I provide code (with details & description) to download gene sequences from GenBank using R. The code allows the user to obtain sequences for multiple species and save them into the same FASTA file. This is a modification of the code I used in Baliga & Law, 2016 (MPE).Read More
Members of the 2013-14 UCSC SCWIBLES team have written a Feature Article on incoporating models when teaching science. It will be in the January edition of The American Biology Teacher.Read More
My previously-mentioned paper on the kinematics of prey capture in three species of cleaner fishes has now been included in the most recent issue (November 2015) of Journal of Morphology.Read More
A recent manuscript I submitted to Molecular Phylogenetics and Evolution has been accepted and is now "In Press".Read More
A new article in Journal of Morphology is now available in Early ViewRead More
I use some data from a recent paper to show the benefits of interactive data visualizationsRead More
Say you have an R script shared between you and several colleagues. You may not be sure that each user with whom you're collaborating has installed all the packages the script will require. This code below provides an easy way to check whether specific packages are in the default Library. If they are, they're simply loaded. If any packages are missing, they're installed (with dependencies) into the default Library and are then loaded.Read More
I've moved to a new domain!Read More
I recently completed my final requirement for advancing to PhD candidacy: giving a departmental seminar to outline my proposed dissertation research. It's amazing how something like this can be simultaneously wonderful and frustrating.Read More
My QE Committee was composed of Dr. Bruce Lyon (chair), Dr. Pete Raimondi, Dr. Peter Wainwright (UC Davis), and, of course, my major advisor, Dr. Rita Mehta. I feel pretty lucky to have had such an amazing array of biologists devoted to helping me create the best dissertation possible. As part of the QE, I composed a research proposal which outlined the complete content of all of my dissertation work and sent it to my committee a few weeks in advance of the QE. This was not a simple task, but I managed to keep everything within a concise 9 pages of text (not including figures or citations) to limit any burden I might place on my committee (they're busy people!).
The exam itself was a great experience. I gave a presentation to my committee to again outline my proposed dissertation work. I was pretty nervous for the first few minutes, but that feeling completely vanished once my committee started asking questions during my presentation. The whole experience morphed into more of a discussion than a strict presentation, and I was quite pleased with the back-and-forth dynamic I had with my committee. This "conversation" lasted almost 3 hours, and I received strong positive comments on my ideas and work. The committee seemed impressed with the work I've done for my first chapter, and helped me brainstorm and further solidify my ideas for my other two chapters. All in all, this exam was not nearly as nerve-wracking as I thought it would be, and was quite honestly fun!
Thankfully, the Mehta Lab has an amazing light microscope: the Leica M80. This microscope is connected to one of the lab computers, which makes it possible to take photos during dissections. Plus, I can make use of this setup for teaching dissection techniques, since the camera that is incorporated into the microscope allows me access to a live view on the computer screen of whatever can be seen through the ocular lens of the scope.
|Anyone sitting next to me can get a live view of whatever I see through the scope. Pretty neat!|
One activity we plan to implement focuses on Leonardo da Vinci's Vitruvian Man drawing. In this lab, students will get the chance to explore the degree to which body proportions are consistent across a variety of individuals. Students will first take measurements on themselves to determine if they each fit da Vinci's assertion that in the ideal human, the span of an individual's arms are equal to his/her height. The students will then pool their data as a class to determine if this is robust across individuals. They are then encouraged to propose other body proportions they would like to explore and are given the chance to measure other students to test their own hypotheses. I think this lab will not only promote these students to be curious about their own bodies, but will also give me the chance to teach them how to use common computer programs (such as MS Excel) to analyze data.
Another activity I would like to do focuses on the mammalian dive response (or dive reflex). A wide variety of mammals (including humans) demonstrate a physiological response when diving into cold water for extended periods. This response is characterized by apnea, bradycardia, and peripheral vasoconstriction. Together, these effects allow the body to conserve oxygen and ensure a more steady supply of blood to vital organs like the brain. In my undergraduate experience at UC Berkeley, I took part in a lab activity during one of my physiology courses that allowed me to experience this firsthand by "diving" into a dishpan of cold water. For the students at Watsonville, I think Sarah and I will "inquirize" this lab activity to see if students can devise their own experiments to determine what factors trigger the dive response in humans.
