Fine-scale patterns of genetic variation indicate non-equilibrium gene frequency divergence in the stream lily, Helmholtzia glaberrima

1. Helmholtzia glaberrima (Philydraceae) is a rare plant, endemic to streams of the border ranges of Queensland and New South Wales, Australia.
2. We used AFLP markers to investigate genetic diversity and patterns of differentiation among 19 populations of H. glaberrima (24 for demographic analyses), and also collected data on the size, distribution and altitude of populations.
3. Based on the distribution of populations, altitude significantly influenced the spatial arrangement of H. glaberrima along stream systems, with population size and frequency greatest in upstream habitat.
4. Patterns of genetic diversity within populations were not related to population size or distribution. Altitude and genetic diversity were related, with upstream and downstream populations having higher genetic diversity than mid-stream populations. Differentiation among populations was pronounced at all spatial scales and did not conform to a hierarchical model of gene flow.
5. Both genetic diversity and differentiation data sets indicated that strong non-equilibrium conditions associated with persistent founder effects, and not landscape characteristics, have shaped patterns of genetic diversity and differentiation in H. glaberrima . Patterns of distribution indicate that populations are distributed over a discontinuous ecological gradient, which becomes marginal at lower altitudes.     

Relationship between biodiversity and landscape structure in the Gyungan stream basin,central Korea

The relationship between landscape structure and biodiversity was investigated in the Gyungan stream basin, central Korea, in order to prepare a biodiversity conservation plan. The study area was divided into upstream, midstream, downstream and Gonjiam stream sub‐watersheds based on the land use pattern of each sub‐watershed. The quality of the terrestrial landscape was assessed by connectivity and percentages of deciduous broad‐leaved forest and urbanized area. The quality of the terrestrial landscape was the highest in the downstream sub‐watershed followed by Gonjiam stream, midstream and upstream sub‐watersheds. The quality of the riparian landscape assessed by percentages of the number and the area that the wetland vegetation elements occupy in the whole area showed a similar trend to that of terrestrial landscape. The diversity of all taxa including fish, reptiles and amphibians, birds, mammals and wetland vegetation except benthic macroinvertebrates was the highest downstream. The diversity of benthic macroinvertebrates was the highest in the Gonjiam stream sub‐watershed. Thus, biodiversity was shown to be the highest in the downstream sub‐watershed, followed, in order, by Gonjiam stream, midstream and upstream sub‐watersheds in proportion to landscape quality. On the other hand, the quality of the aquatic environment based on the ecological score of benthic macroinvertebrate (ESB) index was the highest downstream, followed, in order, by upstream, Gonjiam stream and midstream areas. This trend is different from that of biodiversity. In order to improve landscape quality degraded by excessive land use and to increase biodiversity, we recommended a restoration plan that addresses both ecosystem and landscape.     

Contrasting effects of landscape features on genetic structure in different geographic regions in the ornate dragon lizard,Ctenophorus ornatus

Habitat fragmentation can have profound effects on the distribution of genetic variation within and between populations. Previously, we showed that in the ornate dragon lizard, Ctenophorus ornatus, lizards residing on outcrops that are separated by cleared agricultural land are significantly more isolated and hold less genetic variation than lizards residing on neighbouring outcrops connected by undisturbed native vegetation. Here, we extend the fine‐scale study to examine the pattern of genetic variation and population structure across the species' range. Using a landscape genetics approach, we test whether land clearing for agricultural purposes has affected the population structure of the ornate dragon lizard. We found significant genetic differentiation between outcrop populations (F_ST = 0.12), as well as isolation by distance within each geographic region. In support of our previous study, land clearing was associated with higher genetic divergences between outcrops and lower genetic variation within outcrops, but only in the region that had been exposed to intense agriculture for the longest period of time. No other landscape features influenced population structure in any geographic region. These results show that the effects of landscape features can vary across species' ranges and suggest there may be a temporal lag in response to contemporary changes in land use. These findings therefore highlight the need for caution when assessing the impact of contemporary land use practices on genetic variation and population structure.     

