RAD-Seq Reveals Patterns of Additive Polygenic Variation Caused by Spatially-Varying Selection in the American Eel (Anguilla rostrata)

• Published in: Genome Biology and Evolution
• Main Authors: Babin, Charles, Gagnaire, Pierre-Alexandre, Pavey, Scott, Bernatchez, Louis
• Other Authors: Institut de Biologie Intégrative et des Systèmes Québec (IBIS), Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), Université Paris Sciences et Lettres (PSL)-Université Paris Sciences et Lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement IRD : UR226-Centre National de la Recherche Scientifique (CNRS), University of New Brunswick (UNB)
• Format: Article in Journal/Newspaper
• Language: English
• Published: HAL CCSD 2017
• Subjects: panmixia; spatially-varying selection; environmental association; RAD-sequencing; genome scan; polygenic selection; [SDE.BE]Environmental Sciences/Biodiversity and Ecology; [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE]; [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE]; Subarctic
• Online Access: https://hal.science/hal-02395860; https://hal.science/hal-02395860/document; https://hal.science/hal-02395860/file/Babin,%20GBE,%202017.%20RAD-Seq%20reveals%20patterns%20of%20additive%20polygenic%20variation%20caused%20by%20spatially%20varying%20selection%20in%20the%20Americal%20eel.pdf; https://doi.org/10.1093/gbe/evx226

International audience The American Eel (Anguilla rostrata) has an exceptional life cycle characterized by panmictic reproduction at the species scale, random dispersal, and selection in a highly heterogeneous habitat extending from subtropical to subarctic latitudes. The genetic consequences of spatially-varying selection in this species have been investigated for decades, revealing subtle clines in allele frequency at a few loci that contrast with complete panmixia on the vast majority of the genome. Because reproduction homogenizes allele frequencies every generation, sampling size, and genomic coverage are critical to reach sufficient power to detect selected loci in this context. Here, we used a total of 710 individuals from 12 sites and 12,098 high-quality single nucleotide polymorphisms to re-evaluate the extent to which local selection affects the spatial distribution of genetic diversity in this species. We used environmental association methods to identify markers under spatially-varying selection, which indicated that selection affects $1.5% of the genome. We then evaluated the extent to which candidate markers collectively vary with environmental factors using additive polygenic scores. We found significant correlations between polygenic scores and latitude, longitude and temperature which are consistent with polygenic selection acting against maladapted genotypes in different habitats occupied by eels throughout their range of distribution. Gene functions associated with outlier markers were significantly enriched for the insulin signaling pathway, indicating that the trade-offs inherent to occupying such a large distribution range involve the regulation of metabolism. Overall, this study highlights the potential of the additive polygenic scores approach in detecting selective effects in a complex environment.