NO EFFECT OF ENVIRONMENTAL HETEROGENEITY ON THE MAINTENANCE OF GENETIC VARIATION IN WING SHAPE IN DROSOPHILA MELANOGASTER

Theory suggests that heterogeneous environments should maintain more genetic variation within populations than homogeneous environments, yet experimental evidence for this effect in quantitative traits has been inconsistent. To examine the effect of heterogeneity on quantitative genetic variation, we maintained replicate populations of Drosophila melanogaster under treatments with constant temperatures, temporally variable temperature, or spatially variable temperature with either panmictic or limited migration. Despite observing differences in fitness and divergence in several wing traits between the environments, we did not find any differences in the additive genetic variance for any wing traits among any of the treatments. Although we found an effect of gene flow constraining adaptive divergence between cages in the limited migration treatment, it did not tend to increase within‐population genetic variance relative to any of the other treatments. The lack of any clear and repeatable patterns of response to heterogeneous versus homogeneous environments across several empirical studies suggests that a single general mechanism for the maintenance of standing genetic variation is unlikely; rather, the relative importance of putative mechanisms likely varies considerably from one trait and ecological context to another.     

Environmental Heterogeneity Explains the Genetic Structure of Continental and Mediterranean Populations of Fraxinus angustifolia Vahl

Tree species with wide distributions often exhibit different levels of genetic structuring correlated to their environment. However, understanding how environmental heterogeneity influences genetic variation is difficult because the effects of gene flow, drift and selection are confounded. We investigated the genetic variation and its ecological correlates in a wind-pollinated Mediterranean tree species, Fraxinus angustifolia Vahl, within a recognised glacial refugium in Croatia. We sampled 11 populations from environmentally divergent habitats within the Continental and Mediterranean biogeographical regions. We combined genetic data analyses based on nuclear microsatellite loci, multivariate statistics on environmental data and ecological niche modelling (ENM). We identified a geographic structure with a high genetic diversity and low differentiation in the Continental region, which contrasted with the significantly lower genetic diversity and higher population divergence in the Mediterranean region. The positive and significant correlation between environmental and genetic distances after controlling for geographic distance suggests an important influence of ecological divergence of the sites in shaping genetic variation. The ENM provided support for niche differentiation between the populations from the Continental and Mediterranean regions, suggesting that contemporary populations may represent two divergent ecotypes. Ecotype differentiation was also supported by multivariate environmental and genetic distance analyses. Our results suggest that despite extensive gene flow in continental areas, long-term stability of heterogeneous environments have likely promoted genetic divergence of ashes in this region and can explain the present-day genetic variation patterns of these ancient populations.     

Population Genetic Structure of the Endangered Kaiser’s Mountain Newt,Neurergus kaiseri (Amphibia: Salamandridae)

Species often exhibit different levels of genetic structuring correlated to their environment. However, understanding how environmental heterogeneity influences genetic variation is difficult because the effects of gene flow, drift and selection are confounded. We investigated the genetic variation and its ecological correlates in an endemic and critically endangered stream breeding mountain newt, Neurergus kaiseri, within its entire range in southwestern Iran. We identified two geographic regions based on phylogenetic relationships using Bayesian inference and maximum likelihood of 779 bp mtDNA (D-loop) in 111 individuals from ten of twelve known breeding populations. This analysis revealed a clear divergence between northern populations, located in more humid habitats at higher elevation, and southern populations, from drier habitats at lower elevations regions. From seven haplotypes found in these populations none was shared between the two regions. Analysis of molecular variance (AMOVA) of N. kaiseri indicates that 94.03% of sequence variation is distributed among newt populations and 5.97% within them. Moreover, a high degree of genetic subdivision, mainly attributable to the existence of significant variance among the two regions is shown (θ_CT = 0.94, P = 0.002). The positive and significant correlation between geographic and genetic distances (r = 0.61, P = 0.002) following controlling for environmental distance suggests an important influence of geographic divergence of the sites in shaping the genetic variation and may provide tools for a possible conservation based prioritization policy for the endangered species.     

