John Carlos Garza

The Power of Single-Nucleotide Polymorphisms for Large-Scale Parentage Inference

Likelihood-based parentage inference depends on the distribution of a likelihood-ratio statistic, which, in most cases of interest, cannot be exactly determined, but only approximated by Monte Carlo simulation. We provide importance-sampling algorithms for efficiently approximating very small tail probabilities in the distribution of the likelihood-ratio statistic. These importance-sampling methods allow the estimation of small false-positive rates and hence permit likelihood-based inference of parentage in large studies involving a great number of potential parents and many potential offspring. We investigate the performance of these importance-sampling algorithms in the context of parentage inference using single-nucleotide polymorphism (SNP) data and find that they may accelerate the computation of tail probabilities >1 millionfold. We subsequently use the importance-sampling algorithms to calculate the power available with SNPs for large-scale parentage studies, paying particular attention to the effect of genotyping errors and the occurrence of related individuals among the members of the putative mother–father–offspring trios. These simulations show that 60–100 SNPs may allow accurate pedigree reconstruction, even in situations involving thousands of potential mothers, fathers, and offspring. In addition, we compare the power of exclusion-based parentage inference to that of the likelihood-based method. Likelihood-based inference is much more powerful under many conditions; exclusion-based inference would require 40% more SNP loci to achieve the same accuracy as the likelihood-based approach in one common scenario. Our results demonstrate that SNPs are a powerful tool for parentage inference in large managed and/or natural populations.

Development of a Standardized DNA Database for Chinook Salmon

Abstract An international multi-laboratory project was conducted to develop a standardized DNA database for Chinook salmon (Oncorhynchus tshawytscha ). This project was in response to the needs of the Chinook Technical Committee of the Pacific Salmon Commission to identify stock composition of Chinook salmon caught in fisheries during their oceanic migrations. Nine genetics laboratories identified 13 microsatellite loci that could be reproducibly assayed in each of the laboratories. To test that the loci were reproducible among laboratories, blind tests were conducted to verify scoring consistency for the nearly 500 total alleles. Once standardized, a dataset of over 16,000 Chinook salmon representing 110 putative populations was constructed ranging throughout the area of interest of the Pacific Salmon Commission from Southeast Alaska to the Sacramento River in California. The dataset differentiates the major known genetic lineages of Chinook salmon and provides a tool for genetic stock identification of ...

A comparison of variability and population structure for major histocompatibility complex and microsatellite loci in California coastal steelhead (Oncorhynchus mykiss Walbaum)

The major histocompatibility complex (MHC) contains genes integral to immune response in vertebrates. MHC genes have been shown to be under selection in a number of vertebrate taxa, making them intriguing for population genetic studies. We have conducted a survey of genetic variation in an MHC class II gene for steelhead trout from 24 sites in coastal California and compared this variation to that observed at 16 presumably neutral microsatellite loci. A high amount of allelic variation was observed at the MHC when compared to previously published studies on other Pacific salmonids. Elevated nonsynonymous substitutions, relative to synonymous substitutions, were detected at the MHC gene, indicating the signature of historical balancing selection. The MHC data were tested for correlations to and deviations from the patterns found with the microsatellite data. Estimates of allelic richness for the MHC gene and for the microsatellites were positively correlated, as were estimates of population differentiation (FST). An analysis for FST outliers indicates that the MHC locus has an elevated FST relative to the neutral expectation, although a significant result was found for only one particular geographical subgroup. Relatively uniform allele frequency distributions were detected in four populations, although this finding may be partially due to recent population bottlenecks. These results indicate that, at the scale studied here, drift and migration play a major role in the observed geographical variability of MHC genes in steelhead, and that contemporary selection is relatively weak and difficult to detect.

