Biologist

R-GMT HexMap

Hexmap example

I’m just finishing up a contract making maps of telemetry data from satellite tagged animals. Basically just finding daily positions and making a pretty map out of them. It’s taken me a little while to write the code for it and while I’m not sure a whole lot of other people will be able to use it, I thought it might help one or two people out if I posted it online. The boss ended up wanting that as part of the contract too so pretty good motivation.

It’s not completely automatic but if you want pretty hexmaps of animal positions and you’re reasonably proficient in R (with maybe a little knowledge of GMT), then this may save you a good bit of time (or least let you skip some of the stumbling blocks I ran into). There’s also a function to read the output from the Douglas Argos Filter which could be handy if you’re working with Douglas filtered data in R.

The project page is here. Feel free to leave any comments or suggestions below.

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Programmer

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When Do Leatherback Turtles Migrate South?

ResearchBlogging.orgCover of volume 19 issue 2 Behavioral Ecology

I’ve had this blog a year and a half now and although I’ve had a good time, I’ve never really wrote about anything I’m actually (somewhat) knowledgeable. So I think I’ll do a few posts on leatherback turtles. I’m no turtle expert but I did spend a couple years working on their migration and movement. My first first-author paper just got officially published so I’ll start with that. <ego>It made the cover of Behavioral Ecology</ego> which isn’t really a big deal but I thought it was kind of cool. The paper was about leatherback turtles migrating from their summer feeding grounds near Nova Scotia to head down to wintering and nesting areas in the south. (If you don’t feel like reading all this, you could just skip to the pretty cool {at least to me} movie down at the bottom).

Map of Nova Scotian waters

First a little background. If you don’t know much about Nova Scotian geography, don’t feel too bad a lot of my relatives in Michigan were surprised when I told them I was in Canada but still south of them. Here’s a map for orientation. Leatherback turtles come up to Nova Scotian waters to eat jellyfish in the summer and then head back south to nest, mate and presumably avoid the cold waters. Leatherback turtles are pretty cool animals and I’ll probably do another post with more details on them later. For now, you just need to know they’re big animals reaching more than half a ton and their size, blubber and counter-current heat exchange allow them to maintain a high body temperature in cold waters almost like a warm-blooded animal.

So back to the paper, my coauthor Mike James has tagged a whole bunch of turtles now and we were curious if we could see any pattern in when they begin their migration. One problem was that unlike migratory birds it’s pretty hard to define when a turtle begins migrating. Luckily the state space models of Ian Jonsen provide a method to estimate turtle behavior as either foraging or transiting. By finding the last foraging in a season, we could have a pretty good idea of when the turtles began their migration.

Once we figured out when the turtles began their migration, we tried to figure out what might be triggering it. We guessed it would have something to do with colder temperatures or declining prey abundance. I could get temperature from satellite data but there isn’t an easy way to measure jellyfish (leatherback food) abundance. As a rough proxy, we used chlorophyll estimates from satellite images. As a side note, it’s really cool that NASA provides their data for free. Just to cover as many bases as possible, we threw position, day length, the North Atlantic Oscillation index, water depth and the sex and size of the turtle into the mix and stuck it all into a stats model. After a bit of calculating, the model came back predicting that the position of the turtle and temperature and chlorophyll of the water appear to correlate with departures.

Predicted departure of leatherback turtles

The biggest factor for predicting departure was the position of the turtle. Northern turtles appear to leave earlier than southern turtles and turtles around the longitude of Georges Bank (abundant shelf ecosystem) and Nova Scotia (the study area and lots of jellyfish) stay longer. The contour plot to the right shows the relative probability of departure from low (red) to high (yellow). The contour lines and dates show when we would expect 50% of the turtles in a region to depart. Knowing these dates could be pretty useful for conservation since regulations could be lifted after their departure.

Northern turtles leaving earlier was pretty much what we expected since northern waters get colder sooner. So it was pretty surprising when the model also predicted that turtles are actually more likely to leave when the water is warmer and greener. Now I’m not sure exactly why this is but one possible guess is that warmer chlorophyll-rich waters provide more nourishment sooner and allow turtles to head south earlier. Another possible explanation is that jellyfish population might decrease earlier since many jellyfish die off after reproducing and warmer waters and increased prey allow jellyfish to reproduce sooner. Of course, a final possibility is that the correlation is just a funny coincidence in the data but hopefully this is unlikely.

