The ultimate grad student guide to survive (and pass) qualifying exams

***Updated on 11/24/2014***


Most qualifying exam stories come with the same take home message: it’s the worse moment in the life of a PhD student. My story is no different than the others: several times I considered just walking out the door, heading to the airport and taking the first flight back home; all I put in my stomach in the last three days of the quals process were 24 cans of coke and a giant bag of dinosaur shaped nuggets; I would work 15-20 hrs a day, and often question myself if it was enough; some days I wouldn’t work at all, because my brain just refused to, and the struggle with the endless guiltiness was even worse; I couldn’t sleep the night before my oral exam; during the exam I was so tired and got so nervous that I couldn’t think straight, and said “I don’t know”, s-e-v-e-r-a-l times; at the end, I passed, and I cried (a lot). Not tears of happiness though, those were intentional tears of relief, to wash away tons of stress and personal pressure.

If you’re about to take your quals and just read the above, you probably hate me for being such a Debbie Downer. I’m sorry about that, but I needed to highlight the general negativeness around qualifying exams so you can understand the point I want to make with this post: the hardest part of quals isn’t the tons of papers you have to read, or endless hours working, or deciding how to structure your arguments…the hardest part is to manage your levels of self confidence. If you cannot trust yourself, you can trust me and the other graduate students that contributed with several suggestions to this post. I’ll try my best so our mistakes don’t become yours, and summarize here good and safe strategies for doing well on qualifying exams, as well as the most common self-trapping strategies.

Think about the characters in the Hollywood classic “The good, the bad, and the ugly” when trying to understand how you can win the quals war looking as pretty as Clint Eastwood would, or how you could fail by choosing a bad stratagem, or letting the ugly side of your own self doubts make your life harder than it should be, and even drive you to failure. The advices here are mainly towards the system of qualifying exams at the Ecology, Evolution and Systematics program at the University of Missouri St Louis, however they can be useful to graduate students taking qualifying exams in different areas and institutions as well. The quals in our the department is far from being easy, but it is a fair and very reasonable process. It’s important to highlight here that the qualifying exam structure varies tremendously across graduate programs. At least in the fields of Ecology and Evolution, the common component of all exams is an oral examination with a committee (as far as I know). However, the written part of the quals exams goes from exams lasting a few hours, days, months, or no written component at all. PhD students in our program have one month to write down the answers for five questions: two four page long essays on major theoretical fields that your dissertation fits in, and three shorter, one page long essays on minor, or satellite topics. The written part goes to a committee composed by faculty members who will read the answers and discuss them with the student during in a meeting, which makes up the oral exam of the quals process. The student’s advisor is left out of the entire process, in order to avoid conflict of interests. One of the most distinctive characteristics of our quals at UMSL is that while working on our questions, we are allowed to brainstorm with other people. Hence, you are free to discuss your questions with other people, as long as you use your own words when writing the answers. A solo and silent qualifying structure is common elsewhere.


The good, or Eastwood-style strategies for success:

1) Get your life ready beforehand. If you don’t want to end up like me, eating dinosaur nuggets for three days in a row, stock some provisions beforehand. As if you’re preparing yourself for war or a long hard winter, make sure you have enough food, caffeine and whatever keeps you going. Crock pot-borne food will be your best friends. Warn family, friends and significant others that you’ll be in a on the edge/cave-man mode for a while. They’ll have to bear with a bipolar version of you that, on the blink of an eye, goes from a cold working machine to a highly emotional type that cries watching diaper commercials.

2) Make a work and rest schedule and stick to it. Set up the order of the questions you will answer, and a time frame for each. Include an order of tasks: read -> write -> revise -> break -> next question. The transition from reading to writing is very important, I personally struggle with start writing even after reading more than enough, which is why respecting the schedule is essential.

3) Plan on finishing before the deadline. My deadline was on a Friday. I finished on Tuesday, took a brain break on Wednesday, and revised half on Thursday and half on Friday. Taking a break before doing a final review allows you to set your brain free from your own text, and do a somewhat unbiased review. Sometimes the oral exam is scheduled only a few days after you send the responses to the examination committee –  hence, you want to rest and take it easy at the very end.

4) Tackle the hardest first. If you leave the hardest and the longest parts to the second half of the process, your tiredness and emotional state will affect your progress.

5) Put some endorphin in your blood stream, at least twice a week. Best way of doing it: exercise. Bike to the library, Brainstormwalk around the block, do some jumping jacks, yoga, walk to the coffee shop that is two blocks away…It doesn’t matter how, just find a way to boost your endorphins levels, it’ll help to clean up your head, control your stress and improve your concentration.

6) Brainstorm with your colleagues. Papers shouldn’t be your only learning resource. To me, one of the coolest things in the academic environment is to be able to knock on the door across the hallway and discuss whatever you want with your colleagues. Take advantage of the intellectual environment around you, and learn how to use it in your favor, if you aren’t doing it already.

7) Read about writing. As any method of communication, there are clearly stablished writing techniques out there. My favorite read on the topic is “Gopen and Swan, 1990. The Science of Scientific Writing. American Scientist“. Duke University has a free-web based course on scientific writing:

8) Beat the myth of the professor-enemy. Students of the world: your teachers are not your enemies. I’ve been taking a teacher training course at UMSL this fall, and we discuss a lot about how to be the student’s “best friends” through out their educations journey. However, even when their mentors try and are supportive, students often don’t even acknowledge that their professors are their more powerful allies. Dr Patty Parker, our department chair, pointed out the following after reading the first version of this post: “In general, the faculty completely believe in the students and want them to do well. It may feel like someone is “out to get you” but that is never the case, in my experience. In general, the examiners are supportive of the students and want them to succeed, and understand that everyone is different and responds differently to the particular form of nervousness that comes with qualifying exams. I guess that is my main point: the faculty on the examination committee are humans, too, with feelings and strengths and weaknesses. Remember that we, too, would struggle to formulate strong responses to these same questions. Remember that we are sitting there when someone asks a question, asking ourselves whether we could answer it and how we would answer it.  I am usually extremely impressed with the poise of our students and how they can respond to questions that I think I would struggle to answer“.

