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USGS2020

Using advanced population genomics to better understand the relationship between offshore and spawning habitat use for Atlantic Sturgeon

Atlantic Sturgeon ( Acipenser oxyrinchus oxyrinchus ) are a large-bodied anadromous fish that historically supported important fisheries along the east coast of the United States. Following years of overharvest and habitat degradation, populations experienced severe declines. In 2012, the National Marine Fisheries Service listed Atlantic Sturgeon under the Endangered Species Act (ESA; 61 FR 4722). Their listing named five Distinct Population Segments (DPSs), predicated on genetic groups composed of geographically proximate populations. Federal management of Atlantic Sturgeon presents challenges, as sturgeon from each of the five DPSs mix extensively in coastal and marine habitats yet take and recovery progress must be evaluated separately for each unit. Genetic assignment testing based on mitochondrial and microsatellite markers allows individuals to be assigned back to their natal river and DPS. However, this approach is not perfect and some individuals may be incorrectly assigned. Recent advances in genomics offer the potential of a higher resolution approach to genetic assignment testing, and thus may reduce uncertainty associated with assignment testing. In addition, genomics allows a greater number of markers to be examined from across a broader portion of the sturgeon genome, thus may provide an enhanced perspective of population structure for the species, and potentially allow other previously intractable questions to be addressed (Bernatchez et al. 2017, Supple and Shapiro 2018). We used next-generation sequencing to develop a draft genome for Atlantic Sturgeon and identify single nucleotide polymorphisms (SNPs) that could be used to resolve the natal river and DPS of individual Atlantic Sturgeon. We identified 1,210 candidate SNPs within the nuclear genome as well as 49 SNPs within the mitochondrial genome. After filtering and review, we selected 161 nuclear SNPs and 39 mitochondrial SNPs for further testing and evaluation. We used genotyping-in-thousands by sequencing (GT-seq) to simultaneously sequence nuclear SNP loci, mitochondrial SNP loci, and the existing panel of twelve microsatellite loci. This effort required a pilot sequencing run on a single sturgeon sample to test marker amplification and refine primer strengths, followed by a series of sequencing runs to generate baseline data for 288 individuals representing nine populations of Atlantic Sturgeon in four DPSs. Using baseline data from the nine populations, we ran a series of genomic analyses to characterize diversity within and among populations, providing a benchmark for this species using the new SNP markers. Allelic richness was similar for all populations, although there was a general trend of more northern population containing greater levels of allelic richness. Interestingly, we observed linkage disequilibrium among many pairs of loci within many populations. This might be the result of physical linkage but could also suggest these populations are recovering from genetic bottlenecks and/or are effectively small, leading to specific haplotypes to be favored by chance. Pairwise differentiation among populations varied among the populations ( F ST range: 0.010-0.098) and was significantly correlated ( r = 0.771; P < 0.001) to pairwise F ST observed using microsatellite markers). Population clustering and ordination techniques using the new genomic data both support an overall population structure that is similar to the current DPS management units (which were developed primarily based on microsatellite genetic data). Overall, this suggests that existing microsatellite markers and the panel of SNP markers developed in this study provide similar information about the populations structure and ecology of Atlantic Sturgeon. Given the observed differences in allele frequencies among populations, our genomic baseline supports previous assertations that Atlantic Sturgeon show natal homing, despite mixing extensively in marine waters during non-breeding periods. Lower levels of differentiation between populations in the South Atlantic DPS suggest that populations in this region may have greater levels of gene flow relative to their more northerly conspecifics, which has also previously been suggested based on microsatellite data. The observed differentiation among populations provides the necessary foundation for determining the natal river and DPS of Atlantic Sturgeon using assignment testing. We tested the utility of our new genomic baseline for resolving the population and DPS of Atlantic Sturgeon. Our nuclear SNP markers showed utility for identifying the origin of unknown Atlantic Sturgeon samples, as 86.5% were assigned to the correct DPS and 66.3% were assigned to the correct natal river. However, since this study was funded the Conservation Genetics and Genomics Laboratory at Leetown Science Center has made significant improvements to their microsatellite genetic baseline, which now performs more effectively than our new genomic approach (the genetic baseline includes 12 populations and 5 DPSs, and correctly assigns 95.8% of individuals to DPS and 84.9% of individuals to their natal population using 12 microsatellite loci). We conducted an ad hoc exploration of how additional microsatellite or nuclear SNP loci may further improve the accuracy of assignment testing. We found that additional microsatellite markers are likely to result in greater improvements in assignment efficiency than additional nuclear SNPs. However, a much larger number of SNP loci (which if identified could be sequenced using other methods that are now available; e.g., the RAD-capture approach published by Ali et al. 2016) could produce assignment efficiencies that are greater than what is currently feasible using microsatellites. In the absence of further research and development of additional SNP markers for Atlantic Sturgeon (possibly using an approach other than GT-seq), the existing microsatellite loci are the most effective means available to determine the natal river and DPS of Atlantic Sturgeon encountered in offshore waters. Because our new genomic markers were less effective than the existing panel of 12 microsatellite markers, we chose to use the existing microsatellite markers to assign Atlantic Sturgeon captured in another BOEM-funded study (cooperative agreement M16AC00003; Monitoring endangered Atlantic Sturgeon and commercial finfish habitat use offshore New York) following consultation with our project officer. Using this approach, we genotyped and assigned 186 Atlantic Sturgeon captured in coastal waters off the Rockaway Peninsula, New York. The vast majority of these sturgeon were assigned to the New York Bight DPS (94.62%), and most appear to belong to the Hudson River population (87.10%) with smaller contributions from the Delaware River population (7.53%). Smaller contributions (2.15%) were observed from six other populations, including those from the James, York, Kennebec, Ogeechee, and Edisto rivers. Although most of the fish we assigned were assigned to the nearest spawning rivers (Hudson and Delaware), the contributions from distant rivers is consistent with the propensity of this species to move long distances and form mixed stock aggregations along the continental shelf. This finding indicates that spawning populations (and their corresponding DPS) from distant locations may potentially be impacted by offshore activities. In fact, activities in this region of the New York Bight could negatively impact Atlantic Sturgeon population from at least four different DPSs. Genetic or genomic assignment testing remains an essential tool to characterize potential impacts to Atlantic Sturgeon populations and should be applied more broadly to better characterize potential impacts of activities in other locations.

