Tag Archives: genetics

Genetics schmetics! What is the difference between all the different methods used in conservation genetics?

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Genetics is a powerful tool in the field of conservation, but the topic of genetics is so large that it can sometimes be overwhelming to begin to even understand. So here is a quick cheat sheet on different methods and genetic markers that are used in the field of biology, ecology and conservation in general.

 

Using genetics can help us understand the evolution of an organism, assess the status of a population, and conserve a species.  The basis for all of the is DNA, which can be found in every single cell of all life on earth!

Photo credit: Alex Avila. Fin clip sample preserved in alcohol

Photo Credit: Alex Avila. This is a fin clip, this is all you need to extract DNA ( very tiny sample)

Photo Credit: Alex Avila, tools of the trade

DNA helps us in species identification (very useful when two different species have very similar physical characteristics), understanding taxonomic relationship ( this can be important when making natural resource management decisions and guiding conservation/restoration efforts), determination of hybrids, identifying individuals with in a population, determination of parentage, migration of populations, genetic variation and historical size of populations, and also has forensic applications (like tracking down poachers!). As you can see there are many applications for genetics in conservation, and since DNA can be found anywhere, even in poop, it makes it a great tool for scientists and managers in this field to use.

 

Ok, let’s say I have convinced you that genetics is awesome, but now what? There are so many different methods out there, how do I know which one I should use?

In genetics different methods are known as markers. Which marker you need depends on what you want to learn. Here is a quick reference to what markers to use depending on the questions being asked.

Illustration Credit: Kathleen O’Malley

  • Allozymes: nor really used that much today, but used to be used for population differentiation.
  • RFLPs: were used for population differentiation, DNA fingerprinting, genome mapping and paternity tests
  • AFLPs: used for population differentiation, and genetic mapping
  • mtDNA: also known as mitochondrial DNA is used for population differentiation, phylogeography, phylogenetics, and is only passed down via the mother
  • Y-chomosomes: phylogeography, phylogenetics, and is only found in males
  • Introns: used to study population differentiation, phylogeography, phylogenetics, and selective adaptations
  • Microsatellites: population differentiation, gene flow and migration rates, individual identification, parentage (who’s the daddy), and relatedness
  • SNPs: population differentiation, gene flow and migration, individual identification, parentage, relatedness

 

As you can see, there is some overlap in the markers. In my case I a m studying China rockfish, and looking at how ocean currents affect their dispersal. To do this I am looking at whether the China rockfish in Oregon are connected, via ocean currents to China rockfish in Washington. I had the option of using microsatellites or SNPs for this. Even though both can provide information on gene flow, parentage and relatedness, I chose to work with SNPs because I am interested in a greater level of detail that microsatellites does not produce.

Photo Credit: Alex Avila China rockfish

Photo Credit: Alex Avila

So there you have it, next time you are considering working in the field of conservation, maybe give genetics a try! You’ll find it to be a very powerful tool

 

Here are some really cool examples of real life uses of genetics in conservation:

Wolf conservation: http://www.latimes.com/science/sciencenow/la-sci-sn-wolf-species-20160727-snap-story-20160727-snap-story.html

Whale conservation: http://www.washingtonpost.com/wp-dyn/content/article/2010/04/14/AR2010041402683.html

 

 

A big year for small Dungeness crab megalopae

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Since I am studying the genomics of Dungeness crab megalopae, I first need to catch some megalopae and extract their DNA! Both last year and this year we have collected Dungeness crab megalopae in Yaquina Bay at the Hatfield Marine Science Center. The Dungeness crab megalopae are about the size of the eraser on a pencil.

 

We use a light trap to catch Dungeness crab megalopae. A light trap is a device used to collect the larval stages of marine fishes and invertebrates. A light is placed inside a clear container with several funnel entrances on the outside of the container and a mesh collection chamber on the bottom of the container. Below is a picture of the light trap that we use. The light trap is placed in the water and tied to a dock. The trap floats just under the surface of the water and shines bright like a beacon at night.

Light Trap Used to Collect Dungeness Crab Megalopae

Some larval stages, such as Dungeness crab megalopae, are attracted to light and move towards light sources. This behavior is called positive phototaxis. You have probably seen this phenomenon when you turn on an outdoor-light at night and then within the hour moths are surrounding the light. For this reason, marine light trapping is an effective way to collect live larval fishes, or live Dungeness crab megalopae.

Dungeness Crab Megalopae

At night, Dungeness crab megalopae are attracted to the light in the light trap. They swim towards the trap and through the funnel entrances where they are then entrapped within the container. In the morning, the trap is pulled out of the water and the collection chamber is emptied. We count how many Dungeness crab megalopae are collected each night and preserve a subsample of the megalopae for genomic analyses.