 The bad, or guaranteed failure (or partial failure) strategies, or two ways of shooting your own foot:

Trying to do multiple things at the same time during your quals is a bad idea. Photo from:

Trying to do multiple things at the same time during your quals is a bad idea. Photo from:

1) Multitasking. During your quals, ALL you will do will be your quals. NOTHING ELSE. You should engage in single priority mode. That’s the main reason the quals in our department have been moved to the winter break – there’s the downside of kind of missing all the holiday parties, but the very very very positive side that there’s little overlap with field seasons and conferences, which mostly happen over the summer. Focusing and not multitasking may sound obvious to you, but people don’t follow this rule more often than you’d think, and all cases I’m aware of people that have failed (or partially failed) qualifying exams did something else during that month, which includes distractions from both professional and personal life. So, be careful with this one.

2) Answering “it depends”. For my own qualifying exam, I received the following question for a minor in Conservation Biology: “If scientists readily adopted the phylogenetic species concept and this concept became accepted by policy-makers, how might that impact the U.S. Endangered Species Act?“. The phylogenetic species concept considers species as the smallest monophyletic units in a phylogeny, hence species are irreducible clusters grouped by unique shared characters and ancestry. The U.S. Endangered Species Act (ESA) of 1973 provides legal means for the conservation of wildlife endangered or in threat of extinction, and the ecosystems upon which they depend. The ESA original definition of species included “any subspecies of fish, wildlife or plants”, and having a major flaw of not specifying the species concept under which endangered and threatened taxa are recognized. My answer strategy on that was: “It depends.”. Bad mistake. My arguments were that adopting the phylogenetic species concept in the ESA could be beneficial for giving a standard operational unit for policy makers, besides considerably reducing the number of species in the list, which can be an advantage when resources are limited; however, by adopting the phylogenetic species concept, the ESA would ignore that species are complex evolutionary entities, and should be treated as so. I concluded saying that the species concept adopted should be context dependent. Bad idea again. The problem here was, by being so on the fence I: 1) didn’t prepare myself well enough to defend either side of what I was proposing; and 2) gave my committee the chance to ask me questions that went in any possible direction. I was also told that as a scientist I should be able to give a single answer when policy makers ask my opinion: “People out there want one answer, and it’s your responsibility to be able to provide that single answer”. I still don’t have experience enough to judge these words, but here is my message: if you are asked to give your opinion on something, even if you really believe the answer is “it depends”, pick a side for your own sake.


 The ugly, or the dangerous lack of self confidence:

Have you heard of the impostor syndrome? If you are in your first years in grad school, I bet two phalanges from my right hand that you have it. Impostor syndrome is a term that was coined to describe several types of feelings related to problems with self-acceptance. It’s that constant feeling of being a fraud that comes with a fear of being caught – “what if everybody finds out that I actually know nothing”. It is constantly accompanied by thoughts like: “I’ll never be as good as Mary Jane, or John Smith”. You’re not alone when it comes to feeling like an impostor, but it’s up to you to make your way out of it. You can find out how here and here. As I said earlier, the hardest part of the qualifying exam process is to manage your self confidence. If you are going through the quals process, you earned your place in hell, and you know it wasn’t easy getting there. Think about it.

I’ll be posting two examples of qualifying exam answers in the near future. There’s a lot of anxiety around thinking about what type of questions are asked, and how in depth one should answer these questions. I got the ok from our Department Chair to post examples of questions and answers, and hope you can take advantage of them. Stay tuned.

If you have any other suggestion that I didn’t cover in this post, please post a comment :) !

Not all frogs jump alike – the evolution of landing in frogs

Well, at least they don’t land alike – some prefer a nose-dive style! A group of researchers led by Dr. Rick Essner, from the Southern Illinois University Edwardsville, have recorded the jumping styles of different frogs in slow-motion and found that some frogs, more specifically the ones belonging to the Leiopelmatidae family, don’t know how to land like most frogs. Interestingly, Leiopelmatidae is the basal-most living frog family, indicating frogs first learned how to jump, and only later in their evolutionary history did they develop a way to land that didn’t involve a head or belly flop. Here is a link to their paper.

The Leiopelmatidae:


The frogs we are accustomed to seeing, and that we used to chase when we were kids, have a typical jump that works like this: first there is a propulsion to get the body off ground, then half-way through, the body and limbs will flex in preparation for landing. This mid-air flexion is what prevents them from a head-first collision.

Screen Shot 2014-11-04 at 6.23.07 PM

All frogs (order Anura) can be divided in two main classifications, the basal-most Leiopelmatidae and all other frogs, Lalagobatrachia (Frost et al, 2006). These two groups diverged around 225 million years ago (Roelans and Bossuyt, 2005). The Leiopelmatidae were particularly interesting for this study because according to Dr. Essner they “retained central and behavioral features that are evolutionary informative”. Dr. Essner and his group already knew that these basal frogs swim differently than others. They do a trot-like rather than a kick-like swim. This trot-like style is characterized by asynchronous movement of the hindlimb, while in the kick-like one, frogs extend and flex both their hindlimbs together, which is what all other frogs do. That suggested to the researches that maybe there were other differences in how these frogs moved. So, they set out to test how they jumped and landed. They analyzed slow-motion video footage from five species, three basal leiopelmatidae, Ascaphus montanus, the Rocky Mountain tailed frog, Leiopelma pakeka and L. hochstetteri; and two lalagobatrachians, Bombina orientalis and Lithobates pipiens.


Amphibian Tree of Life, including caecilians, salamanders and all frogs. Not the first frog family is Leiopelmatidae. From

The Lalagobatrachia frogs they observed all had a similar jumping pattern where the “aerial phase [is] characterized by mid-air body and limb rotation in preparation for landing. […] Limb recovery involves protraction, adduction, and extension of the forelimbs, placing them in position to absorb impact forces”. We can call the lalagobatrachians derived frogs, a reference to their more recent placement in the Anuran phylogeny.  The Leiopelamtidae, however, didn’t come programed to flex their hindlimb mid-air, and therefore, land in a belly-flop, abdomen (and sometimes nose) first, and skid to a stop. Like in this video from their study:

Poor guy, but I don’t blame you if you replay that video a couple of times.

