Author Archives: Elizabeth Lee

About Elizabeth Lee

I am a fisheries genomics master's student at Oregon State University's Hatfield Marine Science Center and Coastal Oregon Marine Experiment Station. I am studying the genomic diversity among Dungeness crab megalopae recruits along the Oregon coast. She grew up on the Rhode Island coast, where I developed an interest in marine systems. In 2013, I completed a Bachelor’s degree in Biology studying molecular and ecological systems along the shores of the Chesapeake Bay at St. Mary’s College of Maryland. After graduation, I completed a postbaccalaureate program in bioinformatics at the National Human Genome Research Institute in Bethesda, Maryland. I then conducted fisheries monitoring for the Washington Department of Fish and Wildlife before beginning a master’s program in fisheries genomics at OSU. As a graduate student in the State Fisheries Genetics Lab, I am using genomics approaches to better understand Oregon’s most valuable fishery, Dungeness crab.

Biodiversity in a Changing World: A genetics perspective

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What is Biodiversity?

Biodiversity is the variety of life on Earth (Hooper et al. 2005). It can be studied on many different scales (Oliver et al. 2015). Look out into your backyard and you will see biodiversity; there is grass, there are a few different types of trees, there is a berry bush, there is a vegetable garden, there are birds, there are rabbits, and there are many different types of insects. The variety of plants and animals in your backyard constitutes the biodiversity of your backyard (Hooper et al. 2015). You can also look at biodiversity on a larger scale, such as the biodiversity in your county. In your county, there are many more species of trees, there are several different types of berries, there are many farms growing vegetables, there are many different species of birds, there are larger mammals, there are many types of insects, and there are rivers full of amphibians and fish. In contrast, we can also study biodiversity on a smaller scale; at the genetic scale (Oliver et al. 2015). Consider humans, we are all the same species, but we all look very different from one another. This is because we each have a different set of genes encoded in our DNA which makes each of us unique (Durham 1991). Just like there is genetic diversity in the human population, there is genetic diversity in each of the species we find in our backyard, in our county, or in our oceans (Oliver et al. 2015).

Backyard

What is Resilience and how does it relate to Biodiversity?

Today, we live in an ever-changing environment. It is important to have biodiversity in our environment because it makes our ecosystems more resilient (Oliver et al. 2015). Let’s think about our backyard again. The trees in our backyard provide us with something that we need and want in the hot summer months, shade. Shade is considered an ecosystem service; it is a benefit that humans receive from the environment (McLeod and Leslie 2009). Now imagine a big storm comes through your area and all the cottonwood trees in your backyard fall over with the high winds of the storm. If the only type of tree in your backyard was cottonwood, then you would no longer have shade in the summer. Luckily, you also have maple trees in your backyard. These maple trees have a much larger root system, so they can stay standing through the high winds of the storm. So, even though all the cottonwood trees in your backyard are gone, there are still maple trees to provide you with shade in the summer. Having biodiversity of trees in your backyard allows your backyard to be more resilient to storms. Your backyard changed, but it was still able to provide you with the ecosystem service that you wanted, shade. The biodiversity of your backyard ecosystem allows for resilience.

Cottonwood Tree

Now let’s look at the biodiversity on the smaller scale, let’s consider genetic biodiversity. Your neighbor has only cottonwood trees in their yard; so, you assume that all their trees have blown over in the storm. Yet, when you look over at your neighbor’s backyard, you see that some cottonwood trees are still standing. Why is this? It turns out that while your neighbor does not have a biodiversity of different types of tree species in their backyard, they do have genetic biodiversity in the cottonwoods planted in their backyard.  Some of the cottonwood trees planted in their backyard have genes that code for a larger root system. These trees make up a genetically defined group of cottonwood trees that are different from the genetically defined group of cottonwood trees that blew over. The genetic diversity among cottonwood trees in your neighbor’s backyard allowed for resilience of not only their backyard ecosystem, but also of the cottonwood trees. You still have shade in your backyard, but now you must sit under a maple tree for shade. Your neighbor still has shade, but they can still sit under a cottonwood tree for shade.

