Hierarchical population structure and genetic diversity of lake trout (Salvelinus namaycush) in a dendritic system in Northern Labrador

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Urban population genetics of slum‐dwelling rats (Rattus norvegicus) in Salvador,Brazil

Throughout the developing world, urban centres with sprawling slum settlements are rapidly expanding and invading previously forested ecosystems. Slum communities are characterized by untended refuse, open sewers and overgrown vegetation, which promote rodent infestation. Norway rats (Rattus norvegicus) are reservoirs for epidemic transmission of many zoonotic pathogens of public health importance. Understanding the population ecology of R. norvegicus is essential to formulate effective rodent control strategies, as this knowledge aids estimation of the temporal stability and spatial connectivity of populations. We screened for genetic variation, characterized the population genetic structure and evaluated the extent and patterns of gene flow in the urban landscape using 17 microsatellite loci in 146 rats from nine sites in the city of Salvador, Brazil. These sites were divided between three neighbourhoods within the city spaced an average of 2.7 km apart. Surprisingly, we detected very little relatedness among animals trapped at the same site and found high levels of genetic diversity, as well as structuring across small geographical distances. Most F_ST comparisons among sites were statistically significant, including sites <400 m apart. Bayesian analyses grouped the samples in three genetic clusters, each associated with distinct sampling sites from different neighbourhoods or valleys within neighbourhoods. These data indicate the existence of complex genetic structure in R. norvegicus in Salvador, linked to the heterogeneous urban landscape. Future rodent control measures need to take into account the spatial and temporal linkage of rat populations in Salvador, as revealed by genetic data, to develop informed eradication strategies.     

Urban landscape genetics: canopy cover predicts gene flow between white-footed mouse (Peromyscus leucopus) populations in New York City

In this study, I examine the influence of urban canopy cover on gene flow between 15 white-footed mouse (Peromyscus leucopus) populations in New York City parklands. Parks in the urban core are often highly fragmented, leading to rapid genetic differentiation of relatively nonvagile species. However, a diverse array of 'green' spaces may provide dispersal corridors through 'grey' urban infrastructure. I identify urban landscape features that promote genetic connectivity in an urban environment and compare the success of two different landscape connectivity approaches at explaining gene flow. Gene flow was associated with 'effective distances' between populations that were calculated based on per cent tree canopy cover using two different approaches: (i) isolation by effective distance (IED) that calculates the single best pathway to minimize passage through high-resistance (i.e. low canopy cover) areas, and (ii) isolation by resistance (IBR), an implementation of circuit theory that identifies all low-resistance paths through the landscape. IBR, but not IED, models were significantly associated with three measures of gene flow (Nm from F(ST) , BayesAss+ and Migrate-n) after factoring out the influence of isolation by distance using partial Mantel tests. Predicted corridors for gene flow between city parks were largely narrow, linear parklands or vegetated spaces that are not managed for wildlife, such as cemeteries and roadway medians. These results have implications for understanding the impacts of urbanization trends on native wildlife, as well as for urban reforestation efforts that aim to improve urban ecosystem processes.     

Gene flow among native bush rat,Rattus fuscipes (Rodentia: Muridae), populations in the fragmented subtropical forests of south‐east Queensland

Abstract Many natural populations in areas of continuous habitat exhibit some form of local genetic structure. Anthropogenic habitat fragmentation can also strongly influence the dynamics of gene flow between populations. We used eight microsatellite markers to investigate the population genetic structure of an abundant forest species, the Australian bush rat (Rattus fuscipes), in the subtropical forests of south‐east Queensland. Five sites were sampled, allowing pairwise comparisons within continuous habitat and across clearings. Weak, but significant population differentiation and a significant pattern of isolation by distance was detected over the small scale (<10 km) of this study. Fine‐scale analysis at a single site (<1 km) showed a significant correlation between individual female genetic distance and geographical distance, but no similar pattern among male individuals. There was no evidence of increased population differentiation across clearings relative to comparisons within continuous forest. This was attributed to dispersal within corridors of remnant and revegetated habitat between the forested areas. We concluded that an inherently restricted dispersal ability, female philopatry and natural habitat heterogeneity play an important part in the development of genetic structure among populations of R. fuscipes. It is important to understand the relationship between landscape features and the pattern of gene flow among continuous populations, as this allows us to predict the impact of fragmentation on natural populations.     

