Category Archives: Sounds

Detecting Killer Whales by using DNA

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Sharon Nieukirk, Senior Research Assistant
Sharon Nieukirk

This post comes to us from Sharon Nieukirk, Senior Research Assistant:

Killer Whale

As a marine mammal acoustician (studying the sounds produced by marine mammals) I am typically in an office, and my recorded data come to me. Other members of our team deploy the recorders or “hydrophones” Haru described in a previous blog, and they sway on their moorings in remote oceans of the world, recording the sounds of the sea. However, last week I had a chance to go into the field to collect acoustic data in person as part of an (e)DNA project led by OSU researchers Dr. Scott Baker and Dr. Holger Klinck. The main objective of this project is to “develop next-generation sequencing methodology for detection and species identification of cetaceans using environmental (that’s the “e”) DNA collected from seawater”. What this means in layman’s terms is Dr. Baker is developing a method to detect what species of animals have moved through a portion of a bay or ocean by collecting water samples and looking at the DNA present in that sample.

Neve Baker and Scott Baker
Neve Baker & Scott Baker

Sounds a lot like something out of the TV show CSI, doesn’t it? The method is still under development, and to test this idea the team conducted a series of experiments in the vicinity of killer whales near San Juan Island in Puget Sound. We started with killer whales because the population is well known, the whales are relatively accessible from shore and Puget Sound is a semi-enclosed ocean environment. During August and September, the team spent two weeks at the University of Washington’s Friday Harbor Laboratory (FHL), and launched our small 18’ boat each day to find the whales and sample water. Friday Harbor is an amazing place to work on killer whales; there are numerous researchers working in the area (i.e. NOAA, Center for Whale Research), there is a thriving whale watching industry which also collects killer whale information (Orca Network) and virtually the entire island is “wired for sound” with listening stations set up to monitor the vocalizations of killer whales (Salish Sea Hydrophone Network). After touching base with others working in the area, we’d leave the FHL dock in the early morning, proceed to an area where killer whales had been spotted….and get in line. The number of boats, from both U.S. and Canadian ports, in the vicinity of whales is truly staggering. Luckily, there are strict rules for how you should behave when you are near killer whales… and just in case you forget the rules the volunteers from Soundwatch will pay you a visit.

Soundwatch boat and crew
Soundwatch boat and crew

An advantage of this research technique is that we didn’t need to be close to the whales, we just needed to move into an area where the whales had been. We would wait for the whales to come past us, throw our current drogue in the water to mark the water mass where the whales had been, and then began sampling. Sampling involved taking water samples, towing a net through the water to maximize the chance of concentrating trace DNA and recording sound in the vicinity of the animals.

Collecting water samples in hopes of retrieving killer whale DNA
Current drogue deployed to mark body of water through which killer whales moved. Team would stay and sample the water every 30 minutes while killer whales moved on.
Sharon Nieukirk bundled up on the boat
Sharon Nieukirk bundled up on the boat

Recordings are important as they help us to identify the particular killers whales that passed through the water mass because individual groups of killer whales produce very specific vocalizations (see Listening to Orcas). At the end of the day, we’d head back to FHL, filter the water samples and freeze the filtrate for further analysis. Dr. Baker and Debbie Steel are working hard on analyzing all of the water samples collected during this fieldwork. Stay tuned to see if killer whales have left their mark on the waters of Puget Sound……

Click here to hear an example of sounds we recorded from killer whales while in the field last week (may require headphones).

Killer Whale near San Juan Island
Killer Whale near San Juan Island

 

Under Ocean Sounds – Analyzing the Data

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Anna
Anna

As a research assistant, I do a lot of data analysis for our group. I’ve been learning a lot about the different under ocean sounds we come across and how to find them on a spectrogram to help answer questions that our scientists put forth, but I’ve still got much to learn. I spent years picking out earthquakes and volcanic tremor in the Lau Basin (a very active area under the ocean near Fiji). I was so focused on locating earthquake and volcanic activity for that project, that I pretty much ignored any other random noises. When picking out earthquakes and volcanic tremor, you have to set your scrolling of the spectrograms (spectrograms are pictures of the sounds on a time and frequency view) in a way that you can get through data at a quicker pace and pay attention to the louder events. My screen for looking at earthquake and volcanic activity encompassed 15 or 20 minutes of data in one screen and scrolled fairly quickly. For quieter sounds, like some marine mammals, and especially fish, you are looking at about 1 minute of data per screen and the going is a lot slower!

