Geology topics

Gordon Luikart

Publications and source records attributed to Gordon Luikart.

At least 19 recordsLinked to original sources

USGS2026

Invasive hybridization has unpredicted and variable effects on trout survival in contrasting environments

Invasive hybridization between native and introduced species is widespread, especially in fishes, yet its effects on fitness-related traits across environments remain poorly understood. We combined individual genetic admixture estimates with capture–recapture data to quantify how hybridization between native Westslope Cutthroat Trout ( Oncorhynchus lewisi ) and invasive Rainbow Trout ( Oncorhynchus mykiss ) influences survival. We measured individual survival of 5186 trout across three populations in contrasting environments. Non-native admixture significantly affected survival in two populations, with positive effects during summer and negative effects during winter. Prior research has shown hybridization increases with stream temperature; however, survival patterns did not follow this trend. In a warmer stream, native trout in all size-classes had ≥20% higher annual survival than hybrids, whereas in a cooler stream, juvenile native trout had ≥20% lower survival than hybrids. These findings indicate that hybridization effects on survival are complex and vary among populations, environments, and size-classes. Landscape patterns of hybridization may therefore not reflect local survival (or fitness) outcomes, emphasizing that measures fitness-related traits across populations and environments could elucidate the eco-evolutionary consequences of invasive hybridization.

Canadian Journal of Fisheries and Aquatic Sciences↗

USGS2024

How, what, and where you sample environmental DNA affects diversity estimates and species detection

Environmental DNA (eDNA) is a complex mixture of DNA, varying in particle sizes and distributed heterogeneously in aquatic systems. Optimizing eDNA sampling is crucial for maximizing species detection, particularly in high-risk scenarios like invasive species management. In this study, we compare two eDNA sampling methods - namely tow net and grab sample, where the tow nets process large volumes of water (3500–7000 L) through a 64 μm pore size and the grab samples process 1 L sample at a single point through 0.45–1.2 μm pore size membranes. We compared these methods to ascertain what most influences (1) the detection of invasive species ( Dreissena mussels and Burmese pythons) using qPCR or ddPCR and (2) total diversity monitoring of metazoan, protist, and fungi community using a COI marker and plant communities using the ITS marker. Sampling was conducted across a wide geography and diverse aquatic environments in Minnesota and Florida, USA, and Switzerland. The tow net samples had significantly higher eDNA yield compared to grab samples; however, they exhibited equal or lower alpha diversity of OTUs (Operational Taxonomic Units). The two sampling methods measured different beta diversity of communities detected with the COI marker across all three regions, highlighting the impact of the sampling method on the diversity of eDNA captured. In comparison, the beta diversity of plant eDNA was less impacted by the sampling method. We found no clear difference in detection for the invasive species targets based on the eDNA sampling method. These results underscore the need for pilot studies before conducting biodiversity inventory and monitoring, and a need for a greater understanding of not just how much, but also what, eDNA is captured depending on method choice, considering both spatial and particle size heterogeneity.

Florida, Minnesota↗

USGS2024

Local environments, not invasive hybridization, influence cardiac performance of native trout under acute thermal stress

Climate-induced expansion of invasive hybridization (breeding between invasive and native species) poses a significant threat to the persistence of many native species worldwide. In the northern U.S. Rocky Mountains, hybridization between native cutthroat trout and non-native rainbow trout has increased in recent decades due, in part, to climate-driven increases in water temperature. It has been postulated that invasive hybridization may enhance physiological tolerance to climate-induced thermal stress because laboratory studies indicate that rainbow trout have a higher thermal tolerance than cutthroat trout. Here, we assessed whether invasive hybridization improves cardiac performance response to acute water temperature stress of native wild trout populations. We collected trout from four streams with a wide range of non-native admixture among individuals and with different temperature and streamflow regimes in the upper Flathead River drainage, USA. We measured individual cardiac performance (maximum heart rate, “MaxHR”, and temperature at arrhythmia, “ArrTemp”) during laboratory trials with increasing water temperatures (10–28°C). Across the study populations, we observed substantial variation in cardiac performance of individual trout when exposed to thermal stress. Notably, we found significant differences in the cardiac response to thermal regimes among native cutthroat trout populations, suggesting the importance of genotype-by-environment interactions in shaping the physiological performance of native cutthroat trout. However, rainbow trout admixture had no significant effect on cardiac performance (MaxHR and ArrTemp) within any of the three populations. Our results indicate that invasive hybridization with a warmer-adapted species does not enhance the cardiac performance of native trout under warming conditions. Maintaining numerous populations across thermally and hydrologically diverse stream environments will be crucial for native trout to adapt and persist in a warming climate.

