Geology topics

Patrick W. DeHaan

Publications and source records attributed to Patrick W. DeHaan.

5 recordsLinked to original sources

USGS2025

Placing environmental DNA monitoring for new detections into perspective: Fishes in the Milwaukee River, Wisconsin

Invasive species management frameworks, such as the early detection of and rapid response to invasive species, use monitoring programs to detect new species occurrences. Resource managers use environmental DNA (eDNA) as one tool for these monitoring programs. An eDNA detection in a new location may lack perspective for resource managers and researchers because of the rarity of potential invaders and the randomness in their dispersal and detection. An example monitoring program is the eDNA-based sampling approach used by the U.S. Fish and Wildlife Service for bigheaded carps Hypophthalmichthys spp. in the upper Mississippi River and Great Lakes Basins that collects hundreds of water samples per event. The U.S. Fish and Wildlife Service detected a single positive sample for Bighead Carp Hypophthalmichthys nobilis during the spring 2021 sampling event in the Kinnickinnic River within the Milwaukee River Basin, and detected a second single positive sample for bigheaded carps during the fall 2021 sampling event in the Milwaukee River. The U.S. Fish and Wildlife Service did not detect any bigheaded carps in previous years (2015 to 2020) or in either the spring or fall 2022 sampling events. These detections lacked perspective, such as detection numbers for other species. We reanalyzed the 2021 and 2022 samples for four existing species of fish: two fairly common species (Common Carp Cyprinus carpio and Gizzard Shad Dorosoma cepedianum ) and two fairly rare species (Burbot Lota lota and Grass Carp Ctenopharyngodon idella ). We detected Common Carp during all four sampling events, Gizzard Shad during three of four sampling events, and Burbot and Grass Carp during two of four sampling events. These results demonstrated that current sampling efforts could detect other species, and bigheaded carp eDNA was not common in the Milwaukee River compared to these species. More specifically, this finding indicates bigheaded carp eDNA detections are as rare as, or rarer than, Grass Carp eDNA detections, a recent invader to the basin. Our findings also demonstrated how reanalyzing eDNA samples after positive detections for targeted species can help managers understand the context of the detections and provide perspective for the relative abundance of the targeted species. Additionally, our results highlight the importance of completing long-term eDNA-based monitoring rather than a single sampling or inventory event. These detections may have been missed in a single year or sampling event, whereas a multiyear monitoring program provides an opportunity to observe trends through time.

Wisconsin↗

USGS2025

Spatial variation of eDNA detection across an invasion gradient for invasive species monitoring programs

Spatial and temporal distribution data provide critical information for invasive species management. For example, distribution data can help managers with early detections and guiding other response actions. Environmental DNA (eDNA)-based sampling exists as one tool for monitoring invasive species. As part of bigheaded carp Hypophthalmichthys spp. monitoring efforts in the Illinois River, USA, we compared eDNA-based sampling results at multiple habitats across an invasion gradient in 2015. Greater densities of carp occurred downriver in the Illinois River and lower densities occurred upriver. We sampled from five locations along this gradient and from three habitat types (backwater, main channel, and shoreline) within each location. We sampled each location in April and June. A priori , we hypothesized that more eDNA detections would occur downriver, where higher densities of carp occur; that more eDNA detections would occur in backwater habitats compared to areas of the river with more fish movement; and that more eDNA detections would occur in April, because bigheaded carps are thought to use our sampling areas more during the spring. We compared the proportion of samples positive across this gradient, the habitat type, and the two sampling time periods. The most downriver location had the highest proportion of samples with eDNA detections, the backwater habitats had the highest proportion of samples with eDNA detections, and April had more positive detections than June. Our results highlight the importance of sampling across multiple habitat types and across time to gain a clear understanding of distribution when using eDNA-based sampling. Thus, being cognizant of the interactions between seasonal habitat use and eDNA-based detections is important for managers who rely upon eDNA-based monitoring.

