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.     

Effects of structural connectivity on fine scale population genetic structure of muskrat,Ondatra zibethicus

In heterogeneous landscapes, physical barriers and loss of structural connectivity have been shown to reduce gene flow and therefore lead to population structuring. In this study, we assessed the influence of landscape features on population genetic structure and gene flow of a semiaquatic species, the muskrat. A total of 97 muskrats were sampled from three watersheds near Sudbury, Ontario, Canada. We estimated population genetic structure using 11 microsatellite loci and identified a single genetic cluster and no genetic differences were found among the watersheds as a result of high levels of gene flow. At finer scales, we assessed the correlation between individual pairwise genetic distances and Euclidean distance as well as different models of least cost path (LCP). We used a range of cost values for the landscape types in order to build our LCP models. We found a positive relationship between genetic distance and least cost distance when we considered roads as corridors for movements. Open landscapes and urban areas seemed to restrict but not prevent gene flow within the study area. Our study underlines the high‐dispersal ability of generalist species in their use of landscape and highlights how landscape features often considered barriers to animal movements are corridors for other species.     

Where movement happens: scale‐dependent landscape effects on genetic differentiation in the European tree frog

Functional connectivity among fragmented populations depends on the landscape matrix between occupied habitat patches and its effect on the frequency of animal movement and gene flow. The quantification of landscape effects on gene flow should therefore be scale‐dependent. Here, we explored the impact of different spatial scales in a landscape genetic analysis of the European tree frog Hyla arborea in a fragmented landscape in Switzerland. We examined the effects of landscape elements and geographic distance on genetic differentiation at three distance classes reflecting varying frequencies of tree frog movement. We calculated pairwise F_ST‐values and assembled 16 landscape elements within 1 km wide corridors between all pairs of tree frog breeding sites. Per distance class, we computed a multiple regression model with stepwise backward elimination and permutation testing. At distances of<2 km, only a larger river acted as a barrier to gene flow. At distances>2 km, geographic distance had a negative effect on gene flow as had landscape elements such as forests and roads. In general, hedgerows and various structure‐rich landscape elements positively affected gene flow. As we found distinct scale‐dependent landscape effects on gene flow, future landscape genetic studies should analyse the effects of landscape variables at different spatial dimensions relevant for the movement and dispersal of the study organisms. Corresponding studies should also carefully consider relevant correlations among the landscape elements tested and should preferentially replicate their analysis at the landscape‐level in order to avoid idiosyncratic results owing to the particular scale and landscape studied.     

Streams over mountains: influence of riparian connectivity on gene flow in the Pacific jumping mouse (Zapus trinotatus)

In species affiliated with heterogeneous habitat, we expect gene flow to be restricted due to constraints placed on individual movement by habitat boundaries. This is likely to impact both individual dispersal and connectivity between populations. In this study, a GIS-based landscape genetics approach was used, in combination with fine-scale spatial autocorrelation analysis and the estimation of recent intersubpopulation migration rates, to infer patterns of dispersal and migration in the riparian-affiliated Pacific jumping mouse (Zapus trinotatus). A total of 228 individuals were sampled from nine subpopulations across a system of three rivers and genotyped at eight microsatellite loci. Significant spatial autocorrelation among individuals revealed a pattern of fine-scale spatial genetic structure indicative of limited dispersal. Geographical distances between pairwise subpopulations were defined following four criteria: (i) Euclidean distance, and three landscape-specific distances, (ii) river distance (distance travelled along the river only), (iii) overland distance (similar to Euclidean, but includes elevation), and (iv) habitat-path distance (a least-cost path distance that models movement along habitat pathways). Pairwise Mantel tests were used to test for a correlation between genetic distance and each of the geographical distances. Significant correlations were found between genetic distance and both the overland and habitat-path distances; however, the correlation with habitat-path distance was stronger. Lastly, estimates of recent migration rates revealed that migration occurs not only within drainages but also across large topographic barriers. These results suggest that patterns of dispersal and migration in Pacific jumping mice are largely determined by habitat connectivity.     

