Caren S. Goldberg

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.

Molecular detection of vertebrates in stream water: a demonstration using Rocky Mountain tailed frogs and Idaho giant salamanders.

Stream ecosystems harbor many secretive and imperiled species, and studies of vertebrates in these systems face the challenges of relatively low detection rates and high costs. Environmental DNA (eDNA) has recently been confirmed as a sensitive and efficient tool for documenting aquatic vertebrates in wetlands and in a large river and canal system. However, it was unclear whether this tool could be used to detect low-density vertebrates in fast-moving streams where shed cells may travel rapidly away from their source. To evaluate the potential utility of eDNA techniques in stream systems, we designed targeted primers to amplify a short, species-specific DNA fragment for two secretive stream amphibian species in the northwestern region of the United States (Rocky Mountain tailed frogs, Ascaphus montanus, and Idaho giant salamanders, Dicamptodon aterrimus). We tested three DNA extraction and five PCR protocols to determine whether we could detect eDNA of these species in filtered water samples from five streams with varying densities of these species in central Idaho, USA. We successfully amplified and sequenced the targeted DNA regions for both species from stream water filter samples. We detected Idaho giant salamanders in all samples and Rocky Mountain tailed frogs in four of five streams and found some indication that these species are more difficult to detect using eDNA in early spring than in early fall. While the sensitivity of this method across taxa remains to be determined, the use of eDNA could revolutionize surveys for rare and invasive stream species. With this study, the utility of eDNA techniques for detecting aquatic vertebrates has been demonstrated across the majority of freshwater systems, setting the stage for an innovative transformation in approaches for aquatic research.

Employing Philosophical Dialogue in Collaborative Science

ABSTRACT Integrated research across disciplines is required to address many of the pressing environmental problems facing human societies. Often the integration involves disparate disciplines, including those in the biological sciences, and demands collaboration from problem formulation through hypothesis development, data analysis, interpretation, and application. Such projects raise conceptual and methodological challenges that are new to many researchers in the biological sciences and to their collaborators in other disciplines. In this article, we develop the theme that many of these challenges are fundamentally philosophical, a dimension that has been largely overlooked in the extensive literature on cross-disciplinary research and education. We present a “toolbox for philosophical dialogue,” consisting of a set of questions for self-examination that cross-disciplinary collaborators can use to identify and address their philosophical disparities and commonalities. We provide a brief users manual for this toolbox and evidence for its effectiveness in promoting successful integration across disciplines.

Environmental DNA as a new method for early detection of New Zealand mudsnails (Potamopyrgus antipodarum)

Abstract.  Early detection of aquatic invasive species is a critical task for management of aquatic ecosystems. This task is hindered by the difficulty and cost of surveying aquatic systems thoroughly. The New Zealand mudsnail (Potamopyrgus antipodarum) is a small, invasive parthenogenic mollusk that can reach very high population densities and severely affects ecosystem functioning. To assist in the early detection of this invasive species, we developed and validated a highly sensitive environmental deoxyribonucleic acid (eDNA) assay. We used a dose–response laboratory experiment to investigate the relationship between New Zealand mudsnail density and eDNA detected through time. We documented that as few as 1 individual in 1.5 L of water for 2 d could be detected with this method, and that eDNA from this species may remain detectable for 21 to 44 d after mudsnail removal. We used the eDNA method to confirm the presence of New Zealand mudsnail eDNA at densities as low as 11 to 144 snails/m2 in a eutrophic 5th-order river. Combined, these results demonstrate the high potential for eDNA surveys to assist with early detection of a widely distributed invasive aquatic invertebrate.

