Category Archives: Research

NOAA’s search & tag cruise embarks

NOAA ship Shimad track for 2/16/12

NOAA ship Shimada track for 2/16/12

Last update — 3/2/2012, 10:00

Brad Hanson and his colleagues from the Northwest Fisheries Science Center, including Marla Holt and Dawn Noren, embarked today (2/16/12) from Newport, OR, aboard the NOAA ship Shimada (MMSI 369970147) to search for southern resident killer whales (SRKWs) along the outer coast of Oregon and Washington, and possibly California and British Columbia.  With luck, they will encounter members of J, K, or L pod over the next 3 weeks and be able to gather further information about the wintertime habitat and behaviors of these salmon-seeking orcas that frequent the Salish Sea during the summer.  It’s also possible they may learn more about what may have caused the death of L-112 who washed up at Long Beach (top of ship track map) on 2/11/12.

NPR offered a 1-minute prospectus for the cruise on 2/10/12, but it did not mention satellite tagging.  Instead it only indicated the normal activities would take place — towing hydrophones to listen for calls, whistles, and clicks, and scanning for whales visually with binoculars from the ship’s bridge.  In past winter cruises, they have deployed a small boat upon locating SRKWs to gather fecal and prey fragment samples.

This winter is the first they also have a permit in place to attach barbed satellite tags to specific SRKW individuals. A King 5 story on 1/25/12 suggested they do plan to deploy satellite tags during this cruise.  The question of whether the risks of tagging exceed the potential benefits has split the local research and conservation communities, with Brad advocating it’s worth it while Ken Balcomb of the Center for Whale Research said it’s not.

PDF assessing NWFSC permit (among others)

Candice Calloway-Whiting’s case for not tagging: 1) Added risk of fatalities from infections; 2) interference with care-giving by older females

Huffington Post article quoting Brad’s practical rational for tagging: 1) refining where acoustic detectors are placed and 2) offering new habitat use information to the transboundary orca-salmon meeting in Vancouver this March.

If you’d like to follow the Shimada’s progress this winter, one useful tool is the real-time Automatic Identification Service (AIS) data that is available through sites like  Today they zig-zagged up the coast at about 10 knots.  The forecast is for rough weather tomorrow (Friday) night, so expect to see the Shimada run for the more-protected waters of the Strait of Juan de Fuca.

Update: Monday 2/20/2012 1:10 a.m. (Pacific time)

After returning to Seattle briefly, presumably to wait out bad weather on the outer coast, the Shimada heads back out into the Strait of Juan de Fuca and is passing Race Rocks around midnight or 1 a.m. Pacific Time.

2/20: Shimada departs Seattle & Salish Sea

2/20: Shimada departs Seattle & Salish Sea

About 5 hours later (~6:00 a.m.)  J and possibly K pod calls are heard on the Lime Kiln hydrophones by Jeanne Hyde and Laura Swan.  There aren’t many fixes from AIS in the interim, but around noon the Shimada is moving east near the mouth of the Strait of Juan de Fuca.

Shimada steaming east at 7-10 knots around noon on 2/20

Sometime during daylight hours on 2/20/2012, the NOAA team tagged a J pod whale (J26, or Mike) that returned its first location around 1800. Here is a NOAA web page where the tagging data from SRKWs will be shared — and the first track posted there:

First J pod track

First track of a J pod whale with a satellite tag

And here is a summary of the first tagging event in 2012 by Chris Dunagan of the Kitsap Sun.

Updates on Shimada ship tracks — 2/21-23:


Shimada track on 120221 at 1527 Pacific time

No AIS data are easily available for the 24 hour period between 15:00 on 2/21 and 15:00 on 2/22.  Then the Shimada made a few passes within the Strait of Juan de Fuca between 15:00 on 02/22/2012 and 01:00 on 02/23/2012 (as shown in screengrab below).

Evening to midnight Shimada tracks on 2/22-23

Evening to midnight Shimada tracks on 2/22-23


Updates on 2/25/12:

The Shimada arrived in Port Angeles around 10pm local time on Friday 2/24/2012 to escape a storm that brought 45 knot wind gusts to the mouth of the Strait of Juan de Fuca (see AIS screengrab and plot below).

