Gila spp. (bonytail chub, humpback chub, and roundtail chub) genomic data from various locations including the Colorado River in the Grand Canyon (2020-2024)

These data were compiled to investigate genomic patterns in humpback chub (Gila cypha) sampled from various locations (New Mexico and Utah) including the Colorado River in the Grand Canyon, AZ. Specifically, our objectives were to understand 1) if unique genetic variation persisted in the western Grand Canyon during the period when chub was restricted to warm water refugia and 2) if a behavioral difference between migratory and resident fish in the Little Colorado River led to assortative mating. These data represent anonymous genomic sequences generated as a result of next-generation sequencing. The data release consists of two tab delimited text files that may be used to infer population structure and genetic diversity statistics (gicy_pop4.vcf, gicy_pop5.vcf). These data represent genetic variation on an individual level. These files may be opened and edited in a text editor program, such as Notepad ++ (PC) or BBEdit (Mac). The .vcf file can be loaded into the Stacks population program (Catchen et al. 2013) to calculate genetic diversity statistics or convert to other file formats (e.g., .stru or .ped). The sequencing data were collected in 2021 and leveraged fin clips resulting from sampling between 2015 and 2020. The data were collected by scientists and technicians at the U.S. Geological Survey Southwest Biological Science Center by sequencing a library on an Illumina NovaSeq 6000 (Illumina, San Diego, CA USA). These data can be used to investigate patterns of genetic diversity and structure to illuminate the ecological and evolutionary forces influencing humpback chub.