Cutthroat Trout: Evolutionary Biology and Taxonomy

2018 ◽  
Keyword(s):  
Classification System ◽  
Evolutionary Biology ◽  
Scientific Evidence ◽  
Molecular Genetic ◽  
Cutthroat Trout ◽  
Oncorhynchus Clarkii ◽  
Widespread Species ◽  
Geological Evidence ◽  
New Information ◽  
Western Division

<em>Abstract</em>.—Cutthroat Trout <em>Oncorhynchus clarkii </em>are currently considered a single, widespread species composed of many subspecies following the classification system proposed by Robert J. Behnke in 1979. More recently, molecular genetic and geological evidence has yielded results that are inconsistent with Behnke’s classification, which suggests that a re-evaluation of the existing phylogenetic tree is timely. Additionally, several varieties of Cutthroat Trout are either listed under the U.S. Endangered Species Act or are considered to be at risk by the states in which they reside, making it important that the classification and evolutionary relationships among Cutthroat Trout be based on the best available scientific evidence. In 2015, the Western Division of the American Fisheries Society convened a special workshop in which a panel of experts was asked to weigh carefully evidence on Cutthroat Trout phylogeny and classification, from the oldest published studies to the most recent and answer two questions: (1) does Behnke’s 14-subspecies classification remain scientifically tenable and defensible given all available evidence, and (2) if not, what taxonomic classification does satisfy this array of evidence? From new information, the panel concluded that the existing classification system is no longer supported by existing evidence; however, the panel was unable to reach consensus on what a new phylogeny and classification system should be. In the interim, we suggest that the four major evolutionary lineages of Cutthroat Trout be elevated to full species designation and that several uniquely identifiable evolutionary units receive additional investigation to elucidate additional evolutionary structure. This chapter provides the background and context for topics that are covered in the following chapters and suggests fruitful lines of investigation that should help resolve outstanding questions.

Cutthroat Trout: Evolutionary Biology and Taxonomy

2018 ◽  
Keyword(s):  
Evolutionary Biology ◽  
Cutthroat Trout ◽  
Westslope Cutthroat Trout ◽  
Oncorhynchus Clarkii ◽  
Coastal Cutthroat Trout ◽  
Lahontan Cutthroat Trout ◽  
Museum Samples ◽  
Yellowstone Cutthroat Trout ◽  
The 1960S

<em>Abstract</em>.—There has been considerable interest in the systematics and classification of Cutthroat Trout since the 1800s. Cutthroat Trout native to western North America (currently classified as <em>Oncorhynchus clarkii</em>) have historically been grouped or separated using many different classification schemes. Since the 1960s, Robert Behnke has been a leader in these efforts. Introductions of nonnative trout (other forms of Cutthroat Trout, and Rainbow Trout <em>O. mykiss</em>) have obscured some historical patterns of distribution and differentiation. Morphological and meristic analyses have often grouped the various forms of Cutthroat Trout together based on the shared presence of the “cutthroat mark,” high scale counts along the lateral line, and the presence of basibranchial teeth. Spotting patterns and counts of gill rakers and pyloric caeca have in some cases been helpful in differentiation of groups (e.g., Coastal Cutthroat Trout <em>O. c. clarkii</em>, Lahontan Cutthroat Trout <em>O. c. henshawi</em>, and Westslope Cutthroat Trout <em>O. c. lewisi</em>) currently classified as subspecies. The historical genetic methods of allozyme genotyping through protein electrophoresis and chromosome analyses were often helpful in differentiating the various subspecies of Cutthroat Trout. Allozyme genotyping allowed four major groups to be readily recognized (Coastal Cutthroat Trout, Westslope Cutthroat Trout, the Lahontan Cutthroat Trout subspecies complex, and Yellowstone Cutthroat Trout <em>O. c. bouvieri </em>subspecies complex) while chromosome analyses showed similarity between the Lahontan and Yellowstone Cutthroat trout subspecies complex trout (possibly reflecting shared ancestral type) and differentiated the Coastal and Westslope Cutthroat trouts from each other and those two groups. DNA results may yield higher resolution of evolutionary relationships of Cutthroat Trout and allow incorporation of ancient museum samples. Accurate resolution of taxonomic differences among various Cutthroat Trout lineages, and hybridization assessments, requires several approaches and will aid in conservation of these charismatic and increasingly rare native fishes.