Atlantic Coast↗

USGS2015

Status and conservation of interior Redband Trout in the western United States

In this article we describe the current status and conservation of interior (potamodromous) Redband Trout Oncorhynchus mykiss sspp. throughout its range in the western United States using extant data and expert opinion provided by fish managers. Redband Trout historically occupied 60,295 km of stream habitat and 152 natural lakes. Currently, Redband Trout occupy 25,417 km of stream habitat (42% of their historical range) and 124 lakes or reservoirs. Nonhybridized populations are assumed to occupy 11,695 km (46%) of currently occupied streams; however, fish from only 4,473 km (18%) have been genetically tested. Approximately 47% of the streams occupied by Redband Trout occur on private land, 45% on government lands, and 8% in protected areas. A total of 210 Redband Trout populations, occupying 15,252 km of stream habitat (60% of the current distribution) and 95,158 ha of lake habitat (52%), are being managed as “conservation populations.” Most conservation populations have been designated as weakly to strongly connected metapopulations (125; 60%) and occupy much more stream length (14,112 km; 93%) than isolated conservation populations (1,141 km; 7%). The primary threats to Redband Trout include invasive species, habitat degradation and fragmentation, and climate change. Although the historical distribution of interior Redband Trout has declined dramatically, we conclude that the species is not currently at imminent risk of extinction because it is still widely distributed with many populations isolated by physical barriers and active conservation efforts are occurring for many populations. However, the hybridization status of many populations has not been well quantified, and introgression may be more prevalent than documented here. We recommend (1) collecting additional genetic data and estimating distribution and abundance by means of a more rigorous spatial sampling design to reduce uncertainties, (2) collecting additional information to assess and predict the impacts of climate on populations, and (3) continuing to use this database to evaluate the status of Redband Trout and inform conservation efforts through time.