Inferred foraging locations of northern and southern leatherback turtles and departure tracks

Since turtles didn’t appear to be leaving when the water cooled off, why were they still leaving early from the north? One guess might be that turtles leave earlier from the north if they have farther to swim to their southern nesting grounds but the difference from the southern and northern foraging areas is only about 500 km. Since leatherbacks can easily swim 2 km/hr, they could cover this distance in 10 days or less but we observed differences of more than a month. Without temperature or distance to explain it, the disparity could possibly be related to some difference in habitat quality. Unfortunately this will remain just a hypothesis until we get a lot more data on jellyfish distribution and feeding rates. It is interesting to note that although many leatherbacks are still foraging in southern waters (blue dots in the figure to the right), no northern foraging turtle (red dots) has been observed moving into southern foraging grounds late in the season (red tracks).

Now that you made it through all that text, here’s a video I made of the turtles foraging, transiting and migrating (higher quality here). By the way, it costs quite a bit of work and money to get a transmitter on a leatherback so each one of those points is a good bit of work done by my coauthor Dr. James.

A couple extra interesting things to watch for are turtles hitting the Gulf Stream east of the continental shelf and being swept to the northeast and turtles getting stuck in the Bay of St. Lawrence (there used to be a channel between Cape Breton Island and mainland Nova Scotia but it was recently filled in with a causeway). See the map above if you need help finding those. Anyway, that movie’s pretty much the highlight of my thesis. I must have seen it several dozen times already but I still get a kick out of watching the turtles swim around.

Reference

Sherrill-Mix, S.A., James, M.C., Myers, R.A. (2007). Migration cues and timing in leatherback sea turtles. Behavioral Ecology, 19(2), 231-236. DOI: 10.1093/beheco/arm104

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Leatherback

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Can Elephants Gallop?

ResearchBlogging.org

I watched 10,000 BC yesterday and was pretty disappointed in the animal animations (which were the main reason I went). Most of them looked rather cheap and computer generated. The most unnatural looking was when the elephants galloped with their back feet moving together. That seemed completely wrong to me but I’m no elephant expert so I took a look at the literature when I got home.

You can see tiny bits of the offending gallop in this preview at around the 40 second and 2 minute mark:

If you can manage to get a glimpse of the mammoths’ movement in that, then compare it to this example:

Luckily there is a Nature paper addressing this issue pretty directly. I think the title “Are fast-moving elephants really running?” is a pretty good give away. If you’re getting published in Nature for determining if an animal runs, it’s pretty unlikely said animal is galloping around.

A marked running elephant from Hutchinson et al

So the authors (Hutchinson, Famini, Lair and Kram) went to Thailand, got a bunch of elephants, painted motion capture dots on their joints and had the elephants run a 30 meter dash on video camera. You can see a speedy elephant video in their supplementary material. The elephants reached speeds of 25 km/hr. First to take care of the galloping question:

Elephant footfall patterns from Hutchinson et al

The fastest gait used by elephants has been variously described as a walk, amble, trot, pace, rack or a running walk… …trotting and galloping are running gaits with footfall patterns that are distinct from walking… Our elephants maintained the same walking footfall pattern…

That’s a lot of …’s but I think it gets the point across. Elephants are certainly not galloping. Since that was a little anticlimactic I thought I’d also cover the more interesting question, are elephants running?

The authors first seek to define “running”. Running can be defined as a gait which includes periods where no foot touches the ground and where each foot touches the ground for less than 50% of the time. The second part is new on me but I’m not a kinematicist. It turns out elephants always have at least one foot on the ground but their feet are on the ground only 37% of the time.

Since that didn’t settle the question, the authors turn to physics. The Froude number is a measure of intertia vs gravity often used in boat physics. Apparently scientists also apply it to animals as velocity2/acceleration of gravity/hip height. The authors explain that most animals begin running at at a Froude number of .5 and start to gallop around 2.5. Elephants had Froude numbers as high as 3.4 which seem too high to be a walk.

