Category Archives: Southern resident natural history

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.


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

Updates from NOAA on Elwha science

Yesterday Sarah Morely of NOAA/NWFSC Watershed Program, Fish Ecology Division gave a 40-minute synopsis of the “Elwha River Dam Removal – Past, Present, Future.”  My notes are appended and the NOAA site has an abstract with recommended references (also appended in case the link breaks).

A small (fall) Elwha chinook (dated Oct 4, 2010)

The most interesting aspect of the talk from the perspective of the southern resident killer whales is that no one in the audience, including Mike Ford, offered a clear articulation of the strategy for recovering the Elwha’s chinook salmon — and particularly the possibly extinct spring chinook of 50-kg fame.  Given their strong preference for big chinook (Hanson et al., 2010), the southern residents would presumably benefit most from the fast recovery of the biggest Elwha chinook, but Sarah only indicated that her impression was that the return of salmon to the Elwha was going to more “natural” than managed.  With large salmon and a combined species population potential of ~400,000 fish, we ought to be very clear as a community about the chinook recovery strategy!

That led one audience member to wonder whether the spring run is really extinct and, if so, how long it might take the fall chinook population to naturally fill the spring niche.  He asked whether 25 years might be a good guess for natural recovery of the spring chinook runs if adults are not moved above Glines Canyon dam to facilitate their re-colonization of the upper Elwha and tributaries (as is currently being done at Condit Dam on the White Salmon), but Sarah didn’t volunteer a confirmation or an alternative estimate.  The audience member’s suggestion of possible extinction is echoed on the National Park Service’s web page on the historic range of Elwha chinook:

Very few, if any, spring-run Chinook remain in the Elwha.

This made me realize that I (or some other southern resident stewards) need to dig into the EIS and figure out if the spring chinook are being managed in an optimal way from the perspective of the salmon-eating killer whales.  If they are not, then perhaps we should all make it a priority to change the situation.

In sleuthing around for details on the Elwha chinook runs, I did start to answer a different long-standing question: “Why were the Elwha chinook so big?”  I had heard 2 compelling hypotheses: (1) velocity and vertical barriers are more substantial on the Elwha than on comparable (Olympic) rivers and selected for fish powerful enough to surmount them; and, (2) stream bed gravel size in the Elwha is much larger than on comparable (Olympic) rivers and only bigger salmon could dig in it to build their redds.

The second is refuted by Sarah’s response to a question I asked her after her talk: How does the sediment size distribution in the upper Quinalt compare with that in the upper Elwha?  She said the upper (east?) fork of the Quinalt was chosen as a comparison site because the river bed sediment size distribution is similar to that in the upper Elwha.  Yet the Quinalt does not host gigantic chinook…  But perhaps it has bigger velocity and vertical barriers than the Elwha?

The first hypothesis is addressed in Brenkman et al., 2008 (special issue of Northwest Science).  They describe the velocity and vertical barriers on the Elwha:

The 7.9 km of main stem habitat currently available to anadromous salmonids in the Elwha River will increase to 71 km following dam removal. Possible seasonal velocity barriers exist in three main stem Elwha River canyons during periods of high river flows (Figure 2)—Rica (rkm 26.1 to rkm 27.3), Grand (rkm 31.1 to rkm 35.3), and Carlson Canyons (rkm 53.0 to rkm 54.5). Rica Canyon consists of bedrock, large boulders, and high-velocity water with several cascades and falls up to 1.8 m in height. The upstream portion of Grand Canyon contains several cascades and low waterfalls, and the lower 2.4 km of Grand Canyon contains approximately 15 cascades and falls. Carlson Canyon has a single waterfall that is 2 m in height (Washington Department of Fisheries 1971).
Seasonal velocity barriers in the Elwha River occur where the river channel is constrained by steep canyon walls and boulder- and bedrock- dominated substratum. Canyon reaches have channel gradients that are up to two times steeper (2% in Rica, Grand, and Carlson Canyons) than the average gradient for the entire 69 km of the main stem river (1%). High-flow events resulting from early winter storms and spring runoff create high-velocity cataracts that may constitute seasonal migration barriers to salmonids moving upstream. In contrast to these steep canyons, other sections of the Elwha River are much more gradual, with gradients of 0.3% from the mouth to Elwha Dam, 0.8% from Elwha Dam to Glines Canyon Dam, and 1.4% from Glines Canyon Dam to the headwaters of the main stem.

