The Elwha Restoration Project: Goodbye Dams, Hello Salmon

Imagine that you’re a salmon. You were born in clean, healthy river waters. You grew, smolted, and migrated downstream, eventually reaching the ocean where you would attain your adult size. After a few years, you felt the urge to return to your home stream for your one chance at spawning. You traveled hundreds of miles through the Pacific Ocean and found the mouth of your home river. But when you tried to swim upstream, you found a barrier in the way – a giant wall that prevented you from getting back to your spawning stream.

For many fish in the Elwha River, this is exactly what happened.
Continue reading

Science Story-telling at Restoration 2012 (or, why I think science blogging is important)

Twitter followers will know that I was in a foreign land for most of this past week.  (Are you following me on Twitter?  Because you should be.  I’m @iriskemp)

I’m speaking, of course, about Canada, land of lovely maple leaves and delicious maple syrup.

I spent this past Monday through Thursday on the University of Victoria campus attending Restoration 2012, the annual meeting for the Washington-British Columbia chapter of the American Fisheries Society.

Along with my fellow fisheries friends, Jessica Rohde (@RockyRohde) and Jessie Hale (@HaleJessie), I presented my thoughts about the importance of science communication in today’s world.  While I recognize that the power of social media can be harnessed through many different venues (e.g., Twitter), I focused this presentation on science blogging and it’s assorted benefits.  I also answered some of the most common questions that I hear from scientists when I mention blogging–questions about time commitment, blogging identity, and open science.

If I can be perfectly honest for a moment, I was feeling hesitant about my suitability to give this talk.  I’m not the most prolific science blogger out there–my posting frequency tends to be negatively correlated with my thesis work–nor am I the most well-spoken.  Even though I’ve been blogging for nearly 2 years (!!) now, I still sometimes feel uncomfortable putting myself out there for the world to see.  I think some part of this is my natural tendency towards shy-ness, but also I’m quite prone to imposter syndrome.

But then I realized: I’m living proof that anyone can do this.

I’m not a natural writer.  I’m shy and often insecure.  I’m only at the beginning of my career, with so much more to learn.  But I love science.  And so I blog.  And (I hope), I make a difference.  I make a difference by posting about scientific studies that I find interesting.  I make a difference by showing pictures of my research and my field work, experiences that a non-fisheries scientist may never get to have.  I make a difference by sharing my graduate experiences.  I make a difference simply by being me: a young female scientist who may still have a lot to learn, but who can’t wait to learn it.  I blog because I want to get you as excited about science (and fish) as I am.  I want to show you that I am science.

And I’m hesitant to share my muddled personal details with you.  But I will.  Because?  If I can do this, you can too.

Imagine what a difference we would make as each of us shares our science stories.

Below is a modified version of my presentation slides.  The modifications I made were in order to make the presentation compatible with slideshare; I tend to rely on pictures for the slides and verbalize my thoughts, so I’ve added some text slides for clarity.  (I’m also kinda bummed that I couldn’t get animations to work with slideshare, because I had some fun with those in the actual talk–I like my points to come in one at a time.  Ah well.)

Anyway, I hope you enjoy!

**Edit: I don’t know why the embed code is not working.  Technologically-savvy people, help me out?  The link below DOES work though, so please go there to view my slides.

[slideshare id=12988342&doc=slideshareversionrestoration2012sciencestory-telling-120518175855-phpapp01]

(link to slideshare profile here)

Battling #GradSchoolGuilt

It’s hard to relax when your work is always in the back of your mind.  Your thesis invades all the tiny nooks and crannies of your brain and leaps out at unexpected moments, just to make sure you haven’t forgotten about it—as if you could!  Add to that your classwork and your other commitments, and you find yourself on the express bus to Sleepless City.  At a certain point, you realize you need a break.  But when you turn off the computer, a familiar sinking feeling creeps in…  Yep.  Turns out grad school guilt applies to us science-y folk as well.

Continue reading

English sole & estuaries: how natural chemical markers can reveal habitat importance

If you’re a regular reader, you know I talk a lot about salmon.  And it’s pretty obvious that in anadromous species like salmon, juveniles occupy different habitats than adults (streams, rivers, estuaries vs. the open ocean).  However, it’s not just salmon that show this pattern.  Many coastal species of fishes live in different habitats at different life stages.  High quality juvenile habitats are often called “nurseries”, and these nurseries are what I want to discuss today.

First: how do you define a nursery?  Beck et al. (2001) give this definition: “A habitat is a nursery for juveniles of a particular species if its contribution per unit area to the production of individuals that recruit to adult populations is greater, on average, than production from other habitats in which juveniles occur.”  Basically, if one habitat is contributing disproportionately more fish to the adult population, that habitat can be considered a nursery.

