Cutthroat Trout: Evolutionary Biology and Taxonomy

<em>Abstract</em>.—A Y chromosome marker shared with Rainbow Trout <em>Oncorhynchus mykiss </em>has been sequenced in many Cutthroat Trout <em>O. clarkii </em>subspecies. The marker is found in and inherited through males. It evolves more slowly than the maternally inherited mitochondrial DNA. The marker delineates the four major groups of Cutthroat Trout: the Lahontan Cutthroat Trout <em>O. c. henshawi </em>subspecies complex, the Yellowstone Cutthroat Trout <em>O. c. bouvieri</em> subspecies complex, Westslope Cutthroat Trout <em>O. c. lewisi</em>, and Coastal Cutthroat Trout <em>O. c. clarkii</em>. The paternal inheritance pattern of the Y marker makes it useful for dissecting the origins of fish with mixed ancestries. We describe a case study using both Y and mitochondrial markers in Lahontan Cutthroat Trout subspecies complex trout populations. Our results confirmed Lahontan Cutthroat Trout affinities for the Paiute Cutthroat Trout <em>O. c. seleniris</em> and Willow–Whitehorse Creek Cutthroat Trout. However, we found evidence of a complex ancestry for Guano Creek, Oregon trout, a group that has been proposed by some to be related to the Alvord Cutthroat Trout, a subspecies thought to be extinct.

Cutthroat Trout: Evolutionary Biology and Taxonomy

<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

<em>Abstract</em>.—In the past 17 million years (myr), the topography and drainage systems of the northwestern United States were drastically modified by the Yellowstone–Snake River Plain (YSRP) hotspot and associated east–west extension of the Basin and Range Province. These geologic changes influenced distribution and diversification of Cutthroat Trout <em>Oncorhynchus clarkii</em> and allowed connections between Snake River, Colorado River, and Great Basin fish populations beginning in the late Miocene. Studies of detrital zircon grains in Miocene to Holocene fluvial sands of the Snake River document the eastward migration of the regional drainage divide from central Idaho to northwestern Wyoming. This migration was concomitant with the southwest migration of the North American tectonic plate over the YSRP hotspot. In the late Miocene and Pliocene, since 10 million years before present (Ma), the Chalk Hills and Glenns Ferry lake systems formed on the western Snake River Plain and were hosts to diverse fish fauna. The modern Snake River formed after 3 Ma with the cutting of Hells Canyon and integration of the Snake and Columbia River drainage. In the Great Basin south of the Snake River watershed, Lake Lahontan has a history that goes back to the Miocene. Connections between the western Snake River Plain and the Great Basin were recurrent over the past 10 myr. In southeastern Idaho, the Bear River has had a complex drainage interaction with the Snake River and Bonneville watersheds. Lake Bonneville, in northern Utah, grew during Pleistocene glacial climate regimes. The modern Bear River connection to Lake Bonneville was initiated about 50,000 years before the present. The integration of the Green River with the Colorado River occurred in the late Miocene, developing after breaking of Eocene connections between the Green River and streams draining to the Atlantic Ocean. In sum, geological constraints are compatible with patterns of fish fossils and genetic linkages and identify mechanisms of colonization and isolation of fish populations that have resulted in regional diversification of Cutthroat Trout.

Cutthroat Trout: Evolutionary Biology and Taxonomy

<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

<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

<em>Abstract</em>.—Despite major declines in distribution and abundance of Cutthroat Trout <em>Oncorhynchus clarkii </em>across their native range since European settlement, substantial morphological and genetic diversity remains. For example, recent molecular investigations revealed the presence of six discrete lineages of Cutthroat Trout native to the Southern Rocky Mountains rather than four as previously thought. These include the previously recognized Yellowfin Cutthroat Trout <em>O. c. macdonaldi </em>(extinct) and Rio Grande Cutthroat Trout <em>O. c. virginalis</em>, as well as the true native of the South Platte River basin, located east of the Continental Divide, which we continue to refer to as Greenback Cutthroat Trout. Within the range of Colorado River Cutthroat Trout <em>O. c. pleuriticus</em>, which is located west of the Continental Divide, we highlight two divergent clades that historically occupied upstream, coldwater reaches of the Green River and Colorado River basins. Both are also found outside their historical ranges as well, due to extensive, mostly undocumented stocking in the early 20th century that served to conceal native diversity in the region. An additional clade closely aligned with those two Colorado River groups historically occupied the San Juan River basin. In this chapter, we discuss both molecular and morphomeristic evidence that indicates distinct lineages are aligned with major drainage basins, information that guides ongoing conservation actions.

Cutthroat Trout: Evolutionary Biology and Taxonomy

<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

<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

<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.