Over the Falls? Rapid Evolution of Ecotypic Differentiation in Steelhead/Rainbow Trout (Oncorhynchus mykiss)

Adaptation to novel habitats and phenotypic plasticity can be counteracting forces in evolution, but both are key characteristics of the life history of steelhead/rainbow trout (Oncorhynchus mykiss). Anadromous steelhead reproduce in freshwater river systems and small coastal streams but grow and mature in the ocean. Resident rainbow trout, either sympatric with steelhead or isolated above barrier dams or waterfalls, represent an alternative life-history form that lives entirely in freshwater. We analyzed population genetic data from 1486 anadromous and resident O. mykiss from a small stream in coastal California with multiple barrier waterfalls. Based on data from 18 highly variable microsatellite loci (He = 0.68), we conclude that the resident population above one barrier, Big Creek Falls, is the result of a recent anthropogenic introduction from the anadromous population of O. mykiss below the falls. Furthermore, fish from this above-barrier population occasionally descend over the falls and have established a genetically differentiated below-barrier subpopulation at the base of the falls, which appears to remain reproductively isolated from their now-sympatric anadromous ancestors. These results support a hypothesis of rapid evolution of a purely resident life history in the above-barrier population in response to strong selection against downstream movement.

Rapid parallel evolution of standing variation in a single, complex, genomic region is associated with life history in steelhead/rainbow trout

Rapid adaptation to novel environments may drive changes in genomic regions through natural selection. Such changes may be population-specific or, alternatively, may involve parallel evolution of the same genomic region in multiple populations, if that region contains genes or co-adapted gene complexes affecting the selected trait(s). Both quantitative and population genetic approaches have identified associations between specific genomic regions and the anadromous (steelhead) and resident (rainbow trout) life-history strategies of Oncorhynchus mykiss. Here, we use genotype data from 95 single nucleotide polymorphisms and show that the distribution of variation in a large region of one chromosome, Omy5, is strongly associated with life-history differentiation in multiple above-barrier populations of rainbow trout and their anadromous steelhead ancestors. The associated loci are in strong linkage disequilibrium, suggesting the presence of a chromosomal inversion or other rearrangement limiting recombination. These results provide the first evidence of a common genomic basis for life-history variation in O. mykiss in a geographically diverse set of populations and extend our knowledge of the heritable basis of rapid adaptation of complex traits in novel habitats.

Population structure and genetic diversity of trout (Oncorhynchus mykiss) above and below natural and man-made barriers in the Russian River, California

The effects of landscape features on gene flow in threatened and endangered species play an important role in influencing the genetic structure of populations. We examined genetic variation of trout in the species Oncorhynchus mykiss at 22 microsatellite loci from 20 sites in the Russian River basin in central California. We assessed relative patterns of genetic structure and variation in fish from above and below both natural (waterfalls) and man-made (dams) barriers. Additionally, we compared sites sampled in the Russian River with sites from 16 other coastal watersheds in California. Genetic variation among the 20 sites sampled within the Russian River was significantly partitioned into six groups above natural barriers and one group consisting of all below barrier and above dam sites. Although the below-barrier sites showed moderate gene flow, we found some support for sub-population differentiation of individual tributaries in the watershed. Genetic variation at all below-barrier sites was high compared to above-barrier sites. Fish above dams were similar to those from below-barrier sites and had similar levels of genetic diversity, indicating they have not been isolated very long from below-barrier populations. Population samples from above natural barriers were highly divergent, with large Fst values, and had significantly lower genetic diversity, indicating relatively small population sizes. The origins of populations above natural barriers could not be ascertained by comparing microsatellite diversity to other California rivers. Finally, below-barrier sites farther inland were more genetically differentiated from other watersheds than below-barrier sites nearer the river’s mouth.

Population genetic structure and ancestry of Oncorhynchus mykiss populations above and below dams in south-central California.

Genetic analyses of coastal Oncorhynchus mykiss, commonly known as steelhead/rainbow trout, at the southern extreme of their geographic range in California are used to evaluate ancestry and genetic relationships of populations both above and below large dams. Juvenile fish from 20 locations and strains of rainbow trout commonly planted in reservoirs in the five study basins were evaluated at 24 microsatellite loci. Phylogeographic trees and analysis of molecular variance demonstrated that populations within a basin, both above and below dams, were generally each other’s closest relatives. Absence of hatchery fish or their progeny in the tributaries above dams indicates that they are not commonly spawning and that above-barrier fish are descended from coastal steelhead trapped at dam construction. Finally, no genetic basis was found for the division of populations from this region into two distinct biological groups, contrary to current classification under the US and California Endangered Species Acts.

