Advanced Topics in Conservation Genetics Webinar Series
These webinars provide biologist and managers with the latest techniques in conservation genetics.
This webinar series is for educational purposes only. The opinions, ideas or data presented in this webinar series do not represent FWS policy or constitute endorsement by FWS. Some of the materials and images may be protected by copyright or may have been licenses to us by a third party and are restricted in their use. Mention of any product names, companies, Web links, textbooks, or other references does not imply Federal endorsement.
Advanced Topics in Conservation Genetics Webinar DescriptionsA Call for Tiger Management Using "Reserves" of Genetic Diversity (00:50:00)
Presented by Rachael A. Bay, Uma Ramakrishnan, and Elizabeth A. Hadly. August 2014.
Tigers (Panthera tigris), like many large carnivores, are threatened by anthropogenic impacts, primarily habitat loss and poaching. Current conservation plans for tigers focus on population expansion, with the goal of doubling census size in the next 10 years. Previous studies have shown that because the demographic decline was recent, tiger populations still retain a large amount of genetic diversity. Although maintaining this diversity is extremely important to avoid deleterious effects of inbreeding, management plans have yet to consider predictive genetic models. We used coalescent simulations based on previously sequenced mitochondrial fragments (n = 125) from 5 of 6 extant subspecies to predict the population growth needed to maintain current genetic diversity over the next 150 years. We found that the level of gene flow between populations has a large effect on the local population growth necessary to maintain genetic diversity, without which tigers may face decreases in fitness. In the absence of gene flow, we demonstrate that maintaining genetic diversity is impossible based on known demographic parameters for the species. Thus, managing for the genetic diversity of the species should be prioritized over the riskier preservation of distinct subspecies. These predictive simulations provide unique management insights, hitherto not possible using existing analytical methods.
Presented by Taylor Edwards, University of Arizona. September 16, 2014.
The conservation of tortoises poses a unique situation because several threatened species are commonly kept as pets within their native range. Thus, there is potential for captive populations to be a reservoir for repatriation efforts. As a result of ongoing evolutionary studies on desert tortoises (Gopherus agassizii and G. morafkai) we have assembled a massive genotypic database of 1258 Gopherus samples, spanning the full range of both species in the Mojave and Sonoran deserts plus other congeners. Here, we present the results of two studies where we genotyped captive (pet) tortoises at STR and mitochondrial loci to determine their geographic origins. We performed assignment tests to assess the utility of captive populations for recovery efforts based on genetic affinity to local areas. For G. morafkai in Arizona, we genotyped 180 captive desert tortoises from Kingman (n = 45), Phoenix (n = 113), and Tucson (n = 22), Arizona. We found that >40% of our Arizona captive samples were genetically G. agassizii or hybrid origin. For G. agassizii, we collected samples from 130 captive desert tortoises from three desert communities: two in California (Ridgecrest and Joshua Tree) and the Desert Tortoise Conservation Center (Las Vegas) in Nevada. For our total sample set, only 44% of captive individuals were assigned to local populations based on genetic units derived from the reference database. Our data suggest that captive desert tortoises kept within the native range of both G. agassizii and G. morafkai cannot be presumed to have a genealogical affiliation to wild tortoises in their geographic proximity. Escaped or released captive tortoises have the potential to affect the genetic composition of native populations. Genotyping captive desert tortoises could be used to inform the adoption process, and thereby provide additional protection to native desert tortoise populations. Precautions should be taken before considering the release of captive tortoises into the wild as a management tool for recovery.
Presented by Dr. Mark E. Hauber, Hunter College, City University of New York. November 18, 2014.
Translocations of small or threatened populations to larger or safer localities are the bread and butter of conservation efforts in many regions of the world, especially in insular nations. Translocations are
often highly successful, establishing independent, distant, and protected populations to improve the prospects of species longevity. But translocations also carry potential costs, which may or may not supersede these benefits, especially when there is both connectivity and asymmetry between the source and the destination sites and
populations. Here I review both the behavioral (song culture and species recognition) and the genetic
(theoretical modelling based) evidence for the potential impact of translocation efforts in several contexts
inspired by my own work in New Zealand.
Presented by David S. Blehert, USGS, National Wildlife Health Center. October 30th, 2013.
