To Go Boldly … : The Genomics Frontier of Conservation and Management: Part II


8:00AM Using GT-Seq to Reconstruct Genetic Pedigrees and Examine Relative Fitness of Hatchery- and Natural-Origin Pink Salmon in Prince William Sound, Alaska
  Emily Lescak
The scale of hatchery programs in Alaska has raised concerns about the impact of hatchery-origin fish on the productivity and sustainability of natural stocks. We present the first study to measure fitness (reproductive success, RS) differences between hatchery- and natural-origin Pink Salmon (Oncorhynchus gorbuscha). This research is part of the Alaska Hatchery Research Program, a government-industry-academia project focused on understanding interactions between hatchery- and natural-origin Pink and Chum (O. keta) salmon to inform management decisions regarding hatchery production in Alaska. We used genotyping-in-thousands by sequencing (GT-seq) to genotype thousands of individuals collected in a stream in Prince William Sound at 298 amplicons developed for genetic parentage analysis. We then reconstructed pedigrees and compared the RS of hatchery-origin (identified by thermal otolith marks) to natural-origin salmon collected in the same stream. Results from one stream indicate hatchery-origin Pink Salmon have reduced RS compared to their natural-origin conspecifics and that differences are more pronounced for females. We plan to expand this study to five streams over a seven-year period to add replicate estimates of RS and explore multi-generational fitness trends. This research will inform policy makers on how to balance societal benefits of hatchery programs with conservation risk to natural stocks.
8:20AM North American Canine Ancestry: Development of Large Genetic Datasets for Effective Conservation and Management of Canids.
  Kristin Brzeski
Over ten years after the genomic revolution, researchers regularly use genome sequencing as wildlife management and conservation tool. Through these efforts, we have refined our understanding of many species’ population structure, migration rates, and admixture events, in addition to gaining new knowledge of adaptive processes such as local adaptation and regions under selection during range expansion. Our understanding of canids (wolves, coyotes, foxes, dogs) has been especially enhanced with genomics, where interspecific gene-flow and cryptic genetic ancestry have been identified. This talk will highlight how large, genomic datasets have been leveraged for conservation and management of canids, where results will be presented from The North American Canine Ancestry project. The North American Canine Ancestry project is a collaborative project that has genotyped 1000s of individual canids utilizing Restriction-site Associated DNA sequencing (RADseq) methodologies. Specifically, I will discuss how large genome-wide SNP genotype datasets broaden our understanding of coyote range expansion, red wolf conservation, and fox urbanization.
8:40AM Selection Along Ecological Gradients: Genome-Wide Assessment of Introgression and Adaptive mRNA Loci
  Bradley T Martin
Introgressive hybridization can have evolutionary consequences (e.g., increased adaptive potential) or impact demographic parameters (e.g., outbreeding depression). Importantly, introgression can occur differentially across the genome. Statistical identification of introgression in natural populations has been limited, but with advances in sequencing technologies such studies are now feasible. To assess introgression and selection in three Terrapene taxa inhabiting the southeastern United States we screened thousands of genome-wide Single-Nucleotide-Polymorphisms (SNPs) in 392 individuals. Population structure was assessed using ADMIXTURE, and individuals with mixed ancestry were statistically evaluated for introgression using HyDe, followed by classification into hybrid generations using NewHybrids. Finally, loci were aligned to the Terrapene transcriptome to infer genomic clines indicative of loci under selection. Across four discrete populations, 157 individuals were statistically corroborated as admixed (P<0.05). Introgressed individuals were primarily assigned to the F2 and backcross generations, and admixture patterns generally reflected spatial clines. Ten unique loci under selection aligned to the transcriptome, with the majority seemingly associated with temperature tolerance and anoxia. These data illuminate genome-wide selection gradients and gene flow of three Terrapene taxa inhabiting the southeastern U.S. Furthermore, having a better understanding of the dynamics of introgression occurring in the region will help facilitate effective conservation management strategies
9:00AM Community Genomics of Stream Fish: A Framework for Multi-Species, Comparative Population Genetics Spanning the White River Basin
  Zachery Zbinden
Most population genetic studies focus on one species in a given region. However, further insight can come from examining many species within a region (i.e. community or assemblage) and comparing them to explore the mechanisms of variation of population genetic patterns. We estimate genetic population connectivity for 34 species of stream fish collected at 75 sampling localities across the White River basin in Arkansas and Missouri. We explain variation in population connectivity among species using a multivariate framework incorporating species specific traits such as size and resource use. Until recently, the cost of sequencing proved to be prohibitive, but with advances in next generation sequencing it is now possible to generate data at a much larger scale. Multi-species population genomics, or “Community genomics”, is paramount for testing theoretical frameworks such as the “meta-community” concept, which aims to determine why biodiversity changes across space and time. Community genomics can also provide estimates of population fragmentation, connectivity, and diversity across many species, which can be used to inform management and conservation endeavors. Such a holistic and regional approach to “community conservation” has much to gain from community genomics.