Montana↗

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, ↗

USGS2022

Environmental DNA methods for ecological monitoring and biodiversity assessment in estuaries

Environmental DNA (eDNA) detection methods can complement traditional biomonitoring to yield new ecological insights in aquatic systems. However, the conceptual and methodological frameworks for aquatic eDNA detection and interpretation were developed primarily in freshwater environments and have not been well established for estuaries and marine environments that are by nature dynamic, turbid, and hydrologically complex. Environmental context and species life history are critical for successful application of eDNA methods, and the challenges associated with eDNA detection in estuaries were the subject of a symposium held at the University of California Davis on January 29, 2020 ( https://marinescience.ucdavis.edu/engagement/past-events/edna ). Here, we elaborate upon topics addressed in the symposium to evaluate eDNA methods in the context of monitoring and biodiversity studies in estuaries. We first provide a concise overview of eDNA science and methods, and then examine the San Francisco Estuary (SFE) as a case study to illustrate how eDNA detection can complement traditional monitoring programs and provide regional guidance on future potential eDNA applications. Additionally, we offer recommendations for enhancing communication between eDNA scientists and natural resource managers, which is essential for integrating eDNA methods into existing monitoring programs. Our intent is to create a resource that is accessible to those outside the field of eDNA, especially managers, without oversimplifying the challenges or advantages of these methods.

Estuaries and Coasts↗

USGS2022

A framework to integrate innovations in invasion science for proactive management

Invasive alien species (IAS) are a rising threat to biodiversity, national security, and regional economies, with impacts in the hundreds of billions of U.S. dollars annually. Proactive or predictive approaches guided by scientific knowledge are essential to keeping pace with growing impacts of invasions under climate change. Although the rapid development of diverse technologies and approaches has produced tools with the potential to greatly accelerate invasion research and management, innovation has far outpaced implementation and coordination. Technological and methodological syntheses are urgently needed to close the growing implementation gap and facilitate interdisciplinary collaboration and synergy among evolving disciplines. A broad review is necessary to demonstrate the utility and relevance of work in diverse fields to generate actionable science for the ongoing invasion crisis. Here, we review such advances in relevant fields including remote sensing, epidemiology, big data analytics, environmental DNA (eDNA) sampling, genomics, and others, and present a generalized framework for distilling existing and emerging data into products for proactive IAS research and management. This integrated workflow provides a pathway for scientists and practitioners in diverse disciplines to contribute to applied invasion biology in a coordinated, synergistic, and scalable manner.

Biological Reviews↗

USGS2021

Testing a generalizable machine learning workflow for aquatic invasive species on Rainbow Trout (Oncorhynchus mykiss) in northwest Montana

Biological invasions are accelerating worldwide, causing major ecological and economic impacts in aquatic ecosystems. The urgent decision-making needs of invasive species managers can be better met by the integration of biodiversity big data with large-domain models and data-driven products. Remotely sensed data products can be combined with existing invasive species occurrence data via machine learning models to provide the proactive spatial risk analysis necessary for implementing coordinated and agile management paradigms across large scales. We present a workflow that generates rapid spatial risk assessments on aquatic invasive species using occurrence data, spatially explicit environmental data, and an ensemble approach to species distribution modeling using five machine learning algorithms. For proof of concept and validation, we tested this workflow using extensive spatial and temporal hybridization and occurrence data from a well-studied, ongoing, and climate-driven species invasion in the upper Flathead River system in northwestern Montana, USA. Rainbow Trout (RBT; Oncorhynchus mykiss), an introduced species in the Flathead River basin, compete and readily hybridize with native Westslope Cutthroat Trout (WCT; O. clarkii lewisii), and the spread of RBT individuals and their alleles has been tracked for decades. We used remotely sensed and other geospatial data as key environmental predictors for projecting resultant habitat suitability to geographic space. The ensemble modeling technique yielded high accuracy predictions relative to 30-fold cross-validated datasets (87% 30-fold cross-validated accuracy score). Both top predictors and model performance relative to these predictors matched current understanding of the drivers of RBT invasion and habitat suitability, indicating that temperature is a major factor influencing the spread of invasive RBT and hybridization with native WCT. The congruence between more time-consuming modeling approaches and our rapid machine-learning approach suggest that this workflow could be applied more broadly to provide data-driven management information for early detection of potential invaders.

