Using six microsatellite loci, we characterized the 12 remaining populations of Arctic char Salvelinus alpinus naturally occurring in Maine. More specifically, we challenged the hypotheses based on previous analyses with other markers that (1) Arctic char from Floods Pond (known locally as silver char) represent a distinct evolutionary lineage and (2) all other Arctic char populations from Maine belong to the same evolutionary lineage and therefore do not require individual consideration for conservation. The high level of polymorphism observed at microsatellite loci in this study contrasted sharply with the extremely low levels of variation previously reported at other markers. Analyses confirmed that all lakes possess genetically distinct populations among which gene flow is restricted and on which other evolutionary forces may act independently, enhancing their genetic divergence. However, hierarchical gene diversity, population clustering, and population assignment analyses all indicated that the populations from different drainages did not originate from genetically distinct ancestral population assemblages. Our results thus contradict previous conclusions, as we found that the Arctic char from Floods Pond likely did not originate from a distinct evolutionary lineage. Secondly, although all Maine Arctic char appear to belong to a single evolutionary lineage, sufficient divergence was found to reject the hypothesis that all other populations should be considered as genetically equivalent for conservation. We discuss the implications of these findings for the management and protection of these unique Arctic char populations.

Genotyping errors are present in almost all genetic data and can affect biological conclusions of a study, particularly for studies based on individual identification and parentage. Many statistical approaches can incorporate genotyping errors, but usually need accurate estimates of error rates. Here, we used a new microsatellite data set developed for brown rockfish (Sebastes auriculatus) to estimate genotyping error using three approaches: (i) repeat genotyping 5% of samples, (ii) comparing unintentionally recaptured individuals and (iii) Mendelian inheritance error checking for known parent-offspring pairs. In each data set, we quantified genotyping error rate per allele due to allele drop-out and false alleles. Genotyping error rate per locus revealed an average overall genotyping error rate by direct count of 0.3%, 1.5% and 1.7% (0.002, 0.007 and 0.008 per allele error rate) from replicate genotypes, known parent-offspring pairs and unintentionally recaptured individuals, respectively. By direct-count error estimates, the recapture and known parent-offspring data sets revealed an error rate four times greater than estimated using repeat genotypes. There was no evidence of correlation between error rates and locus variability for all three data sets, and errors appeared to occur randomly over loci in the repeat genotypes, but not in recaptures and parent-offspring comparisons. Furthermore, there was no correlation in locus-specific error rates between any two of the three data sets. Our data suggest that repeat genotyping may underestimate true error rates and may not estimate locus-specific error rates accurately. We therefore suggest using methods for error estimation that correspond to the overall aim of the study (e.g. known parent-offspring comparisons in parentage studies).

Upper Columbia River spring-run Chinook salmon are listed as endangered under the Endangered Species Act (ESA). Forensic genetic analyses are needed to assist the National Oceanic and Atmospheric Administration Fisheries Office of Law Enforcement (NOAA Fisheries OLE) during criminal investigations of ESA take violations. Previous genetic studies using allozyme markers have demonstrated that the spring-run and summer-run of Chinook salmon in the Upper Columbia River are genetically differentiated. Because many of the carcasses collected as forensic evidence are of compromised quality, we have developed a PCR based assay to distinguish between the spring-run and the summer-run Chinook salmon in the upper Columbia River Basin. A total of 347 Chinook salmon samples from the upper Columbia River in Washington State were surveyed for single nucleotide polymorphisms (SNPs) using PCR-RFLP at two nuclear genetic loci (Somatolactin and Cytochrome p450A), and a mitochondrial locus (Cytochrome Oxidase III/ND3). We found near fixed differences in our SNP baseline between the summer-run and the spring-run Chinook salmon in the upper Columbia River at these loci enabling us to assign individuals to the most likely population of origin with a high degree of accuracy.

The Mid-Lake Reef Complex (MLRC) is a large area of deep reefs that separate the two main basins of Lake Michigan. In an attempt to evaluate which of several strains of lake trout Salvelinus namaycush stocked in Lake Michigan are actively spawning at the MLRC, eggs that had been deposited by spawning lake trout were collected at three sites on East Reef. These eggs were incubated and shown to be viable and capable of developing to the emergent fry stage. The samples were genotyped at four microsatellite loci, and a proportional admixture analysis was performed to estimate the genetic contribution of the four predominant lake trout hatchery strains used to stock the MLRC. These estimates were then compared with the abundance of each strain stocked since 1985. The point admixture estimates indicated unequal spawning success among strains in the wild. Specifically, the Seneca Lake strain appeared to be the most successful, while the Lewis Lake strain was the least successful and may not be spawning in the wild. The implications for conservation management are also discussed.