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Snake valley – full version
Species with large geographic distributions often exhibit complex patterns of diversity that can be further complicated by human activities. Cutthroat trout Oncorhynchus clarkii are one of the most widely distributed freshwater fish species in western North America exhibiting substantial phenotypic and genetic variability; however, fish stocking practices have translocated populations outside of their native range and may have obscured intraspecific boundaries.
This study focuses on cutthroat trout populations representing three distinct evolutionary clades that are found intermixed within a contact zone between the Bonneville and upper Snake River watersheds in the western United States.
We used mitochondrial and microsatellite genetic data, as well as historical stocking records, to evaluate whether populations of cutthroat trout in the contact zone are native or are introduced. We found ificant genetic differentiation and fine-scale genetic population structure that was organized primarily by watershed boundaries. While we detected increased genetic diversity in some areas in close proximity to the greatest of stocking events, the highly organized population structure both within and between areas of the contact zone indicates that the snake valley f95 are native to the watersheds.
Intermixing of distinct evolutionary lineages of cutthroat trout appears to be the result of historical connections between paleodrainages. Our analyses provide a context for understanding how genetic data can be used to assess the status of populations as native or introduced. Natural geological processes may have a substantial influence on population structure and gene flow by altering the landscape through volcanism, glaciation, mountain building, and plate tectonics [ 12 ].
Similarly, habitat variability can lead to ecological specialization and genetic differentiation through behavioral, morphological, or physiological adaptation.
Given sufficient time, natural isolating mechanisms can lead to local adaptive differentiation and speciation, creating a complex mosaic of unique populations organized by geographic and habitat-related features [ 23 ].
Although natural processes can sub-divide populations and promote diversification, human activities can obscure natural evolutionary patterns [ 4 — 6 ]. The translocation of species outside of their native range is arguably one of the most important human mediated factors that complicates native species distribution patterns [ 47 — 9 ]. For species with extensive geographic structuring, disentangling natural and human-mediated factors affecting their distribution can be difficult, but is critical to the development of management plans for protecting species and their role within ecosystems.
In freshwater ecosystems, natural features commonly isolate populations because many aquatic animals cannot move around physical barriers that extend across the land-water interface [ 10 ]. As a result, the contemporary distribution of aquatic taxa is often a reflection of once widely inter-connected populations subsequently isolated by natural events such as major changes in climate and hydrological conditions [ 1112 ]. In western North America, the Great Basin and adjacent regions include a vast area of deserts and mountains snake valley f95 watersheds that have experienced wetter and cooler periods with high levels of connectivity followed by periods of desiccation [ 13 — 15 ].
During pluvial times, lakes covered large areas of the Great Basin allowing widespread dispersal of aquatic species; however, when the climate became more arid, connections were lost and populations isolated [ 15 — 17 ]. Over time, isolated populations accumulated differences as selection acted on adaptive variation or as small populations became subject to genetic drift, creating genetically distinct endemic taxa [ 23 ].
A variety of aquatic taxa have been identified with localized endemic species in remnant aquatic habitat of arid regions, including amphibians, mollusks, insects, and fish [ 1318 — 20 ]. The geographic proximity, but phylogenetic distinctiveness of such taxa, often creates a mosaic of adjacent ranges separated by movement barriers across snake valley f95 landscapes [ 161920 ].
Understanding the range and extent of endemic taxa is essential for protecting and conserving native biodiversity. Yet, as human activities continue to expand in areas such as the Great Basin, translocations of closely related species outside of their native range is becoming an increasing concern as it threatens the genetic integrity of native populations, decreasing their abundance through competition or predation [ 21 — 24 ].
In addition to historical geographic features, contemporary processes have been instrumental in shaping the genetic population structure of fish species through various human activities [ 52526 ]. Increasingly, the movement of freshwater fish species to areas outside of their native range has become a common occurrence, often to support the demand for recreational fishing opportunities and to supplement natural populations [ 27 ].
The cutthroat trout Oncorhynchus clarkii is one of the most widespread freshwater fish species native to western North America and is also a popular sport fish that has been propagated and translocated from relatively few hatchery stocks [ 28 — 30 ].
Cutthroat trout trace their ancestry in North America to between eight and 16 million years BP [ 3132 ], and as such, natural geological events have influenced their distribution and diversification throughout their range [ 33 ]. In western North America, ificant changes in watershed connectivity and landscape topology have occurred from processes associated with mountain building, volcanism, and altered flow regimes of rivers during multiple periods of climatic cooling and glaciation [ 33 — 38 ].
As result of these processes, cutthroat trout have diversified into genetically distinct taxa; largely organized by geographic features such as major watershed boundaries [ 3940 ]. Furthermore, the contemporary distribution of cutthroat trout has been complicated snake valley f95 hatchery propagation and translocation to areas outside of their natural range of diversification.
While geographic features can largely explain the main axes of cutthroat trout diversification and distribution, overlap in the distribution of some cutthroat trout taxa, and the widespread stocking of hatchery fish have created confusion about whether some cutthroat trout populations are native or have been introduced [ 64142 ].
With ongoing efforts to restore and recover endangered cutthroat trout subspecies, determining the extent and frequency of native populations is of vital importance to developing management plans. Bonneville cutthroat trout O. However, even early genetic investigations revealed an additional evolutionary lineage present in the southwestern portions of the Bonneville watershed that is as divergent as populations ased as Bonneville or Yellowstone cutthroat trout [ 3143 ].
Snake valley – full version
Later genetic studies also documented a distribution of haplotypes thought to be representative of Bonneville cutthroat trout in areas of the upper Snake River [ 33 ]. More recent genetic studies of cutthroat trout revealed an intermixing of these evolutionary lineages in a contact zone surrounding the southern portion of the upper Snake River and northern portions of the Bonneville Basin, with one lineage being more closely related to populations from the Colorado River watershed [ 41 ].
