Genomic footprints of speciation in Atlantic eels ( Anguilla anguilla and A. rostrata )

• Published in: Molecular Ecology
• Main Authors: Jacobsen, Magnus W., Pujolar, Jose Martin, Bernatchez, Louis, Munch, Kasper, Jian, Jianbo, Niu, Yongchao, Hansen, Michael M.
• Other Authors: Danish Council for Independent Research, Natural Sciences, Elisabeth og Knud Petersen's Foundation
• Format: Article in Journal/Newspaper
• Language: English
• Published: Wiley 2014
• Subjects: Genetics; Ecology, Evolution, Behavior and Systematics; Anguilla anguilla
• Online Access: http://dx.doi.org/10.1111/mec.12896; https://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1111%2Fmec.12896; https://onlinelibrary.wiley.com/doi/pdf/10.1111/mec.12896

Abstract The importance of speciation‐with‐geneflow scenarios is increasingly appreciated. However, the specific processes and the resulting genomic footprints of selection are subject to much discussion. We studied the genomics of speciation between the two panmictic, sympatrically spawning sister species; European ( Anguilla anguilla ) and American eel ( A. rostrata ). Divergence is assumed to have initiated more than 3 Ma, and although low gene flow still occurs, strong postzygotic barriers are present. Restriction‐site‐associated DNA ( RAD ) sequencing identified 328 300 SNP s for subsequent analysis. However, despite the presence of 3757 strongly differentiated SNP s ( F ST > 0.8), sliding window analyses of F ST showed no larger genomic regions (i.e. hundreds of thousands to millions of bases) of elevated differentiation. Overall F ST was 0.041, and linkage disequilibrium was virtually absent for SNP s separated by more than 1000 bp. We suggest this to reflect a case of genomic hitchhiking, where multiple regions are under directional selection between the species. However, low but biologically significant gene flow and high effective population sizes leading to very low genetic drift preclude accumulation of strong background differentiation. Genes containing candidate SNP s for positive selection showed significant enrichment for gene ontology ( GO ) terms relating to developmental processes and phosphorylation, which seems consistent with assumptions that differences in larval phase duration and migratory distances underlie speciation. Most SNP s under putative selection were found outside coding regions, lending support to emerging views that noncoding regions may be more functionally important than previously assumed. In total, the results demonstrate the necessity of interpreting genomic footprints of selection in the context of demographic parameters and life‐history features of the studied species.