Alberta, British Columbia, Montana↗

USGS2021

A new approach to evaluate and reduce uncertainty of model-based biodiversity projections for conservation policy formulation

Biodiversity projections with uncertainty estimates under different climate, land-use, and policy scenarios are essential to setting and achieving international targets to mitigate biodiversity loss. Evaluating and improving biodiversity predictions to better inform policy decisions remains a central conservation goal and challenge. A comprehensive strategy to evaluate and reduce uncertainty of model outputs against observed measurements and multiple models would help to produce more robust biodiversity predictions. We propose an approach that integrates biodiversity models and emerging remote sensing and in-situ data streams to evaluate and reduce uncertainty with the goal of improving policy-relevant biodiversity predictions. In this article, we describe a multivariate approach to directly and indirectly evaluate and constrain model uncertainty, demonstrate a proof of concept of this approach, embed the concept within the broader context of model evaluation and scenario analysis for conservation policy, and highlight lessons from other modeling communities.

BioScience↗

USGS2021

Opportunities and challenges of macrogenetic studies

The rapidly emerging field of macrogenetics focuses on analysing publicly accessible genetic datasets from thousands of species to explore large-scale patterns and predictors of intraspecific genetic variation. Facilitated by advances in evolutionary biology, technology, data infrastructure, statistics and open science, macrogenetics addresses core evolutionary hypotheses (such as disentangling environmental and life-history effects on genetic variation) with a global focus. Yet, there are important, often overlooked, limitations to this approach and best practices need to be considered and adopted if macrogenetics is to continue its exciting trajectory and reach its full potential in fields such as biodiversity monitoring and conservation. Here, we review the history of this rapidly growing field, highlight knowledge gaps and future directions, and provide guidelines for further research.

Nature Reviews Genetics↗

USGS2021

Macrogenetic studies must not ignore limitations of genetic markers and scale

Millette et al . (Ecology Letters, 2020, 23:55–67) reported no consistent worldwide anthropogenic effects on animal genetic diversity using repurposed mitochondrial DNA sequences. We reexamine data from this study, describe genetic marker and scale limitations which might lead to misinterpretations with conservation implications, and provide advice to improve future macrogenetic studies.

Ecology Letters↗

USGS2020

Detecting population declines via monitoring the effective number of breeders (Nb)

Estimating the effective population size and effective number of breeders per year ( N b ) can facilitate early detection of population declines. We used computer simulations to quantify bias and precision of the one-sample LDNe estimator of N b in age-structured populations using a range of published species life history types, sample sizes, and DNA markers. N b estimates were biased by ~5%–10% when using SNPs or microsatellites in species ranging from fishes to mosquitoes, frogs, and seaweed. The bias (high or low) was similar for different life history types within a species suggesting that life history variation in populations will not influence N b estimation. Precision was higher for 100 SNPs ( H ≈ 0.30) than for 15 microsatellites ( H ≈ 0.70). Confidence intervals (CIs) were occasionally too narrow, and biased high when N b was small ( N b < 50); however, the magnitude of bias would unlikely influence management decisions. The CIs (from LDNe ) were sufficiently narrow to achieve high statistical power (≥0.80) to reject the null hypothesis that N b = 50 when the true N b = 30 and when sampling 50 individuals and 200 SNPs. Similarly, CIs were sufficiently narrow to reject N b = 500 when the true N b = 400 and when sampling 200 individuals and 5,000 loci. Finally, we present a linear regression method that provides high power to detect a decline in N b when sampling at least five consecutive cohorts. This study provides guidelines and tools to simulate and estimate N b for age structured populations ( https://github.com/popgengui/agestrucnb/ ), which should help biologists develop sensitive monitoring programmes for early detection of changes in N b and population declines.