While salmon are generally capable of jumping 1.8-2m barriers, their ability to do so is limited by the pool size (particularly depth), relative position of the pool and the hydraulic jump, and degree of aeration in the pool.  I’ve yet to find these details, but if they don’t exist, I know what I’m doing on my next hike up the Elwha drainage!


Sept 16 was beginning of deconstruction of dams. Deconstruction will take another 2-3 days. Salmon recovery is expected to take decades.


Global distribution of dams and reservoirs is extensive in termparate regions. Global Water System Project Database, 2011 (McGill University)

Poff & Hart, 2002, Bioscience: increased dam removal over last 30 (now 40?) years is due to replacement generally being more expensive than removal, BUT most removed dams have been small.

Imminent NW removals – Elwha, White Salmon, Sandy River, Marmot Dam on Little Sandy River, Rogue, Calapooia (Umpqua), Kalamat

Lower Elwha (190? 1913) and Glines dams (1932? 1927) reduced sediment, river movement, woody debris, as well as salmon populations. They will be removed concurrently in controlled increments over 2-3 years (to minimize impacts of sediment to fish as well as benthic organisms.

Link to web cam of sediment plume? (Bureau of Reclamation is managing erosion of 18 M m^3 of sediment, 50% fine, 30% coarse, suspended sediment concentrations of >10,000 ppm)

Monitoring efforts and objectives

Objectives: 1) Establish baselines (advanced) and 2) evaluate response to dam removal (just getting started)

Research areas: Former reservoirs, Nearshore (consortium of Fresh/Kagley/+), River ecosystem

Nearshore (slides from Kurt, but also USGS+ collaborators)

  • Monthly sampling (Mar-Sep) since 2006; 37m beach seine plus environmental data
  • Community composition doesn’t change much between years, but is a little different between their reference areas and the area expected to be impacted by sediments.

River ecosystem (Floodplain dynamics, aquatic foodwebs, fish recolonization [enumeration, distribution, predicted movements, genetic work])

Floodplain dynamics Pess, Beechie, LEKT, USGS, USFWS

  • Channel age, connectivity, distribution
  • Riparian vegetation diversity
  • Kloehn et al 2008, Influence of dams on river-floodplain dynamics in the Elwha River, Washington. Northwest Science 82.
  • Trout dominate surface water channels; Coho dominate in groundwater channels.
  • George snorkels to measure residual pool depth, pebble counts and spawnable area and fine sediment sampling.
  • 14 monitoring sites (7 below Elwha, 7 above Elwha; 2 mainstem, 2 tributaries, 10 floodplain)

Aquatic Foodwebs

  • Morley, Coe, LEKT, USGS
  • Nutrient Limitation, primary production, benthic invertebrate, marine derived nutrient transfer
  • Morley et al. 2008. Benthic invertebrate and periphyton in the Elwha River basin: current conditions and predicted response to dam removal. Northwest Science 82.
  • Duda et al., 2010. Isotope patterns.
  • River is nutrient limited in non-winter months by nitrogen and secondarily phosphorous
  • Elwha Fish Weir (species, sex, length, Tags (CWT, ?), scales, fin clip
  • Blue View (Keith Denton and 1 other) is helping with enumerating Coho when fish weir is non-functional in high flow periods.
  • Genetics of O. mykiss (resident rainbow and steelhead): see 3 gene pools or distinct populations: 3 native, 1 non-native (lower, resident, Trout Lake); no hatchery influence upstream of dams.
  • McMillan looking at resident rainbows vs anadromous steelhead metrics.
  • Kinsey Frick: Spawning movements of adult salmonids during dam removal. Catching fish in weir, tagging with radio tags, and releasing above
  • 20 chinook released above dam; relocated 3-4 that had found spawning habitat in lower Elwha while some returned to spawn below the dam. Plans to tag more chinook as well as other salmonids.

On-line resources


  • Do you have plans to monitor hatchery stock status and impacts? At recent symposium, Norm Dicks mentioned that Chambers Creek (non-native steelhead) may be an issue, plus it is also focus of current law suit.
  • There used to be spring and fall chinook. The spring were the big ones and likely are extinct. Will spring chinook be brought in or are fall chinook expected to fill in that gap?
  • Me: How will chinook recovery be managed? Why was this approach taken, while more direct facilitation was done on White Salmon?
  • The Condit removal is supposed to take 3-5 days; why should the Elwha take so much longer?
Big Elwha salmon

Big Elwha salmon (from LEKT?)