Towards the end of this month, I'll begin making appearances in Sarah's classes to run these labs and also generally assist her in teaching. I'm always excited to try something new, but I also have a few concerns. As a TA, my students only had to come to our discussion sections on a voluntary basis. Thus, the students who showed up on a weekly basis were generally the more academically-driven crowd, and were a self-selected group. At Watsonville, this will not be the case. I'm curious to see how well the students will respond to inquiry-based learning given the notion that the students themselves do not necessarily want to be in school -- they're there because they have to be. I feel inquiry-based approaches are probably very effective only in motivated students, and I'm curious to see how we might deal with apathy in the classroom.
My first goal in working with Sarah was to introduce her to the vast diversity of coral reef fishes, placing an emphasis on the family Labridae. Through my visits to various natural history museums, I've built a sizable collection of labrid fishes. For each labrid species, I have started collecting an ontogenetic size series of at least 15 specimens so that I can examine trends in the scaling of morphological traits over ontogeny. I'm particularly interested in testing the hypothesis that labrid species that undergo dramatic shifts in feeding ecology over ontogeny also undergo shifts in morphological characters related to feeding in a more drastic manner than species that don't show dietary shifts.
|Sarah Baumgart is always enthralled by the peculiar morphology of Gomphosus varius, the bird wrasse.|
In the near future, I will enlist Sarah's help in capturing high-speed video of cleaning behavior in labrid fishes (particularly in Labroides dimidiatus). This will not be a simple task, as cleaners are often quite difficult to keep alive in an aquarium setting. Furthermore, since I aim to build kinematic profiles of cleaning behavior, I'll need to devise a clever way to ensure I capture the cleaners in a lateral view. I'm very excited to begin this project, which will ultimately constitute its own chapter in my dissertation.
Why So Difficult?
Why is it so hard to tell these two species apart? Just look at the photo below. Both the black prickleback and the monkeyface prickleback are highly-elongate, intertidal crevice-dwelling fishes with similar coloration patterns. Both have terminal mouths with large, fleshy lips and have dorsal and anal fins that seem to be almost continuous with their caudal fins. Plus, it doesn't help that they have overlapping ranges along the Pacific coast, especially along California.
|Upon first inspection, the black (left) and monkeyface (right) pricklebacks look almost identical.|
|Can you tell them apart based on their tails?|
Clue #1: Pectoral Fin Size
Quite possibly the easiest and quickest way to differentiate between the two species is to examine the pectoral fins. The black prickleback's pectoral fins are quite reduced, looking like minute flaps compared to those of the monkeyface prickleback.
|The black prickleback's (left) pectoral fins are quite reduced in size when compared to those of the monkeyface prickleback (right).|
Clue #2: Fleshy Lump and Head Shape
The monkeyface prickleback has a characteristic fleshy lump of fatty tissue that occupies the top of head, a trait that is absent in the black prickleback. As a result, the monkeyface prickleback seems to have a more rounded cranial shape than its torpedo-like cousin.
|The monkeyface prickleback (top) has a characteristic fleshy lump on its head, a trait|
which is absent in its cousin, the black prickleback (bottom).
Clue #3: Dorsal Ray Spines
Although I do not have a picture to show for this one, take my word for it: this is another easy way to differentiate the two. Run your fingers along the dorsal fin of your fish. If it feels spiny, it's probably the black prickleback. The monkeyface prickleback has no spines in its dorsal fin -- just soft fin rays -- and is much softer to the touch. You'll have a much easier time grabbing hold of a monkeyface prickleback than a black prickleback.
|Think you know the difference now?|
|It seems kind of obvious now, doesn't it?|
|A face only a mother could love: a rather large specimen of monkeyface prickleback (Cebidichthys violaceus).|
In my ongoing quest to know more about this local species, I came across the work of Dr. Michael Horn, of Cal State Fullerton (CSUF), who has spent much of his life documenting the dietary trends of the Stichaeids of the California coast. In particular, Horn noted that the monkeyface prickleback undergoes a dramatic shift in diet over ontogeny: it goes through a carnivorous stage as a juvenile before making a transition to herbivory as it grows longer than 45mm standard length. A series of papers from the 2000s by Horn and colleagues highlight the fascinating trends in gut morphology and enzymatic activity of this Stichaeid.