Molecular Ecology Resources↗

USGS2020

Hybridization alters growth and migratory life-history expression of native trout

Human-mediated hybridization threatens many native species, but the effects of introgressive hybridization on life-history expression are rarely quantified, especially in vertebrates. We quantified the effects of non-native rainbow trout admixture on important life-history traits including growth and partial migration behavior in three populations of westslope cutthroat trout over five years. Rainbow trout admixture was associated with increased summer growth rates in all populations and decreased spring growth rates in two populations with cooler spring temperatures. These results indicate that non-native admixture may increase growth under warmer conditions, but cutthroat trout have higher growth rates during cooler periods. Non-native admixture consistently increased expression of migratory behavior, suggesting that there is a genomic basis for life-history differences between these species. Our results show that effects of interspecific hybridization on fitness traits can be the product of genotype-by-environment interactions even when there are minor differences in environmental optima between hybridizing species. These results also indicate that while environmentally mediated traits like growth may play a role in population-level consequences of admixture, strong genetic influences on migratory life-history differences between these species likely explains the continued spread of non-native hybridization at the landscape-level, despite selection against hybrids at the population-level.

Montana↗

USGS2020

Are environmental DNA methods ready for aquatic invasive species management?

Multiple studies have demonstrated environmental (e)DNA detections of rare, invasive species. However, invasive species managers struggle with using eDNA results because detections might not indicate species presence. We evaluated if eDNA methods have matured to a point where they can be widely applied to aquatic invasive species management. We found that eDNA methods meet legal standards for being admissible as evidence in most courts, suggesting that eDNA method reliability is not the problem. Rather, we suggest that the interface between results and management needs attention since there are few tools for integrating uncertainty into decision-making. Solutions include decision support trees based on molecular best practices that integrate the temporal and spatial trends in eDNA positives relative to human risk tolerance.

Trends in Ecology and Evolution↗

USGS2019

Improved detection of rare, endangered and invasive trout using a new large-volume sampling method for eDNA capture

Environmental DNA (eDNA) detection probability increases with volume of water sampled. Common approaches for collecting eDNA samples often require many samples since these approaches usually use fine filters, which restrict the volume of water that can be sampled. An alternative to collecting many, small volume water samples using fine filters may be to collect fewer, large volume water samples using coarse filters that do not clog as rapidly. We used mesocosm experiments and field evaluations to compare coarse filter‐large water volume samples (hereafter large volume filter samples) versus fine filter‐small water volume samples (hereafter small volume filter samples) for detection and quantification of rainbow trout ( Oncorhynchus mykiss ) and bull trout ( Salvelinus confluentus ) DNA. We found that large volume filter sampling can be an effective approach for detecting DNA of low‐density target taxa. In mesocosm experiments, large‐volume and small‐volume water samples detected similar quantities of rainbow trout DNA. In the field, large volume samples more frequently detected bull trout DNA, had higher bull trout DNA copy number, and higher total DNA concentrations than small volume samples. However, sampling higher water volumes increased the potential for PCR inhibition so the DNA workflow had to be altered for large volume samples. Combining larger water volume samples with other strategies, like increasing PCR sensitivity and the number of PCR replicates, will improve detection of rare species, which is crucial for advancing conservation and ecological understanding.

Montana↗

USGS2019

Challenges in Columbia River fisheries conservation: Response to Duda et al.