Difficulties in detecting the causative agent of bat white-nose syndrome (WNS), Pseudogymnoascus (formerly Geomyces) destructans, in the presence of closely related fungi previously limited our ability to define the ecology of this emergent wildlife disease. We have addressed this challenge by developing a highly specific and sensitive real-time TaqMan PCR test. We have subsequently used this test to characterize the distribution and persistence of P. destructans in the environment. Soil samples collected in winter 2008-2009 from 55 bat hibernacula, both within and outside the known range of WNS at that time, were analyzed. The fungus was only detected from sites within the known range of WNS, indicating that P. destructans was not widely distributed in North American bat hibernacula prior to the emergence of WNS.
Presented by Dr. Hugh Britten, University of South Dakota; Dr. Emy Monroe and Kris Lah, USFWS. April 23, 2015.
The Hine’s emerald dragonfly, Somatochlora hineana, is the only dragonfly on the US Endangered Species List. The species recovery plan divides the current range of the dragonfly into a Northern Recovery Unit consisting of sites in northeastern Wisconsin, and Upper Peninsula and northern Lower Peninsula of Michigan and a Southern Recovery Unit with sites in southwestern Wisconsin, northeastern Illinois, and southeastern Missouri based on floristic and geologic considerations. Recently, disjunct sites have been located in southwestern Wisconsin and southern Ontario, Canada. It was extirpated from its type locality in Ohio by the early 1960s. It exists in fragmented fen habitats in association with the devil crayfish, Cambarus diogenes, that provides refugia for larval dragonflies during winter and dry periods of the year. We focused our efforts on two focal areas: 1) the relatively pristine Door Peninsula, WI, which appears to be the species’ demographic stronghold and 2) highly urbanized sites in the vicinity of Chicago, IL, along the Des Plaines River. The impetus for the work was the construction of a 6-lane interstate highway bridge across the Des Plaines River through Hine’s emerald dragonfly habitat. The talk will focus on our efforts to non-destructively sample DNA from larval and adult dragonflies and the delineation of Recovery Units and populations based on 10 microsatellite markers. We will discuss the implications of our results for dragonfly re-introductions and population augmentations into restored/created habitat areas. We will briefly speculate on the role of the bridge as a barrier to dragonfly dispersal and the apparent relative roles of gene flow and census population size for the persistence of the dragonfly in the Des Plaines River Valley.
Presented by Dr. Chris Funk, Associate Professor of Biology at Colorado State University. May 8, 2014
Conservation Units (CUs) are population units identified within species that are used to help guide management and conservation efforts, such as Evolutionarily Significant Units (ESUs) and Management Units (MUs). Identifying CUs is an essential first step in conservation so that managers and policy makers know the boundaries of the population units they are trying to conserve. In addition to delineating CUs, a long-standing but elusive goal has been to detect and conserve adaptive differences among CUs. Genomic data—genetic information at thousands to millions of loci of a sample of organisms—have the potential to revolutionize our understanding of adaptive differentiation and the delineation of CUs. I have three aims of my webinar. My first aim is to outline several considerations when using genomic data to delineate CUs. My second aim is to describe a new framework my collaborators and I developed for using genomic data to delineate CUs and characterize adaptive differentiation among them and to discuss how to use this information to inform management decisions. My last aim is to highlight important remaining questions in this field and suggest future research to address them.
Advanced Topics in Conservation Genetics. Presented by Dr. Sean Hogan, National Institute for Mathematical and Biological Synthesis at the University of Tennessee, Knoxville. August 19, 2015.
Presented by Emy Monroe, Geneticist for USFWS Region 3, La Crosse Fish Health Center. February 19, 2014.
Environmental DNA (eDNA) has been used as an early detection tool for aquatic invasive species. eDNA is genetic material shed by living or dead organisms into the environment in urine, feces, mucous, or sloughed cells and can be detected by polymerase chain reaction which targets specific species DNA in environmental samples. Monitoring efforts with eDNA for Bighead and Silver Carp in the Chicago Area Waterway (CWS) were initiated in 2009 by the University of Notre Dame, and then continued by the US Corps of Engineers from 2010 to 2012. Along with eDNA in 2010, complementary field sampling with traditional gears was added to the monitoring program with interagency cooperation among the FWS and Illinois Department of Natural Resources. In 2013, the FWS assumed responsibility for both eDNA and traditional monitoring in the CAWS and also expanded eDNA monitoring to the Great Lakes, and Ohio and Mississippi Rivers. The current FWS Asian carp eDNA monitoring program employs rigorous quality control measures outlined in the Quality Assurance Project Protocol (QAPP), which has been peer reviewed by three external groups. However, additional research to refine and improve eDNA techniques is currently ongoing in a multi-agency cooperative eDNA calibration study (ECALS). Results from ECALS are validated in multi-laboratories and then incorporated annually into the QAPP to increase confidence in the interpretation of eDNA results as well as improve efficiency and reduce costs.
