Estimating levels of introgression between Gila trout (Oncorhynchus gilae) and rainbow trout (O. mykiss) using next-generation sequencing data

Authors: David Camak, Thomas F. Turner

Year: 2016 (xlviii)

Abstract

Gila trout (Oncorhynchus gilae) is a federally protected species in the family Salmonidae and is confined to headwater streams in the Gila and San Francisco Rivers in New Mexico and Arizona. Currently, there are five recognized relict and genetically distinct lineages of Gila trout found in the Upper Gila River (Main Diamond, South Diamond, Whiskey, and Iron Creeks) and San Francisco River (Spruce Creek) drainages based on various genetic markers. Understanding levels of introgression is crucial for management and conservation of genetic diversity. Previous genetic data suggested admixture with Gila trout individuals from the Iron Creek lineage and rainbow trout (O. mykiss), via illegal stocking or movement over barriers. Despite shared allozyme and microsatellite alleles between Iron Creek and rainbow trout, mtDNA analyses indicate no shared haplotypes. Gila and rainbow trout are close relatives that shared a common ancestor about 2 million years ago. Shared alleles could result from common recent ancestry rather than introgression. We used next-generation sequencing and SNP genotyping in an effort to increase resolution of genetic variation and gain a better insight into levels of introgression between Gila and rainbow trout lineages. About thirty individuals from each relict Gila trout lineage and source rainbow trout lineages were sequenced and genotyped. Preliminary results are consistent with previous data, indicating five distinct Gila trout lineages with varying levels of diversity within each lineage. Between the five relict Gila trout lineages and rainbow trout, there was no indication of phylogenetic incongruence, suggesting that introgression has not been substantial among the lineages. However, preliminary results are based on averages across/within lineages, which may underrepresent hybrid origins, especially if introgression has been low.