This summer, Dr. Horn was kind enough to invite me to his lab at CSUF so that I may view his collection of monkeyface pricklebacks. He has quite a large collection of Stichaeids caught from tidepools, with some jars dating back to the early '70s. I learned a lot from this experience, especially when it comes to eying the subtle differences between C. violaceus and its close cousin Xiphister atropurpureus, the black prickleback (which I will highlight in my next post).
|San Simeon, CA seems to be a pretty good site to find monkeyface pricklebacks.|
|This black prickleback doesn't look too happy to have been stuck in a jar of |
ISO for the last 30 years. Also, I think he looks a little bit like Jason Segal.
The Division of Fishes does not reside in Washington D.C. (where the NMNH is), but is actually located a short train-ride away in Suitland, Maryland. The collection is housed in the Museum Support Center, pictured below.
|The Smithsonian Institution's Museum Support Center, located in Suitland, Maryland|
|Walking around in here made me want to play Mirror's Edge.|
Similar to how things are set up at the CAS and LACM, the Division of Fishes' collection is set up like an academic library, with rows of specimens organized by family.
|At least four of the rows pictured here are dedicated to wrasses (Family: Labridae).|
|Just a few hundred jars of specimens. No big deal.|
The friendly staff of the Division of Fishes were kind enough to set me up in my own office, dedicated to visiting researchers. I gathered that the Division hosts about 150 visitors per year, which probably keeps them quite busy, so I appreciated their hospitality.
|My workstation for the day. Comfy chair!|
|No Escort Required.|
|Some of these jars date back to the late 1800s. The fish inside smelled quite lovely...|
|Labroides bicolor: juvenile (L) and adult (R)|
|Thalassoma lutescens: juveniles (L), terminal adult male (R)|
|I always have fun photographing Gomphosus varius, the bird wrasse.|
|More Thalassoma lutescens|
|Just the right sizes of Halichoeres argus to borrow for my work.|
|Totally unrelated -- just wanted to throw this in, too|
I'll first be paired with a partner teacher from Watsonville High, who will work with me in the Mehta Lab at UCSC this summer. In this research partnership, my teacher partner will assist me in collecting and analyzing data for my dissertation work. This will be a win-win situation for both of us: I'll directly benefit by having a research assistant, and my teacher partner will learn techniques used in comparative anatomy and see how researchers work.
During the academic school year, I will travel to Watsonville High School a few times per week to not only design and implement lab exercises (which we call "modules"), but also to be the "fun science guy". The SCWIBLES program places special emphasis on inquiry-based learning techniques, whereby students are educated about a concept (as a form of "scaffolding"), and are then encouraged to design their own experiments to further develop their knowledge. As a scientist, I'm very interested in helping students develop their analytical skills to properly implement the scientific method. I'm also very curious to see how effective inquiry-based teaching methods can be in piquing natural curiosity. I'm sure it will be a rewarding experience!
Note: there seems to be a set resolution for uploading videos into this blog. To watch these videos in higher resolution, please click on the video title itself (inside the video frame) to view it on my YouTube channel.
In this first video, we see an individual bluestreak cleaner wrasse (Labroides dimidiatus) cleaning a blue and yellow fusilier (Caesio teres). As the cleaning bout begins, the fusilier slows to a grinding halt. It eventually remains stationary as the cleaner wrasse inspects its body and dorsal fin. This behavior is common in clients; they often wait patiently as the cleaners work their magic.
When I observed the same individual of Labroides dimidiatus as above cleaning diamondfish (Monodactyus argenteus), I noticed that the cleaner tended to inspect only the cranial region of this client species, largely ignoring the rest of the body.
Cleaners often work in pairs, and that's what this video highlights. The client this time is a sailfin tang (Zebrasoma veliferum). Notice how it enters a trance-like state as the cleaners surround it and inspect for parasites. Of all the species I observed at the Aquarium of the Pacific, the sailfin tang was by far the most common client for Labroides dimidiatus.
