Andrew Storfer

Putting the "landscape" in landscape genetics.

Landscape genetics has emerged as a new research area that integrates population genetics, landscape ecology and spatial statistics. Researchers in this field can combine the high resolution of genetic markers with spatial data and a variety of statistical methods to evaluate the role that landscape variables play in shaping genetic diversity and population structure. While interest in this research area is growing rapidly, our ability to fully utilize landscape data, test explicit hypotheses and truly integrate these diverse disciplines has lagged behind. Part of the current challenge in the development of the field of landscape genetics is bridging the communication and knowledge gap between these highly specific and technical disciplines. The goal of this review is to help bridge this gap by exposing geneticists to terminology, sampling methods and analysis techniques widely used in landscape ecology and spatial statistics but rarely addressed in the genetics literature. We offer a definition for the term ‘landscape genetics’, provide an overview of the landscape genetics literature, give guidelines for appropriate sampling design and useful analysis techniques, and discuss future directions in the field. We hope, this review will stimulate increased dialog and enhance interdisciplinary collaborations advancing this exciting new field.

Landscape genetics: where are we now?

Landscape genetics has seen rapid growth in number of publications since the term was coined in 2003. An extensive literature search from 1998 to 2008 using keywords associated with landscape genetics yielded 655 articles encompassing a vast array of study organisms, study designs and methodology. These publications were screened to identify 174 studies that explicitly incorporated at least one landscape variable with genetic data. We systematically reviewed this set of papers to assess taxonomic and temporal trends in: (i) geographic regions studied; (ii) types of questions addressed; (iii) molecular markers used; (iv) statistical analyses used; and (v) types and nature of spatial data used. Overall, studies have occurred in geographic regions proximal to developed countries and more commonly in terrestrial vs. aquatic habitats. Questions most often focused on effects of barriers and/or landscape variables on gene flow. The most commonly used molecular markers were microsatellites and amplified fragment length polymorphism (AFLPs), with AFLPs used more frequently in plants than animals. Analysis methods were dominated by Mantel and assignment tests. We also assessed differences among journals to evaluate the uniformity of reporting and publication standards. Few studies presented an explicit study design or explicit descriptions of spatial extent. While some landscape variables such as topographic relief affected most species studied, effects were not universal, and some species appeared unaffected by the landscape. Effects of habitat fragmentation were mixed, with some species altering movement paths and others unaffected. Taken together, although some generalities emerged regarding effects of specific landscape variables, results varied, thereby reinforcing the need for species‐specific work. We conclude by: highlighting gaps in knowledge and methodology, providing guidelines to authors and reviewers of landscape genetics studies, and suggesting promising future directions of inquiry.

Landscape genetics of the blotched tiger salamander (Ambystoma tigrinum melanostictum)

The field of landscape genetics has great potential to identify habitat features that influence population genetic structure. To identify landscape correlates of genetic differentiation in a quantitative fashion, we developed a novel approach using geographical information systems analysis. We present data on blotched tiger salamanders (Ambystoma tigrinum melanostictum) from 10 sites across the northern range of Yellowstone National Park in Montana and Wyoming, USA. We used eight microsatellite loci to analyse population genetic structure. We tested whether landscape variables, including topographical distance, elevation, wetland likelihood, cover type and number of river and stream crossings, were correlated with genetic subdivision (FST). We then compared five hypothetical dispersal routes with a straight‐line distance model using two approaches: (i) partial Mantel tests using Akaikes information criterion scores to evaluate model robustness and (ii) the BIOENV procedure, which uses a Spearman rank correlation to determine the combination of environmental variables that best fits the genetic data. Overall, gene flow appears highly restricted among sites, with a global FST of 0.24. While there is a significant isolation‐by‐distance pattern, incorporating landscape variables substantially improved the fit of the model (from an r2 of 0.3 to 0.8) explaining genetic differentiation. It appears that gene flow follows a straight‐line topographic route, with river crossings and open shrub habitat correlated with lower FST and thus, decreased differentiation, while distance and elevation difference appear to increase differentiation. This study demonstrates a general approach that can be used to determine the influence of landscape variables on population genetic structure.

