Sunday, July 21, 2013


Frankenfish. For me, the word conjures an image of a child’s drawing of a fish—huge teeth, multi-colored and distorted, coloring outside the lines—a cross between Jaws and Nemo. This is what the news media has lovingly dubbed the genetically engineered (GE) Atlantic salmon, which recently passed (pending public comments) the FDA after nearly 17 years in review. The FDA concluded the fish would have “no significant impact” (e.g. it poses neither significant health or environmental risks). The public comment period is now over, and the AquAdvantage Salmon is now undergoing final review—if it passes, it will be the first GE animal to enter the markets.

The AquAdvantage Salmon (as it’s being marketed by AquaBounty) was developed by scientists at the University of Newfoundland, and adds two genes (a promoter gene from the Ocean Pout and a growth hormone gene from faster-growing Chinook salmon) in order to allow the salmon to produce growth hormone all year long instead of seasonally, thus achieving full size in about half the time of a wild Atlantic salmon.

A genetically-engineered salmon and regular salmon of the same age
The aptly named Ocean Pout
So what are the potential problems concerning GE animals? (I use the term genetically engineered rather than genetically modified, as genetic modification has been going on for hundreds of years, since the Middle Ages when destriers were bred for size to be able to hold knights in armor. Genetic engineering is the more recent practice of directly manipulating an organism’s genome using biotechnology). Obviously, GE animals are a facet of the wide-spread and ongoing ethical debate over GMO foods, but here I will focus on the potential environmental impacts of GE organisms.

Genetic modification in Westeros
One of the major environmental concerns with GE plants (like Monsanto’s pesticide-producing corn) is that insects and weeds will evolve resistance, instigating an evolutionary arms race—‘superweeds’ demand the invention of GE plants with even higher levels of pesticide production, which will in turn breed super-superweeds, etc.. The main concern with GE animals is that if they escape, they will compete and/or interbreed with local populations, with unknown consequences. For salmon, this is already a problem with current hatchery and aquaculture practices, but in this case there is concern that the transgene conferring elevated growth rates will give GE salmon a competitive advantage over wild populations. However, AquaBounty is taking serious measures to ensure that its fish will not interbreed (more below), and the GE salmon will grow faster, but not larger, than wild salmon.

The most recent news flurry about GE Atlantic salmon was sparked by a study from ecologist Peter Westley. A few weeks before this study hit the mainstream news, Westley came and gave a seminar to the UC Santa Cruz Ecology department, presenting the results of his lab studies on potential interspecific hybridization between AquAdvantage salmon and wild brown trout. (An amiable man and good speaker, Westley did a good job of diplomatically presenting the science without expressing his personal opinion on whether GE salmon should enter the market, a challenge for all scientists, especially concerning controversial topics). In his study, he and his colleagues found that under lab conditions, transgenic hybrids (i.e. offspring of a wild brown trout and a GE salmon) outcompeted both GE and wild salmon.1 While this study validates concerns about the potential risks of interbreeding between GE salmon and other closely related species (as well as wild salmon), these studies are necessarily limited to laboratories, making it difficult to know the actual environmental consequences should GE salmon escape.

AquaBounty has devised a triply secure method against the possibility of GE salmon escaping and interbreeding with wild populations: the GE salmon will be sterile, all female, and raised in land-locked pens in Panama (where local water temperatures are inhospitable to the salmon, should they escape). The all-female population will be created using gynogenesis, and sterility will be achieved by making the fish triploid (3 chromosomes) via heat and pressure shock on the eggs.2

Process of AquAdvantage salmon production
(figure from FDA report)
So the question remains, is the risk of putting GE salmon on the market worth taking? Let’s consider the alternative. People LOVE salmon—it’s delicious. So at the heart of this debate, it’s a matter of supply and demand. Our current salmon supply comes from a combination of wild populations, supplemental hatchery production, and farmed salmon. Wild salmon populations are in trouble—and on many rivers, hatchery fish have already interbred with wild fish populations, decreasing their genetic diversity (some rivers, such as the Sacramento in California, would likely not have salmon populations at all anymore if it weren’t for hatchery production). And many large salmon aquaculture operations (the source of farmed fish) raise their fish in net-pens in the ocean (see previous post), making the risk of escape and interbreeding more likely than for AquaBounty’s proposed operation.