The effect of landscape features on population genetic structure in Yunnan snub-nosed monkeys (Rhinopithecus bieti) implies an anthropogenic genetic discontinuity

The Tibetan Plateau is one of the top 10 biodiversity hotspots in the world and acts as a modern harbour for many rare species because of its relatively pristine state. In this article, we report a landscape genetic study on the Yunnan snub-nosed monkey ( Rhinopithecus bieti ), a primate endemic to the Tibetan Plateau. DNA was extracted from blood, tissue and fecal samples of 135 wild individuals representing 11 out of 15 extant monkey groups. Ten microsatellite loci were used to characterize patterns of genetic diversity. The most striking feature of the population structure is the presence of five subpopulations with distinct genetic backgrounds and unique spatial regions. The population structure of R. bieti appears to be shaped by anthropogenic landscape features as gene flow between subpopulations is strongly impeded by arable land, highways and human habitation. A partial Mantel test showed that 36.23% ( r  =   0.51, P  =   0.01) of the genetic distance was explained by habitat gaps after controlling for the effect of geographical distance. Only 4.92% of the genetic distance was explained by geographical distance in the partial Mantel test, and no significant correlation was found. Estimation of population structure history indicates that environmental change during the last glacial maximum and human impacts since the Holocene, or a combination of both, have shaped the observed population structure of R. bieti . Increasing human activity on the Plateau, especially that resulting in habitat fragmentation, is becoming an important factor in shaping the genetic structure and evolutionary potential of species inhabiting this key ecosystem.     

Uncovering the features of population genetic structures by the descriptive method of "genetic landscape"]

It was found that using surnames as genetical markers in rural Russian populations gives adequate results under conditions of working on the area not extending over the territory of 2 or 3 adjacent regions. Schematic drawings of genetic landscapes in 4 regions of the Kirov district and in 2 regions of the Adyg district are presented. Analysis of anomalous features of equidistant lines has been performed.     

Effects of landscape features and demographic history on the genetic structure of Testudo marginata populations in the southern Peloponnese and Sardinia

Testudo marginata, the largest European land tortoise, is suffering habitat degradation and destruction. Some populations, in markedly degraded habitats, are characterized by divergent morphotypes. However, the evolutionary significance of these morphotypes is of debate. Using 11 polymorphic microsatellites, we studied: (1) marginated tortoises from Sardinia that display a divergent morphotype – this population was potentially introduced from Greece; and (2) an area in the southern Peloponnese that includes a small and degraded zone in which marginated tortoises are dwarf. Genetic analyses run without any a priori assignment clearly acknowledge the specimens sampled in the territory of the dwarf form as a single group whilst Sardinian specimens are clustered with other specimens from the northern part of the area sampled in Greece. Demographic analyses suggest that Sardinian tortoises originated recently from some of the populations sampled in the northern part of the area sampled in Greece. Over locations sampled in Greece, a landscape‐genetic analysis allowed us to detect potential landscape features that may reduce gene flow between the dwarf form territory and surrounding areas. Our results suggest that the territory of the dwarf form is particularly propitious for marginated tortoises and that conservation regulations in Greece should be reinforced to protect this area from increasing impact of human activities changing from traditional agriculture to mechanization and extensive use of chemicals. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 105 , 591–606.     

Fine-scale analysis reveals cryptic landscape genetic structure in desert tortoises

Characterizing the effects of landscape features on genetic variation is essential for understanding how landscapes shape patterns of gene flow and spatial genetic structure of populations. Most landscape genetics studies have focused on patterns of gene flow at a regional scale. However, the genetic structure of populations at a local scale may be influenced by a unique suite of landscape variables that have little bearing on connectivity patterns observed at broader spatial scales. We investigated fine-scale spatial patterns of genetic variation and gene flow in relation to features of the landscape in desert tortoise (Gopherus agassizii), using 859 tortoises genotyped at 16 microsatellite loci with associated data on geographic location, sex, elevation, slope, and soil type, and spatial relationship to putative barriers (power lines, roads). We used spatially explicit and non-explicit Bayesian clustering algorithms to partition the sample into discrete clusters, and characterize the relationships between genetic distance and ecological variables to identify factors with the greatest influence on gene flow at a local scale. Desert tortoises exhibit weak genetic structure at a local scale, and we identified two subpopulations across the study area. Although genetic differentiation between the subpopulations was low, our landscape genetic analysis identified both natural (slope) and anthropogenic (roads) landscape variables that have significantly influenced gene flow within this local population. We show that desert tortoise movements at a local scale are influenced by features of the landscape, and that these features are different than those that influence gene flow at larger scales. Our findings are important for desert tortoise conservation and management, particularly in light of recent translocation efforts in the region. More generally, our results indicate that recent landscape changes can affect gene flow at a local scale and that their effects can be detected almost immediately.     