Genetic population structure of the Dakota skipper (Lepidoptera: Hesperia dacotae): A North American native prairie obligate

A range-wide survey of Dakotaskipper (Hesperia dacotae) populationsassessed levels of genetic variability andgeographic scale of population structure inthis species of conservation concern. Thisspecies exists on isolated patches of nativetall- and mixed-grass prairie within a highlymodified landscape dominated by agriculture. It has been extirpated from the southernportion of its range and has sufferedrange-wide declines. Nine populations weresampled from western Minnesota, eastern SouthDakota, and southern Manitoba. Starch gelelectrophoresis was used to resolve 21 isozymeloci in 278 Dakota skippers. Dakota skipperpopulations were approximately as variable asother lepidopterans found in isolated habitats. Genetic distances indicated that Manitobapopulations were somewhat distinct from ones inMinnesota and South Dakota. Isolation-by-distance was detected range-wideand among the seven southern-most populations. Genetically effective immigration rates weresmall at both range-wide and regional scalesand effective populations sizes were lowsuggesting that Dakota skipper populations aregenetically isolated from one another, althoughthey were likely more connected in the recentpast. Genotype assignment tests revealed twoclusters of populations in Minnesota and SouthDakota that were not apparent from theisolation-by-distance results. Significantheterozygote deficiencies relative toHardy-Weinberg expectations and high inbreedingcoefficients suggest structure within samplelocations. Management recommendations includethe maximization of effective population sizein each Dakota skipper population to offset theeffects of drift and habitat corridors in somecases. Habitat management should consider thewithin-site population structure and possibletemporal population structure detected in thisstudy.     

Do landscape processes predict phylogeographic patterns in the wood frog?

Understanding factors that influence population connectivity and the spatial distribution of genetic variation is a major goal in molecular ecology. Improvements in the availability of high-resolution geographic data have made it increasingly possible to quantify the effects of landscape features on dispersal and genetic structure. However, most studies examining such landscape effects have been conducted at very fine (e.g. landscape genetics) or broad (e.g. phylogeography) spatial scales. Thus, the extent to which processes operating at fine spatial scales are linked to patterns at larger scales remains unclear. Here, we test whether factors impacting wood frog dispersal at fine spatial scales are correlated with genetic structure at regional scales. Using recently developed methods borrowed from electrical circuit theory, we generated landscape resistance matrices among wood frog populations in eastern North America based on slope, a wetness index, land cover and absolute barriers to wood frog dispersal. We then determined whether these matrices are correlated with genetic structure based on six microsatellite markers and whether such correlations outperform a landscape-free model of isolation by resistance. We observed significant genetic structure at regional spatial scales. However, topography and landscape variables associated with the intervening habitat between sites provide little explanation for patterns of genetic structure. Instead, absolute dispersal barriers appear to be the best predictor of regional genetic structure in this species. Our results suggest that landscape variables that influence dispersal, microhabitat selection and population structure at fine spatial scales do not necessarily explain patterns of genetic structure at broader scales.     

Landscape effects on the contemporary genetic structure of Ruffed Grouse (Bonasa umbellus) populations

The amount of dispersal that occurs among populations can be limited by landscape heterogeneity, which is often due to both natural processes and anthropogenic activity leading to habitat loss or fragmentation. Understanding how populations are structured and mapping existing dispersal corridors among populations is imperative to both determining contemporary forces mediating population connectivity, and informing proper management of species with fragmented populations. Furthermore, the contemporary processes mediating gene flow across heterogeneous landscapes on a large scale are understudied, particularly with respect to widespread species. This study focuses on a widespread game bird, the Ruffed Grouse (Bonasa umbellus), for which we analyzed samples from the western extent of the range. Using three types of genetic markers, we uncovered multiple factors acting in concert that are responsible for mediating contemporary population connectivity in this species. Multiple genetically distinct groups were detected; microsatellite markers revealed six groups, and a mitochondrial marker revealed four. Many populations of Ruffed Grouse are genetically isolated, likely by macrogeographic barriers. Furthermore, the addition of landscape genetic methods not only corroborated genetic structure results, but also uncovered compelling evidence that dispersal resistance created by areas of unsuitable habitat is the most important factor mediating population connectivity among the sampled populations. This research has important implications for both our study species and other inhabitants of the early successional forest habitat preferred by Ruffed Grouse. Moreover, it adds to a growing body of evidence that isolation by resistance is more prevalent in shaping population structure of widespread species than previously thought.     