Factors influencing detection of eDNA from a stream‐dwelling amphibian

Environmental DNA (eDNA) methods for detecting and estimating abundance of aquatic species are emerging rapidly, but little is known about how processes such as secretion rate, environmental degradation, and time since colonization or extirpation from a given site affect eDNA measurements. Using stream‐dwelling salamanders and quantitative PCR (qPCR) analysis, we conducted three experiments to assess eDNA: (i) production rate; (ii) persistence time under different temperature and light conditions; and (iii) detectability and concentration through time following experimental introduction and removal of salamanders into previously unoccupied streams. We found that 44–50 g individuals held in aquaria produced 77 ng eDNA/h for 2 h, after which production either slowed considerably or began to equilibrate with degradation. eDNA in both full‐sun and shaded treatments degraded exponentially to <1% of the original concentration after 3 days. eDNA was no longer detectable in full‐sun samples after 8 days, whereas eDNA was detected in 20% of shaded samples after 11 days and 100% of refrigerated control samples after 18 days. When translocated into unoccupied streams, salamanders were detectable after 6 h, but only when densities were relatively high (0.2481 individuals/m2) and when samples were collected within 5 m of the animals. Concentrations of eDNA detected were very low and increased steadily from 6–24 h after introduction, reaching 0.0022 ng/L. Within 1 h of removing salamanders from the stream, eDNA was no longer detectable. These results suggest that eDNA detectability and concentration depend on production rates of individuals, environmental conditions, density of animals, and their residence time.

Comparative landscape genetics of two pond-breeding amphibian species in a highly modified agricultural landscape

Evaluating fine‐scale population structure of multiple species in the same landscape increases our ability to identify common patterns as well as discern ecological differences among species’ landscape genetic relationships. In the Palouse bioregion of northern Idaho, USA, 99% of the native prairie has been converted to nonirrigated agriculture and exotic grasslands. Columbia spotted frogs (Rana luteiventris) and long‐toed salamanders (Ambystoma macrodactylum) in this area breed almost entirely in artificial ponds on private land. We used genetic distances (FST and Dc) derived from eight microsatellite loci in 783 samples to evaluate the relationships among sympatric breeding populations (N = 20 and 26) of these species in a 213‐km2 landscape. Both species showed a pattern of isolation by distance that was not improved when distance was measured along drainages instead of topographically corrected straight lines (P < 0.01). After testing for autocorrelation among genetic distances, we used an information theoretic approach to model landscape resistance based on slope, soil type, solar insolation, and land cover, and multi‐model inference to rank the resistance of landscape surfaces to dispersal (represented by genetic distance). For both species, urban and rural developed land cover provided the highest landscape resistances. Resistance values for long‐toed salamanders followed a moisture gradient where forest provided the least resistance, while agriculture and shrub/clearcut provided the least resistance for Columbia spotted frogs. Comparative landscape genetics can be a powerful tool for detecting similarities and differences between codistributed species, and resulting models can be used to predict species‐specific responses to landscape change.

Critical considerations for the application of environmental DNA methods to detect aquatic species

Summary Species detection using environmental DNA (eDNA) has tremendous potential for contributing to the understanding of the ecology and conservation of aquatic species. Detecting species using eDNA methods, rather than directly sampling the organisms, can reduce impacts on sensitive species and increase the power of field surveys for rare and elusive species. The sensitivity of eDNA methods, however, requires a heightened awareness and attention to quality assurance and quality control protocols. Additionally, the interpretation of eDNA data demands careful consideration of multiple factors. As eDNA methods have grown in application, diverse approaches have been implemented to address these issues. With interest in eDNA continuing to expand, supportive guidelines for undertaking eDNA studies are greatly needed. Environmental DNA researchers from around the world have collaborated to produce this set of guidelines and considerations for implementing eDNA methods to detect aquatic macroorganisms. Critical considerations for study design include preventing contamination in the field and the laboratory, choosing appropriate sample analysis methods, validating assays, testing for sample inhibition and following minimum reporting guidelines. Critical considerations for inference include temporal and spatial processes, limits of correlation of eDNA with abundance, uncertainty of positive and negative results, and potential sources of allochthonous DNA. We present a synthesis of knowledge at this stage for application of this new and powerful detection method.

