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Geology topics

Keith N. Turnquist

Publications and source records attributed to Keith N. Turnquist.

9 recordsLinked to original sources
USGS2021

The genetic composition of wild recruits in a recovering lake trout population in Lake Michigan

Strain performance evaluations are vital for developing successful fishery management and restoration strategies. Here, we utilized genotypes from 36 microsatellites to investigate hatchery strain contribution to collections of naturally produced lake trout ( Salvelinus namaycush ) sampled across Lake Michigan. Strain composition varied by area, with recoveries of Seneca Lake strain exceeding expectations based on stocking records in northern Lake Michigan but performing similarly to other strains in southern Lake Michigan. Interstrain hybrids were present at moderate frequencies similar to expectations based on simulations, suggesting that strains are interbreeding randomly. We hypothesize that the superior performance of the Seneca Lake strain in northern Lake Michigan is partially due to adaptive advantages that facilitate increased survival in areas with high mortality from sea lamprey ( Petromyzon marinus ) predation, such as northern Lake Michigan. However, when this selective pressure is lessened, the Seneca Lake strain performs similarly to other strains. Our study demonstrates that strain performance can vary across small spatial scales and illustrates the importance of conducting thorough strain evaluations to inform management and conservation.

Lake Michigan↗
USGS2020

Defining the need for genetic stock assignment when describing stock demographics and dynamics: An example using Lake Whitefish in Lake Michigan

Genetic stock assignment is not routinely used when describing the dynamics and demographics of individual stocks supporting mixed-stock fisheries, and capture location and timing are often used as alternative assignment methods. However, variation in stock demographics and dynamics may not be accounted for if stock assignments based on capture location or timing do not accurately reflect genetic assignments. We used Lake Whitefish Coregonus clupeaformis in Lake Michigan as a model fishery to determine whether stock mixing could undermine efforts to describe stock status when using October capture location as a proxy for genetic stock assignment. Accuracy of stock assignments based on October capture location ranged from 54% to 100% among management zones. Metrics describing length and age distributions, weight at length, fecundity, and growth varied among genetic stocks. Stock-specific metrics were typically similar between stock assignment methods (capture location versus genetics) because only one or two genetic stocks were collected in most locations and the majority of those fish were from spatially proximal stocks with similar metrics. However, more extensive mixing of Lake Whitefish stocks has been documented; thus, using capture location for stock assignment could result in incorrect conclusions regarding stock status and harvest management depending on stock composition. Ambiguity in genetic stock assignments was a problem in two management zones, where between 23% and 42% of Lake Whitefish did not assign to a specific stock with a probability of at least 0.70. In the future, using genomic techniques rather than microsatellites may provide different conclusions regarding genetic stock structure; these differences could affect the accuracy of using capture location for stock assignment. Use of capture location as a proxy for genetic stock assignment may not be warranted for all mixed-stock fisheries but may be appropriate when stock mixing is limited or is restricted to stocks with consistently similar characteristics.

Michigan, Wisconsin↗
USGS2019

Discriminating among Pacific salmon, Rainbow Trout, and Atlantic Salmon species using common genetic screening methods

The five most common species of Pacific salmon, Rainbow Trout (steelhead) Oncorhynchus spp., and Atlantic Salmon Salmo salar intermingle in the North Pacific Ocean and its freshwater tributaries. Efficient morphological methods for distinguishing among these species are sometimes limited by condition of the specimen (degraded or missing morphology), life history stage, or training of the observer. Researchers have successfully applied various genetic methods to distinguish among these species when morphological analyses are not possible, but they cannot easily incorporate these methods into standard fish and wildlife population monitoring analysis workflows. Here we test five 5′–3′ exonuclease (TaqMan) assays developed from mitochondrial genes and provide novel methods that take advantage of TaqMan output to distinguish among these species. We found that combinations of as few as two of the five assays were adequate to distinguish all species. TaqMan chemistry is designed to interrogate a single nucleotide locus. We also explore the basis for the variation in the observed scatter plot distributions (variation in florescent signals) and show that this variation is due to nucleotide diversity in and near the probe site. Because the SNPs underlying the assays developed here are all physically close to one another along the mitochondrial genome, the potential exists to develop a single DNA sequence-based assay to discriminate among salmon species. This single assay can be added to a genotyping-by-sequencing panel to identify and exclude nontarget species from analyses.

Journal of Fish and Wildlife Management↗
USGS2018

Stock structure, dynamics, demographics, and movements of walleyes spawning in four tributaries to Green Bay

To test assumptions related to the current conceptual model for walleye Sander vitreus management in Green Bay, we evaluated whether: 1) spawning aggregations in the Fox, Menominee, Oconto, and Peshtigo rivers represent genetically distinct stocks; 2) population dynamics and demographics vary among walleye spawning at these locations; 3) walleye spawning in these rivers contribute to the fishery in northern Green Bay, and 4) walleye spawning in these rivers exhibit spawning site fidelity or if they stray among rivers. Genetic differentiation among the four tributaries was low and sex-specific total length (TL), mean TL at age 5, and age-class diversity were generally similar among rivers and observed differences were not consistent. Movements of walleye inferred from angler tag returns suggest that walleye spawning (and tagged) in the four tributaries typically remain within southern Green Bay; however, this assertion may be confounded by the distribution of angling effort that provides tag recoveries. Straying rates among rivers ranged from 0 to 23% and were likely sufficient to preclude genetic differentiation among stocks. Collectively, results suggest that walleye spawning in the Fox, Menominee, Oconto, and Peshtigo rivers do not function as separate stocks and do not significantly contribute to the fishery outside of southern Green Bay. The primary assumption of the current conceptual model that remains to be tested is whether the walleye fishery in southern Green Bay is supported primarily by fish spawning in these four rivers, or if there are substantial contributions from fish spawning at other unknown locations.