North American Journal of Fisheries Management↗

USGS2016

DNA and dispersal models highlight constrained connectivity in a migratory marine megavertebrate

Population structure and spatial distribution are fundamentally important fields within ecology, evolution, and conservation biology. To investigate pan-Atlantic connectivity of globally endangered green turtles ( Chelonia mydas ) from two National Parks in Florida, USA, we applied a multidisciplinary approach comparing genetic analysis and ocean circulation modeling. The Everglades (EP) is a juvenile feeding ground, whereas the Dry Tortugas (DT) is used for courtship, breeding, and feeding by adults and juveniles. We sequenced two mitochondrial segments from 138 turtles sampled there from 2006-2015, and simulated oceanic transport to estimate their origins. Genetic and ocean connectivity data revealed northwestern Atlantic rookeries as the major natal sources, while southern and eastern Atlantic contributions were negligible. However, specific rookery estimates differed between genetic and ocean transport models. The combined analyses suggest that post-hatchling drift via ocean currents poorly explains the distribution of neritic juveniles and adults, but juvenile natal homing and population history likely play important roles. DT and EP were genetically similar to feeding grounds along the southern US coast, but highly differentiated from most other Atlantic groups. Despite expanded mitogenomic analysis and correspondingly increased ability to detect genetic variation, no significant differentiation between DT and EP, or among years, sexes or stages was observed. This first genetic analysis of a North Atlantic green turtle courtship area provides rare data supporting local movements and male philopatry. The study highlights the applications of multidisciplinary approaches for ecological research and conservation.

Florida↗

USGS2015

Post-release monitoring of Antillean manatees: an assessment of the Brazilian rehabilitation and release programme

Mammalian reintroduction programmes frequently aim to reconnect isolated sub-populations and restore population viability. However, these long-term objectives are rarely evaluated due to the inadequacy of post-release monitoring. Here, we report the results of a unique long term telemetry-based monitoring programme for rehabilitated Antillean manatees (Trichechus manatus manatus) reintroduced into selected sites in northeast Brazil with the aim of reconnecting isolated relict populations. Twenty-one satellite-tagged rehabilitated manatees, 13 males and 8 females, were released into the wild from two sites between November 2008 and June 2013. Individual accumulation curves were plotted and home ranges were calculated through the fixed kernel method using 95% of the utilization distribution. The number and size of the Centres of Activity (COAs) were calculated using 50% of the utilization distribution. Manatees displayed a dichotomous pattern of movement, with individuals either characterized by sedentary habits or by much more extensive movements. Moreover, home range size was not significantly influenced by gender, age at release or release site. COAs were strongly associated with sheltered conditions within reefs and estuaries, and also by the presence of freshwater and feeding sites. Our data confirm that manatee reintroductions in Brazil have the potential to reconnect distant sub-populations. However, pre-release identification of potential long-distance migrants is currently unfeasible, and further analysis would be required to confirm genetic mixing of distant sub-populations.

Animal Conservation↗

USGS2021

Intended consequences statement

As the biodiversity crisis accelerates, the stakes are higher for threatened plants and animals. Rebuilding the health of our planet will require addressing underlying threats at many scales, including habitat loss and climate change. Conservation interventions such as habitat protection, management, restoration, predator control, translocation, genetic rescue, and biological control have the potential to help threatened or endangered species avert extinction. These existing, well-tested methods can be complemented and augmented by more frequent and faster adoption of new technologies, such as powerful new genetic tools. In addition, synthetic biology might offer solutions to currently intractable conservation problems. We believe that conservation needs to be bold and clear-eyed in this moment of great urgency.