Genetic structure of the cyclic fossorial water vole (Arvicola terrestris): landscape and demographic influences

Genetic structure can be strongly affected by landscape features and variation through time and space of demographic parameters such as population size and migration rate. The fossorial water vole (Arvicola terrestris) is a cyclic species characterized by large demographic fluctuations over short periods of time. The outbreaks do not occur everywhere at the same time but spread as a wave at a regional scale. This leads to a pattern of large areas (i.e. some hundreds of km2), each with different vole abundances, at any given time. Here, we describe the abundance and genetic structures in populations of the fossorial water vole. We use the data to try to understand how landscape and demographic features act to shape the genetic structure. The spatial variability of vole abundance was assessed from surface indices, collected in spring 2002 (April) in eastern central France. Genetic variability was analysed using eight microsatellite loci at 23 localities sampled between October 2001 and April 2002. We found some congruence between abundance and genetic structures. At a regional scale, the genetic disruptions were associated with both sharp relief and transition between an area of low abundance and another of high abundance. At a local scale, we observed a variation of the isolation-by-distance pattern according to the abundance level of vole populations. From these results we suggest that the dispersal pattern in cyclic rodent populations varies throughout the demographic cycle.     

Fine-scale spatial genetic structure and gene dispersal in Silene latifolia

Plants are sessile organisms, often characterized by limited dispersal. Seeds and pollen are the critical stages for gene flow. Here we investigate spatial genetic structure, gene dispersal and the relative contribution of pollen vs seed in the movement of genes in a stable metapopulation of the white campion Silene latifolia within its native range. This short-lived perennial plant is dioecious, has gravity-dispersed seeds and moth-mediated pollination. Direct measures of pollen dispersal suggested that large populations receive more pollen than small isolated populations and that most gene flow occurs within tens of meters. However, these studies were performed in the newly colonized range (North America) where the specialist pollinator is absent. In the native range (Europe), gene dispersal could fall on a different spatial scale. We genotyped 258 individuals from large and small (15) subpopulations along a 60 km, elongated metapopulation in Europe using six highly variable microsatellite markers, two X-linked and four autosomal. We found substantial genetic differentiation among subpopulations (global F_ST=0.11) and a general pattern of isolation by distance over the whole sampled area. Spatial autocorrelation revealed high relatedness among neighboring individuals over hundreds of meters. Estimates of gene dispersal revealed gene flow at the scale of tens of meters (5–30 m), similar to the newly colonized range. Contrary to expectations, estimates of dispersal based on X and autosomal markers showed very similar ranges, suggesting similar levels of pollen and seed dispersal. This may be explained by stochastic events of extensive seed dispersal in this area and limited pollen dispersal.     

Spatial and ecological population genetic structures within two island‐endemic Aeonium species of different niche width

The Crassulacean genus Aeonium is a well‐known example for plant species radiation on oceanic archipelagos. However, while allopatric speciation among islands is documented for this genus, the role of intra‐island speciation due to population divergence by topographical isolation or ecological heterogeneity has not yet been addressed. The aim of this study was to investigate intraspecific genetic structures and to identify spatial and ecological drivers of genetic population differentiation on the island scale. We analyzed inter simple sequence repeat variation within two island‐endemic Aeonium species of La Palma: one widespread generalist that covers a large variety of different habitat types (Ae. davidbramwellii) and one narrow ecological specialist (Ae. nobile), in order to assess evolutionary potentials on this island. Gene pool differentiation and genetic diversity patterns were associated with major landscape structures in both species, with phylogeographic implications. However, overall levels of genetic differentiation were low. For the generalist species, outlier loci detection and loci–environment correlation approaches indicated moderate signatures of divergent selection pressures linked to temperature and precipitation variables, while the specialist species missed such patterns. Our data point to incipient differentiation among populations, emphasizing that ecological heterogeneity and topographical structuring within the small scales of an island can foster evolutionary processes. Very likely, such processes have contributed to the radiation of Aeonium on the Canary Islands. There is also support for different evolutionary mechanisms between generalist and specialist species.     

