Author Archives: scottveirs

VENUS hydrophones going deeper, reporting more

Thanks to Jim Cummings of the Acoustic Ecology Institute, some news caught my ear in this article from the Times Colonist on the hydrophones deployed off the Fraser River delta.  There’s also a good bit of supposition without much science to back it up…

The key news I gleaned is that the hydrophones will be moved in a couple weeks from 170m depth to 300m.  I also was happy to learn that someone at VENUS (Richard Dewey) appears to be paying attention to the issue of noise pollution from the perspective of the southern resident killer whales.  Indeed, it seems he’s got a bit of a publicity campaign started.  He’s been on Canadian radio (CBC’s BC Almanac) talking about the hydrophones and has posted a nice YouTube video about underwater ship noise and potential impacts on orcas.

Listen to:  an excerpt with only the hydrophone portion of the broadcast; the full BC Almanac podcast (45 min including other news).

It will be great if they publish some of their work soon, or put a few more recordings in their research highlight section of their web site.  In the video they suggest they may be observing amplitude compensation at increased levels of ship noise, which they could accomplish by localizing calls with their calibrated array.  For now, you can at least listen in (nearly live) and browse the many hours of ship noise.  Checking again on their website, I’m also pleased to see they are now reporting occasionally on interesting acoustic events:

http://venus.uvic.ca/data/data-plots/strait-of-georgia-plots/sog-east-highlights-hydrophone/whale-sounds/

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!

Chum salmon: orca prey around Puget Sound

As the southern residents are visiting Puget Sound today, I’m inspired to learn a bit more about chum and where to view the fall runs.

The Washington Department of Fish and Wildlife has some good background information in their section on Chum Salmon Stories.  Of particular import to the southern residents is the fact that Chum salmon are the most abundant salmon species in Washington State.  In “Respect” Jim Aimes writes points out that recent chum runs are about has good as they have ever been, in contrast to the declines experienced many Puget Sound chinook and coho populations:

If we consider only naturally produced fish, the most abundant salmon in Washington State are chum salmon. In case you missed that – chum salmon are the most abundant wild salmon in our state! This is probably the best kept “secret” in the salmon business. In the five-year period 1994-1998, over 6.5 million wild chum salmon returned to Washington waters. Of that total, approximately 6.2 million wild chum returned to Puget Sound and over 300,000 were destined for coastal streams. Given the very real problems faced by wild fish and the recent tales about the supposed imminent demise of all wild salmon, these chum returns are pretty remarkable.

Chum salmon are also very successful at a number of hatcheries, although they seldom receive the emphasis provided to chinook and coho salmon. The majority of hatchery chum programs are located in the Puget Sound region; producing fish from WDFW, tribal, and federal facilities. The return of hatchery-origin chum for the above 5 years (1994-1998) was nearly 2.6 million fish. Combine the wild and hatchery returns for those 5 years and the total is over 9 million fish, or an average annual return of more than 1.8 million chum.

For guidance on how to view these fantastic fish, here is a blurb from WDFW with a link to the Piper’s Creek (Carkeek Park) population:

Various chum salmon stocks spawn in Washington streams from August through March. The duration of spawning for individual streams, however, is typically much shorter; usually one to two months. The best time to view chum salmon in local streams is November and December, when the large runs of fall chum are spawning.

There are a number of visitor-friendly locations where chum salmon spawning (both wild and hatchery fish) can be observed. This page will identify a number of these locations, and will provide travel information and the best season for chum salmon viewing. The initial location will be the Kennedy Creek Salmon Trail in the Olympia area, with more locations to be added in the near future.

And here is a nice piece on the fall chum runs of the Kitsap Peninsula and Chico Creek in particular by Chris Dunagan.

Marine acoustics talks in Victoria (live blog)

This week the Canadian Acoustical Association is running a conference on marine and environmental sound (abstracts).  Below are notes from talks that relate to the southern resident killer whales, presented in near-real-time.

9:00 Keynote: The Marine Soundscape and the Effects of Noise on Aquatic Animals

Christine Erbe

Marine soundscapes include natural sounds (e.g. from rain), marine organisms, and human sources.  Christine played a wide variety of sounds from many of these sources, highlighting along the way the opportunity to listen live for southern residents in Washington State and British Columbia.  Most amazing were recordings of belugas, aptly known as “sea canaries,” and humpbacks singing over mid-frequency sonar.

