Patrick W. DeHaan

Spatial patterns of hybridization between bull trout, Salvelinus confluentus, and brook trout, Salvelinus fontinalis in an Oregon stream network.

Hybridization with introduced species represents a serious threat to the persistence of many native fish populations. Brook trout (Salvelinus fontinalis) have been introduced extensively throughout the native range of bull trout (S. confluentus) and hybridization has been documented in several systems where they co-exist and is seen as a significant threat to the persistence of bull trout populations. We identified a group of diagnostic microsatellite loci to differentiate bull trout and brook trout and then used these loci to examine the spatial distribution of hybrids in the Malheur River basin, Oregon USA. In random samples of approximately 100 fish from each of three creeks we identified 181 brook trout, 112 bull trout and 14 hybrids. Although bull trout, brook trout and hybrids were found in all three creeks, they were not evenly distributed; brook trout were primarily found in the lower sections of the creeks, bull trout further upstream, and hybrids in the areas of the greatest overlap. One creek with a population of brook trout in a headwater lake provided an exception to this pattern; brook trout were found distributed throughout the creek downstream of the lake. Several post-F1 hybrids were identified suggesting that hybrids are reproducing in the Malher River Basin. Mitochondrial DNA analysis indicated that both female bull trout and brook trout are involved in hybridization events. Analysis of population structure suggested that brook trout have established multiple spawning populations within the Malheur system. Data presented in this study suggest that relative abundance of brook trout and habitat quality are important factors to consider when evaluating the threat of hybridization to bull trout populations.

Use of genetic tags to identify captive-bred pallid sturgeon ( Scaphirhynchus albus ) in the wild: improving abundance estimates for an endangered species

The ability to distinguish captive-bred and natural-origin individuals in the wild is critical for evaluating the impact of captive breeding programs on natural populations. Continued persistence of endangered pallid sturgeon (Scaphirhynchus albus) in the Missouri River is largely dependent on captive breeding efforts that spawn natural-origin adults in fish hatcheries and release their progeny into the wild. Prior to release, hatchery-origin individuals are physically marked so they can be distinguished from natural-origin individuals when recaptured. During the years 2004–2006, 24 unmarked juvenile pallid sturgeon tissue samples were collected in the Missouri River downstream of Gavins Point Dam, South Dakota, USA that were presumed natural-origin. However, these individuals were similar in size to hatchery-origin fish released in this area raising concerns that these individuals were actually hatchery-origin fish with lost or malfunctioning tags. We used microsatellite based parentage analysis to determine if the unmarked fish were members of hatchery families that had been released in this area. This retrospective genetic tagging approach revealed that 23 of 24 unmarked fish were indeed hatchery-origin. The origin of the remaining individual remains unknown because genetic samples were not available from all of the families released below the dam and the unassigned fish may have originated from one of these un-sampled families. These results provide important insight into the conservation status of endangered pallid sturgeon as well as provide data important for guiding management decisions. Our results also demonstrate the efficacy of using genetic tags as an alternative or complimentary approach to physically marking individuals.

Genetic Structure, Evolutionary History, and Conservation Units of Bull Trout in the Coterminous United States

Abstract The bull trout Salvelinus confluentus is a broadly distributed char in northwestern North America that has undergone significant population declines. This species is currently protected under the Endangered Species Act across its range in the coterminous United States. To clarify patterns of phylogenetic structure and to assist with identification of conservation units, we examined genetic variation within and among 75 representative bull trout populations sampled throughout the USA. Genealogies from a 520-base-pair portion of the mitochondrially encoded NADH dehydrogenase 1 gene (ND-1) revealed reciprocal monophyly between coastal and interior lineages that differed by 1.34% in DNA sequence. The geographic distribution of the two lineages was divided by the Cascade Mountains, a pattern that likely reflects postglacial dispersal from separate glacial refugia. Analysis of microsatellite variation revealed that 76% of populations had an estimated effective population size less than 50 and indicated...

Genetic Population Structure of Olympic Peninsula Bull Trout Populations and Implications for Elwha Dam Removal

Abstract In the Elwha River, two hydroelectric dams constructed nearly a century ago fragment previously continuous habitat and isolate migratory bull trout. Removal of the dams is scheduled to begin in 2011, and represents an opportunity to help recover this threatened species. Large-scale disturbance is expected when accumulated sediments behind the dams are released downstream, which may initially negatively affect bull trout. To inform restoration planning, we investigated levels of genetic variation within and among bull trout populations from six Olympic Peninsula watersheds with an emphasis on the Elwha River. We determined genetic relationships among Elwha bull trout from four distinct river sections and performed population assignments for fish collected from the lower Elwha and Dungeness rivers. There were greater levels of variation and gene flow in coastal watersheds (Hoh, South Fork Hoh, Kalaloch) compared to populations isolated by dams (Elwha, North Fork Skokomish). Elwha bull trout represented an independent spawning population and were highly differentiated from other populations. Bull trout from the Elwha (n = 21) and Dungeness (n = 18) estuaries all assigned to the river they there were collected from. Despite long-term fragmentation, there was no significant genetic variation among Elwha bull trout separated by the dams, although fish from the Elwha headwaters were genetically distinct. Results suggest that bull trout still migrate downstream through both Elwha River dams and that anadromous bull trout will likely help to recolonize the Elwha River following dam removal. Baseline data from this study will be useful for monitoring bull trout recovery following dam removal.