Presented by Pat Dehaan, Geneticist with the USFWS's Abernathy Fish Technology Center. February 9, 2016.
Redband trout, a subspecies of Oncorhynchus mykiss, are found in the Columbia, Fraser, and Sacramento river systems as well as the Upper Klamath Lake Basin and the northern Great Basin. The abundance of redband trout has declined across the subspecies range and many natural resource agencies are working to conserve redband trout. In 2007 the Oregon Department of Fish and Wildlife (ODFW) began a six year study to assess the abundance and distribution of redband trout in the northern drainages of the Great Basin in Oregon. As part of that study, genetic samples were collected from 23 redband trout populations across six subbasins in order to gain a better understanding of the level of genetic variation within and among redband trout populations. Using a panel of 96 single nucleotide polymorphism (SNP) markers, we examined the level of genetic variation among subbasins and among populations within subbasins, the levels of genetic diversity within populations, and the level of introgression between native redband trout and introduced hatchery fish. Great Basin redband trout formed three distinct genetic groups suggesting multiple colonization events from different evolutionary lineages. Despite historic and contemporary isolation among many populations, our data suggest that there has been recent gene flow among some populations of redband trout. Estimates of genetic diversity within subbasins and within populations ranged widely, with the greatest estimates observed in the Fort Rock populations and the lowest estimates observed in two isolated populations in the Catlow Valley. Despite extensive stocking efforts, coastal-origin hatchery fish have not replaced native redband trout in the northern Great Basin. The level of introgression between native redband trout and hatchery-origin fish varied among subbasins, among populations, and among individuals within populations. Redband trout in the northern Great Basin represent a unique genetic legacy and data presented in this study will be useful for helping to design conservation plans for redband trout in this unique environment.
Presented by Dr. Steve Fain, USFWS. July 16, 2014.
Caviar is among the world’s most valuable wildlife products. Exploitation of sturgeon and paddlefish for the caviar trade has severely reduced abundance, and harvest of most species is regulated under CITES. International trade requires that importing nations verify the species source of caviars they receive; the US domestic trade has no such requirement. We report the results of forensic species identifications of US caviar imports from 1998 to 2008 and of US domestic market caviars from 1997 to 1998. Twelve species were identified overall and species origins were mislabeled three times as often among US domestic market caviars (14.7 %) as among imports (4.9 %). Industry practices associated with the re-packaging of caviars for domestic markets and re-export from intermediate countries have created opportunities for the co-mingling of legitimate caviars with those from illegal, unreported and unregulated sources.
Presented by Dr. Robin Waples, NOAA, October 15, 2014.
Illegal, Unreported and Unregulated fishing has had a major role in the overexploitation of global fish populations. In response, international regulations have been imposed and many fisheries have been 'eco-certified' by consumer organizations, but methods for independent control of catch certificates and eco-labels are urgently needed. Here we show that, by using gene-associated single nucleotide polymorphisms, individual marine fish can be assigned back to population of origin with unprecedented high levels of precision. By applying high differentiation single nucleotide polymorphism assays, in four commercial marine fish, on a pan-European scale, we find 93–100% of individuals could be correctly assigned to origin in policy-driven case studies. We show how case-targeted single nucleotide polymorphism assays can be created and forensically validated, using a centrally maintained and publicly available database. Our results demonstrate how application of gene-associated markers will likely revolutionize origin assignment and become highly valuable tools for fighting illegal fishing and mislabelling worldwide.
Presented by Dr. Suresh A. Sethi, Regional Biometrician, USFWS Conservation Genetics Laboratory, Anchorage, AK. April 9, 2014.
Genetic mark recapture studies use individuals’ genotypes as identifying marks for subsequent statistical modeling to estimate abundance, survival, movement, and other population parameters. They present advantages over traditional tagging programs which rely on physically handling organisms at close range to deploy marks and allow for passive sampling of individuals through hair traps, scat collection surveys, or sampling by long-range biopsy gear. Genetic mark recapture studies, however, come with their own set of problems, chiefly that genotyping error and/or lack of discriminatory power amongst individuals can lead to errors in estimating population parameters. In this talk, I will present an overview of the application of genetic mark recapture studies and also examine solutions to dealing with genotyping error and lack of discriminatory power in estimating population parameters.