Illinois↗

USGS2022

Rapid SNP genotyping, sex identification, and hybrid-detection in threatened bull trout

We developed new bull trout genetic markers using Restriction-site Associated DNA sequencing (RAD-seq) to improve our ability to address questions important for their conservation and management. Samples from across the species range were sequenced and 5020 high quality single nucleotide polymorphism (SNP) loci were discovered, including hundreds with high heterozygosity ( H > 0.30). We developed 63 high-heterozygosity bull trout polymorphic SNPs and one sex-identification SNP and tested them on range-wide samples. In addition, we tested previously published SNP assays including 11 species-diagnostic SNPs differentiating bull trout from brook trout and 3 brook trout variable SNPs on a broad set of range-wide samples. Genotypes from the sex-identification SNP showed 95% agreement with the field sex identification across 113 samples. The eleven species-diagnostic loci reliably discriminated between known brook trout, bull trout, and F 1 hybrid control samples. These SNP assays will facilitate genotyping of partially degraded museum fin clips, and tissues with low DNA content such as scales and otoliths. Finally, these loci will allow rapid genotyping for improved resolution of bull trout population structure, sex ratios, movement patterns, and introgressive hybridization with non-native brook trout for a wide range of management questions.

British Columbia, Idaho, Montana, Nevada, Oregon, ↗

USGS2019

Simulating demography, genetics, and spatially explicit processes to inform reintroduction of a threatened char

The success of species reintroductions can depend on a combination of environmental, demographic, and genetic factors. Although the importance of these factors in the success of reintroductions is well‐accepted, they are typically evaluated independently, which can miss important interactions. For species that persist in metapopulations, movement through and interaction with the landscape is predicted to be a vital component of persistence. Simulation‐based approaches are a promising technique for evaluating the independent and combined effects of these factors on the outcome of various reintroduction and associated management actions. We report results from a simulation study of bull trout ( Salvelinus confluentus ) reintroduction to three watersheds of the Pend Oreille River system in northeastern Washington State, USA. We used an individual‐based, spatially explicit simulation model to evaluate how reintroduction strategies, life history variation, and riverscape structure (e.g., network topology) interact to influence the demographic and genetic characteristics of reintroduced bull trout populations in three watersheds. Simulation scenarios included a range of initial genetic stocks (informed by empirical bull trout genetic data), variation in migratory tendency and life history, and two landscape connectivity alternatives representing a connected network (isolation‐by‐distance) and a fragmented network (isolation‐by‐barrier, using the known existing barriers). A novel feature of these simulations was the ability to consider the interaction of both demographic and genetic (i.e., demogenetic) factors in riverscapes with implicit asymmetric movement probabilities across the barriers. We found that connectivity (presence or absence of barriers) had the largest effect on demographic and genetic outcomes over 200 yr, with a greater effect than both initial genetic diversity and life history variation. We also identified regions of the study system in which bull trout populations persisted across a wide range of demographic, life history, and environmental connectivity parameters. Finally, we found no evidence that initial neutral genetic diversity influenced genetic diversity and structure after 200 yr; instead, genetic drift due to stray rate and population isolation dominated and erased any initial differences in genetic diversity. Our results highlight the utility of spatially explicit demogenetic approaches in exploring and understanding population dynamics—and their implications for management strategies—in fresh waters.

Washington↗

USGS2015

Genetic diversity is related to climatic variation and vulnerability in threatened bull trout

Understanding how climatic variation influences ecological and evolutionary processes is crucial for informed conservation decision-making. Nevertheless, few studies have measured how climatic variation influences genetic diversity within populations or how genetic diversity is distributed across space relative to future climatic stress. Here, we tested whether patterns of genetic diversity (allelic richness) were related to climatic variation and habitat features in 130 bull trout ( Salvelinus confluentus ) populations from 24 watersheds (i.e., ~4–7th order river subbasins) across the Columbia River Basin, USA. We then determined whether bull trout genetic diversity was related to climate vulnerability at the watershed scale, which we quantified on the basis of exposure to future climatic conditions (projected scenarios for the 2040s) and existing habitat complexity. We found a strong gradient in genetic diversity in bull trout populations across the Columbia River Basin, where populations located in the most upstream headwater areas had the greatest genetic diversity. After accounting for spatial patterns with linear mixed models, allelic richness in bull trout populations was positively related to habitat patch size and complexity, and negatively related to maximum summer temperature and the frequency of winter flooding. These relationships strongly suggest that climatic variation influences evolutionary processes in this threatened species and that genetic diversity will likely decrease due to future climate change. Vulnerability at a watershed scale was negatively correlated with average genetic diversity ( r = −0.77; P < 0.001); watersheds containing populations with lower average genetic diversity generally had the lowest habitat complexity, warmest stream temperatures, and greatest frequency of winter flooding. Together, these findings have important conservation implications for bull trout and other imperiled species. Genetic diversity is already depressed where climatic vulnerability is highest; it will likely erode further in the very places where diversity may be most needed for future persistence.

Global Change Biology↗