DNA

You planted certain trees in your backyard and continued to maintain the health of these trees; this is a way in which your backyard was managed. By maintaining a diversity of trees species or genetic diversity of cottonwood trees, you can make your backyard ecosystem more resilient to environmental effects (Bagley et al. 2002). Just like you can manage your backyard to be more resilient to storms and a changing environment, we can manage other natural resources to maintain a heathy, productive, and resilient ecosystem that will continue to provide humans with the services that they want and need from the natural environment (McLeod and Leslie 2009; Berks 2012; Lester et al. 2010).

Genetic Diversity and Dungeness Crab

In Oregon, fisheries are an important natural resources that provide us with many ecosystem services, including food. Just like shade is an ecosystem service we obtain from the trees in our backyard, seafood is an ecosystem service provided by the ocean. One of the most valuable ocean fisheries in Oregon is the Dungeness crab fishery (Rasmuson 2013). In order to continue catching and eating this natural resource into the future, the fishery is managed. There is uncertainty in what environmental changes or extreme events will occur in the marine ecosystems in the future, but understanding and maintaining the genetic diversity of the Dungeness crab can provide a foundation for a species that has greater resilience to change. It is inevitable that environmental events will negatively impact some of the Dungeness crab along our coasts, but diversity of the population’s genetic composition can increase the likelihood that some of the Dungeness crab will survive. Genetic diversity of the Dungeness crab along our coasts is just one of many aspects of the species that can influence how plentiful the Dungeness crab fishery is along our coasts in the future.

Dungeness Crab

Dungeness crab DNA sequencing and big data

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We have been collecting the megalopae life stage of Dungeness crab along the Oregon coast and extracting DNA from these individual megalopae. The next step is to sequence the Dungeness crab megalopae DNA so we can conduct statistical analyses that will help us understand how oceanographic conditions impact the Dungeness crab megalopae recruitment and the genomic composition of Dungeness crab along the West Coast of the United States.

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

Before jumping into the details to genomic sequencing, imagine you are given a stack of 100 cover-less books and told that there are several different book series mixed within this stack. You are asked to categorize the books by series.

What if you were given a pile of 100 books and asked to categorize them by book series?

You could read every book, but this might take a very long time… And, it may not be necessary to read every book cover-to-cover if your only goal is to categorize the books by series and not necessarily understand the storyline details of each book. Right?

So, what if instead of reading all 100 books, you systematically read the first paragraph of each chapter. Would you have enough information about each book to group the books into series? Chances are that each series has their own characters, settings, themes, or writing styles. By reading the first paragraph of each chapter in each book, you would be able to pick-up on the characters, settings, themes, or writing styles of each book that differentiate each series. You could then group the books together that had the same characters, settings, themes, or writing styles.

We do something similar with Dungeness crab DNA. Sequencing the Dungeness crab megalopae DNA involves reading the ‘A’s, ‘T’s, ‘G’s, and ‘C’s that make up the DNA and then comparing the patterns of ‘A’s, ‘T’s, ‘G’s, and ‘C’s between individual crab megalopae to look for differences. Considering that the size of the Dungeness crab genome (all of its DNA) is quite large, it would be a costly, time-intensive, and computationally-intensive process to sequence the entire genome of every megalopae we want to analyze.

After collecting Dungeness crab megalopae and extracting DNA from individual megalopae, we use sequencing machines to read the DNA. But instead of reading the entire genome, we read many small sections from across the genome. This type of DNA sequencing is called reduced representation sequencing. Similar to the pile of books example, after this type of sequencing we couldn’t tell you everything about the genome of that particular Dungeness crab, but we would know enough about the individual crabs (or “books”) to tell if they are different from each other and if they were members of different groups (or from different “book series”).

Reduced Representation Sequencing (Truong 2012)

If the groups of crabs (“book series”) differentiate significantly, we can call them different populations. Alas, this is why we call ourselves population geneticists. We know that all Dungeness crab are of the species Dungeness crab (Cancer magister) and that all “books” are of the species “book.” But with population genetics, we are looking within species to to determine if there are sub-populations (or “book series”) within the species. Because of the social, economic, and ecological value of the Dungeness crab species along the West Coast, it is important that we understand the population genetics of the species so that we can continue to sustainability harvest this valuable fishery.

Dungeness Crab Commercial Fishery

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.