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Discovery and validation of species–specific diagnostic SNP markers for the endangered San Diego fairy shrimp (Branchinecta sandiegonensis) and the versatile fairy shrimp (Branchinecta lindahli)

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Abstract

Because only 3–7% of historically present vernal pool habitat remains in coastal San Diego County, conservation efforts must prioritize both the maintenance of these pools and the genomic integrity of their inhabitants. Coastal vernal pools found in southern California are home to the federally endangered San Diego fairy shrimp Branchinecta sandiegonensis. Simovich et al. (J Crustac Biol 33:730–740, 2013) characterized hybridization between B. sandiegonensis and the versatile fairy shrimp (Branchinecta lindahli) using morphological characters, but these characters are only found in adult females. To detect adult female, male and juvenile hybrids in the wild, we developed a genomic hybrid index comprised of 20 SNP loci using 16 individuals with no morphological evidence of hybridization, collected from populations unlikely to facilitate introgression. These loci have alternatively fixed alleles between the two species. This genomic hybrid index was validated using 426 individuals from 27 localities using morphology and habitat information. Our data suggest that some artificial and disturbed pool basins harbor hybrids, and thus have the potential to be stepping-stones for the future spread of hybrids. This genomic hybrid index will be a useful tool for identifying putative Branchinecta hybrids from both mature and immature life history stages, and aid in the monitoring and recovery of non-admixed B. sandiegonensis.

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Acknowledgements

The authors would like to thank Charles Black for help with sample collection and his insights on fairy shrimp biology. We thank David Carlson, Shahan Derkarabetian for their assistance in transcriptome assembly and SNP discovery as well as Cheryl Hayashi, William Walton and the anonymous reviewer for providing helpful suggestions regarding manuscript preparation. We also thank the genomic services laboratory at Hudson Alpha Institute for Biotechnology for help with sample preparation and technicians at the University of Arizona Genetics Core for help with multiplex optimization. Funding for this study was granted by the San Diego Association of Governments (SANDAG), U.S. Department of the Navy (Cooperative Agreement N62473-14-2-0001), California Department of Fish and Wildlife and U.S. Fish and Wildlife Service (Cooperative Endangered Species Conservation Fund/Section 6 Grant P1382012). All ‘‘take’’ was conducted under the supervision of Marie Simovich as authorized under US Fish and Wildlife Service Permit TE-787037-4.

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Authors and Affiliations

  1. Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, CA, 92182-4614, USA

    Ketan V. Patel, Andrew J. Bohonak, Natalie S. Goddard & Nicholas S. Graige

  2. University of San Diego, 5998 Alcala Park, San Diego, CA, 92110, USA

    Marie A. Simovich

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  1. Ketan V. Patel
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  2. Andrew J. Bohonak
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  3. Marie A. Simovich
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  4. Natalie S. Goddard
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  5. Nicholas S. Graige
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Correspondence to Ketan V. Patel.

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Patel, K.V., Bohonak, A.J., Simovich, M.A. et al. Discovery and validation of species–specific diagnostic SNP markers for the endangered San Diego fairy shrimp (Branchinecta sandiegonensis) and the versatile fairy shrimp (Branchinecta lindahli). Conservation Genet Resour 10, 897–905 (2018). https://doi.org/10.1007/s12686-017-0912-0

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