Category Archives: marine mammal

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!

Orca refuge: a gift for endangered killer whales

Mother and calf seeking refuge

This Friday, January 15, 2010, is the deadline for public comment on the proposed orca conservation area along the west side of San Juan Island. All marine conservationists should consider commenting on these precedent-setting rules: comment via email | comment via web form.  (Official background and the PDF of proposed rule are on the NOAA web page.)

If you are short on time, you can simply sign the petition in support of the proposed rules.  The petition will be submitted to NOAA by the comment deadline.

Give a New Year’s gift to the southern residents  — comment on these precedent-setting rules before midnight (EST for web submittal; PST for emailed comments) this Friday, January 15, 2010: comment via email | comment via web form.

“Current regulations in the U.S. to protect marine mammals stem from the whaling era and focus on prohibiting individual acts that harm marine mammals.  If our society is to protect marine life from today’s threats, the regulatory process will need to change to protect the quality of habitats on which marine mammals depend.” — Peter Tyack, Physics Today, November, 2009.

Researchers call for orca conservation zone in B.C.

Dec 23 Vancouver Sun article about a forth-coming science paper that proposes a conservation zone that overlaps with the proposed orca sanctuary boundaries:

Wildlife researchers have identified the key feeding area for a critically endangered population of killer whales near Vancouver Island and proposed the creation of a unique, miniature conservation zone for the few square kilometres encompassing the animals’ favourite seafood restaurant.

The international team of scientists, including University of British Columbia biologist Rob Williams and colleagues from Britain and the U.S., spent four months in the summer of 2006 painstakingly monitoring the movements of a three-pod population of killer whales in waters off B.C. and Washington state that numbers just 87 individuals — so few that every animal has been identified from distinctive markings.

The researchers found the whales were about three times more likely to feast on Chinook salmon — their preferred meal — in a narrow coastal strip south of Washington’s San Juan Island than anywhere else in their summer range.

In an article published in the latest issue of the journal Animal Conservation, the scientists propose strict protections on this whale-dining “hot spot,” arguing that the no go zone is small enough to establish a practical system for diverting all boat traffic but large enough to guarantee the whales unfettered feeding.

“Protecting even small patches of water can provide conservation benefits, as long as we choose the spots wisely,” said lead researcher Erin Ashe, a biologist at Scotland’s University of St. Andrews, in a summary of the study.

+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.
Technorati Tags: ,

Seattle Metropolitan on orcas raising their voices

WhalesInteresting to see the Holt et al, 2009, paper still in the popular press.  This article provides a nice summary and connects the study to the proposed orca-vessel regulations.

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)