Light Trap Floating Below the Surface in Yaquina Bay

Our light trapping for Dungeness crab megalopae in Yaquina Bay follows methods from Dr. Alan Shanks’ Lab at the University of Oregon’s Oregon Institute of Marine Biology (OIMB) on Coos Bay in Charleston, Oregon. At OIMB, the Shanks Lab has been light trapping and documenting the daily abundances of Dungeness crab megalopae for over a decade. They are studying how oceanographic conditions impact Dungeness crab megalopae recruitment patterns. Dr. Leif Rasmuson, a 2011-2012 Malouf Scholar, worked on this long-term project.

You may remember from my first post, that I am specifically looking at how coastal upwelling, the timing of spring transition, and the Pacific Decadal Oscillation influence annual Dungeness crab genetic composition. The reason I am studying these three specific ocean conditions is because Shanks and colleagues have found relationships between these three ocean conditions and the annual abundance of recruiting megalopae collected by light trap in Coos Bay, Oregon.

Megalopae Light Trapping Locations in Oregon 
(Photo Adapted from Rasmuson 2013)

The Dungeness crab megalopae recruitment season is April through September each year. In 2017, we caught a total of 12,000 megalopae in Yaquina Bay throughout the season. Currently, we are only two and a half months into the 2018 Dungeness crab megalopae recruitment season, but it is already turning out to be a big year for megalopae recruitment catches. This year we have caught over a half-million Dungeness crab megalopae in our Yaquina trap! And the Shanks Lab at OIMB has also been seeing record numbers of megalopae recruits this year. It is a very exciting time to be studying Dungeness crab megalopae!

A Big Daily Catch of Dungeness Crab Megalopae in the Yaquina Bay Light Trap (May 2018)

So, I mentioned that we preserve some megalopae from the light trap for later genomic analysis. To study the genomic composition of Dungeness crab megalopae, we need to extract the DNA from the megalopae. In fisheries genetics, we immediately preserve fish or crab tissue while in the field by placing a fish fin, a crab leg, or a full megalopae into a plastic tube of ethanol. This ensures that the DNA does not degrade before we can extract the DNA from the fish or crab tissue.

Preserved Megalopae Collected from Yaquina Bay, Newport, Oregon
(Photo by Ketchum 2017)

DNA extraction sounds like it might be a complicated process, but it is relatively a simple protocol. You can actually extract your own DNA quite easily with ingredients from under your sink! Take a look at the below video if you want to try and extract your own DNA!

 

When we extract fish or crab DNA in the laboratory, we use slightly different chemicals than in the above video, small plastic tubes instead of plastic cups, a heating step to break the double stranded DNA into single strands, and a centrifuge machine and filters to separate the DNA from the rest of the solution. Think of the centrifuge machine like the spin cycle on your washing machine. The wet clothes spin at high speed and the water is removed from the clothes by being forced out of the small holes in the sides of washing machine like a filter. You are left with only dry clothes and no water, just like you are left with only DNA and not the liquids you used to extract the DNA.

Laboratory DNA Extraction
(Photo from http://2017.igem.org/)

We extract the DNA from many Dungeness crab megalopae collected throughout the 2017 and the 2018 recruitment season. The next step is to determine the sequence of ‘A’s, ‘T’s, ‘G’s, and ‘C’s in the extracted DNA so we can conduct genomic analyses and better understand how ocean conditions are impacting the genomics of Dungeness crab.

What’s so big about Dungeness crab?

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Hi, I’m Elizabeth Lee, and I am an Oregon State University master’s student with Dr. Kathleen O’Malley in the State Fisheries Genetics Lab at Hatfield Marine Science Center in Newport, Oregon. My first quarter as Malouf Scholar has been quite busy, but before I dive into my Fall quarter, let me provide a little background on my research.

When you think of the Oregon Coast, what comes to mind? Maybe rocky coastlines? Tides pools? Seals? Beaches? Boats? Seafood? Dungeness crab?

Oregon Coast, Yaquina Head Lighthouse, Newport, Oregon

Oregon Coast Tide Pools
Newport, Oregon

If “Dungeness crab” didn’t come to mind, you need to spend more time along the Oregon Coast! Dungeness crab (Cancer magister) is Oregon’s most valuable single-species commercial fishery. Its cultural, historical, economical, and ecological importance along the Oregon coast is prominent.

Dungeness Crab
(Photo: Delecia Loper)

In 2017, 20.4 million pounds of Dungeness crab were landed by commercial fishing vessels in Oregon, totaling $62.7 million in ex-vessel value. These may seem like large numbers to you, but I will argue, that from the perspective of my discipline, there’s another aspect of Dungeness crab that’s even bigger. The genome of the Dungeness crab.

