Data from: Can AFLP genome scans detect small islands of differentiation? The case of shell sculpture variation in the periwinkle Echinolittorina hawaiiensis
Tice, Kimberly A, University of Hawaii at Manoa
Carlon, David B
Published May 11, 2011 on Dryad.
Cite this dataset
Tice, Kimberly A; Carlon, David B (2011). Data from: Can AFLP genome scans detect small islands of differentiation? The case of shell sculpture variation in the periwinkle Echinolittorina hawaiiensis [Dataset]. Dryad. https://doi.org/10.5061/dryad.q6t5g
Genome scans have identified candidate regions of the genome undergoing selection in a wide variety of organisms, yet have rarely been applied to broadly dispersing marine organisms experiencing divergent selection pressures, where high recombination rates can reduce the extent of linkage disequilibrium and the ability to detect genomic regions under selection. The broadly dispersing periwinkle Echinolittorina hawaiiensis exhibits a heritable shell sculpture polymorphism that is correlated with environmental variation. To elucidate the genetic basis of phenotypic variation, a genome scan using over 1000 AFLP loci was conducted on smooth and sculptured snails from divergent habitats at four replicate sites. Approximately 5% of loci were identified as outliers with Dfdist, while no outliers were identified by BayeScan. Closer examination of the Dfdist outliers supported the conclusion that these loci were false positives. These results highlight the importance of controlling for Type I error by using multiple outlier detection approaches, multitest corrections, and replicate population comparisons. Assuming shell phenotypes have a genetic basis, our failure to detect outliers suggests that the life history of the target species needs to be considered when designing a genome scan.
Echinolittorina hawaiiensis samples were collected in the field, and DNA was extracted and amplified using 8 AFLP primer combinations. Chromatograms were analyzed using GeneMapper, and genotypes were determined using the programs Peakmatcher and AFLPScore. Descriptions for column headings can be found in the ReadMe file.