Jennifer L. Nielsen

Thermally Stratified Pools and Their Use by Steelhead in Northern California Streams

Abstract Thermal stratification occurred in pools of three rivers in northern California when inflow of cold water was sufficiently great or currents were sufficiently weak to prevent thorough mixing of water of contrasting temperatures. Surface water temperatures in such pools were commonly 3–9°C higher than those at the bottom. Cold water entered pools from tributaries, intergravel flow through river bars, and streamside subsurface sources. In Redwood and Rancheria Creeks, cold water was protected where gravel bars encroached into pools that were scoured along bedrock banks, creating isolated backwaters. Sixty-five percent of the juvenile steelhead Oncorhynchus mykiss found in the Rancheria Creek study reaches moved into adjacent stratified pools during periods of high ambient stream temperatures (23–28°C). Fish showed a decline in forage behavior and increased agonistic activity just before movement into stratified pools. In the Middle Fork Eel River, pools deeper than 3 m stratified when surface flow ...

Microhabitat-Specific Foraging Behavior, Diet, and Growth of Juvenile Coho Salmon

Abstract Observations of behavior were made on marked juvenile coho salmon Oncorhynchus kisutch in pools in Huckleberry Creek, Washington. Fish exhibited two distinct types of forage behavior during observations made from May to August 1988 and from June to August 1989. Some coho salmon formed dominance hierarchies wherein fish defended forage stations in ranks determined by an individuals ability or willingness to defend access to drifting food. Other coho salmon foraged as nonhierarchical floaters. Eight percent of marked individuals changed their foraging behavior class during their first summer. Focal point velocity (FPV) differentiated specific microhabitats used by these two foraging behavior classes. Coho salmon in dominance hierarchies (FPV > 0.06 m/s) fed most frequently on drifting invertebrates, which contributed 81% of their energy intake. Floaters (FPV ≤ 0.06 m/s) fed by patrolling large forage arenas, where they fed opportunistically on items delivered by aerial drop and instream drift. Ene...

Mitochondrial DNA and Nuclear Microsatellite Diversity in Hatchery and Wild Oncorhynchus mykiss from Freshwater Habitats in Southern California

Abstract We examined mitochondrial control-region haplotype diversity and allelic frequency distributions for three polymorphic microsatellite loci in 541 coastal Oncorhynchus mykiss collected from six habitats associated with different levels of human activity and ocean access in southern California. Extensive urbanization, climatic unpredictability, and the accelerated rate of decline in anadromous fish suggested a probable loss of genetic diversity in this area due to habitat fragmentation, geographic isolation, and population bottlenecks. Unexpectedly high levels of genetic diversity were found in southern California populations of O. mykiss. Haplotype diversity (H S) was highest in anadromous fish (H S = 0.74) and lowest in the Whale Rock Hatchery trout (H S = 0.32). The proportion of variation attributable to population differentiation among habitat groups (G ST) was 10%. Haplotype frequencies showed a close relationship between anadromous steelhead and resident rainbow trout from closed habitats (D...

Scientific Sampling Effects: Electrofishing California's Endangered Fish Populations

Abstract Standard methods used by biologists around the world for sampling fish populations and determining fish and habitat relationships primarily involve electrofishing. With the recent listings of coastal salmon and steelhead as threatened or endangered, one must ask how electrofishing-induced injury to fish in rare populations relates to “take” under the U.S. Endangered Species Act. Issues related to electrofishing are under discussion in California as federal and state agencies determine how to approach permitting for monitoring and research activities in rivers containing protected fish populations. Many problems have been discussed in the literature based on short-and long-term injury to individual fish from different forms of electrofishing. To date no standard approach for this technology exists that will allow effective surveys without probable injury to some portion of the fish population. How electrofishing injuries made at the individual fish level translate into population effects has not b...

Biogeographic analysis of Pacific trout (Oncorhynchus mykiss) in California and Mexico based on mitochondrial DNA and nuclear microsatellites

The Pacific basin trout were traditionally classified as members of the Atlantic lineage Salmo, based on analyses of morphology and life history characteristics. This chapter explores the biogeographic analysis of pacific trout ( Oncorhynchus mykiss ) in California and Mexico. DNA studies of Pacific salmonids were initially concentrated on mitochondrial DNA (mtDNA) markers due to the relatively rapid rate of evolution in this maternally inherited molecule and the ease of extraction and amplification of mtDNA. The primary methods and material used in these studies were sampling protocols, extracting mtDNA from fin clips, microsatellites, and an analytical approach for sequences obtained from the mtDNA. Analysis of Variance (ANOVA) and factor analysis using Principal Components (PCA) were used to describe biogeographic associations between genotype (mtDNA or microsatellite allelic diversity) and sample location (longitude and latitude). The results for the changes found in mitochondrial control region variable sites and nucleotides are shown in this chapter using a tabular representation. While dealing with the biogeographic concordance in these studies, a significant correlation was observed in mtDNA haplotype variation. The phylogeographic structure for mtDNA was significantly associated with both longitude and latitude in western trout populations.