Population structure, habitat features and genetic structure of managed red deer populations

Management of game ungulates alters population structure and habitat features, with potential effects on genetic structure. Here, we study 26 red deer (Cervus elaphus) populations in Spain. We used census data and habitat features as well as genetic information at 11 microsatellite markers from 717 individuals. We found that metapopulations presented a distribution associated with forest interruptions. Within metapopulations, fences did not have a significant effect on red deer genetic structure. The metapopulations we studied presented similar population structure, but they differed in habitat features and genetic structure. The metapopulation with higher resource availability showed a genetic structure pattern in which genetic relatedness between geographically close individuals was high while relatedness between geographically distant individuals was low. Contrarily, the metapopulation with lower resource availability presented a genetic structure pattern in which the genetic relatedness between individuals of different populations was independent of the geographic distance. We discuss the possible connection between resource availability and genetic structure. Finally, we did not find any population or environmental variable related to genetic differentiation within metapopulations.     

Spatial heterogeneity in landscape structure influences dispersal and genetic structure: empirical evidence from a grasshopper in an agricultural landscape

Dispersal may be strongly influenced by landscape and habitat characteristics that could either enhance or restrict movements of organisms. Therefore, spatial heterogeneity in landscape structure could influence gene flow and the spatial structure of populations. In the past decades, agricultural intensification has led to the reduction in grassland surfaces, their fragmentation and intensification. As these changes are not homogeneously distributed in landscapes, they have resulted in spatial heterogeneity with generally less intensified hedged farmland areas remaining alongside streams and rivers. In this study, we assessed spatial pattern of abundance and population genetic structure of a flightless grasshopper species, Pezotettix giornae, based on the surveys of 363 grasslands in a 430‐km² agricultural landscape of western France. Data were analysed using geostatistics and landscape genetics based on microsatellites markers and computer simulations. Results suggested that small‐scale intense dispersal allows this species to survive in intensive agricultural landscapes. A complex spatial genetic structure related to landscape and habitat characteristics was also detected. Two P. giornae genetic clusters bisected by a linear hedged farmland were inferred from clustering analyses. This linear hedged farmland was characterized by high hedgerow and grassland density as well as higher grassland temporal stability that were suspected to slow down dispersal. Computer simulations demonstrated that a linear‐shaped landscape feature limiting dispersal could be detected as a barrier to gene flow and generate the observed genetic pattern. This study illustrates the relevance of using computer simulations to test hypotheses in landscape genetics studies.     

Spatial genetic structure of a small rodent in a heterogeneous landscape

Gene flow in natural populations may be strongly influenced by landscape features. The integration of landscape characteristics in population genetic studies may thus improve our understanding of population functioning. In this study, we investigated the population genetic structure and gene flow pattern for the common vole, Microtus arvalis, in a heterogeneous landscape characterised by strong spatial and temporal variation. The studied area is an intensive agricultural zone of approximately 500 km² crossed by a motorway. We used individual-based Bayesian methods to define the number of population units and their spatial borders without prior delimitation of such units. Unexpectedly, we determined a single genetic unit that covered the entire area studied. In particular, the motorway considered as a likely barrier to dispersal was not associated with any spatial genetic discontinuity. Using computer simulations, we demonstrated that recent anthropogenic barriers to effective dispersal are difficult to detect through analysis of genetic variation for species with large effective population sizes. We observed a slight, but significant, pattern of isolation by distance over the whole study site. Spatial autocorrelation analyses detected genetic structuring on a local scale, most probably due to the social organisation of the study species. Overall, our analysis suggests intense small-scale dispersal associated with a large effective population size. High dispersal rates may be imposed by the strong spatio-temporal heterogeneity of habitat quality, which characterises intensive agroecosystems.     

