Phylogenomics of an endangered beetle reveals challenges and opportunities for broader conservation planning in a rapidly disappearing desert ecosystem

Authors: RUBINOFF, DANIEL - University Of Hawaii; REIL, J. BRADLEY - University Of Hawaii; OSBORNE, KENDALL - Osborne Biological Consulting; GREGORY, CHRISTOPHER - Us Fish And Wildlife Service; Geib, Scott; DUPUIS, JULIAN - University Of Hawaii

Submitted to: Biodiversity and Conservation Journal
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/30/2020
Publication Date: 4/16/2020
Citation: Rubinoff, D., Reil, J., Osborne, K., Gregory, C., Geib, S.M., Dupuis, J. 2020. Phylogenomics of an endangered beetle reveals challenges and opportunities for broader conservation planning in a rapidly disappearing desert ecosystem. Biodiversity and Conservation Journal. 29:2185-2200. https://doi.org/10.1007/s10531-020-01968-w.
DOI: https://doi.org/10.1007/s10531-020-01968-w

Interpretive Summary: The Casey’s June Beetle is an endangered beetle living in the Coachella Valley of California. Habitat fragmentation from human development is impacting its populations. Looking at both mitochondrial and genome wide marker data cryptic diversity among Dinacoma in Southern CA was detected, and confirmed that the endangered Casey’s June beetle (D. caseyi) is a distinct species from D. marginata sister species. Even though dispersal of this species due to flightless females is restricted, there was no fine-scale population structure within this species, and in order to best conserve the genetic makeup of this group, conservation across localities should be considered, as genetic exchange in widespread species cannot be assumed. This information can be used to inform land managers on how to best conserve this endangered species.

Technical Abstract: There is growing evidence for the decline of cryptic species across the planet as a result of human activities. Accurate data regarding patterns of poorly known or hard-to-find species diversity is essential for the recognition and conservation of threatened species and ecosystems. Casey’s June beetle Dinacoma caseyi is a federally listed endangered species restricted to the Coachella Valley in southern California, where rapid development is leading to habitat fragmentation. This fragmentation may be disproportionately impacting a wide-range of poorly-dispersing, cryptic species, including Casey’s June beetle, which has flightless females. We characterized 1,876 single nucleotide polymorphisms from across the genome along with 1480bp of mitochondrial DNA of all confirmed extant Dinacoma populations. We found that Dinacoma is isolated into three distinct species, including evidence for a previously undescribed species revealed during this study. Each is restricted to a small part of the inland desert region. Our results suggest unappreciated and fine scale diversity, which may be reflected in the other cryptic species of the region. Patterns of diversity in non-vagile species should guide ongoing conservation planning in the region. These results show that genetic exchange within the one remaining island of beetle habitat (Palm Canyon Wash) is not limited. However, non vagile species, such as Casey’s June beetle, may not colonize suitable but fragmented habitat islands which presents risks to the species due to habitat loss and periodic natural events that may put the single population at risk of extirpation.