Presented by Dr. Andrew Whiteley, Department of Environmental Conservation, University of Massachusetts Amherst. February 10, 2015.
Fragmentation effects on natural populations are pervasive and have wide-ranging management implications. I will focus on native populations of the brook trout in eastern North America and discuss fragmentation effects on headwater stream systems from a genetics and evolutionary perspective. Brook trout populations are highly fragmented, particularly in the southern portion of the native range. We have demonstrated that this leads to small, genetically depauperate populations that are likely to have lower resilience to environmental change. We are initiating a genetic monitoring program that will help identify population strongholds and isolated populations that are currently at most jeopardy. The effective number of breeders (Nb) is a genetic metric that appears to be extremely promising in this regard. Once the most threatened populations are identified, a possible management action involves the movement of a small number of individuals form a nearby source population, so-called genetic rescue. We have an ongoing experimental test of genetic rescue underway in a series of four brook trout populations in Virginia. I will summarize these results from this experimental work and discuss genetic rescue in the context of additional management options to maintain population resilience.
Presented by Patrick DeHaan, USFWS, Abernathy Fish Technology Center Conservation Genetics Lab. December 4, 2013.
Genetic stock ID involves collecting unknown origin individuals and using their genotype to determine their most likely stock, population, or management unit of origin. This technique has been utilized for several decades by fisheries managers for determining the stock of origin for fish collected in commercial and recreation fisheries and for setting harvest quotas. Recently biologists and managers have utilized this technique to address a number of additional conservation issues including broodstock selection, examining movement patterns, and fish transport. This presentation will outline the concept of genetic stock ID and provide examples of how it has been utilized for fish and wildlife conservation and management. The presentation will focus on the development and implementation of a long-term monitoring program that utilizes genetic stock ID to aid upstream transport of federally threatened bull trout collected below impassible dams on the Clark Fork River in Idaho and Montana. A series of three dams constructed without fish passage facilities have prevented migratory bull trout in the Lake Pend Oreille and Clark Fork River system from returning to their natal spawning tributaries for nearly 100 years. To address fish passage issues in the watershed, a baseline dataset of 41 bull trout populations from the watershed was assembled and used to develop a real-time genotyping and analysis protocol to determine the population and management unit of origin for individuals collected below Clark Fork River dams. Self-assignment tests and analysis of blind samples indicated that unknown origin individuals could be assigned to their management region of origin with a high degree of confidence. Genetic assignment tests could then be used to help inform fish passage decisions; specifically, whether fish collected below dams should be transported upstream to access spawning habitat above the dams. Since 2004 this protocol has been used to provide genetic assignments for nearly 400 bull trout collected below Clark Fork River dams and over 300 of these fish were transported upstream of one or more dams based on their genetic assignments. The use of genetic stock ID has helped biologists re-establish important migratory corridors for bull trout in the Clark Fork River and has helped increase the number of spawning adults in several small populations upstream of mainstem dams.
Presented by Dr. David Nelson and Dr. Paul Gugger , University of Maryland Center for Environmental Science’s Appalachian Laboratory in Frostburg, MD. May 26, 2016.
Growing concern over greenhouse gas emissions associated with energy production from the combustion of fossil fuels has prompted a proliferation of renewable-energy production in the United States and abroad. Despite the environmental benefits associated with renewable-energy development, recent studies also highlight potential negative impacts on wildlife, including the largely unanticipated and widespread mortality of bats and birds at utility-scale wind-energy facilities. Determining whether different species are vulnerable to population declines resulting from wind-turbine fatalities, as well as other threats, is thus a question of major conservation and resource-management importance. However, this question is often difficult to address because little is typically known regarding the movement and diversity and population structure of affected species. In this presentation we will (1) summarize our recent work using stable hydrogen isotope and population genetic data to determine the summering grounds, effective size, structure, and temporal stability of hoary (Lasiurus cinereus) and eastern red (L. borealis) bats killed at wind-energy facilities in the central Appalachian Mountains, (2) highlight other recent studies applying stable isotope, genetic, and/or genomic techniques to these species and silver-haired bats (Lasionycteris noctivagans) elsewhere in North America, and (3) discuss prospects for future research to better understand the movement ecology and population structure of these species in the context of wind-energy development.