Cutthroat Trout: Evolutionary Biology and Taxonomy

2018 ◽  
Keyword(s):  
Rainbow Trout ◽  
Rocky Mountains ◽  
Evolutionary Biology ◽  
Cutthroat Trout ◽  
Taxonomic Revision ◽  
River Basins ◽  
Evidence Based ◽  
Oncorhynchus Clarkii ◽  
Southern Rocky Mountains ◽  
Green Lineage

<em>Abstract</em>.—One objective of systematics is to recognize species in a manner that minimizes the disparity between species as real entities in nature and species as a Linnaean category. Reconciliation requires a conceptualization of species consistent with evolutionary processes that yields predictive delimitation criteria. Here we review the unified species concept (USC) and its associated delimitation criteria as a prelude to revising the taxonomy of Cutthroat Trout <em>Oncorhynchus clarkii</em>. Additionally, in the context of the conceptualizing species as a separately evolving metapopulation, we briefly review how climate change may have influenced the connectivity and isolation of Cutthroat Trout within and among river basins, with a focus mainly on the Cutthroat Trout of the Southern Rocky Mountains. We summarize evidence based on delimitation criteria that distinguishes Rainbow Trout <em>O. mykiss</em> and Cutthroat Trout, Gila Trout<em> O. gilae </em>and Rainbow Trout, and blue lineage and green lineage Cutthroat Trout from the Southern Rocky Mountains. We advocate adopting the USC as a guide for taxonomic revision of Cutthroat Trout, recommend eliminating subspecies as a valid taxonomic designation, and expect—based on our evaluation of three pairs of species—that the taxonomy of Cutthroat Trout will be revised in ways that elevate some recognized subspecies to species status.

Cutthroat Trout: Evolutionary Biology and Taxonomy

2018 ◽  
Keyword(s):  
Evolutionary Biology ◽  
Species Concept ◽  
Management Strategies ◽  
Cutthroat Trout ◽  
Ecological Processes ◽  
Oncorhynchus Clarkii ◽  
Voucher Specimens ◽  
Captive Propagation ◽  
Analytical Tools

<em>Abstract</em>.—The broad distribution and regional variation of Cutthroat Trout <em>Oncorhynchus clarkii </em>across western North America has led to considerable interest in the different forms from both scientific and recreational perspectives. This volume represents an attempt to describe this observed diversity with the most current information available and suggests a revised taxonomy for Cutthroat Trout. However, what is proposed in this volume will be subject to change or refinement as new techniques and analytical tools become available. In particular, remaining uncertainty would benefit from a comparison of all described lineages with a common set of morphological and genetic markers. A range-wide collection of voucher specimens will help to document variation in these characteristics, and we encourage field biologists to prioritize these collections. Future revisions will benefit from agreement on a species concept and explicitly state the assumptions of the chosen species concept. We encourage collaboration between managers and taxonomists to accurately delineate units of conservation that can be used by decision makers tasked with ensuring the long-term persistence of Cutthroat Trout lineages. The proposed taxonomic revisions herein validate many of the ongoing management strategies to conserve Cutthroat Trout, but we advise additional consideration of life-history diversity as an attainable management target. For long-term persistence of all Cutthroat Trout, maintaining and expanding the availability of high quality, well-connected stream and lake habitats will be a necessary first step to achieving desired conservation outcomes. Moreover, restoring and protecting ecological processes are key to conserving the diversity found within and among lineages of Cutthroat Trout. In systems where native Cutthroat Trout have been extirpated or suppressed, captive propagation and translocation are two potentially available tools to re-establish or reinvigorate populations. Last, we encourage fisheries managers and taxonomists to embrace the challenges that come with conserving locally unique forms of wide-ranging species like Cutthroat Trout.

Cutthroat Trout: Evolutionary Biology and Taxonomy

2018 ◽  
Keyword(s):  
Life History ◽  
Evolutionary Biology ◽  
Conservation Management ◽  
Cutthroat Trout ◽  
Life History Strategies ◽  
Oncorhynchus Clarkii ◽  
The Past ◽  
Management Plans ◽  
Anthropogenic Processes ◽  
Bonneville Basin

<em>Abstract</em>.— Cutthroat Trout <em>Oncorhynchus clarkii </em>of the Yellowstone River, Snake River, and Bonneville Basin exhibit tremendous diversity in the habitats and landscapes in which they are found, diversity in the life-history strategies they employ, and diversity in the coloration and spotting patterns they display. This chapter reviews substantial research conducted over the past 35 years that has described this diversity and the historical and more recent anthropogenic processes that have shaped it and highlights key findings that should be considered during taxonomic reassessments and the writing of conservation management plans.