Spatial autocorrelation analysis offers new insights into gene flow in the Australian bush rat,Rattus fuscipes

Dispersal is a fundamental process that influences the response of species to landscape change and habitat fragmentation. In an attempt to better understand dispersal in the Australian bush rat, Rattus fuscipes, we have combined a new multilocus autocorrelation method with hypervariable microsatellite genetic markers to investigate fine-scale (< or = 1 km) patterns of spatial distribution and spatial genetic structure. The study was conducted across eight trapping transects at four sites, with a total of 270 animals sampled. Spatial autocorrelation analysis of bush rat distribution revealed that, in general, animals occurred in groups or clusters of higher density (< or = 200 m across), with intervening gaps or lower density areas. Spatial genetic autocorrelation analysis, based on seven hypervariable microsatellite loci (He = 0.8) with a total of 80 alleles, revealed a consistent pattern of significant positive local genetic structure. This genetic pattern was consistent for all transects, and for adults and sub-adults, males and females. By testing for autocorrelation at multiple scales from 10 to 800 m we found that the extent of detectable positive spatial genetic structure exceeded 500 m. Further analyses detected significantly weaker spatial genetic structure in males compared with females, but no significant differences were detected between adults and sub adults. Results from Mantel tests and hierarchical AMOVA further support the conclusion that the distribution of bush rat genotypes is not random at the scale of our study. Instead, proximate bush rats are more genetically alike than more distant animals. We conclude that in bush rats, gene flow per generation is sufficiently restricted to generate the strong positive signal of local spatial genetic structure. Although our results are consistent with field data on animal movement, including the reported tendency for males to move further than females, we provide the first evidence for restricted gene flow in bush rats. Our study appears to be the first microsatellite-based study of fine-scale genetic variation in small mammals and the first to report consistent positive local genetic structure across sites, age-classes, and sexes. The combination of new forms of autocorrelation analyses, hypervariable genetic markers and fine-scale analysis (< 1 km) may thus offer new evolutionary insights that are overlooked by more traditional larger scaled (> 10 km) population genetic studies.     

Marine landscapes and population genetic structure of herring (Clupea harengus L.) in the Baltic Sea

Numerically small but statistically significant genetic differentiation has been found in many marine fish species despite very large census population sizes and absence of obvious barriers to migrating individuals. Analyses of morphological traits have previously identified local spawning groups of herring (Clupea harengus L.) in the environmentally heterogeneous Baltic Sea, whereas allozyme markers have not revealed differentiation. We analysed variation at nine microsatellite loci in 24 samples of spring-spawning herring collected at 11 spawning locations throughout the Baltic Sea. Significant temporal differentiation was observed at two locations, which we ascribe to sympatrically spawning but genetically divergent 'spawning waves'. Significant differentiation was also present on a geographical scale, though pairwise F(ST) values were generally low, not exceeding 0.027. Partial Mantel tests showed no isolation by geographical distance, but significant associations were observed between genetic differentiation and environmental parameters (salinity and surface temperature) (0.001 < P < or = 0.099), though these outcomes were driven mainly by populations in the southwestern Baltic Sea, which also exhibits the steepest environmental gradients. Application of a novel method for detecting barriers to gene flow by combining geographical coordinates and genetic differentiation allowed us to identify two zones of lowered gene flow. These zones were concordant with the separation of the Baltic Sea into major basins, with environmental gradients and with differences in migration behaviour. We suggest that similar use of landscape genetics approaches may increase the understanding of the biological significance of genetic differentiation in other marine fishes.     

Genetic structure of the endangered perennial plant Eryngium alpinum (Apiaceae) in an alpine valley

We investigated the genetic structure of Eryngium alpinum (Apiaceae) in an Alpine valley where the plant occurs in patches of various sizes. In a conservation perspective, our goal was to determine whether the valley consists of one or several genetic units. Habitat fragmentation and previous observations of restricted pollen/seed dispersal suggested pronounced genetic structure, but gene dispersal often follows a leptokurtic distribution, which may lead to weak genetic structure. We used nine microsatellite loci and two nested sampling designs (50 × 50 m grid throughout the valley and 2 × 2 m grid in two 50 × 10 m quadrats). Within the overall valley, F -statistics and Bayesian approaches indicated high genetic homogeneity. This result might be explained by: (1) underestimation of long-distance pollen/seed dispersal by in situ experiments and (2) too recent fragmentation events to build up genetic structure. Spatial autocorrelation revealed isolation by distance on the overall valley but this pattern was much more pronounced in the 50 × 10 m quadrats sampled with a 2-m mesh. This was probably associated with limited primary seed dispersal, leading to the spatial clustering of half-sibs around maternal plants. We emphasize the interest of nested sampling designs and of combining several statistical tools.  © 2008 The Linnean Society of London, Biological Journal of the Linnean Society , 2008, 93 , 667–677.     