Great Lakes Piping Plovers (00:49:15)
Presented by Sarah Saunders, University of Minnesota. May 19, 2015.
Adaptation depends on the additive genetic variance for fitness and its component traits. Yet estimating additive genetic variance and heritability for wild populations is challenging because determining relatedness of individuals is difficult. We used 20 years (1994–2013) of phenotypic records from mark-recapture data and a multi-generational pedigree to estimate quantitative genetic variation in three fitness-related traits in Great Lakes piping plovers (Charadrius melodus), an endangered wild shorebird. Genetic and environmental components of variance as well as heritabilities were estimated using Bayesian inference for animal models. Phenotypic variation in age-corrected chick mass was composed of a significant additive genetic component (h2 = 0.27; 95% credible interval: 0.16–0.38), and hatch year, common maternal environment, and hatch site effects. Conversely, natal dispersal distance and female breeding time were not significantly heritable (h2 = 0.03; 95% CI: 0.0–0.11; h2 = 0.08, 95% CI: 0.0–0.22, respectively). Rather, environmental factors (e.g., breeding site) are the main sources of variation in these two traits. Variation in female breeding time was minimally influenced by her mate and was moderately repeatable. The low potential for natal dispersal and breeding time to evolve may limit the ability of this population to adapt to climate change long-term. However, trait alteration could occur by a phenotypically plastic response, allowing rapid adjustment to novel environmental conditions and short-term persistence. Depending on the relative contribution of genetic and environmental influences on the trait(s) of interest, results from quantitative genetic studies can also help identify management priorities for endangered populations.
Presented by Sarah Fitzpatrick, Department of Biology, Colorado State University. March 17, 2015.
A fundamental, but unresolved question in conservation biology is how does gene flow affect fitness and population dynamics? Gene flow may wipe out local distinctiveness or introduce disease. But on the other hand, gene flow can rescue populations from negative inbreeding effects or infuse small populations with the genetic variation needed to adapt to a changing climate. My research addresses this question using a model system for studying evolution in the wild: the Trinidadian guppy. The guppy is a small freshwater fish that is far from imperiled, but populations isolated in headwater streams make it an excellent proxy for other small and fragmented populations. I conducted a large-scale mark-recapture and genetic monitoring effort in two freshwater streams in Trinidad to study the effects of gene flow from translocated guppies on native populations that were previously isolated from gene flow. I began monitoring the native guppies before gene flow and tracked genetic composition of the population, individual fitness, and population dynamics for 26 months (8 guppy generations) after gene flow began. I will summarize the results from this study and discuss lessons we can learn from model systems and how they could be applied to conservation and management.
Advanced Topics in Conservation Genetics. Presented by Dr. Mitchell E McGlaughlin, Associate Professor, School of Biological Sciences, University of Northern Colorado. September 16, 2015.
Since its origin, the field of conservation genetics has been dominated by research focused on determining levels of genetic diversity within and among populations of rare taxa. Although empirical data has documented the relationship between levels of genetic diversity and ‘evolutionary potential,’ many conservation genetic studies fail to answer questions important to the short-term management and conservation of rare taxa. However, genetic data provides a relatively unbiased tool that can be used to assess if conservation goals are being achieved. An area where genetic data is likely to be useful is assessing levels of diversity within ex situ seed collections. Ex situ seed collections seek to establish plant resources that can be used in restoration and reintroduction efforts, and that hedge against stochastic population losses. The value of ex situ seed collections will be impacted by how much of the available wild diversity is captured. The current work examined genetic diversity and population structure in the wild and the effect of sampling intensity on the genetic diversity of ex situ seed collections for the endangered annual plant Sibara filifolia (Brassicaceae), Santa Cruz Island Rock Cress, which is endemic to the California Channel Islands. Simulated sampling for ex situ seed collections found that 10 individuals was sufficient to capture 90% of the diversity for normalized measures (NE, HO, and HE) in a depauperate population, while 30 individuals was necessary in a diverse population. Sampling 125 or 60 individuals was necessary to capture 90% of all the alleles present for depauperate and diverse populations, respectively. These findings indicate that theoretical guidelines for ex situ seed collections that recommend targeting 50 individuals per population overestimate the sampling effort required to adequately preserve common alleles, but may underestimate the effort necessary to capture most alleles in wild populations. Furthermore, this research shows how genetic data can be used to address questions that enhance the management of rare and endangered taxa and move beyond solely measuring levels of genetic diversity.
