Quantification of genome-wide inbreeding in Bonytail (Gila elegans) and preliminary evaluation of reproductive success in Cibola High Levee Pond

Authors: Guilherme Caeiro-Dias, Megan Osborne, Thomas Turner

Year: 2024

Abstract

Bonytail is among the most imperiled fishes in North America and is considered functionally extinct in the wild. Nonnative predators are one of the main culprits of population decline and remain the greatest challenge for recovery of Bonytail. Hatchery production has been a key element to preventing extinction of the species. The original broodstock of Bonytail was founded in 1981 by breeding 5 sires and 6 dams; however, eight or less individuals contributed to the offspring produced from spawning efforts. Subsequent efforts to secure additional wild individuals from Lake Mohave to supplement the broodstock were unsuccessful and therefore, existing genetic variation in Bonytail is derived from the initial founders. Given this demographic history, we first quantified individual inbreeding by calculating the proportion of the genome in runs of homozygosity (RoH) using two genomes. We found a substantial fraction of the genome in RoH for both individuals (11.2% and 13.3%) as consequence of bottlenecks that occurred in the past century. In addition to traditional hatchery production, allowing Bonytail to breed and recruit in off-channel habitats, free of nonnative predators, is an important element of management of the species. Cibola High Levee pond (CHL) and ponds at Imperial National Wildlife Refuge (INWR) are backwaters adjacent to the Colorado River that have been stocked with Bonytail. In these off-channel Bonytail breed and recruit. We developed a Genotyping-in-Thousands by sequencing (GT-seq) panel containing 231 SNP-based genetic markers that reflects the genome-wide genetic diversity, and it is suitable for parentage analysis. Using this panel, we evaluated genetic diversity in INWR (ponds 2, 5, and 6) and CHL pond and evaluated parent-offspring relationships in CHL pond. We report preliminary results that reveal important difference between these backwaters. Future work should include multiple generations from each pond to estimate variance of reproductive success, to understand population dynamics in each pond, and compare those dynamics between INWR and CHL.