Shimada track into Port Angeles from 8pm local time on 2/24.

Shimada runs for Port Angeles at 13 knots from 8pm local time on 2/24.

35 knot winds send the Shimada to port on 2/25

Updates on 2/27/12:

The highlighted text was changed in this 2/27 screengrab of the NOAA orca tagging web site.  It indicates that the first tag provided data for only 3 days, though the group’s research permit states “Tags would be expected to stay attached for up to 25 weeks and are designed to release after one year.”  What a drag for Mike that so little data was transmitted…  At least he gave us an example of how far out on the shelf J pod goes, though (foraging?) at Swiftsure and La Perouse Banks is not new information.

Full track of J pod whale

3 day track of a J pod whale

The Shimada departed Port Angeles on 2/26/12 at 10 a.m. after weathering a storm.  The latest track (below, as of 03:00 on 2/27/2012) suggests that after crossing the Strait of Juan de Fuca, the NOAA team moved north at 5-8 knots from False Bay at around noon.  That could be a speed consistent with traveling killer whales, but no SRKW vocalizations were reported by humans on the San Juan Island hydrophones on 2/26/12 (though transient calls were heard at Lime Kiln around 17:00).  The Shimada proceeded at those speeds until reaching the south arm of the Fraser River where they turned around at about 19:00 and increased speed to 8-10 knots.  They passed False Bay going south at about midnight and then proceeded out the Strait of Juan de Fuca.

Screen Shot 2012-02-27 at 12.50.27 PM

Shimada track for 2/26-27/2012.

Updates on 2/28/12:

The Shimada began a search pattern today, zig-zagging south along the outer coast of Washington at about 8 knots.  The screengrab below shows their track from midnight until 4pm local time on 2/28/12.

Shimada track for 2/28/2012 00:00-04:00 Pacific time.

Shimada track for 2/28/2012 00:00-04:00 Pacific time.

The weather forecast suggests they’re in for a pretty rough ride, though weather is expected to moderate on Wednesday:

849 AM PST TUE FEB 28 2012






Oops.  Looks like the turned back and as of Tuesday 2/28/2012 at 17:10 were searching in the more-sheltered Strait of Juan de Fuca


Scant AIS data suggest Shimada returning to Salish Sea.

Updates Wednesday 2/29/2012:



Shimada patrols Strait from 2/28 19:00 to 2/29 08:24

Shimada feb 29 2012 data show the Shimada criss-crossed the shelf at 6-9 knots from 17:00-22:00 on Wed 2/29/2012.

The Shimada slowed to 3-4 knots near Sooke around 8 a.m. on Wednesday 2/29.  It is possible that the decrease in speed and changes of direction were related to an effort to observe the Bigg’s killer whales that were reported by Ron Bates on Orca Network’s Facebook page ~6-7 hours later: “T20 & T21 4.4 Nautical N.E of Race Rocks 1445.” AIS data for 2/29/2012 show a search pattern in the Strait of Juan de Fuca. Speed begins is mostly ~6 knots, but slows to 3-4 during direction changes near Sooke and increases to about 10 knots during return to inland waters.

Graphical synopsis of the first 2 weeks:

The NOAA team seems to have been concentrating on the Strait of Juan de Fuca in its search for killer whales the last two weeks.

Shimada ship tracks for first 2 weeks of February 2012 cruise.

Shimada ship tracks for first 2 weeks of February 2012 cruise.

NOAA's search pattern in the Strait of Juan de Fuca

NOAA's search pattern in the Strait of Juan de Fuca

Updates on 3/2/2012:

On 3/1 Orca Network reported on their Facebook Page this notice from John Ford:

A J pod sighting from yesterday, sent by John Ford of DFO’s Pacific Biological Station:
We observed J pod southbound off Nanaimo at 1800 yesterday (2/29). They were heading (south) towards Dodd Narrows when we left them at dark.

Shortly afterwards the Shimada returned from the shelf and began patrolling Active and Boundary Passes.


Shimada track for Wed 2/29 @ 1800 to Thur 3/01 @ 1751.

Subsequently, they have been cruising in that area and Georgia Strait, mostly at 6-8 knots, but with one burst near East Point at 12 knots.


