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Can AFLP genome scans detect small islands of differentiation? The case of shell sculpture variation in the periwinkle Echinolittorina hawaiiensis
Author(s) -
TICE K. A.,
CARLON D. B.
Publication year - 2011
Publication title -
journal of evolutionary biology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.289
H-Index - 128
eISSN - 1420-9101
pISSN - 1010-061X
DOI - 10.1111/j.1420-9101.2011.02314.x
Subject(s) - biology , replicate , genome , amplified fragment length polymorphism , evolutionary biology , linkage disequilibrium , outlier , population , false positive paradox , selection (genetic algorithm) , genetics , gene , haplotype , allele , artificial intelligence , statistics , genetic diversity , demography , mathematics , sociology , computer science
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 (LD) 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 D fdist , whereas no outliers were identified by B aye S can . Closer examination of the D fdist outliers supported the conclusion that these loci were false positives. These results highlight the importance of controlling for Type I error 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.