Many california native inland desert fish species are at risk from the immediate threat of drought and the longer-term impacts of climate change

These fish live in isolated, potentially ephemeral habitats (springs and cienegas) and are susceptible to stochastic events that can result in local extirpation or extinction, such as extreme water temperature and salinity changes due to variability in water supply, desiccation of habitat, and human activities such as habitat modification and invasive species introductions. As such, all california species of cyprinodon pupfish are either a california species of special concern or threatened or listed as an endangered species at state and/or federal levels. Facilitated introductions to new habitats have resulted in successful establishment of new or reintroduced populations for these species, but these actions can result in strong genetic 'founder effects' and/or genetic drift over time in small, isolated populations (allendorf, 1986; frankham, ballou, & briscoe, 2002; NEI, maruyama, & chakraborty, 1975). Genetic evaluation of these populations is critical for a landscape-scale monitoring program that seeks to address the long-term genetic challenges of these isolated populations within the multi-species pupfish complex.owens pupfish (c. Radiosus) have been listed under the federal endangered species act since 1967. All extant members of this species are descended from nearly 400 fish that were relocated from a drying pond (the last known population of owens pupfish) to bureau of land management (BLM) spring in 1969 (miller & pister, 1971; pister, 1993), as all other historical populations had been extirpated from their native habitats. These BLM spring fish served as a source population for a complex history of population founding, extirpation, RE-founding, and relocation across multiple locations in owens valley. The five currently extant populations of owens pupfish (BLM spring, mule spring, letter ponds, marvin's marsh, and well 368) are being used as source populations for the current species management action to set up a larger refuge population at river spring lakes ecological reserve. In this proposal, we will sequence, assemble, and annotate reference genomes for all seven california pupfish species, which will then be used to evaluate current and future conservation activities for this native and threatened fish complex. Once all species reference genomes are created, we will design a pan-species genetic assay that can be used across all california pupfish species. This assay will consist of specific and targeted DNA sequencing the genome at hundreds of sequence variants to assess overall genetic diversity both within and between pupfish species. After assay validation, we will employ the assay to examine diversity of the owens pupfish populations across all five current source populations, as well as within the recently established refuge population at river spring lakes ecological reserve. Using the assay, we will attempt to identify the proportion of each donor population of origin within samples at the reserve, aiding species management in ensuring appropriate conservation of source populations which are proven successful in the establishment of this reserve population.