Shimada track 3/1 through 3/2 @ 09:22.


Virus implicated in Fraser sockeye (and chinook?) mortality

The idea that a virus may play a part in the unpredictable Fraser river sockeye returns is (month) old news, but this article in Scientific American is the first to mention chinook that I’ve seen.  Perhaps the fate of the southern resident killer whales (who specialize on Fraser chinook in the summertime) is more connected than we thought to whatever marine factors govern the population dynamics of Fraser River sockeye?

“One of the most important findings of this study was the fact that salmon were already compromised before entering the river” on their journey home to spawn, she wrote. The scientists are currently studying juvenile salmon to see if the genomic signature is already present before they go out to the open ocean. Miller-Saunders also reports “there is some indication that the signature may be in Chinook and coho” salmon, too.

Infrared detection of marine mammals

Live blog of a talk by Joseph Graber on “Land-based Infrared Imagery for Marine Mammal Detection” at UW/APL on March 10, 2011.

Admiralty Inlet tidal currents can exceed 3 m/s and is therefore a valuable prospect for tidal power generation.  The Inlet is also a migration corridor for marine mammals, most importantly southern resident killer whales.

Infrared radiation has a range of bands from about 1-10 micrometers. In July 2010 at Lime Kiln State Park, we tested a FLIR A40 IR camera, as well as Canon VB-C50FSi and Flea B/W digital cameras.  On July 7 we imaged 84 surfacing whales.

Here’s an example of the footage from the Northwest National Marine Renewable Energy Center (NNMREC):

The key to detecting marine mammals is to detect the change in the temperature (T) contrast between the sea and the dorsal fin when a killer whale surfaces.  The mean temperature difference was about 2 oC.

How does it work? “Increased sky reflectivity at high incident angles lowers the apparent sea surface T and enhances detection.”

At 182m the camera only yielded one pixel to represent an orca which makes detection difficult beyond ~75m.   At greater ranges, detection can be assisted by blows which are sometimes discernible at ranges >100m when dorsal fins are hard to resolve. 

For clear conditions, T sky < T sea (about 4.3-7.3 oC vs 10.1 oC for the sea from a nearby buoy).

Ambient light, fog, and sea state can affect detection distance and reliability for visual and IR cameras.

Automated detection for IR could be accomplished by monitoring thermal gradients. Joe used thresholds (area, orientation, perimeter, and eccentricity) and frame-to-frame comparisons (to remove sporadic detections). This simple algorithm produced hits for 85% of a subset of the killer whales imaged in the Lime Kiln tests.

Flushed chemicals reach orca habitat in less than 4 days

Live-blogged notes from a UW Water Seminar talk by Rick Keil’s student Brittany Kimball

Spicing Up the Sound: Cooking Spices and Aberrant Chemicals in Puget Sound and How They Get There
Sound Citizen collects water samples from around the region to understand the transport of common household chemicals from human sources into the marine environment.  An added benefit is that the educational message is positive (e.g. associated with holiday cooking), in contrast to typical discouraging environmental news.  With funding primarily from Washington Sea Grant, the undergraduate-driven project provides citizen scientists with kits for collecting water samples (about 40-75 kits returned per month since December 2008).

Analysis measures concentrations of: spices (27), solvents, perfumes, endocrine disruptors, and (soon) soaps and more.

Oregano — spikes in early May due to spring growth

Linalool — a scent from flowers (also common in household products) peaks naturally in June/July

Cinammon — can differentiate between cooked and metabolized (trans-cinnamic acid); based on 2007 data from treated sewage effluent peaks ~4 days after Thanksgiving (thyme also peaks 4 days after)

Vanillin — both natural and synthetic (ethyl vanillin, 4x more flavorful, so common in candy); peaks on memorial day, Christmas, Thanksgiving, Valentines day, 4th of July, Labor day; natural vanillin peaks during winter holidays (when real vanilla extract is used) while synthtic peaks during summer (possibly due to mass consumption of ice cream).

Chemicals in personal care products (e.g. musks, other fragrances…) and industrial products (e.g. insecticides, fertilizers) are detected about as commonly as spices in the samples.  Lawn care chemicals peak in summer, while ibuprofen and estrogens peak in winter (a function of runoff and overflow from sewage treatment plants?).