Effect of migration and environmental heterogeneity on the maintenance of quantitative genetic variation: a simulation study

The paradox of high genetic variation observed in traits under stabilizing selection is a long‐standing problem in evolutionary theory, as mutation rates appear too low to explain observed levels of standing genetic variation under classic models of mutation–selection balance. Spatially or temporally heterogeneous environments can maintain more standing genetic variation within populations than homogeneous environments, but it is unclear whether such conditions can resolve the above discrepancy between theory and observation. Here, we use individual‐based simulations to explore the effect of various types of environmental heterogeneity on the maintenance of genetic variation (V_A) for a quantitative trait under stabilizing selection. We find that V_A is maximized at intermediate migration rates in spatially heterogeneous environments and that the observed patterns are robust to changes in population size. Spatial environmental heterogeneity increased variation by as much as 10‐fold over mutation–selection balance alone, whereas pure temporal environmental heterogeneity increased variance by only 45% at max. Our results show that some combinations of spatial heterogeneity and migration can maintain considerably more variation than mutation–selection balance, potentially reconciling the discrepancy between theoretical predictions and empirical observations. However, given the narrow regions of parameter space required for this effect, this is unlikely to provide a general explanation for the maintenance of variation. Nonetheless, our results suggest that habitat fragmentation may affect the maintenance of V_A and thereby reduce the adaptive capacity of populations.     

Gene flow and genetic drift in urban environments

Evidence is growing that human modification of landscapes has dramatically altered evolutionary processes. In urban population genetic studies, urbanization is typically predicted to act as a barrier that isolates populations of species, leading to increased genetic drift within populations and reduced gene flow between populations. However, urbanization may also facilitate dispersal among populations, leading to higher genetic diversity within, and lower differentiation between, urban populations. We reviewed the literature on nonadaptive urban evolution to evaluate the support for each of these urban fragmentation and facilitation models. In a review of the literature with supporting quantitative analyses of 167 published urban population genetics studies, we found a weak signature of reduced within‐population genetic diversity and no evidence of consistently increased between‐population genetic differentiation associated with urbanization. In addition, we found that urban landscape features act as barriers or conduits to gene flow, depending on the species and city in question. Thus, we speculate that dispersal ability of species and environmental heterogeneity between cities contributes to the variation exhibited in our results. However, >90% of published studies reviewed here showed an association of urbanization with genetic drift or gene flow, highlighting the strong impact of urbanization on nonadaptive evolution. It is clear that species biology and city heterogeneity obscure patterns of genetic drift and gene flow in a quantitative analysis. Thus, we suggest that future research makes comparisons of multiple cities and nonurban habitats, and takes into consideration species' natural history, environmental variation, spatial modelling and marker selection.     

Genetic variation within and among populations of a dominant desert tree Haloxylon ammodendron (Amaranthaceae) in China

BACKGROUND AND AIMS: China is one of the countries most severely affected by desertification. Haloxylon ammodendron (Amaranthaceae) is an ecologically important component of the desert ecosystem and is one of the main tree species used for restoration, yet we know little about its genetic structure. METHODS: Genetic variation within and between nine populations of H. ammodendron from two regions of China was investigated using ISSR (inter-simple sequence repeat) markers. KEY RESULTS: Eight primers used in this study amplified 219 reproducible bands of which 184 (84 %) were polymorphic. Analysis of molecular variance (AMOVA) revealed high genetic variation within populations (97.63 %) and low genetic differentiation between regions (0.62 %) and among populations (1.75 %). CONCLUSIONS: It is suggested that the present genetic structure could have arisen by high levels of gene flow. The gene flow among populations observed here is probably mainly attributable to pollen movement. The genetic structure also has important implications in ecological restoration practice.     

Migration load in plants: role of pollen and seed dispersal in heterogeneous landscapes

Evolution of local adaptation depends critically on the level of gene flow, which, in plants, can be due to either pollen or seed dispersal. Using analytical predictions and individual-centred simulations, we investigate the specific influence of seed and pollen dispersal on local adaptation in plant populations growing in patchy heterogeneous landscapes. We study the evolution of a polygenic trait subject to stabilizing selection within populations, but divergent selection between populations. Deviations from linkage equilibrium and Hardy-Weinberg equilibrium make different contributions to genotypic variance depending on the dispersal mode. Local genotypic variance, differentiation between populations and genetic load vary with the rate of gene flow but are similar for seed and pollen dispersal, unless the landscape is very heterogeneous. In this case, genetic load is higher in the case of pollen dispersal, which appears to be due to differences in the distribution of genotypic values before selection.     

