Paul Moran

Developments in molecular genetic techniques in fisheries

The use of molecular genetic techniques in fisheries research has increased dramatically over the past several years, largely due to the increased availability of techniques and an increased awareness of the value of genetic data. Today, the boundaries of fisheriesrelated molecular genetic research encompass topics from the identification of markers for stock discrimination (Park et al., 1993) to the genetics of pathogenic organisms of commercially important species (Meyers et al., 1992) to the expression of growth factors during maturation (Duguay et al., 1992). We cannot hope to cover all of these applications in the space of this review but we would like to at least acknowledge the breadth of research that is being conducted. With that said, we shall focus primarily on molecular methods as they relate to population genetic/evolutionary questions, because most data (in terms of volume and diversity) exist for these applications, and this is our area of research. Research in this area generally involves the characterization of molecular genetic variants that can be used as genetic markers.

Molecular Markers Distinguish Coastal Cutthroat Trout from Coastal Rainbow Trout/Steelhead and Their Hybrids

Abstract A major cause of population declines among interior cutthroat trout subspecies Oncorhynchus clarki ssp.is hybridization with introduced rainbow trout O. mykiss ssp. Coastal cutthroat trout O. c. clarki have also experienced population declines in recent decades and are known to hybridize with coastal rainbow trout/steelhead O. m. irideus. However, unlike interior cutthroat trout, coastal cutthroat trout are naturally sympatric with coastal rainbow trout/steelhead, and the role of hybridization in their population declines remains unclear. Further, little is known about the spatial and temporal distributions of hybridization in these coastal subspecies. As a step toward better characterization of this hybridization, we developed a suite of species-specific DNA markers for coastal cutthroat trout and coastal rainbow trout/steelhead. Of 11 loci presented here, 8 exhibit fixed differences between coastal cutthroat trout and coastal rainbow trout/steelhead. The other three loci revealed frequency diff...

Genetic Stock Identification of Steelhead in the Columbia River Basin: An Evaluation of Different Molecular Markers

Abstract Protein genetic markers (allozymes) have been used during the last decade in a genetic stock identification (GSI) program by state and federal management agencies to monitor stocks of steelhead Oncorhynchus mykiss in the Columbia River basin. In this paper we report new data for five microsatellite and three intron loci from 32 steelhead populations in the three upriver evolutionarily significant units (ESUs) and compare the performance of allozyme, microsatellite, and intron markers for use in GSI mixture analyses. As expected, microsatellites and introns had high total heterozygosity (H T) values; but there was little difference among marker classes in the magnitude of population differentiation as estimated by Wrights fixation index (F ST), which ranged from 0.041 (microsatellite loci) to 0.047 (allozyme loci) and 0.050 (intron loci). For allozyme and microsatellite loci, the relationships among populations followed the patterns of geographic proximity. In computer-simulated mixture analyses,...

A centralized model for creating shared, standardized, microsatellite data that simplifies inter-laboratory collaboration

We demonstrate an efficient model for standardizing microsatellite DNA data among laboratories studying Oncorhynchus mykiss. Eight laboratories standardized 13 microsatellite loci following allele nomenclature of a central laboratory (average inter-laboratory genotyping concordance >98%). Following this central model, we have currently standardized 298 alleles from throughout the species native range. Although we focus here on O. mykiss, our experiences and recommendation apply equally to other broadly distributed species that may benefit from multi-laboratory collaborative data collection.

Major Lineages and Metapopulations in Columbia River Oncorhynchus mykiss Are Structured by Dynamic Landscape Features and Environments

Abstract It is widely recognized that genetic diversity within species is shaped by dynamic habitats. The quantitative and molecular genetic patterns observed are the result of demographics, mutation, migration, and adaptation. The populations of rainbow trout Oncorhynchus mykiss in the Columbia River basin (including both resident and anadromous forms and various subspecies) present a special challenge to understanding the relative roles of those factors. Standardized microsatellite data were compiled for 226 collections (15,658 individuals) from throughout the Columbia and Snake River basins to evaluate the genetic patterns of structure and adaptation. The data were primarily from fish of the anadromous life history form, and we used a population grouping procedure based on principal components and hierarchical k-means clustering to cluster populations into eight aggregates or groups with similar allele frequencies. These aggregates approximated geographic regions, and the two largest principal componen...

Diminished Reproductive Success of Steelhead from a Hatchery Supplementation Program (Little Sheep Creek, Imnaha Basin, Oregon)

Abstract Hatchery supplementation programs are designed to enhance natural production and maintain the fitness of the target population; however, it can be difficult to evaluate the success of these programs. Key to the success of such programs is a relatively high reproductive success of hatchery fish. This study investigated the relative reproductive success (RRS) of steelhead Oncorhynchus mykiss (anadromous rainbow trout) by creating pedigrees for hatchery and natural spawning steelhead. We genotyped adult steelhead that returned to a weir and were released upstream to spawn in Little Sheep Creek, a tributary to the Imnaha River in eastern Oregon. The broodstock for this supplementation program were originally chosen from natural-origin steelhead returning to the weir and in subsequent years consisted of both natural- and hatchery-origin individuals. Microsatellite analyses showed the broodstock to be genetically similar to the natural population across years. We also genotyped adult resident rainbow t...

