Using Genetic and Genomic Data to Understand Movement Dynamics: How Organisms Assort Themselves on a Riverscape/Landscape and What this Means for Conservation

SYMPOSIUM Description: The focus of this symposium will be on the use of genetic and genomic data to characterize population genetic structure for both terrestrial and aquatic organisms using a landscape genetics approach. The landscape/riverscape approach integrates data on geographic and environmental features to explain patterns of genetic population structure and as such combines the fields of landscape ecology and population genetics. Connectivity among populations is a key parameter for long-term population viability and persistence for many organisms both in both terrestrial and aquatic ecosystems, where natural landscapes have shaped the spatial and temporal patterns of individual movement. Identifying the features of natural landscapes that promote or reduce connectivity as well as the potential impacts of anthropogenic disturbance – habitat fragmentation, degradation or reduction and synergistic effects of climate change – on these evolutionary patterns has become a focus of conservation science. This symposium will explore movement patterns for a diversity of taxa in both intact and disturbed habitats under a changing climate.

8:00AM Environmental DNA – Real Time Results in the Field to Confirm the Presence of Target Species
  Jacob W. Riley
Sampling for environmental DNA (eDNA) has emerged as a reliable and cost-effective method for biomonitoring for species at risk and invasive species. As compared with conventional field surveys, sampling for eDNA is rapid, less labor-intensive, and provides an objective way to confirm species presence or absence. A field-based eDNA sampling and testing tool has recently emerged and provides real-time results in the field. We will compare the pros and cons of this new tool with conventional laboratory eDNA methods and eDNA sampling versus traditional aquatic sampling techniques. We will review the results of the proof-of-concept testing that has been conducted on pilot projects to confirm the presence of fish and aquatic species, along with the quality control measures that have been built into the tool to provide reliable results. eDNA is a powerful and sensitive new sampling technology with the ability to detect a single fish in a stream for only 17 hours while minimizing costs and impacts to rare, threatened and endangered species and their habitat. We will review examples of how eDNA sampling has been incorporated into fisheries and aquatic monitoring projects to augment conventional survey approaches to address research questions and lessons learned from these pilot projects.
8:20AM Assessing the Genetic Impact of a Dam on Native Fish Populations: A Midwest River Case Study
  Rebecca Gehri, Daniel Zielinski, Kristen Gruenthal, Wesley Larson
The fragmentation of river systems by dams can have a genetic impact on fish populations due to reductions in gene flow and subsequent genetic drift. The Union Street Dam on the Boardman River in Michigan is an impassable earthen dam built roughly 150 years ago. Beginning in 2020, the dam will be replaced with a fish passage facility. The objective of our study is to determine if the populations of five fish species above and below the Union Street Dam are significantly differentiated and/or show differences in diversity. We investigated five native species with varying life histories, generation times, and migratory behaviors: white sucker (Catostomus commersonii), yellow perch (Perca flavescens), walleye (Sander vitreus), smallmouth bass (Micropterus dolomieu), and rock bass (Ambloplites rupestris). We collected fin clips from fifty fish above and below the dam for each species and used RAD sequencing to examine differences in population structure and diversity. Our results will provide a baseline to quantify the genetic change of fish populations once the Union Street Dam is removed and connectivity is restored in the Boardman River.
8:40AM Using RAD-Sequencing to Assess the Landscape Genomics of Listed Vernal Pool Anostracans in California
  Shannon Rose Kieran, Joshua Hull, Andrea Schreier, Amanda Finger
The decline of California’s vernal pools to below 5% pre-Spanish Settlement levels has driven a statewide effort to conserve these habitats and the organisms that inhabit them. Conserving the genetic diversity of a species is vital when considering their potential to adapt in the face of threats like climate change. Previous work using small numbers of mitochondrial markers to investigate the genetics and genomics of California’s vernal pool anostracans (Crustacea: Branchiopoda) have been inconclusive. To increase our understanding of anostracan genetic diversity, we undertook a rangewide sampling effort for four species: Linderiella occidentalis, Branchinecta lynchi, Branchinecta mesovallensis and Branchinecta conservatio. We analyzed samples from vernal pools throughout California over two years using the high-throughput RAD-sequencing method. We identified approximately 1000 RAD loci and compared genetic diversity and genetic distance across populations and species throughout their ranges to better understand how they relate to each other and the landscape. We found non-geographic patterns of genetic distance that suggest both short- and long-range dispersal mechanisms for these species. Our findings provide new tools to conservationists seeking to preserve these species and their threatened habitat.