Questions I didn’t ask:

  1. What is evidence of 100 lb chinook? Have all sources of evidence been pursued? (Middens? Interviews? Historic photographs? Written accounts? Inference from tree ring growth rate and/or isotope ratios?)  What is the source and story of the photo in your title slide (shown at right and credited to LEKT = Lower Elwha Klallum Tribe)?
  2. Are sediment size distributions similar in Quinalt to in the Elwha? Are such distributions governing invertebrate community structure?
  3. Why is recovery expected to take decades? (Urgency is lent by the SRKW’s need and preference for chinook.)

Follow research to do:

  • Frick re plans for upper Glines?
  • Is “out-planting” mentioned in the EIS?
  • Ask Eric Anderson how long fall chinook would take to fill niche of spring chinook.
  • Surely there are studies of how fast adaptation occurs from other removals or mitigation efforts?
  • How much sediment is behind Condit?

Clipping from the NWFSC talk announcement web site:

Elwha River Dam Removal: Past, Present, and Future

Date and Time: October 06, 2011, 11:00-12:00 Pacific Time Zone [Check U.S. Time clock for your local time]
Location: NOAA Northwest Fisheries Science Center (NWFSC) (2725 Montlake Boulevard East, Seattle, WA 98112; Map to NWFSC), Room: Auditorium.
Speaker(s): Sarah Morley (Research Ecologist, Watershed Program, Fish Ecology Division, NOAA NWFSC)
Speaker’s Email:
OneNOAA Seminar Sponsor: NOAA NWFSC Monster Seminar JAM
Abstract: The removal of the Elwha River dams on the Olympic Peninsula of Washington State is a unique opportunity to examine ecosystem recovery on a watershed scale, and has spurred collaborative research efforts among divergent groups. For the past century, the two dams have blocked the upstream movement of anadromous fish to over 90% of the watershed, and restricted the downstream movement of sediment, wood, and other organic materials to the lower river and estuary. Populations of all five Pacific salmon species and steelhead in the Elwha are critically low, habitat complexity decreased in the middle and lower river, and downstream coastal habitats are sediment starved. Simultaneous deconstruction of the two dams began in September 2011 and will take three years to complete. During and after that time, researchers are examining dam removal effects in three geographic regions: the soon-to-be former reservoirs, across the river floodplain, and in the nearshore environment. Short-term (< 3 years post dam removal) monitoring is focused on the projected downstream transport of approximately four million cubic meters of fine sediments accumulated in the reservoir deltas, associated peaks in river and estuary turbidity levels, and re-vegetation of the reservoir themselves. Longer-term effects of dam removal (> 5 years) to be evaluated are the delivery of gravels and cobbles to the lower river and nearshore, the re-establishment of a natural wood delivery regime, the re-colonization of the upper watershed by anadromous fish, and the associated effects on aquatic and riparian foodwebs. This talk will provide an overview of the Elwha restoration project, but particularly highlight the research of NWFSC researchers examining river floodplain dynamics, salmon re-colonization, and aquatic foodwebs. The removal of the Elwha Dams has been long awaited by the Lower Elwha Klallam Tribe and others and will provide ongoing learning opportunities for future dam removal efforts across the United States and elsewhere.
About the Speaker: Sarah Morley is a field ecologist whose research focuses on biological assessment-using biota to evaluate the condition of a place and better identify the causes of degradation. Within this broad framework, she has conducted research on the effects of urbanization on the health of Puget Sound streams and evaluated the effectiveness of restoration actions on streams and rivers across the Pacific Northwest. Recent projects include examining the effects of shoreline armoring on the biota of the Duwamish River estuary, the effectiveness of green stormwater management strategies in improving urban stream health, and aquatic foodweb effects of dam removal on the Elwha River. Sarah holds a B.S. in Environmental Science from U.C. Berkeley and an M.S. in Aquatic and Fisheries Sciences from the University of Washington. She has been a member of the Watershed Program at the Northwest Fisheries Science Center since 2000.

