Genetics to Genomics: What We’ve Learned over the Last 10 Years and What’s Next for Wildlife

ROOM: Room 140 – Aztec
We have undoubtedly entered the genomic era of molecular ecology, which is characterized by the examination of whole genomes and the availability of large amounts of genetic data for numerous wildlife species. But how has this ‘big-data’ era of genetics impacted wildlife conservation and management? What are the most recent advancements in molecular ecology and how can we leverage these methods for wildlife management? This symposium aims to answer these questions with talks focused on both methodological advancements and empirical studies. We will begin the symposium with presentations detailing practical aspects of genomic research for those new to population genomic studies. Next, research talks will focus on comparative results between traditional genetic methods and genomic sequencing, highlighting similarities and new discoveries attainable with ‘big-data’ methods that are applicable to wildlife management. The symposium will end with presentations addressing some of the newest applications of molecular ecology for wildlife management, such as ecological epigenetics. Please join us for an engaging lineup of talks that will be accessible for anyone interested in how genomics can improve wildlife management, no genetic experience required!

1:10PM Genetics to Genomics: What We’ve Learned and What’s Next for Wildlife Management
  Emily Latch
The genomic era is here. Genomic approaches in conservation and management are increasingly common, and are being used to address a widening array of questions. But how has genomics impacted wildlife conservation and management? And how can we best leverage advances in genomics for wildlife management? In this talk to introduce the symposium, I will provide a summary of common genomic methods used in wildlife research, emphasizing ways to match genomic approaches with research questions. I will address practical questions for the professional wildlife manager, providing guidelines for people who are thinking about undertaking population genomics studies. I will compare results generated from traditional genetic methods with those from genomic data. Highlighting both methodological advancements and empirical studies, I will summarize the advances in wildlife management and conservation that have been made using genomic methods over the last 15 years, and how genomic approaches can help shape the future of wildlife conservation and management.
1:30PM SNP-Based Assessment of Genetic Diversity and Population Structure in Northern Bobwhite
  Damon L. Williford; Randy W. DeYoung; Leonard A. Brennan
The northern bobwhite (Colinus virginianus) is a small, terrestrial species of New World quail that was historically distributed throughout much of the eastern United States and Mexico. Studies based on mitochondrial DNA and nuclear microsatellites have shown that the northern bobwhite exhibits weak population structure. However, broad geographic distribution and substantial morphological variation suggests adaptive genetic variation that may not be detected by neutral markers. Therefore, we examined the genetic diversity and population structure of northern bobwhite populations west of the Mississippi River, including Sonoran masked bobwhites (C. v. ridgwayi). using 2,137 polymorphic single nucleotide polymorphisms (SNPs) obtained through restriction-site associated DNA sequencing. Masked bobwhites had the lowest genetic diversity and were the most greatly differentiated, whereas little structure was evident among the 5 populations in the United States. We identified 2 candidate genes for positive selection by FST outlier tests: interleukin-1 receptor accessory protein-like 2 and YTH domain containing 2 genes. Genetic differentiation among Sonoran and United States populations was probably the result of long-term geographic isolation of masked bobwhites due to increasing aridity in southwestern North America that began after the end of the Pleistocene. Lack of population structure among bobwhites in the United States may be due to combined effects of post-Pleistocene range expansion, long-distance dispersal, flexible mating system, and high effective population size. Masked bobwhites should be managed as a distinct unit due to its long-term isolation, whereas bobwhites in the United States should be managed on a regional basis with emphasis placed on preserving, restoring, and enlarging landscapes containing suitable habitat.
1:50PM High-Throughput Sequencing Used to Compare Neutral and Adaptive Genetic Variation among Tamaulipan Ocelot Populations
  J. P. Leonard
The ocelot (Leopardus pardalis) is an endangered felid whose range in the United States is restricted to 2 isolated populations in southern Texas. Previous studies have found reduced genetic variation within these populations through the use of neutral genetic markers. To better assess the genetic health of these populations and advise future translocation efforts, an examination of functional genetic variation is also necessary. The major histocompatibility complex (MHC) is a genomic region that codes for antigen-presenting molecules that play a role in the adaptive immune response. Our goals were to compare changes in MHC allele frequencies over time between ocelot populations in Texas and Mexico, test for the presence of selection on MHC alleles, and determine if alleles have been lost over time due to inbreeding and genetic drift. We amplified exon 2 of the MHC DRB for 53 ocelots from both Texas populations and from Tamaulipas, Mexico, using polymerase chain reaction. We obtained nucleotide sequences using paired-end sequencing on the Illumina platform. To test for the historical signature of selection on specific antigen-binding sites, we used the program OMEGAMAP. This program uses a Bayesian framework to estimate residue-specific posterior probabilities of natural selection, using the nonsynonymous to synonymous substitution ratio (dN/dS), in the presence of recombination. We identified 16 unique alleles, 6 of which had not been previously described in ocelots. Antigen-binding sites showed high dN/dS ratios, indicating a high posterior probability of positive selection on these sites. The 6 newly identified alleles all showed >98% sequence similarity to previously published ocelot DRB sequences, and showed no insertions, deletions or premature stop codons. We found private alleles in all 3 ocelot populations, suggesting that translocations between populations might help maintain MHC variation within Texas ocelot populations.