Conservation Science and Practice↗

USGS2004

Evaluating mixed samples as a source of error in non-invasive genetic studies using microsatellites

The use of noninvasive genetic sampling (NGS) for surveying wild populations is increasing rapidly. Currently, only a limited number of studies have evaluated potential biases associated with NGS. This paper evaluates the potential errors associated with analysing mixed samples drawn from multiple animals. Most NGS studies assume that mixed samples will be identified and removed during the genotyping process. We evaluated this assumption by creating 128 mixed samples of extracted DNA from brown bear (Ursus arctos) hair samples. These mixed samples were genotyped and screened for errors at six microsatellite loci according to protocols consistent with those used in other NGS studies. Five mixed samples produced acceptable genotypes after the first screening. However, all mixed samples produced multiple alleles at one or more loci, amplified as only one of the source samples, or yielded inconsistent electropherograms by the final stage of the error-checking process. These processes could potentially reduce the number of individuals observed in NGS studies, but errors should be conservative within demographic estimates. Researchers should be aware of the potential for mixed samples and carefully design gel analysis criteria and error checking protocols to detect mixed samples.

Molecular Ecology↗

USGS2017

Status of White Sturgeon (Acipenser transmontanus Richardson, 1863) throughout the species range, threats to survival, and prognosis for the future

White Sturgeon, Acipenser transmontanus (WS), are distributed throughout three major river basins on the West Coast of North America: the Sacramento-San Joaquin, Columbia, and Fraser River drainages. Considered the largest North American freshwater fish, some WS use estuarine habitat and make limited marine movements between river basins. Some populations are listed by the United States or Canada as threatened or endangered (upper Columbia River above Grand Coulee Dam; Kootenai River; lower, middle and, upper Fraser River and Nechako River), while others do not warrant federal listing at this time (Sacramento-San Joaquin Rivers; Columbia River below Grand Coulee Dam; Snake River). Threats that impact WS throughout the species’ range include fishing effects and habitat alteration and degradation. Several populations suffer from recruitment limitations or collapse due to high early life mortality associated with these threats. Efforts to preserve WS populations include annual monitoring, harvest restrictions, habitat restoration, and conservation aquaculture. This paper provides a review of current knowledge on WS life history, ecology, physiology, behavior, and genetics and presents the status of WS in each drainage. Ongoing management and conservation efforts and additional research needs are identified to address present and future risks to the species.

Journal of Applied Ichthyology↗

USGS2016

Identification of the major capsid protein of erythrocytic necrosis virus (ENV) and development of quantitative real-time PCR assays for quantification of ENV DNA

Viral erythrocytic necrosis (VEN) is a disease of marine and anadromous fish that is caused by the erythrocytic necrosis virus (ENV), which was recently identified as a novel member of family Iridoviridae by next-generation sequencing. Phylogenetic analysis of the ENV DNA polymerase grouped ENV with other erythrocytic iridoviruses from snakes and lizards. In the present study, we identified the gene encoding the ENV major capsid protein (MCP) and developed a quantitative real-time PCR (qPCR) assay targeting this gene. Phylogenetic analysis of the MCP gene sequence supported the conclusion that ENV does not group with any of the currently described iridovirus genera. Because there is no information regarding genetic variation of the MCP gene across the reported host and geographic range for ENV, we also developed a second qPCR assay for a more conserved ATPase-like gene region. The MCP and ATPase qPCR assays demonstrated good analytical and diagnostic sensitivity and specificity based on samples from laboratory challenges of Pacific herring Clupea pallasii . The qPCR assays had similar diagnostic sensitivity and specificity as light microscopy of stained blood smears for the presence of intraerythrocytic inclusion bodies. However, the qPCR assays may detect viral DNA early in infection prior to the formation of inclusion bodies. Both qPCR assays appear suitable for viral surveillance or as a confirmatory test for ENV in Pacific herring from the Salish Sea.

