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Trevor J. Krabbenhoft

Publications and source records attributed to Trevor J. Krabbenhoft.

13 recordsLinked to original sources
USGS2026

A genomic tool to tackle cryptic diversity demonstrates the potential for off-target use of GT-seq panels

A comprehensive understanding of life history is vital to successful species conservation and management. When different life history stages are accompanied by considerable morphological or cryptic variation, such as the egg and larval phases exhibited by most fishes, genomic tools are essential for identifying species so that early-life ecology questions can be studied. Genotyping-in-thousands by sequencing (GT-seq) has recently emerged as a targeted and efficient approach for species identification. We leveraged existing genomic and transcriptomic data to develop a GT-seq panel capable of differentiating the members of the Coregonus artedi complex, a radiation of salmonids in the Laurentian Great Lakes whose members are indistinguishable with mitochondrial DNA barcoding loci and are the focus of bi-national conservation initiatives. Our panel of 494 loci was able to assign fishes in the C. artedi complex to species and lake. We examined cross-amplification in other coregonines with overlapping distributions and found that congeneric Lake Whitefish ( C. clupeaformis ) cross-amplified at 94% of loci and confamilial Round and Pygmy Whitefish ( Prosopium spp.) cross-amplified at 42% and 38% of loci, respectively. We adapted bioinformatic probes to account for Prosopium -specific variants including 22 new SNPs and developed a whitelist of 428 SNPs capable of distinguishing these whitefishes. Finally, we demonstrated performance by identifying 3,066 coregonine larvae and juveniles collected in spring 2019-2021 from Lake Superior. These results hold promise for future insights into the species-specific ecology of early life coregonines and demonstrate the flexibility of GT-seq panels, which may cross-amplify hundreds of informative genome-wide loci in related taxa.

BioRxiv↗
USGS2025

Speciation genomics in the tiger whiptail lizards ( Aspidoscelis tigris complex)

The transition from small genetic to genome-scale datasets for studying biodiversity has revealed that genetic exchange through introgressive hybridization is a widespread phenomenon in nature. Despite this, a lack of high-quality reference genomes for most non-model species limits our understanding of the impact of this process for many taxonomic groups. This restricts the range of insights that genomic tools can provide for conservation biologists, who often hope to employ genomic datasets to accurately identify historically isolated lineages to protect and to predict their evolutionary fate in the face of environmental change. Tiger whiptail lizards ( Aspidoscelis tigris complex) are an abundant and important ecological component of ecosystems across the southwestern United States. In this study, we assembled and annotated a chromosome-level reference genome for A. t. stejnegeri from coastal California. We then used this reference genome to reconstruct patterns of speciation and admixture within the larger species complex, finding evidence that gene flow is widespread both geographically and across the genome.

northern Mexico, southwestern United States↗
USGS2024

Origin of the Laurentian Great Lakes fish fauna through upward adaptive radiation cascade prior to the Last Glacial Maximum

The evolutionary histories of adaptive radiations can be marked by dramatic demographic fluctuations. However, the demographic histories of ecologically-linked co-diversifying lineages remain understudied. The Laurentian Great Lakes provide a unique system of two such radiations that are dispersed across depth gradients with a predator-prey relationship. We show that the North American Coregonus species complex (“ciscoes”) radiated rapidly prior to the Last Glacial Maximum (80–90 kya), a globally warm period, followed by rapid expansion in population size. Similar patterns of demographic expansion were observed in the predator species, Lake Charr ( Salvelinus namaycush ), following a brief time lag, which we hypothesize was driven by predator-prey dynamics. Diversification of prey into deep water created ecological opportunities for the predators, facilitating their demographic expansion, which is consistent with an upward adaptive radiation cascade. This study provides a new timeline and environmental context for the origin of the Laurentian Great Lakes fish fauna, and firmly establishes this system as drivers of ecological diversification and rapid speciation through cyclical glaciation.

Communications Biology↗
USGS2023

Climate impacts to inland fishes: Shifting research topics over time

Climate change remains a primary threat to inland fishes and fisheries. Using topic modeling to examine trends and relationships across 36 years of scientific literature on documented and projected climate impacts to inland fish, we identify ten representative topics within this body of literature: assemblages, climate scenarios, distribution, climate drivers, population growth, invasive species, populations, phenology, physiology, and reproduction. These topics are largely similar to the output from artificial intelligence application (i.e., ChatGPT) search prompts, but with some key differences. The field of climate impacts on fish has seen dramatic growth since the mid-2000s with increasing popularity of topics related to drivers, assemblages, and phenology. The topics were generally well-dispersed with little overlap of common words, apart from phenology and reproduction which were closely clustered. Pairwise comparisons between topics revealed potential gaps in the literature including between reproduction and distribution and between physiology and phenology. A better understanding of these relationships can help capitalize on existing literature to inform conservation and sustainable management of inland fishes with a changing climate.

