Microsatellite variation reveals similar population genetic structure for two species of rockfish (Sebastes borealis and Sebastes paucispinis) with different life histories

Thesis (M.S.) University of Alaska Fairbanks, 2002Rockfish belong to the speciose genus Sebastes (72 species described in the Northeast Pacific). Basic biological and life history information for many rockfish species is limited. Little is known about juvenile recruitment, and identification in early life stages is difficult because the larvae of congeners look similar and often occur in spatial and temporal association. Population genetic structure is an important element for characterization of species or populations, and may provide information on productivity and life history. Eight micro satellite loci were evaluated for variability in analyses of genetic structure for two species of rockfish: the deepwater shelf rockfish bocaccio (S. paucispinis) and the demersal shortraker rockfish (S. borealis) of the continental slope. Tests of homogeneity provided evidence of similar geographically based structure in both species, which is consistent with a neighbor model of gene flow. Structure inferred from this study provides information on the sizes of the basic units of productivity, which may aid in management and conservation efforts.Ch. 1. Microsatellite variation indicates population genetic structure of Bocaccio (Sebastes paucispinis) -- ch. 2. Population structure of Alaskan Shortraker rockfish, Sebastes borealis, inferred from microsatellite variation -- Conclusion

All landscape variable values

Measurements for all landscape variables both at natal site and along migration paths for every collection locality

Tag sequences and population genetic stats

Tag sequences for all of the RAD loci used in this study. Additionally, the mapping position in the O. mykiss genome and summary population genetic statistics for each population

All landscape variable values

Measurements for all landscape variables both at natal site and along migration paths for every collection locality

Full RAD Loci Stats

Large table including stats for each RAD locus globally and by population. The RAD sequence, mapping position to the O. mykiss assembly, and outlier classification are included for each locus. Additionally, the genotype success rate, observed heterozygosity, expected heterozygosity, minor allele frequency, and HWE corrected P.val (FDR) are included globally and for each population

Top BLAST hits

Top BLAST hits for loci identified by the majority of outlier tests (3/4) and GEA analyses (2/3). For each SNP, the environmental association and category (if applicable) are included. Additionally, the top BLAST hit and nearest gene (within 10 kb) are included with their GO terms

Top BLAST hits

Top BLAST hits for loci identified by the majority of outlier tests (3/4) and GEA analyses (2/3). For each SNP, the environmental association and category (if applicable) are included. Additionally, the top BLAST hit and nearest gene (within 10 kb) are included with their GO terms

Pairwise FST Table

Pairwise population FST calculated by hierfstat. FST values are represented between each cluster (k=3), globally between populations, and between populations within each genetic cluster

Pairwise FST Table

Pairwise population FST calculated by hierfstat. FST values are represented between each cluster (k=3), globally between populations, and between populations within each genetic cluster

Full RAD Loci Stats

Large table including stats for each RAD locus globally and by population. The RAD sequence, mapping position to the O. mykiss assembly, and outlier classification are included for each locus. Additionally, the genotype success rate, observed heterozygosity, expected heterozygosity, minor allele frequency, and HWE corrected P.val (FDR) are included globally and for each population