Recruitment, kin and the spatial genetic structure of a caddisfly Plectrocnemia conspersa in a southern English stream

1. Our objectives were to examine small‐scale patterns in oviposition and genetic relatedness in a population of the stream‐dwelling caddis Plectrocnemia conspersa and, in particular, to look for any evidence of the spatial proximity of close kin and, therefore, ‘patchy recruitment’. 2. In order to examine the distribution of related larvae at the beginning of the aquatic phase, we searched the stream for egg masses. Spatially and temporally structured samples of larvae were then collected from the stream over four sample dates within one generation. The genetic relatedness of these field‐collected larvae, estimated using six polymorphic microsatellite loci, was subsequently compared with that of larvae reared from individual egg masses in the laboratory. 3. Egg masses were laid in clusters or ‘hot spots’ along the stream. The mean relatedness coefficient within reared egg masses ranged from 0.327 to 0.525, and differed significantly from that estimated for the population as a whole (0.070), indicating that the markers were sufficiently powerful to identify groups of siblings. Each egg mass was likely to be the progeny of one father, although the possibility of a small contribution from a second male could not be excluded for a few masses. 4. Mean relatedness within the spatially structured groups of larvae in the stream, even those in close proximity to each other, did not differ from the background population level estimate, suggesting that siblings disperse away from each other very quickly and that kin structure does not persist over time. 5. Changes in spatial genetic structure late in the larval life indicated that neighbouring larvae were less closely related than the population overall, possibly suggesting some direct or indirect means of avoiding kin when approaching the onset of pupation. 6. Our counts of egg masses suggested that survival through the egg stage and early larval life was apparently very high (>50%) for a non‐social insect, and may be a consequence of the colonial net that is briefly occupied by first instar larvae. 7. The number of egg masses laid in the stream (approximately 400 in the sample year), the lack of a spatial genetic structure showing evidence of families even early in larval life, and the high survival of eggs and early instar larvae, all refute the ‘patchy recruitment hypothesis’ for this species.     

Temporal population genetic structure of eastern mosquitofish in a dynamic aquatic landscape

We analyzed the effect of periodic drying in the Florida Everglades on spatiotemporal population genetic structure of eastern mosquitofish (Gambusia holbrooki). Severe periodic drying events force individuals from disparate sources to mix in dry season relatively deep-water refuges. In 1996 (a wet year) and 1999 (a dry year), we sampled mosquitofish at 20 dry-season refuges distributed in 3 water management regions and characterized genetic variation for 10 allozyme and 3 microsatellite loci. In 1996, most of the ecosystem did not dry, whereas in 1999, many of our sampling locations were isolated by expanses of dried marsh surface. In 1996, most spatial genetic variation was attributed to heterogeneity within regions. In 1999, spatial genetic variation within regions was not significant. In both years, a small but significant amount of variation (less than 1% of the total variation) was partitioned among regions. Variance was consistently greater than zero among long-hydroperiod sites within a region, but not among short-hydroperiod sites within a region, where hydroperiod was measured as time since last marsh surface dry-down forcing fishes into local refuges. In 1996, all sites were in Hardy-Weinberg equilibrium. In 1999, we observed fewer heterozygotes than expected for most loci and sites suggesting a Wahlund effect arising from fish leaving areas that dried and mixing in deep-water refuges.     

Multiscale analysis of Hymenocallis coronaria (Amaryllidaceae) genetic diversity, genetic structure, and gene movement under the influence of unidirectional stream flow

Understanding gene movement patterns in unidirectional flow environments and their effect on patterns of genetic diversity and genetic structure is necessary to manage these systems. Hypotheses and models to explain genetic patterns in streams are rare, and the results of macrophyte studies are inconsistent. This study addresses Ritland's (Canadian Journal of Botany 67: 2017-2024) unidirectional diversity hypothesis, the one-dimensional stepping stone model, and the metapopulation model within and among populations. Hymenocallis coronaria, an aquatic macrophyte of rocky river shoals of the SE USA, was sampled in four river basins. Within populations and among populations <16.2 km apart had significant isolation by distance. However, the rate of gene flow decay was not consistent with a one-dimensional stepping stone model, nor was evidence strong or consistent for Ritland's hypothesis. Some evidence indicates that localized metapopulation processes may be affecting genetic diversity and structure; however, gene flow patterns inconsistent with the assumptions of the linear and unidirectional models are also a possible influence. We discuss three variants on the one-dimensional stepping stone model. Future research in linear environments should examine the expectations of these models. This study is also one of the first efforts to calculate population genetic parameters using a new program, TETRASAT.     

