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Marine Ecology Progress Series

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MEPS 595:149-156 (2018)  -  DOI:

Evaluation and application of BIOPOLE, a biopsy device for in situ non-lethal tissue extraction for fishes

Joshua G. Smith1,*, Dan Malone1, Diana S. Baetscher2,3, Mark H. Carr1

1University of California, Santa Cruz, Department of Ecology and Evolutionary Biology, Santa Cruz, CA 95060, USA
2University of California, Santa Cruz, Department of Ocean Sciences, Santa Cruz, CA 95060, USA
3Southwest Fisheries Science Center, National Marine Fisheries Service, Santa Cruz, CA 95060, USA
*Corresponding author:

ABSTRACT: With the rapidly expanding use of genetics for basic research, conservation, and management purposes, efficient in situ, non-lethal tissue sampling methods have wide application. We designed, applied, and evaluated a device designed to collect non-lethal tissue samples in situ from nearshore marine fishes. Using SCUBA, tissue samples were collected in the field with a biopsy pole (BIOPOLE) from a total of 1591 adults of 4 demersal (Scorpaenichthys marmoratus, Hexagrammos decagrammus, Sebastes chrysomelas, Ophiodon elongatus) and 1 mid-water (Sebastes atrovirens) fish species that ranged in total length from 15 to 75 cm. DNA concentration, samples per unit effort (SPUE; mean no. of ind. collected d-1), and extended monitoring of lethality and sub-lethal effects (i.e. infection) of the BIOPOLE were compared against the commonly employed fin-clip technique for fishes captured using hook-and-line fishing. Mean DNA concentration of a subset of 20 tissue samples collected with the BIOPOLE (11.53 µg ml-1) was less than fin-clipped individuals (62.50 µg ml-1), but nonetheless produced high-quality genotypes using a PCR-based protocol. BIOPOLE was more successful in obtaining tissue samples from target species (SPUE: 21.37) over hook-and-line fishing (SPUE: 8.19). Extended monitoring in a laboratory open seawater system showed no lethal or sub-lethal effects post-biopsy. BIOPOLE presents an efficient non-lethal device for obtaining tissue samples from species accessible by SCUBA or snorkeling when genetic analyses are of interest. Furthermore, the utility of BIOPOLE is highly desirable when target species are difficult to collect with more conventional methods, or when management or conservation concerns prohibit bycatch or the lethal take of samples.

KEY WORDS: Genetic sampling · Tissue collection · Biopsy probe · Fishes · Non-lethal sampling · SCUBA

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Cite this article as: Smith JG, Malone D, Baetscher DS, Carr MH (2018) Evaluation and application of BIOPOLE, a biopsy device for in situ non-lethal tissue extraction for fishes. Mar Ecol Prog Ser 595:149-156.

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