While similarities of native fish fauna between the Bonneville Basin and upper Snake River have long been associated with pluvial events, such as the Bonneville Flood that connected the two watersheds about 17, years ago [ 4445 ], translocations of hatchery trout are common and may also explain unexpected distribution patterns of cutthroat trout subspecies [ 3946 ]. In this study, we used population genetic data to determine if there is evidence for natural admixture of cutthroat trout between the upper Snake River and the adjacent Bonneville Basin or if the intentional translocation of closely related snake valley f95 explains the current distribution of cutthroat trout within the study area.
Sampling locations of cutthroat trout according to stream name within the Bonneville Basin and upper Snake River in western North America. s in parentheses indicate population ID reported in Table 1.
Connections and containers: using genetic data to understand how watershed evolution and human activities influence cutthroat trout biogeography
Bold line indicates the boundary separating the upper Snake River from the Bonneville Basin. Dashed line represents the division between the Malad River watershed within the Bear River watershed. Inset map indicates estimated boundary for the native range of Bonneville blue polygon and Yellowstone yellow polygon subspecies of cutthroat trout within the western United States. Genetic analyses provide a powerful tool to resolve the status of populations whose taxonomy and biogeography are poorly understood [ 47 ]. Many studies have used genetic approaches to determine source populations of introduced species [ 4849 ], identify invasive species [ 4750 ], or simply to uncover genetic differences that occur between known native and introduced populations [ 5152 ].
In some instances, the distribution of populations is such that it is not clear whether specific populations are native or introduced because individuals may be morphologically indistinguishable from each other despite exhibiting genetic differences [ 53 ]. Population genetic data can be used to identify evidence of recent translocations through snake valley f95 of genetic differentiation, diversity, and structure [ 47485455 ].
Here, we examine the population genetic structure of cutthroat trout along a contact zone where multiple evolutionary clades are intermixed to determine if secondary contact is a consequence of natural processes or recent human-mediated introductions. To describe genetic variation of cutthroat trout in the contact zone, we collected tissue samples from individuals representing 30 populations within the Bonneville Basin and upper Snake River Fig 1. We haphazardly sampled cutthroat trout from headwater streams with backpack electro-fishing.
In most instances, we sampled 25 fish from each location, but in four locations we collected fewer fish Table 1. Once captured, each fish was fin-clipped for genetic analysis and then released near the point of capture. All sampling locations were pd to be native populations of cutthroat trout, except Six Mile Creek in the Raft River watershed.
Six Mile Creek was chemically treated to remove the fish population because it was introgressed with non-native rainbow trout Oncorhynchus mykiss and subsequently recolonized using cutthroat trout from neighboring Eight Mile Canyon Creek D. We included Six Mile Creek as a method for comparison describing the genetic population structure of a known translocated population of cutthroat trout. We examined the diversity and geographic distribution of cutthroat trout lineages by comparing mitochondrial mtDNA haplotypes from all study populations.
Sequences were edited and aligned to a reference cutthroat trout sequence using Sequencer v. We estimated haplotype and nucleotide diversity, as well as haplotype frequency, using DnaSp v.
To illustrate evolutionary relationships, we constructed a phylogenetic tree with representatives of each unique ND2 haplotype from this study, and a single representative sequence from other subspecies of cutthroat trout, including: Colorado River cutthroat trout O. Phylogenetic trees were constructed using the Tamura-Nei substitution model with invariant sites based on jModeltest [ 59 ]. The final phylogenetic tree was generated with bootstrap replicates as implemented in the program PhyML [ 60 ] and edited in FigTree ver.
Mitochondrial DNA sequence diversity was examined at various spatial scales using an Analysis of Molecular Variance AMOVA partitioning pairwise differences between sequences among watersheds, among populations within watersheds, and within populations using Arlequin ver.
Estimates of genetic population structure, organization, and diversity were compared using nuclear microsatellite loci. We subsequently used GeneMapper software ver. All peaks were verified manually to ensure accuracy. Microsatellite diversity and fine scale genetic structure were examined using the of alleles per loci, average heterozygosity, allelic richness, and pairwise genetic differentiation F ST with Microsatellite Analyzer MSA, ver.
Snake valley – full version
We used MSA to test for population level differences in the of alleles per locus and heterozygosity to identify diversity measures that could indicate stocking or natural causes. FSTAT was used to test for ificant differences in allelic richness based on 10, permutations. Analyses for pairwise genetic differentiation estimates were calculated in Arlequin with 10, iterations.
Geographic structuring of genetic data was visualized both at the population level as well as at the watershed level, using a neighbor-ing tree and population asment tests. If cutthroat trout populations have a natural distribution history, the neighbor-ing tree and clustering should group by watershed and migration should be between neighboring populations. Alternatively, the absence of geographic structure or migration events between watersheds would indicate a ificant influence of non-native introductions.
For the neighbor-ing tree, we estimated genetic distance using Cavalli-Sforza chord distance [ 69 ] and constructed the tree using Phylip ver.
We generated a bootstrap tree using bootstrap replicates and visualized it in FigTree. In addition to illustrating geographic structure using genetic distance, patterns of migration and population clustering were examined using GeneClass2 [ 71 ] and Structure ver. We identified migrants between populations through asment tests that as each individual to the most likely population of origin using genetic similarity. To assess geographic genetic structure, we estimated the of populations K with Structure using an individual-based Bayesian asment method, based on no prior information of population origin.
For the Structure analysis, five independent runs for each K 2—30 were conducted using the admixture model atiterations with a burn-in ofTo visualize the asment of each population in the resulting clusters, we used the programs Clumpp ver.