Predicting land use change: comparison of models based on landowner surveys and historical land cover trends

To make informed planning decisions, community leaders, elected officials, scientists, and natural resource managers must be able to evaluate potential effects of policies on land use change. Many land use change models use remotely-sensed images to make predictions based on historical trends. One alternative is a survey-based approach in which landowners’ stated intentions are modeled. The objectives of our research were to: (1) develop a survey-based landowner decision model (SBM) to simulate future land use changes, (2) compare projections from the SBM with those from a trend-based model (TBM), and (3) demonstrate how two alternative policy scenarios can be incorporated into the SBM and compared. We modeled relationships between land management decisions, collected from a mail survey of private landowners, and the landscape, using remotely-sensed imagery and ownership parcel data. We found that SBM projections were within the range of TBM projections and that the SBM was less affected by errors in image classification. Our analysis of alternative policies demonstrates the importance of understanding potential effects of targeted land use policies. While policies oriented toward increasing enrollment in the Conservation Reserve Program (CRP) resulted in a large (11–13%) increase in CRP lands, policies targeting increased forest thinning on private non-industrial lands increased low-density forest projections by only 1%. The SBM approach is particularly appropriate for landscapes including many landowners, because it reflects the decision-making of the landowners whose individual actions will result in collective landscape change.

Quantification and reduction of bias from sampling larvae to infer population and landscape genetic structure

A well‐designed sampling scheme is critical for obtaining accurate results from population genetic studies. Larval samples contain only the genetic material of successful breeders, often of a single year, and may be biased towards particular families. To quantify the bias of using larval samples to infer population and landscape genetic structure and explore how this bias may be reduced using sibship analysis, we analysed eight microsatellite loci from 484 tissue samples of larvae and adults of Columbia spotted frogs (Rana luteiventris) and long‐toed salamanders (Ambystoma macrodactylum) at nine breeding sites in north Idaho. Differences in allele frequencies between adult and larval samples were not detected after full‐siblings were removed from the larval data set for Columbia spotted frogs; for long‐toed salamanders, these differences remained at two out of four ponds. Data from Columbia spotted frog larvae indicated higher levels of differentiation among populations (median difference in FST = 0.020, P < 0.01), as predicted by population genetic theory, whereas data from larval samples of long‐toed salamanders showed some evidence of lower levels of differentiation among populations (median difference in FST = 0.012, P = 0.06). For both species, removing all but one individual from each full‐sibling family led to parameter estimates that were closer to those calculated from adult samples for both population and landscape genetic measures. Removal of full‐siblings is likely to improve estimates of population genetic parameters; however, knowledge of the species’ breeding system is essential for understanding additional sources of bias when inferring population genetic structure from larval samples.

Diversification and asymmetrical gene flow across time and space: lineage sorting and hybridization in polytypic barking frogs

Young species complexes that are widespread across ecologically disparate regions offer important insights into the process of speciation because of their relevance to how local adaptation and gene flow influence diversification. We used mitochondrial DNA and up to 28 152 genomewide single nucleotide polymorphisms from polytypic barking frogs (Craugastor augusti complex) to infer phylogenetic relationships and test for the signature of introgressive hybridization among diverging lineages. Our phylogenetic reconstructions suggest (i) a rapid Pliocene–Pleistocene radiation that produced at least nine distinct lineages and (ii) that geographic features of the arid Central Mexican Plateau contributed to two independent northward expansions. Despite clear lineage differentiation (many private alleles and high between‐lineage FST scores), D‐statistic tests, which differentiate introgression from ancestral polymorphism, allowed us to identify two putative instances of reticulate gene flow. Partitioned D‐statistics provided evidence that these events occurred in the same direction between clades but at different points in time. After correcting for geographic distance, we found that lineages involved in hybrid gene flow interactions had higher levels of genetic variation than independently evolving lineages. These findings suggest that the nature of hybrid compatibility can be conserved overlong periods of evolutionary time and that hybridization between diverging lineages may contribute to standing levels of genetic variation.