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Santa Cruz, CA

Vikram Baliga, PhD Candidate at UC Santa Cruz, member of the Mehta Lab. Areas of study: ecology, ontogeny, morphometrics, and comparative methods.

Blog

A Hassle-Free Way to Verify that R Packages are Installed and Loaded

Vikram Baliga

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.

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Another Year, Another Milestone: The Qualifying Exam

Vikram Baliga

What a great end to the Fall quarter! I'm happy to report that last week, I passed my Qualifying Exam (QE) to advance to PhD candidacy. I am not truly a "PhD Candidate" just yet though -- the last remaining hurdle is for me to give a seminar to the EEB Department, which I will do in the upcoming Winter quarter.

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!


Fun with Dissections!

Vikram Baliga

I just wanted to share one quick little update. I've been working more with my labrid (wrasse) specimens over the past few weeks, and have started to dissect out a few muscles. I'm chiefly interested in removing the adductor mandibulae and sternohyoideus muscles. The adductor mandibulae is a collection of muscles that function to close the jaws -- quite important for species that rely on biting. The sternohyoideus muscle acts to retract and depress the hyoid bar (a.k.a. the "bony tongue") and is quite integral to the process of suction feeding (side note: humans have a homologous sternohyoid muscle) I'm interested in understanding how large (by mass) each of these muscles is not only in different species of wrasses, but also how muscle sizes scale across ontogeny within each species. I'd like to gather data to test the hypothesis that labrids that show strong dietary shifts over ontogeny also show larger scaling differences over ontogeny in muscles related to feeding.

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!

My Foray into Inquiry-Based Teaching

Vikram Baliga

As the title suggests, I've started writing a few inquiry-based lab activities with Sarah Baumgart, my partner-in-crime through the SCWIBLES program. Sarah teaches both general biology (10th-11th grade) and anatomy & physiology (11th-12th grade) at Watsonville High School. With her strong background in human anatomy and my training in comparative vertebrate morphology, I feel we will make an excellent team in the classroom.

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.

Summer Research Update

Vikram Baliga

Through my SCWIBLES Fellowship, I've been partnered with Sarah Baumgart, an anatomy & physiology teacher at Watsonville High School. Sarah has been kind enough to assist me with various aspects of my dissertation research this summer.

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.
Sarah is quite the natural! I have led her through the basics of how to take morphological measurements of each specimen’s overall body shape and size, as well as the basics of skinning fishes to prepare them for the clearing & double-staining process. Our sessions have been highly productive, and I am continually impressed with the thoroughness and care that Sarah exhibits. I owe her a lot of credit in helping me describe the overall body shape characteristics of a variety of labrid fishes this summer.

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.

Black vs. Monkeyface Pricklebacks: Subtle Differences

Vikram Baliga

In my recent visit to the Horn Lab at CSUF, I got a chance to look at many members of the Stichaeid family. As I was hunting through Dr. Horn's jars for specimens of monkeyface prickleback (Cebidichthys violaceus), I noticed how easy it is to confuse this species with the black prickleback (Xiphister atropurpureus). As such, I figured I would dedicate a post to highlight the differences between the two species' morphologies so that anglers (and fellow lab researchers!) can better tell what exactly they're handling. If you're into game fishing and would like to know how to tell your black pricklebacks from your monkeyfaces, this post is for you.


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.


Test Yourself
Think you know the difference now?
It seems kind of obvious now, doesn't it?


Happy poke-poling!

Monkeyface Project & Horn Lab Visit

Vikram Baliga

One of my ongoing sideprojects involves understanding the cranial morphology of the monkeyface prickleback, Cebidichthys violaceus. This species is found along the Pacific coast, ranging from Oregon to Baja California, and inhabiting rocky intertidal and tidepool habitats. Commonly confused with being a type of eel (it's even known as the monkeyface eel), this species is actually a member of Stichaeidae, a family found in the Perciform order. Famous for their distinct, lumpy foreheads, these fish are often caught by anglers using a method called "poke-poling".

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.

Monkeyface measuring!

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.

Building Ontogenetic Series III: Smithsonian National Museum of Natural History

Vikram Baliga

In my ongoing quest to obtain specimens for my dissertation research, I managed to find my way to the world's largest collection of fishes: the Smithsonian Institution's National Museum of Natural History (NMNH). The Division of Fishes works tirelessly to collect and catalogue marine & freshwater fishes from around the world. Their collection contains over 24,000 of the roughly 32,000 recognized species of fish worldwide. This collection is so large, that only 35% of the estimated 6.2 million individual specimens have been computer cataloged. Fortunately for me, their efforts are currently focused on obtaining and cataloging Caribbean and Indo-Pacific fishes. These geographic areas are home to the many wrasses, gobies, (marine) angelfishes, and damselfishes that I am analyzing for my dissertation work. As I fortuitously found myself on the East Coast thanks to a good friend's wedding, I decided to visit the NMNH during the same trip. In this visit, I was able to fill in many of the gaps in my current collection (which consists of specimens borrowed from the Cal Academy and the LACM, bought (and euthanized) from the pet trade, and generously donated by Dr. Peter Wainwright).