Emergence of long‐term balanced polymorphism under cyclic selection of spatially variable magnitude

A fundamental question in evolutionary biology is what promotes genetic variation at nonneutral loci, a major precursor to adaptation in changing environments. In particular, balanced polymorphism under realistic evolutionary models of temporally varying environments in finite natural populations remains to be demonstrated. Here, we propose a novel mechanism of balancing selection under temporally varying fitnesses. Using forward‐in‐time computer simulations and mathematical analysis, we show that cyclic selection that spatially varies in magnitude, such as along an environmental gradient, can lead to elevated levels of nonneutral genetic polymorphism in finite populations. Balanced polymorphism is more likely with an increase in gene flow, magnitude and period of fitness oscillations, and spatial heterogeneity. This polymorphism‐promoting effect is robust to small systematic fitness differences between competing alleles or to random environmental perturbation. Furthermore, we demonstrate analytically that protected polymorphism arises as spatially heterogeneous cyclic fitness oscillations generate a type of storage effect that leads to negative frequency dependent selection. Our findings imply that spatially variable cyclic environments can promote elevated levels of nonneutral genetic variation in natural populations.     

Weak impact of fine‐scale landscape heterogeneity on evolutionary potential in Arabidopsis lyrata

Microhabitat heterogeneity can lead to fine‐scale local adaptation when gene flow is restricted, which may be important for the maintenance of genetic variation within populations. This study tested whether microhabitat heterogeneity was associated with trait differences in a population of Arabidopsis lyrata and studied its impact on the genetic variance–covariance (G) matrix. Maternal seed families were collected from dune tops and bottoms, two microhabitats known to vary significantly in water availability. In a common garden experiment, replicate individuals per family were raised under wet and dry conditions, and physiological, morphological and life‐history traits were assessed. Plants from the two microenvironments differed in their response to treatment in two performance components, in stomata density and most strongly in flowering time. Under wet conditions, plants originating from dune bottoms flowered 4 weeks earlier than those from dune tops. Only one of three G‐matrix comparisons revealed that habitat heterogeneity and evolutionary potential were positively linked. The number of independent trait dimensions was larger in the entire population than within subpopulations separated by microhabitat under wet conditions. However, the size of the G‐matrix was no larger in the entire population than within subpopulations separated by microhabitat, and trait correlation structure between microhabitats and treatments was not significantly different. These results indicate that fine‐scale habitat heterogeneity likely led to local adaptation, which weakly affected levels of across‐trait genetic variation.     

Genetic differentiation and gene flow among populations of the alpine butterfly, Parnassius smintheus, vary with landscape connectivity

Levels of gene flow among populations vary both inter- and intraspecifically, and understanding the ecological bases of variation in levels of gene flow represents an important link between the ecological and evolutionary dynamics of populations. The effects of habitat spatial structure on gene flow have received considerable attention; however, most studies have been conducted at a single spatial scale and without background data on how individual movement is affected by landscape features. We examined the influence of habitat connectivity on inferred levels of gene flow in a high-altitude, meadow-dwelling butterfly, Parnassius smintheus. For this species, we had background data on the effects of landscape structure on both individual movement and on small-scale population genetic differentiation. We compared genetic differentiation and patterns of isolation by distance, based on variation at seven microsatellite loci, among three regions representing two levels of connectivity of high-altitude, nonforested habitats. We found that reduced connectivity of habitats, resulting from more forest cover at high altitudes, was associated with greater genetic differentiation among populations (higher estimated FST), a breakdown of isolation by distance, and overall lower levels of inferred gene flow. These observed differences were consistent with expectations based on our knowledge of the movement behaviour of this species and on previous population genetic analyses conducted at the smaller spatial scale. Our results indicate that the role of gene flow may vary among groups of populations depending on the interplay between individual movement and the structure of the surrounding landscape.     