9:00AM Local Adaptation in Steelhead across Aquatic Landscapes of the Columbia River
  Shawn R. Narum
Anadromous species such as steelhead trout (Oncorhynchus mykiss) undergo long-distance migrations across geographical regions that consist of highly heterogeneous habitats. This may lead to local adaptation and signatures of adaptive variation associated with phenotypic traits that may be distinct across broad aquatic landscapes. Extensive genomics research in steelhead has revealed strong signals of local adaptation in steelhead throughout the Columbia River. This includes results from gene-environment association tests that provide evidence that adaptive allele frequencies are more commonly significant for steelhead in the migratory corridor compared to their natal habitat (91.2% versus 8.8% of adaptive loci, respectively). Additional studies have identified that balancing selection maintains variation for phenotypic traits such as arrival timing to spawning grounds (premature vs. mature) and age-at-maturity (1-ocean vs. 2-ocean) in steelhead throughout the Columbia River. Genes of major effect have been identified for these two traits and development of markers from these candidate genes enable monitoring of phenotypic and genetic variation in natural populations or hatchery-reared stocks. This is a promising approach to maintain a broad portfolio of phenotypic diversity in steelhead that can buffer against exploitation and increase species persistence in disturbed ecosystems.
9:20AM The Genetic Ramifications of Translocation on Bighorn Sheep Genetic Diversity, Population Structure, and Hybridization
  Joshua Jahner, Marjorie Matocq, Jason Malaney, Mike Cox, Peregrine Wolff, Mitchell Gritts, Thomas Parchman
Bighorn sheep (Ovis canadensis) are an iconic western North American species that have been heavily managed throughout their range. Dramatic declines in the early 20th century decimated populations and led to the extirpation of bighorn sheep from a large proportion of their range. For several decades, state and federal agencies employed hundreds of translocations to recolonize previously occupied habitat with individuals from remnant herds. However, nearly all of these translocations took place without prior genetic information, leading to concerns about resulting genetic diversity, connectivity, local adaptation, and hybridization within and among these populations. Here, we use a genotyping-by-sequencing (GBS) approach to generate genetic information at several thousand loci for hundreds of bighorn sheep individuals across Nevada, a state with a particularly complicated translocation history involving several genetic lineages. Our results document the erosion of natural population genetic structure following translocations, characterize the degree of hybridization among subspecies, and provide support for the existence of a previously hypothesized Great Basin lineage of desert bighorn sheep. Further, our results demonstrate how genome-wide datasets can be leveraged to guide conservation by shedding light on the outcomes of past restoration practices, even in organisms with complicated management histories.
09:40AM Break
1:10PM A Population-Genomics Approach to Estimating Migration Among Genetically Similar Subpopulations
  Timothy Smyser, Eric C. Anderson, Michael Tabak, Kim Pepin, Amy Davis, Antoinette J Piaggio, Ryan Miller
We developed a population-genomics method that integrates cluster analysis, assignment testing, and permutation approaches to identify genetic migration when subpopulations are closely related and sample sizes are small. Using a supervised analysis in a leave-one-out (LOO) framework, we iteratively queried the genetic origin of individuals while all other samples served as references for the spatial subpopulation in which they were collected. When subpopulations are only modestly differentiated, individuals would be expected to have low strength of assignment (Q) to their subpopulation of origin. Accordingly, we randomly resampled alleles from the observed dataset to create parallel simulated datasets. We repeated the LOO analysis with the simulated datasets to describe expected Q-values for simulated residents from the described subpopulations and then extended this approach for descendants and grand descendants of migrants. From the derived Q-values, we developed decision rules to classify the migration history of observed individuals. We illustrate this method for invasive subpopulations of feral swine (Sus scrofa) distributed throughout Missouri. Our analysis revealed rampant translocation among subpopulations and releases from exogenous sources. This method is computationally efficient, can resolve connectivity among closely related subpopulations across multiple generations, and offers the transparency of permuted distributions to quantify patterns of migration.
1:30PM A Novel Quantitative Framework for Riverscape Genetics Highlights the Importance of Mainstem Channels for Brook Trout Population Connectivity
  Shannon White, Ephraim Hanks, Tyler Wagner
Riverscape genetics analyses fail to accommodate the spatial autocorrelation structure of linear stream networks and the bidirectional gene flow that occurs in riverine systems. To address these challenges, we present a novel framework for the design and analysis of riverscape genetics studies, including the development of the bidirectional gene flow in riverscapes (BGFR) model. Using the BGFR model, we completed an analysis of riverscape genetics for Brook Trout (Salvelinus fontinalis) in a northcentral Pennsylvania watershed. Our results suggested that gene flow was higher in mainstem than in tributary stream segments and was higher in the downstream direction. Additionally, we found negative effects of stream intermittency and physical movement barriers including waterfalls, impoundments, and permanently dry stream segments. These findings have significant implications for brook trout conservation, as climate change and anthropogenic disturbance will alter hydrologic regimes, which could decrease the ability of brook trout to use the mainstem as a seasonal movement corridor and increase the periodicity of flow in tributary channels. This case study highlights the utility of our framework for riverscape genetics, particularly the ability to rigorously test hypotheses about factors that influence gene flow in riverine networks.