Such a simple maneuver, you would think, to flex you limbs before you have to skid your way through a stop. Maybe the art of jumping and landing had evolved together. Apparently not in frogs. The fact that the most basal lineages can’t perform such maneuver indicates that frogs first evolved how to jump, and the landing skills were only developed much later on, in the ancestrals of the lalagobatrachian frogs. According to the authors: “The switch to lalagobatrachian landing and swimming behavior appears to have involved a simple evolutionary change in the timing of limb muscle motor patterns, shifting the onset of hindlimb flexors to an earlier point in the stride cycle.” There seems to be no difference in the morphology of these frogs that could influence how they land, and what makes a difference is simply the timing of their limbs flexion.

“All else being equal, if A. montanus shifted the onset of recovery so that flexion began at mid-flight it would land on its limbs like other frogs.” – Essner et al.

It is worth mentioning that these basal frogs are tiny, as you can see in the picture below where the for is next to a dime. Their smaller size probably helps in their rough landing. They also have large, shield-shaped cartilages, which could soften the uncontrolled landing.

Ascaphus montanus next to a dime. Photo from

Ascaphus montanus next to a dime. Photo from

By now you could be thinking: how did jumping evolve, and is there any relation of how these frogs differ in how they land to primitive terrestrial fishes, or did jumping evolve independently more than once? Well, we don’t know it, but Dr. Essner and his collaborators are currently investigating how jumping involved in anurans.

A very important point to be taken from their work is that when looking at morphological traits to understand evolutionary history, we tend to ignore behavioral aspects that may involve multiple ways of using the same available structures. This paper proves that to make an engine work, it takes much more than just having the right tools.

For more information, read the article: Essner, Richard L, Daniel J Suffian, Phillip J Bishop, and Stephen M Reilly. 2010. “Landing in Basal Frogs: Evidence of Saltational Patterns in the Evolution of Anuran Locomotion.” Naturwissenschaften 97 (10): 935–39. doi:10.1007/s00114-010-0697-4.

Photo courtesy of Dr. Essner.

Photo courtesy of Dr. Essner.

Interbreeding, introgression and human evolution: Neanthertal cousins responsible for high altitude adaptation in Tibetans

Tibetans ability to survive in the mountains, where there is 40% less oxygen than at sea level, was donated by Denisovans, which are Neanthertals close relatives. Photo: Lhasa girl, Gaelle Morand, from

Tibetans ability to survive in the mountains, where there is 40% less oxygen than at sea level, was donated by Denisovans, which are Neanthertals close relatives. Photo: Lhasa girl, Gaelle Morand, from

When I think about Tibetans, what first comes to my mind is the expression of enlightenment in their faces. Maybe because to survive at 14,000 ft of elevation, one needs to have something else, which can be either lots of wisdom or an especial adaptation craved in the genes. In a recent study published in Nature, researches found that this something else that makes Tibetans so successful at colonizing high elevation areas are haplotypes donated by Denisovan hominins through DNA introgression. In a multi-national collaboration, Huerta-Sanchez and colleagues investigated the genetic variation of the gene EPAS1, linked to adaptation to low oxygen levels in high altitudes. When ordinary, non-adapted to high altitude, people are exposed to environments with low concentration of oxygen (hypoxia) the body enters in a compensatory mode. Hemoglobin levels increase, the number of red blood cells boosts, the heart starts to overwork in order to deliver oxygen to all demanding tissues, and finally, blood pressure ramps up to the risk of heart failure and damage to the peripheral circulation. All that doesn’t happen to Tibetans though. Their hemoglobin levels aren’t boosted because of the low oxygen levels, in fact they present similar adaptations of other mammalian species that live in high altitude, such as pigs and antelopes: they have thin walled pulmonary vascular structure, which translates into high gas exchange efficiency, and their blood flows at a higher velocity, meaning that tissues get their oxygen delivered even when the supply is low. All these anatomic and physiologic variations have a direct implication on reproductive success, since women that lack high-altitude adaptation usually have miscarriages due to eclampsia, or fetal heart failure. Given such a tuned phenotype-environment adaptation, one can ask how evolution of altitude adaptation in the Tibetan population took place. In order to disentangle this evolutionary history, Huerta-Sanchez and colleagues put their bet on using SNPs (see bellow) to understand the genetic variability of one gene, EPAS1, a transcription factor associated with the activation of several other genes regulated by oxygen concentration.

Thanks to Denisovans, Tibetans physiology make them well equipped to survive hypoxia. Photo by Lynn Johnson, Nat Geo.

Thanks to Denisovans, Tibetans physiology make them well equipped to survive hypoxia. Photo by Lynn Johnson, Nat Geo.

Data from Single Nucleotide Polymorphisms (SNPs) analysis have been contributing to understand how altitude adaptation took place. A SNP is a single nucleotide difference in a DNA sequence. These unique changes on the basic building blocks of genes can be associated to several phenotypic differences detectable between populations of the same species. Human arrival in the Tibetan plateau took place in the Last Glacial Maximum, around 25 thousand years ago. Since then, about 1,100 generations of Tibetans have been surviving under high-elevation-related hypoxia – sufficient time for fixation of alleles that confer altitude adaptation. Just looking at the gene EPAS1, Tibetans have shown to present a remarkable SNP diversity when compared to their closely related ethnic group, the Han Chinese, showing the fastest allelic change observed in any human genome to date – how impressive! But, what is the deal with populations that are not highly differentiated, but present considerable difference in the frequency at which specific mutations happen, like Tibetans and Han Chinese for EPAS1 SNPs? Huerta-Sanchez and colleagues hypothesized that the source of variation may come from donor populations. They first tried to understand how so much variation in such a short genomic region evolved, by testing two models of selection that simulate how EPAS1 haplotype diversity evolved: 1) selection under standing variation, assuming that Tibetans already had the beneficial haplotype when they colonized high altitude environments; or 2) selection under de novo mutation, which predicts that beneficial haplotype showed up and was fixed in the population after establishment in high altitudes. Surprisingly, the high haplotype diversity found in Tibetan EPAS1 couldn’t be explained by neither of the models of evolution, which supported the hypothesis that a donor population contributed to the fast EPAS1 diversification: in other words, DNA introgression lead to adaptation.

Haplotype network. Each pie chart is a haplotype, and colors within each pie chart represent the proportions of individuals from all populations that share the same haplotype. The Tibetan haplotypes are closer to the Denisovan than they are from any other modern human population a pattern expected under introgression. Figure and legend adapted from Huerta-Sanchez 2014.