River network architecture,genetic effective size and distributional patterns predict differences in genetic structure across species in a dryland stream fish community

Dendritic ecological network (DEN) architecture can be a strong predictor of spatial genetic patterns in theoretical and simulation studies. Yet, interspecific differences in dispersal capabilities and distribution within the network may equally affect species’ genetic structuring. We characterized patterns of genetic variation from up to ten microsatellite loci for nine numerically dominant members of the upper Gila River fish community, New Mexico, USA. Using comparative landscape genetics, we evaluated the role of network architecture for structuring populations within species (pairwise F_ST) while explicitly accounting for intraspecific demographic influences on effective population size (N_e). Five species exhibited patterns of connectivity and/or genetic diversity gradients that were predicted by network structure. These species were generally considered to be small‐bodied or habitat specialists. Spatial variation of N_e was a strong predictor of pairwise F_ST for two species, suggesting patterns of connectivity may also be influenced by genetic drift independent of network properties. Finally, two study species exhibited genetic patterns that were unexplained by network properties and appeared to be related to nonequilibrium processes. Properties of DENs shape community‐wide genetic structure but effects are modified by intrinsic traits and nonequilibrium processes. Further theoretical development of the DEN framework should account for such cases.     

The influence of landscape structure on occurrence, abundance and genetic diversity of the common frog, Rana temporaria

Human‐caused habitat destruction and modification constitute one of the largest threats to population persistence and biodiversity, and are also suspected to be the major cause behind the global decline of amphibian populations. We assessed the potential role of agriculture‐related habitat fragmentation on population size and genetic variability in the common frog (Rana temporaria) by recording the occurrence, population density and genetic diversity in three geographically disparate regions in Sweden – each containing landscapes of high and low agricultural activity – and related these to landscape variables extracted from digital maps. We found a highly significant region‐by‐landscape interaction in occurrence, population density and genetic diversity revealing a reversed response to agriculture from south to north: while the effects of agriculture on R. temporaria populations were negative in the south, there were no effects in the central region, whereas positive effects were observed in the north. Spatial autocorrelation analyses of genetic data revealed that populations in high agricultural activity areas were more isolated than populations in low activity areas both in the southern and central regions of Sweden. Landscape diversity showed a strong positive correlation with both density and occurrence of frogs in Sweden as a whole, as well as in the southern region. Also, negative effects of roads and positive effects of ditches on genetic diversity were found in the south. Overall, these results suggest clear but regionally opposite effects of habitat structure on the population size and genetic diversity of amphibian populations. This means that the management strategy aiming to maximize the size and genetic diversity of local common frog populations, and perhaps also those of other amphibian populations, should account for regional differences in existing land‐use patterns.     

Spatio-environmental determinants of the genetic structure of three steppe species in a highly fragmented landscape

Habitat fragmentation can lead to substantial genetic depletion. As a consequence, restoration schemes often involve the introduction of propagules into isolated plant populations to improve genetic diversity. To avoid introducing maladapted seed material, such measures need to account for landscape genetic processes. However, surprisingly little is known as to whether different species within a distinct fragmented ecosystem respond similarly or idiosyncratically to eco-geographical variation.Using AFLP markers, we studied the population genetic structure in three species of the highly fragmented Kulunda steppe (South Siberia): Adonis villosa, Jurinea multiflora and Paeonia hybrida. In each population, we conducted a vegetation survey. We performed Mantel tests and an RDA approach to investigate how genetic structure was affected by three spatio-environmental variables: spatial distance, floristic composition and climate.Despite strong fragmentation, genetic diversity was moderate (A. villosa, J. multiflora) to high (P. hybrida), while differentiation was weak (A. villosa) to moderate (P. hybrida, J. multiflora). Mantel tests showed that spatial distance correlated with genetic distance in A. villosa and P. hybrida. Floristic composition was significantly associated with genetic differentiation in A. villosa. Climate did not have an effect on genetic structure in any species.All three species are long-lived, which may contribute to explaining why genetic effects of recent fragmentation are still limited. We highlight that floristic composition can be a powerful predictor of population differentiation in species that show rather stable conditions in their recent population histories (e.g. A. villosa). This can have important implications for identifying source populations where restoration actions involve the (re)introduction of propagules. In contrast, for P. hybrida and J. multiflora, we could not identify deterministic drivers of differentiation. We advocate that future studies should aim at disentangling the interactive effects of varying life cycles, eco-evolutionary population histories and spatio-environmental heterogeneity in fragmented landscapes.