Odontocetes generate sound within their nasal system, not the larynx.  Echolocation clicks include energy at frequencies as high as 180 kHz for some porpoises. Pile driving recorded near Australia has a power spectrum with a very broad peak centered near 200 Hz.

The effects of noise on aquatic animals can be graded from most severe to weak: damage, temporary threshold shifts, out to behavioral response.

Graded effects of noise on aquatic animals

There is little data on chronic effects of noise. We can model cumulative sound exposure, but measuring the exposure directly will be challenging. [Perhaps Marla’s recent DTAG deployments on southern residents will help calibrate models made with regional ambient noise and ship traffic data?]

10:20 How deep do you call? Depth localization in Southern Resident killer whales using passive acoustics.

Jason Wood

We recorded 189 minutes of southern resident calls and clicks as they transited Admiralty Inlet where Snohomish Public Utility District is prospecting for tidal power.  We used a 4-element vertical array and localized the sound source by measuring the time of arrival differences (TOADs) between the different elements.  TOADs were computed using cross-correlation for calls and hand-picking of first arrivals for clicks.  The technique was validated using light bulbs as a synthetic source at known depths.

Of 510 calls and 145 independent clicks, about 80% of calls and clicks were made shallower than 30m, but some sounds (about 5%) were emitted at 60 m or deeper.  So killer whales are using the full depth of the prospective tidal turbine location.  Adjusting the source depths using the light bulb calibration (mean error of localization is 13 m deeper than actual bulb), our depth distribution compares well to the time-depth-recorder data from southern residents throughout their critical habitat (kindly shared with us by Robin Baird).

We also grouped our data by behavioral state of the pod during acoustic observations.  One surprise was that the depth of sounds made during social behavior were significantly deeper than other behavioral states.  Also, the mean depth of calls during foraging was the same as the mean depth of the clicks.

11:00 Assessing the effects of mid-frequency sonar on cetaceans in Southern California

Mariana Melcon

Looked for echolocation clicks of beaked whales (power at 30-60 kHz, depending on species) and periods of mid-frequency active sonar (MFA, 1-8 kHz) in HARP data (sampling at 200kHz).  Beaked whales click 30-50% less often during MFA exposures.  [Did southern residents click less during the Shoup incident?]

Transients harrassed near Shelton, WA

Interesting Kiro 7 video report regarding harassment of killer whales in Puget Sound during 2010.

And here’s a sighting report from Orca Network that is probably related:

Sighted 2 Orca for sure, when they came back east I thought at one point there were 3. They were in Hammersley Inlet at approximately N 047 12.360 – W 123 1.66, traveling west at 9 AM. East at 11AM. On the way west they were surfacing a lot. On the way east, they sounded right about the listed location and did not surface again in sight (I can see east to about 47 11.943). There was some construction noises going on at Skookum point – loud miter saw. The inlet is only 1/4 mile wide, and they were on the side opposite of me – much deeper water. I have noticed several harbor seals around in the morning lately – there must be food in the area. — Willard.

L pod was sighted that day in Haro Strait, so there are some indications these were transients who are listed as threatened under the ESA and also protected by the MMPA.  Fines could go even higher than $10k if the harassment was criminal, as opposed to civil.

King5 TV shows infrared video of orcas

Tonight reporter Gary Chitten and cameraman Pete Cassam from King 5 Television broadcast a nice story about the successful first test of a FLIR camera for detecting killer whales at night.  The pilot study was designed by Jim Thomson of the UW Applied Physics Lab, his Master’s student Joe Graber, and his other staff.  In collaboration with Jason Wood, Research Curator for The Whale Museum, and with the cooperation of Whale Watch State Park, the camera was deployed atop the Lime Kiln lighthouse where orcas commonly pass by close to shore during the summer months.

Two orcas surface in an infrared image

In just a week of effort, a suite of useful data were collected that are allowing Joe to assess to what extent automated signal processing algorithms can reliably detect orcas at night when they are up to 300 yards from the camera.  Preliminary results suggest that a human can identify whales among the noise generated by waves at 300 yards, but the computer isn’t very reliable much further out than 100 yards.  Perhaps a higher-resolution, top-of-the-line camera could improve the detection range?