Journal of Veterinary Diagnostic Investigation↗

USGS2008

Delayed genetic effects of habitat fragmentation on the ecologically specialized Florida sand skink ( Plestiodon reynoldsi )

Populations rarely show immediate genetic responses to habitat fragmentation, even in taxa that possess suites of traits known to increase their vulnerability to extinction. Thus conservation geneticists must consider the time scale over which contemporary evolutionary processes operate to accurately portray the effects of habitat isolation. Here, we examine the genetic impacts of fragmentation on the Florida sand skink Plestiodon reynoldsi , a sand swimming lizard that is highly adapted to the upland scrub habitat of central Florida. We studied fragments located on the southern Lake Wales Ridge, where human activity in the latter half of the 20th century has modified the natural patchiness of the landscape. Based on a relaxed molecular clock method, we estimate that sand skinks have persisted in this region for approximately 1.5 million years and that the time frame of human disturbance is equivalent to fewer than 30 skink generations. Using genotypes from eight microsatellite loci, we screened for molecular signatures of this disturbance by assessing congruence between population structure, as inferred from spatially-informed Bayesian assignment tests, and the current geography of scrub fragments. We also tested for potential intrapopulation genetic effects of inbreeding in isolated populations by comparing the average pairwise relatedness of individuals within fragments of different areas and isolation. Our results indicate that although some patches show a higher degree of relatedness than expected under random mating, the genetic effects of recent isolation are not evident in this part of the species’ range. We argue that this result is an artefact of a time-lag in the response to disturbance, and that species-typical demographic features may explain the genetic inertia observed in these populations.

Conservation Genetics↗

USGS2003

Sediment-starved sand ridges on a mixed carbonate/siliciclastic inner shelf off west-central Florida

High-resolution side-scan mosaics, sediment analyses, and physical process data have revealed that the mixed carbonate/siliciclastic, inner shelf of west-central Florida supports a highly complex field of active sand ridges mantled by a hierarchy of bedforms. The sand ridges, mostly oriented obliquely to the shoreline trend, extend from 2 km to over 25 km offshore. They show many similarities to their well-known counterparts situated along the US Atlantic margin in that both increase in relief with increasing water depth, both are oriented obliquely to the coast, and both respond to modern shelf dynamics. There are significant differences in that the sand ridges on the west-central Florida shelf are smaller in all dimensions, have a relatively high carbonate content, and are separated by exposed rock surfaces. They are also shoreface-detached and are sediment-starved, thus stunting their development. Morphological details are highly distinctive and apparent in side-scan imagery due to the high acoustic contrast. The seafloor is active and not a relict system as indicated by: (1) relatively young AMS 14C dates (< 1600 yr BP) from forams in the shallow subsurface (1.6 meters below seafloor), (2) apparent shifts in sharply distinctive grayscale boundaries seen in time-series side-scan mosaics, (3) maintenance of these sharp acoustic boundaries and development of small bedforms in an area of constant and extensive bioturbation, (4) sediment textural asymmetry indicative of selective transport across bedform topography, (5) morphological asymmetry of sand ridges and 2D dunes, and (6) current-meter data indicating that the critical threshold velocity for sediment transport is frequently exceeded. Although larger sand ridges are found along other portions of the west-central Florida inner shelf, these smaller sand ridges are best developed seaward of a major coastal headland, suggesting some genetic relationship. The headland may focus and accelerate the N-S reversing currents. An elevated rock terrace extending from the headland supports these ridges in a shallower water environment than the surrounding shelf, allowing them to be more easily influenced by currents and surface gravity waves. Tidal currents, storm-generated flows, and seasonally developed flows are shore-parallel and oriented obliquely to the NW-SE trending ridges, indicating that they have developed as described by the Huthnance model. Although inner shelf sand ridges have been extensively examined elsewhere, this study is the first to describe them in a low-energy, sediment-starved, dominantly mixed siliciclastic/carbonate sedimentary environment situated on a former limestone platform. ?? 2003 Elsevier B.V. All rights reserved.

Florida↗

USGS2023

Toward invasive mussel genetic biocontrol: Approaches, challenges, and perspectives

Invasive freshwater mussels, such as the zebra ( Dreissena polymorpha ), quagga ( Dreissena rostriformis bugensis ), and golden ( Limnoperna fortunei ) mussel have spread outside their native ranges throughout many regions of the North American, South American, and European continents in recent decades, damaging infrastructure and the environment. This review describes ongoing efforts by multiple groups to develop genetic biocontrol methods for invasive mussels. First, we provide an overview of genetic biocontrol strategies that have been applied in other invasive or pest species. Next, we summarize physical and chemical methods that are currently in use for invasive mussel control. We then describe the multidisciplinary approaches our groups are employing to develop genetic biocontrol tools for invasive mussels. Finally, we discuss the challenges and limitations of applying genetic biocontrol tools to invasive mussels. Collectively, we aim to openly share information and combine expertise to develop practical tools to enable the management of invasive freshwater mussels.