1:50PM Native Fishes in the Truckee River: Are in-Stream Structures and Patterns of Population Genetic Structure Related?
  Mary M. Peacock, Mae Gustin, Evon Hekkala, Tim Loux
In-stream structures are recognized as significant impediments to movement for freshwater fishes. Patterns of genetic structure on a riverscape can provide information on which structures represent barriers and under what flow conditions. Here we characterize the impact of 41 dam and diversion structures on movement dynamics under varying flow conditions for a suite of six native fishes found in the Truckee River of California and Nevada. Genetic data were used to estimate total allelic diversity, effective population size and genetic population structure. Although there is spatial overlap among species within the river, there are clear differences in species distributions. Observed population genetic structure was associated with in-stream structures, but only under low flow conditions. High total discharge in 2006 allowed fish to move over potential barriers resulting in no observed population genetic structure for any species in 2007. The efficacy of in-stream structures to impede movement and isolate fish emerged only after multiple years of low flow conditions. Flow management may mitigate restricted movement of fishes due to in-stream barriers however, as flow dynamics are likely to be altered under global climate change, fragmentation due to barriers could isolate fishes into small subpopulations susceptible to both demographic and genetic losses.
2:10PM Population Connectivity and Chronic Wasting Disease Susceptibility of White-Tailed Deer in Arkansas: A Landscape Genomics Approach
  Marlis Douglas, Tyler K Chafin, Bradley T Martin, Zachery Zbinden, Cory Gray, Christopher Middaugh, Jennifer Ballard, Don White, Michael Douglas
Chronic Wasting Disease (CWD) is a highly infectious, fatal, neurological prion disease affecting deer, elk, and moose. In Arkansas, CWD has been found in 580 white-tailed deer and 16 elk since first detected in autumn 2015. Because the disease is transmitted via direct and indirect contact between uninfected and infected hosts, major factors affecting the potential for CWD spread across the landscape are: 1) rate of dispersal between herds and 2) rate of disease penetration within herds. The present study addresses both of these issues by combining next-generation genomic methods with traditional genetic screening approaches to understand how patterns of dispersal and disease susceptibility covary with landscape features across Arkansas. To infer population structure and connectivity, we sequenced >50,000 SNP markers for 896 white-tailed deer, and applied landscape genetic methods to understand patterns of population differentiation and landscape resistance statewide. We then assayed the same individuals for certain known variants that have been associated with differential disease susceptibility in other states using targeted sequencing of the PRNP gene. Understanding the landscape features modulating dispersal and the distribution of susceptibility-linked PRNP variants across Arkansas will allow stakeholders to more effectively gauge potential risk for disease spread.
2:30PM An Eco-Evolutionary Metapopulation Model for Simulating Effects of Riverscapes on Population Demogenetics: Case Studies from the Lower Pend Oreille Watershed, Washington, USA
  Casey Day, Erin Landguth
Landscape genetics has primarily focused on the degree to which landscapes facilitate or impede dispersal movement and gene flow between populations. In contrast, metapopulation ecology has focused on the effects of local environmental conditions on demographic processes such as colonization and extinction. Naturally, the need to incorporate complex demographics into studies of landscape genetics has become more apparent. Here we present Cost-Distance MetaPOPulation, a program for the simulation of changes in genotype frequency as a function of individual-based movement, complex spatial population dynamics, and landscape characteristics and configuration. CDMetaPOP is a flexible simulation modeling framework that can be adapted to any system in which movement patterns, demographic parameters, and spatial environmental conditions can be described. Using the riverscape of the Lower Pend Oreille River watershed in Washington State, we present a few of the possible applications of CDMetaPOP for asking questions about the interactions among landscapes, animal behavior, and population demogenetics. These include (1) applying alternative harvest scenarios for the control of invasive brook trout, (2) designing optimal reintroduction strategies for bull trout, and (3) developing relationships between specific genotypes and riverscape environments to identify the ecological drivers of adaptive genetic variation and rates of hybridization.
2:50PM Refreshment Break
3:20PM Choose Your SNPs Well: Common and Rare Genetic Variants Describe Population Genetic Structure and Historical Movement in Catostomus Suckers
  Elizabeth Mandeville
Population genetic studies using high resolution genomic datasets now routinely involve thousands of variable loci. A relatively unexplored aspect of these datasets is how choices when filtering SNPs for inclusion in analyses affect our ability to describe population genetic structure. Appropriate filtering is particularly important for studies with conservation and management applications, as over-estimating or under-estimating population structure and genetic diversity can lead to negative impacts for threatened species or wasted conservation effort. At the same time, the information contained in different potential datasets can reveal different aspects of genetic structure within species. We applied these principles to describe within-species population genetic structure for five species of Catostomussuckers in the Upper Colorado River basin in the US mountain west. We found that genetic structure at common genetic variants within species provides a perspective consistent with geography – populations that are physically more distant from one another are most genetically divergent, and genetic signatures of known barriers to fish movement were evident. We also used rare genetic variants to examine fine-scale, recent connectivity between river basins. Our results indicated different rates of rare allele sharing across populations, and therefore suggested different dispersal rates, for the two threatened native species.