Second: so how do you determine if a habitat is a nursery for a particular species?  Let’s look at one study that did just that: JA Brown (2006) investigated whether estuaries along the California coast could act as nursery habitats for English sole (Pleuronectes vetulus for those of you who, like me, love scientific nomenclature).

Image courtesy of, photographer Østergaard, Thorke A.S.

JA Brown looked at the chemical composition of English sole otoliths to determine a) whether otolith compositions were different in estuarine and coastal habitats and b) whether this could be used to determine the contribution of each habitat type to the adult population.

The otolith is a calcified structure in the head of a fish (basically, an ear bone).  As the fish grows, the otolith grows as well, adding a new layer each day.  This creates daily banding patterns and annual growth patterns (commonly, slow growth -> thin bands, while fast growth -> thick bands).  These bands are used to age the fish similar to how you would age a tree by counting its rings.  Otoliths are metabolically inert, so once a layer is added, its chemical composition does not change.  Finally, the deposition of elements into an otolith layer can be influenced by the outside environment (e.g., temperature, salinity).  Therefore, different habitats can produce otoliths with different chemical compositions.

From Brown (2006), an English sole otolith:

Fig. 2. Pleuronectes vetulus. Juvenile core isolated from otoliths of adult English sole in a multistep process. An isomet saw was used to remove edge material from the rostrum and post-rostrum along Cuts A and B, and to make a thin section approximately 300 μm thick along the sagittal plane (plane of this page). A microdrill was used to remove right and left sides from the thin section by drilling along translucent band corresponding to 1st winter (Paths C and D)

Brown’s first question was: is there a chemical tag that can distinguish English sole living in estuaries from English sole living in coastal habitats?  She analyzed the chemical composition of otoliths from juvenile fish caught in each type of habitat and found that strontium (Sr) and lithium (Li) concentrations differed between estuaries and coastal habitats and that Sr:Ca and Li:Ca ratios could be used to separate fish from each type of habitat.

Brown’s second question: what is the contribution of each habitat type to the adult population of English sole?

She created two juvenile classification models under different assumptions.  English sole are mostly non-migratory; however, some individuals might move along the coast.  So Brown created a model for each movement type: one model assumed juvenile migration and the other assumed no juvenile migration.  She then used a linear discriminant-function analysis to assign fish to estuarine or coastal habitats for each model.  (For non-statistical-minded folks: basically, this analysis allows you to categorize your data into groups based on certain features–in this case, Sr and Li concentrations.)

For juvenile fish, she compared the model classification results to the known habitat of the fish (where they caught it).  Under each model, classification accuracy was over 75%.  She then analyzed the otolith cores from adult fish–only looking at the juvenile portion of the otolith–to see in what habitat these fish had been in as juveniles.  Both models showed that about half the adult fish were from estuarine habitats.  Brown went through several tests of other assumptions (for example, whether the otolith cutting technique and potential contamination might significantly affect the results).  In all cases, about half the adult fish had spent their juvenile life stage in an estuarine habitat.

So okay, about half of the adult English sole were from estuaries.  What does that tell us about the contribution of estuaries as opposed to coastal habitats?  Not too much–until you consider the area of each habitat.  For example, in Monterey Bay, estuarine habitat comprises about 6% of the available juvenile habitat.  But that 6% contributes approximately half the adult English sole in the region!  Definitely a disproportionate contribution.

A GoogleMaps image of Elkhorn Slough, CA: the only estuary in Monterey Bay.

Other research on English sole suggests that estuaries can support higher densities and faster growth rates than coastal habitats can.  Those findings and the results of Brown’s work suggest that California estuaries can serve as nursery habitats for English sole.  Unfortunately, estuaries are often vulnerable to habitat loss from things like erosion, pollution, and urbanization.  Research like Brown’s, which shows the importance of certain estuaries to fish populations, help us realize that we should be concerned about targeting these areas for environmental monitoring and protection.

This is merely an overview of JA Brown’s work.  She goes in-depth in her 2006 paper about her collection methods, otolith procedures, and statistical analyses–topics which I have skimmed over here.  I definitely recommend you go and read the paper in its entirety.  It’s cool stuff.

Brown, JA.  2006.  Using the chemical composition of otoliths to evaluate the nursery role   of estuaries for English sole Pleuronectes vetulus populations.  Mar. Ecol. Prog. Ser. 306: 269-281.