Discovery and characterization of single-nucleotide polymorphisms in steelhead/rainbow trout, Oncorhynchus mykiss

Single‐nucleotide polymorphisms (SNPs) have several advantages over other genetic markers, including lower mutation and genotyping error rates, ease of inter‐laboratory standardization, and the prospect of high‐throughput, low‐cost genotyping. Nevertheless, their development and use has only recently moved beyond model organisms to groups such as salmonid fishes. Oncorhynchus mykiss is a salmonid native to the North Pacific rim that has now been introduced throughout the world for fisheries and aquaculture. The anadromous form of the species is known as steelhead. Native steelhead populations on the west coast of the United States have declined and many now have protected status. The nonanadromous, or resident, form of the species is termed rainbow, redband or golden trout. Additional life history and morphological variation, and interactions between the forms, make the species challenging to study, monitor and evaluate. Here, we describe the discovery, characterization and assay development for 139 SNP loci in steelhead/rainbow trout. We used EST sequences from existing genomic databases to design primers for 480 genes. Sanger‐sequencing products from these genes provided 130 KB of consensus sequence in which variation was surveyed for 22 individuals from steelhead, rainbow and redband trout groups. The resulting TaqMan assays were surveyed in five steelhead populations and three rainbow trout stocks, where they had a mean minor allele frequency of 0.15–0.26 and observed heterozygosity of 0.18–0.35. Mean FST was 0.204. The development of SNPs for O. mykiss will help to provide highly informative genetic tools for individual and stock identification, pedigree reconstruction, phylogeography and ecological investigation.

Patterns of Historical Balancing Selection on the Salmonid Major Histocompatibility Complex Class II β Gene

Allelic variation in the major histocompatibility class (MHC) IIB gene of salmonids is analyzed for patterns indicative of natural selection acting at the molecular level. Sequence data for the second exon of this MHC gene were generated for 11 species in three salmonid genera: Oncorhynchus, Salmo, and Salvelinus. Phylogenetic analysis of nucleotide sequences revealed: (1) monophyletic grouping of alleles from each genus, (2) transspecies evolution of alleles within Salmo and Salvelinus, and (3) differential patterns of transspecies evolution within the genus Oncorhynchus. Within Oncorhynchus, five of seven species had alleles that were species-specific or nearly so, while the remaining two, O. mykiss and O. clarkii, retained ancestral polymorphisms. The different patterns in Oncorhynchus and the other two genera could be due to historical demographic effects or functional differences in MHC molecules in the three genera, but the two hypotheses could not be distinguished with the current dataset. An analysis of recombination/gene conversion identified numerous recombinant alleles, which is consistent with what has been found in other vertebrate taxa. However, these gene conversion events could not account for the species-specific allelic lineages observed in five of the Oncorhynchus species. Analyses of the relative rates of nonsynonymous and synonymous substitutions revealed the signature of selection on the class IIB gene in all 11 of the salmonid species for both the ABS and the non-ABS codons. Codon-based analyses of selection identified seven codons that have experienced selection in the majority of the species. More than half of these sites were mammalian ABS codons, but several were not, suggesting subtle functional differences in the mammalian and teleost fish MHC molecules.

Temporal recruitment patterns and gene flow in kelp rockfish (Sebastes atrovirens)

Pelagic dispersal of marine organisms provides abundant opportunity for gene flow and presumably inhibits population genetic divergence. However, ephemeral, fine‐scale, temporal and spatial genetic heterogeneity is frequently observed in settled propagules of marine species that otherwise exhibit broad‐scale genetic homogeneity. A large variance in reproductive success is one explanation for this phenomenon. Here, genetic analyses of 16 microsatellite loci are used to examine temporal patterns of variation in young‐of‐year kelp rockfish (Sebastes atrovirens) recruiting to nearshore habitat in Monterey Bay, California, USA. Population structure of adults from central California is also evaluated to determine if spatial structure exists and might potentially contribute to recruitment patterns. Genetic homogeneity was found among 414 young‐of‐year sampled throughout the entire 1998 recruitment season. No substantial adult population structure was found among seven populations spanning 800 km of coastline that includes the Point Conception marine biogeographic boundary. Comparison of young‐of‐year and adult samples revealed no genetic differentiation and no measurable reduction in genetic variation of offspring, indicating little variance in reproductive success and no reduction in effective population size for this year class. Simulation analyses determined that the data set was sufficiently powerful to detect both slight population structure among adults and a small reduction in effective number of breeders contributing to this year class. The findings of high gene flow and low genetic drift have important implications for fisheries management and conservation efforts.