A Highlight of Molecular Ecology outside of Academia

I’ve recently made a career change. Actually, I’m not even sure whether to call it that, or the next step of a natural, if meandering progression of a scientist not on the academic career path. Even though I see more and more articles and social media threads showcasing the career opportunities outside of academics and the need to emphasize those opportunities, it can still feel like a walk in the wilderness to someone with a non-medical, non-human, non-microbial genetics background.  With genetics and genomics data gathering and analysis skills, it SEEMS like it would be easy to slide into a biomedical lab, either with the government, or private industry, though the job applications tend to require clinical lab experience as well as expertise  with data and analyses on a scale much larger than what the typical ecological geneticist is used to.  On my job seeking journey, I worried that I would have to give up “interesting” science in favor of drug testing and humanGWAS data analysis or continue to look for the unicorn research position whereI had job stability and could work on projects with a more conservation and ecological slant.  

Luckily, I managed to land at Eagle Fish Genetics Lab (EFGL) in Eagle, Idaho where resources and funding are available to power large scale genetics projects that inform management decisions affecting endangered and threatened fish species along with the management of non-native and invasive species.  There are several conservation genetics labs across the country that have created a similar niche where applied and pure research is being conducted (see Robin Waple’s illustrious career at NOAA’s Northwest Fisheries Science Center, for one example).  The projects here at EFGL fall into three major categories: Genetic Stock Identification (GSI), Parentage Based Tagging (PBT), and Sex Marker Discovery. Every year, juvenile and adult steelhead and Chinook salmon return to the Lower Granite Dam on the Snake River. These fish are genotyped using a species-specific SNP panel consisting of several hundred markers. The genotypes are compared to baseline genetic data of known stocks in the region to ascertain the stock composition of the returning fish.

In addition, hatchery supplementation of several species is employed throughout the Columbia River and Snake River Basin. Several hatcheries rear smolts to be released at various places throughout the river systems in order to decrease fishing pressure on the natural populations.  The broodstock generating the smolts are replaced annually. Since 2008, there has been a concerted effort to genotype every broodstock fish at every hatchery facility (~17,000 fish per year), so that any hatchery-generated fish collected in the system can be traced back to their broodstock parents using genetic pedigree information. The success of PBT relies upon the thorough genotyping of the broodstock annually.  This is accomplished using the Genotyping-in-Thousands by sequencing (GTseq) methodology.  Beyond yearly monitoring of hatchery and wild populations, the data generated can be used to assess the most effective hatchery practices, salmonid life history harvest patterns, and trait heritability.

A taste of the management effort via hatchery supplementation that goes
into steelhead and Chinook in Idaho. Map by Dylan Kovis

Another focus of EFGL work is finding genetic markers to determine the sex of various fish species as a way to track the success of Trojan Y invasive species control.  In this scenario, males are exposed to estradiol, a female hormone, which causes some to produce eggs. These feminized males are mated with untreated males, which results in ~25% YY “super” or “Trojan” males. Any subsequent cross with the resultant YY fish will result in male progeny.  The hope is to extirpate the non-native population with continued releases of Trojan males.  A codominant, genetic marker that can distinguish XY males from YY males helps to track the efficacy and efficiency of the technique. We employ the modified RadSeq protocol, BestRAD, to a mixture of phenotypically male and female samples, then use Stacks (see previous TME posts here and here for an overview and interview with the author, Julian Catchen) and Python scripts to sort putative SNPs into piles that segregate with sex. Though steelhead and Chinook salmon are the main species of interest, other projects involve carp, burbot, sculpins, and other species of salmonids.

It takes a village to collect, inventory, extract, genotype, and analyze these samples annually. The jobs here at this facility include technicians, biologists (including geneticists), a data manager, and a supervisor and we work in close proximity to a fish health lab, a wildlife forensics lab, and many personnel tasked with maintaining the on-site Sockeye salmon hatchery.  At EFGL, the technicians are well versed in DNA extraction (often performing several hundred to thousands of them per project), SNP genotyping, and RadSeq to name a few.  There are also ample opportunities to help with fish sampling throughout the state and spawning events within hatcheries.The biologists/geneticists coordinate the various projects and analyze the data for reports and manuscripts.  The data manager is the gate keeper making sure that all samples sent to the facility have all the required labeling and metadata and those in the field taking samples across the region are adequately briefed and prepared. The data manager also runs QC scripts on sequencing runs and maintains a gigantic database of sampling, pedigree, and genotype information on every fish that we’ve sampled.  The database system we use is Progeny (designed for human disease pedigree data, of course) and it ain’t cheap (naturally), but considering the enormity of the task at hand, and the fact that it’s built for storing metadata AND genotypes, it does a great job.

My motivation for providing this brief overview of the facility here is to pique the interest of  beginning researchers thinking about their future career paths and assuage some doubts about opportunities for those not interested in the academic career eight-lane highway (that may end in a brick wall with a tunnel painted on it). If you are in the early stages of your career, and you want some experience in a lab generating and analyzing genomic data for a project likely to have a beginning and end during your tenure, I suggest you seek out these types of programs.  Furthermore, if the thought of relentless and never ending grant writing (and the stress of running out of funding) leaves you cold, a well-funded wildlife genetics lab with multiple long-term, ongoing projects on species people love to hunt/fish/photograph/eat may be the niche you are looking for. Not to say that opportunities are not available for securing your own funding and/or pursuing a pet project, necessarily, though that would be lab specific. Collaborations within the agency, with other non-profits and governmental agencies, and academic labs are common as well.

Another motivation of mine is to put these types of labs on the radar of researchers that are attempting to ramp up their program to larger scale/higher throughput pipelines.  If you are overwhelmed with data and sample tracking and organization or concerned about tailoring protocols and/or scripts to fit your needs, it may be that wildlife genetics labs have already done the tweaking and QC for you and some of those resources can be found outside of the primary literature (e.g agency reports, https://www.monitoringresources.org/).  Reaching out to your fellow scientists at wildlife labs would surely be mutually beneficial. Lastly, and most importantly, tell your students interested in wildlife genetics and bioinformatics about these  jobs!  Sure, they’re rare, but so are tenure track positions.

For a little more detail about our little corner of the world, click here.

Sockeye salmon in the Snake River basin are endangered.  Therefore, every wild fish is brought into the hatchery to spawn.  Every female is crossed with two males and vice versa. The left photo shows the deft harvesting of milt from a male. The center photo is of eggs harvested from a single female.  EVERY SINGLE EGG is accounted for throughout the process.  Finally, in the right photo, a marriage betwixt the two. Photo by Katharine Coykendall

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