On the spatial scale of dispersal in coral reef fishes

Marine biologists have gone through a paradigm shift, from the assumption that marine populations are largely ‘open’ owing to extensive larval dispersal to the realization that marine dispersal is ‘more restricted than previously thought’. Yet, population genetic studies often reveal low levels of genetic structure across large geographic areas. On the other side, more direct approaches such as mark‐recapture provide evidence of localized dispersal. To what extent can direct and indirect studies of marine dispersal be reconciled? One approach consists in applying genetic methods that have been validated with direct estimates of dispersal. Here, we use such an approach—genetic isolation by distance between individuals in continuous populations—to estimate the spatial scale of dispersal in five species of coral reef fish presenting low levels of genetic structure across the Caribbean. Individuals were sampled continuously along a 220‐km transect following the Mesoamerican Barrier Reef, population densities were estimated from surveys covering 17 200 m² of reef, and samples were genotyped at a total of 58 microsatellite loci. A small but positive isolation‐by‐distance slope was observed in the five species, providing mean parent‐offspring dispersal estimates ranging between 7 and 42 km (CI 1–113 km) and suggesting that there might be a correlation between minimum/maximum pelagic larval duration and dispersal in coral reef fishes. Coalescent‐based simulations indicate that these results are robust to a variety of dispersal distributions and sampling designs. We conclude that low levels of genetic structure across large geographic areas are not necessarily indicative of extensive dispersal at ecological timescales.     

Spatial genetic structure in a metapopulation of the land snail Cepaea nemoralis (Gastropoda: Helicidae)

Habitat fragmentation is a major force affecting demography and genetic structure of wild populations, especially in agricultural landscapes. The land snail Cepaea nemoralis (L.) was selected to investigate the impact of habitat fragmentation on the spatial genetic structure of an organism with limited dispersal ability. Genetic and morphological patterns were investigated at a local scale of a 500 m transect and a mesoscale of 4 x 4 km in a fragmented agricultural landscape while accounting for variation in the landscape using least-cost models. Analysis of microsatellite loci using expected heterozygosity (HE), pairwise genetic distance (FST/1-FST) and spatial autocorrelograms (Moran's I) as well as shell characteristics revealed spatial structuring at both scales and provided evidence for a metapopulation structure. Genetic diversity was related to morphological diversity regardless of landscape properties. This pointed to bottlenecks caused by founder effects after (re)colonization. Our study suggests that metapopulation structure depended on both landscape features and the shape of the dispersal function. A range of genetic spatial autocorrelation up to 80 m at the local scale and up to 800 m at the mesoscale indicated leptokurtic dispersal patterns. The metapopulation dynamics of C. nemoralis resulted in a patchwork of interconnected, spatially structured subpopulations. They were shaped by gene flow which was affected by landscape features, the dispersal function and an increasing role of genetic drift with distance.     

Habitat‐specific population structure in native western flower thrips Frankliniella occidentalis (Insecta,Thysanoptera)

Invasions by pest organisms are among the main challenges for sustainable crop protection. They pose a serious threat to crop production by introducing a highly unpredictable element to existing crop protection strategies. The western flower thrips Frankliniella occidentalis (Insecta, Thysanoptera) managed to invade ornamental greenhouses worldwide within < 25 years. To shed light on possible genetic and/or ecological factors that may have been responsible for this invasion success, we studied the population genetic structure of western flower thrips in its native range in western North America. Analysis of nucleotide sequence variation and variation at microsatellite loci revealed the existence of two habitat‐specific phylogenetic lineages (ecotypes) with allopatric distribution. One lineage is associated with hot/dry climates, the second lineage is restricted to cool/moist climates. We speculate that the ecological niche segregation found in this study may be among the key factors determining the invasion potential of western flower thrips.     

Spatial structure of lemming populations (Dicrostonyx groenlandicus) fluctuating in density

The pattern and scale of the genetic structure of populations provides valuable information for the understanding of the spatial ecology of populations, including the spatial aspects of density fluctuations. In the present paper, the genetic structure of periodically fluctuating lemmings (Dicrostonyx groenlandicus) in the Canadian Arctic was analysed using mitochondrial DNA (mtDNA) control region sequences and four nuclear microsatellite loci. Low genetic variability was found in mtDNA, while microsatellite loci were highly variable in all localities, including localities on isolated small islands. For both genetic markers the genetic differentiation was clear among geographical regions but weaker among localities within regions. Such a pattern implies gene flow within regions. Based on theoretical calculations and population census data from a snap-trapping survey, we argue that the observed genetic variability on small islands and the low level of differentiation among these islands cannot be explained without invoking long distance dispersal of lemmings over the sea ice. Such dispersal is unlikely to occur only during population density peaks.     