Small-Scale Genetic Structure and Variation in Steelhead of the Grande Ronde River, Oregon, USA

Abstract Patterns of genetic variation in summer-run steelhead Oncorhynchus mykiss from the Grande Ronde River, Oregon, were evaluated with 20 microsatellite loci to determine the level of fine-scale genetic structure and influences from hatchery-reared stocks. Included were temporal collections of three wild populations (Lookingglass Creek, Catherine Creek, and the upper Grande Ronde River) and one hatchery population (Wallowa Hatchery). Average gene diversity was moderate to high in all collections (range = 0.794–0.815). Genetic variance among sample locations was greater than that of temporal collections within sites, as pairwise exact tests within populations were not significant except for Lookingglass Creek (P = 0.00005). Structure among the four populations was evident from pairwise tests, which yielded 23 significant results from 28 comparisons (adjusted critical value = 0.0018), but Catherine Creek collections were not significantly different from Wallowa Hatchery collections. None of the eight c...

The utility and limitations of genetic data for stock identification and management of North Pacific rockfish (Sebastes spp.)

Rockfishes (Sebastes spp.) represent a speciose and ecologically important group of marine fishes found in both the Pacific and Atlantic oceans, with approximately 105 species found world-wide (Hyde and Vetter 2007). They also comprise the majority of species found in the Pacific groundfish fishery. Thorough species assessments in terms of harvest management have been done for only 11 species, and of the 11 species, seven have been declared overfished. Having accurate genetic information is critical to the continuing effort at stock assessments, but sampling is often difficult in marine fishes. Genetic techniques are a powerful tool in the effort to better characterize the ecology of these species. These techniques can be used to investigate multiple biological traits, including species identity, intra- and interspecific genetic variation, migration patterns, and effective population size. There are important caveats and limitations when applying specific genetic methods, especially in marine species that lack discrete spawning aggregates. Nevertheless, it is clear from a review of recent literature that genetic tools have already provided very specific insight regarding rockfish population dynamics. The results are diverse and difficult to synthesize; however, existing studies show five primary patterns to population groupings in rockfishes: no obvious pattern of structure, structure consistent with isolation by distance, structure evident but inconsistent with isolation by distance, structure that correlates to oceanographic features, and potential genetic introgression. Clearly the study of rockfish population genetics is poised for rapid expansion that will unquestionably aid management of the rockfish fisheries and general understanding of rockfish evolutionary systematics. A principle challenge at this point is to derive generalized inferences from such a diverse array of study results across the vast North Pacific range of Sebastes. This review summarizes existing genetic studies in Sebastes spp. in the North Pacific to assist in identifying knowledge gaps for this ecologically important and diverse group.

Multiple paternity is prevalent in Pacific ocean perch (Sebastes alutus) off the Oregon coast, and is correlated with female size and age

The need to rebuild Pacific ocean perch, Sebastes alutus, populations on the west coast of the United States has precipitated a need to better understand the life history characteristics of this rockfish species. One such characteristic is mating behavior, which has the potential to influence the amount of genetic diversity in a population. We documented and examined the frequency of multiple mating in Pacific ocean perch collected off the Oregon coast using five microsatellite loci. We found that 47 of 66 (71.2%) females examined had broods sired by multiple males. The mean number of sires per brood was 1.92 (SD = 0.76) and ranged from 1–4. Polyandrous females were significantly larger and had an older average age than monogamous females. Our results suggest that polyandrous behavior among female Pacific ocean perch off the coast of Oregon is prevalent, is related to female size and age, and should be preserved by maintaining a natural age structure in this population.

Polymerase Chain Reaction Inhibition in Historical Fish Scale Mounting Cards

Abstract In the case of Pacific salmon Oncorhynchus spp., as in that of other fish species, the ability to amplify specific DNA sequences from historical scale samples offers the opportunity to infer past population genetic structure and better understand how human activities may have changed natural populations. We extracted DNA from fish scales of various ages using two different methods and tested polymerase chain reaction (PCR) amplification of nuclear and mitochondrial products of various sizes. Our results provide further insight into some important limitations in working with historical DNA samples. We found evidence suggesting the presence of an inhibitory compound associated with the gummed scale collection cards that copurified with the DNA. Our results demonstrated that the putative inhibitory material was free in solution and not bound to the scale DNA. Long recognized in other genetic literature, PCR inhibition has only recently been reported in historical studies of fish. This paper provides...