Presented by Dr. Gregory Moyer, Regional Geneticist for the USFWS’s Southeast Region. January 30, 2014.
The southeastern United States is a recognized hotspot of biodiversity for a variety of aquatic taxa, including fish, amphibians, and mollusks. Unfortunately, the great diversity of the area is accompanied by a large proportion of species at risk of extinction. Gap analysis was employed to assess the representation of evolutionary hotspots in protected lands where an evolutionary hotspot was defined as an area with high evolutionary potential and measured by atypical patterns of genetic divergence, genetic diversity, and to a lesser extent genetic similarity across multiple terrestrial or aquatic taxa. A survey of the primary literature produced 16 terrestrial and 14 aquatic genetic datasets for estimation of genetic divergence and diversity. Relative genetic diversity and divergence values for each terrestrial and aquatic dataset were used for interpolation of multispecies genetic surfaces and subsequent visualization using ArcGIS. The multispecies surfaces interpolated from relative divergences and diversity data identified numerous evolutionary hotspots for both terrestrial and aquatic taxa, many of which were afforded some current protection. For instance, 14% of the cells identified as hotspots of aquatic diversity were encompassed by currently protected areas. Additionally, 25% of the highest 1% of terrestrial diversity cells were afforded some level of protection. In contrast, areas of high and low divergence among species, and areas of high variance in diversity were poorly represented in the protected lands. Of particular interest were two areas that were consistently identified by several different measures as important from a conservation perspective. These included an area encompassing the panhandle of Florida and southern Georgia near the Apalachicola National Forest and a large portion of the coastal regions of North and South Carolina. Our results must be interpreted with caution given the sparse sampling of populations in many of the datasets; however, our results show the utility of genetic datasets for identifying cross-species patterns of genetic diversity and divergence (i.e., evolutionary hotspots) in aquatic and terrestrial environments for use in conservation design and delivery across the southeastern United States.
Presented by Dr. Megan Osborne, University of New Mexico September 2, 2014.
The Arkansas River Shiner is a federally threatened species that has been extirpated throughout much of its native range (Arkansas River drainage) and remaining populations are highly imperiled. Prior to 1978, this species was accidently introduced to the Pecos River (Rio Grande drainage) and has since persisted for over 30 years. We examined several factors that could be responsible for high introduced genetic diversity including (a) multiple introductions from genetically distinct sources (b) introduction of individuals from a genetically diverse source followed by rapid population expansion, (c) presence of life-history traits that foster propagule diversity and wide spatio-temporal demographic and genetic mixing; and (d) introduction to a suitable habitat in the non-native range. Threats to native Arkansas River Shiner have increased due to ongoing drought and water resource development, thus a finding of high diversity in the Pecos River suggests conservation significance of this non-native population. Further, it identifies the Pecos River as both a refuge for native endemic fishes and of genetic diversity of introduced, yet threatened, species.
Presented by Dr. Meredith Bartron, Northeast Fishery Center (USFWS) and Dr. Jeff Olsen, Conservation Genetics Laboratory (USFWS). July 2013.
Rapid advances in the field of molecular genetics continue to provide new tools for research, management and conservation. One such genetic tool is environmental DNA (eDNA) analysis. eDNA refers to DNA that organisms leave behind or shed as they pass through the environment. This shed DNA can be detected using routine molecular techniques such as the polymerase chain reaction (PCR) to amplify species-specific genes, potentially linking the organism to the environment without actually observing the organism. eDNA analysis is currently being evaluated and applied for uses such as surveillance and control of aquatic invasive species, identification and monitoring of endangered species, and analysis of biodiversity. In this webinar, we will explore the methodologies and potential uses of eDNA analysis for monitoring, managing and conserving fishery resources and aquatic habitat. We also will provide an overview of eDNA (general field collection and laboratory protocols and analysis) as well as an overview of the interpretation and application of results (including issues such as false positive and false negative results, PCR inhibition, and contamination).
Presented by Dr. Justin Bohling, USFWS. December 6, 2017.