iScience↗

USGS1991

Spatial heterogeneity of mitochondrial DNA and allozymes among populations of white-tailed deer and mule deer

A white-tailed deer ( Odocoileus virginianus ) population in northeastern Minnesota and a mule deer ( O. hemionus ) population in the Bridger Mountains Montana, have previously been shown to be spatially subdivided into contiguous subpopulations. We assessed the degree of genetic differentiation among subpopulations and tested the hypothesis that differentiation will be greater for mitochondrial DNA (mtDNA) than for nuclear-encoded allozymes. Differentiation of the white-tailed deer subpopulations was significant for two allozyme loci but not for mtDNA, and the overall degree of differentiation was low. Gene flow, recent founding of the subpopulations, and polygamous breeding structure may all have contributed to this pattern. Greater differentiation was evident among disjunct populations than between the contiguous subpopulations of white-tailed deer. The contiguous mule deer subpopulations were significantly differentiated for mtDNA and one allozyme locus. Differentiation was greater for mtDNA than for allozymes. These results are consistent with demographic data that indicate mule deer males disperse more than do females. Disjunct mule deer populations may be similar or dramatically different in mtDNA haplotype frequencies that do not necessarily vary with geographic distance. Current and historical gene flow and breeding structure will influence population genetic patterns.

Journal of Heredity↗

USGS2003

Effective number of breeding adults in Bufo bufo estimated from age-specific variation at minisatellite loci

Estimates of the effective number of breeding adults were derived for three semi-isolated populations of the common toad Bufo bufo based on temporal (i.e. adult-progeny) variance in allele frequency for three highly polymorphic minisatellite loci. Estimates of spatial variance in allele frequency among populations and of age-specific measures of genetic variability are also described. Each population was characterized by a low effective adult breeding number ( N b ) based on a large age-specific variance in mini-satellite allele frequency. Estimates of N b (range 21–46 for population means across three loci) were ≊ 55–230-fold lower than estimates of total adult census size. The implications of low effective breeding numbers for long-term maintenance of genetic variability and population viability are discussed relative to the species' reproductive ecology, current land-use practices, and present and historical habitat modification and loss. The utility of indirect measures of population parameters such as N b and N e based on time-series data of minisatellite allele frequencies is discussed relative to similar measures estimated from commonly used genetic markers such as protein allozymes.

Leicestershire region↗

USGS2015

Re-colonization by common eiders Somateria mollissima in the Aleutian Archipelago following removal of introduced arctic foxes Vulpes lagopus

Islands provide refuges for populations of many species where they find safety from predators, but the introduction of predators frequently results in elimination or dramatic reductions in island-dwelling organisms. When predators are removed, re-colonization for some species occurs naturally, and inter-island phylogeographic relationships and current movement patterns can illuminate processes of colonization. We studied a case of re-colonization of common eiders Somateria mollissima following removal of introduced arctic foxes Vulpes lagopus in the Aleutian Archipelago, Alaska. We expected common eiders to resume nesting on islands cleared of foxes and to re-colonize from nearby islets, islands, and island groups. We thus expected common eiders to show limited genetic structure indicative of extensive mixing among island populations. Satellite telemetry was used to record current movement patterns of female common eiders from six islands across three island groups. We collected genetic data from these and other nesting common eiders at 14 microsatellite loci and the mitochondrial DNA control region to examine population genetic structure, historical fluctuations in population demography, and gene flow. Our results suggest recent interchange among islands. Analysis of microsatellite data supports satellite telemetry data of increased dispersal of common eiders to nearby areas and little between island groups. Although evidence from mtDNA is suggestive of female dispersal among island groups, gene flow is insufficient to account for recolonization and rapid population growth. Instead, near-by remnant populations of common eiders contributed substantially to population expansion, without which re-colonization would have likely occurred at a much lower rate. Genetic and morphometric data of common eiders within one island group two and three decades after re-colonization suggests reduced movement of eiders among islands and little movement between island groups after populations were re-established. We predict that re-colonization of an island group where all common eiders are extirpated could take decades.