Cutthroat Trout: Evolutionary Biology and Taxonomy

2018 ◽  
Keyword(s):  
Evolutionary Biology ◽  
Cutthroat Trout ◽  
River Basins ◽  
Lake Basin ◽  
Evolutionarily Significant Unit ◽  
Oncorhynchus Clarkii ◽  
Northern Nevada ◽  
Lahontan Cutthroat Trout ◽  
Carson River ◽  
Evolutionary Units

<em>Abstract</em>.—Lahontan Cutthroat Trout (LCT) <em>Oncorhynchus clarkii henshawi </em>and Paiute Cutthroat Trout (PCT) <em>O. c. selernis </em>are found in the Lahontan hydrographic basin of northern Nevada, northeastern California, and southeastern Oregon and together form the Lahontan Basin evolutionary lineage of Cutthroat Trout <em>O. clarkii</em>. The Alvord Cutthroat Trout <em>O. c. </em>ssp. native to the Alvord Lake subbasin in the northwestern Lahontan Basin was also part of this lineage but went extinct due to Rainbow Trout <em>O. mykiss </em>introgression in the mid-20th century. Both LCT and PCT are federally listed as threatened under the U.S. Endangered Species Act. Given its historic distribution in a single small stream and both phenotypic and genetic distinctiveness, PCT is currently recognized as a separate evolutionarily significant unit (ESU). For LCT, three ESUs are identified based upon meristic, morphological, ecological, and genetic data. These putative LCT ESUs separate lacustrine forms in the western Lahontan Basin (Truckee, Carson, and Walker River basins) from largely fluvial forms in the eastern Lahontan Basin (Humboldt and Reese River basins) and northwestern Lahontan Basin (Quinn River, Coyote Lake, and Summit Lake basins). The more recent recognition of a much longer evolutionary history of Cutthroat Trout and several influential genetic papers identifying previously unrecognized diversity within Cutthroat Trout have prompted a need to re-evaluate the overall taxonomy of this species. Here, we review earlier literature and draw on new information from recent studies to delineate uniquely identifiable evolutionary units within the Lahontan Basin lineage of Cutthroat Trout. Though in several cases various anthropogenic and natural influences have made definitive conclusions difficult, based on this collective information and the goal of conserving potentially important genetic, evolutionary, and life history diversity, we propose recognition of six uniquely identifiable evolutionary units within the Lahontan Cutthroat Trout lineage: (1) Paiute Cutthroat Trout—upper East Carson River; (2) western Lahontan Basin—Truckee, Walker, and Carson rivers together with Summit Lake; (3) northwestern Lahontan Basin—Quinn River; (4) eastern Lahontan Basin—Humboldt and Reese rivers; (5) Lake Alvord basin—Virgin-Thousand and Trout Creek drainages; and (6) Coyote Lake basin—Willow and Whitehorse rivers.

Cutthroat Trout: Evolutionary Biology and Taxonomy

2018 ◽  
Keyword(s):  
Evolutionary Biology ◽  
Colorado River ◽  
Species Concept ◽  
Cutthroat Trout ◽  
Rocky Mountain ◽  
Zoological Nomenclature ◽  
High Likelihood ◽  
Westslope Cutthroat Trout ◽  
Systematic Revision ◽  
Oncorhynchus Clarkii

