Michael A. Banks

Influence of barriers to movement on within-watershed genetic variation of coastal cutthroat trout

Because human land use activities often result in increased fragmentation of aquatic and terrestrial habitats, a better understanding of the effects of fragmentation on the genetic heterogeneity of animal populations may be useful for effective management. We used eight microsatellites to examine the genetic structure of coastal cutthroat trout (Oncorhynchus clarki clarki) in Camp Creek, an isolated headwater stream in western Oregon. Our objectives were to determine if coastal cutthroat trout were genetically struc- tured within streams and to assess the effects of natural and anthropogenic barriers on coastal cutthroat trout genetic variation. Fish sampling occurred at 10 locations, and allele frequencies differed significantly among all sampling sections. Dispersal barriers strongly influenced coastal cutthroat trout genetic structure and were associated with reduced genetic diversity and increased genetic differentiation. Results indicate that Camp Creek coastal cutthroat trout exist as many small, partially independent populations that are strongly affected by genetic drift. In headwater streams, barriers to movement can result in genetic and demographic isolation leading to reduced coastal cutthroat trout genetic diversity, and potentially compromising long-term population persistence. When habitat fragmentation eliminates gene flow among small populations, similar results may occur in other species.

Differentiating salmon populations at broad and fine geographical scales with microsatellites and single nucleotide polymorphisms

Single nucleotide polymorphisms (SNPs) are appealing genetic markers due to several beneficial attributes, but uncertainty remains about how many of these bi‐allelic markers are necessary to have sufficient power to differentiate populations, a task now generally accomplished with highly polymorphic microsatellite markers. In this study, we tested the utility of 37 SNPs and 13 microsatellites for differentiating 29 broadly distributed populations of Chinook salmon (n = 2783). Information content of all loci was determined by In and , and the top 12 markers ranked by In were microsatellites, but the 6 highest, and 7 of the top 10 ranked markers, were SNPs. The mean ratio of random SNPs to random microsatellites ranged from 3.9 to 4.1, but this ratio was consistently reduced when only the most informative loci were included. Individual assignment test accuracy was higher for microsatellites (73.1%) than SNPs (66.6%), and pooling all 50 markers provided the highest accuracy (83.2%). When marker types were combined, as few as 15 of the top ranked loci provided higher assignment accuracy than either microsatellites or SNPs alone. Neighbour‐joining dendrograms revealed similar clustering patterns and pairwise tests of population differentiation had nearly identical results with each suite of markers. Statistical tests and simulations indicated that closely related populations were better differentiated by microsatellites than SNPs. Our results indicate that both types of markers are likely to be useful in population genetics studies and that, in some cases, a combination of SNPs and microsatellites may be the most effective suite of loci.

A latitudinal cline in the Chinook salmon (Oncorhynchus tshawytscha) Clock gene: evidence for selection on PolyQ length variants

A critical seasonal event for anadromous Chinook salmon (Oncorhynchus tshawytscha) is the time at which adults migrate from the ocean to breed in freshwater. We investigated whether allelic variation at the circadian rhythm genes, OtsClock1a and OtsClock1b, underlies genetic control of migration timing among 42 populations in North America. We identified eight length variants of the functionally important polyglutamine repeat motif (PolyQ) of OtsClock1b while OtsClock1a PolyQ was highly conserved. We found evidence of a latitudinal cline in average allele length and frequency of the two most common OtsClock1b alleles. The shorter 335 bp allele increases in frequency with decreasing latitude while the longer 359 bp allele increases in frequency at higher latitudes. Comparison to 13 microsatellite loci showed that 335 and 359 bp deviate significantly from neutral expectations. Furthermore, a hierarchical gene diversity analysis based on OtsClock1b PolyQ variation revealed that run timing explains 40.9 per cent of the overall genetic variance among populations. By contrast, an analysis based on 13 microsatellite loci showed that run timing explains only 13.2 per cent of the overall genetic variance. Our findings suggest that length polymorphisms in OtsClock1b PolyQ may be maintained by selection and reflect an adaptation to ecological factors correlated with latitude, such as the seasonally changing day length.

Which genetic loci have greater population assignment power

SUMMARY WHICHLOCI is a program that determines the relative discriminatory power of alternate genetic loci and loci combinations for population assignment of individuals. AVAILABILITY http://www.oregonstate.edu/dept/comes/genetics/software.htm

Candidate loci reveal genetic differentiation between temporally divergent migratory runs of Chinook salmon (Oncorhynchus tshawytscha).

