Category Archives: Northern residents

Scientists seek to silence sonar in the Salish Sea

The following open letter was sent today to Governmental and Naval leaders on both sides of the U.S.-Canada border.  As of 3/11/2012 it has been signed by 20 biologists and bioacousticians who have studied the killer whales of the Salish Sea.  (When sent initially, 16 had signed).



Silence Sonar in the Salish Sea

As biologists and bioacousticians who study killer whales of the Salish Sea, we ask that the U.S. Navy and Canadian Navy cease using sonar in their critical habitat.  Polluting their environment with intense underwater noise like the “pings” from mid-frequency active sonar poses significant risks to these Federally-listed species.

On February 6, 2012, the Canadian Naval frigate HMCS Ottawa used its sonar system in critical habitat of the endangered Southern Resident Killer Whales during a training exercise east of Victoria, B.C. The calls of the Southern Residents’ K and L pods were heard 18 hours later in Haro Strait, and sub-groups of K and L pods were identified 36 hours after the sonar use in Discovery Bay – a location where Southern Residents have never been sighted in 22 years of records. These observations are reminiscent of an incident in May, 2003, when the USS Shoup’s sonar training exercise caused similar unusual nearshore surface milling behavior of Southern Residents in Haro Strait.

New limits should be put on the use of mid-frequency active (MFA) sonar, particularly in the critical habitat of the Southern Residents.  Killer whales are sensitive to the frequencies emitted by MFA sonar (2-10 kHz) and use the same frequency range to communicate with calls and whistles.  Because MFA sonar is intense (source levels ~220-235 underwater decibels), it could permanently or temporarily deafen whales that are unexpectedly nearby and thereby impact their ability to forage, navigate, and socialize. Even temporary threshold shifts could be deleterious because the recovery of the Southern Residents hinges on their use of echolocation to find, identify, and acquire their primary prey, Pacific salmon.

Current procedures for mitigating underwater military noise are inadequate to protect either the resident or transient ecotypes. These procedures depend on the ability to detect whales within 1000 yards (U.S.) or 4000 yards (Canada), which neither passive acoustic listening nor visual surveillance can reliably accomplish. The unprecedented sighting of Southern Residents in Discovery Bay suggests that they may have been present during the pre-dawn sonar exercise on February 6 while remaining undetected by the Canadian Navy’s marine mammal monitoring procedures.  Moreover, we know from the 2003 Shoup incident and the scientific literature that MFA sonar can disrupt marine mammal behavior well beyond the current mitigation distances, particularly in the sound propagation conditions of the Salish Sea.

We therefore urge the U.S. and Canadian Navies to restrict MFA sonar and other intense underwater sound sources in all training and testing conducted in the Salish Sea.  By protecting the whales’ acoustic habitat, our Navies can help further their respective country’s obligations to ensure the recovery of these endangered iconic populations while still fulfilling their important National security missions.

Signed (alphabetically):

  1. David Bain, Ph.D
  2. Robin Baird, Research Biologist, Cascadia Research Collective
  3. Stefan Bråger, Research Director/Curator, The Whale Museum
  4. John Calambokidis, Research Biologist, Cascadia Research Collective
  5. Fred Felleman, Vice-President, Board of Directors, The Whale Museum
  6. Andrew Foote, Postdoctoral Fellow, University of Copenhagen, Denmark
  7. Deborah Giles, MSc, PhD Candidate/Research Biologist, UC Davis
  8. Rachael Griffin, B.Sc. Marine Biology, Aquagreen Marine Research, Victoria, BC
  9. Erin Heydenreich, Field Biologist, Senior staff at the Center for Whale Research
  10. Cara Lachmuth, MSc., Contract Biologist, Victoria, BC
  11. Patrick Miller, Lecturer, School of Biology, University of St Andrews, Scotland
  12. Joseph Olson, President, Cetacean Research Technology
  13. Richard Osborne, Ph.D., Research Associate, The Whale Museum
  14. Paul Spong, Director, OrcaLab and Pacific Orca Society, Alert Bay, BC
  15. Helena Symonds, Director, OrcaLab and Pacific Orca Society, Alert Bay, BC
  16. Scott Veirs, President, Beam Reach Marine Science and Sustainability School
  17. Val Veirs, Professor of Physics, Colorado College
  18. Monika Wieland, BA in Biology, Reed College
  19. Jason Wood, Ph.D., Research Associate, The Whale Museum
  20. Harald Yurk, Research Associate, Vancouver Aquarium