Haplotype network. Each pie chart is a haplotype, and colors within each pie chart represent the proportions of individuals from all populations that share the same haplotype. The Tibetan haplotypes are closer to the Denisovan than they are from any other modern human population a pattern expected under introgression. Figure and legend adapted from Huerta-Sanchez 2014.

Work inside the Denisova cave in Siberia, where Denisovan, Neanthertal and modern humans took shelter from the cold generation after generation, during thousands of years. Photo from:

Work inside the Denisova cave in Siberia, where Denisovan, Neanthertal and modern humans took shelter from the cold generation after generation, during thousands of years. Photo from:

By searching for possible donor populations in several genomic databases, the authors found that Tibetans shared several haplotypes with the Denisovan individuals, popularly known as being the Neanthertal cousins. The Denisovan fossil record, even though only composed as whole by two phalanges and two teeth, have rendered amazing insights into hominin evolution since their discovery four years ago, in a cave in Siberia. What Huerta-Sanches and co-authors visualized when they looked at the haplotype networks to understand the relationships between Denisovan, Tibetan and 26 other modern human populations haplotype diversity of the EPAS1 gene was striking: the Tibetan haplotypes are closer to the Denisovan than they are from any other modern human population, a pattern only expected under introgression. Adaptation to high altitude amongst Tibetans may have been facilitated by gene flow from other hominins that may already have been adapted to those environments. This fantastic finding leads to an infinite network of questions: What is the relationship between Tibetans and other human populations adapted to high altitudes, like Basques in the Pyrenees and several ethnic groups in the Andes?  How does the genetic variation of other hypoxia-related genes look like? Are Tibetans good marathonists? How culturally different were Homo sp. populations interbreeding around 30 thousand years ago, did they speak the same language, how different they looked, how long did they interbred for? Should Tibetans thank the DNA donation by creating a new holiday called National Denisovan Day? Well, I suppose this is one of the beauties of science, one question answered, so many more to go.

Thanks to Dr Hughes, who chose this paper to be discussed in the seminar lead by him about Next Generation Sequencing at the Bio Department of the University of Missouri St Louis!

Huerta-Sanchez et al. 2014. Altitude adaptation in Tibetans caused by introgression of Denisovan-like DNA, Nature 512, 194–197. 

The role of dispersal in Neotropical avian diversity

In a paper published in Nature last month by Brian T. Smith (American Museum of Natural History) and collaborators argue that the strongest predictors of avian speciation in the Amazon are the amount of time a species lineage has endured in the landscape, and how well a bird can move through that landscape. Their results suggest that the dispersal abilities of the birds and how long their lineage has persisted are important drivers of the high biodiversity in the Amazon.

The authors start the introduction by reminding us that we, scientists, usually link the biodiversity of the Neotropics to two major hypotheses:

1) large-scale landscape changes that generate bio-diversification by population fragmentation followed by isolation, and

2) the formation of a geographically structured landscape matrix on which diversification occurred.

The first, commonly known as vicariance, involves reconfigurations of the landscape, such as the separation of continents by plate tectonics, the uplift of mountains or the formation of large rivers. Since the study involves the avian fauna of the Neotropic region, the large-scale events considered by the authors that could drive biodiversity patterns are the Andean mountain uplift, and the formation of the (very large) Amazonian rivers. This first hypothesis is easier to understand: big mountain or rivers separate populations, which can no longer exchange genes and start differentiating from one another to the point where the different sides will have completely separate evolutionary futures.

The second hypothesis involves organisms’ ability to persist in a structured landscape, which does not necessarily need to change. In this case, allopatric speciation would follow dispersal events, and thus, organism-specific abilities to persist and disperse in the landscape are the principal drivers of speciation. Species with lower dispersal abilities have a lower chance of navigating the landscape and, therefore, tend to accumulate higher genetic differentiation between populations. Higher differentiation, in turn, leads to higher speciation rates.

Figure 1 from Smith et al. 2014. Main landscape barriers and data points in the Neotropics.

Figure 1 from Smith et al. 2014. Main landscape barriers and data points in the Neotropics.

To test these two hypotheses, the authors used 2,500 individuals from 27 widespread bird lineages in the Neotropics. To prevent biases of current taxonomic limitations, authors considered lineages instead of species, i. e., they used monophyletic groups as their definition of a lineage instead of going by current taxonomic nomenclature.

They looked at relatively recently diversified lineages that have their distribution interrupted by the Andes, the Isthmus of Panama and large rivers of the Amazon Basin (the Amazon, Madeira and Negro rivers).

To get around hypothesis 1, the authors tested whether the timing of divergence events were congruent with a single episode of vicariance associated with barrier formation, the Andean uplift. To test hypothesis 2, they compared the different dispersal abilities of lineages to their diversification rate. The idea being that species with lower dispersal abilities accumulate higher genetic differentiation between populations, which, in turn, leads to higher speciation rates. The measures of dispersal are based on “foraging stratum (a measure of dispersal ability linked to the behavior of birds: canopy, high dispersal ability or understory, low dispersal ability) and niche breadth (an indirect measure of dispersal ability based on habitat preference)”.

Birds included in the study. Bird drawings from Smith et al. (2014), originally from del Hoyo et al. (2013) Handbook of the Birds of the World.

Birds included in the study.
Bird drawings from Smith et al. (2014), originally from del Hoyo et al. (2013) Handbook of the Birds of the World.

What their genetic data indicate is that there was not a single divergence event, but rather between 9 and 29, and the timing of these events were not synchronous. Most of the species diversity originated during the Pleistocene, i.e. after the Neogene formation of the landscape matrix. If any of the vicariance events predicted to affect speciation (Andean uplift, Isthmus of Panama, Amazonian rivers formation) had been the source of the diversification, the lineage divergence time would be synchronous, since they were being affected by the same event, considering these are relatively recently divergent species. However, wouldn’t only older divergence events be affected by old vicariance events? How well we can test this is entirely dependent on how well the old phylogenetic node divergences can be estimated. In the paper, the authors acknowledge that they “… do not reject the possibility that the initial geographical isolation of populations at deeper phylogenetic scales was due to vicariance associated with the Andean orogeny or with the emergence of other landscape features”.