2:10PM Optimizing Disease Management of Prairie Dogs with Population Genomics
  Rachael Giglio; Tonie Rocke; Jorge Osorio; Emily Latch
Plague, caused by the bacterium Yersinia pestis, triggers outbreaks that result in severe declines in prairie dog populations (typically killing >90% of a colony). However, it is not clear how plague moves among prairie dog colonies. It is unlikely that prairie dogs are effective transmission vectors among colonies, because they live in highly structured social groups and rarely travel between colonies. Their fleas, Oropsylla hirsuta and Oropsylla tuberculata cynomuris, are implicated in the spread of plague, but it remains unknown how they move among colonies if movement is not prairie dog-mediated. Since fleas require a host for mobility, we suggest that an alternative host to these presumed specialist fleas exists and moves them among colonies. To identify a likely alternative host, we examined a colony of white-tailed prairie dogs (Cynomys leucurus). We found that genetic structure in white-tailed prairie dogs was not concordant with either O. hirsuta or O. t. cynomuris. This pattern supports the hypothesis that prairie dogs do not move fleas among prairie dog colonies and that an alternative host to the fleas likely exists. We found that the deer mouse, Peromyscus maniculatus, is a likely alternative host to prairie dog fleas due to their abundance, range of habitat, and resistance to plague. Further, both deer mice and prairie dog fleas exhibited higher rates of gene flow than prairie dogs. By understanding how plague spreads among prairie dog colonies, we may target management to prevent epizootics.
2:30PM Conservation Genomics of Declining Cascades Frogs at the Southern Edge of Their Range
  Bennett Hardy; Emily K. Latch; Karen L. Pope
Cascades frogs (Rana cascadae) in the southern Cascades Range of California have been declining over the last 30 years, primarily due to the fungal pathogen, Batrachochytrium dendrobatidis (Bd). In the Lassen Region of the southern Cascades, at least six of the eleven remaining localities face extirpation within 50 years. These small and isolated populations are prone to negative genetic effects including reduced diversity and increased inbreeding which could potentially exacerbate declines. We used thousands of polymorphic SNP loci generated from high-throughput sequencing to characterize fine-scale patterns of genetic structure in these imperiled populations, as well as from relatively stable populations in the adjacent Klamath Mountains of California and central Cascades of Oregon to prioritize populations for conservation. Genetic variation was low in the Lassen Region and there was little gene flow among isolated populations; weak gene flow followed a pattern of isolation-by-distance. SNPs were well suited to quantifying fine-scale structure in these low-diversity populations and provided high-resolution data. Our results also support previous work indicating that Cascades frogs in California are divergent from those in Oregon. Assessing the genetic structure of remaining Cascades frog populations is key to the success of future management actions (i.e. translocation, population re-establishment, captive breeding).
2:50PM Refreshment Break
3:20PM Importance of Genomics and Hybrid Phenotypes in the Mallard Complex: Establishing a Working Field Key Requires Vetting Phenotypic Characters with Genomic Techniques
  Philip Lavretsky
Novel genomic techniques that permit the access of large portions of the genome provide researchers the necessary genetic differences to be able to differentiate between even the most shallow divergences and/or species with wide-spread hybridization. Here, I present the utility of two new methods, ddRAD-seq and sequence capture, as they are applied to species within the New World Mallards. Employed molecular techniques yielded ~3,500 markers (~20,000 SNPs) scattered across the genome’s of Mallards, American Black Ducks, Mottled Ducks, and Mexican Ducks. Genetic data was able to resolve complex evolutionary relationships, population structure, and reliably identify hybrids among any of the species. Characters truly diagnostic of hybrid ancestry were identified by vetting individuals as hybrid or pure and conducting association tests with various phenotypic characters. For example, using un-vetted phenotypic characters, identification has been <60% correct when calling hybrids between mallards and either American black ducks or mottled ducks; however, the recent completion of a genetically vetted field key increased field identification of hybrids to >95% between mottled ducks and mallards. Additionally, I present novel methods in which empirical genomic data is used to simulate expected assignment probabilities for first generation hybrids (F1) and subsequent backcrosses (F2 and on). Not only does this provide data that would otherwise be unfeasible via breeding experiments, but researchers have a means to test for prevalence and rate of hybridization by identifying the number and generational hybrid classes in their sampling set. Finally, I use sequence capture methods on historical (1860-1910) mallards and American black ducks to demonstrate how such methods now allow researchers to use historical samples to test for changes with present day populations. These results demonstrate how novel genomic techniques can have an immediate and real world application towards the conservation and management of wild populations.
