Analysis of microsatellite DNA resolves genetic structure and diversity of chinook salmon (<i>Oncorhynchus tshawytscha</i>) in California's Central Valley

Abstract

We use 10 microsatellite DNA markers to assess genetic diversity within and among the four runs (winter, spring, fall, and late fall) of chinook salmon (Oncorhynchus tshawytscha) in California's Central Valley. Forty-one population samples are studied, comprising naturally spawning and hatchery stocks collected from 1991 through 1997. Maximum likelihood methods are used to correct for kinship in juvenile samples and run admixture in adult samples. Through simulation, we determine the relationship between sample size and number of alleles observed at polymorphic microsatellite markers. Most samples have random-mating equilibrium proportions of single and multilocus genotypes. Temporal and spatial genetic heterogeneity is minimal among samples within subpopulations. An F ST of 0.082 among subpopulations, however, indicates substantial divergence among runs. Thus, with the exception of our discovery of two distinct lineages of spring run, genetic structure accords with the diverse chinook life histories seen in the Central Valley and provides a means for discrimination of protected populations. Résumé : Nous nous sommes servis de dix marqueurs microsatellites de l'ADN pour estimer la diversité génétique dans et entre les quatre remontes (hiver, printemps, automne et fin de l'automne) de quinnat (Oncorhynchus tshawytscha) dans la vallée centrale de la Californie. Nous avons étudié 41 échantillons de populations, représentant des poissons à reproduction naturelle et des stocks d'écloserie, prélevés entre 1991 et 1997. Les méthodes du maximum de vraisemblance ont servi à faire la correction pour la parenté génétique dans les échantillons de juvéniles et pour le mélange des remontes dans les échantillons d'adultes. Par la simulation, nous déterminons la relation entre la taille de l'échantillon et le nombre d'allèles observés aux marqueurs polymorphes microsatellites. La plupart des échantillons présentent des proportions équilibrées d'appariement aléatoire de génotypes à un et à plusieurs locus. L'hétérogénéité génétique temporelle et spatiale est minime entre les échantillons au sein des sous-populations. Un F ST de 0,082 entre les sous-populations indique toutefois une divergence substantielle entre les remontes. Ainsi, à l'exception de notre découverte de deux lignées distinctes dans la remonte du printemps, la structure génétique concorde avec les divers cycles biologiques du quinnat observés dans la vallée centrale et fournit un moyen de distinguer les populations protégées. [Traduit par la Rédaction] Banks et al. 927

What sampling is needed for reliable estimations of genetic diversity in Fraxinus excelsior L. (Oleaceae)?

“…1) out of 31 possible alleles. Our results are similar to those for trout populations measured also with microsatellites whose sampling requirement is between 200 and 300 individuals if most of the alleles are to be captured (Banks, et al, 2000). If hypervariable microsatellites are the chosen tool for population diversity measures and allelic richness and inclusion of rare alleles the conservation goal, population sizes that need to be sampled and preserved will necessarily be large.…”

“…In consequence, accuracy is measured with a bias estimator, and precision with standard errors and related measures. We combined the methods proposed by (Banks et al, 2000) to measure allelic diversity by Monte Carlo resampling and those by (Kirst et al, 2005) to measure the accuracy of the estimations through the use of mean square errors (MSE). Therefore, resampling without replacement from the whole adult population (N = 579) was performed for samplings efforts of n = 1, 2, 3, .…”

Science Advancements Key to Increasing Management Value of Life Stage Monitoring Networks for Endangered Sacramento River Winter-Run Chinook Salmon in California

“…Sacramento and Chipps Island trawls are considered two high-priority locations for genetic monitoring of SRWRC for four reasons: (1) Although this monitoring review focuses primarily on advances for SRWRC, the resolution of the current genetic baseline provides high-precision identification of both ESA-listed salmon runs in the Central Valley (i.e., SRWRC and wild spring-run Chinook from Deer, Mill, and Butte creeks; Banks et al 2000;Seeb et al 2007;Anderson et al 2008;Banks et al 2014;Clemento et al 2014). However, there are challenges in distinguishing the late-fall run from fall run, and in identifying wild Feather River spring-run Chinook Salmon, because of introgression with fall-run Chinook Salmon (Clemento et al 2014).…”

“…• Current and previous Central Valley AT tagging programs have provided important new insights into migration rates, reach-specific survival estimates, behaviors at junctions, and survival related to environmental co-variates (reviewed in Perry et al 2016) • Extensively used in Columbia River Basin to estimate survival of juvenile salmon through dams (McMichael et al 2010) • Real-time receivers can provide in-season detections and fish distribution and movement data, and with modeling support can be used to monitor in-season survival standards 18 VOLUME 15, ISSUE 3, ARTICLE 1 long-term viability, especially given their recent population bottlenecks and low genetic diversity (Banks et al 2000;Lindley et al 2007). Monitoring within-population genetic diversity, effective population size, relative reproductive success of individuals as a function of origin (hatchery versus wild), and spawning behavior (timing and location) provide important insights into how management actions (e.g., hatchery broodstock management) and water project operations (e.g., water temperature, flow timing, and the magnitude of flow releases) may influence the population's long-term genetic integrity.…”

Yuba River analysis aims to aid spring-run chinook salmon habitat rehabilitation

“…Four distinct races of anadromous chinook salmon occupy the Sacramento/San Joaquin river system (Banks et al 2000), but for spawning they all prefer common physical attributes of a river: cool temperature, gravel and cobble bed material, low depth (about 0.5 to 4 feet) and moderate velocity (2 to 4 feet per second). The spring-run chinook salmon is a federally threatened species that is differentiated by the time at which adults migrate from the ocean to fresh water systems (Yoshiyama et al 1996).…”