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...


It's easy to see the drastic changes in coloration over ontogeny in Labroides bicolor, the bicolor (cleaner) wrasse. The juvenile form (L) presents with a dark lateral stripe; the adult (R) develops darker coloration over the anterior half of its body. Does anything else change? I'll be able to answer that question in a few months.

Labroides bicolor: juvenile (L) and adult (R)
We see another obvious transition in Thalassoma lutescens (the yellow-brown wrasse): there's a huge distinction in coloration between juveniles (L) and terminal adult males (R). This species cleans predominately as juveniles, and shifts to eating crabs, molluscs, and shrimps as adults. Are these transitions in color pattern and diet accompanied by transitions in musculoskeletal morphology?
Thalassoma lutescens: juveniles (L), terminal adult male (R)

More pictures, you say? Sure, why not?

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.






I'm quite happy with what I gained from this visit -- the specimens I have requested to use for my work should be shipped to me within a few months. I'll be able to make a lot progress over this summer and gather valuable data for my proposal defense, which I'm planning to hold in the fall. I had a blast talking with the staff of the Division of Fishes, and I am grateful for their support of my research. I always enjoy making visits to museum collections, and this one was no exception.



Totally unrelated -- just wanted to throw this in, too

I'm going to be a SCWIBLEr

Vikram Baliga

This year marks an exhilarating change in my grad school career. I have been selected to receive an NSF GK-12 graduate fellowship as part of a graduate training program for STEM students at UC Santa Cruz. This program, entitled Santa Cruz-Watsonville Inquiry-Based Learning in Environmental Sciences, or SCWIBLES, makes it possible for fellows like me to further develop our scientific communication skills by working with high school students. Although I really enjoyed being a TA for classes at UCSC, I'm excited to develop inquiry-based curricula for students at Watsonville High School in Watsonville, CA.

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!

Species of the Moment: Labroides dimidiatus

Vikram Baliga

I had the good fortune of visiting the Aquarium of the Pacific in Long Beach, CA again not too long ago. While I was there, I spent hours gawking at the tropical pacific reef galleries they have on display there. Not only are there over 1,000 animals on display in these galleries, but also there are several individuals of Labroides dimidiatus, the bluestreak cleaner wrasse. I was again able to shoot some videos, this time armed with a slightly-better camera.

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

Announcing: My New YouTube Channel

Vikram Baliga

I'm happy to announce that I have created my own channel on YouTube. In this channel, I will be sharing videos that relate somehow to my dissertation work here at UC Santa Cruz. Thus far, I have uploaded some videos of interesting fish that I took at the Aquarium of the Pacific in Long Beach, CA.

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

Building Ontogenetic Series II: Visiting the LACM

Vikram Baliga

Since my parents live in southern California, I figured I'd make the most of my Spring Break by scheduling a visit to the Ichthyology-Herpetology department at the LA County Museum of Natural History (LACM). In this visit, I had the pleasure of meeting the Collections Manager (and all-around great guy), Rick Feeney. Very much like the Cal Academy, the LACM houses many, many specimens that are organized in shelves -- reminiscent of most libraries. According to Rick, the collection contains over 5 million specimens.

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!


In my ongoing quest to build ontogenetic series for Labrid fishes, I took advantage of the LACM's beautiful collection. Rick Feeney was quite generous with the number of specimens he was willing to loan to me -- he let me get away with 91 little fishies. Here are the spoils!

First up, we have Thalassoma bifasciatum, also known as the bluehead wrasse. This Caribbean species is probably most well-known for being a protogynous hermaphrodite, although many other wrasses exhibit this condition as well. Thus, the largest individuals in a population tend to be terminal-phase males, who exhibit a distinct coloration. If they leave or die, large females will often change sex secondarily. Bluehead wrasses often eat zooplankton and small benthic crustaceans, but can also consume echinoderms and molluscs. This species is also a facultative (juvenile) cleaner of ectoparasites.

A size series of Thalassoma bifasciatum (LACM 54098-040).


Next, we have Halichoeres bivittatus. I already have a few specimens of this species from the Cal Academy, which I highlighted in a previous post. Another protogynous hermaphrodite from the Atlantic, this species also forms leks during breeding. Also unlike T. bifasciatum, this species can undergo sex reversal. Whether any of this helped inspire the common name of "slippery dick wrasse" is a mystery to me. Anyway, this species is a gastropod-eater and occasional piscivore. As I mentioned before, this species is also a facultative (juvenile) cleaner!
A size series of Halichoeres bivittatus (a.k.a H. bivittata, LACM 2479-000).


These weird fellows below are specimens of Gomphosus varius, the bird wrasse. This Indo-Pacific species uses its elongate jaws to pick off small benthic invertebrates from coral or rocky crevices. Interestingly, this species does not clean, even though it possesses jaws that are conducive to a "picking" feeding mode. I guess it goes to show that there's a lot more to cleaning than having (presumably) adequate morphology -- behavioral ecology plays a huge role in determining the evolutionary trajectory of mutualistic behavior.
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.