At this point, it seems we are stuck trying identify the lesser of several evils. The bigger picture problem is how we are going to feed a growing world population. Fish is a relatively cheap protein source, and GE salmon grow faster than regular farmed salmon on less feed, thereby efficiently creating more marketable fish in a shorter time. Put this way, AquaBounty starts to sound a lot like CAFOs, with the associated problems of crowded conditions, disease, and use of antibiotics… and this is already a problem with current aquaculture operations. In the case of CAFO animals, there are no wild cow or chicken populations that we’re trying to protect by supplying an alternative, but there are movements towards locally sustainable farming (with the associated increases in cost per pound). So regardless of whether it’s traditional aquaculture or GE salmon aquaculture, the conditions under which the fish are raised should be an important consideration for both health-conscious and environmentally-conscious consumers.

1) Krista B. Oke, et al. (2013). “Hybridization between genetically modified Atlantic salmon and wild brown trout reveals novel ecological interactions.” Proceedings of the Royal Society B.

Tuesday, June 4, 2013

Re-inspired! Banff, birds, and bad-ass statistics


Some people are fortunate enough to be passionate about their jobs. They are also probably familiar with the roller-coaster love-hate relationship that comes along with this passion. This is especially true in grad school, where passion for your (often outdoor) research is then traded for long hours at the computer, doing data analysis and statistics. And I’m one of those people that thinks statistics is fun, but after hundreds of hours, I’m often in the “hate” phase of the roller-coaster. The solution? A week-long course explaining the guts of statistical models, held in a spectacular location, that can re-ignite your faith in statistics and even broaden (if possible) your love of nature.

This past week I took a course in mixed effects models, which happened to be located in Banff, Alberta. (I had to convince my advisor that this was not the reason I signed up for the course.) Banff is as spectacular as the hype might lead you to believe – it reminded me of a cross between leafy-green New England and Aspen Colorado (but with more epic-looking mountains). I had, without doubt, the most amazing few days of wildlife viewing of my life. I headed up to Moraine Lake at 5a.m. one morning for some dawn photography with a friend from the modeling course, and in quick succession, we came across a porcupine, 5 Snowshoe hares, 2 pika, and the incredibly elusive wolverine, an animal that I never really expected to see in my lifetime. I saw its dark shaggy back disappearing into the underbrush, and then it was gone.

On the Bow River, north of Banff
A gray dawn at Moraine Lake
We spent daytime hours in a sort of endurance-learning fiesta – like drinking from a fire-hose, as one girl put it – absorbing as much statistical knowledge as possible while it washed over us in voluminous waves. But luckily it was light from 5am-10pm, and we were able to explore before and after class… and sometime during these days in Banff, I re-discovered my interest in birds. I’m not sure why I’ve never really taken to birding – my husband is a birder, as are many of my friends (one of whom is so enthusiastic that he plans to tattoo an image of the 600th bird he sees onto his butt). But the fact is, I’ve had only a passing interest… until this trip. Perhaps it was seeing the Great Gray Owl close-up in a meadow one of the evenings, staring at us with yellow-eyed suspicion, a bird I’ve been obsessed with seeing ever since listening to its incessant evening hoots while living in Yosemite. Or perhaps it was the early morning trip to Moraine Lake, where my birder friend was able to pick out species after species from the dawn cacophony of calls, a language he spoke but I didn’t. Regardless, my interest was piqued.

And really, when you think about it, why isn’t everyone obsessed with birds? They are brightly-colored animals that FLY and are related to dinosaurs. Perhaps it’s a matter of novelty. If birds existed only in Africa, we’d probably all be dying to take a bird-safari to go see the colorful flying mini-dinosaurs. Who cares about lions!

So I spent my 3-days of backpacking in the Banff wilderness with binoculars in hand, re-discovering the joy of stop-and-go hiking as I birded my way along the trails. Incidentally, it helped my birding skills considerably that I didn’t fall into my usual zone-out hiking style, due to the fear of a grizzly round every bend. That’s pretty good incentive to stay alert. (It’s also surprisingly hard to keep up a steady stream of whistling while hiking uphill.) My birding efforts were rewarded by many cool species (see below), among them a Ruffed Grouse that I nearly ran into, perched silently on a branch by the trail. (Thankfully, since my only experience with Grouse has been as a master of camouflage, staying perfectly still until you’re right on top of it, when it explodes from the underbrush with a thunderclap.)