9:20AM National Center for Genome Analysis Support (NCGAS): Providing Cyberinfrastructure to a National Community
  Thomas Doak
NCGAS is funded through an NSF to provide support to NSF researchers working the field of genomics (‘omics generally). Support includes access to national academic supercomputers, curated software sets specific to the genomics field, and consultation on the use of research-grade cyberinfrastructure and genomic analysis. NCGAS provides researchers free access to needed computational resources, bioinformatic workflows, and training to use these resources.Beyond NSF researchers, NCGAS currently works with researchers with NIH, USDA, Army, etc. funding The largest impact NCGAS has in computational science is to establish a model of a “scientific service center” focused on a particular subdiscipline, independent of federally-funded cyberinfrastructure computational resources. That is, we have decoupled federal funding for supercomputers and federal funding for application support. This ensures that a community relatively new to use of supercomputers—ex. biology—has NSF support attuned to the needs of a research community. NCGAS is a collaborative project between Indiana University (IU) and the Pittsburgh Supercomputing Center (PSC) at Carnegie Mellon University, both of which provide significant HPC facilities, human resources, and administrative support. NCGAS also acts as a gateway to XSEDE supercomputers, is a level 2 Service Provider, and is Domain Champion for genomics and field stations.
09:40AM Break
10:10AM Assessing Genomic Inbreeding in Island Wolves Using High-Quality and Non-Invasively Collected Samples
  Katherine E. Zarn
Alexander Archipelago wolves (Canis lupus ligoni) in Southeast Alaska have been petitioned for listing under the Endangered Species Act three times since 1993 due to concerns about declining populations and habitat loss. A key consideration is the vulnerability of genetically isolated island populations, thus quantifying inbreeding, genetic connectivity, and structure in island and mainland wolves is essential for designating population boundaries and quotas for harvest to ensure long-term sustainability. To support informed management, we designed a custom hybridization-based capture targeting 100k genome-wide loci in Southeast Alaskan wolves. Our high-throughput genotyping protocol was designed for compatibility with DNA from tissues and non-invasive samples. We found this approach well-suited for estimating genomic inbreeding using high-quality samples, and for assessing genetic variation and structuring in wolf populations across the region. Sequencing coverage across the non-invasive samples was highly variable, indicating the need for further optimization to ensure high genotyping success rates for these sample types. We present a comparison of inbreeding estimates from island and mainland wolves using runs of homozygosity. This study provides the foundation for utilizing non-invasive samples in population genomic analyses to inform management and ensure long-term sustainability of wolves in Southeast Alaska.
10:30AM Use of Genomic Methods for Enhancing Conservation Efforts in the Endangered Razorback Sucker, Xyrauchen Texanus (Cypriniformes: Catostomidae)
  Thomas Dowling
Razorback sucker Xyrauchen texanus (RBS) is a fish endemic to the Colorado River of western North America. This once common species has become endangered due to modification of habitat, especially the presence of predatory non-native species that prevent natural recruitment. Microsatellites and mtDNA have been used to monitor transmission of genetic variation for >20 years, yielding important information on the effectiveness of management actions for conserving RBS. We recently implemented a variety of genomic methods to improve genetic monitoring efforts and inform management. RAD-seq data were used to identify single nucleotide polymorphisms (SNPs) for parentage analysis and population genomic studies. Samples included adult males and females, which allowed us to identify male-specific markers for genetic sex identification, and larvae produce by some of these adults, allowing us to test the effectiveness of these markers for parentage analysis. Nanopore and Illumina sequencing were used to assemble the RBS genome, allowing for identification of linkage relationships for these markers. Transcriptomes were characterized from year-old hatchery fish with vastly different growth rates to assess factors responsible for this phenomenon. Taken in total, these methods illustrate the utility and power obtainable by applying genomic approaches to conservation and management of endangered species.
