Diagnostic single nucleotide polymorphisms for identifying westslope cutthroat trout (Oncorhynchus clarki lewisi), Yellowstone cutthroat trout (Oncorhynchus clarkii bouvieri) and rainbow trout (Oncorhynchus mykiss)

Kalinowski, Steven T.; Novak, Ben J.; Drinan, Daniel P.; Jennings, Ryan deM.; Vu, Ninh V.

doi:10.1111/j.1755-0998.2010.02932.x

Cited by 20 publications

(20 citation statements)

References 13 publications

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“…Two diagnostic loci with SNPs unique to westslope cutthroat trout, Yellowstone cutthroat trout ( Oncorhynchus clarkii bouvieri ), and rainbow trout ( Oncorhynchus mykiss ) were used (WebTable 2; Kalinowski et al . ; Campbell et al . ).…”

Section: Methodsmentioning

confidence: 99%

Environmental DNA in lake sediment reveals biogeography of native genetic diversity

Nelson‐Chorney

Davis

Poesch

et al. 2019

Frontiers in Ecol & Environ

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Understanding the historical distributions of species is vital to the conservation and restoration of native species, yet such information is often qualitative. We show that the paleolimnological history of threatened freshwater fishes can be reconstructed using species‐diagnostic markers amplified from environmental DNA deposited in lake sediments (lake sedDNA). This method was validated through the detection of lake sedDNA from non‐native trout (Yellowstone cutthroat trout, Oncorhynchus clarkii bouvieri), which corroborated historical records of human‐mediated introductions. We also discovered native trout (westslope cutthroat trout, Oncorhynchus clarkii lewisi) lake sedDNA that predated human‐mediated introductions of freshwater fishes in a watershed with high topographical relief. This unexpected result revealed that the westslope population was of native origin and requires immediate conservation protection. Our findings demonstrate that lake sedDNA can be used to determine the colonization history of freshwater fishes and the structure of ecosystems, aiding in the identification of native ranges, novel native diversity, and introductions of non‐native species.

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Section: Methodsmentioning

confidence: 99%

Environmental DNA in lake sediment reveals biogeography of native genetic diversity

Nelson‐Chorney

Davis

Poesch

et al. 2019

Frontiers in Ecol & Environ

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“…Because it is becoming common to generate several thousand SNP loci for a study, they are rapidly becoming a popular source of diagnostic markers both for taxonomic studies as well as management of units of conservation concern (Kalinowski et al . , Funk et al . , Sousa and Hey , Cronin et al .…”

Section: Discussionmentioning

confidence: 99%

Diagnosability of mtDNA with Random Forests: Using sequence data to delimit subspecies

Archer

Martien

Taylor

2017

Marine Mammal Science

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We examine the use of an ensemble method, Random Forests, to delimit subspecies using mitochondrial DNA (mtDNA) sequences. Diagnosability, a measure of the ability to correctly determine the taxon of a specimen of unknown origin, has historically been used to delimit subspecies, but few studies have explored how to estimate it from DNA sequences. Using simulated and empirical data sets, we demonstrate that Random Forests produces classification models that perform well for diagnosing subspecies and species. Populations with strong social structure and relatively low abundances (e.g., killer whales, Orcinus orca) were found to be as diagnosable as species. Conversely, comparisons involving subspecies that are abundant (e.g., spinner and spotted dolphins, Stenella longirostris and S. attenuata), are only as diagnosable as many population comparisons. Estimates of diagnosability reported in subspecies and species descriptions should include confidence intervals, which are influenced by the sample sizes of the training data. We also stress the importance of reporting the certainty with which individuals in the training data are classified in order to communicate the strength of the classification model and diagnosability estimate. Guidance as to ideal minimum diagnosability thresholds for subspecies will improve with more comprehensive analyses; however, values in the range of 80%–90% are considered appropriate.

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“…; Kalinowski et al. ); however, the small geographic range of the Sicklefin Redhorse may warrant future genetic research designed to identify historical introgression between the Black Redhorse and Sicklefin Redhorse as a means to establish Sicklefin Redhorse historical occupancy and justify future reintroductions. Furthermore, historical stocking programs have unintentionally introduced genetically undesirable progeny ranging from those exhibiting reduced genetic diversity (e.g., Sicklefin Redhorse: Moyer et al.…”

Section: Discussionmentioning

confidence: 99%

Behavior and Reproductive Ecology of the Sicklefin Redhorse: An Imperiled Southern Appalachian Mountain Fish

Favrot

Kwak

2018

Trans Am Fish Soc

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Many nongame fishes are poorly understood but are essential to maintaining healthy aquatic ecosystems globally. The undescribed Sicklefin Redhorse Moxostoma sp. is a rare, imperiled, nongame fish endemic to two southern Appalachian Mountain river basins. Little is known of its behavior and ecology, but this information is urgently needed for conservation planning. We assessed the spatial and temporal bounds of spawning migration, quantified seasonal weekly movement patterns, and characterized seasonal and spawning behavior using radiotelemetry and weir sampling in the Hiwassee River basin, North Carolina–Georgia, during 2006 and 2007. Hiwassee River tributaries were occupied predominantly during the fish's spawning season, lower reaches of the tributaries and the Hiwassee River were primarily occupied during the postspawning season (i.e., summer and fall), and lower lotic reaches of Hiwassee River (upstream from Hiwassee Lake) were occupied during winter. Adults occupied Hiwassee Lake only as a movement corridor during spawning migrations. Both sexes conducted upstream spawning migrations simultaneously, but males occupied spawning tributaries longer than females. Sicklefin Redhorse exhibited interannual spawning‐area and tributary fidelity. Cold water temperatures associated with hypolimnetic releases from reservoirs and meteorological conditions influenced spawning migration distance and timing. During 2007, decreased discharges during the spawning season were associated with decreases in migration distance and spawning tributary occupancy duration. Foraging was the dominant behavior observed annually, followed by reproductive behaviors (courting and spawning) during the spawning season. No agonistic reproductive behavior was observed, but females exhibited a repetitious postspawning digging behavior that may be unique in the family Catostomidae. Our findings suggest that protection and restoration of river continuity, natural flow regimes, seasonally appropriate water temperatures, and geographic range expansion are critical components to include in Sicklefin Redhorse conservation planning. Fisheries and ecosystem managers can use our findings to justify sensitive management decisions that conserve and restore critical streams and rivers occupied by this imperiled species.

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Diagnostic single nucleotide polymorphisms for identifying westslope cutthroat trout (Oncorhynchus clarki lewisi), Yellowstone cutthroat trout (Oncorhynchus clarkii bouvieri) and rainbow trout (Oncorhynchus mykiss)

Cited by 20 publications

References 13 publications

Environmental DNA in lake sediment reveals biogeography of native genetic diversity

Environmental DNA in lake sediment reveals biogeography of native genetic diversity

Diagnosability of mtDNA with Random Forests: Using sequence data to delimit subspecies

Behavior and Reproductive Ecology of the Sicklefin Redhorse: An Imperiled Southern Appalachian Mountain Fish

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