Analyses of Genetic Variation in Populations of Oregon Chub, a Threatened Floodplain Minnow in a Highly Altered Environment

Abstract The Oregon chub Oregonichthys crameri is a small floodplain minnow endemic to the Willamette River basin of western Oregon. Historically the species was widely abundant and probably relied on periodic floods for dispersal and genetic exchange among populations. The species has declined substantially in the past 100 years due to habitat alterations and the introduction of nonnative species and is currently listed as threatened under the U.S. Endangered Species Act. Information on the level of genetic variation within and among populations did not exist when the species was listed or when a recovery plan was being developed. In this study, we used a suite of nine microsatellite loci to characterize genetic variation within and among 16 sampling locations and provide information to help guide future recovery efforts. Even though many locations are presently isolated from one another, we observed relatively high levels of genetic variation within collections. Temporal samples revealed that the levels...

Historical and contemporary forces shape genetic variation in the Olympic mudminnow (Novumbra hubbsi), an endemic fish from Washington State, USA

Genetic data have become increasingly useful for conservation planning when data regarding population status and long-term viability is limited. The Olympic mudminnow is the only fish species endemic to Washington State, USA. The species is an increasing priority for conservation given its limited distribution and increasing habitat loss. Presently, information important for developing conservation plans including population abundance data, knowledge of population boundaries, and estimates of gene flow among populations are limited. We used microsatellite markers to assess the level of genetic variation within and among Olympic mudminnow collections from 23 sites across the species range. Genetic variation within collections ranged widely and was greatest within the Chehalis River Basin, a former glacial refugium. Analysis of population boundaries showed that each collection site represented a unique population with the exception of collections made within two large wetland and stream complexes. Genetic variation among populations appears to be strongly influenced by glacial history and the species’ life history. Populations originating from the Chehalis River glacial refugium clustered together in multiple analyses and populations from the Olympic Coast, which persisted in separate refugia and have limited capacity for dispersal, showed a high level of differentiation. Competing theories existed regarding the origins of disjunct populations in east Puget Sound and genetic data showed that these populations represent undocumented introductions rather than a glacial remnant or historic colonization from the Chehalis refugium. Data presented in this study will help fill important information gaps and advance conservation planning for this species.

Characterization of tetranucleotide microsatellite loci for Olympic mudminnow (Novumbra hubbsi)

We describe the isolation and amplification of 21 potential tetranucleotide microsatellites for the Olympic mudminnow (Novumbra hubbsi). After initial testing, eight microsatellites were removed from future analysis for non-resolvable electropherograms. The remaining 13 loci were screened against a total of 772 individuals from 12 populations. The thirteen polymorphic loci amplified between four and forty-eight alleles per locus with expected heterozygosities ranging from 0.41 to 0.95. These markers should aid in conservation and the description of population structure of this state sensitive species.

Novel SNP Genotyping Assays Facilitate Species Identification of Salvelinus Collected in a Recreational Fishery

AbstractMembers of the genus Salvelinus often occur sympatrically, exhibit a high degree of phenotypic plasticity, and commonly hybridize. These factors often complicate species identification and hybrid detection based solely on morphology. Many species and populations of Salvelinus are threatened or endangered and accurate species identification and hybrid detection are important for conservation. Single nucleotide polymorphism (SNP) markers offer several advantages over other classes of genetic markers for species identification. We used DNA sequences from six species of Salvelinus to identify 16 SNPs that exhibited fixed differences among species and 16 additional SNPs that were variable within different species. These markers were used for species identification of putative Bull Trout Salvelinus confluentus that were misidentified as Lake Trout S. namaycush in a recreational fishery in Lake Pend Oreille, Idaho. The markers developed in this study will be useful for Salvelinus species identification a...

Influence of Introduction History on Genetic Variation in Introduced Populations: A Case Study of Oregon Chub

AbstractPopulation introductions and reintroductions have become a common tool for conserving threatened species, but oftentimes introduced populations have reduced the genetic diversity compared with the source population they were founded from. Population introductions played an important role in the recovery of the Oregon Chub Oregonichthys crameri, a small floodplain minnow found in western Oregon. Unlike many introduction efforts, introduced populations of Oregon Chub were founded using large numbers of individuals (hundreds in many cases) and each population had a unique introduction history (e.g., number of founders, source populations selected, duration of the introduction effort). We used microsatellite loci to examine 13 introduced populations and their respective sources to evaluate how well the introduction program captured genetic diversity present in the wild populations. Genetic variation was reduced by roughly 25% in one introduced population, and three introduced populations showed eviden...