And so, like a meditation retreat, grad school-style, my week of re-inspiration is complete. It’s hard to write engagingly about statistics, but I’ll say that mixed effects models are immensely important for ecological analysis, since they allow you to take into account (rather than ignore) individual variation… which is pretty much a given in ecology. And for my data, which features 200+ fish all behaving slightly differently, this is a definite necessity for teasing apart any patterns. Data analysis, here I come (again).

Banff wildlife bonanza (e.g. all the species I saw during my trip):

Grizzly Bear


Red squirrel
Elk (my photo)

Great Gray Owl

Snowshoe hare
Least chipmunk

Ruffed Grouse (my photo)
Clark's Nutcracker
Northern Goshawk
Black-capped Chickadee
Yellow-rumped Warbler
Dark-eyed Junco
Chipping Sparrow

Canada Geese
Varied Thrush
Common Merganser

Stellar's Jay
Quoth the raven, 'Nevermore'

Friday, May 24, 2013

Striped bass: will eating them all solve the problem?

A few weeks ago, I had the opportunity to help out a labmate with her research on the Mokelumne River (and take a classic fish photo.) Unfortunately, I didn’t catch it angling… an electro-fishing boat caught it. For those who haven’t heard of this, it’s a boat that sends out pulses of electricity through the water to momentarily stun fish, a common way to catch them for fisheries research. Cheating? Perhaps. But the fish aren’t hurt, and it’s a whole lot easier (though less fun) than fishing all day to catch your sample size quota.
Striped bass classic shot
E-fishing boat courtesy of collaborator EBMUD:
the hanging metal cables shock the water
We were up on the Mokelumne, which joins the Sacramento-San Joaquin Delta near San Francisco, to remove all the striped bass from a pool below an irrigation dam. California’s Sacramento-San Joaquin Delta is plagued by many problems, and foremost among them is the conflict over water needs between agriculture and ESA-listed native fish populations, including salmon, steelhead, and Delta smelt. As a result, a lot of effort goes into trying to figure out what is causing high mortality in native fish populations, and what can be done to boost survival. One possible culprit: striped bass.

The last thing the juvenile salmon sees (looking down the striped bass gullet)
Striped bass are native to the Eastern U.S., and were introduced to the west coast as a game fish, a sadly familiar story. (As an interesting sidenote, Wikipedia lists many common local names for striped bass, including striper, linesider, rock... and my favorite, pimpfish). Striped bass eat juvenile salmon (see my post from last October), so one suggestion for boosting salmon populations is to decrease predation pressure by attempting a large-scale striped bass removal, through unlimited fishing allowances. But will this work?

My labmate is looking at an interesting aspect of this question. She is measuring juvenile salmon mortality as the fish move past an irrigation dam, both when striped bass are present in the pool below the dam, and when they are absent (through removal). The idea is to see if salmon mortality drops dramatically when the bass are absent, or if other predators in the system (some of them native, like the pikeminnow) fill the predatory niche, making removal ineffective… or perhaps even exacerbating the problem, since striped bass also prey on some of the other fish that eat salmon. If striped bass are removed, this would release these other predator populations from bass predation pressure as well, and could potentially cause a sharp rise in other predator populations. (For a more complete, interesting discussion of this topic, check out well-known fisheries biologist Peter Moyle’s post on the California WaterBlog).

The fieldwork for this project was quite fun, involving many slippery, spiny fish and a beautiful day in the California sun. I joined in for the bass removal day, so a group of juvenile salmon had already been released through the dam the previous day and mortality measured while striped bass were present. We were there to remove most of the striped bass, prior to another salmon release. To remove striped bass from the pool, an electro-fishing boat made four passes through the pool below the dam, shocking the water and catching a cross-section of the fish community each time. Striped bass key in on pools below dams, where salmon coming through are funneled through a small area in large numbers, providing an easy feast for waiting predators, so this pool is usually full of bass around this time of spring, when juvenile Chinook are out-migrating to the ocean.

