Sunday, July 24, 2016

Can you hear me now?

Figuring out the loudness at which an animal is vocalizing is a deceivingly difficult question to answer.  To investigate this question of loudness, we use an equation that, on the surface, is deceivingly simple – the sonar equation. 

SL = RL + TL

Source level (the actual loudness of the call) is equal to the received level (the loudness of the call when it gets to the hydrophone) plus the transmission loss (the amount of loudness that’s lost over the distance between the caller and the hydrophone).  How bad could it be?

Calculating received levels – this involves a few pieces of information.  First, you need to know when your animal is actually vocalizing.  I’ve browsed through dozens of hours of acoustic data from the 2015 season and have marked hundreds of calls from harbor seal males.  Lucky for me harbor seals call almost nonstop; at least finding the calls is easy enough.  I also need to know some information about my hydrophone, mainly the sensitivity.  Different hydrophones have different sensitivity levels, which influences the calls it can pick up.  A more sensitive hydrophone can pick up quieter calls than a less sensitive hydrophone.  Then, after I’ve input these hydrophone parameters, with the flick of my magic acoustic wand, a program called Raven will give me a received level.  Step one is complete.

Pretty picture from Strawberry Island to break from the scienceness of this blog post (Photo: L. Matthews)

Transmission loss is a bit more of a beast.  Back in the 1980’s, Malme and Miles came to Glacier Bay and investigated how sound travels underwater in this environment.  Turns out that sound attenuates at a rate of 15log(r), where r is the distance from the vocalizing animal to the hydrophone.  So if I want to quantify how much loudness is lost between my animal and my array, I need to know from where my animal is calling.  Enter acoustic localization. 

Sound is a pressure wave traveling through a medium.  In water, sound travels approximately 1500 m/s.  Depending on where an animal is located when it calls, the vocalization will travel through the water and arrive on the different hydrophones in our hydrophone array at different times.  The call will get to the closest hydrophone first, and the farthest hydrophone last.  You can see what I mean in the spectrogram below.  Each line is a different hydrophone, and this particular calling animal is closest to the second hydrophone.

I am lucky enough to be collaborating with a group at Cornell University called the Bioacoustics Research Program.  They’re the ones who make the software that I use to do the acoustic localization.  It’s been an up and down process to get this localization up and running, but after a few rounds of troubleshooting, it’s working with a fair amount of consistency.  It’s a slow and time-consuming part of calculating source levels, but so far I’ve managed to locate over 250 harbor seal vocalizations. 

Harbor seals called here.

Then there’s some coding involved to get the actual distances between the caller and the hydrophone, and a little excel spreadsheet organizing, but then it’s just plugging and chugging to get a number for a source level.  Sweet science victory. 

Hello sweet angel.  (Photo: L. Matthews)

I’ve always been intimidated by calculating source levels, and rightfully so.  There are a lot of different pieces that have to fall into place for everything to turn out correctly.  In my downtime on Strawberry Island, I’ve been slowly but surely chipping away at my source level analysis.  The island seems to be a good place to hunker down and focus.  Somehow it’s so much easier to be on my computer and not get distracted when the internet is just a distant memory….

Working hard on the beach.

Now that I’m getting baseline estimates of how loud harbor seals are vocalizing, I can start to answer another question.  Do harbor seals change their source levels when there are vessels nearby?  We see this phenomenon in many species, including humans.  When our environment is loud, we get louder so that other people can hear us.  I’m curious to see if harbor seals do the same thing.

Cruise ships are a regular occurrence during the summer (Photo: L. Matthews)

FUN SCIENCE FACT #36: Sound travels almost 5x faster underwater compared to in air.  From the hydrophones, we can hear a cruise ship coming almost 45 minutes before it gets to the island.

Friday, July 15, 2016

Mysterious little harbor seals...

So far, the harbor seal data collection has gone about as good as could be expected for any new protocol.  I had a few set backs early on with equipment, which have since been resolved, and there’s also been a lot of forward progress, which is great.  The part I’m struggling the most with, actually, is the part I thought wouldn’t be a problem at all – where are the seals that are vocalizing underwater. 

Harbor seal in the foreground, glacier in the background (Photo: L. Matthews)

I looked at the acoustic data from last year, and harbor seals are vocalizing all the time.  During the breeding season, male harbor seals set up underwater territories and defend them acoustically – makes sense that they would vocalize all the time.  I kayaked around our survey area the first few days we were here, and harbor seals are popping up everywhere – seems like there would be a lot of territories. 

In an ideal world, I drop a hydrophone from my kayak near where an individual is vocalizing, that individual vocalizes for a bit and then pops his head up out of the water to take a few breaths.  When that individual is at the surface, I take his photo and his position.  If I do this enough times, I can get a general idea of the size of size of this animal’s territory and compare that to the locations of the vocalizations underwater.   I can also associate the vocalizations I’ve recorded to specific animals and look at variation in vocalizations between individuals.