PLOS Climate↗
USGS2022

Concordant patterns of morphological, stable isotope, and genetic variation in a recent ecological radiation (Salmonidae: Coregonus spp.)

Groups of sympatric taxa with low interspecific genetic differentiation, but considerable ecological differences, offer great opportunities to study the dynamics of divergence and speciation. This is the case of ciscoes ( Coregonus spp.) in the Laurentian Great Lakes, which are characterized by a complex evolutionary history and are commonly described as having undergone an adaptive radiation. In this study, morphometrics, stable isotopes and transcriptome sequencing were used to study the relationships within the Coregonus artedi complex in western Lake Superior. We observed general concordance for morphological, ecological and genomic variation, but the last was more taxonomically informative as it showed less overlap among species in multivariate space. Low levels of genetic differentiation were observed between individuals morphologically identified as Coregonus hoyi and C. zenithicus , which could be evidence of incomplete lineage sorting or recent hybridization between the two groups. Transcriptome-based single nucleotide polymorphisms exhibited significant divergence for genes associated with vision, development, metabolism and immunity among species that occupy different habitats. This study highlights the importance of using an integrative approach when studying groups of taxa with a complex evolutionary history, as individual-level analyses of multiple independent data sets can provide a clearer picture of the patterns and processes associated with the origins of biodiversity.

Michigan, Minnesota, Ontario, Wisconsin↗
USGS2022

Reducing uncertainty in climate change responses of inland fishes: A decision-path approach

Climate change will continue to be an important consideration for conservation practitioners. However, uncertainty in identifying appropriate management strategies, particularly for understudied species and regions, constrains the implementation of science-based solutions and adaptation strategies. Here, we share a decision-path approach to reduce uncertainty in climate change responses of inland fishes to inform conservation and adaptation planning. With the Fish and Climate Change database (FiCli), a comprehensive, online, public database of peer-reviewed literature on documented and projected climate impacts to inland fishes, users can identify relevant studies and associated management recommendations via geographic regions, response types (i.e., fish assemblage dynamics, demographic, distributional, evolutionary, phenological), fish taxa, and traits (e.g., thermal guilds, feeding type, parental care, habitat type) and use a suite of summary tools to make more informed decisions. For both data-rich and data-poor scenarios, we demonstrate that this approach can reduce uncertainty in understanding climate change responses. Using thermal sensitivity as an example, we also establish the utility of FiCli database to address other user-defined, management-relevant questions via supplementary analyses. This decision-path approach can be applied to rapid assessments, management decisions, and policy development and may serve as a model for other conservation decision-making processes.

Conservation Science and Practice↗
USGS2021

Managing for RADical ecosystem change: Applying the Resist-Accept-Direct (RAD) framework

Ecosystem transformation involves the emergence of persistent ecological or social–ecological systems that diverge, dramatically and irreversibly, from prior ecosystem structure and function. Such transformations are occurring at increasing rates across the planet in response to changes in climate, land use, and other factors. Consequently, a dynamic view of ecosystem processes that accommodates rapid, irreversible change will be critical for effectively conserving fish, wildlife, and other natural resources, and maintaining ecosystem services. However, managing ecosystems toward states with novel structure and function is an inherently unpredictable and difficult task. Managers navigating ecosystem transformation can benefit from considering broader objectives, beyond a traditional focus on resisting ecosystem change, by also considering whether accepting inevitable change or directing it along some desirable pathway is more feasible (that is, practical and appropriate) under some circumstances (the RAD framework). By explicitly acknowledging transformation and implementing an iterative RAD approach, natural resource managers can be deliberate and strategic in addressing profound ecosystem change.

Frontiers in Ecology and the Environment↗
USGS2020

Nanopore amplicon sequencing reveals molecular convergence and local adaptation of rhodopsin in Great Lakes salmonids

Local adaptation can drive diversification of closely related species across environmental gradients and promote convergence of distantly related taxa that experience similar conditions. We examined a potential case of adaptation to novel visual environments in a species flock (Great Lakes salmonids, genus Coregonus ) using a new amplicon genotyping protocol on the Oxford Nanopore Flongle and MinION. We sequenced five visual opsin genes for individuals of C. artedi , C. hoyi , C. kiyi , and C. zenithicus. Comparisons revealed species-specific differences in a key spectral tuning amino acid in rhodopsin (Tyr261Phe substitution), suggesting local adaptation of C. kiyi to the blue-shifted depths of Lake Superior. Ancestral state reconstruction demonstrates that parallel evolution and “toggling” at this amino acid residue has occurred several times across the fish tree of life, resulting in identical changes to the visual systems of distantly related taxa across replicated environmental gradients. Our results suggest that ecological differences and local adaptation to distinct visual environments are strong drivers of both evolutionary parallelism and diversification.