The irrigation dam and pool
We took striped bass diet samples to get an idea of what proportion of the bass diet is made up of juvenile salmon. This is done through gastric lavage (aka making the fish barf by flushing them out with water). The only downside to this is that the spines on the dorsal fin of striped bass are surprisingly sharp, and fish are slippery and wiggly. Suffice it to say that I got some war wounds.

Barfing a fish
One striped bass' breakfast
We then returned all other fish species to the pool, but retained the striped bass and transported them to another river later that day. It will be interesting to see the results of this research. However, I doubt very much that removing all striped bass from the Sacramento-San Joaquin system will be enough to cause significant increases in salmon populations. The Delta is a highly altered system—it used to be an extensive wetland, and is now mostly agricultural fields and channelized habitat—so extensive habitat restoration will likely be needed to help restore native salmon populations. However, this is a complex question that deserves its own post. Stay tuned.

But predator removal could well be a part of the solution, and hopefully this study will help us determine whether this is true. Striped bass for dinner, anyone?

The crew (fish and human)
And most importantly... when you're doing fieldwork in the sun all day,
you have to be innovative about how to keep the chocolate snacks from melting

Thursday, May 9, 2013

Stuck between a creek and a hot place: Why our rivers are getting warmer

 When I give my ‘elevator-speech’ summary of my research—I study the effects of hot river temperatures on juvenile salmon behavior and the importance of coolwater refugia…—a common question I get is, ‘But why are river temperatures rising?’ Sometimes people are a little abashed about asking, since it seems like a simple question… but really, it’s a great question, and the answer has considerable nuance.

A recent study of 40 rivers across the U.S. found that most showed significant increases in water temperature over the past half-century.1 A combination of factors affect stream temperatures, including air temperatures, amount of solar input, and land-use (e.g. urbanization, farming, and river management). This makes sense both intuitively and from experience—rivers in tropical climates are on average warmer than in the Arctic, and small high mountain streams are colder than large rivers near their delta (where they are both larger and less shaded, and are therefore open to a lot more solar radiation).

Air temperature is a strong predictor of water temperature, and increases in air temperatures due to global warming are causing a trend of increasing stream temperatures.1,2 However, this is not the whole story. Urban areas create ‘heat islands’ that can increase water temperatures both through hotter ambient air temperatures, as well as heated water run-off from hot pavement. In addition, land-uses such as irrigation and dams can exacerbate the warming trend further, by storing water in slow-moving or shallower areas (such as irrigation ditches and reservoirs) where it heats up before returning to the river. For example, on the Klamath River where I do my research, the Iron Gate Dam (lowest of 6 on the river) is an old dam that releases water downriver from the top of the reservoir, water that has been sitting in the sometimes 100°F summer heat all day. As a result, summer water temperatures on the Klamath can reach ~80°F (26°C), which feels like bathwater, and is nearly lethal for coldwater-adapted fish like salmon.

There are many problems associated with rising river temperatures, and not just for salmon. Warmer water temperatures can cause increases in primary productivity and lower dissolved oxygen levels, effects that cascade up through the ecosystem, changing aquatic habitat structure and availability, invertebrate community composition, habitat suitability for many fish species, and often making the ecosystem more susceptible to invasive species. On the Klamath River, the summer hot water temperatures combined with eutrophication (excess nutrients, often from farm run-off) cause massive green-algae blooms in the reservoir by late summer, which get released downstream and turn the whole river green.
The Klamath River during an algae bloom
Halting the trend in rising water temperatures is linked to the problem of stopping increasing air temperatures (and rising atmospheric carbon dioxide), and will not be a quick fix. However, there is significant mitigation and restoration that we can do to lessen the impact of elevated water temperatures, solutions ranging from urban greening to dam removal to in-stream habitat restoration. This is where my research fits in—salmon are a coldwater fish, and on rivers like the Klamath, summer water temperatures can reach levels that are sometimes lethal. As a result, the fish seek out colder areas in the river (coolwater refugia), often created by incoming coldwater tributaries. Protecting and restoring these refugia are an important way that we can mitigate the effects of hot summer rivers temperatures on salmon.