<em>Abstract</em>.—The 2015 special workshop on the taxonomy and evolutionary biology of Cutthroat Trout highlighted the need for a modern systematic revision of Cutthroat Trout. Pending such a revision, the consensus of this panel was that Cutthroat Trout taxonomy should be based on the unified species concept. The current classification of Cutthroat Trout is based on Benhke’s “major and minor subspecies,” which is incompatible both with the unified species concept, which logically excludes subspecies, and the International Code for Zoological Nomenclature, which does not recognize major and minor subspecies. A compromise, interim classification is proposed, which captures Benhke’s ideas about Cutthroat Trout evolution and other recent information and retains trinomials for his “minor” subspecies, entities deserving re-evaluation in any subsequent systematic revision. Four species are recognized in this interim classification: Coastal Cutthroat Trout <em>Oncorhynchus clarkii</em>, Westslope Cutthroat Trout <em>O. lewisi</em>, Lahontan Cutthroat Trout <em>O. henshawi</em>, and Rocky Mountain Cutthroat Trout <em>O. virginalis</em>. The latter two contain recognized, named subspecies—<em>O. henshawi</em> with four (one extinct) and <em>O. virginalis</em> with seven (one extinct). Substantial nomenclatural problems are described, such that some common names are likely to be more stable than some scientific names until problems are resolved. Significant among these nomenclatural problems are the need to stabilize Rocky Mountain Cutthroat Trout <em>Salar virginalis</em> Girard with a neotype selection; the recognition of <em>Salmo stomias</em> Cope as a synonym of Rio Grande Cutthroat Trout <em>Salar virginalis</em> Girard and, consequently, the absence of a scientific name for Greenback Cutthroat Trout; the high likelihood that <em>Salmo bouvieri</em> Bendire is not a Yellowstone Cutthroat Trout; the high likelihood that the surviving syntype of <em>Salmo pleuriticus</em> Cope is a Westslope Cutthroat Trout and not a Colorado River Cutthroat Trout; and the related need to stabilize <em>S. pleuriticus</em> Cope, either with a lectotype designation from the surviving syntype, which might place <em>S. pleuriticus</em> Cope as a synonym of Westslope Cutthroat Trout, or, if it can be justified, a neotype designation using a Colorado River specimen.

Cutthroat Trout: Evolutionary Biology and Taxonomy

2018 ◽  
Keyword(s):  
Phylogenetic Relationships ◽  
Evolutionary Biology ◽  
Sequence Data ◽  
Cutthroat Trout ◽  
Future Research ◽  
Oncorhynchus Clarkii ◽  
Mtdna Phylogeny ◽  
History Of ◽  
Phylogenetic Hypotheses ◽  
Fossil Data

<em>Abstract</em>.—North American trout have undergone a long and complicated taxonomic history and this holds for taxonomic designations of Cutthroat Trout <em>Oncorhynchus clarkii</em>. Current Cutthroat Trout taxonomy recognizes a monophyletic species comprising 11–16 subspecies. The complex geological and climatic history of western North America is postulated to have strongly influenced differentiation among Cutthroat Trout subspecies. Early studies relied on morphological and meristic data in conjunction with fossil data and known aquatic connections within and among hydrological basins to infer the phylogenetic history of Cutthroat Trout. More recently, molecular studies incorporating karyotypes, allozymes, restriction fragment length polymorphisms, and mitochondrial DNA (mtDNA) sequence data have tested these early phylogenetic hypotheses and yielded additional insights into Cutthroat Trout evolution, although some phylogenetic relationships remain unresolved. In this study, we analyzed DNA sequence data from approximately half of the mitochondrial genome (8,057 base pairs) to better resolve phylogenetic relationships and estimate divergence times among Cutthroat Trout lineages. Herein, we present a well-resolved mtDNA phylogeny and discuss Cutthroat Trout evolution in a phylogeographic framework, as well as clarify current taxonomic implications and make recommendations for future research directions.

Cutthroat Trout: Evolutionary Biology and Taxonomy

2018 ◽  
Keyword(s):  
Evolutionary Biology ◽  
Cutthroat Trout ◽  
River Basins ◽  
Nucleotide Polymorphisms ◽  
Westslope Cutthroat Trout ◽  
Glacial Cycles ◽  
Oncorhynchus Clarkii ◽  
Coeur D'alene ◽  
1 John ◽  
John Day

<em>Abstract</em>.—Identifying units of conservation of aquatic species is fundamental to informed natural resources science and management. We used a combination of mitochondrial and nuclear molecular methods to identify potential units of conservation of Westslope Cutthroat Trout <em>Oncorhynchus clarkii lewisi</em>, a taxon native to montane river basins of the northwestern United States and southwestern Canada. Mitogenomic sequencing identified two major lineages composed of nine monophyletic clades, and a well-supported subclade within one of these, largely delineated by river basins. Analyses of microsatellites and single nucleotide polymorphisms corroborated most of these groupings, sometimes with less resolution but demonstrating more complex connections among clades. The mitochondrial and nuclear analyses revealed that Pleistocene glacial cycles profoundly influenced the distribution and divergence of Westslope Cutthroat Trout, that this taxon crossed the Continental Divide in two separate events, and that genetically pure but nonindigenous fish were widely distributed. Herein, we recognize nine geographically discrete, cytonuclear lineages largely circumscribed by major river basins as potential units of conservation: (1) John Day; (2) Coeur d’Alene; (3) St. Joe; (4) North Fork Clearwater; (5) Salmon; (6) Clearwater headwaters; (7) Clearwater–eastern Cascades; (8) neoboreal, consisting of most of the Columbia upstream from central Washington, the Fraser in British Columbia, and the South Saskatchewan in Alberta; and (9) Missouri.