The King 5 piece did an admirable job of conveying the importance of passive acoustic monitoring when attempting to detect approaching orcas.  While infrared cameras may ultimately be able to detect killer whales up to a kilometer away, the loud calls and clicks made by the whales can be detected at 10 times that range when background noise levels are low.  Together, infrared video cameras and real-time hydrophone networks constitute our best nighttime chance of knowing whether and when to shut down a turbine to mitigate it’s potential impacts on the fragile southern resident killer whale population.  Sighting networks like Orca Network and human eyes at tidal turbine sites will be critical supplemental techniques for tracking whales during the day.

$1-10k fines for proximity to orcas

It’s nice to see WDFW making public (see below) the consequences of violating the State and Federal laws governing how vessels may interact with killer whales.  I’ve added these details to the Beam Reach wiki page regarding orca-boat rules.

WDFW NEWS RELEASE
Washington Department of Fish and Wildlife
600 Capitol Way North, Olympia, WA 98501-1091

http://wdfw.wa.gov/

June 1, 2010

Rocky Beach, (360) 902-2510

WDFW cautions boat owners
to steer clear of orca whales

OLYMPIA – With summer approaching, the Washington Department of Fish and Wildlife (WDFW) is reminding recreational boaters to give orca whales and other marine mammals a wide berth.

State law requires boaters to stay at least 100 yards away from southern resident orca whales. Boaters who unexpectedly come into closer proximity to an orca are required to stop immediately and allow the whales to pass.

These and other state regulations apply to a variety of small watercraft, including tour boats, private powerboats, sailboats, kayaks, canoes and personal floatation devices.

Federal law also includes broad restrictions against disturbing or harassing any marine mammal, said Mike Cenci, WDFW’s deputy chief of enforcement.

“Boaters have a responsibility to keep their distance from these amazing animals,” Cenci said.  “Human disturbances, including boat traffic, can interfere with their ability to feed, communicate with one another and care for their young.”

Cenci noted that WDFW has issued 10 citations and dozens of warnings to recreational boaters since 2008, when the Legislature approved the state law regulating boating activity around orca whales.

Violating the state law can result in a fine of up to $1,025. The maximum fine under federal law is $10,000.

The southern resident orca population, which currently includes about 90 whales, is classified as “endangered” by both the State of Washington and the federal government.

Those animals, which mostly travel the waters of northern Puget Sound, account for the majority of orca whales found in Washington from early spring to late fall, said Rocky Beach, WDFW wildlife diversity division manager. Major threats to their survival include the declining abundance of salmon, exposure to pollutants and disruptions from passing vessels.

Under state law, it is unlawful to:

  • Approach within 100 yards of a southern resident whale.
  • Cause a vessel or other object to approach within 100 yards of a southern resident whale.
  • Intercept a southern resident whale by remaining in its path until it comes within 100 yards of a vessel.
  • Fail to disengage the transmission of a vessel that is within 100 yards of a southern resident whale.
  • Feed a southern resident whale.

Additional information about the state law is available on the WDFW website at http://wdfw.wa.gov/wlm/diversty/soc/orca/ . Whale-watching guidelines are available at http://www.bewhalewise.org .


This message has been sent to the WDFW News Releases & Weekender mailing list.
Visit the WDFW News Release Archive at:
http://wdfw.wa.gov/do/newreal/

Shall orca fans boycott CA tomatoes?

This well-written story about the CA salmon fishery in the High Country News connects the fate of southern residents with the agricultural industry of the Central Valley.

The past five years have already been harrowing, with a round of fishing bans to protect declining salmon runs in the Klamath River near the California-Oregon border. While those stocks are now in better shape, the main population of local salmon — the celebrated Sacramento River fall run of chinooks — is in steep decline. For the past two years, the federal government has banned commercial salmon fishing in California and most of Oregon.

Then, in April, Collins and other fishermen received what seemed like good news. The Pacific Fishery Management Council, a 14-member assembly that makes fishing recommendations to the federal government, voted to open salmon season in California and Oregon. But, particularly in California, the season will be just a fraction of what it once was: Beginning July 1, some 400 commercial fishing boats could be chasing roughly 33,500 salmon.

“It works out to about 90 fish a boat. Eight years ago, you’d catch that in a morning,” Collins says, and then pauses. “I’m hoping a lot of guys aren’t going to bother.”

In comparison, the southern resident orca population needs about 1000 good-sized chinook per day.  So, the limited opening that the Pacific Fishery Management Council has allowed could potentially reduce Southern Resident food supply by about one month.  We’ll have to delve into the PFMC analysis to understand what led them to decide that allowing OR and CA fishers to harvest 93,000 salmon from all runs would be “safe.”  Is that “safe” for the salmon populations, the orca populations, the human fishers’ livelihood, or some subset of influential politicians?