Juvenile salmon piling into a thermal refugia on the
Klamath River (photo by Kyle Swann) 
It’s important to note that knowledge of the long-term trends in river water temperatures, as well as the data that produced the now famous graphs of rising C02 trends, would not be possible without long-term monitoring projects that were established years ago. These kinds of long-term programs are hard to fund and maintain, yet are essential if we want to understand how our environment is changing over time—this is an interesting problem that my lab is currently researching. Stay tuned!

1) Kauschal, S. et al. (2010). “Rising stream and river temperatures in the United States.” Frontiers in Ecology and the Environment.

2) Webb, B. et al. (2007). “Long-term changes in river temperature and the influence of climatic and hydrological factors.” Hydrological Sciences Journal.

Tuesday, April 30, 2013

Fish ‘n’ Chips… in Laos?

I had the best fish and chips of my life last week, and I was nowhere near England. We were traveling in Thailand and Laos for the past two weeks. In Luang Prabang, Laos, a sleepy river town along the Mekong River, still touched by the influence of French colonization (at least in cuisine and architecture), after three days of weathering the near 110F heat (and ~80% humidity), we treated ourselves to some Western food for dinner. I had a brief internal struggle over whether I should order fish and chips in Asia, but then desire took over, and I went for it. (However, I shouldn’t have worried, given the deliciousness of the Pain au Chocolat all over town). And what I realized—in between exclaiming for the 27th time to Pete how delicious it was—is that I’ve never really liked fish and chips because of the fish (not because of the way it was cooked). Fishy-tasting haddock has nothing on the light, fresh Mekong mystery fish. Inevitably, this got me curious about Mekong fish species, and the state of the fishery there.

Delicious Laotian food, featuring brown sticky rice and chicken laap

It turns out that the Mekong has the second highest fish species richness in the world, surpassed only by the Amazon.1 Some of its native fish species look as though they have been lifted straight from the Pleistocene—600lb giant catfish (which I admit I fantasized would leap out of the water by our boat), and a freshwater stingray that supposedly reaches 1200 pounds! However, in what is a sadly familiar story, the fish diversity is threatened, as many of these species are suffering severe population declines from a combination of overfishing, water pollution, and upstream dams. This is particularly concerning for a country where much of the rural population relies on local fish as the cheapest source of protein.1 At the moment, the main threat to these fish is hydropower development, which under certain development projections could cut off 81% of the Lower Mekong Basin to fish migration, and turn 43% of the this section of river into a reservoir.2 There are currently 16 dams in the Lower Mekong, 47 more planned for completion by 2015, and 77-88 more to be completed by 2030… an astounding rate of development.2 But unlike the U.S., which is currently removing more dams than it’s building, many developing countries are still in the dam building phase. As well as being concerning, this presents an opportunity to research alternative, or at least more environmentally sound, solutions. Perhaps we should move to Laos.

Mekong River at sunset, Luang Prabang
Local fish at market
 We got to observe some interesting native fishing practices while in Laos. On our daytrip up the Mekong to a cave full of over 4000 Buddha statues, we saw people in small wooden fishing boats whacking the water with long sticks. At first, we couldn’t fathom what they were doing—the parting of the Mekong?—but then we saw them jump in the water and haul in fishing nets. Somehow, slapping the water with the poles was encouraging, or even herding, the fish into the nets. Unfortunately we didn’t have a chance to find out what kind of fish they were catching… but perhaps it’s the same kind that ended up in my belly later that night.

Fisherman on the Mekong
On the boat trip up to Pak Ou Caves
While I’m not sure what kind of fish was served up in the fish and chips that warm night in Luang Prabang—the awkwardness of the language barrier dissuaded me from asking—one way that we, as consumers, can have some sway over the commercial fishery is by being informed fish buyers. My husband and I often embarrass whomever we’re dining out with by asking the waiter where the fish came from (yes, Portlandia style, although I usually forbear from asking the fish’s name). In fact, on our trip to Thailand, we were eating out in an elegant Bangkok restaurant with family, and Pete and I began discussing where the salmon might have come from… only to be greeted by a snort of laughter from across the table. My sister-in-law and her friend had made a bet that we would ask about the salmon (while they cringed in embarrassment)… and indeed, they were right.