“Although highly suggestive of multiple dispersal events, this variation could be explained by a single vicariant event associated with the Andean uplift if the dispersal restrictions imposed by the barrier were heavily dependent on dispersal ability, such as was reported for a taxonomically diverse group of marine organisms isolated by the formation of the Isthmus of Panama. In a similar fashion, the emerging Andes could have first become a barrier for bird lineages with low dispersal abilities, with fragmentation of the distributions of more dispersive lineages occurring later. However, we detected no significant associations between dispersal abilities and divergence times across the Andes and the Isthmus of Panama that would support a model of ecologically mediated vicariance for these barriers.”

What about hypothesis 2? They found that whether a bird lineage inhabits canopy or understory affected the species diversity of that lineage. Since they used foraging strata as a proxy for dispersal ability, this result corroborates with the idea that dispersal-limited lineages (occupying forest understory) are significantly more diverse. The longer a lineage has persisted through time was also a good predictor of species diversity, i.e., older lineage accumulated more differentiation.

“The accumulation of bird species in the Neotropical landscape occurred through a repeated process of geographical isolation, speciation and expansion, with the amount of species diversity within lineages influenced by how long the lineage has persisted in the landscape and its ability to disperse through the landscape matrix.”

All in all, the paper doesn’t refute the vicariance hypothesis, but highlights the role of dispersal. These findings add to the ever-increasing pile of possible explanations for the higher diversity of the tropics and its heated discussion.

Smith, Brian Tilston, John E McCormack, Andrés M Cuervo, Michael J Hickerson, Alexandre Aleixo, Carlos Daniel Cadena, Jorge Pérez-Emán, et al. 2014. “The Drivers of Tropical Speciation.” Nature, September. doi:10.1038/nature13687.

Mastering scariness: the mechanisms behind hooding and growling in cobras

Snake charming is a very popular and ancient performance in Africa and Asia, which takes advantage of the natural defensive behavior of cobras of forming a hood.

Snake charming is a very popular and ancient performance found in Africa and Asia, in which flute players takes advantage of the natural defensive behavior of cobras of forming a hood. Picture from:

The second Ultimate Vert Bio Challenge is a warm up for Halloween, about one of the most terrifying, albeit amazing, creatures in nature: Cobras! These reptiles found their place in the animal kingdom hall of fame due to snake charming, a very ancient and popular performance in African and Asian countries,  in which a flute player pretends to hypnotize a cobra. What snake charmers actually do is take advantage of the defensive behavior called hooding, which cobras naturally perform by standing vertically, flaring the neck laterally and compressing it dorsoventrally. But, precisely, what adaptations in the skeleton and musculature of the cobras allow them to perform such a scarring defensive hooding display? When comparing X-rays of king cobras displaying hooding to cobras in a relaxed state, one is able to see how, in order to flare the hood, these snakes can rotate the ribs in two planes, frontal and transverse. The rotating movement of the ribs allow these bones to protract (move towards the head), and elevate (flatten and move dorsally), anchoring the muscles associated to the hood. Rib rotation is initiated by contraction of two muscles in the head, followed by contraction of intercostal muscles to support the protracted and elevated ribs. How long cobras can keep up with the defensive display depends on the amount of visual stimuli, or how threatened they feel, as well as intra- and inter- specific variation. However, there is evidence from laboratory observations that they are able to maintain the hood flared for at least 10 min, and up to 80 min!

Young BA, Kardong KV. 2010. The functional morphology of hooding in cobras.J Exp Biol. 213, 1521-8.

Young BA, Kardong KV. 2010. The functional morphology of hooding in cobras.J Exp Biol. 213, 1521-8.

I wouldn't hold a king cobra for a million dollars...wait, maybe for that money I would..but I definitely wouldn't smile while doing it like this guy does.  Picture from: http-//

I wouldn’t hold a king cobra for a million dollars…wait, maybe for that money I would..but I definitely wouldn’t smile while doing it like this guy does. Picture from: http-//

If you think hooding is enough to make cobras one of the most frightful creatures out there, you probably haven’t seen a video of a cobra hooding and growling at the same time. Yes, growling. Super laud nasty scary growling. Check out the video bellow:

Most snakes are able to produce hissing-like vocalizations at a frequency of 7,500 Hz, whereas cobras’ vocalizations lie at much lower frequencies, around 700 Hz, which is what characterizes them as growlers. The production of low frequency sound is possible due to the presence of a structure called tracheal diverticula. These are sacs associated to the trachea, which work as low frequency resonating chambers for the air flushed down the respiratory passageway. Interestingly, the only snake that has tracheal diverticula and is also able to growl, is the cobra’s favorite snack, the mangrove rat snake. This is considered to be a case of vocal Batesian mimicry, in which the mangrove rat snake mimics the vocalization of the more threatening cobras. The venom of mangrove rat snake is not toxic to humans, whereas cobras can inject up to 7 ml of venom in a single bite, and can kill a person in less than half an hour. We’re aware that cobras are predated by honey badgers (because they just don’t care), but I wonder what was the actual evolutive pressure through time to select for such a nasty defensive apparatus! Any thoughts?

Just to prove that King cobras can also look cute! Picture from:

Just to prove that King cobras can also look cute! Picture from:×200.jpg


Zombies of the ocean: the mechanism behind shark tonic immobility

Shark in tonic immobility state.

Shark in tonic immobility state.

My true passion in science is ecology and evolution of host-parasite systems. However,vertebrate evolution was what really caught my attention when I first started to study biology. Just based on the number of fans the movie Jurassic Park has, I’m sure I’m not alone with my fascination by vertebrate biology and evolution. Luckily, I got the chance to TA the Vertebrate Biology Lab at UMSL, which is an anatomy lab that I try to teach in an evolutionary, ecological and behavioral context. This Fall, I’ve decided to spice things up, and proposed to the students what I called the “Ultimate Vert Bio Challenge”. The idea here is to get our brains around some of the coolest, but, complex and most times under studied, facts involving vertebrates. In this first challenge, students had to try to explain the mechanism involved on shark tonic immobility (TI), a very popular topic referred to as ‘shark hypnosis’ or ‘zombie sharks’ in the media, and recently featured on Discovery Channel’s shark week (see video bellow).

Tonic immobility is assumed to be a behavioral strategy of preys – but, what does it mean when a predator presents the same type of behavior? Figure from the book Epossumondas Plays Possum, by Salley and Stevens.