Cleaning can attract a lot of attention, especially when it occurs in special zones termed "cleaning stations". This individual bluestreak cleaner wrasse (Labroides dimidiatus) first inspects the pelvic fins and the underside of the body of a sailfin tang (Zebrasoma veliferum). A nearby Millet butterflyfish (Chaetodon miliaris) notices this activity and approaches the wrasse, hoping to be inspected as well. The cleaner briefly inspects the pelvic fins of the butterflyfish before speeding off.
Even when not cleaning, the bluestreak cleaner wrasse (Labroides dimidiatus) will attract attention. The individual in this video does not seem to be all that interested in cleaning. Notice how each individual the cleaner wrasse approaches slows down, allowing time for the cleaner to inspect it. This behavior seems to occur automatically -- the clients slow to a halt even when the cleaner is not interested.
I hope I have given you more insight on the behavior of this fascinating species. As noted before, these videos (and more) have been posted to my YouTube channel, which is available at: http://www.youtube.com/user/VBaligaUCSC. Thanks for watching!
|Labroides dimidiatus and Monodactyus argenteus|
|Screenshot of the channel|
In the coming months, I will acquire live specimens of an obligate cleaner (either Labroides dimidiatus or Labroides bicolor) and a client species (most likely Zebrasoma veliferum) and house them together in one of my tanks at the Mehta Lab at UCSC. Using high-speed video, I will record the cleaning activity I observe in order to study the kinematics of cleaning behaviors. Once analyzed, these videos will also be uploaded to the YouTube channel. Stay tuned!
Channel available at: http://www.youtube.com/user/VBaligaUCSC
|Each of these rows contains hundreds of jars of fish specimens.|
|You're not a true ichthyologist unless you come up with jokes like this.|
|Found this little gem lying around. Quality entertainment!|
|A size series of Thalassoma bifasciatum (LACM 54098-040).|
|A size series of Halichoeres bivittatus (a.k.a H. bivittata, LACM 2479-000).|
|Size series of Gomphosus varius (LACM 57407-001).|
|Some more specimens of Gomphosus varius (LACM 37434-005).|
Another familiar face: Halichoeres nicholsi, the spinster wrasse. This facultative (juvenile) species is found in the eastern Pacific. Although it may be hard to really notice by looking at faded museum specimens, this species has very distinct coloration patterns for the juvenile and adult phases. Juveniles have a more blotchy/spotted coloration whereas adults are more uniform in color with a broad bar behind the head.
|A size series of Halichoeres nicholsi (LACM 32499-027).|
|Two juvenile specimens of Halichoeres nicholsi (LACM 43924-005).|
The tubelip wrasse, Labrichthys unilineatus, is the most closely-related non-cleaning species to the obligate Labroides and facultative Labropsis cleaners in Labridae. Members of this monophyletic group, called the "labrichthynes", are known for having tube lips. Unlike its sister taxa, L. unilineatus does not clean, and instead feeds on coral polyps.
|A few specimens of Labrichthys unilineatus (LACM 42489-026).|
Back to the world of Thalassoma: next we have Thalassoma hardwicke. This species, known as the sixbar wrasse for its characteristic stripes, can be found in the Indo-Pacific. It is not a cleaner, but rather a benthic invertivore.
|A size series of Thalassoma hardwicke (a.k.a. T. hardwickei, LACM 51859-049).|
|A few larger specimens of Thalassoma hardwicke (a.k.a. T. hardwickei, LACM 38210-004).|
The final species I will highlight tonight is Halichoeres dispilus, the chameleon wrasse. Found in the eastern Pacific, this species feeds on benthic and pelagic invertebrates, but is not a cleaner. Large individuals have been observed to be piscivorous.
|A size series of Halichoeres dispilus (LACM 8104-000).|
|More specimens of Halichoeres dispilus (also from LACM 8104-000).|
|Two additional juveniles of Halichoeres dispilus (LACM 43822-001).|
I was fortunate enough to be able to borrow all of the specimens I have shown here, plus a few more. Much to my delight, Rick Feeney was fine with having me clear & stain these specimens, which is a pretty tall order. As such, I am very thankful to Rick and the rest of the staff at the Museum of Natural History. They run an amazing Ichthyology-Herpetology department, and made me feel very welcome working there for the day.
|A great group of folks -- the Ichthyology-Herpetology staff at the LA County Museum of Natural History.|