Salient Publications

  • Duda, J. J., H. Coe, S. A. Morley, K. Kloehn. 2011. Establishing Spatial Trends in Water Chemistry and Stable Isotopes (d15N and d13C) in the Elwha River Prior to Dam Removal: A Foodweb Perspective. River Research and Applications. doi:10.1002/rra.1413
  • Kloehn, K.K., T.J. Beechie, S.A. Morley, H.J. Coe, and J.J. Duda. 2008. Influence of dams on river-floodplain dynamics in the Elwha River, Washington. Northwest Science 82: 224-235.
  • Morley, S.A., J.J. Duda, H.J. Coe, K.K. Kloehn, and M.L. McHenry. 2008. Benthic Invertebrates and Periphyton in the Elwha River Basin: Current Conditions and Predicted Response to Dam Removal. Northwest Science 82:179-196.
  • Morley, S. A., P. S. Garcia, T. R. Bennett, P. Roni. 2005. Juvenile salmonid (Oncorhynchus spp.) use of constructed and natural side channels in Pacific Northwest Rivers. Canadian Journal of Fisheries and Aquatic Sciences, 62:2811-2821.
  • Pess, G. R., S. A. Morley, J. L. Hall, R. K. Timm. 2005. Monitoring floodplain restoration. Pages 127-166 in Roni, P. (Ed.) Methods for monitoring stream and watershed restoration. American Fisheries Society, Bethesda, Maryland.

Explosive Condit dam removal: more Columbia salmon on winter menu?

Kim Pokorny of the Oregonian reports progress on cleaning up the White Salmon River, a tributary on the lower Columbia, in preparation for an October 26 explosive removal.  This is good news for future foraging by southern resident killer whales who are known to target main stem Columbia fish when foraging on the Washington and Oregon coasts.

On Oct. 26, after years of wrangling among Washington’s Klickitat and Skamania counties and the environmental and tribal groups that teamed with dam operator PacifiCorp, a hole will be blown through the bottom of the dam and about 2.2 million cubic yards of sediment will pour through and rush three miles downriver to the confluence of the White Salmon and Columbia rivers.

It will be interesting to compare the sediment and fish dynamics between this dredging and explosive technique with the more progressive removal of the Elwha dams.  This is the fall of falling dams!  Hurrah!

L pod in SF Bay

I love this quote from a spokeswoman from the Marine Sanctuary outside of San Francisco Bay where L pod was observed foraging last week:

“It’s nice they’re showing up, but it’s too bad there’s not enough food for them up north,” Schramm said.

That’s pretty funny since L pod is almost surely pursuing salmon of the Sacramento and San Joaquin River Basin — populations which have been plagued by dismal returns in recent years, despite seeing the best returns last fall since 2006.  So, what struggling northern river systems and salmon populations is she pondering?  (The Columbia I hope!)

It goes to show you that we Washingtonians have a lot of communicating about orcas and their prey to do with the keepers of other river systems that feed the southern residents, particularly during the winter.

> Read the whole story

> Take action for CA fish

> Tell Representatives to save CA fish

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!

Prey relationship talks

8:35 John Ford, resident KW foraging ecology

What may have caused the simultaneous declines in the N and S residents during the late 1990s?  Nutritional stress?

We compared expected and observed births and deaths, where expectations were based on period of unlimited growth (’73-’90).  There were two phases of increased mortality in adult/juvenile fe/males: late 90s for N and S, mid-80s for southern and A pods.

Sockeye outnumber Chinook by 1000x in areas where residents forage during the summer.  Yet Sockeye make up less than 1% of diet during sampling period (May-Oct).  Only adult males don’t bring prey (of all species) to the surface for sharing.  This indicates that our surface prey fragment sampling technique isn’t biased.  Additionally, sockeye swim shallow and Chinook deep, but we’ve only sampled 3 sockeye predation events.

Sub-adults show some preference for smaller fish like Pink and Chum that make up about about 20% of their diet.  Recent winter sampling show continued chinook preference: 2 samples in Jan from N residents; 2 from J pod near Nanaimo Chinook.  They didn’t see enhanced mortality in weaners (expected in mammals under nutritional stress), perhaps because of prey sharing. Mortality lags chinook abundance by 1 year.

The Chinook abundance index is a bit below average currently, so we expect high mortalities next year.  A research priority is to identify important Chinook stocks for whales (Brian Gisborn, Brad Hanson).  How many are hatchery fish?

9:01 Jennifer (for Brad), species and stock ID for southern residents

Goals were to supplement Ford’s prey samples (beyond J pod), to collect fecal/regurgitation samples (to avoid potential bias in surface fragment sampling), and to define foraging surface behavior.  We now have ~150 fecal samples and 250 foraging samples that have been analyzed genetically.