Interannual genetic heterogeneity of pollen pools accepted by Quercus salicina individuals

Since flowering often varies among years in wind-pollinated woody species, the genetic composition of pollen pools accepted by seed parents can differ between years. The interannual heterogeneity of pollen flow may be important for maintaining genetic diversity within populations because it can increase genetic variation within populations and the effective sizes of the populations. In this study we examined heterogeneity, using paternity analysis and analysis of molecular variance, in the genetic composition of pollen pools among different reproductive years for six Quercus salicina seed parents in an 11.56-ha plot in a temperate old-growth evergreen broadleaved forest. The genotypes at seven microsatellite loci were determined for 111 adult trees and 777 offspring of the six seed parents in 2-5 reproductive years. Genetic differentiation of pollen pools among different reproductive years for each seed parent was significant over all seed parents and for each of four seed parents that were analysed for more than 2 years, but not for either of the other two seed parents (analysed for 2 years). For both the pollen pools originating from inside the plot and those originating from outside it, genetic differentiation among different reproductive years for each seed parent was significant over all seed parents. However, among-year genetic differentiation in the pollen pools originating from within the plot was detected for all four of the seed parents that were analysed for more than 2 years, but for only one of the four in the pools originating from outside the plot. Genetic diversity (estimated as allelic richness and gene diversity) was higher for pollen pools over all reproductive years than for pollen pools in single years. These results indicate that the year-to-year genetic variation of pollen pools increases genetic diversity in offspring and is strongly affected by the variation in pollen parents within the plot because of their high pollination contributions. The high year-to-year variation in pollen parents within the plot and overall supports the hypothesis that the offspring produced across years represent a larger genetic neighbourhood.     

Patterns of gene flow and population genetic structure in the canyon treefrog, Hyla arenicolor (Cope)

Patterns of gene flow and genetic structuring were examined in the canyon treefrog, Hyla arenicolor (Cope). Hierarchical analysis of genetic variation was performed on mitochondrial cytochrome b haplotypes from 323 individuals, representing 32 populations from previously described phylogeographic regions. Results from AMOVA revealed that 60.4-78.9% of the recovered genetic variation was the result of differences in the appointment of genetic variation between subdivisions of the primary phylogeographic regions. In contrast, populations only contained between 13.9 and 30.1% of the observed haplotypic variation. Gene flow estimates based on calculations of phi ST revealed moderate levels of gene flow within phylogeographic regions, but there was no evidence of gene flow between these regions, suggesting that geographical boundaries were probably important in the formation of phylogeographic structure in H. arenicolor. Phylogeographic regions exhibited very different patterns of gene flow. One region showed evidence of recent colonization. Another region exhibited very limited gene flow. Moderate to high estimates of gene flow were obtained for populations from two distinct phylogeographic regions characterized by mesic and xeric environments. Isolation by distance was observed in both regions suggesting that these regions are in genetic equilibrium. Because gene flow is extremely unlikely between the populations in the xeric region, this result is interpreted as historical gene flow. These results indicate that isolation-by-distance effects may still be observed even when population genetic structure and gene flow are the result of historical association.     

ECOLOGICAL HISTORY AND EVOLUTION IN A NOVEL ENVIRONMENT: HABITAT HETEROGENEITY AND INSECT ADAPTATION TO A NEW HOST PLANT

Environmental heterogeneity has often been implicated in the maintenance of genetic variation. However, previous research has not considered how environmental heterogeneity might affect the rate of adaptation to a novel environment. In this study, I used an insect-plant system to test the hypothesis that heterogeneous environments maintain more genetic variation in fitness components in a novel environment than do uniform environments. To manipulate recent ecological history, replicate populations of the dipteran leafminer Liriomyza trifolii were maintained for 20 generations in one of three treatments: a heterogeneous environment that contained five species of host plant, and two uniform environments that contained either a susceptible chrysanthemum or tomato. The hypothesis that greater genetic variance for survivorship and developmental time on a new host plant (a leafminer-resistant chrysanthemum) would be maintained in the heterogeneous treatment relative to the uniform environments was then tested with a sib-analysis and a natural selection experiment. Populations from the heterogeneous host plant treatment had no greater genetic variance in either larval survivorship or developmental time on the new host than did populations from either of the other treatments. Moreover, the rate of adaptation to the new host did not differ between the ecological history treatments, although the populations from the uniform chrysanthemum treatment had higher mean survivorship throughout the selection experiment. The estimates of the heritability of larval survivorship from the sib-analysis and selection experiment were quite similar. These results imply that ecologically realistic levels of environmental heterogeneity will not necessarily maintain more genetic variance than uniform environments when traits expressed in a particular novel environment are considered.     

