Estimation of genotyping error rate from repeat genotyping, unintentional recaptures and known parent–offspring comparisons in 16 microsatellite loci for brown rockfish (Sebastes auriculatus)

Abstract

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).

Seasonal changes in abundance and compelling evidence of migration for 2 rockfish species (Sebastes auriculatus and S. caurinus) inhabiting a nearshore, temperate-water artificial reef

“…We could not determine whether the brown rockfish recaptures identified by Hess et al (2012) that were at liberty for more than one year remained on the reef year-round or left the reef in the winter and returned during the summer (i.e., migrated), although only one of the fish was recaptured in the winter. The recapture data indicate some degree of reef fidelity for some brown rockfish at PHAR.…”

“…The genetic data were compiled from a study in which molecular markers had been used to estimate genotyping error rates from brown rockfish captured at PHAR (Hess et al 2012). In that study, 718 brown rockfish ranging in length from 10 to 37 cm (M [mean]=22; SD [standard deviation]=7.1) were sampled and returned alive to their point of capture during all seasons between spring of 2004 and summer of 2009.…”

“…Fifty-one (7%) of the 718 brown rockfish ≥10 cm sampled by Hess et al (2012) were fish that had been recaptured (2 of these were recaptured twice) according to genotype matching. The number of days at liberty between first and final capture ranged from 1 to 1518 (M=615; SD=448.8).…”

“…Four different divers conducted surveys on the north side of the transect center-lines; but nearly all (~96%) of those surveys were conducted by just 2 divers. All scuba divers had extensive experience in surveying rockfish on Puget Sound rocky reefs prior to Fishery Bulletin 114(3) participating in this study, and they periodically used hand-held graduated staffs to calibrate their visual estimates of fish length.The genetic data were compiled from a study in which molecular markers had been used to estimate genotyping error rates from brown rockfish captured at PHAR (Hess et al 2012). In that study, 718 brown rockfish ranging in length from 10 to 37 cm (M [mean]=22; SD [standard deviation]=7.1) were sampled and returned alive to their point of capture during all seasons between spring of 2004 and summer of 2009.…”

Allele Size Miscalling due to the Pull-Up Effect Influencing Size Standard Calibration in Capillary Electrophoresis: A Case Study Using HEX Fluorescent Dye in Microsatellites

“…In this process, incorrect microsatellite genotype scoring can occur at many steps [3][4][5][6][7]. Stutter, null alleles and allelic dropout are the three major problems, which have been discussed extensively [5,7].…”