This spring, Democratic Congressmen Jim Costa and Dennis Cardoza and Republican George Radanovich, who represent the valley, wrote to Gary Locke, the Cabinet secretary who oversees the federal salmon-protection program, to decry a “double standard” of allowing salmon fishing while farmers still face water cutbacks. Then in April, Dianne Feinstein, the Democratic senator and former mayor of San Francisco, joined Costa and Cardoza in again complaining that “tens of thousands of acre-feet (of water) are now flowing unchecked past the pumps and into the ocean.”

Despite those water cutbacks, California still managed to grow its largest tomato crop in history last year. The 13.3-million-ton harvest was so big, in fact, that some farmers tilled a portion of their crop back into the ground. “It’s the greediest bunch of creeps I’ve ever seen in my life,” says fisherman Collins. “We haven’t worked in two years, and they’re crying like little girls.”

Perhaps it’s time to ascertain which crops are most water-intensive and to a coast-wide or even Inter/national boycott of them.  The article suggests cotton and tomatoes.  What other crops would be a worthy target?  Would progressive stores like Trader Joe’s or Whole Foods participate?  Or would this need to be a grassroots effort activated by orca enthusiasts around the country and globe?

BP threatens Northwest’s orcas

Heraldnet.com
This morning, John Burbank scribed a disconcerting account of oil politics in the southern residents’ backyard.  The following paragraphs provide a glimpse into how the complex interactions of the petroleum industry and our State political system increase risks for killer whales in the Northwest.

BP also has its own salaried lobbyist dedicated to keeping watch over the Legislature. Their man in Olympia is William Kidd, whom BP pays $120,000 a year to prevent any new taxes or regulations from becoming law. He also has an expense account to wine and dine legislators. For example, Kidd took Rep. Jeff Morris, D-Mount Vernon, out to dinner on July 12 in Boise. He took Morris out to dinner again on July 14. And again on Sept. 2. And again on Nov. 4 and Nov. 5 in Regina, Saskatchewan. And again on Dec. 8 in San Diego. (Lobbyist expenses are public records in Washington, and available at www.pdc.wa.gov. )

What’s all the interest in Jeff Morris? He is the speaker pro tem, sort of like vice president of the House of Representatives. He also sits on the House Technology, Energy and Communications Committee, which deals with energy production. He is the CEO of Energy Horizons, which is sponsored by the oil company ConocoPhillips, and by the giant utility Pacificorps, among others. Morris’ district includes Anacortes, home of two oil refineries, and is close to two more refineries, including the BP refinery in Blaine recently cited for 13 serious safety violations.

So why not wine and dine Rep. Morris and make sure that a word here or there could cast doubt about legislation for cleaning up Puget Sound? It is money well spent. BP refines 225,000 barrels of crude oil a day in Washington. The Clean Water Act would have cost BP at least $200,000 a day in new fees. Paying Kidd $120,000 a year and picking up the meal tabs for a few legislators was a wise investment — for BP, not for us. Not for Puget Sound. And not for our future.

We have at least 5 refineries in western Washington: 2 in Anacortes (Tesoro and Shell), Tacoma (U.S. Oil & Refining), 1 in Blaine (BP’s Cherry Point Refinery), and 1 in Ferndale (Conoco Phillips).  Anyone know how much oil is transported to/from each of these facilities, and by what means (tankers, pipeline, rail, truck, etc)?

Salmon & orcas in Patagonia catalog

The new Patagonia catalog (out yesterday) has a full page spread by Steven Hawley entitled “The Idaho Tide.”  It eloquently connects the wolves of Idaho’s Frank Church Wilderness with Snake River salmon and the southern residents, and it includes a great paragraph (below) with a quote-worthy line by Ken Balcomb:

“I think any reasonable biologist will tell you the only way to take advantage of [the intact salmon habitat left on the Snake River] is to tear out the dams.” — Ken Balcomb, Center for Whale Research

The full text of the piece is appended (and archived as a PDF). Inspired readers can take action here (too bad such a link wasn’t provided in the catalog!)…

Thanks to Dan Drais of Save Our Wild Salmon for the heads up on this one.  Watch for Hawley’s new book next year, “Recovering the Lost River” (the Columbia).