Eric C. Anderson

An improved method for predicting the accuracy of genetic stock identification

Estimating the accuracy of genetic stock identification (GSI) that can be expected given a previously collected baseline requires simulation. The conventional method involves repeatedly simulating mixtures by resampling from the baseline, simulating new baselines by resampling from the baseline, and analyzing the simulated mixtures with the simulated baselines. We show that this overestimates the predicted accuracy of GSI. The bias is profound for closely related populations and increases as more genetic data (loci and (or) alleles) are added to the analysis. We develop a new method based on leave-one-out cross validation and show that it yields essentially unbiased estimates of GSI accu- racy. Applying both our method and the conventional method to a coastwide baseline of 166 Chinook salmon (Onco- rhynchus tshawytscha) populations shows that the conventional method provides severely biased predictions of accuracy for some individual populations. The bias for reporting units (aggregations of closely related populations) is moderate, but still present.

Assessing the power of informative subsets of loci for population assignment: standard methods are upwardly biased

It is well known that statistical classification procedures should be assessed using data that are separate from those used to train the classifier. This principle is commonly overlooked when the classification procedure in question is population assignment using a set of genetic markers that were chosen specifically on the basis of their allele frequencies from amongst a larger number of candidate markers. This oversight leads to a systematic upward bias in the predicted accuracy of the chosen set of markers for population assignment. Three widely used software programs for selecting markers informative for population assignment suffer from this bias. The extent of this bias is documented through a small set of simulations. The relative effect of the bias is largest when screening many candidate loci from poorly differentiated populations. Simple unbiased methods are presented and their use encouraged.

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.

Steelhead Growth in a Small Central California Watershed: Upstream and Estuarine Rearing Patterns

We monitored growth and life history pathways of juvenile steelhead Oncorhynchus mykiss and compared growth rates between the upper watershed and estuary in Scott Creek, a typical California coastal stream. Growth in the upper watershed was approximately linear from May to December for age-0 fish. For passive integrated transponder (PIT) tagged, age-1þ fish, growth transitioned to a cyclic pattern, peaking at 0.2% per day during February-April, when maximum flows and temperatures of 7-128C occurred. Growth of PIT-tagged fish then slowed during August-September (0.01% per day), when temperatures were 14-188C and flows were low. During each spring, smolts (mean fork length (FL) 6 SE ¼ 98.0 6 1.2 mm) and fry migrated to the estuary; some fish remained there during summer-fall as low flows and waves resulted in seasonal sandbar formation, which created a warm lagoon and restricted access to the ocean. Growth in the estuary-lagoon was much higher (0.2-0.8% per day at 15-248C). Our data suggest the existence of three juvenile life history pathways: upper-watershed rearing, estuary-lagoon rearing, and combined upper- watershed and estuary-lagoon rearing. We present a model based upon the above data that reports size at age for each juvenile life history type. The majority of fish reaching typical steelhead ocean entry sizes (;150- 250 mm FL; age 0.8-3.0) were estuary-lagoon reared, which indicates a disproportionate contribution of this habitat type to survival of Scott Creek steelhead. In contrast, steelhead from higher latitudes rear in tributaries during summer, taking several years to attain ocean entry size.

Mapping migration in a songbird using high-resolution genetic markers

Neotropic migratory birds are declining across the Western Hemisphere, but conservation efforts have been hampered by the inability to assess where migrants are most limited—the breeding grounds, migratory stopover sites or wintering areas. A major challenge has been the lack of an efficient, reliable and broadly applicable method for measuring the strength of migratory connections between populations across the annual cycle. Here, we show how high‐resolution genetic markers can be used to identify genetically distinct groups of a migratory bird, the Wilsons warbler (Cardellina pusilla), at fine enough spatial scales to facilitate assessing regional drivers of demographic trends. By screening 1626 samples using 96 highly divergent single nucleotide polymorphisms selected from a large pool of candidates (~450 000), we identify novel region‐specific migratory routes and timetables of migration along the Pacific Flyway. Our results illustrate that high‐resolution genetic markers are more reliable, precise and amenable to high throughput screening than previously described intrinsic marking techniques, making them broadly applicable to large‐scale monitoring and conservation of migratory organisms.