We have scientists who have developed software to help automatically detect certain sounds in the data we collect. This doesn’t work for every type of sound and has varying degrees of accuracy, depending on other sounds present that may be in the same frequency range. Next up, I’ll be learning about one of these programs called Ishmael (developed by Dr. David Mellinger – he’s on our People Page) and, with the help of Sara Heimlich (also on our People Page), seeing if it can do a good job picking out orca sounds right off of South Beach here in Newport. I have found many of these orca sounds manually, but at 1 minute of data per screen, it would be very time consuming to go through all of the data that way. Check back later, and I’ll let you know how the automatic detection software does.

VIBESv5Noise in the ocean has become a hot topic lately in the media. (It’s incredible just how loud ship noise can be. Even louder: icebergs grounding and calving). How does man-made and other noise in the ocean affect fish, or marine mammals who depend on sound to navigate, hunt, find food, or communicate? These are questions scientists are busy trying to answer. VIBES, our new group acronym, stands for Volcanic, Ice, Biological, and Earthquake Sounds in the ocean. We also record surf and man-made sounds like oil drilling, ship noise, wave energy technology, and anything else you can think of down there.

Following are some examples of what I see in the data we get back from our under ocean recordings and the sounds that accompany them. Please let me know your best guess for the final sound!

(Note: sound clips for most of these encompass the data between the 2 fine white lines shown on the spectrograms, and are best heard on decent speakers or through headphones.)

Earthquakes in the Lau Basin
Earthquakes in the Lau Basin
Orcas off South Beach in Newport, Oregon
Orcas off South Beach in Newport, Oregon
Orcas and Ship Noise off South Beach in Newport, OR
Orcas and Ship Noise off South Beach in Newport, OR
Volcanic Tremor in the Lau Basin
Volcanic Tremor in the Lau Basin
Seismic Air Gun Shooting for imaging purposes in the Lau Basin
Seismic Air Gun Shooting for imaging purposes in the Lau Basin
Brydes Whale in the Lau Basin
Brydes Whale in the Lau Basin
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Elementary acoustics

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When I’m asked, “What do you do?” my answer, “Ocean Acoustics” is often followed by a puzzled look. And when I think about it, with good reason. Underwater acoustics can be a dense subject, difficult to describe in a short sentence with many different areas of focus. A few weeks ago, a presentation on representing science in social media (http://blogs.oregonstate.edu/bioacoustics/scicomm) by a few of the graduate students in our program, sparked the idea for this new path of communication and outreach for our group. The intent of this new blog effort is to share the science, research and all of the challenges and triumphs we go through to get to the point of discovery and results. By sharing some of the day-to-day activities and projects of our diverse group we hope to make underwater ocean acoustics research more accessible and interesting to a broad audience.

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So in that light, I’ll share a recent journey I took into the wild-lands of an elementary school classroom to talk about sound in the ocean with a group of first graders. It was a tough room. Hard stares were directed my way as they determinedly chewed their popcorn snacks with looks of, “Well? Show us what you’ve got.” I brought in about 20 different biological, natural and man-made sounds that ranged from local recordings of whales, ships and a wave energy conversion device made right off the coast 5 miles from their classroom to ice noise recorded on the other side of the earth near Antarctica. I also brought in a collage of pictures composed of each type of sound with the words written in bold letters. After a very brief introduction on ocean acoustics, I told them about each sound we were going to hear and they were to guess at the source from the collage of images on the board. I played the sounds through a small sub-woofer and satellite speakers so we could shake the fluorescent lights in the classroom and give the kids some “boom” with the lower frequency signals. After a few rounds of playback and guesses were made, the room began to loosen up. I started to see a lot of smiles and excitement growing in every little face. Hands were shooting up around the room at each question. We talked about high and low frequencies and I started out each new guess with the question of whether they thought the sound had a biological, natural or man-made origin. Still not sure that last one sank in with all of them. The magic and fun of listening to sounds in the ocean was alive. After we’d finished the playbacks I took a poll to find out their favorite sound. Result: earthquake just barely won out over the blue whale!? That almost never happens. Must have impressed them with the sub-woofer turned up. At the end of the 40 minutes the kids’ tough stares had turned into smiles and I hope they learned some new things, particularly about sound in the oceans. I even think I might have made a few new friends.

 

Well, now it’s your turn. Guess the nature of sounds A and B below. Are they biological, natural process, or man-made? Send us a comment and let us know what you think they are.

Welcome to our blog and we hope you’ll come back for more.

 

 

 

Sounds

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Here is where we will post sound clips or blogs about sounds. Subcategories will include earthquakes, volcanoes, ice, man-made, and biological sounds. Come back soon!