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: http://cdn.fansided.com/wp-content/blogs.dir/75/files/2013/07/snake-charmer.jpg

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-//static.panoramio.com/photos/large/100885070.jpg

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-//static.panoramio.com/photos/large/100885070.jpg

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: http://www.snaketype.com/wp-content/uploads/king_cobra_200-623x200.jpg

Just to prove that King cobras can also look cute! Picture from: http://www.snaketype.com/wp-content/uploads/king_cobra_200-623×200.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…

jaramillo2

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

jaramillo3

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.

jaramillo6

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 robbie.eugraph.com.


 

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 http://robbie.eugraph.com/photos/thesis

Rhododendron racemosum – 2800 meters 
http://robbie.eugraph.com/photos/thesis

Rhododendron impeditum – 3800 meters http://robbie.eugraph.com/photos/thesis

Rhododendron impeditum – 3800 meters
http://robbie.eugraph.com/photos/thesis

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…

Dirty-Dancing-the-80s-19478090-400-323

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.

Herpes viruses got a friend: Helminth parasites can promote the reactivation of latent viral infections

In a fascinating story about co-infections and co-evolution, helminth parasites play a role in a two-signal reactivation pathway of latent infections of herpes-like viruses. 

The helminth Heligmosomoides polygyrus can re-activate latent herpes viruses through the modulation of transcriptior factors and inhibition of anti-viral cytokines. Photograph by Constance Finney.

The helminth Heligmosomoides polygyrus can re-activate latent herpes viruses through the modulation of transcriptor factors and inhibition of anti-viral cytokines. Photograph by Constance Finney.

We all know at least one person who has exhibited the signs of an infection by herpes viruses, as well as their complaints about how this inconvenient infection might re-occur after long dormant periods. In fact, more than 90% of the human population is accounted to latently carry viruses of the herpes family. Although most research on disease mechanisms and host immunity have focused on one-host-one-parasite systems, most vertebrates are known to carry a vast community of parasites, that can behave much like herpes viruses do, alternating between latent and active phases. There is evidence that parasites can interact when in co-infection, however little is known about the precise mechanisms through which these organisms deal with each other when exploring a common host.

In a study published this month in the Science magazine, researchers investigate how helminth parasites influence the end of the latency stages of herpes viruses in murine rodents. The researchers experimentally infect rodents with a herpes-like virus modified to express luciferase – a bioluminescent enzyme that can be used to track the viral replication inside the host. Then, they challenged the same rodents with infections of two different types of helminths, Heligmosomoides polygyrus and Schistosomiasis mansoni, and found out that both parasites promote viral reactivation. Interestingly, the helminths elicit viral ‘awakening’ through a cascade of cell-mediate immunity that starts with the activation of lymphocytes Th2. Once activated by helmintic infections, Th2 cells produce IL-4, which is the crucial factor on the re-activation of herpes viruses. The exit from the latency state is dependent on the expression of one viral gene (gene50), and such expression relies on the bond of a single signaling molecule to gene50. The misfortune of the host and the beauty of co-evolution come from the fact that IL-4, which synthesis is a product of the helminth presence, is the the activator of this one signaling molecule that promotes the expression of the gene necessary for the ‘awakening’ of the herpes virus. Also, IL-4 not only promotes viral gene expression, but also blocks the activity of anti-viral cytokines. Hence, the viruses only exit the latent state when the host immune system provides an ideal medium for their proliferation, by both stimulating viral re-activation and inhibiting anti-viral immunity – all thanks to helminths parasites. What a fine example of co-evolution and organismal adaptation! 

How helminths go viral: Helminth infection activates TH2 cells to release IL-4 and IL-13, both of which ligate the IL-4 receptor (IL-4R) on M2 macrophages. In M2 macrophages harboring latent herpesvirus, the IL-4R activates host cell STAT6, which then acts directly on the key viral gene that initiates viral replication. Figure and caption adapted from Maizels and Gause 2014.

How helminths go viral: Helminth infection activates TH2 cells to release IL-4 and IL-13, both of which ligate the IL-4 receptor (IL-4R) on M2 macrophages. In M2 macrophages harboring latent herpesvirus, the IL-4R activates host cell STAT6, which then acts directly on the key viral gene that initiates viral replication. Figure and caption adapted from Maizels and Gause 2014.

Reese et al, 2014. Helminth infection reactivates latent γ-herpesvirus via cytokine competition at a viral promoter. Science Vol. 345 no. 6196 pp. 573-577.

Males can be the fragile sex for Leishmania parasites: sex-biased disease incidence in human populations of central Amazonia

When it comes to sex differences on the incidence of cutaneous leishmaniasis, male bias can exist even when exposure time is comparable among men and women.

Cutaneous leishmaniasis is a vector transmitted disease characterized by skin lesions that develop near or at the bite site of the vectors. Image from http://upload.wikimedia.org/wikipedia/commons/c/ca/Cutaneous_Leishmaniasis.jpg.