With the new mass spectrometer, we can measure oleic acids (olive oil soaps), steric acids, and more…

Don’t miss our high school action projects on Feb 3-4.  Student posters will be presented then at Mary Gates Hall.

Orca genetics talk by Phillip Moran

Using next generation sequencing to generate whole mitochondrial genomes for population genetics and phylogeography of cetaceans

Dr. Phillip Morin, Protected Resources Division, Southwest Fisheries Science Center

Abstract and bio

Live blog notes:

Hoelzel et al 2002 found extremely low genetic diversity in control region (1000 base pairs): only 13 haplotypes from 100 samples from global killer whales. LeDuc et al 2008 increased to 35 haplotypes in ~>180 samples, but still very little global structure in phylogenetic tree.

But there are good reasons to use whole mitochondrial genome (16.4 kilobase genome) broken into 2-3 overlapping products (4.8-9.4 kb). Next generation sequencing uses highly parallel sequencing of small (30-350bp) fragments, but generate 100 million to 10 billion copies very economically and quickly.

Gathered north pacific samples (only 5 offshore), including ENA (Eastern North Atlantic who differ most in tooth wear) type 1 and 2, offshore, resident, transient, unknown. Also had samples from Antarctic whales and by Andy Foote from N Atlantic whales. We used Baysian techniques and publicly available mitochondrial priors from a wide range of marine mammals and managed to date divergence in killer whales to ~700,000 years ago.

Killer whale mitogenetics show that transients diverged ~700ky ago. In comparison, residents and offshores diverged much more recently, ~175ky ago (e.g. conventional wisdom: beginning of the pliocene). Antarctic B/C diverged from each other 150ky ago, and from A/GoM 335ky. Nuances are: proximity of ENA (1/2) and a Hawaii whale to North Pacific residents/offhores hints of exchange through the Northwest passage; some Antarctic A individuals have a haplotype close to transients, suggesting there may be even more types of killer whales in Antarctica (Bob plans to find out).

De Queiroz, 2007: helps in defining of species/subspecies — a hot topic for killer whales

  • B/C Antarctic types have strong morphological, feeding behavior and prey, group size, and genetic differences.  Foote et al. 2010.
  • N Pac transients: should be distinct species, primarily due to genetic divergence, though they also differ in morphology, feeding behavior and prey, group size, acoustics, fatty acids, contaminants.
  • Resident/Offshores we tend to believe are different sub-species, or species awaiting more evidence.  We have especialluy little info about offshores (only 5 samples and minimal behavioral differences).
  • North Atlantic situation is undetermined.

So, we had this low world-wide diversity (even in microsatellites — why?).  With whole mitogenome, we have strong association of ecotypes and genotypes.  For species with low mtDNA sequence diversity or poor phylogenetics, these new techniques can be very useful!

Other species that could benefit:

  • Blue whales (taxonomy and population structure, using SNPs)
  • Fin whales (150 mitogenomes sequenced but not analyzed; clear need for analysis of whether N Pac and Atlantic are really the same species (likely a historic taxonomic mistake)
  • Sperm whales (even less diverse than KWs — globally about 30 haplotypes, but 90% of samples fall into 3 haplotypes)
  • Turtles (effectively dinosaurs — been around for millions of years w/only 7 species and handful of haplotypes; SNPs may help describe population structure of leatherback and green turtles that move around the globe and are currently hard to genotype to source location when caught in longline fisheries)

Mike Ford Q: have you estimated historic population sizes from your results?  We’ve only recently started those analyses and we’re overwhelmed with data.  A current Masters student is looking at rates of patterns of evolution in mitochondrial genome.  Hoping to fund a post-doc (or any other collaborators!) to look at historic population size.

Q: Did you differentiate between N Pacific residents: We had 1? southern resident and a couple from Russia, but no BC residents.

Q: What’s difference between ecotype and subspecies?  It’s a really tough call (demographically distinct, DPS, evolutionarily distinct…).  In my mind, a subspecies is one in which you have multiple lines of evidence (not necessarily including genetic) suggesting distinctive evolutionary trajectories.  There is likely gene flow in delphinids (some evidence from microsatellite data, but some is suspect inference).