Gene flow and endangered species translocations: a topic revisited

Understanding the evolutionary role of gene flow is pivotal to the conservation of endangered populations. Gene flow can be enhanced through population translocations that are conducted to maintain genetic variation and combat the negative consequences of inbreeding depression (two of the major concerns in the conservation of subdivided or isolated populations). While researchers have given extensive consideration to the idea that gene flow can act as a creative evolutionary force by maintaining genetic variation or spreading adaptive gene complexes, the focus of this paper is to investigate gene flow as a force that constrains local adaptation. I briefly review the theoretical basis of and summarize empirical studies that indicate gene flow can constrain local adaptation, and may thereby lower short-term population fitness. This review suggests that knowledge of gene flow rates and understanding ecological differences among populations is necessary before embarking on a program to artificially enhance gene flow.

Perspectives on the use of landscape genetics to detect genetic adaptive variation in the field

Understanding the genetic basis of species adaptation in the context of global change poses one of the greatest challenges of this century. Although we have begun to understand the molecular basis of adaptation in those species for which whole genome sequences are available, the molecular basis of adaptation is still poorly understood for most non‐model species. In this paper, we outline major challenges and future research directions for correlating environmental factors with molecular markers to identify adaptive genetic variation, and point to research gaps in the application of landscape genetics to real‐world problems arising from global change, such as the ability of organisms to adapt over rapid time scales. High throughput sequencing generates vast quantities of molecular data to address the challenge of studying adaptive genetic variation in non‐model species. Here, we suggest that improvements in the sampling design should consider spatial dependence among sampled individuals. Then, we describe available statistical approaches for integrating spatial dependence into landscape analyses of adaptive genetic variation.

Parasite local adaptation: Red Queen versus Suicide King

Parasites are generally expected to be locally adapted to their hosts, but the basis of this prediction involves two distinct areas of research: coevolutionary studies of infectivity and epidemiological studies of optimal virulence. The distinction between infectivity and virulence is sometimes blurred but is crucial to our understanding of parasite local adaptation. Recent theoretical and empirical work has greatly improved our understanding of the evolutionary processes affecting local infectivity adaptation. However, in spite of the attention paid to the evolution of virulence, only a few recent models have explicitly studied spatial variation in optimal virulence. Our understanding of parasite local adaptation will continue to improve through studies of the genetic basis of infectivity, research on spatial variation in optimal virulence in multiple-deme systems, and the combination of these two interacting components of parasite infection in theoretical and empirical studies.

Finding the genomic basis of local adaptation: Pitfalls, practical solutions, and future directions

Uncovering the genetic and evolutionary basis of local adaptation is a major focus of evolutionary biology. The recent development of cost-effective methods for obtaining high-quality genome-scale data makes it possible to identify some of the loci responsible for adaptive differences among populations. Two basic approaches for identifying putatively locally adaptive loci have been developed and are broadly used: one that identifies loci with unusually high genetic differentiation among populations (differentiation outlier methods) and one that searches for correlations between local population allele frequencies and local environments (genetic-environment association methods). Here, we review the promises and challenges of these genome scan methods, including correcting for the confounding influence of a species’ demographic history, biases caused by missing aspects of the genome, matching scales of environmental data with population structure, and other statistical considerations. In each case, we make suggestions for best practices for maximizing the accuracy and efficiency of genome scans to detect the underlying genetic basis of local adaptation. With attention to their current limitations, genome scan methods can be an important tool in finding the genetic basis of adaptive evolutionary change.