In an interesting example of how effective consumer pressure can be, a professor at UC Santa Cruz recently had his Marine Conservation class research which food markets in town sold environmentally sustainable fish, and then create a little pamphlet ranking them (red/yellow/green). Within a week, he got a call from one of the yellow-ranked stores asking how they could change. They were concerned about their public image. Shame, as it turns out, is an excellent motivator. (Even more so than guilt).

We have incredible power as consumers. And the more people that ask where fish comes from when they sit down to eat, the less socially weird it becomes. As “dancing guy” shows, be the one to set the trend…

1) Mekong River Commission (2010). "State of the Basin Report, 2010." MRC, Vientiane, Laos.
2) Baran, E. et al. (2012). “Fish Biodiversity Research in the Mekong Basin.” Ecological Research Monographs.

Thursday, March 28, 2013

Who’s eating all the fish?

What are the major causes of salmon mortality? Unsurprisingly, this is one of the major questions in salmonid research. Of the thousands of eggs that an individual adult female salmon lays, on average only 1-2 adults return to successfully spawn. Salmon have a complex life history, spanning both freshwater and marine realms; there are many opportunities for them to die along the way, but it’s not always easy for researchers to parse out what’s killing them, and at which life stage.

This week, I helped out one of my lab-mates who’s studying one aspect of this complex question. She’s trying to figure out whether bird predation is a major cause of juvenile steelhead mortality in several small creeks just north of Santa Cruz, California. However, quantifying predation can be extremely difficult—the challenge is not just to show whether one animal is eating another, but also to quantify the predation rate (i.e. what percentage of the out-migrating juvenile salmon population is being eaten?). To do this, she and several researchers at the National Marine Fisheries Service lab in Santa Cruz came up with an ingenious method. A local biologist discovered a PIT tag (a small tag used to individually ID fish) on the nearby Año Nuevo Island, sparking the question: are birds eating young salmon in the creek and estuary and then depositing the tags (i.e. crapping them out) on the island?

The old foghorn keeper's house from the late 19th century
Año Nuevo Island is a beautiful state reserve just off the coast north of Santa Cruz, and provides important breeding and resting habitat for Northern Elephant Seals, California and Stellar’s Sea Lions, Rhinoceros Auklets, Brandt’s Cormorants, and Western gulls. At this time of year, its beaches and rocky terraces are teeming with wildlife—elephant seal pups, abandoned by their mothers and resting until they’re ready to start their own ocean journey, lie in adorable, fat, glassy-eyed piles. Huge droves of California sea lions blanket the beaches as well, barking noisily. And Western gulls add to the relentless cacophony; it’s a place that is at once peaceful and frantic, depending on your mood and ability to filter out the constant noise.
Sea lions and elephant seals blanketing the beach of the island
Wallowing baby elephant seals
We made a research trip out to the island yesterday to search for the PIT tags, heading across the ~1km stretch of ocean in a tiny dingy, banging the sides to scare off over-curious marine mammals. Our mission was to use a PIT tag detector to scan as much of the island as possible (marine mammals permitting)—the detector picks up the individual tag ID if it’s near a tag. Luckily, we didn’t need to actually find or retrieve the tags, since they are about the size of a grain of rice. Data on how many PIT tags are found and the detection likelihood, combined with data on total out-migrating salmon population size, will allow us to estimate avian predation rates on juvenile salmon in nearby creeks. In addition, the tags will tell us which particular individual fish were eaten, allowing us to quantify the characteristics of these fish to see if there is size-based mortality (i.e. were these fish disproportionately small or large compared to the average size of fish in the out-migrating population?)

Western gulls staking out their territory
Scanning for PIT tags
Estimating predation rates, as well as pinpointing potential predators, is an important step towards good management practices. So what are the potential predators that could be depositing these tags on the island? Possible culprits include avian predators—Western gulls and Brandt’s cormorants both use Año Nuevo Island for breeding—but also California sea lions, who also eat salmon. Determining which of these possible predators is actually depositing the tags on the island requires more (past and ongoing) research, including several studies analyzing the diet and movement patterns of Western gulls.