Phenotypic differentiation of the Solidago virgaurea complex along an elevational gradient: Insights from a common garden experiment and population genetics

Plant species distributed along wide elevational or latitudinal gradients show phenotypic variation due to their heterogeneous habitats. This study investigated whether phenotypic variation in populations of the Solidago virgaurea complex along an elevational gradient is caused by genetic differentiation. A common garden experiment was based on seeds collected from nine populations of the S. virgaurea complex growing at elevations from 1,597 m to 2,779 m a.s.l. on Mt. Norikura in central Japan. Population genetic analyses with microsatellite markers were used to infer the genetic structure and levels of gene flow between populations. Leaf mass per area was lower, while leaf nitrogen and chlorophyll concentrations were greater for higher elevations at which seeds were originally collected. For reproductive traits, plants derived from higher elevations had larger flower heads on shorter stems and flowering started earlier. These elevational changes in morphology were consistent with the clines in the field, indicating that phenotypic variation along the elevational gradient would have been caused by genetic differentiation. However, population genetic analysis using 16 microsatellite loci suggested an extremely low level of genetic differentiation of neutral genes among the nine populations. Analysis of molecular variance also indicated that most genetic variation was partitioned into individuals within a population, and the genetic differentiation among the populations was not significant. This study suggests that genome regions responsible for adaptive traits may differ among the populations despite the existence of gene flow and that phenotypic variation of the S. virgaurea complex along the elevational gradient is maintained by strong selection pressure.     

Genetic variation of Sherardia arvensis L. – How land use and fragmentation affect an arable weed

The distribution of arable weeds extends over regions, where the species occur naturally in different kinds of habitats and regions, where they are mainly limited to arable fields.Here, we present a comparative study on the genetic structure of the arable weed Sherardia arvensis L. comprising populations from Mediterranean grasslands in Southern France and populations from arable fields in Germany. Enhanced by intensified land use since the 1960th, overall population density in Germany is very low compared to the density of populations in Southern France. We tested whether genetic variation within and among populations differ between France and Germany due to different patterns of distribution and land use. Therefore, we analysed 231 individuals of S. arvensis from 24 populations using AFLPs. Based on fragment analysis data we compared spatial genetic structure and genetic variation of populations from the two regions.Genetic variation within populations from the two regions (Shannon Index = 0.13 for both) and genetic variation among populations (26.8% and 30.0% in an analysis of molecular variance) were comparable. In both regions a drift-migration model supported the assumption of gene flow between populations. However, a clear correlation of geographical and genetic distances could only be reported for the indigenous populations from France (r = 0.46; P = 0.02), whereas in Germany a spatial genetic relationship between populations was missing (r = 0.16; P = 0.21).Our study revealed that neither French nor German populations are genetically impoverished. For French populations further the spatial genetic structure suggests that there is current gene flow between populations through pollinators and seed dispersal by cattle. For German populations comparable levels of genetic diversity and gene flow were detected, but gene flow was random. This can be traced back in all likelihood to diffuse dispersal by agriculture and the mechanical reshuffling of the individuals from the soil seed bank.     

Genomic evidence for divergence with gene flow in host races of the larch budmoth

Ecological divergence in the face of gene flow has recently become implicated as a potentially important cause of speciation and adaptive radiation. Here, we develop a genomic approach to test for divergent selection in sympatric host races of the larch budmoth Zeiraphera diniana (Lepidoptera: Tortricidae). We analysed hundreds of amplified fragment length polymorphism markers in 92 individuals in sympatric and allopatric populations, and in two backcross broods used to map the markers to individual chromosomes. The results directly confirm the existence of natural hybridization and demonstrate strong heterogeneity between chromosomes in terms of molecular divergence between host races (the average level of divergence was FST = 0.216). However, genomic heterogeneity was not found when we analysed divergence between geographically separated populations of the same host race. We conclude that the variance of the level of sympatric divergence among chromosomes is the footprint of divergent selection acting on a few linkage groups, combined with appreciable gene flow that homogenizes between-race variation at the remaining linkage groups. These results, coupled with other recent multilocus analyses of sister species pairs, demonstrate that selection-driven sympatric phase of genetic divergence in the presence of gene flow is a likely feature of speciation.     