The development of high-throughput DNA sequencing technology has revolutionized the field of genetics, offering unprecedented resolution into genetic, population, and evolutionary processes. However, these data do not exist in a vacuum: many species have already been investigated with many alternative types of genetic markers. Different marker types have different properties and interpretations,creating the need to compare the inferences derived from different types of datasets. Here I present a study of population genomics of an endangered freshwater fish, the bull trout. Native to the Pacific Northwest of North America, bull trout populations have been extensively surveyed using a variety of genetic markers. Along with collaborators, I generated genomic-level data derived using Restriction-site Associated DNA sequencing (RADseq) of 24 bull trout populations from the United States and compared it to microsatellite data produced for the same sample of individuals. Both marker types detected the primary phylogenetic division in the species, but the RADseq data did so more reliably and with higher resolution. The RADseq data identified further hierarchical structuring that corresponded with biogeographic expectations. For some populations the relationships inferred by the two marker types were in direct conflict. RADseq also revealed introgression between bull trout lineages that were not inferred by the microsatellites. This case study presents a scenario that is likely to become more common as genomics becomes broadly applied to non-model species. Moving forward, geneticists must take care to reconcile past findings with modern genomic data and work with natural resource managers to explain the implications of these conflicts.
Presented by Dr. Craig Steele, Fisheries Research Biologist, Pacific States Marine Fisheries Commission- Eagle Fish Genetics Lab. June 26, 2014.
The role of molecular methods in fisheries management has reached a milestone. Parentage-Based Tagging (PBT), an emerging genetic-based tagging methodology, was only recently envisioned but is already providing information that previously was impossible or impractical to collect with traditional tagging methods. PBT provides the same information as traditional tags but when fully implemented can “tag” 100% of hatchery-origin fish. The principle application of PBT is to provide information on the origin and age of hatchery fish, but implementation of PBT can also be used to generate additional information such as effective population size of hatchery stocks, genetic diversity of hatchery populations, inter-hatchery stray rates, relative reproductive success rates, heritability estimates, and effects of rearing conditions on size and returns. Since 2008, a collaborative sampling effort by state, tribal, and federal agencies has resulted in the genetic sampling of nearly all Chinook and steelhead broodstock at hatcheries in the Snake River Basin of Idaho, Oregon, and Washington. This regional implementation of PBT has genetically tagged approximately 12 million smolts per year for each species. The Idaho Department of Fish and Game is committed to utilizing PBT as a tool for fisheries management and collaborative efforts are now underway to expand PBT sampling of broodstock outside the Snake River Basin.
Presented by Dr. Chad Ferguson, Ohio EPA and Dr. Michael Blum, Tulane University. December 10, 2014.
reproduction and population connectivity will better enable mussel conservation programs to sustain long-term population viability particularly restocking and recovery programs. Here we used genetic methods to characterize population structure, dispersal potential, and reproductive strategies in the freshwater mussel Lampsilis cardium from Twin Creek and Big Darby Creek (Ohio, USA). We genotyped adults and individual glochidia at 12 microsatellite loci to assess local population structure relative to within-population patterns of relatedness and parentage. Local populations within watersheds were weakly structured, and within-population estimates of relatedness identified probable full- and half-siblings several kilometers apart. Parent–offspring comparisons provided evidence of multiple paternity in single broods and identified the likely father of 3 glochidia from 1female’s brood 16.2 km upstream of the mother, indicating that long-distance transport of spermatozoa can promote population connectivity within watersheds. Given that lampsilines and other unionoids exhibit similar reproductive strategies, it is possible that other species are capable of long-distance fertilization. If so, fertilization in populations of many freshwater mussels might not be limited by local density of breeding adults. Therefore, the prospects for recovery of imperiled freshwater mussels might be better than what is now expected.
Presented by Dr. Jill Hamilton, North Dakota State University. November 16, 2016.
In a rapidly changing climate, there is an increased need to both quantify the threat of climate change and better understand populations’ ability to respond to climate change. This ability to respond may in part depend upon the genetic makeup or genomic architecture underlying phenotypic traits important to adaptation in a changing climate. This research examines the genetic basis of adaptation in a changing climate focusing on long-lived forest trees linking phenotype, genotype and environment. Specifically, we will consider adaptive introgression in forest tree hybrid zones and evaluate its importance to climate adaptation and ask whether climate pre-adaptation may facilitate colonization in novel environments.
Presented by Dr. Christian Smith, USFWS. January 20, 2015.