Alaska↗

USGS2017

Molecular phylogeny of the Nearctic and Mesoamerican freshwater mussel genus Megalonaias

Megalonaias is the most geographically widespread genus of the subfamily Ambleminae and is distributed across much of the eastern half of North America, from Minnesota to Nicaragua. Despite the large geographic distribution, the species-level diversity of Megalonaias is quite depauperate (2 spp.), suggesting the genus may not be constrained by the same physical, ecological, or physiological barriers that limit dispersal in many other amblemines. However, this hypothesis is contingent on the assumption that the current taxonomy of Megalonaias accurately reflects its evolutionary history, which remains incompletely understood due to the marginalization of Mesoamerican populations in systematic research. Using one mitochondrial (COI ) and one nuclear marker ( ITS1 ) sequenced from 41 individuals distributed across both the Nearctic and Mesoamerican ecoregions, we set out to better understand the species boundaries and genetic diversity within Megalonaias . The reconstructed molecular phylogeny and the observed genetic diversity suggests that Megalonaias is a monotypic genus and that Megalonaias nickliniana , currently considered a federally endangered species, is not a valid species. These results are discussed in the context of their systematic and conservation implications, as well as how the unusual life history strategy of Megalonaias may be influencing its molecular diversity.

Hydrobiologia↗

USGS2016

Mixed stock analysis of Lake Michigan's Lake Whitefish Coregonus clupeaformis commercial fishery

Lake whitefish ( Coregonus clupeaformis ) support the primary commercial fishery in Lake Michigan. Discrete genetic stocks of lake whitefish have been identified and tagging data suggest stocks are mixed throughout much of the year. Our objectives were to determine if (1) differential stock harvest occurs in the commercial catch, (2) spatial differences in genetic composition of harvested fish were present, and (3) seasonal differences were present in the harvest by commercial fisheries that operate in management zones WI-2 and WFM-01 (Green Bay, Lake Michigan). Mixed stock analysis was conducted on 17 commercial harvest samples (n = 78–145/sample) collected from various ports lake-wide during 2009–2010. Results showed significant mixing with variability in stock composition across most samples. Samples consisted of two to four genetic stocks each accounting for ≥ 10% the catch. In 10 of 17 samples, the stock contributing the largest proportion made up < 60% of the harvest. In general, seasonal and annual differences existed in the proportional stock contribution at a single capture location. Samples from Wisconsin's primary commercial fishing management zone (WI-2) were composed predominately of fish from the Big Bay de Noc (Michigan) stock as opposed to the geographically proximate, North–Moonlight Bay (Wisconsin) stock. These findings have implications for management and allocation of fish to various quotas. Specifically, geographic location of harvest, the current means of allocating harvest quotas, is not the best predictor of genetic stock harvest.

Lake Michigan↗

USGS2011

Young (<7 Ma) gold deposits and active geothermal systems of the Great Basin: Enigmas, questions, and exploration potential