Tonic immobility is assumed to be a behavioral strategy of preys – but, what does it mean when a predator presents the same type of behavior? Figure from the book Epossumondas Plays Possum, by Salley and Stevens.

TI is a behavioral strategy found in several species of vertebrates, such as  rabbits, chickens, hummingbirds, opossums, lizards, humans, and even in invertebrates, such as the red-flour beetle. In terrestrial vertebrates, TI is characterized as an unlearned and reversible behavior, in which the animal involuntarily enters a dead-like state characterized by motor inhibition. It is a behavioral display commonly associated with stress and fear responses to predators – hence a very widespread strategy among prey species. If TI is a response to predation, why the heck sharks, one of the sea’s top predators, can also be induced into a TI state? The TI mechanism is somewhat understood in terrestrial vertebrates: it involves activity of the hypothalamic-adrenal-axis, production of corticosteroids and muscle contraction. In contrast, in sharks and other elasmobranchs, TI is characterized by muscle relaxation. It is known that sharks experience physiological stress when in TI, due to high levels of carbon dioxide in the blood caused by inefficient ventilation while immobilized and turned upside down. However, the precise mechanism of TI in sharks has yet to be determined.

To get some insights on the possible mechanistic pathway of this phenomena, I got in touch with Dr Stephen Kajiura, the PI of the Elasmobranch Research Laboratory, at the Florida Atlantic University. Dr Kajiura mentioned that the consensus is that we just don’t know what the precise mechanism is. When I asked him to speculate what he believes the mechanism could be, he stated: “Since it (TI) works when the animal is flipped upside down, I would suspect that the mode of action is initiated by the vestibular system.  Another option is that the position causes blood flow to the brain to be compromised causing the animal to pass out.  In the wild, these animals are only likely to be flipped upside-down when being mated and it would probably be adaptive to be somewhat passive during that procedure to avoid being damaged by the mate’s teeth.” Another fact frequently pictured in shark TI videos are divers rubbing the animal’s snout with metal gloves, to stimulate the shark’s Ampullae of Lorenzini (AOL), an electro-receptive sensory system. This often misleads us to believe that AOL disruption is somehow the mechanism behind TI. Dr Kajiura explains that “it is possible to flip the sharks in the absence of any metal glove and get the same result.  AOL detect changes in electric fields so the shark may be momentarily confused by the metal glove, which might help to get it flipped upside-down, but remaining in TI is accomplished without any metal.  Again, we flip sharks with just our bare hands and get the same result so AOL are not likely the mechanism“. What is your hypothesis about the mechanism responsible for turning sharks into zombies?

Thanks to Dr Stephen Kajiura for kindly answering my questions so promptly!!

Long field seasons: how to prepare for one

Planning for a long field season next summer? Here is some advice for you. 

Recently, Leticia Soares wrote a post giving advice to students who are planning their first field season. Well, let’s be honest, we all could learn a thing or two (or a gazillion, in my case) about having a successful field season. Together, we decided that this was a topic worth extending, and we invited a few friends from the University of Missouri – St. Louis (UMSL) to give us (and you) some extra advice. In a previous post, Robbie Hart gave us some food for thought while in the field. In this post, you can read Mari Jaramillo‘s tips on how to plan for long periods in the field. She is a PhD candidate who works with avian malaria in the Galapagos islands. That’s right, she works in the Galapagos!! (sigh). Mari is a student in Dr. Patricia Parker’s lab at UMSL, and you can read more about her work at the end of this post.  

Taken at Tortuga Bay, Santa Cruz Island.

Taken at Tortuga Bay, Santa Cruz Island.

If you are lucky, field work doesn’t only take place during summer. Depending on the nature of your project you might need to stay at the field for extended periods of time, which for a field biologist is not hard at all. The hardest thing is probably leaving; you may be so comfortable you may want to make it your home…

But at some point you ought to know when you have collected enough data. No need to start crying and pouting though, the preliminary analysis of these data will point you in the right direction in future field seasons needed to complete your project.

Planning for extended field seasons is not that different from shorter ones, there’s just a lot more of it! Start thinking way ahead of time about the things that may take a while to get and be proactive about it. Lists are crucial! Ask yourself what things are indispensable for your research, for your assistants and for yourself and write these things down on a field or personal notebook. Also, you and your advisor will be glad if you check the list, item by item, with them or with your teammates that have been to the field site before. You could also send a list of personal items to your assistants and colleagues so they too are prepared for the field conditions and make sure they know about things that they are going to live without, like fresh water or electricity. Now, it doesn’t matter where and for how long you are going if all items in your list are checked off, you are good to go! And if you didn’t include it in your list, after all the scrutiny…


…the truth is you will likely be fine without it.


Field conditions and protocols are different from place to place; make sure you get acquainted with the rules and regulations of the different parks or reserves that you will be working at. Embrace the rules! You may find some of these rules are a pain in the %#$, but there is usually a pretty good reason behind them. Most of my field experience comes from work in the Galapagos Islands. These islands are a world icon and for that reason the park rules are more strict and extensive than anywhere else I have ever been. But I wouldn’t worry; there is a whole lot to enjoy as a scientist in these islands that no one else ever gets to experience!

The stars of the Pacific sky. Credit: Jeisson Zamudio.

The stars of the Pacific sky. Credit: Jeisson Zamudio.

If your work involves being away and isolated for long periods of time, you need to think survival!

Cover yours and everyone else’s basic needs and you will have a happy team! This means: food and water, a well-equipped first aid kit, a comfortable and warm place to sleep, a stove, gas or fuel and cooking equipment, duct tape (YES! Duct tape is a must!), rope, and never forget the matches!! I usually take a bunch of lighters and carry them in Ziploc bags in different places. Trust me, you do not want your field team to be eating cold food for two and a half months! This leads me to something I forgot to mention (and my advisor reminded me of), notice I said a ‘bunch of lighters’, not just one? Always take a spare, especially for items that are important for your work!! There are certain places in the Galapagos where you can head to do field work and find yourself in real isolation; it may take hours (and hundreds of dollars) for boats to get there, if an important piece of equipment brakes you’ll be glad to have a spare one!

Also, make your own plan of what to do in case something unusual happens or in case of an emergency and make sure everyone knows that plan. When the basics are covered, give yourself and your team a place to talk about the research each day. I usually break the group into two-people teams that go out and work all day to come back to camp before sunset. We may or may not have a cooking schedule (I’ve recently learned big groups alaways need schedules), but we usually eat dinner together, talk about how the day went and plan for the next day.

