Isolation and characterization of polymorphic microsatellite loci in the endangered San Diego fairy shrimp ( Branchinect
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MICROSATELLITE LETTERS
Isolation and characterization of polymorphic microsatellite loci in the endangered San Diego fairy shrimp (Branchinecta sandiegonensis) Joelle M. Andrews • Andrew J. Bohonak Marie A. Simovich
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Received: 11 November 2013 / Accepted: 25 November 2013 / Published online: 6 December 2013 Ó Springer Science+Business Media Dordrecht 2013
Abstract A set of ten polymorphic microsatellite loci were isolated and characterized for the endangered San Diego fairy shrimp (Branchinecta sandiegonensis). These loci were amplified on a set of 24 fairy shrimp collected from vernal pools located throughout San Diego County. The loci selected are highly variable across a wide sampling range (3–29 alleles per locus, 3–20 heterozygotes observed). After directly testing for Mendelian inheritance through family screens, eight markers did not show evidence of null alleles. This novel set of microsatellite markers will be useful in future genetic studies to assess intraspecific diversity, population connectivity and mating patterns. Keywords Vernal pools Fairy shrimp Anostraca Branchinecta Microsatellites Population genetics
The San Diego fairy shrimp (Branchinecta sandiegonensis) inhabits a narrow, discontinuous range of vernal pool habitat on coastal chaparral-covered mesas and inland foothills of southern California, and is the most commonly found fairy shrimp species in this range (Eriksen and Belk 1999). Loss of vernal pool habitat in San Diego due to J. M. Andrews (&) A. J. Bohonak Department of Biology, San Diego State University, 5500 Campanile Dr., San Diego, CA 92182-4614, USA e-mail: [email protected] A. J. Bohonak e-mail: [email protected] M. A. Simovich Department of Biology, University of San Diego, 5998 Alcala´ Park, San Diego, CA 92110, USA e-mail: [email protected]
human disturbance has been extensive, with only small remnants of most vernal pool landscapes remaining (Bauder and McMillan 1998). As a result, Branchinecta sandiegonensis was listed as an endangered species (U.S. Fish and Wildlife Service [USFWS] 1997) among other sensitive species unique to these habitats. Here, we report the isolation and characterization of polymorphic B. sandiegonensis microsatellite loci that will be useful in future population genetic studies. Genomic DNA from 10 adult B. sandiegonensis individuals, each from a different population, was extracted using the DNeasy Blood and Tissue kit (Qiagen), and sent to Genetic Identification Services (GIS; Chatsworth CA, USA) to develop eight enriched microsatellite libraries with CA-, GA-, AAC-, CAG-, AAG-, ATG-, TACA-, and TAGA- repeats. Following digestion of genomic DNA with HindIII restriction enzyme, fragments 350–700 bp long were subjected to magnetic bead capture using biotinylated capture molecules. Enriched fragments were ligated into pUC19 plasmids and electroporated into E. coli. Colonies containing the insert were isolated and plasmid DNA was amplified via PCR. Resulting PCR products were sequenced using Amersham’s DYEnamicTM ET Terminator Cycl
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