Young gold systems in the Great Basin (£ 7 Ma), though not as well studied as their older counterparts, comprise a rapidly growing and in some ways controversial group. The gold inventory for these systems has more than doubled in the last 5 years from roughly 370 tonnes (12 Moz) to 890 tonnes (29 Moz). Although these deposits are characterized by low grades, tonnages can be high and stripping ratios low, and they have been mined profitably, as exemplified by Florida Canyon and Hycroft. Active geothermal systems in the Great Basin also comprise a rapidly growing group, as evidenced by a number of recent discoveries of geothermal groundwater and a more than 50% increase in electricity production capacity from these systems in the last 5 years. Many young gold deposits are closely associated with active geothermal systems, suggesting that gold deposits may be forming today in the Great Basin. Measured or estimated geothermal reservoir temperatures commonly approach or exceed 200∞C, and other characteristics and processes (advanced argillic caps, hydrothermal eruption breccias) of these young deposits resemble those of nearby Tertiary precious metal deposits. Nonetheless, many young gold systems, especially in Nevada, are not associated with coeval igneous rocks. Similarly, almost all electricity-grade geothermal systems in Nevada are not associated with Quaternary silicic volcanic rocks, and have lower temperature gradients, lower 3He/4He ratios, and lower dissolved trace element concentrations than most magmatic-heated geothermal systems elsewhere in the world. The increasing economic significance of young gold deposits and active geothermal systems justifies more research to better understand their origins, particularly because in some aspects they remain enigmatic and controversial. Are young gold deposits in Nevada truly amagmatic, or have they received metal and fluid contributions from magmas deeper within the crust? Has gold in these deposits been remobilized from older gold mineralization? Current research is investigating these and other questions to improve our genetic understanding of these young gold systems, which in turn can lead to improved exploration targeting. The recent rapid growth in resources for both young gold deposits and geothermal systems underscores their underdeveloped exploration potential. Even though many young gold deposits exhibit relatively shallow hot-springs-style mineralization, their young age may preclude exposure by erosion. Uplift along active normal faults has exposed some deposits (e.g., Florida Canyon, Dixie Comstock, Wind Mountain), but in other areas, such as the Walker Lane, where strike-slip faulting is prevalent, the opportunities for exposure can be limited. Many active geothermal systems are also concealed below the surface in that hot springs or steam vents may be absent above areas of thermal groundwater. With sources of energy to support mine production becoming more problematic, the potential advantages of simultaneously exploring for young gold deposits and spatially associated geothermal systems are becoming more apparent. Exploration methods recently proven effective in geothermal exploration that can be adapted to gold exploration include temperature surveys, hyperspectral remote sensing, geophysical surveys, water analyses, and detailed mapping of geothermal-related features and related fault systems.

Conference Paper↗

USGS2017

The Southern Appalachian Brook Trout management conundrum: What should restoration look like in the 21st Century?

Brook Trout Salvelinus fontinalis in the southern Appalachian portion of their range have been isolated in remote headwater systems for millennia. Recent genetic investigations indicate extremely low allelic diversity, heterozygosity and effective population sizes in many streams. In populations restored using multiple source stocks, limited introgression has been observed despite source stocks being collected from streams within the same subwatershed. It remains unclear if pre- and/or post-reproductive isolating mechanisms are restricting effective gene flow among source stocks in restored streams. Objectives of this study were to: 1) identify environmental variables contributing to assortative mating, and 2) use common garden crossings to determine if wild type brood stock crossings resulted in physiologically viable offspring. We observed markedly different fertilization success rates within-population (66.7%) and betweenpopulation (91.7%) from the 42 crosses (N=18 control, N=24 treatment). Moreover, we observed significant (P < 0.05) differences between within-population and between-population groups in each of our linear mixed effects global models for each trial stage of development (i.e., fertilization rate, eyed egg rate, and hatch rates). Tukey’s HSD comparisons revealed only one significantly (P < 0.003) different fertilization rate among the forty five pairwise comparisons in each of our three stages of trails. In addition, we observed differential peaks of gamete production within and among source stream brood stock, despite common garden conditions, that appeared to have limited fertilization success rates between interstream and control groups. Despite differential peak gamete timing, intrastream crosses performed equally, and, in some instances, better than those between control groups. Our results suggest differential responses to shared environmental conditions (i.e., temperature and/or photoperiod) may contribute to mismatched spawning phenology (i.e., gamete production timing) among restoration founder stocks leading to introgression (i.e., genetic admixture). The application of contemporary genetic techniques could help determine if these possible local adaptations are genetically fixed or may break down over time in restored populations with mixed source stocks. These findings demonstrate the need to apply contemporary conservation genetics tools to future wild trout restoration projects using translocated source stock towards the goal of “genetically-robust”, naturally reproducing populations with the ability to cope with current and future perturbations.

North Carolina, Tennessee↗