Evidence for the genetic basis and epistatic interactions underlying ocean‐ and river‐maturing ecotypes of Pacific Lamprey ( Entosphenus tridentatus ) returning to the Klamath River, California

Abstract Surveys of genomic variation have improved our understanding of the relationship between fitness‐related phenotypes and their underlying genetic basis. In some cases, single large‐effect genes have been found to underlie important traits; however, complex traits are expected to be under polygenic control and elucidation of multiple gene interactions may be required to fully understand the genetic basis of the trait. In this study, we investigated the genetic basis of the ocean‐ and river‐maturing ecotypes in anadromous Pacific lamprey ( Entosphenus tridentatus ). In Pacific lamprey, the ocean‐maturing ecotype is distinguished by advanced maturity of females (e.g., large egg mass) at the onset of freshwater migration relative to immature females of the river‐maturing ecotype. We examined a total of 219 adult Pacific lamprey that were collected at‐entry to the Klamath River over a 12‐month period. Each individual was genotyped at 308 SNPs representing known neutral and adaptive loci and measured at morphological traits, including egg mass as an indicator of ocean‐ and river‐maturing ecotype for females. The two ecotypes did not exhibit genetic structure at 148 neutral loci, indicating that ecotypic diversity exists within a single population. In contrast, we identified the genetic basis of maturation ecotypes in Pacific lamprey as polygenic, involving two unlinked gene regions that have a complex epistatic relationship. Importantly, these gene regions appear to show stronger effects when considered in gene interaction models than if just considered additive, illustrating the importance of considering epistatic effects and gene networks when researching the genetic basis of complex traits in Pacific lamprey and other species.