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Opportunity at National Oceanic & Atmospheric Administration (NOAA)

Next Generation Sequencing to Evaluate Fish Assemblages in the California Current

Location

National Marine Fisheries Service, Southwest Fisheries Science Center

RO# Location
26.03.37.C0057 La Jolla, CA 92038

Advisers

Name E-mail Phone
Thompson, Andrew Richard andrew.thompson@noaa.gov 858-546-7132

Description

Advances in genetic technology holds the promise to greatly augment marine ecosystem monitoring in the coming decades. In particular, next generation sequencing (NGS) can provide DNA analyses that are orders of magnitude more sensitive than techniques implemented just 10 years ago. This project will focus on the development of genetic tools to bulk-identify fishes collected in plankton samples. Larval fishes collected through plankton sampling have helped elucidate fish population dynamics in the California Current over the past 70 years. However, traditional larval fish sampling techniques that rely on visual morphological identification are labor and time intensive. The primary goal of this project is to evaluate the accuracy of NGS to quantify the presence/absence of all species of larval fishes found in plankton samples collected off California, Oregon, and Washington.

Hundreds of plankton samples have already been collected for this project from the California Current Ecosystem. During this project we will first use traditional, morphological identification methods to determine which fish larvae and eggs are in each sample. Next, we will conduct Sanger sequencing (i.e., a small amount of tissue will be taken from each individual and sequenced one by one). The larvae and eggs will then be returned to the original sample. The entire sample will then be ground up and subjected to bulk tissue extraction. We will then apply NGS to this DNA to determine which of the known species are detected in each sample. In addition, we will extract DNA directly from the ethanol that is used to preserve each samples and again conduct NGS. As such, we will evaluate how well NGS can identify species presence/absence from both ethanol preservative and actual tissue.

Once NGS techniques to identify larvae and eggs from plankton samples are perfected, we will turn to archived ethanol-preserved plankton samples and to build unique time-series of genetically identified fishes. Utilization of NGS should help optimize fisheries sampling in the upcoming decade.

 

Keywords:
Larval fish; Marine monitoring; Ecosystem; Genetics; Next generation sequencing; MIseq; California Current; Integrated ecosystem assessment;

Eligibility

Citizenship:  Open to U.S. citizens, permanent residents and non-U.S. citizens
Level:  Open to Postdoctoral and Senior applicants

Stipend

Base Stipend Travel Allotment Supplementation
$56,000.00 $2,000.00

Experience Supplement:
Postdoctoral and Senior Associates will receive an appropriately higher stipend based on the number of years of experience past their PhD.

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