Cutthroat Trout: Evolutionary Biology and Taxonomy

2018 ◽  
Author(s):  
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Rainbow Trout ◽  
Evolutionary Biology ◽  
Isolation By Distance ◽  
Cutthroat Trout ◽  
Population Connectivity ◽  
Oncorhynchus Clarkii ◽  
Habitat Alterations ◽  
Coastal Cutthroat Trout

<em>Abstract</em>.—We examined patterns of dispersal and colonization after Cordilleran glaciations, population connectivity, levels of genetic diversity, and potential impacts of anthropogenic changes to Coastal Cutthroat Trout <em>Oncorhynchus clarkii clarkii</em>. Populations were mostly small with restricted dispersals but exchanged one to two migrants per generation on average. Genetic differences among local populations of Coastal Cutthroat Trout accounted for approximately three-fourths of the total genetic variation among groups, with differences among different geographical groups accounting for the rest. Because of this, hierarchical geographical population structure was difficult to detect except at small geographical scales that reflected local dispersal and gene flow or at broad geographical scales that reflected divergence associated with long-term isolation during Cordilleran glacial advances. Evolutionary processes such as gene flow and genetic drift reflected in isolation by distance occurred at distances up to 600–700 km but mostly lesser distances, whereas divergence associated with Pleistocene glaciation occurred at 1,900 km or greater. Glacial refugia existed south of the Salish Sea along the Washington, Oregon, and California coasts; in the Haida Gwaii or Alexander Archipelago; and possibly near the central coast of British Columbia near Bella Coola. Throughout the range, hybridization with Rainbow Trout <em>O. mykiss </em>or steelhead (anadromous Rainbow Trout) appears to occur naturally at low levels, but releases of hatchery-produced <em>O. mykiss </em>can lead to higher levels of hybridization and rarely hybrid swarms. Degraded habitat may contribute to hybridization, but most anthropogenic habitat alterations reduce habitat quantity and quality and disrupt opportunities for dispersal, contributing to declines in abundance, population connectivity, and genetic diversity.

The genetic legacy of more than a century of stocking trout: a case study in Rocky Mountain National Park, Colorado, USA

2015 ◽  
Vol 72 (10) ◽  
pp. 1565-1574 ◽  
Author(s):  
Sierra M. Love Stowell ◽  
Christopher M. Kennedy ◽  
Stower C. Beals ◽  
Jessica L. Metcalf ◽  
Andrew P. Martin
Keyword(s):  
National Park ◽  
Molecular Genetic ◽  
Cutthroat Trout ◽  
Rocky Mountain ◽  
Rocky Mountain National Park ◽  
Oncorhynchus Clarkii ◽  
Continental Divide ◽  
Molecular Genetic Data ◽  
Northern Colorado

Human introductions can obscure the diversity and distribution of native biota; hybridization with and replacement by introduced congeners is a primary conservation threat, particularly in salmonids. Cutthroat trout (Oncorhynchus clarkii) are an important component of biodiversity in the American West, and all recognized subspecies are targets for state and federal conservation efforts. Rocky Mountain National Park (RMNP) in northern Colorado is a microcosm of trout introductions that happened worldwide. We used a combination of extensive stocking records and molecular genetic data to ask whether native trout populations persist despite stocking and whether patterns in the distribution of cutthroat trout clades could be explained by source and intensity of stocking. Nearly 15 million cutthroat trout were stocked into RMNP from a mosaic of sources in the 20th century. A single lineage of cutthroat trout was historically native to each side of the Continental Divide in RMNP, but we detected at least five divergent clades of cutthroat trout in 34 localities on both sides of the Divide. The distribution of lineages was predicted by stocking pressure and source but not by which lineage was historically native. The future of mixed and non-native cutthroat trout populations in RMNP poses a substantial conservation challenge.

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