The salmonid fisheries of the Columbia River Basin (CRB) have enormous socioeconomic, cultural, and ecological importance to numerous diverse stakeholders (e.g., state, federal, tribal, nonprofit), and there are a wide array of opinions and perspectives on how these fisheries should be managed. Although we appreciate Duda et al.’s commentary, it offers only one perspective of many in this context. The objective of our paper (Hand et al. 2018) was to provide justification for “the importance of social–ecological perspectives when communicating conservation values and goals, and the role of independent science in guiding management policy and practice for salmonids in the CRB”. However, we did not intend to strictly advocate for a single course of action, and the available space within our paper’s Panel 1 limited us from engaging in a thorough ecological debate.

Frontiers in Ecology and the Environment↗

USGS2018

A social–ecological perspective for riverscape management in the Columbia River Basin

Riverscapes are complex, landscape-scale mosaics of connected river and stream habitats embedded in diverse ecological and socioeconomic settings. Social–ecological interactions among stakeholders often complicate natural-resource conservation and management of riverscapes. The management challenges posed by the conservation and restoration of wild salmonid populations in the Columbia River Basin (CRB) of western North America are one such example. Because of their ecological, cultural, and socioeconomic importance, salmonids present a complex management landscape due to interacting environmental factors (eg climate change, invasive species) as well as socioeconomic and political factors (eg dams, hatcheries, land-use change, transboundary agreements). Many of the problems in the CRB can be linked to social–ecological interactions occurring within integrated ecological, human–social, and regional–climatic spheres. Future management and conservation of salmonid populations therefore depends on how well the issues are understood and whether they can be resolved through effective communication and collaboration among ecologists, social scientists, stakeholders, and policy makers.

Columbia River Basin↗

USGS2017

Demographic modelling reveals a history of divergence with gene flow for a glacially tied stonefly in a changing post-Pleistocene landscape

Aim Climate warming is causing extensive loss of glaciers in mountainous regions, yet our understanding of how glacial recession influences evolutionary processes and genetic diversity is limited. Linking genetic structure with the influences shaping it can improve understanding of how species respond to environmental change. Here, we used genome-scale data and demographic modelling to resolve the evolutionary history of Lednia tumana , a rare, aquatic insect endemic to alpine streams. We also employed a range of widely used data filtering approaches to quantify how they influenced population structure results. Location Alpine streams in the Rocky Mountains of Glacier National Park, Montana, USA. Taxon Lednia tumana , a stonefly (Order Plecoptera) in the family Nemouridae. Methods We generated single nucleotide polymorphism data through restriction-site associated DNA sequencing to assess contemporary patterns of genetic structure for 11 L. tumana populations. Using identified clusters, we assessed demographic history through model selection and parameter estimation in a coalescent framework. During population structure analyses, we filtered our data to assess the influence of singletons, missing data and total number of markers on results. Results Contemporary patterns of population structure indicate that L. tumana exhibits a pattern of isolation-by-distance among populations within three genetic clusters that align with geography. Mean pairwise genetic differentiation ( F ST ) among populations was 0.033. Coalescent-based demographic modelling supported divergence with gene flow among genetic clusters since the end of the Pleistocene (~13-17 kya), likely reflecting the south-to-north recession of ice sheets that accumulated during the Wisconsin glaciation. Main conclusions We identified a link between glacial retreat, evolutionary history and patterns of genetic diversity for a range-restricted stonefly imperiled by climate change. This finding included a history of divergence with gene flow, an unexpected conclusion for a mountaintop species. Beyond L. tumana , this study demonstrates the complexity of assessing genetic structure for weakly differentiated species, shows the degree to which rare alleles and missing data may influence results, and highlights the usefulness of genome-scale data to extend population genetic inquiry in non-model species.

Montana↗

USGS2017

No evidence for ecological segregation protecting native trout from invasive hybridization

We appreciate the comments of Young et al. (2017) on our recent paper (Muhlfeld et al., 2017) concerning spatiotemporal dynamics of hybridization between native westslope cutthroat trout ( Oncorhynchus clarkii lewisi ; WCT) and introduced coastal rainbow trout ( Oncorhynchus mykiss irideus ; RBT). Nevertheless, we believe there is no evidence for “ecological segregation” protecting WCT from hybridization with invasive RBT. Here we consider their three major arguments for ecological segregation and find their conclusions invalid.

Global Change Biology↗