoring these collections at five microsatellite loci. Statistically significant positive spatial autocorrelation was detected indicating the presence of fine-scale genetic structure within the area. Repeated autocorrelation analyses with varied minimum distance classes (50–500 m) detected positive spatial genetic structure up to 400 m. Therefore nonrandom evolutionary processes (e.g., isolation by distance) can cause fine-scale genetic structure in C. formosus. The implications of this research for future broad-scale population studies of this species are that population samples should be separated by at least 400 m to be considered statistically independent. Sampling designs that account for fine-scale genetic structure will better characterize heterogeneity distributed across the landscape by avoiding the effects of pseudo replication.

Spatial analysis of within-population microsatellite variability reveals restricted gene flow in the Pacific golden chanterelle (Cantharellus formosus)

We examined the within-population genetic structure of the Pacific golden chanterelle (Cantharellus formosus) in a 50 y old forest stand dominated by Douglas-fir (Pseudotsuga menziesii) and western hemlock (Tsuga heterophylla) with spatial autocorrelation analysis. We tested the null hypothesis that multilocus genotypes possessed by chanterelle genets were randomly distributed within the study area. Fruit bodies from 203 C. formosus genets were collected from a 50 ha study plot. One hundred six unique multilocus genotypes were identified after scoring these collections at five microsatellite loci. Statistically significant positive spatial autocorrelation was detected indicating the presence of fine-scale genetic structure within the area. Repeated autocorrelation analyses with varied minimum distance classes (50-500 m) detected positive spatial genetic structure up to 400 m. Therefore nonrandom evolutionary processes (e.g., isolation by distance) can cause fine-scale genetic structure in C. formosus. The implications of this research for future broad-scale population studies of this species are that population samples should be separated by at least 400 m to be considered statistically independent. Sampling designs that account for fine-scale genetic structure will better characterize heterogeneity distributed across the landscape by avoiding the effects of pseudo replication.

Within-population genetic variation in the distylous Primula veris: Does floral morph anisoplethy matter in fragmented habitats?

We studied genetic variation and structure in 24 populations of Primula veris , a distylous self-incompatible perennial herb that in Flanders (northern Belgium) occurs in fragmented habitats of the intensively used agricultural landscape. Distyly, which favours cross-fertilization, is characterized in this species by two genetically determined floral morph types (‘pin’ or ‘thrum’). Using 30 allozyme loci, we investigated within-population and within-morph genetic variation and structure in relation to distyly (stochastic morph bias and pin frequency), demography (population size, plant density), and evidence of recent bottlenecks. No significant relationship was found between genetic patterns and stochastic morph bias. However, F IS values were lower when pin frequency increases in the population. This may be explained by the partial self-compatibility of the pin morph, which, in conditions of pollination disruption, as observed for P. veris in fragmented habitats, may favour intra-pin outcrosses and increase mating opportunities in the population. A lower within-population structure can be expected because of a higher density of compatible mates and more random matings. Pin and thrum individuals showed similar levels of genetic variation. Three populations revealed a significant genetic differentiation between pin and thrum morphs ( F ST ⩾ 0.0 4 9 ), as a result of recent bottlenecks, spatial segregation of the morphs and/or disturbance of demographic processes. From our findings, we may hypothesize future changes in population mating processes in fragmented habitats, which might lead to pin excesses. However, due to slowing down life-history traits (long-lived perenniality and clonality), and demographic stochasticity randomly changing morph frequency, this may take time before being expressed. Evaluating the impact of morph frequencies on population dynamics is therefore essential for implementing conservation strategies of heterostylous plant species.

Seed gene flow and fine-scale structure in a Mediterranean pine ( Pinus pinaster Ait.) using nuclear microsatellite markers.

The Mediterranean populations of maritime pine ( Pinus pinaster Ait.) are typically small and have a scattered distribution, being threatened by human activities and forest fires. In the framework of the genetic-resources conservation program of this species, a native multi-age stand located in a Mediterranean area (central Spain) was studied using three highly polymorphic nuclear microsatellites (SSRs). Spatial autocorrelation analysis was conducted using Moran's index in order to detect fine-scale structure in both natural regeneration and mature trees. The spatial pattern of seed flow based on dispersed progeny was studied using a highly reliable subset of parent-offspring matches obtained by means of parentage analysis and simulation-based calculation of statistical confidence. Maritime pine showed a fine-scale structure at the seedling stage. In natural regeneration, the autocorrelograms indicated a patch size of approximately 10 m. The fine-scale structure seems to be produced by a restricted seed gene flow. In fact, there was an excess of parent-offspring matches in a radius of 15 m from the parent trees. Pines with a heavy seed, such as P. pinaster, are expected to have a short dispersal distance, thus producing a fine-scale structure. However, the fine-scale structure did not persist in the mature trees. Within-population genetic structure in Mediterranean pines may be affected by a number of post-dispersal events (e.g. mortality due to the severity of the Mediterranean climate and animal-mediated secondary dispersal during the summer period). Thus, great alteration in the pattern produced by the initial seed rain and differences in genetic structure between tree cohorts are expected.

Spatial genetic structure and non-equilibrium demographics within plant populations

Spatial genetic structure within plant populations is primarily determined by the effects of limited seed and pollen dispersal. In the absence of selfing, spatial genetic structure and limited pollen flow are generally considered to be the primary controlling factors of the dynamics of biparental inbreeding and inbreeding depression. However, in some cases spatial structure may depend on specific demographic processes. Most theoretical studies have focused on the long-term or equilibrium structure of genetic variation, which allows, if demographic considerations are simple enough, a system to be collapsed into a single standardized measure (such as Wright's neighborhood size) of total pollen and seed dispersal distances. Specific demographic considerations may take many forms and strengths. In this paper we examine some particular cases that illustrate a wide range of effects on spatial genetic structure, and identify some of the most critical parameters. For example, Cecropia obtusifolia is a canopy-gap-filling, dioecious species. Perennially, the highly limited availability of habitat forces the removal of seedlings and the associated strong but ephemeral genetic structure, leaving one or a few trees to fill in each canopy gap. The structure among reproductive adults is minor and in line with standard amounts and forms expected for a wind-pollinated species. In contrast, Silene dioica is a dioecious, bee-pollinated, gravity-seed-dispersed perennial, and a colonizer or early successional species. In certain regions of Sweden, S. dioica grows primarily on uplifting islands that undergo rapid succession, and S. dioica exhibits exhibits extreme levels of spatial autocorrelation, caused by highly limited seed and pollen flow at a specific spatial scale that corresponds to demographic patches. Moreover, the types of genotypic concentrations in space vary, being dominated by matrilineal relationships. The availability of habitat rapidly increases, then rapidly decreases (with analogous changes in population growth rates), and, combined with a long-life, causes the genetic structure to exist on such a time scale that it appears to be the main form of within-population genetic structure for the species in this region. Clonal reproduction may have marked effects on the spatial genetic structure of plant populations. For monoecious, self-compatible species, clonal groups may increase effective selfing, whereas in dioecious plants any effects on the development of IBD may be more subtle. We examine a number of dioecious plants with a variety of spatial distributions of clones and populations, existing for various time scales. The demographics of clonal structure may interact with spatial-temporal demographics and structure of the genetic variation.