Also, the definition of nursery as stated above is from this paper:

Beck, MW, Heck, KL Jr, Able, KW, Childers, DL, Eggleston, DB, Gillanders, BM, Halpern, B, Hays, CG, Hoshino, K, Minello, TJ, Orth, RJ, Sheridan, PF, & Weinstein, MP.  2001.  The identification, conservation, and management of estuarine and marine nurseries for fish and invertebrates.  BioScience 51: 633-641.

Links to Check Out

If you’re interested in Infectious Salmon Anemia or salmon diseases in general, the USGS Western Fisheries Research Center has released a short YouTube video.  Go watch it!

Also, the University of Washington’s American Fisheries Society student sub-unit (also known as the much less tongue-twisty AFSUW) has a new website!  This is a shameless promo, since I am currently the VP for AFSUW and had a hand in the making of the website.  But if I may say so myself, the new site is pretty darn cool.  Go check it out–we love feedback!

In which Iris recovers from finals and posts pictures of cute animals.

Finals are over!  Finally!

My brain is mushy.  And I went to San Diego for the weekend.  So now I will proceed to make your brains mushy too, by posting pictures of adorable animals that I took at the San Diego Zoo.  Think of it as zombie protection.  Zombies hate mushy brains.  You’re welcome.

(lots o’ pictures below the fold)

Continue reading

A Secret about Salmon Virus

Anyone seen today’s Seattle Times?  I walked past a paper box this morning and this headline jumped out:


(It then proceeded to dance wildly down the street.  But that’s a story for another day.)

Anyway, what’s up with this story?  That headline sounds scary.  Here’s the low-down:

10 years ago, in 2002, a visiting researcher (Molly Kibenge) took samples of Pacific salmon on Vancouver Island.  She found evidence of salmon virus (a strain of infectious salmon anemia, or ISA) in 117 wild fish.  However, though the virus was present, there was no illness.  Molly Kibenge concluded that a non-lethal strain of ISA might exist naturally in wild Pacific salmon*.  However, her results and prepared write-up were not published.  So no one outside Canada knew about it.  After this year’s initial ISA scare, she went to her lab colleague (Simon Jones), who works for DFO Canada, to pursue publication of her results.  But he said that his agency disputed her results and did not give his permission for publication.

Molly Kibenge’s work suggests that wild Pacific salmon might contain a natural variant of ISA.  Thus, it is less likely than previously thought that ISA in wild Pacific salmon started in farmed fish.  Basically, ISA in wild Pacific salmon carries less risk than previously thought, since this strain appears to be local and non-lethal.

Let’s sum up:

Boo to Canada, for not letting anyone else in on this–especially because access to this work would likely have mitigated the fall-out of this fall’s virus-scare.

But YAY for those results, because they point to the conclusion that we should not be overly worried about the two wild sockeye that tested ISA-positive at Simon Fraser University.

However–as is always the case in science–we need more data.  I hope U.S. and Canadian officials continue the push for increased monitoring and virus testing of wild Pacific salmon.  If Molly Kibenge’s work can be verified and her conclusions supported, we’ll all breathe a big sigh of relief.

Link to the story: read it for yourself!

*Edited to add:

I’ve been corrected in the comments: Molly Kibenge did not find a naturally-occurring local strain of ISA in Pacific salmon.  She found the European strain, which does suggest introduction of the virus to the Pacific from Atlantic fish.  However, the strain was non-lethal.  My apologies for the confusion.

Infectious Salmon Anemia: the news keeps coming

Typical ISA lesions. Source: Merck Animal Health

Canada: government says that all tests were negative–oh wait, one was positive…but the sample was degraded and not repeatable, so technically it counts as a negative?  They say that there’s nothing to suggest that infectious salmon anemia (ISA) is present of British Columbia or in the North Pacific at all.  Dr. Rick Routledge, the professor who initially tested the salmon and announced the presence of ISA, says that the government shouldn’t simply dismiss the one positive and should do further sampling and testing.

Norway: A Norwegian lab conducted independent testing of the samples and came up with results that Canadian government officials say are consistent with Canada’s tests.  Except while Canada says there’s no ISA, Dr. Nylund says that results are inconclusive but do suggest that ISA is present in wild Pacific sockeye.

United States: U.S. officials fear that Canada has motivations to misrepresent the results.  They want to do testing of their own.  Canadian Peter King of DFO says that the samples are so degraded that sharing them would not be “good science”.  But Washington officials, Alaska officials, U.S. agencies, and tribes are developing a sampling program of their own.

Stay tuned…Salmongate, as some are calling it, isn’t over yet.

Some links:

Seattle Times article: No B.C. salmon virus, Canada says

A blog Superheroes4Salmon: Positively Negative-How the CFIA failed to defuse ISA in BC.  Includes photos of internal documents and several other links.