The following recipients were copied on the email:

  • Senator Patty Murray
  • Senator Maria Cantwell
  • Representative Norm Dicks
  • Representative Jay Inslee
  • Governor Chris Gregoire
  • Will Stelle, NOAA NW Regional Administer
  • Lynne Barre, NOAA NW Regional Office
  • Brad Hason, NOAA NWFSC
  • Dr. John Ford, DFO
  • Admiral Cecil D. Haney, Commander U.S. Pacific Fleet
  • Rear Admiral Douglass T. Biesel, Commander Navy Region Northwest
  • Renee Wallis, Navy Region NW
  • Lieutenant Diane Larose, Canadian Navy Public Affairs

Regional “Points of Contact” (POCs) for further information:

Admiral Cecil D. Haney
Commander U.S. Pacific Fleet
(808) 471-9727

Rear Admiral Douglass T. Biesel
Commander Navy Region Northwest
(360) 396-1630

Lieutenant Diane Larose
Navy Public Affairs
(250) 363-5789

Canadian recovery plans need public comment

Thanks to Cathy Bacon for forwarding this notice regarding Canadian “action plans” for recovering the northern and southern resident killer whale populations. It will be interesting to see to what extent managing salmon (farmed or wild) for killer whales is mentioned in the plans… Discuss here and comment officially when you can!

> From: “XPAC Species at Risk”
> Date: January 18, 2012 11:35:42 AM PST
> Subject: Resident Killer Whale Action Planning process Consultations
> Microsoft Word PictureFisheries and Oceans Canada Pêches et Océans Canada
> January 18, 2012
> Picture (Metafile)
> To: Stakeholders, Interested Individuals, and Organizations:
> Re: Northern and Southern Resident Killer Whale Action Planning process Consultations
> Fisheries and Oceans Canada (DFO) is pleased to invite you to participate in consultations on the development of the Northern and Southern Resident Killer Whale Action Plan. We are interested in your feedback as we develop and prioritize actions in support of recovery of Resident Killer Whale populations in Canadian Pacific waters.
> The Minister of Fisheries and Oceans Canada is required to develop a recovery strategy and action plan for all threatened or endangered aquatic species listed under the Species at Risk Act (SARA), and appreciates your input. Northern and Southern Resident Killer Whales are listed as Threatened and Endangered respectively, and a recovery strategy for these populations is posted on the SARA National Registry:
> If you would like to know more about the Northern and Southern Resident Killer Whale populations and how their recovery may affect you, or if you would like to provide comments on the draft actions supporting recovery of these populations, we will be conducting meetings during the month of February (open house from 6:00 pm to 7:00 pm; public meeting from 7:00 pm to 9:00 pm).
> February 2, 2012 Victoria, BC The Maritime Museum of BC
> February 9, 2012 Vancouver, BC Vancouver Maritime Museum
> February 23, 2012 Port Hardy, BC Quarterdeck Inn Marina Resort
> Please see for further information, or contact us directly at the numbers below.
> Sincerely,
> Sheila Thornton Paul Cottrell
> SARA Recovery Planner Marine Mammal Coordinator
> Fisheries and Oceans Canada Fisheries and Oceans Canada
> 200-401 Burrard Street 200-401 Burrard Street
> Vancouver, BC V6C 3S4 Vancouver, BC V6C 3S4
> Tel: 604-666-2043 Tel: 604-666-9965
> Fax: 604-666-3341 Fax: 604-666-3341

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!