Landscape barriers reduce gene flow in an invasive carnivore: geographical and local genetic structure of American mink in Scotland

To be effective, management programmes geared towards halting or reversing the spread of invasive species must focus on defined and defensible areas. This requires knowledge of the dispersal of non-native species targeted for control to better understand invasion and recolonisation scenarios. We investigated the genetic structure of invasive American mink ( Neovison vison ) in Scotland, and incorporated landscape genetic approaches to examine resultant patterns in relation to geographical features that may influence dispersal. Populations of mink sampled from 10 sites in two regions (Argyll and Northeast Scotland) show a distinct genetic structure. First, the majority of pairwise population comparisons yielded F _ST values that were significantly greater than zero. Second, amova revealed that most of the genetic variance was attributable to differences among regions. Assignment tests placed 89 or more of individuals into their sampled region. Bayesian clustering methods grouped samples into two clusters according to their region of origin. Wombling approach identified the Cairngorms Mountains as a major impediment to gene flow between the regions. Mantel pairwise correlations between genetic and geographical distances estimated as least-cost distance assuming a linear increase in the cost of movement with increasing elevation were higher than Euclidean distances or distance along waterways. Spatial autocorrelation analyses revealed stronger spatial structuring for females than for males. These results suggest that gene flow by American mink is restricted by landscape features (mountain ranges) and that eradication attempt should in the first instance break down the connectivity between management units separated by mountains.     

Scale-dependent diversity effects of seed dispersal by a wild herbivore in fragmented grasslands

Dispersal limitation between habitat fragments is a known driver of landscape-scale biodiversity loss. In Europe, agricultural intensification during the twentieth century resulted in losses of both grassland habitat and traditional grassland seed dispersal vectors such as livestock. During the same period, populations of large wild herbivores have increased in the landscape. Usually studied in woodland ecosystems, these animals are found to disperse seeds from grasslands and other open habitats. We studied endozoochorous seed dispersal by roe deer (Capreolus capreolus) in fragmented grasslands and grassland remnants, comparing dispersed subcommunities of plant species to those in the established vegetation and the seed bank. A total of 652 seedlings of 67 species emerged from 219 samples of roe deer dung. This included many grassland species, and several local grassland specialists. Dispersal had potentially different effects on diversity at different spatial scales. Almost all sites received seeds of species not observed in the vegetation or seed bank at that site, suggesting that local diversity might not be dispersal limited. This pattern was less evident at the landscape scale, where fewer new species were introduced. Nonetheless, long-distance dispersal by large wild herbivores might still provide connectivity between fragmented habitats within a landscape in the areas in which they are active. Finally, as only a subset of the available species were found to disperse in space as well as time, the danger of future biodiversity loss might still exist in many isolated grassland habitats.     

Maintenance of high pollen dispersal in Eucalyptus wandoo, a dominant tree of the fragmented agricultural region in Western Australia

Pollen dispersal was investigated in five remnant populations of Eucalyptus wandoo, a dominant insect-pollinated tree in the fragmented agricultural region of southern Western Australia. Paternity analysis using six microsatellite loci identified a pollen source for 45% of seedlings, and the remainder were assumed to have arisen from pollen sources outside the stands. Outcrossing was variable, ranging from 52 to 89%, and long distance pollen dispersal was observed in all populations with up to 65% of pollen sourced from outside the populations over distances of at least 1 km. Modelling dispersal functions for pollination events within the two larger populations showed little difference between the four two-parameter models tested and indicated a fat-tailed dispersal curve. Similarity of direct and indirect historical estimates of gene flow indicates maintenance of gene flow at levels experienced prior to fragmentation. The study revealed extensive long distance pollen dispersal in remnant patches of trees within a fragmented agricultural landscape in the southern temperate region and highlighted the role of remnant patches in maintaining genetic connectivity at the landscape scale.     