3:40PM Population Genetic Inferences in Eastern Coyotes: Comparing Microsatellites to Genome-Wide SNPs to Elucidate Patterns of Genetic Diversity and Admixed Ancestry
  Elizabeth Heppenheimer
Human-mediated range expansions have increased in recent decades and represent unique opportunities to evaluate the genetic outcomes of establishing peripheral populations across broad expansion fronts. Over the past century, one of the most extreme examples of an extensive range expansion includes the coyote (Canis latrans), which now inhabit every state in the continental United States. Coyote expansion into eastern North America was facilitated by anthropogenic landscape changes and followed two distinct expansion fronts. The northern expansion extended through the Great Lakes region and southern Canada, where hybridization with remnant wolf populations was common. The southern and more recent expansion front occurred approximately 40 years later and across territory where gray wolves have been historically absent and remnant red wolves were extirpated in the 1970s. Our initial microsatellite survey of eastern coyote populations suggested that population structure corresponded to a north-south divide, consistent with the two known expansion routes, and identified a mid-Atlantic contact zone between these two populations. Our follow-up study employed genome-wide markers to quantify which regions of the eastern coyote genome have introgressed from wolf populations as a result of interspecific hybridization. We further explored how introgression varies along a latitudinal gradient and conducted genomic cline analysis to identify wolf-derived loci that may be under directional selection in eastern coyote populations.
4:00PM Beyond Population Genomics- Ecological Epigenetics and Application to Wildlife Management
  Kristin E. Brzeski
Environmental epigenetics is a burgeoning field in ecology and evolution. Recent sequencing advances have created a whole new area of research where we can evaluate complex epigenetic effects in natural, non-model systems. This has management and conservation implications because wildlife can have epigenetic responses to environmental stress with downstream fitness consequences. DNA methylation is one of the best studied epigenetic mechanisms and unlike DNA mutations, can be influenced directly by the environment. Thus, DNA methylation may be an important process by which animals respond to environmental stress and perturbations such as contaminants. This presentation will introduce epigenetics and its application to wildlife management and conservation. I will also highlight the application of epigenetic studies in natural systems by presenting a case study investigating the interactions between toxin exposure and DNA methylation in songbirds. Please join us for an introduction to a new and exciting area of study in wildlife genetics.
4:20PM Sage-Grouse Management in the Genomics Age: Insights Into Local Genetic Adaptation and Population Differentiation
  Kevin P. Oh; Cameron L. Aldridge; Sara J. Oyler-McCance
Identifying and preserving unique genetic adaptations is an important consideration for conservation and management strategies, particularly for species with geographic distributions that span diverse ecological conditions. Contemporary sequencing technology has now made it possible to probe the genome for potential genetic adaptations with unprecedented resolution in species of conservation concern. We recently completed sequencing the genomes of both Gunnison Sage-grouse (Centrocercus minimus) and Greater Sage-grouse (C. urophasianus). We are leveraging these new genomic resources to investigate differentiation of satellite populations, as well as metabolic adaptations to different types of sagebrush diets within and among both sage-grouse species. Using whole-genome resequencing from birds sampled across the West, we have identified several promising candidate genes underlying sage-grouse dietary adaptations. We also present results of whole-genome scans to examine regions within the genome with elevated divergence between populations and species. We discuss potential implications of these analyses for common management practices including translocation of birds, and sagebrush restoration efforts.
4:40PM Molecular Underpinnings of Sarcoptic Mange Susceptibility and Severity in Yellowstone Wolves
  Alexandra DeCandia; Quin Pompi; Emily Almberg; Daniel Stahler; Bridgett vonHoldt
A classic paradigm in population genetics and species management posits that molecular variation buffers against individual and population level disease risk. This variation is thought to confer multiple defense strategies, thus limiting a pathogen’s ability to exploit common weaknesses. As a result, numerous studies characterize variation in genes with known immune function, such as the major histocompatibility complex (MHC) gene family. Yet a more inclusive understanding of molecular variation is needed, as studies increasingly delve into genome-wide analyses and consider untraditional forms of variation (such as commensal microbes or gene regulatory diversity) that may also affect disease susceptibility and severity on both individual and population scales. Using sarcoptic mange in Yellowstone National Park (YNP) wolves as our study system, we seek to apply an integrative molecular approach to the study of wildlife disease. We start by surveying MHC variation and performing a family-based association study with genome-wide data to identify loci linked with mange susceptibility and severity. Critically, these analyses consider both traditional immune genes and loci often excluded from targeted immunogenetic approaches. Of equal importance, they are conducted in a natural population of reintroduced carnivores currently experiencing disease-mediated morbidity and mortality. Through their highly resolved pedigree and detailed longitudinal data, YNP wolves enable integration of environmental, demographic, and genomic parameters when evaluating risk factors of disease. Their ongoing sample collection allows for additional analyses that consider the roles of epigenetic and microbial variation in disease state (planned for the upcoming field season). It is our hope that this study will illustrate the importance of considering multiple facets of molecular variation in the complex ecology of wild vertebrates and disease, and that others will adopt this approach for better monitoring, management, and evolutionary inference going forward.

Organizers: Kristin Brzeski, Princeton University, Princeton, NJ; Randall DeYoung, Caesar Kleberg Wildlife Research Institute Texas A&M University-Kingsville, Kingsville, TX; Emily Latch, University of Wisconsin-Milwaukee, Milwaukee, WI
Supported by: TWS Molecular Ecology Working Group

Location: Albuquerque Convention Center Date: September 25, 2017 Time: 1:10 pm - 5:00 pm