Some field experiences may be overwhelming, especially if it is the first time in a new place or leading a big group of people. You’re usually very busy and constantly planning for the next step… but I guess my best word of advice would be to stop and look around. I mean, really look around. You may be working with a single species but give yourself time to observe its surroundings, its habitat and its interactions with other organisms. Field work is a whole learning experience on its own, take advantage of it. And learn from others too, listen to other people’s ideas and suggestions; some people may surprise you with their creativity.


Lastly, know that things never go exactly as planned. When this happens, IMPROVISE!

Even if that means adding sea water to the rice because you forgot to bring the salt, holding your arm up next to the roof drain at 3am to collect rain water for cooking because they told you there would be water up in the hut and there isn’t, or brushing your teeth with noodle water. Aah! All the good things about field work!



About Mari Jaramillo: I am an Ecuadorian biologist and have been doing field work in the Galapagos since 2008. I began as a field assistant in different projects with PhD students from Australia and Germany. I eventually ended up working with Dr. Sharon Deem, DVM, and Dr. Patricia Parker in a project under the Wildcare Center for Avian Health in the Galapagos Islands of the Saint Louis Zoo. Then I was awarded one of the scholarships for two Ecuadorian students established by Dr. Parker, Dr. Hernán Vargas and The Peregrine Fund to complete a master’s degree working with the Galapagos hawk. My master’s project (at UMSL) studied the impacts of ungulate (mainly goat) eradication on the diet of the Galapagos hawk on Santiago Island. This project required me to lead big groups of people to an uninhabited island for long periods of time (up to 2 1/2 mo) and very hard work. For my PhD I switched back to work with avian diseases. I’d like to break down the disease dynamics of avian malaria in this somewhat isolated archipelago to understand which are the main players in transmission and what is its effect on the endemic avifauna. However, I return to Santiago often to lead field seasons for the long term monitoring of the hawk population run by Dr. Parker in collaboration with Dr. Vargas and others (GNP, CDF).

Getting your statistician side out of the closet

anxiety3Ecology is a science that demands from researchers a decent amount of mathematical thinking and good analytical skills.  To be fair, these are must have traits for all of us working in this data-rich era. Despite the obvious mathematical reasoning that comes with studying how organisms and populations thrive, interact and evolve, most ecology graduate programs don’t provide a formal mathematical training for students, thought advanced stats and programming courses are offered in most departments out there. I see this trend as a “lets go straight to what matters” type-of-strategy for learning and teaching analytical methods in ecology graduate programs – which works, but is this the best strategy? I believe the lack of a more traditional training on the basic stuff, such as algebra and probability theory, makes it really hard for early-career ecologists to get their statistics skills developing in a steep learning curve. Fortunately, there are ways to overcome that – and the sooner the better to start going around these limitations through working on improving math and programming skills.

As an ecologist ‘under development’, I believe the first way to get around the limitations in our analytical training is by losing the fear of math: in other words, get the puppy face off and go rough my friend, throw yourself in the mud, and have fun trying to walk on very slippery terrain until you become a pro at doing so. My inspiration for writing this post comes from my recent experience as an ecologist in an environmetrics conference: Graybill/ENVR Conference  – Modern  Statistical Methods for Ecology. The Graybill Conference is hosted every year by the Department of Statistics of the Colorado State University, and it’s a great opportunity to get to know people that are the actual developers of the statistical approaches we apply in ecology and evolution. Some topics discussed in the conference were hierarchical modeling, occupancy modeling, modeling spatial data, latent variable modeling, and estimating species diversity taking phylogenetics into account. As any other ordinary grad student in Ecology, I also didn’t receive a formal mathematical training, besides undergrad level calculus zillions of years ago. Hence, I definitely wasn’t able to understand most talks as thoroughly and completely as I (probably) would in an ecology-related conference. However, I was indeed able to scoop enough information that will help me to improve my work in progress–and that’s exactly what I was looking for. If you’re a grad student in ecology, and frequently find yourself trying to answer questions that would take advantage of a more advanced statistical approach, keep an eye on environmetrics meetings and workshops, as these might be a handy resource for you.

If this post inspired you, check out these links:

I’ll leave you with a remarkable quote from S. J. Gould in the book “The Mismeasure of Man”, which always inspires me to go beyond in my learning process, in an attempt to understand this beautiful thing called nature.

“We naturally favor, and tend to overextend, exciting novelties in vain hope that they may supply general solutions or panaceas–when such contributions really constitute more modest (albeit vital) pieces of a much more complex puzzle.”

Field work’s yin and yang, lessons from China

Following up our “Field preparation” series, Robbie Hart from the Missouri Botanical Garden in St. Louis gives us some extra advice on how to prepare for the unforeseen during your field time. Thanks, Robbie, for this great post!

Robbie Hart is a 7th-year Ph.D. candidate at UMSL. He’s spent about half of his time since coming to St. Louis away at his field site in Himalayan China, monitoring the effects of climate change on Rhododendron flowering time along a gradient 2600-4100 m above sea level. He’s now writing up his dissertation and working at the Missouri Botanical Garden, where he continues to focus on climate change impacts on high-elevation Himalayan plants. There’s more about his work, and some pictures of his field sites at


Planning is a feedback loop.