The view from my kayak office is kind of amazing (Photo: L. Matthews)

After some days of dropping the hydrophone and listening, I found a few places where the harbor seals roared loudly.  I sat in these spots and watched and waited for a harbor seal to pop up within sight range of the kayak, but nothing!  Multiple times now, we’ve made recordings of harbor seals, and we’re definitely close to where they’re vocalizing, but they never actually make an appearance at the surface.

I don’t know why it appears that my vocalizing animals never come to the surface.  I’ve got a little tinkering to do with the data that might clue us in as to where they are, but as of right now, your guess is as good as mine.

FUN SCIENCE FACT #45: Harbor seals may not be very agile on land, but in the water, they can swim up to 15mph to escape predators.  Most of the time though, they cruise around at a much more casual pace.

Harbor seal swimming gracefully in the cold waters of Glacier Bay (Photo: L. Matthews)

Friday, July 8, 2016

Always Listening, Sometimes Watching

Everyday the Strawberry Island field team wakes up and starts off the morning watching either whales or seals.  We take a break, watch some more whales and seals, take another break, and end our evening watching whales and seals again.  And throughout all of our data collection of marking what the animals are doing at the surface, our hydrophones are recording what the animals are saying underwater.  We do our best to try and understand what the whales and the seals do at the surface during all times of the day, but even at our best we can only watch some of the time.

Humpback whales are a common site near Strawberry Island (Photo: L. Matthews)

Acoustics is a great way to monitor animal behavior for a variety of reasons.  One of these reasons is that we can leave our hydrophones underwater to record animal vocalizations for months at a time.  No matter the time of day or type of weather, the hydrophones are archiving the acoustic behavior of all the whales and seals in and around the array.  And then, when we pick up our hydrophones at the end of the season, we can correlate the behavioral data we collected all summer to the acoustic data.  Our hydrophones are arranged in such a way that by using recordings from all four of them, we can determine the location of the vocalizing animal.  Acoustic localization plus behavioral data equals a lovely picture of what's happening in the survey area.

Spectrogram of a harbor seal roar recorded in Glacier Bay
Harbor seal (Phoca vitulina) in Glacier Bay (Photo: L. Matthews)

Understanding the correlation between what the animals are doing and what they are saying is an important link in the field of animal bioacoustics.  If we can relate these two datasets – the visual observations and the acoustic data – it will hopefully give us insights into what the animals are doing even when we’re not watching. 

FUN SCIENCE FACT #44: The clocks we use to synchronize our hydrophones for localization are among the most precise clocks in the world.  We're talking military-grade clocks (because that's a thing).  The only more accurate clock is the one on your cell phone. 

Sunday, July 3, 2016

Alaskan Adventure

Eighteen days ago I was dropped off on an island in Glacier Bay National Park with five other people, a dozen tarps, a fair amount of scientific equipment, thirteen 5-gallon water jugs, and 36 bear cans filled to the brim with food appropriate for a camp stove.  The goals: shore-based data collection on the behaviors of humpback whales and kayak-based data collection on the surface positions of harbor seals.

This fieldwork is part of my PhD research (the harbor seal part, at least), and it’s related to the hydrophone deployment I wrote about last year.  What I failed to write about more recently was that we deployed those same hydrophones in the same general area for a second year of data collection.  These hydrophones sit on the ocean floor all summer and listen to the sounds of harbor seals, humpback whales, and vessels.  The data from these hydrophones allows us to assess how noise from passing vessels affects the vocal behavior of two of Glacier Bay’s marine mammal species.  Last year there was a field team on this island collecting humpback whale behavioral data for the dissertation of my Glacier Bay counterpart, Michelle Fournet.  This year, I’ve tagged along with the humpback whale team to organize a harbor seal data collection initiative that will beef-up a chapter of my own dissertation. 

Harbor seal (Phoca vitulina) in Glacier Bay (Photo: L. Matthews)

The island is Strawberry Island.  It sits west of the Beardslee Island complex and has a perfect view over the area in which our hydrophones are deployed.  From the eastern point of Strawberry Island, you can see humpback whales and harbor seals, as well as Stellar sea lions, harbor porpoises, and sea otters.  And off in the distance, two black bears comb the rocky shores to the south of our camp.  The salmonberries are ripe, the forest is dense, and the views are incredible. 

The orange star is the location of our camp, the green markers are the locations of our hydrophones

Strawberry Island has a pretty stellar backdrop.  (Photo: L. Matthews)

We’ve just returned from the first of four stints on the island.  Each stint lasts around eighteen days, then there’s a four-day break off the island in the local town of Gustavus (real showers, cell phone service, and the best Rueben money can buy).  Overall we’re off to a great start – the entire field team is trained on all the protocols and we’ve already collected some great data.  Excited to see what’s to come in stint number two!

FUN SCIENCE FACT #43:  Humpback whales have the potential to lose up to 1/3 of their body weight during the winter.  When considering that humpback whales upwards of 70,000 pounds, that's a pretty impressive number of pounds to lose.