Feces were screened for rockfish, sole, starry flounder, pacific halibut,  Irish lords, herring, sculpin, sable fish, greenling, lingcod, cabezon, and squid.  Thus far, we have detected (rarely) rockfish, sole, Pacific halibut, and lingcod.

Prey sampling results — Steelhead may be imporant in May.  Chinook dominate from May-September.

Fecal sampling results — Chinook dominate in May-September, but Chum is also important in September.

Breakdown of Chinook stocks is based on GAPS database which gives genetic profile for each river from 20k sampled fish.  They appear to be eating Chinook in rough proportion to what is available (most dense by number? biomass?).

Future work is focused on bioenergetics (how many fish do they consume and do they impact the stocks?) and availability (Is background noise impeding foraging efficiency?).  We need samples in Sept-Dec and May!

Eric Ward, risk analysis

Developed a fecundity model which was age specific (the rate of maturity is much faster than rate reproductive senesence).  Extrinsic factors were prey, contaminants, anthropogenic events (oil spills).  Can’t assess oil spill risks and disease risks (due to lack of data), nor do extant data help us characterize the variability of fecundity between sub-populations (e.g. pods) and indivduals.

Used Pacific Fisheries Management Council (PFMC) indices (terminal run) from to characterize prey.  Also look at Pacific Salmon Commission (PSC) relative index.  Ballard locks was used to get a U.S. sockeye time series to compare with the big (25 million) Fraser sockeye runs.  Used ENSO and PDO time series to characterize climatic variability.

Is the SR production different from NR?  It looks similar (~90+% of NR production rate).  High probability of prey (Chinook) correlates highly w/fecundity.  Late run Fraser and Oregon coastal stocks are driving the correlation of the prey variable.

U.S.+Canada recovery process, U.S. whale watching industry

10:00 Lynne Barre, NWFSC

  • Critical habitat can be modified.  A future step is designating habitat outside of the inland waters of WA.
  • Recovery plan implementation was started in 2003, well before the endangered listing in 2005.
  • Proposed regulations are under review… no date given for when rule-making will occur.
  • Consultations regarding potential impacts result in letters of concurrence or biological opinions; records are kept in public on their website…
  • Prevention of oil spills is a high priority (WDFW is adding the Oct 2007 workshop‘s hazing plan as appendix to the Northwest response plan)

10:30 Paul Cottrell, DFO (taking over for Marilyn Joyce as of last October, was originally a marine mammal biologist)

  • Canadian recovery strategy encompasses both northern and southern residents; transients (300-400 in population, rising with growing pinniped population) are listed as threatened and a recovery strategy is forthcoming; offshores are currently listed as species of concern, but are under review for upgrading to threatened.
  • Southern residents were originally listed under COSEWIC (coh-see-wick); Recovery strategy was published on the SARA Registry in March , 2008
  • Considering general regulations in addition to 100m approach limits; SARA has specific prohibitions
  • Marine Mammal Response Network (headed by Lisa Stavings) is doing a series of workshops and has monitoring handouts for volunteers
  • There is a potential mechanism for licensing (schedule 6), however it is not an option in the regulations that are being amended.  If industry continues to grow, a licensing schedule could be implemented through a public review process.

Suzanne Russell, NMFS/NWFSC, “People of the U.S. Whale Watching Industry”

  • Goal is to collect baseline data on the socio-cultural nature of the industry
  • Started with a voluntary survey in June-November, 2006 (112 returns, 64% response rate); supplemented with interviews and field observations
  • Analyzed overall, and broken down by sector (motorized vessel, kayak, land); further broken down by motorized vessel type (Tiers based on USCG regs — >65′ inspected, <65′ inspected multiple vessels, <65′ inspected single vessel, etc), as well as geographically (mainland vs island), and in some cases non/owner.
  • Results (details coming in a forthcoming report)
  1. Demographics: majority in industry are >45y and have some college education; biggest boats are all based on mainland; owners have typically been in industry the longest are predominanty in kayak, island groups, while land-based portion of industry is relatively new.
  2. Big boats operate out of mainland and operate more tours overall; more multiple daily trips are made out of Islands.
  3. Boats have become bigger and faster over the years; companies have expanded to other wildlife (beyond orcas).
  4. Effects on the local community: many responses emphasized educational effect (e.g. taking school groups out)

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!