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

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

Surprisingly little population genetic structure in a fungus‐associated beetle despite its exploitation of multiple hosts

In heterogeneous environments, landscape features directly affect the structure of genetic variation among populations by functioning as barriers to gene flow. Resource‐associated population genetic structure, in which populations that use different resources (e.g., host plants) are genetically distinct, is a well‐studied example of how environmental heterogeneity structures populations. However, the pattern that emerges in a given landscape should depend on its particular combination of resources. If resources constitute barriers to gene flow, population differentiation should be lowest in homogeneous landscapes, and highest where resources exist in equal proportions. In this study, we tested whether host community diversity affects population genetic structure in a beetle (Bolitotherus cornutus) that exploits three sympatric host fungi. We collected B. cornutus from plots containing the three host fungi in different proportions and quantified population genetic structure in each plot using a panel of microsatellite loci. We found no relationship between host community diversity and population differentiation in this species; however, we also found no evidence of resource‐associated differentiation, suggesting that host fungi are not substantial barriers to gene flow. Moreover, we detected no genetic differentiation among B. cornutus populations separated by several kilometers, even though a previous study demonstrated moderate genetic structure on the scale of a few hundred meters. Although we found no effect of community diversity on population genetic structure in this study, the role of host communities in the structuring of genetic variation in heterogeneous landscapes should be further explored in a species that exhibits resource‐associated population genetic structure.     

Assortative mating and gene flow generate clinal phenological variation in trees

ABSTRACT: BACKGROUND: On-going climate change is shifting the timing of bud burst (TBB) of broad leaf and conifer trees in temperate areas, raising concerns about the abilities of natural populations to respond to these shifts. The level of expected evolutionary change depends on the level and distribution of genetic variation of TBB. While numerous experimental studies have highlighted the role of divergent selection in promoting clinal TBB differentiation, we explored whether the observed patterns of variation could be generated by the joint effects of assortative mating for TBB and gene flow among natural populations. We tested this hypothesis using an in silico approach based on quantitative genetic models. RESULTS: Our simulations showed that genetic clines can develop even without divergent selection. Assortative mating in association with environmental gradients substantially shifted the mean genetic values of populations. Owing to assortative mating, immigrant alleles were screened for proximal or distant populations depending on the strength of the environmental cline. Furthermore, we confirmed that assortative mating increases the additive genetic variance within populations. However, we observed also a rapid decline of the additive genetic variance caused by restricted gene flow between neighboring populations resulting from preferential matings between phenologically-matching phenotypes. CONCLUSIONS: We provided evidence that the patterns of genetic variation of phenological traits observed in forest trees can be generated solely by the effects of assortative mating and gene flow. We anticipate that predicted temperature increases due to climate change will further enhance genetic differentiation across the landscape. These trends are likely to be reinforced or counteracted by natural selection if phenological traits are correlated to fitness.     

Recent range expansion and agricultural landscape heterogeneity have only minimal effect on the spatial genetic structure of the plant pathogenic fungus Mycosphaerella fijiensis

Understanding how geographical and environmental features affect genetic variation at both the population and individual levels is crucial in biology, especially in the case of pathogens. However, distinguishing between these factors and the effects of historical range expansion on spatial genetic structure remains challenging. In the present study, we investigated the case of Mycosphaerella fijiensis—a plant pathogenic fungus that has recently colonized an agricultural landscape characterized by the presence of potential barriers to gene flow, including several commercial plantations in which disease control practises such as the use of fungicides are applied frequently, and low host density areas. We first genotyped 300 isolates sampled at a global scale on untreated plants in two dimensions over a 50 × 80-km area. Using two different clustering algorithms, no genetic structure was detected in the studied area, suggesting expansion of large populations and/or no influence of potential barriers. Second, we investigated the potential effect of disease control practises on M. fijiensis diversity by comparing populations sampled in commercial vs food-crop plantations. At this local scale, we detected significantly higher allelic richness inside commercial plantations compared with the surrounding food-crop plantation populations. Analysis of molecular variance indicated that 99% of the total genetic variance occurred within populations. We discuss the suggestion that high population size and/or high migration rate between populations might be responsible for the absence of any effect of disease control practises on genetic diversity and differentiation.