10:50AM Examining Domestication Selection in a Conservation Hatchery for Delta Smelt
  Ensieh Habibi
Examining domestication selection in a conservation hatchery for Delta Smelt A refuge population of the threatened Delta Smelt has been maintained at the Fish Conservation and Culture Laboratory (FCCL) since 2008, to prevent total extinction of the species if it disappears in the wild. Despite neutral variation not showing differentiation between the wild and captive populations, there is evidence of genetic adaptation to captivity at the FCCL. To investigate domestication selection, we used RAD-sequencing to collect genomic data on archived FCCL samples. We grouped 240 individuals for sequencing based on their domestication index (levels of hatchery ancestry; DI). After sequencing, we carried out genotype analysis to detect SNPs associated with domestication selection. Using Fst analysis, we observed 90 outliers SNPs on 11 RadTags with the highest Fst value. We then looked at allele frequency differences of the 90 SNPs in each group and compared them with each other. The results show a large shift in allele frequency between wild group and the three hatchery groups, early, medium, and late generations. The allele frequency differences are evidence that domestication selection occurred during early generations. The results of this study illuminate the differentiation between the wild and captive populations that is not captured by the neutral markers used for genetic management.
11:10AM Investigating Local Adaptation and Plasticity of an Estuarine-Dependent Teleost, Spotted Seatrout (Cynoscion Nebulosus)
  Jingwei Song
The resilience of organisms to climate change depends on their evolutionary potential and phenotypic plasticity, however, models aimed at predicting the trajectory of species under future climate change scenarios rarely incorporate these factors. We tested for evidence of evolutionary thermal adaptation and phenotypic plasticity in northern and southern populations of Spotted seatrout, Cynoscion nebulosus, by comparing metabolic phenotypes, gene expression and adaptive genomic variation. Using intermittent respirometry, fish from the northern population exhibited standard metabolic rates up to 35% higher than their southern counterparts when measurements were made at the same temperatures between 5°C to 30°C. FST-based and gene-environment association analyses of DArTseq data identified 40 SNPs as outliers, and 20 of these loci showed significant associations with minimum winter water temperatures between populations. Annotations of significant markers revealed putative functions in transcription regulation, cell cycle, and cellular transport. Ongoing analyses of gene expression is being used to determine whether distinct sets of genes are differentially regulated between populations in response to thermal stress. This study advances our understanding of thermal adaptation in an aquatic ectotherm and can be incorporated into mechanistic models to predict future responses of spotted seatrout.
11:30AM Delimitation of Genetic Diversity in Rhinichthys Osculus of the Owens and Amargosa River Basins: Implications for Biodiversity Conservation and Management
  Steven Mussmann
Aquatic fauna of the Owens and Amargosa Rivers persist in the harsh, arid landscape of the Mojave Desert. The fishes of this region, assumed relicts of Pleistocene-age lacustrine environments with fluvial connections, are now isolated in the few areas where water persists. Narrow endemism is thus common, particularly for the many forms of Speckled Dace (Rhinichthys osculus). Its diversity in this region has been defined by five proposed subspecies. We conducted a population-level assessment of Speckled Dace by contrasting genetic diversity among the Amargosa and Owens basins by employing next generation DNA sequencing techniques – specifically double digest restriction site associated DNA (ddRAD) sequencing. We recovered 12,000 ddRAD loci to evaluate samples collected over the past 30 years using phylogenetic and population genetic methods. We established that six genetically distinct groups existed in this region using Bayes factor delimitation analyses, with one group experiencing a potentially recent extinction. FST outlier loci were used to explore localized adaptative diversification. Evidence demonstrates that genetic differentiation has been driven both by recent pluvial connections among populations and geographic isolation. The results of this study promote the case for conservation protections and management of these critically endangered fishes.

Organizers: Marlis Douglas, Michael E. Douglas, Kristin Brzeski, Emily Latch
Supported by: AFS Genetics Section, TWS Molecular Ecology Working Group

Location: Reno-Sparks CC Date: October 2, 2019 Time: 8:00 am - 11:50 am