Q: Is there an issue with nodes evolving at different rates?  Our MS student is working on that and has a manuscript in preparation, but we’re still confident in our times.

Q: What are the different potentials of mitochondrial, microsatellites, and SNPs as tools for understanding evolution?  I hate microsatellites because we don’t understand them, especially their mutation rates (overestimate gene flow and underestimate divergence time)!  They indicate divergence, but aren’t diverging linearly in time.  SNPs are so simple in comparison!

+3dB noise reduces ‘effective listening area’ 30% - website of the Acoustic Ecology Institute

Jim Cummings of the Acoustic Ecology Institute has posted another great synopsis of an important new bioacoustics paper that has big implications for southern resident killer whales.  After defining a new bioacoustic metric “effective listening area” (which is MUCH more intuitive than “active space”), the authors clarify how slight increases in ambient noise can have big impacts for animals that need to listen to sounds that are normally barely audible.

The authors note analyses of transportation noise impacts often assert that a 3dB increase in noise – a barely perceptual change – has “negligible” effects, whereas in fact this increased noise reduces the listening area of animals by 30%. A 10dB increase in background noise (likely within a few hundred meters of a road or wind farm, or as a private plane passes nearby) reduces listening area by 90%.

We know that most commercial ships and recreational boats raise the ambient noise levels near killer whales by 20-30dB for periods of ~30 or 3 minutes, respectively, as the vessels and whales pass by each other.  Clearly it is time to articulate in what common situations the southern residents need to perceive barely audible signals — like distant inter-pod communication signals or echolocation returns from prey — and to model the reduction in listening area during typical noise exposures.  This paper suggests the results may be disconcerting even though southern residents are keystone predators (though one has to wonder if transients appreciate the advantage of the acoustic cloak a noisy freighter offers when trying to pick off a resident calf).

Scientific literature reference:
Barber, Crooks, Fristrup. The costs of chronic noise exposure for terrestrial organisms. Trends in Ecology and Evolution, 2010.
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NOAA finds SRKWs offshore on day 4!

Just got an exciting email from Dr. Marla Holt, bioacoustician on the NOAA cruise that aims to understand how the southern residents utilize the outer coast of Washington. They departed last Monday and are scheduled to return April 9th, making for a significantly longer cruise than in past years.

Since big ocean-going research boats like the McArthur II cost on the order of $20k/day, it’s GREAT news that they have not only encountered L pod, but also obtained some information about what the orcas are eating. It will be fascinating to learn which fish they are consuming on the outer coast at this time of year…

NOAA R/V McArthur II

Marla writes:

Things are going really well.  We found L pod on the 4th day at sea!!! The NOAA ship McArthur II detected all of L pod just north of Grays Harbor, WA in the middle of the night last night (~0330 March 26). We lost them acoustically but then found them visually and acoustically in the mid morning and were able to deploy the small boat (RHIB).  The whales were spread out and traveling south most of the day.  Brad and the rest of the crew got photo IDs and some prey samples, stayed with them day until 1830.  Last visual sighting was at dusk when they grouped back up and became quiet. Hopefully we will stick with them through the night to get more samples tomorrow (3/27).

Congrats to Brad, Marla, and the rest of salty surveillance team!

Orcasphere library revamped

Theses and grey literature related to southern residents can be hard to find and share.  The Orcasphere library eases your pain by providing such documents in PDF format.  Recent additions are the theses of Sara Heimlich-Boran and  Monika Wieland.  Other hard-to-obtain theses that have been archived are those by: Fred Felleman, Rich Osborne, Andy Foote, Shannon McCluskey, and Donna Hauser.

Please comment here if you know of other materials that should be added!

J8 Subpod – Day 2

43 28.2N 123 04.9W Travelling down-island, close to shore. 28 vessels within a 2-mile radius, the top count this season. I promise there are vocals in there…. somewhere… Actually, toward the end of this sample I have J8 pinging the hydrophone from negligible range (Kerri, it was an accident, I promise).

Listen here (2.5MB)

J8 Subpod

48 29.11N 122 43.64W Travelling up-island slowly, occassional milling. Eerie vocals.

Listen here (1.1MB)