Dungeness Crab Pots, Newport, Oregon

Let’s take a trip back to Biology 101, remember all the ‘A’s, ‘T’s, ‘G’s, and ‘C’s that make up your DNA? These ‘A’s, ‘T’s, ‘G’s, and ‘C’s (or bases) pair-up to form the double stranded structure that holds the blueprints that makes each of us unique (or DNA). The complete DNA blueprints (or genome) of the Dungeness crab is over 2 billion base pairs long! And, every cell in its shell-encrusted body has a copy of these 2 billion base pairs. So, although we catch tens-of-millions of pounds of Dungeness crab per year in Oregon, the genetic composition that makes a Dungeness crab a Dungeness crab, is even larger!

DNA Diagram
(Figure: Wikimedia Commons)

Considering the importance of Dungeness crab along the West Coast, one would assume we know a lot about the Dungeness crab’s genome and genetics. But in fact, we do not. The O’Malley Fisheries Genetics Lab undertook one of the first large-scale genetics projects on Dungeness crab. They sampled over 7,000 adult Dungeness crab off the coasts of Washington, Oregon, and California to understand the population genetic structure, genetic connectivity, and genetic diversity of Dungeness crab within the California Current System (Jackson et al. 2017)

Dungeness Crab West Coast Range
(Figure: Rasmuson, 2013)

By determining the pattern of ‘A’s, ‘T’s, ‘G’s, and ‘C’s within the crab genome, we can study the genetic structure, genetic connectivity, and the genetic diversity of the population. These findings are informative for managers and conservationists. Defining the population genetic structure of Dungeness crab is important for determining how groups of crab in the ocean are connected and allows managers to define stocks within the fishery. Assessing the genetic diversity within and among populations provides insight into the species ability to respond to environmental changes.

Dungeness Crab
(Photo: Wikimedia Commons)

In their coast-wide population genetics study, Jackson et al. (2017) found that Dungeness crab were highly connected genetically within the California Current System. Interestingly, they found inter-annual variability in the degree of genetic connectivity. This suggests that inter-annual variations in oceanographic conditions are affecting the genetic population structure of Dungeness crab. Specifically, the strength and timing of coastal upwelling, the timing of spring transition, and the phase of the Pacific Decadal Oscillation that effects of the strength of the off-shore current systems.

So, how is it that these large-scale oceanographic conditions might be affecting the bottom-dwelling Dungeness crab? Because of the complex life cycle of Dungeness crab.

Dungeness Crab Life Cycle
(Adapted from: Wild and Tasto, 1983)

Before Dungeness crab become 6 ¼-inch-bottom-dwelling (benthic) harvestable organisms in the ocean, they spend 3-4 months as very small, floating (pelagic) larvae within the water column. The pelagic larvae are moved offshore and are dispersed for 3-4 months along the west coast by the ocean currents. The time-period the larvae spend in the ocean current systems and the strength of the ocean currents influence where the larvae finally land on the bottom at the completion of their 3-4 month ocean journey. When the Dungeness crab larvae land along our coasts, we call this process recruitment. After recruitment, the juvenile crabs grow into bottom-dwelling adult crabs.

Dungeness Crab Larval Recruits (Megalopae)
Yaquina Bay, Newport, Oregon

As a graduate student, I am studying the genetic structure and diversity of Dungeness crab larvae that are recruiting to our Oregon Coast. By combining this genetic information with information about the oceanographic conditions and ocean currents along our coast, we can better understand the inter-annual variability that is observed within the adult Dungeness crab genetic population structure. The findings of my research can inform scientists and managers about the population of Dungeness crab off our coasts. Our genetic research is one of the many research projects that can help us tackle the complex questions of ‘how’ and ‘why’ the Dungeness crab fishery and population changes from year-to-year.

I am looking forward to keeping you all updated on my Dungeness crab genomics research this year. And in the meantime, I am enjoying the start of the 2018 Dungeness crab commercial season in Newport, Oregon!

 

References:

Jackson, T. M., Roegner, G. C., & O’Malley, K. G. (2017). Evidence for interannual variation in genetic structure of Dungeness crab (Cancer magister) along the California Current System. Molecular ecology.

Rasmuson, L. K. (2013). The biology, ecology and fishery of the Dungeness crab, Cancer magister. In Advances in marine biology (Vol. 65, pp. 95-148). Academic Press.

Wild, P. W., & Tasto, R. N. (Eds.). (1983). Life history, environment, and mariculture studies of the Dungeness crab, Cancer magister, with emphasis on the central California fishery resource. State of California. The Resources Agency. Department of Fish and Game.