As a final shot, Hutchinson and his coauthors decided to look at the movement of the center of mass. They explain that in a run the center of mass is lowest at midstride, while in a walk it is highest. Since they couldn’t directly measure the center of mass, the scientists used the position of the elephant’s shoulder and hip to estimate it. Funnily enough, the shoulder and hip were moving in opposite directions with the shoulder indicating walking and the hips indicating running.

So it looks like fast-moving elephants aren’t walking but they’re not really running either. They certainly were not galloping. Which brings us back to the movie 10,000 BC. I can’t understand why they wouldn’t do even rudimentary research (or watch Lord of the Rings which if I remember right got the gait correct) into the movement of animals filling such a central role in the movie. The galloping mammoths look completely fake even without knowing anything about elephants. But I guess with the general lack of concern for history, it’s not too surprising they wouldn’t worry too much about accurate biology either.

Reference

Hutchinson, J.R., Famini, D., Lair, R., Kram, R. (2003). Biomechanics: Are fast-moving elephants really running?. Nature, 422(6931), 493-494. DOI: 10.1038/422493a

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Fiber Made Out of Viruses?

ResearchBlogging.org M13 virus from Chiang et al. 2007

With advancing nanotechnology, people often need to make custom fibers with special properties such as conducting electricity or sticking to certain substances. These fibers can be created using fancy synthetic materials and complicated chemistry. Or as Chiang and coathors suggest you could try to make fibers out of viruses after modifying the viral DNA to perform the desired task. I’m not sure this is actually all that much easier but it sure seems cooler and perhaps (hopefully) as things develop it actually will be more cost effective.

Procedure for creating virus fiber from Chiang et al. 2007 Viral fibers from Chiang et al. 2007

To put their money where their hypothesis was, Chiang et al. set out to make custom fibers from a virus called M13. The M13 virus is a bacteriophage (a virus that infects bacteria) that looks like a string (instead of the little lunar lander shape in all the textbook virus illustrations). Interestingly, it’s made up of only a handful of proteins; a couple on one end, a couple on the other end, and then a bunch of repeats of a single protien to make a long tube covering it’s DNA. To make virus fiber, the research take a concentrated solution of viruses and squirt it from a syringe into a bath of glutaraldehyde. The glutaraldehyde forms links between neighboring viruses to form a continuous fiber. The researchers found they could adjust the glutaraldehyde concentration, the rate of syringe ejection and how much pull was applied to the fiber to make virus fibers with differing characteristics. They even took the fibers they made and tested them in fiber strength tests. It turns out virus fibers are about as strong as nylon.

To really highlight the benefits of viruses, they also used genetically modified forms of M13 whose DNA coded for proteins that bond well with certain substances. By modifying the highly repeated protein forming the viral tube, they can make viruses (called E4) that really stick to quantum dots. They then used this virus to make fiber containing high concentrations of quantum dots (good for optical sensors [or whatever uses people come up with for quantum dots]). To really show off, they also found a modified M13 virus (p8#9) that showed high affinity to gold (much like my fiancee) and used it to make gold coated virus fibers (think microscopic wires).

When I saw that picture of viral fibers, I was pretty amazed. I’ve always thought of viruses as invisible and problematic (not helped by the fact that I’m fighting off a cold right now) but here these researchers are making real world useful things out of them. And they can manipulate the genetics of the virus to add custom special properties. It’s really cool to see how biotechnology is progressing.

Reference

Chiang, C., Mello, C., Gu, J., Silva, E., Van Vliet, K., Belcher, A. (2007). Weaving Genetically Engineered Functionality into Mechanically Robust Virus Fibers. Advanced Materials, 19(6), 826-832. DOI: 10.1002/adma.200602262

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Gay Flies and White Genes

A while back (since I’m extremely slow on posting things), PZ Myers had an interesting post on a mutation that can turn fruit flies bisexual. Commenter Apikoros pointed to an even more interesting (i.e. has pretty pictures) paper about another mutation that turns male flies gay. Given the series of insect mating posts on here, I had to take a look. First a bit about the genetics. Fruit flies have a white gene which codes for pigment production (white [an absence of pigments] being the trait that is expressed in flies when the mutation is present). The gene is made of 2600 base pairs (the rungs of the DNA helix ladder) on the X chromosome coding for a protien made up of 687 amino acids. Interestingly, the protien is 58% similar to a related protien found in humans.