Local adaptation is a dynamic process driven by selection that can vary both in space and time. One important temporal adaptation for migratory animals is the time at which individuals return to breeding sites. Chinook salmon (Oncorhynchus tshawytscha) are excellent subjects for studying the genetic basis of temporal adaptation because their high seasonal homing fidelity promotes reproductive isolation leading to the formation of local populations across diverse environments. We tested for adaptive genetic differentiation between seasonal runs of Chinook salmon using two candidate loci; the circadian rhythm gene, OtsClock1b, and Ots515NWFSC, a microsatellite locus showing sequence identity to three salmonid genes central to reproductive development. We found significant evidence for two genetically distinct migratory runs in the Feather River, California (OtsClock1b: FST = 0.042, P = 0.02; Ots515NWFSC: FST = 0.058, P = 0.003). In contrast, the fall and threatened spring runs are genetically homogenous based on neutral microsatellite data (FST = –0.0002). Similarly, two temporally divergent migratory runs of Chinook salmon from New Zealand are genetically differentiated based on polymorphisms in the candidate loci (OtsClock1b: FST = 0.083, P‐value = 0.001; Ots515NWFSC: FST = 0.095, P‐value = 0.000). We used an individual‐based assignment method to confirm that these recently diverged populations originated from a single source in California. Tests for selective neutrality indicate that OtsClock1b and Ots515NWFSC exhibit substantial departures from neutral expectations in both systems. The large FST estimates could therefore be the result of directional selection. Evidence presented here suggests that OtsClock1b and Ots515NWFSC may influence migration and spawning timing of Chinook salmon in these river systems.

Reduced reproductive success of hatchery coho salmon in the wild: insights into most likely mechanisms

Supplementation of wild salmonids with captive‐bred fish is a common practice for both commercial and conservation purposes. However, evidence for lower fitness of captive‐reared fish relative to wild fish has accumulated in recent years, diminishing the apparent effectiveness of supplementation as a management tool. To date, the mechanism(s) responsible for these fitness declines remain unknown. In this study, we showed with molecular parentage analysis that hatchery coho salmon (Oncorhynchus kisutch) had lower reproductive success than wild fish once they reproduced in the wild. This effect was more pronounced in males than in same‐aged females. Hatchery spawned fish that were released as unfed fry (age 0), as well as hatchery fish raised for one year in the hatchery (released as smolts, age 1), both experienced lower lifetime reproductive success (RS) than wild fish. However, the subset of hatchery males that returned as 2‐year olds (jacks) did not exhibit the same fitness decrease as males that returned as 3‐year olds. Thus, we report three lines of evidence pointing to the absence of sexual selection in the hatchery as a contributing mechanism for fitness declines of hatchery fish in the wild: (i) hatchery fish released as unfed fry that survived to adulthood still had low RS relative to wild fish, (ii) age‐3 male hatchery fish consistently showed a lower relative RS than female hatchery fish (suggesting a role for sexual selection), and (iii) age‐2 jacks, which use a sneaker mating strategy, did not show the same declines as 3‐year olds, which compete differently for females (again, implicating sexual selection).

Influence of habitat discontinuity, geographical distance, and oceanography on fine-scale population genetic structure of copper rockfish (Sebastes caurinus)

The copper rockfish is a benthic, nonmigratory, temperate rocky reef marine species with pelagic larvae and juveniles. A previous range‐wide study of the population‐genetic structure of copper rockfish revealed a pattern consistent with isolation‐by‐distance. This could arise from an intrinsically limited dispersal capability in the species or from regularly–spaced extrinsic barriers that restrict gene flow (offshore jets that advect larvae offshore and/or habitat patchiness). Tissue samples were collected along the West Coast of the contiguous USA between Neah Bay, WA and San Diego, CA, with dense sampling along Oregon. At the whole‐coast scale (~2200 km), significant population subdivision (FST = 0.0042), and a significant correlation between genetic and geographical distance were observed based on 11 microsatellite DNA loci. Population divergence was also significant among Oregon collections (~450 km, FST = 0.001). Hierarchical amova identified a weak but significant 130‐km habitat break as a possible barrier to gene flow within Oregon, across which we estimated that dispersal (Nem) is half that of the coast‐wide average. However, individual‐based Bayesian analyses failed to identify more than a single population along the Oregon coast. In addition, no correlation between pairwise population genetic and geographical distances was detected at this scale. The offshore jet at Cape Blanco was not a significant barrier to gene flow in this species. These findings are consistent with low larval dispersal distances calculated in previous studies on this species, support a mesoscale dispersal model, and highlight the importance of continuity of habitat and adult population size in maintaining gene flow.