Wisconsin↗
USGS2017

Genetic structure of muskellunge in the Great Lakes region and the effects of supplementation on genetic integrity of wild populations

Muskellunge ( Esox masquinongy ) are important apex predators that support numerous recreational fisheries throughout the Great Lakes region. Declines in muskellunge abundance from historical overharvest and environmental degradation have threatened the viability of many populations and prompted significant restoration efforts that often include stocking. The goal of our study was to investigate contemporary population structure and genetic diversity in 42 populations of muskellunge sampled across the Great Lakes region to inform future management and supplementation practices. We genotyped 1896 muskellunge ( N = 10–123/population) at 13 microsatellite loci. The greatest genetic variation was between populations of Great Lakes origin and populations of Northern (inland) origin, with both groups also exhibiting significant substructure (overall F ST = 0.23). Genetic structure was generally correlated with geography; however, we only found marginal evidence of isolation by distance, likely due to high genetic differentiation among proximate populations. Measures of genetic diversity were moderate across most populations, but some populations displayed low diversity consistent with small population sizes or historical bottlenecks. Many of the populations studied displayed evidence of historic introductions and supplemental stocking, including the presence of individuals with primarily non-native ancestry as well as interlineage hybrids. Our results suggest that the historic population structure of muskellunge is largely intact across the Great Lakes region, but also that stocking practices have altered this structure to some degree. We suggest that future supplementation practices use local sources where possible, and incorporate genetic tools including broodstock screening to ensure that non-native muskellunge are not used to supplement wild populations.

Great Lakes↗
USGS2016

Diet overlap and predation between largemouth bass and walleye in Wisconsin lakes using DNA barcoding to improve taxonomic resolution

Over the last decade, the abundance of Largemouth Bass Micropterus salmoides has increased in many northern Wisconsin lakes, causing concern among anglers and biologists regarding the potential for Largemouth Bass to negatively affect populations of Walleye Sander vitreus through predation or competition for prey. Our objectives were to determine whether (1) diet overlap and predation occurred between adult Walleyes and Largemouth Bass in four northern Wisconsin lakes and (2) the use of DNA barcoding to reduce unidentifiable fish in diet samples affected conclusions regarding diet overlap. A single occurrence of Walleye predation was observed in the diets of 945 Largemouth Bass. Moderate to high diet overlap was observed between Largemouth Bass and Walleyes throughout much of the study period. The use of DNA barcoding reduced the amount of unidentified fish in diets to <1% and showed that failure to identify fish or fish parts can affect conclusions regarding diet overlap. Largemouth Bass predation is probably not a primary factor affecting Walleye abundance in the lakes we selected, but observed diet overlap suggests the potential for competition between the two species.

Wisconsin↗
USGS2015

Validation of eDNA markers for New Zealand mudsnail surveillance and initial eDNA monitoring at Mississippi River Basin sites

The performance of newly developed New Zealand mudsnail ( Potamopyrgus antipodarum ; NZMS) genetic markers for environmental (eDNA) analysis of water were compared across two laboratories. The genetic markers were tested in four quantitative polymerase chain reaction assays targeting two regions of the NZMS mitochondrial genome, specifically the cytochrome c oxidase subunit 1 (coi) and cytochrome b (cytb) genes. In a blind study, analysts tested each sample eight times with each assay. There were 10 expected-negative samples from the Black River in La Crosse, Wisconsin, 10 expected-positive samples from the Black Earth Creek in Black Earth, Wisconsin, and 10 known-positive samples from the Black River spiked with NZMS DNA. Previously extracted samples, kept at the Upper Midwest Environmental Sciences Center, were pooled by sample location and then equal quantities were distributed between the Upper Midwest Environmental Sciences Center and the Molecular Conservation Genetics Laboratory at the University of Wisconsin-Stevens Point for analysis. The assays tested were (1) the assay targeting cytb with a minor groove binder probe described by Goldberg and others (2013), (2) the cytb assay with a modified double-quenched probe, (3) an assay targeting coi with a double-quenched probe, and (4) a duplex reaction combining the modified cytb assay and the coi assay. Samples were considered positive for the presence of NZMS DNA when quantitative polymerase chain reaction amplification and probe signal was higher than the normalized threshold value above baseline fluorescence. For the duplex assay, samples were considered positive only when both probe signals were higher than the normalized threshold value above baseline fluorescence. Positive results were then confirmed by sequencing the products. All four assays detected the DNA of NZMS in all expected-positive and known-positive samples in both labs. The modified cytb assay, the coi assay, and the duplex assay all failed to detect the DNA of NZMS in all expected-negative samples in both labs. The cytb assay, as described by Goldberg and others (2013), failed to detect the DNA of NZMS in all expected-negative samples for the Molecular Conservation Genetics Laboratory, but some reactions resulted in positive detection in late cycles for 9 of the 10 expected-negative samples at the Upper Midwest Environmental Sciences Center. Amplicons for expected-negative samples with positive reactions were sent for sequencing, and none were confirmed as NZMS. Six amplicons failed to give readable sequences, and three gave sequences without similarity to any known sequence in GenBank. Amplicons from each assay for one representative positive sample were sequenced and identified as NZMS with greater than 99 percent identity. The duplex assay was chosen as the most efficient assay and was used at the Upper Midwest Environmental Sciences Center to analyze triplicate samples from 29 streams in Wisconsin, 8 streams in Illinois, and 8 streams in Iowa. In order to verify results, additional triplicate samples were collected from two of the streams in Iowa and two of the streams in Wisconsin for analysis at the Molecular Conservation Genetics Laboratory. All samples at all sites were negative for NZMS DNA.

Illinois, Iowa, Wisconsin↗