Multiple paternity increases effective population size

*NOAA Southwest Fisheries Science Center, National MarineFisheries Service, 110 Shaffer Road, Santa Cruz, CA 95060,USA, †Department of Ecology and Evolutionary Biology,University of California, Santa Cruz, CA, USA, ‡Department ofApplied Math and Statistics, University of California, SantaCruz, CA, USAReceived 11 March 2009; revision received 30 April 2009;accepted 5 May 2009The effective size, N

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.

Bayesian inference of species hybrids using multilocus dominant genetic markers

Neutral genetic markers are useful for identifying species hybrids in natural populations, especially when used in conjunction with statistical methods like the one implemented in the software NewHybrids. Here, a short description of the extension of NewHybrids to dominant markers is given. Subsequently, an extensive series of simulations of amplified fragment length polymorphism (AFLP) data is performed to evaluate the prospects for hybrid identification with (possibly non-diagnostic) dominant markers. Distinguishing between F1s and F2s is shown to be difficult, possibly requiring upwards of 100 AFLP markers to be done accurately. Discriminating between pure-bred and non-pure (hybrid) individuals, however, is shown to be much easier, requiring perhaps as few as 10 dominant markers, even from relatively weakly diverged species.

A role for migration‐linked genes and genomic islands in divergence of a songbird

Next‐generation sequencing has made it possible to begin asking questions about the process of divergence at the level of the genome. For example, recently, there has been a debate around the role of ‘genomic islands of divergence’ (i.e. blocks of outlier loci) in facilitating the process of speciation‐with‐gene‐flow. The Swainsons thrush, Catharus ustulatus, is a migratory songbird with two genetically distinct subspecies that differ in a number of traits known to be involved in reproductive isolation in birds (plumage coloration, song and migratory behaviour), despite contemporary gene flow along a secondary contact zone. Here, we use RAD‐PE sequencing to test emerging hypotheses about the process of divergence at the level of the genome and identify genes and gene regions involved in differentiation in this migratory songbird. Our analyses revealed distinct genomic islands on 15 of the 23 chromosomes and an accelerated rate of divergence on the Z chromosome, one of the avian sex chromosomes. Further, an analysis of loci linked to traits known to be involved in reproductive isolation in songbirds showed that genes linked to migration are significantly more differentiated than expected by chance, but that these genes lie primarily outside the genomic islands. Overall, our analysis supports the idea that genes linked to migration play an important role in divergence in migratory songbirds, but we find no compelling evidence that the observed genomic islands are facilitating adaptive divergence in migratory behaviour.

Large-scale parentage analysis reveals reproductive patterns and heritability of spawn timing in a hatchery population of steelhead (Oncorhynchus mykiss)

Understanding life history traits is an important first step in formulating effective conservation and management strategies. The use of artificial propagation and supplementation as such a strategy can have numerous effects on the supplemented natural populations and minimizing life history divergence is crucial in minimizing these effects. Here, we use single nucleotide polymorphism (SNP) genotypes for large‐scale parentage analysis and pedigree reconstruction in a hatchery population of steelhead, the anadromous form of rainbow trout. Nearly complete sampling of the broodstock for several consecutive years in two hatchery programmes allowed inference about multiple aspects of life history. Reconstruction of cohort age distribution revealed a strong component of fish that spawn at 2 years of age, in contrast to programme goals and distinct from naturally spawning steelhead in the region, which raises a significant conservation concern. The first estimates of variance in family size for steelhead in this region can be used to calculate effective population size and probabilities of inbreeding, and estimation of iteroparity rate indicates that it is reduced by hatchery production. Finally, correlations between family members in the day of spawning revealed for the first time a strongly heritable component to this important life history trait in steelhead and demonstrated the potential for selection to alter life history traits rapidly in response to changes in environmental conditions. Taken together, these results demonstrate the extraordinary promise of SNP‐based pedigree reconstruction for providing biological inference in high‐fecundity organisms that is not easily achievable with traditional physical tags.