The genetic structure of populations of Metrioptera bicolor in a spatially structured landscape: effects of dispersal barriers and geographic distance

The stability and long-term survival of animal populations in fragmented landscapes largely depends on the colonisation of habitat patches and the exchange of individuals between patches. The degree of inter-patch dispersal, in turn, depends on the dispersal abilities of species and the landscape structure (i.e. the nature of the landscape matrix and habitat distribution). Here, we investigated the genetic structure of populations of Metrioptera bicolor, a wing-dimorphic bush cricket, in a spatially structured landscape with patches of suitable habitat distributed within a diverse matrix of different habitat types. Using six microsatellite markers, we assessed the effects of geographic distance and different matrix types on the extent of genetic differentiation among 24 sampling sites. We found that forest and a river running through the study area both impede inter-patch dispersal. The presence of these two matrix types was positively correlated with the extent of genetic differentiation between sites. In addition, we found a significant positive correlation between pairwise genetic and geographic distances for a subsample of sites which were separated only by arable land or settlements. For the complete data set, this correlation could not be found. This is most probably because the adverse effect of forest and river on gene flow dominates the effect of geographic distance in our limited set of patches. Our analyses clearly emphasize the differential resistance of different habitat types on dispersal and the importance of a more detailed view on matrix “quality” in metapopulation studies.     

Landscape features affect gene flow of Scottish Highland red deer (Cervus elaphus)

Landscape features have been shown to strongly influence dispersal and, consequently, the genetic population structure of organisms. Studies quantifying the effect of landscape features on gene flow of large mammals with high dispersal capabilities are rare and have mainly been focused at large geographical scales. In this study, we assessed the influence of several natural and human-made landscape features on red deer gene flow in the Scottish Highlands by analysing 695 individuals for 21 microsatellite markers. Despite the relatively small scale of the study area (115 × 87 km), significant population structure was found using F -statistics ( F _ST = 0.019) and the program structure , with major differentiation found between populations sampled on either side of the main geographical barrier (the Great Glen). To assess the effect of landscape features on red deer population structure, the ArcMap GIS was used to create cost-distance matrices for moving between populations, using a range of cost values for each of the landscape features under consideration. Landscape features were shown to significantly affect red deer gene flow as they explained a greater proportion of the genetic variation than the geographical distance between populations. Sea lochs were found to be the most important red deer gene flow barriers in our study area, followed by mountain slopes, roads and forests. Inland lochs and rivers were identified as landscape features that might facilitate gene flow of red deer. Additionally, we explored the effect of choosing arbitrary cell cost values to construct least cost-distance matrices and described a method for improving the selection of cell cost values for a particular landscape feature.     

Genetic discontinuities in roe deer (Capreolus capreolus) coincide with fenced transportation infrastructure

Linear landscape elements may act as barriers to the movement of wildlife, inducing genetic sub-structure because barriers impair gene flow. This effect often occurs in response to transportation infrastructure such as freeways, requiring expensive measures, such as overpasses, to re-establish connectivity among separated populations. Here, we present a landscape genetic study using a spatial overlay of landscape elements and genetic clustering based on nuclear microsatellites in roe deer. Our results show that fenced freeways appeared as the main obstacles to gene flow in roe deer within a nationally important wildlife corridor in Switzerland. On the other hand, a wide river only showed a weak barrier effect, whereas a highly frequented but unfenced railway track had no detectable effect on gene flow. Landscape genetic overlays proved helpful in the communication with practical environmental management, as they are intuitively appealing. Furthermore, the chosen approach pointed to the need for setting priorities for building wildlife passages as a connectivity measure in the study landscape and sets the reference line for testing the effectiveness of the measures taken.     