Most coho salmon (Oncorhynchus kisutch) in Washington State spawn at three years of age, creating the potential for three temporal populations or “broodlines” at each spawning site. This is generally prevented by a portion of males in each site that mature and reproduce as two-year olds, resulting in population structure in which the geographic component is stronger than the temporal component. The Quilcene National Fish Hatchery selected against latest returning coho salmon by excluding all but the earliest returning fish from its broodstock for an unknown number of generations, and restricted gene flow among broodlines by excluding two-year old males for 27 generations. The resulting hatchery population exhibited three distinct broodlines which returned in alternating years: an “early” broodline which arrived one month before the wild fish; a “late” broodline which arrived at the same time as the wild fish; and a “middle” broodline which arrived in between these two. We evaluated temporal and geographic components of population genetic structure in coho salmon from the Quilcene National Fish Hatchery and nine other sites from Puget Sound and the Strait of Juan de Fuca using 10 microsatellite loci. Genetic diversity at the Quilcene National Fish Hatchery was lowest in the early broodline and highest in the late broodline. Divergence among broodlines was generally much lower than divergence among sites, rendering the term broodline irrelevant for most sites. Divergence among broodlines at the Quilcene National Fish Hatchery, however, was greater than that observed at any other site, and was also greater than that observed between any of the sites. This apparent reversal of the relative magnitudes of temporal and geographic components for this species emphasizes the importance of variable age-at-maturity in shaping population genetic structure.
Presented by Dr. Clint Muhlfeld, Research Aquatic Ecologist and Professor, USGS: Northern Rocky Mountain Science Center, Glacier National Park; University of Montana. December 8, 2016.
Climate change will decrease worldwide biodiversity through a number of potential pathways, including invasive hybridization (cross-breeding between invasive and native species). How climate warming influences the spread of hybridization and loss of native genomes poses difficult ecological and evolutionary questions with little empirical information to guide conservation management decisions3. Here we combine long-term genetic monitoring data with high-resolution climate and stream temperature predictions to evaluate how recent climate warming has influenced the spatio-temporal spread of human-mediated hybridization between threatened native westslope cutthroat trout (Oncorhynchus clarkii lewisi) and non-native rainbow trout (Oncorhynchus mykiss), the world’s most widely introduced invasive fish4. Despite widespread release of millions of rainbow trout over the past century within the Flathead River system5, a large relatively pristine watershed in western North America, historical samples revealed that hybridization was prevalent only in one (source) population. During a subsequent 30-year period of accelerated warming, hybridization spread rapidly and was strongly linked to interactions between climatic drivers—precipitation and temperature—and distance to the source population. Specifically, decreases in spring precipitation and increases in summer stream temperature probably promoted upstream expansion of hybridization throughout the system. This study shows that rapid climate warming can exacerbate interactions between native and non-native species through invasive hybridization, which could spell genomic extinction for many species.
Presented by Wade D. Wilson, USFWS, Southwestern Native Aquatic Resources and Recovery Center, Dexter, NM. April 23, 2014.
Genetic information is an integral part of the recovery process. Having genetically diverse populations allows individuals in those populations, and ultimately the entire species, to have the evolutionary adaptive potential needed for long-term survival and recovery. Documents outlining the recovery process are many, but the Recovery Plan and a Genetics Management Plan are two documents that can incorporate detailed genetic information for the species of interest. This presentation will cover how these two plans can be used to outline the genetic information needed to manage species for recovery.
Presented by Dr. Mary Curtis, Senior Forensic Scientist, Genetics, USFWS National Fish and Wildlife Forensic Laboratory. September 25, 2013.
Wildlife forensic science is the application of a range of scientific disciplines to legal cases involving non-human biological evidence. These disciplines include genetics, morphology, chemistry, pathology, and veterinary sciences. The National Fish and Wildlife Forensic Laboratory (NFWFL) of the U.S. Fish and Wildlife Service is the only accredited full-service forensic laboratory in the United States dedicated to providing scientific support for Federal wildlife crime investigations, including analytical services and expert witness testimony. The NFWFL also acts as the designated analytical facility for the INTERPOL Wildlife Crime Working Group and the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES). The Genetics Section of the NFWFL uses traditional and state of the art genetic techniques for species identification, individual identification and matching, and determination of geographic provenance for a variety of North American and international species of interest to law enforcement, conservation, and management. This webinar will present an overview of the unique role that wildlife forensic genetics plays in the conservation genetics community.