3:40PM Detecting Genomic Variation Underlying Differential Run Timing of Coho Salmon in the Wenatchee River
  Rebekah L. Horn, Cory M. Kamphaus, Keely Murdoch, Shawn R. Narum
Coho salmon (Oncorhynchus kisutch) were listed as extirpated in the mid-1990s in the interior reaches of the Columbia River watershed. Starting in the late 1980s, the Columbia River Treaty tribes were successful in starting a re-introduction program. The Yakama Nation Wenatchee River Coho salmon re-introduction program has established a Mid-Columbia River Coho salmon stock incorporating naturally occurring phenotypic characteristics into their broodstock to facilitate local adaptation. Broodstock are collected at Dryden and Tumwater Dams on the Wenatchee River, however, only ~32% of Coho salmon successfully ascend Tumwater Canyon, a 15km high-gradient reach located between the dams. Fish that successfully ascend the canyon generally arrive early in the season (mid-October); in other salmonids, return timing has been shown to be under genetic control. To further understand how migration timing may impact Coho salmon’s ability to adapt to local landscapes, low-coverage whole genome re-sequencing (lcWGR) was performed on adult fish returning early in the season to Dryden Dam and those successfully ascending Tumwater Canyon. The lcWGR resulted in 70% genome coverage at 10X. After filtering, over 10 million SNPs were retained for assessing genomic differences in run timing of Wenatchee River Coho salmon.
4:00PM Non-Native Introgression Alters Seasonal Growth and Migratory Patterns of Native Salmonids in Three Wild Populations
  Jeffrey Strait, Lisa Eby, Ryan Kovach, Clint Muhlfeld, Matthew C. Boyer, Stephen Amish, Gordon Luikart
Human-induced hybridization with non-native species is a major conservation problem threatening numerous fish taxa. We quantified the effects of non-native rainbow trout admixture on individual growth rates and life history strategy (fluvial vs stream resident) in three populations of westslope cutthroat trout spanning different environmental conditions. Within each creek, we individually marked (n > 7000), recaptured (n=1558), and genotyped Oncorhynchus spp.for five years. We determined emigration via weir traps and stationary PIT tag antennae in each tributary. While there was no significant effect of rainbow trout admixture on growth in the winter/spring period, individual admixture was positively related to summer growth and the propensity to express a migratory life history strategy. These results suggest that introgression from rainbow trout provides a growth advantage during the warmest period of the year and that hybrids tend to express a migratory life history at a higher rate than non-admixed westslope cutthroat trout. This study demonstrates variable impacts of rainbow trout admixture on seasonal growth rates in wild populations, with implications for climate warming driving admixture. Finally, we hypothesize that different growth and migratory behavior of hybrids will influence population dynamics and landscape patterns of invasion.
4:20PM Landscape Genetics of the Pygmy Rabbit (Brachylagus idahoensis) across the Sagebrush Sea of the Great Basin.
  Marjorie Matocq, Thomas Dilts, Eveline Larrucea, Peter Weisberg, Miranda Crowell, Kevin Shoemaker
Understanding the causes and consequences of reduced gene flow remains a primary goal of landscape genetics. In this study we tested two hypotheses that potentially explain genetic differentiation across the southern portion of the range of the pygmy rabbit. The first hypothesis is that extensive pluvial lakes that existed during the Pleistocene are primarily responsible for modern patterns of genetic subdivision. The second hypothesis is that the modern distribution of sagebrush is the primary determinant of genetic differentiation across this portion of the pygmy rabbit’s range. We calculated least-cost paths, cost-weighted distance, and cumulative current between thirteen populations of pygmy rabbit. Our results show strong support for the sagebrush hypothesis with over 70% of genetic differentiation explained by the modern distribution of sagebrush, while the pluvial lake hypothesis explained relatively little variation. Especially in central and eastern Nevada, our analyses suggest that multiple pathways of connectivity through sagebrush may enhance gene flow. In contrast, the Mono Basin populations of pygmy rabbit are genetically distinct and largely isolated because of lack of sagebrush habitat between this region and the more contiguous range. Our results highlight the importance of continuous sagebrush habitat in maintaining genetic connectivity in pygmy rabbit.

Organizers: Mary M. Peacock, Elizabeth Mandeville
Supported by: Genetics Section, AFS

Location: Reno-Sparks CC Date: October 3, 2019 Time: 8:00 am - 5:00 pm