Humpback whale in Glacier Bay (Photo: L. Matthews)

Tuesday, November 10, 2015

Things went wrong. They weren’t our fault. We fixed them anyway.

A few months ago, I went to Alaska to help drop very expensive science to the bottom of the ocean.  Last week, I went back to Alaska to try and pick it back up.  “Try” is the operative word here, because often times, when you drop equipment into the ocean, you have no idea if you’ll ever see it again…

To catch up on some background info for this project, you can read my previous blog post.  But to summarize it really quickly, grad student Michelle Fournet (OSU) and I are looking at the effects of vessel noise on humpback whale and harbor seal vocalizations, respectively.  This project is all taking place in Glacier Bay National Park, Alaska.  At the end of May, we deployed four hydrophones to monitor the underwater soundscape. 

I flew in to Gustavus, Alaska on a Tuesday evening with Michelle and our friend/field assistant/resident electrician David.  It was a beautiful flight.

This flight is always a treat. (Photo: L. Matthews)

We spent all day Wednesday prepping for the recovery of our four little hydrophone babies.  Eight foot long hydrophone babies.  100-pound hydrophone babies.  Hydrophone babies full of five months worth of acoustic recordings.  Hydrophone babies that hold the keys to both mine and Michelle’s dissertations. 

The aforementioned hydrophone babies, pre-deployment.  (Photo: L. Matthews)

In theory, we knew exactly what was going to happen during the recovery.  Each hydrophone is snuggly situated in an aluminum cage.  Each cage is connected to an acoustic release via 500 ft. of line.  The acoustic release is key – that’s how we get our hydrophones back.  When the time comes to retrieve them, we send an acoustic signal from the boat to the release.  This acoustic signal tells the release to float to the surface.  Then, once the release is spotted, we can pull it on deck, connect the attached line to a crane, and reel up the 500 ft. of line and the accompanying hydrophone.  Michelle, David, and I talked through this recovery protocol with Chris Gabriele, a biologist in Glacier Bay National Park, at least 30 times.  We were still nervous to see how it all played out.  You see, sometimes, when you send the acoustic signal to the release, it doesn’t work.  Nothing floats to the surface.  The hydrophone remains on the ocean floor, patiently waiting. 

Schematic of hydrophone set-up in Glacier Bay (not to scale)

We met up with Paul and John Martin of the M/V Lite Weight (our recovery vessel) early on Thursday morning.  We arrived at our first hydrophone location about an hour later.  We sent the acoustic signal to the release.  And then we waited.  All eyes on deck scanned the water’s surface for any sign of our buoyant yellow friend.

It was about a minute later when the release was spotted!  Celebration commenced.  Hugs, laughter, a solitary joyful tear; we were all so pleased that it had worked.  We turned our attention back to the water only to realize that the release was gone.  GONE!  The tides had pulled it below the surface.  Well, now what?

So much water.  No releases to be seen.  (Photo: D. Culp)

Do we wait for the tides to calm down?  Do we put out grappling hooks to try and snag it?  Do we stare dismally at the water until it magically reappears?  The answer is D, all of the above. 

The release was re-spotted about 45 minutes later and pulled on deck.  We still don't know exactly why or how it returned to the surface.  It's possible that the tides let up a bit.  It's also possible that there were some issues with the line and it needed some extra time to sort itself out.  Whatever the case may be, we will definitely be taking extra precautions next year to ensure that this isn't a recurring problem.  

Acoustic release fresh from the ocean!  (Photo: L. Matthews)

The crew of the Lite Weight worked their magic and before we knew it, the hydrophone and its cage were safely on deck.  Success!

Yaaaaaaay!!!  (Video: L. Matthews)

I’ll keep this short and just tell you that despite temporarily losing 3 of our 4 releases to the whims of the tides, we had four hydrophones on the deck of the boat by 1pm.  It was an amazing feeling!  All of that science we dropped off five months ago was finally back!

The recovery team minus David (Photo: D. Culp)

The tides were a challenge – the releases weren’t supposed to disappear back underwater.  But we pulled it together and overall had a very successful recovery.  This, however, was not the end of our troubles.  There was a suite of technical issues that arose as we prepped the hydrophones to be shipped back to Oregon for data processing.  These technical issues were also challenging and unforeseen.  Luckily, the team rallied and managed to solve every challenge that came our way.  In the end, we summarized the trip by saying, “things went wrong, they weren’t our fault, but we fixed them anyway."  It was a solid week of science.

FUN SCIENCE FACT #42: The highest tides in the world can be found in the Bay of Fundy, Canada, which separates New Brunswick from Nova Scotia.  The difference between high and low tide in the Bay is upwards of 16m!  That's taller than a 3-story building!  Glad we weren't trying to recover hydrophones in that part of the ocean...

Tides in the Bay of Fundy (Photo: Steve Brown)