Use of Genetic Stock Identification Data for Comparison of the Ocean Spatial Distribution, Size at Age, and Fishery Exposure of an Untagged Stock and Its Indicator: California Coastal versus Klamath River Chinook Salmon

AbstractManaging weak stocks in mixed-stock fisheries often relies on proxies derived from data-rich indicator stocks, although there have been limited tests of the appropriateness of such proxies. For example, full cohort reconstruction of tagged Klamath River fall-run Chinook Salmon Oncorhynchus tshawytscha of northern California enables the use of detailed models to inform management. Information gained from this stock is also used in the management of the untagged, threatened California Coastal Chinook Salmon (CCC) stock, where it is assumed that a cap on Klamath harvest rates effectively constrains impacts on CCC to acceptable levels. To evaluate use of this proxy, we used a novel approach based on genetic stock identification (GSI) data to compare the two stocks’ size at age and ocean distribution (as inferred from spatial variation in CPUE), two key factors influencing fishery exposure. We developed broadly applicable methods to account for both sampling and genetic assignment uncertainty in estima...

Population Structure of Three Species of Anisakis Nematodes Recovered From Pacific Sardines (Sardinops sagax) Distributed Throughout the California Current System

abstract:  Members of the Anisakidae are known to infect over 200 pelagic fish species and have been frequently used as biological tags to identify fish populations. Despite information on the global distribution of Anisakis species, there is little information on the genetic diversity and population structure of this genus, which could be useful in assessing the stock structure of their fish hosts. From 2005 through 2008, 148 larval anisakids were recovered from Pacific sardine (Sardinops sagax) in the California Current upwelling zone and were genetically sequenced. Sardines were captured off Vancouver Island, British Columbia in the north to San Diego, California in the south. Three species, Anisakis pegreffii, Anisakis simplex ‘C’, and Anisakis simplex s.s., were identified with the use of sequences from the internal transcribed spacers (ITS1 and ITS2) and the 5.8s subunit of the nuclear ribosomal DNA. The degree of nematode population structure was assessed with the use of the cytochrome c oxidase 2 (cox2) mitochondrial DNA gene. All 3 Anisakis species were distributed throughout the study region from 32°N to 50°N latitude. There was no association between sardine length and either nematode infection intensity or Anisakis species recovered. Larval Anisakis species and mitochondrial haplotype distributions from both parsimony networks and analyses of molecular variance revealed a panmictic distribution of these parasites, which infect sardines throughout the California Current ecosystem. Panmictic distribution of the larval Anisakis spp. populations may be a result of the presumed migratory pathways of the intermediate host (the Pacific sardine), moving into the northern portion of the California Current in summer and returning to the southern portion to overwinter and spawn in spring. However, the wider geographic range of paratenic (large piscine predators), and final hosts (cetaceans) can also explain the observed distribution pattern. As a result, the recovery of 3 Anisakis species and a panmictic distribution of their haplotypes could not be used to confirm or deny the presence of population subdivision of Pacific sardines in the California Current system.

Survival and life history characteristics among wild and hatchery coho salmon (Oncorhynchus kisutch) returns: how do unfed fry differ from smolt releases?

Survival and life history characteristics were evaluated for a coho salmon (Oncorhynchus kisutch) integrated hatchery program using two stocking strategies. Fish were released as unfed fry or smolts and returned as adults, and then molecular analysis was employed to pedigree the entire population. We showed that mean adult survival of individuals released as unfed fry was less than that of individuals released as smolts (0.03% vs. 2.39%). The relative reproductive success (RRS) of the fry release strategy to wild spawning was significantly greater for one of two cohorts, whereas the smolt release strategy to wild RRS was significantly greater for both cohorts. Fish released as smolts were significantly smaller upon returning as adults than either those released as unfed fry or wild returns. Mean run timing was also significantly biased towards an earlier run time for hatchery-released fish when compared with the wild component. The incidence of jacking (males maturing at age 2) was greater among fish stoc...