Oncorhynchus at the southern extent of their range : a study of mtDNA control-region sequence with special reference to an undescribed subspecies of O. mykiss from Mexico

Nucleotide sequences from the right-domain of salmonid mitochondrial DNA (mtDNA) control region flanking the phenylalanine tRNA gene (tRNAPhe) were determined for 5 species and 14 subspecies of Oncorhynchus at the southern extent of their range. In all but one population, the right domain contained two 72 bp tandem repeats located between the tRNAPhe gene and the conserved sequence block CSB-3. At the species level we found 46–83% homology between these two repeats. The repeat closest to tRNAPhe contained 43% of the phylogenetically informative sites. The largest number of transversions (N=6) were found outside of both repeat sequences. Phylogenetic inference based on mtDNA right-domain sequence was congruent with other analyses at the species level, but gave variable results in association drawn at the subspecific level. The right-domain contained three highly conserved sequences corresponding to the mtDNA transcription factor, and the heavy- and light-strand promoters. In four O. mykiss from Rio Yaqui, Mexico, the repeat containing the heavy-strand promoter (HSP) was deleted. The mtDNA HSP is responsible for transcription of the 16S and 12S rRNAs, 12 of the 13 protein-coding genes, and most of the tRNA genes. Rio Yagui trout showed no heteroplasmy or tissue specificity for this deletion. This HSP deletion suggests the possibility of a primitive transcriptional promoter with bidirectional capacity in this species, similar to that reported in avian and amphibian mtDNA. These data expand our understanding of genetic diversity in Oncorhynchus at the southern extent of their range with a knowledge of the evolutionary mechanisms that may have led to that diversity.

Threatened fishes of the world : Oncorhynchus mykiss nelsoni Evermann, 1908 (Salmonidae)

Common names: Baja California rainbow trout, San Pedro Mártir rainbow trout, Nelson’s trout. Conservation status: Rare according to Secretariá de Desarollo Social (1994) due to its restricted distribution and low abundance; special concern according to Williams et al. 1989. Identification: Snyder 1926; pp. 44–47 in Needham & Gard (1959); typically have 61–62 vertebra and 125–140 scales in the lateral series, but lack diagnostic taxonomic characters which allow separation from coastal rainbow trout (Behnke 1992); unique rare allele that codes for enzyme creatine kinase (CK-2; Berg 1987); unique dominant alleles for three nuclear microsatellites (Nielsen et al. 1996). Photograph by Phil Pister from Rio St. Domingo, June 1984. Distribution: The original distribution of O.m. nelsoni was in the 24 km section of the Rio Santo Domingo from Rancho San Antonio to the base of a high waterfall that blocks upstream migration (Snyder 1926, Smith 1991). Present confirmed distribution in upper drainage of two main basins, Santo Domingo and San Rafael (Ruiz-Campos & Pister 1995). Abundance: Arroya La Zanja in Santo Domingo drainage 0.25 fish m stream; upper Arroyo San Rafael 0.13–0.43 fish m stream; rare or absent from several tributary locations and lower basin type localities for O.m. nelsoni (Ruiz-Campos & Pister 1995). Habitat and ecology: Baja trout reside in remote, fragile ecosystems found at headwaters locations in two Baja California drainages (540–2030 m above sea level). Both basins contain arid stream systems in batholithic terrain. Perennial flows occur in headwaters, but streams are intermittent in middle and lower courses during dry conditions. Stream mouths are frequently blocked from the ocean by formation of sandbars. Trout are primarily found in larger, deep (1–2 m) pools with heavy riparian (willows and cottonwood) and aquatic vegetation. The ancestor of this trout has been speculated to have been an anadromous coastal steelhead trout from southern California (Evermann 1908, Smith 1991), however, Behnke (1992) suggests an ancestral mixture of primitive forms of both redband and coastal rainbow trout. Recent genetics work showed the Baja trout are fixed for a mitochondrial DNA (mtDNA) haplotype identical to the dominant north-coast steelhead lineage (Nielsen et al. 1994). Most population structure for mtDNA can be traced back to the Pleistocene. Therefore, this association could have resulted from ancestral steelhead straying into Baja rivers a long time ago. Baja trout do carry unique microsatellite alleles that allow diagnostic differentiation from all coastal steelhead and rainbow trout (Nielsen et al. 1996). Only the Little Kern River golden trout, O.m. whitei (Evermann) share these unique microsatellite alleles with Nelson’s trout. Reproduction: Spawning and reproductive behavior are similar to non-migratory resident strains of rainbow trout found in arid habitats throughout southern California (Ruiz-Campos 1993). Threats: Anthropogenic activities including habitat degradation due to grazing and forest practices; introduction of exotics or non-native trout genotypes that threaten introgression and competition for limited habitat; unregulated sport fishing that threatens to eliminate reproductive segments of the population; small isolated populations that are vulnerable to extinction due to natural disasters such as forest fires and severe floods.