Fine-scale population structure and riverscape genetics of brook trout (Salvelinus fontinalis) distributed continuously along headwater channel networks

Linear and heterogeneous habitat makes headwater stream networks an ideal ecosystem in which to test the influence of environmental factors on spatial genetic patterns of obligatory aquatic species. We investigated fine-scale population structure and influence of stream habitat on individual-level genetic differentiation in brook trout (Salvelinus fontinalis) by genotyping eight microsatellite loci in 740 individuals in two headwater channel networks (7.7 and 4.4 km) in Connecticut, USA. A weak but statistically significant isolation-by-distance pattern was common in both sites. In the field, many tagged individuals were recaptured in the same 50-m reaches within a single field season (summer to fall). One study site was characterized with a hierarchical population structure, where seasonal barriers (natural falls of 1.5-2.5 m in height during summer base-flow condition) greatly reduced gene flow and perceptible spatial patterns emerged because of the presence of tributaries, each with a group of genetically distinguishable individuals. Genetic differentiation increased when pairs of individuals were separated by high stream gradient (steep channel slope) or warm stream temperature in this site, although the evidence of their influence was equivocal. In a second site, evidence for genetic clusters was weak at best, but genetic differentiation between individuals was positively correlated with number of tributary confluences. We concluded that the population-level movement of brook trout was limited in the study headwater stream networks, resulting in the fine-scale population structure (genetic clusters and clines) even at distances of a few kilometres, and gene flow was mitigated by 'riverscape' variables, particularly by physical barriers, waterway distance (i.e. isolation-by-distance) and the presence of tributaries.     

Functional connectivity in replicated urban landscapes in the land snail (Cornu aspersum)

Urban areas are highly fragmented and thereby exert strong constraints on individual dispersal. Despite this, some species manage to persist in urban areas, such as the garden snail, Cornu aspersum, which is common in cityscapes despite its low mobility. Using landscape genetic approaches, we combined study area replication and multiscale analysis to determine how landscape composition, configuration and connectivity influence snail dispersal across urban areas. At the overall landscape scale, areas with a high percentage of roads decreased genetic differentiation between populations. At the population scale, genetic differentiation was positively linked with building surface, the proportion of borders where wooded patches and roads appeared side by side and the proportion of borders combining wooded patches and other impervious areas. Analyses based on pairwise genetic distances validated the isolation‐by‐distance and isolation‐by‐resistance models for this land snail, with an equal fit to least‐cost paths and circuit‐theory‐based models. Each of the 12 landscapes analysed separately yielded specific relations to environmental features, whereas analyses integrating all replicates highlighted general common effects. Our results suggest that urban transport infrastructures facilitate passive snail dispersal. At a local scale, corresponding to active dispersal, unfavourable habitats (wooded and impervious areas) isolate populations. This work upholds the use of replicated landscapes to increase the generalizability of landscape genetics results and shows how multiscale analyses provide insight into scale‐dependent processes.     

Natural and anthropogenic determinants of genetic structure in the largest remaining population of the endangered golden-brown mouse lemur, Microcebus ravelobensis

Genetic differentiation between natural populations is best understood as a result of both natural and anthropogenic factors. Genetic studies on large populations still living under relatively undisturbed conditions are extremely valuable to disentangle these influences. The effect of three natural (geographic distance, landscape, dispersal) factors and two anthropogenic factors (road, savannah) on gene flow was analyzed in the largest remaining forest region in the range of the endangered golden-brown mouse lemur in Madagascar. A total of 187 individuals from 12 sites were sampled and genotyped at eight polymorphic microsatellite loci. All sites exhibited similar levels of genetic variation. The level of genetic differentiation was low to moderate with pairwise F(ST) values ranging from -0.002 to 0.12, but most were significant and all sites exhibited high self-assignment rates. A spatial autocorrelation analysis was performed at two geographic scales revealing a pattern of isolation-by-distance and suggesting that no clear differences exist between male and female local dispersal. Two Bayesian approaches revealed that a stretch of savannah represented a significant barrier to movement, whereas the influence of the road on gene flow was less clear. Finally, we found that landscape characteristics, in particular altitude, play a role in the functional connectivity of the sites. The study underlines the importance of studies in relatively undisturbed conditions for the interpretation of population genetics data in fragmented environments. The results are discussed in terms of their conservation relevance for forest-dwelling animals such as most primate species.