Fragmentation of Atlantic Forest has not affected gene flow of a widespread seed‐dispersing bat

Habitat loss and resultant fragmentation are major threats to biodiversity, particularly in tropical and subtropical ecosystems. It is increasingly urgent to understand fragmentation effects, which are often complex and vary across taxa, time and space. We determined whether recent fragmentation of Atlantic forest is causing population subdivision in a widespread and important Neotropical seed disperser: Artibeus lituratus (Chiroptera: Phyllostomidae). Genetic structure within highly fragmented forest in Paraguay was compared to that in mostly contiguous forest in neighbouring Misiones, Argentina. Further, observed genetic structure across the fragmented landscape was compared with expected levels of structure for similar time spans in realistic simulated landscapes under different degrees of reduction in gene flow. If fragmentation significantly reduced successful dispersal, greater population differentiation and stronger isolation by distance would be expected in the fragmented than in the continuous landscape, and genetic structure in the fragmented landscape should be similar to structure for simulated landscapes where dispersal had been substantially reduced. Instead, little genetic differentiation was observed, and no significant correlation was found between genetic and geographic distance in fragmented or continuous landscapes. Furthermore, comparison of empirical and simulated landscapes indicated empirical results were consistent with regular long‐distance dispersal and high migration rates. Our results suggest maintenance of high gene flow for this relatively mobile and generalist species, which could be preventing or significantly delaying reduction in population connectivity in fragmented habitat. Our conclusions apply to A. lituratus in Interior Atlantic Forest, and do not contradict broad evidence that habitat fragmentation is contributing to extinction of populations and species, and poses a threat to biodiversity worldwide.     

The consequences of tree disease and pre-emptive felling on functional and genetic connectivity for woodland invertebrates

Trees outside woodlands facilitate dispersal of woodland invertebrates and may buffer against fragmentation impacts. European ash (Fraxinus excelsior) is common outside woodlands but is threatened by the fungal disease ash dieback (Hymenoscyphus fraxineus). Loss of ash trees to disease or pre-emptive felling could represent a substantial loss in connectivity. We assess the impact of tree disease and the pre-emptive felling of non-woodland ash trees on dispersal and gene flow of woodland invertebrates. We use a stochastic individual-based modelling platform, RangeShifter, to explore impacts of tree loss on the spatial dynamics of ‘virtual’ ash-reliant insects, species which depend on ash to complete their life cycle, with varying dispersal abilities and population densities. We simulate the loss of individual trees in and out of woodlands using current tree cover data from 24 real-world landscapes and estimate functional and genetic connectivity in relation to species-specific habitat-dependent movement costs and the likelihood to move in a straight line. Removal of 10% of ash trees resulted in an increase in dispersal mortality of up to 14.6%, and an increase in isolated woodlands (receiving no immigrants) of up to 2.9%. In some landscapes this resulted in increased isolation by distance (IBD - correlation between genetic and geographic distance). Carrying capacity impacted the proportion of isolated patches and IBD. Species experiencing high dispersal cost were less successful at dispersing under high tree loss, and this decreased geneflow. The consequences of tree loss for woodland connectivity are influenced by the species dispersal traits, but the consequences for gene flow depends on the arrangement of trees within the landscape. Therefore, the focal landscape must be represented explicitly when predicting the impacts of tree diseases on connectivity for a given species.     

Population genetics of orchid bees in a fragmented tropical landscape

The prospects for persistence of bees living in fragmented landscapes is a topic of considerable interest due to bees’ importance as pollinators of agricultural crops and wild plants, coupled with the ubiquity of native habitat loss and evidence that bees may be declining worldwide. Population persistence in fragmented areas depends on dispersal potential and maintenance of gene flow among fragments of habitat. Here we used population genetic techniques to characterize, for two equally abundant orchid bee species that differ in their physiology and ecology, levels of genetic differentiation among fragments of tropical forest in southeastern Costa Rica in a ~200 km² landscape. We measured population differentiation with ϕ_PT (an analogue to the traditional summary statistic Fst), as well as two measures that may more accurately reflect the level of differentiation when highly variable loci are used: G’st and D_est. We also calculated pairwise genetic distances among individuals and conducted Mantel tests to test the correlation of genetic and geographic distance, for each species. We found strong differences in genetic structure between the species. Contrary to our expectations, each measure of genetic structure revealed that the larger-bodied species, Eulaema bombiformis, had higher levels of differentiation than the smaller species, Euglossa championi. Furthermore, for Eulaema bombiformis there was a significant positive correlation of genetic and geographic distance while for Euglossa championi there was no significant positive correlation. Our results demonstrate that bee species can have strikingly different levels of gene flow in fragmented habitats, and that body size may not always act as a useful proxy for dispersal, even in closely related taxa.     

