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Phylogenomics reveals conservation challenges and opportunities for cryptic endangered species in a rapidly disappearing desert ecosystem

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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 1876 single nucleotide polymorphisms from across the genome along with 1480 bp 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.

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Data availability

Raw ddRAD reads are available on NCBI. BioProject: PRJNA552048; SRA: SRR9646661-SRR9646708. Sanger sequencing data is available on BOLD and GenBank MT324554-MT324591.

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Acknowledgements

We dedicate this paper to the memory of Chris Gregory, USFWS, who tirelessly advocated for the thorough investigation and protection of all threatened species, and without whom this project would have never been completed. Noelle Ronan (USFWS) provided valuable feedback, comments and support. ddRAD library construction was performed with the support of Angela Kauwe (USDA-ARS). HiSeq 4000 sequencing was provided by the Vincent J. Coates Genomics Sequencing Laboratory at UC Berkeley, supported by NIH S10 OD018174 Instrumentation Grant. This research was funded by the United States Fish and Wildlife Service, with additional funding provided by The College of Tropical Agriculture and Human Resources, University of Hawaii at Manoa; USDA Cooperative State Research, Education and Extension (CSREES), Grant/Award Number: HAW00942-H. USDA is an equal opportunity employer. Mention of trade names or commercial products in this publication is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the USDA.

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Authors and Affiliations

  1. Department of Plant and Environmental Protection Sciences, University of Hawai’i at Mānoa, 3050 Maile Way, 310 Gilmore Hall, Honolulu, HI, 96822, USA

    Daniel Rubinoff, J. Bradley Reil & Julian R. Dupuis

  2. Osborne Biological Consulting, 6675 Avenue Juan Diaz, Riverside, CA, 92509, USA

    Kendall H. Osborne

  3. U.S. Department of Agriculture-Agricultural Research Service, Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center, Hilo, HI, 96720, USA

    Scott M. Geib & Julian R. Dupuis

  4. (Posthumous) U.S. Fish and Wildlife Service, 777 East Tahquitz Canyon Way, Suite 208, Palm Springs, CA, 92262, USA

    Christopher J. Gregory

  5. Department of Entomology, University of Kentucky, S-225 Agricultural Sciences Center North, Lexington, KY, 40546, USA

    Julian R. Dupuis

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  1. Daniel Rubinoff
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  2. J. Bradley Reil
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  3. Kendall H. Osborne
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Correspondence to Daniel Rubinoff.

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Communicated by Anurag Chaurasia.

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Rubinoff, D., Reil, J.B., Osborne, K.H. et al. Phylogenomics reveals conservation challenges and opportunities for cryptic endangered species in a rapidly disappearing desert ecosystem. Biodivers Conserv 29, 2185–2200 (2020). https://doi.org/10.1007/s10531-020-01968-w

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