Having a set packing list is important when you’re traveling out of the range of Amazon 2-day shipping. Even more vital is a set methodology when you’re trying to collect data while exhilarated, exhausted, exposed to the elements, or all of the above. However, recognize that planning ahead, while essential, is uninformed by the potent realities of how things actually work in practice. Maybe you can’t actually sample 100 trunks without walking across a contested international border. Maybe the idea of a straight-line transect which seemed doable from the perspective of a map doesn’t seem as realistic when you’re staring down a cliff. Ultimately, you’ll never be able to plan perfectly for fieldwork until the project is actually complete, and the final product will always be a compromise between what you did and what you now know you should have done. Don’t fight it, because this is inescapable – just be a little flexible, a little firm, and find the point of compromise that works for your project.
There’s a book by Trevor Legget called ‘Zen and the Ways’, where he talks about two terms one encounters in Japanese martial arts: isshin and zanshin. I’m fairly certain I’m butchering them, but I see isshin (‘one-heart’) as a single-minded focus, an in-the-moment ‘zenning out’ on the task at hand. This is certainly how I get through the taxing or difficult periods of data collection in the field, and I think it’s true of others. There just isn’t another way to sit in a hailstorm for another four hours trying to write with frozen fingers, or to make it up that last mountain pass with a press full of collections on your back. Zanshin(‘remaining heart’) is a wider awareness, meta-level thinking about what you’ve done, why you’ve done it, and what you’re going to do.
Perhaps true samurai, or tenured faculty, can always maintain the right balance of isshin and zanshin. For me, it’s harder – it’s easy to get stuck in just getting the planned work done. Equally, it can also be a trap to constantly be questioning yourself or changing methods, and end up with data that’s not comparable, not efficiently collected, or not collected at all. I think it can be important to plan in times to stop and cultivate zanshin. In the evenings, or those break days that Leticia mentioned (in her previous post to the Naked Darwin), take some time over your well-deserved beer to evaluate and evolve your plans. During the work days, focus on getting things done, and file away those nagging doubts for the appropriate time.


Some rules of thumb which probably hold true no matter how your plan evolves
Back up your data. If you can’t get it in the cloud, make two or three digital copies and keep them in physically separated locations (keydrives, camera cards, etc.). If you can’t do that, make physical copies. You’re never going to get that year back if all of the data you collected during it goes up in smoke.

Don’t be afraid to ask questions. It’s a new field site, country, species, discipline, culture, method, or trail. Someone (or maybe almost everyone) knows more than you do. Ask for advice! I’m always scared to do this, and it always, always is worth it.

Don’t just take data, take metadata. Take much more than you think you need. Whether it’s in a fieldbook, or going through and putting tags on your photos, don’t underestimate your power to forget things in a day or a year. You *will* be grateful that you wrote down that person’s full name, detailed your custom designed sampling scheme, drew a map of where that nest is, or took a photo of your altimeter between every photo you took a photo of a species on your alpine transect. Data is your friend. Metadata is your friend with benefits.

Remember your limits, and those of others with you, and communicate about them. These aren’t always the safest conditions. Just because you can’t catch your breath and are feeling dizzy, doesn’t mean that the team member ahead of you knows that you’re getting mountain sickness. Alternately, just because you’re feeling tired but can totally make that last push to collect another sample doesn’t mean that everyone on your team can.


View from my rooftop on Yunnan, China

Yulong Mountain, Robbie’s field site

Rhododendron racemosum – 2800 meters above sea level

Rhododendron racemosum – 2800 meters

Rhododendron impeditum – 3800 meters

Rhododendron impeditum – 3800 meters

Courtesy of Robbie Hart.


Summer time, field work time: a beginners guide for a successful field season

I never valued summer enough before I started grad school in the US.  I come from a place where summer never goes away, and where changes in the rainfall make up the seasons. But nowadays, after some winters have passed, I get it , and I share the american obsession with the hot and shinny days.  

the notebook 9

All because, during summer, you can spend some time with Ryan Gosling at the beach…

weekend at bernies

or hang out with your buddies at Bernie’s…


and maybe even take some dance lessons…you never know.

But, if your are in grad school, summer time most likely means: Field work!

The reality of doing field work in the Caribbean - you gotta leave all that fun behind you.

The reality of doing field work in the Caribbean – you gotta leave all that fun behind you.

Field work can be one of the most inspiring, energizing, fruitful, and stressful moments of your research work. Here, I share some thoughts I gathered after some field seasons during my years in grad school.

If you are in the first year of your degree, and have just started a research project, chances are that you still have lots to define, understand and narrow down (including your questions and hypothesis). Usually, the field season that takes place in the first year is the one where you’ll rule out what can and cannot be done, as well as what can be improved in your research. The first planning strategy for a successful first field season is to always have at least two back up plans for everything, meaning that if plan A is your ideal scenario of how things will work, you should also have plan B and C for less ideal working situations. The second planning strategy that cannot be highlighted enough is: LISTS! You can avoid forgetting materials and equipments by retracing your work in the field several times, and listing everything you will need to get the work done. I usually bring some copies of the list of materials to the field, to make the organization on the way back easier. Third, have your methods very well clear for yourself, and for the ones that will work with you. Oh man…such an important detail that is frequently forgotten…specially if you’re coordinating interns for the first time. Have a data collection and annotation guide, and make sure that in the field, you and whoever you’re working with keep a copy of it (and shamelessly use it when needed). The last, but not least, advice is: prepare beforehand a detailed field schedule and stick to it – don’t forget to include rest days if you’re staying in the field for prolonged periods. The amount of days you’ll be able to have a healthy and efficient performance in the field depends from person to person, and on the type of field work, of course. Some people are ok and functional with working in the field for a long period of time. In my case, more than 30 consecutive days of waking up at 4 am, and working 15 hrs a day, usually don’t work very well. My ideal schedule is 15-20 work days followed by 1-2 days off.

After the field, organize the data as soon as you can, making a summary of effort and accomplishments. In my case, for instance, my field work involves mist netting birds, taking blood samples, and making blood smears. Thus, my field work summary consists of total captures per location and species, as well as detailed info on sampling location, and mist net hours (which gives me sampling effort, and also gives me an idea of my sampling efficiency). With the summary in hands, it is a good moment to ask yourself wether your project deserves a second field season or not. And, believe me, It’s OK if the answer is no – at this point drastic changes can be very beneficial – and better than sticking with something that has been tagged to failure. Reasons you should consider moving on towards something else can include: 1) overly expensive project for the amount of resources available for you; 2) excessively time consuming data collection (be realistic and think about statistic significance); 3) megalomania – oh yeah, there is a limit for what you can handle in the life-time of a PhD.

Like sex, jeans and hot yoga, field work only gets better with time – you become more efficient, more adapted to it, and more aware of your (and your project’s) limits. My final thought is: be a biologist, be an ecologist, be a naturalist, and enjoy your summers of field work. At some point in your degree summer time will mean lab work time, or data analysis time, or writing time…which are not bad, but cannot be done outdoors!

Good times during field work in the Caribbean. From left to right: Maria Pil, me and Bob Ricklefs.

Good times during field work in the Caribbean. From left to right: Maria Pil, me and Bob Ricklefs.