Dispersal and genetic structure in the American marten, Martes americana

Natal dispersal in a vagile carnivore, the American marten (Martes americana), was studied by comparing radio-tracking data and microsatellite genetic structure in two populations occupying contrasting habitats. The genetic differentiation determined among groups of individuals using F(ST) indices appeared to be weak in both landscapes, and showed no increase with geographical distance. Genetic structure investigated using pairwise genetic distances between individuals conversely showed a pattern of isolation by distance (IBD), but only in the population occurring in a homogeneous high-quality habitat, therefore showing the advantage of individual-based analyses in detecting within-population processes and local landscape effects. The telemetry study of juveniles revealed a leptokurtic distribution of dispersal distances in both populations, and estimates of the mean squared parent-offspring axial distance (sigma2) inferred both from the genetic pattern of IBD and from the radio-tracking survey showed that most juveniles make little contribution to gene flow.     

Influence of habitat discontinuity, geographical distance, and oceanography on fine-scale population genetic structure of copper rockfish (Sebastes caurinus)

The copper rockfish is a benthic, nonmigratory, temperate rocky reef marine species with pelagic larvae and juveniles. A previous range-wide study of the population-genetic structure of copper rockfish revealed a pattern consistent with isolation-by-distance. This could arise from an intrinsically limited dispersal capability in the species or from regularly-spaced extrinsic barriers that restrict gene flow (offshore jets that advect larvae offshore and/or habitat patchiness). Tissue samples were collected along the West Coast of the contiguous USA between Neah Bay, WA and San Diego, CA, with dense sampling along Oregon. At the whole-coast scale (approximately 2200 km), significant population subdivision (F(ST) = 0.0042), and a significant correlation between genetic and geographical distance were observed based on 11 microsatellite DNA loci. Population divergence was also significant among Oregon collections (approximately 450 km, F(ST) = 0.001). Hierarchical amova identified a weak but significant 130-km habitat break as a possible barrier to gene flow within Oregon, across which we estimated that dispersal (N(e)m) is half that of the coast-wide average. However, individual-based Bayesian analyses failed to identify more than a single population along the Oregon coast. In addition, no correlation between pairwise population genetic and geographical distances was detected at this scale. The offshore jet at Cape Blanco was not a significant barrier to gene flow in this species. These findings are consistent with low larval dispersal distances calculated in previous studies on this species, support a mesoscale dispersal model, and highlight the importance of continuity of habitat and adult population size in maintaining gene flow.     

Population structure of spotted salamanders (Ambystoma maculatum) in a fragmented landscape

Understanding the impacts of landscape-level processes on the population biology of amphibians is critical, especially for species inhabiting anthropogenically modified landscapes. Many pond-breeding amphibians are presumed to exist as metapopulations, but few studies demonstrate the extent and consequences of this metapopulation structure. Gene flow measures may facilitate the construction of more realistic models of population structure than direct measures of migration. This is especially true for species that are cryptic, such as many amphibians. We used eight polymorphic microsatellite loci to determine the genetic population structure of spotted salamanders ( Ambystoma maculatum ) breeding at 17 ponds in northeastern Ohio, a landscape fragmented by roads, agriculture, urban areas and the Cuyahoga River. Using a variety of analyses (Bayesian clustering, F -statistics, AMOVA) we generated a model of salamander population genetic structure. Our data revealed patterns of genetic connectivity that were not predicted by geographical distances between ponds (no isolation by distance). We also tested for a relationship between population structure and several indices of landscape resistance, but found no effect of potential barriers to dispersal on genetic connectivity. Strong overall connectivity among ponds, despite the hostile habitat matrix, may be facilitated by a network of riparian corridors associated with the Cuyahoga River; however, high gene flow in this system may indicate a general ability to disperse and colonize beyond particular corridors.     

