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Evaluating manta ray mucus as an alternative DNA source for population genetics study: underwater-sampling, dry-storage and PCR success.

Kashiwagi T, Maxwell EA, Marshall AD, Christensen AB - PeerJ (2015)

Bottom Line: Advanced genetic analyses can contribute relevant information on effective population size and connectivity among populations although acquiring sufficient regional sample sizes can be challenging.DNA stored on cards was found to be reliable for PCR-based population genetics studies.We successfully amplified mtDNA ND5, nuclear DNA RAG1, and microsatellite loci for all samples and confirmed sequences and genotypes being those of target species.

View Article: PubMed Central - HTML - PubMed

Affiliation: Molecular Fisheries Laboratory, University of Queensland , St. Lucia, QLD , Australia ; Marine Megafauna Foundation , Truckee, CA , USA ; Current affiliation: Center for Fisheries, Aquaculture and Aquatic Sciences, Southern Illinois University Carbondale , Carbondale, IL , USA.

ABSTRACT
Sharks and rays are increasingly being identified as high-risk species for extinction, prompting urgent assessments of their local or regional populations. Advanced genetic analyses can contribute relevant information on effective population size and connectivity among populations although acquiring sufficient regional sample sizes can be challenging. DNA is typically amplified from tissue samples which are collected by hand spears with modified biopsy punch tips. This technique is not always popular due mainly to a perception that invasive sampling might harm the rays, change their behaviour, or have a negative impact on tourism. To explore alternative methods, we evaluated the yields and PCR success of DNA template prepared from the manta ray mucus collected underwater and captured and stored on a Whatman FTA™ Elute card. The pilot study demonstrated that mucus can be effectively collected underwater using toothbrush. DNA stored on cards was found to be reliable for PCR-based population genetics studies. We successfully amplified mtDNA ND5, nuclear DNA RAG1, and microsatellite loci for all samples and confirmed sequences and genotypes being those of target species. As the yields of DNA with the tested method were low, further improvements are desirable for assays that may require larger amounts of DNA, such as population genomic studies using emerging next-gen sequencing.

No MeSH data available.


Tissue sampling with a biopsy tip and a hand spear.
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fig-1: Tissue sampling with a biopsy tip and a hand spear.

Mentions: Apart from land-based sampling at fish landing sites, manta ray tissue samples are typically collected underwater while SCUBA or free diving using hand spears with biopsy punch tips (Fig. 1). As manta rays are a major attraction for tourism (O’Malley, Lee-Brooks & Medd, 2013), such sampling activity may not be popular or discouraged in some areas where people fear that the technique might harm the rays, change their behaviour or have a negative impact on tourism (Braithwaite, 2010; Huntingford et al., 2006; Rose et al., 2014). Availability of alternative and less invasive methods to collect DNA from manta rays would increase sampling opportunities.


Evaluating manta ray mucus as an alternative DNA source for population genetics study: underwater-sampling, dry-storage and PCR success.

Kashiwagi T, Maxwell EA, Marshall AD, Christensen AB - PeerJ (2015)

Tissue sampling with a biopsy tip and a hand spear.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4581770&req=5

fig-1: Tissue sampling with a biopsy tip and a hand spear.
Mentions: Apart from land-based sampling at fish landing sites, manta ray tissue samples are typically collected underwater while SCUBA or free diving using hand spears with biopsy punch tips (Fig. 1). As manta rays are a major attraction for tourism (O’Malley, Lee-Brooks & Medd, 2013), such sampling activity may not be popular or discouraged in some areas where people fear that the technique might harm the rays, change their behaviour or have a negative impact on tourism (Braithwaite, 2010; Huntingford et al., 2006; Rose et al., 2014). Availability of alternative and less invasive methods to collect DNA from manta rays would increase sampling opportunities.

Bottom Line: Advanced genetic analyses can contribute relevant information on effective population size and connectivity among populations although acquiring sufficient regional sample sizes can be challenging.DNA stored on cards was found to be reliable for PCR-based population genetics studies.We successfully amplified mtDNA ND5, nuclear DNA RAG1, and microsatellite loci for all samples and confirmed sequences and genotypes being those of target species.

View Article: PubMed Central - HTML - PubMed

Affiliation: Molecular Fisheries Laboratory, University of Queensland , St. Lucia, QLD , Australia ; Marine Megafauna Foundation , Truckee, CA , USA ; Current affiliation: Center for Fisheries, Aquaculture and Aquatic Sciences, Southern Illinois University Carbondale , Carbondale, IL , USA.

ABSTRACT
Sharks and rays are increasingly being identified as high-risk species for extinction, prompting urgent assessments of their local or regional populations. Advanced genetic analyses can contribute relevant information on effective population size and connectivity among populations although acquiring sufficient regional sample sizes can be challenging. DNA is typically amplified from tissue samples which are collected by hand spears with modified biopsy punch tips. This technique is not always popular due mainly to a perception that invasive sampling might harm the rays, change their behaviour, or have a negative impact on tourism. To explore alternative methods, we evaluated the yields and PCR success of DNA template prepared from the manta ray mucus collected underwater and captured and stored on a Whatman FTA™ Elute card. The pilot study demonstrated that mucus can be effectively collected underwater using toothbrush. DNA stored on cards was found to be reliable for PCR-based population genetics studies. We successfully amplified mtDNA ND5, nuclear DNA RAG1, and microsatellite loci for all samples and confirmed sequences and genotypes being those of target species. As the yields of DNA with the tested method were low, further improvements are desirable for assays that may require larger amounts of DNA, such as population genomic studies using emerging next-gen sequencing.

No MeSH data available.