William R. Ardren

Methods of parentage analysis in natural populations

The recent proliferation of hypervariable molecular markers has ushered in a surge of techniques for the analysis of parentage in natural and experimental populations. Consequently, the potential for meaningful studies of paternity and maternity is at an all‐time high. However, the details and implementation of the multifarious techniques often differ in subtle ways that can influence the results of parentage analyses. Now is a good time to reflect on the available techniques and to consider their strengths and weaknesses. Here, we review the leading techniques in parentage analysis, with a particular emphasis on those that have been implemented in readily useable software packages. Our survey leads to some important insights with respect to the utility of the different approaches. This review should serve as a useful guide to anyone who wishes to embark on the study of parentage.

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...

Use of Parentage Analysis to Determine Reproductive Success of Hatchery‐Origin Spring Chinook Salmon Outplanted into Shitike Creek, Oregon

Abstract Removal of fish passage barriers provides Pacific salmon Oncorhynchus spp. and steelhead O. mykiss the opportunity to recolonize previously accessible habitat, though the time scale of natural recolonization may not be sufficient for management or conservation goals. One strategy for accelerating recolonization is to outplant hatchery-origin adults into newly restored habitats. In this paper, we describe how genetic parentage analysis was used to determine the reproductive success of adult stream-type spring Chinook salmon O. tshawytscha taken from two localized hatchery stocks and outplanted into a stream. We defined reproductive success as the production of migratory juveniles. In 2002 and 2003, 83 and 265 adult hatchery salmon, respectively, were outplanted into Shitike Creek, Oregon, a tributary to the Deschutes River. Using 11 microsatellite markers, 799 and 827 migratory juveniles from the two brood years were genotyped and matched back to potential outplanted parents using genetic parentag...

Morphological, Physiological, and Genetic Techniques for Improving Field Identification of Steelhead, Coastal Cutthroat Trout, and Hybrid Smolts

Abstract In streams with sympatric populations of steelhead Oncorhynchus mykiss and coastal cutthroat trout O. clarkii clarkii (hereafter, cutthroat trout), life history descriptions and smolt production estimates may be hampered by misclassification of hybrids as steelhead or cutthroat trout. Additionally, important morphological and physiological differences between hybrid and non-hybird smolts are often unknown. Therefore, we assessed field classification and created classification models to quantify and reduce misclassification rates among migrating steelhead, cutthroat trout, and hybrid smolts. Field misclassifications of smolts with steelhead or cutthroat trout genotypes were low (1% and 2%, respectively). However, field misclassification of fish with hybrid genotypes was high, with 11% of the hybrids being misclassified as steelhead and 42% of the hybrids being misclassified as cutthroat trout. Hybrid smolts were larger, had lower gill Na+, K+-ATPase activities, and lower condition factors than steelhead but were similar to cutthroat trout smolts in these same measurements. Additionally, statistical classification analyses using morphological traits including subterminal jaw slash intensity, hyoid teeth presence, maxillary length, breaks of pigment along outer margin of adipose fin, condition factor, and migration date improved classification error rates of hybrids from 53% to 21%. In systems with sympatric populations of steelhead and cutthroat trout, we recommend a thorough evaluation of field-based identification methods with genetic techniques to assess the effectiveness of field-based classification in addition to examining important life history differences among steelhead, cutthroat trout, and their hybrids.

Ancestry, population structure, and conservation genetics of Arctic grayling (Thymallus arcticus) in the upper Missouri River, USA

We genotyped Arctic grayling (Thymallus arcticus) at 10 microsatellite loci in 18 samples (n = 726) from Mon- tana, Wyoming, and Saskatchewan to determine genetic relationships among native, captive, and naturalized populations in the upper Missouri River basin, to assess patterns in genetic diversity, and to infer recent demographic histories. Sub- stantial genetic subdivision was observed among sample populations (global FST = 0.10). Canadian populations have been isolated from Missouri River populations long enough for mutation to cause genetic differences between regions (mean pairwise FST = 0.18, RST = 0.54). Within the Missouri River basin, most naturalized lacustrine populations traced their an- cestry to Red Rock lakes. Two populations in headwater lakes within the Big Hole River watershed appear to be native. We found neither evidence for introgression of Canadian-origin grayling nor any effect of hatchery stocking in native pop- ulations. The native fluvial Big Hole River group was genetically distinct and most diverse (HE = 0.89), whereas native Madison River and Red Rock lakes populations exhibited lower genetic diversity (HE = 0.74 and 0.80, respectively) and evidence of recent bottlenecks. The existing Big Hole and Red Rock populations are at low abundance but do not appear to be at immediate risk of inbreeding depression (Ne = 207.7-228.2).

Characterization of 12 highly variable tetranucleotide microsatellite loci for Arctic grayling (Thymallus arcticus) and cross amplification in other Thymallus species.

We describe the isolation and development of 12 polymorphic tetranucleotide microsatellite loci for Arctic grayling (Thymallus arcticus). In a sample of 46 fish, we observed between three and 20 alleles per locus. All 12 of these loci were also polymorphic in at least one of the following Thymallus species and subspecies: T. burejensis, T. amurensis, T. thymallus, T. brevirostris, T. grubii, T. arcticus baicalensis and T. arcticus pallasi. These loci will aid in our understanding of the population genetics, behaviour and conservation of grayling species throughout the northern hemisphere.

Evidence of Panmixia between Sympatric Life History Forms of Coastal Cutthroat Trout in Two Lower Columbia River Tributaries

Abstract Coastal cutthroat trout Oncorhynchus clarkii clarkii exhibit resident and migratory life history strategies that often occur sympatrically, but the relationship between these forms within a population is poorly characterized. Through use of passive integrated transponder technology, migratory and resident coastal cutthroat trout were identified in two lower Columbia River tributaries (Abernathy Creek and the Chinook River) separated by more than 80 km. Genetic data from 17 highly variable microsatellite loci were used to ascertain the genetic population structure of these life history forms within and between streams. No distinct genetic separation was observed between the life history forms within a stream, as assessed by four different statistical approaches: permutation tests based on the genetic differentiation index F ST, principal components analysis of individuals, analysis of molecular variance, and contingency tests of allele frequency heterogeneity. Genetic differences were an order of ...

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...