Scientists are often trying to insert new or modified genes into fruit flies. It’s usually difficult to tell if their gene has been successfully inserted so researchers add their gene next to an obvious marker gene. White vs. pigmented flies provide a good marker so scientists created an artificial white imitator gene called mini-white. Scientists stick the desired gene and the mini-white gene together and then insert them into white fly embryos. Any flies that grow up with dark eyes should also have the test gene. To allow even further control, scientists attach DNA that acts as a heat activated switch to the control gene. They can then turn on their target gene whenever they want by heating up the flies.

Now being able to flip a switch in an animals genetics is already pretty cool but now we get to the interesting part. Unknown to scientists, the heat activated switch activates genes on both sides of it. This means that after heating both the target gene and mini-white suddenly flood into the fly. This influx of mini-white produces some rather odd effects. To quote from Zhang and Odenwald, the scientists that noticed this:

Male-male interactions in fruit flies from Zhang and Odenwald

[After heating], transformant males displayed their wings in a spread outward and upward position. Close examination of these males revealed that many had protracted phalli. … Coincident with the extended-wings posture was the onset of vigorous male-male courtship.

The picture to the right shows some of this courtship. The arrow points to a poor ignored female. Again I think the researchers describe the courtship best:

Chain leaders frequently courted members of their own chains, creating courtship circles and lariats. The male-male courtship activities included touching partners with forelegs, unilateral 90° wing extensions (a display that was followed by the extended-wings posture), licking the partner’s genitalia, and curling the abdomen to achieve genital-genital contact. While participants repeated their courtship routines multiple times, no repelling signals were detected-i.e., wing flicking or face kicking.

Comparison of mutant and non mutant male-male interactions in fruit flies from Zhang and Odenwald

Since this was a pretty odd phenomenon, Zhang and Odenwald decided to investigate a bit further. As shown in the picture to the left, they looked at heated normal flies (left), heated mini-white flies (middle) and non-heated mini-white flies (right). Only the heated mini-white flies form the conspicious homosexual chains (the arrow points to females hiding in the corner). To test for pheremones, they tried pumping air from the homosexual bottles to the non-homosexual bottles and switching bottles but nothing happened. Interestingly, they found that even non-modified males would eventually join in the homosexual activities if most males (> 80%) in the bottle were participating mini-white flies. But that was likely a behavioral side effect and didn’t really help explain what was going on. They tried adding or removing different target genes to the mini-white and heat switch DNA but that did not change the results. They tested the children of homosexual flies and found that the homosexual trait associated with whichever chromosome had the inserted mini-white gene. They even fed mutagen to mini-white flies that altered the DNA sequence of mini-white and found that these broken mini-white flies did not exhibit homosexuality. So they are pretty sure they know that abnormal production of min-white can trigger homosexual behavior.

But they are unsure why a pigment producing protien could have such obvious behavioral effects. Interestingly, white protien is also important in transporting trytophan (yes the Thanksgiving turkey sleepiness protien [although that’s mostly a myth]). A decrease in tryptophan has been observed to cause male-male mounting in rats and rabbits. In addition, serotonin (a product of trytophan) depleted cats also exhibit homosexual behavior. This led Zhang and Odenwald to hypothesize that abnormal influx of white gene expression was causing a depletion of tryptophan and serotonin and leading to homosexual behavior although this still needs further investigation.

So this was a pretty cool and obvious demonstration of how genes, molecular pathways and behaviors are tied together both in a single animal and over quite different species (and how can you not like a paper describing “courtship chains and lariats”).

References

S.-D. Zhang & W. F. Odenwald 1995. Misexpression of the White (w) Gene Triggers Male-Male Courtship in Drosophila. Proceedings of the National Academy of Sciences 92:5525-5529

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