Landscape genetics of high mountain frog metapopulations

Explaining functional connectivity among occupied habitats is crucial for understanding metapopulation dynamics and species ecology. Landscape genetics has primarily focused on elucidating how ecological features between observations influence gene flow. Functional connectivity, however, may be the result of both these between‐site (landscape resistance) landscape characteristics and at‐site (patch quality) landscape processes that can be captured using network based models. We test hypotheses of functional connectivity that include both between‐site and at‐site landscape processes in metapopulations of Columbia spotted frogs (Rana luteiventris) by employing a novel justification of gravity models for landscape genetics (eight microsatellite loci, 37 sites, n = 441). Primarily used in transportation and economic geography, gravity models are a unique approach as flow (e.g. gene flow) is explained as a function of three basic components: distance between sites, production/attraction (e.g. at‐site landscape process) and resistance (e.g. between‐site landscape process). The study system contains a network of nutrient poor high mountain lakes where we hypothesized a short growing season and complex topography between sites limit R. luteiventris gene flow. In addition, we hypothesized production of offspring is limited by breeding site characteristics such as the introduction of predatory fish and inherent site productivity. We found that R. luteiventris connectivity was negatively correlated with distance between sites, presence of predatory fish (at‐site) and topographic complexity (between‐site). Conversely, site productivity (as measured by heat load index, at‐site) and growing season (as measured by frost‐free period between‐sites) were positively correlated with gene flow. The negative effect of predation and positive effect of site productivity, in concert with bottleneck tests, support the presence of source–sink dynamics. In conclusion, gravity models provide a powerful new modelling approach for examining a wide range of both basic and applied questions in landscape genetics.

ATRAZINE INCREASES RANAVIRUS SUSCEPTIBILITY IN THE TIGER SALAMANDER, AMBYSTOMA TIGRINUM

Pathogenic diseases and environmental contaminants are two of the leading hypotheses for global amphibian declines, yet few studies have examined the influence of contaminants on disease susceptibility. In this study, we examined effects of ecologically relevant doses of atrazine (0, 1.6, 16, and 160 microg/L), sodium nitrate (0, 6.8, 68 mg/L), and their interactions on susceptibility of four laboratory-bred tiger salamander families to Ambystoma tigrinum virus (ATV), a pathogen implicated in global amphibian die-offs. Salamanders were from Arizona populations where a coevolutionary history with ATV is supported, and thus cofactors rather than recent introduction may contribute to disease epizootics. Use of atrazine and nitrogenous fertilizers are ubiquitous; therefore, the impact of these cofactors on disease susceptibility is an important consideration. Atrazine and sodium nitrate significantly decreased peripheral leukocyte levels, suggesting an impact of these contaminants on the immune system. As expected from this result, atrazine significantly increased susceptibility of larvae to ATV infection. In contrast, nitrate had a marginally significant main effect and significantly decreased infection rate at the highest level. However, neither atrazine nor sodium nitrate had significant effects on viral copy number per individual. These results suggest that ecologically relevant concentrations of atrazine and nitrates have immunosuppressive effects, and atrazine may contribute to ATV epizootics, raising concerns about the influence of contaminants on diseases in general.

GENE FLOW AND INEFFECTIVE ANTIPREDATOR BEHAVIOR IN A STREAM-BREEDING SALAMANDER

Predators often feed on prey that show ineffective antipredator behavior. Gene flow among populations may constrain evolution of effective antipredator ability in larvae of the streamside salamander, Ambystoma barbouri, a species that occupies distinctly different habitats with conflicting selection pressures. Some streams are ephemeral, where larvae should be active to feed and reach metamorphosis before stream drying. In contrast, other streams are more permanent and contain pools with predatory fish, where larvae should remain inactive to avoid fish predation. Feeding rates and predator escape behavior were assayed for laboratory‐reared larvae from 15 populations. Larval survival was also compared among populations in artificial streams with natural predators. Five populations represented streams subjected to fish predation along a gradient of genetic and geographic isolation from populations without fish; the remaining 10 populations were ephemeral and without fish. Individuals from populations with fish had significantly stronger behavioral responses to fish (i.e., decreased feeding rate associated with the presence of fish and increased escape response) than individuals from fishless populations. Larvae from populations containing fish that were more isolated from fishless populations showed stronger antipredator responses than less isolated populations. Further, larvae from more isolated populations survived longer in the predation experiment, indicating that the behaviors measured were related with survival. These results suggest that gene flow between populations with conflicting selection pressures limits local adaptation in some salamander populations with fish. While previous studies have typically focused on the role of gene flow in pairs of populations, the results of this study suggest that gene flow is acting to swamp local adaptation across several populations.