Genetic evidence for landscape effects on dispersal in the army ant Eciton burchellii

Inhibited dispersal, leading to reduced gene flow, threatens populations with inbreeding depression and local extinction. Fragmentation may be especially detrimental to social insects because inhibited gene flow has important consequences for cooperation and competition within and among colonies. Army ants have winged males and permanently wingless queens; these traits imply male‐biased dispersal. However, army ant colonies are obligately nomadic and have the potential to traverse landscapes. Eciton burchellii, the most regularly nomadic army ant, is a forest interior species: colony raiding activities are limited in the absence of forest cover. To examine whether nomadism and landscape (forest clearing and elevation) affect population genetic structure in a montane E. burchellii population, we reconstructed queen and male genotypes from 25 colonies at seven polymorphic microsatellite loci. Pairwise genetic distances among individuals were compared to pairwise geographical and resistance distances using regressions with permutations, partial Mantel tests and random forests analyses. Although there was no significant spatial genetic structure in queens or males in montane forest, dispersal may be male‐biased. We found significant isolation by landscape resistance for queens based on land cover (forest clearing), but not on elevation. Summed colony emigrations over the lifetime of the queen may contribute to gene flow in this species and forest clearing impedes these movements and subsequent gene dispersal. Further forest cover removal may increasingly inhibit Eciton burchellii colony dispersal. We recommend maintaining habitat connectivity in tropical forests to promote population persistence for this keystone species.     

Effects of landscape matrix on population connectivity of an arboreal mammal,Petaurus breviceps

Ongoing habitat loss and fragmentation is considered a threat to biodiversity as it can create small, isolated populations that are at increased risk of extinction. Tree‐dependent species are predicted to be highly sensitive to forest and woodland loss and fragmentation, but few studies have tested the influence of different types of landscape matrix on gene flow and population structure of arboreal species. Here, we examine the effects of landscape matrix on population structure of the sugar glider (Petaurus breviceps) in a fragmented landscape in southeastern South Australia. We collected 250 individuals across 12 native Eucalyptus forest remnants surrounded by cleared agricultural land or exotic Pinus radiata plantations and a large continuous eucalypt forest. Fifteen microsatellite loci were genotyped and analyzed to infer levels of population differentiation and dispersal. Genetic differentiation among most forest patches was evident. We found evidence for female philopatry and restricted dispersal distances for females relative to males, suggesting there is male‐biased dispersal. Among the environmental variables, spatial variables including geographic location, minimum distance to neighboring patch, and degree of isolation were the most important in explaining genetic variation. The permeability of a cleared agricultural matrix to dispersing gliders was significantly higher than that of a pine matrix, with the gliders dispersing shorter distances across the latter. Our results added to previous findings for other species of restricted dispersal and connectivity due to habitat fragmentation in the same region, providing valuable information for the development of strategies to improve the connectivity of populations in the future.     

Gene flow and functional connectivity in the natterjack toad

Functional connectivity is a key factor for the persistence of many specialist species in fragmented landscapes. However, connectivity estimates have rarely been validated by the observation of dispersal movements. In this study, we estimated functional connectivity of a real landscape by modelling dispersal for the endangered natterjack toad (Bufo calamita) using cost distance. Cost distance allows the evaluation of 'effective distances', which are distances corrected for the costs involved in moving between habitat patches in spatially explicit landscapes. We parameterized cost-distance models using the results of our previous experimental investigation of natterjack's movement behaviour. These model predictions (connectivity estimates from the GIS study) were then confronted to genetic-based dispersal rates between natterjack populations in the same landscape using Mantel tests. Dispersal rates between the populations were inferred from variation at six microsatellite loci. Based on these results, we conclude that matrix structure has a strong effect on dispersal rates. Moreover, we found that cost distances generated by habitat preferences explained dispersal rates better than did the Euclidian distances, or the connectivity estimate based on patch-specific resistances (patch viscosity). This study is a clear example of how landscape genetics can validate operational functional connectivity estimates.