Lake Superior↗
USGS2020

Responding to ecosystem transformation: Resist, accept, or direct?

Ecosystem transformation can be defined as the emergence of a self‐organizing, self‐sustaining, ecological or social–ecological system that deviates from prior ecosystem structure and function. These transformations are occurring across the globe; consequently, a static view of ecosystem processes is likely no longer sufficient for managing fish, wildlife, and other species. We present a framework that encompasses three strategies for fish and wildlife managers dealing with ecosystems vulnerable to transformation. Specifically, managers can resist change and strive to maintain existing ecosystem composition, structure, and function; accept transformation when it is not feasible to resist change or when changes are deemed socially acceptable; or direct change to a future ecosystem configuration that would yield desirable outcomes. Choice of a particular option likely hinges on anticipating future change, while also acknowledging that temporal and spatial scales, recent history and current state of the system, and magnitude of change can factor into the decision. This suite of management strategies can be implemented using a structured approach of learning and adapting as ecosystems change.

Fisheries↗
USGS2020

FiCli, the Fish and Climate Change Database, informs climate adaptation and management for freshwater fishes

Inland fishes provide important ecosystem services to communities worldwide and are especially vulnerable to the impacts of climate change. Fish respond to climate change in diverse and nuanced ways, which creates challenges for practitioners of fish conservation, climate change adaptation, and management. Although climate change is known to affect fish globally, a comprehensive online, public database of how climate change has impacted inland fishes worldwide and adaptation or management practices that may address these impacts does not exist. We conducted an extensive, systematic primary literature review to identify peer-reviewed journal publications describing projected and documented examples of climate change impacts on inland fishes. From this standardized Fi sh and Cli mate Change database, FiCli (pronounced fick-lee), researchers and managers can query fish families, species, response types, or geographic locations to obtain summary information on inland fish responses to climate change and recommended management actions. The FiCli database is updatable and provides access to comprehensive published information to inform inland fish conservation and adaptation planning in a changing climate.

Scientific Data↗
USGS2017

Global synthesis of the documented and projected effects of climate change on inland fishes

Although climate change is an important factor affecting inland fishes globally, a comprehensive review of how climate change has impacted and will continue to impact inland fishes worldwide does not currently exist. We conducted an extensive, systematic primary literature review to identify English-language, peer-reviewed journal publications with projected and documented examples of climate change impacts on inland fishes globally. Since the mid-1980s, scientists have projected the effects of climate change on inland fishes, and more recently, documentation of climate change impacts on inland fishes has increased. Of the thousands of title and abstracts reviewed, we selected 624 publications for a full text review: 63 of these publications documented an effect of climate change on inland fishes, while 116 publications projected inland fishes’ response to future climate change. Documented and projected impacts of climate change varied, but several trends emerged including differences between documented and projected impacts of climate change on salmonid abundance ( P = 0.0002). Salmonid abundance decreased in 89.5% of documented effects compared to 35.7% of projected effects, where variable effects were more commonly reported (64.3%). Studies focused on responses of salmonids (61% of total) to climate change in North America and Europe, highlighting major gaps in the literature for taxonomic groups and geographic focus. Elucidating global patterns and identifying knowledge gaps of climate change effects on inland fishes will help managers better anticipate local changes in fish populations and assemblages, resulting in better development of management plans, particularly in systems with little information on climate change effects on fish.

Reviews in Fish Biology and Fisheries↗
USGS2016

Climate change effects on North American inland fish populations and assemblages

Climate is a critical driver of many fish populations, assemblages, and aquatic communities. However, direct observational studies of climate change impacts on North American inland fishes are rare. In this synthesis, we (1) summarize climate trends that may influence North American inland fish populations and assemblages, (2) compile 31 peer-reviewed studies of documented climate change effects on North American inland fish populations and assemblages, and (3) highlight four case studies representing a variety of observed responses ranging from warmwater systems in the southwestern and southeastern United States to coldwater systems along the Pacific Coast and Canadian Shield. We conclude by identifying key data gaps and research needs to inform adaptive, ecosystem-based approaches to managing North American inland fishes and fisheries in a changing climate.

Fisheries↗