Geology topics

Kristen Gruenthal

Publications and source records attributed to Kristen Gruenthal.

3 recordsLinked to original sources

USGS2021

eDNA metabarcoding outperforms traditional fisheries sampling and reveals fine-scale heterogeneity in a temperate freshwater lake

Understanding biodiversity in aquatic systems is critical to ecological research and conservation efforts, but accurately measuring species richness using traditional methods can be challenging. Environmental DNA (eDNA) metabarcoding, which uses high-throughput sequencing and universal primers to amplify DNA from multiple species present in an environmental sample, has shown great promise for augmenting results from traditional sampling to characterize fish communities in aquatic systems. Few studies, however, have compared exhaustive traditional sampling with eDNA metabarcoding of corresponding water samples at a small spatial scale. We intensively sampled Boardman Lake (1.4 km 2 ) in Michigan, USA, from May to June in 2019 using gill and fyke nets and paired each net set with lake water samples collected in triplicate. We analyzed water samples using eDNA metabarcoding with 12S and 16S fish-specific primers and compared estimates of fish diversity among methods. In total, we set 60 nets and analyzed 180 1 L lake water samples. We captured a total of 12 fish species in our traditional gear and detected 40 taxa in the eDNA water samples, which included all the species observed in nets. The 12S and 16S assays detected a comparable number of taxa, but taxonomic resolution varied between the two genes. In our traditional gear, there was a clear difference in the species selectivity between the two net types, and there were several species commonly detected in the eDNA samples that were not captured in nets. Finally, we detected spatial heterogeneity in fish community composition across relatively small scales in Boardman Lake with eDNA metabarcoding, but not with traditional sampling. Our results demonstrated that eDNA metabarcoding was substantially more efficient than traditional gear for estimating community composition, highlighting the utility of eDNA metabarcoding for assessing species diversity and informing management and conservation.

Michigan↗

USGS2021

Efficient genotyping with backwards compatibility: Converting a legacy microsatellite panel for muskellunge (Esox masquinongy) to genotyping-by-sequencing chemistry

Microsatellites have been a staple of population genetics research for over three decades, and many large datasets have been generated with these markers. Microsatellites have been used, for example, to conduct genetic monitoring and construct large multigeneration pedigrees as well as genotype thousands of individuals from a given species to create high-resolution baselines of spatial genetic structure. However, the capillary electrophoresis (CE) approach used to genotype microsatellites is inefficient compared to newer genotyping-by-sequencing (GBS) approaches, and researchers have begun transitioning away from CE. Backward compatibility between GBS and CE would facilitate a seamless transition to a more efficient chemistry, while ensuring that research based on CE panels could continue. Here, we explore the feasibility of converting a legacy panel of 15 microsatellites developed for muskellunge ( Esox masquinongy ) from CE to GBS chemistry. Muskellunge are an important sportfish in the Great Lakes region, and the existing microsatellite panel has been used to genotype thousands of samples to develop a region-wide baseline of genetic structure. We successfully converted all 15 microsatellites to GBS chemistry. GBS produced high genotyping rates (98%) and had high concordance with CE microsatellite genotypes (99%). Conversion to GBS required redesign of some primers and pairs to shorten amplicon length and adjust melting temperatures, optimization of primer concentrations, and comparisons with CE genotypes to optimize GBS genotyping parameters; however, none of these steps were especially onerous. Our results demonstrate that it is highly feasible to convert legacy CE panels to GBS, ensuring seamless continuation of important, often long-term research.

Conservation Genetics Resources↗

USGS2020

A GT-seq panel for walleye (Sander vitreus) provides important insights for efficient development and implementation of amplicon panels in non-model organisms

Targeted amplicon sequencing methods, such as genotyping-in-thousands by sequencing (GT-seq), facilitate rapid, accurate, and cost-effective analysis of hundreds of genetic loci in thousands of individuals. Development of GT-seq panels is nontrivial, but studies describing trade-offs associated with different steps of GT-seq panel development are rare. Here, we construct a dual-purpose GT-seq panel for walleye ( Sander vitreus ), discuss trade-offs associated with different development and genotyping approaches, and provide suggestions for researchers constructing their own GT-seq panels. Our GT-seq panel was developed using an ascertainment set consisting of restriction site-associated DNA data from 954 individuals sampled from 23 populations in Minnesota and Wisconsin, USA. We conducted simulations to test the utility of all loci for parentage analysis and genetic stock identification and designed 600 primer pairs to maximize joint accuracy for these analyses. We then performed three rounds of primer optimization to remove loci that overamplified and our final panel consisted of 436 loci. We also explored different approaches for DNA extraction, multiplexed polymerase chain reaction (PCR) amplification, and cleanup steps during the GT-seq process and discovered the following: (i) inexpensive Chelex extractions performed well for genotyping; (ii) the exonuclease I and shrimp alkaline phosphatase (ExoSAP) procedure included in some current protocols did not improve results substantially and was probably unnecessary; and (iii) it was possible to PCR amplify panels separately and combine them prior to adapter ligation. Well-optimized GT-seq panels are valuable resources for conservation genetics and our findings and suggestions should aid in their construction in myriad taxa.

Minnesota, Wisconsin↗