Cutaneous leishmaniasis is a vector transmitted disease characterized by skin lesions that develop near or at the bite site of the vectors. Image from wikipedia.

Cutaneous leishmaniasis (CL) is a tropical neglected disease that occurs in Central and South America, as well as in some regions of the African continent and the Middle East. Ulcerative lesions that develop at or near the vector’s bite site typically characterize CL, which is caused by parasites of the genus Leishmania, and transmitted by phlebotominae sand flies. According to the World Health Organization (WHO), in 2013 there were almost 100 thousand new cases reported all over the world. CL is considered a neglected disease because its mitigation receives less effort than it should, since the disease does not cause mortality. However, individuals presenting sings and symptoms of CL usually live in impoverished regions, can suffer from social exclusion because of the cutaneous nature of the lesions, besides having do deal with a medical treatment that can cause severe and debilitating side effects.

Cutaneous leishmaniasis incidence is lower among females, even when exposure time is comparable between sexes. This suggests the influence of endocrine-related immune factores, which make females better equipped agains parasitic infections. Image: Bettmann/CORBIS

Cutaneous leishmaniasis incidence is lower among females, even when exposure time is comparable between sexes. This suggests the influence of endocrine-related immune factors, which make females better equipped against parasitic infections. Image: Bettmann/CORBIS

In South America, the disease cycle is mainly sylvatic, meaning that humans are accidental disease hosts. Generally, in forested areas, sand flies would feed on sloths, armadillos and other small mammals, and humans would get occasionally infected if they were exposed to habitats where both vectors and wild hosts are found. Since men are usually the ones that engage in activities that involve being in contact with habitats where transmission is likely, such as hunting and logging, disease incidence tends to be higher among males than their female counterparts.  However, experimental infections in mice has also revealed that females, not only tend to develop the disease less often than males, but also present less severe lesions when clinical symptoms are present. Hence, one can ask whether male-biased disease incidence is solely due to differential exposure or is also a consequence of sex-related differences in the immune ability to cope with Leshmania spp. infection.

That was exactly the question I tackled for my MSc thesis research in the Instituto Nacional the Pesquisas da Amazônia. The study was just published on line in the journal Tropical Medicine and International Health, in which we investigated whether sex-biased CL incidence levels off when exposure time to CL vector habitats is comparable among sexes. We compared disease incidence between two populations from central Amazon: one composed by rural settlers, where exposure is male biased; and other composed by field researchers of the Biological Dynamics of Forest Fragments Project, where both males and females are similarly exposed to forested environments. Interestingly, at low levels of exposure disease incidence is higher among males in both populations, suggesting the existence of a sex-related and endocrine-mediated immunity against these parasitic infections. However, as exposure time increases, this suggested effect of higher immunity among females wears off, and disease incidence becomes comparable among sexes. Another relevant finding was that CL incidence among field researchers is eleven times higher than among rural settlers, which brings to attention a new disease risk group that deserves awareness.

This study was advised by Dr Gonçalo Ferraz, and co-advised by Dr Fernando Abad-Franch, in a collaboration between the Instituto Nacional de Pesquisas da Amazônia (INPA), the Biological Dynamics of Forest Fragments Project (INPA/Smithsonian Tropical Research Institute), and the Instituto Leônidas e Maria Deane (FIOCRUZ-AM).  I am very grateful to all of those who answered my epidemiological questionnaire and made this study happen!

Soares, L., Abad-Franch, F. and Ferraz, G. (2014), Epidemiology of cutaneous leishmaniasis in central Amazonia: a comparison of sex-biased incidence among rural settlers and field biologists. Tropical Medicine & International Health. doi: 10.1111/tmi.12337

Careers in Biology: Curators, what they do and how they do it

What is the role of curators in herbariums and museums? Do curators have to do research? Do they apply for grants? How stressful is their job?  These and more questions will be answered in this post of Careers in Biology, in which Dr. Charlotte Taylor explains her job as a curator of the Herbarium in the Missouri Botanical Garden (MOBOT). The summary presented here was prepared by our guest blogger and PhD student Haydée Hernández, with contributions of the UMSL grad students Priya Maharaj, Vona Kuczynska and Alicia Marty.

In this column of The Naked Darwin, you will find interviews with outstanding professionals that have devoted their careers to different fields of Biology. Here, they share their expertise in their career, and we hope our readers can gain from the knowledge and advice they will share. The interviews are performed by students from the University of Missouri-St Louis, who are taking the seminar “Careers in Biology” offered by Dr. Parker.

 

WordCloudCuratorsDr. Charlotte Taylor’s research focus is in floristics and systematics of Neotropical and Malagasy plants of the family Rubiaceae. This interview session with Dr. Taylor was particularly exciting, because although most people have visited museums and botanical gardens, few know what happens behind the scenes. Curators are important personnel of these interesting places. They are the managers of the herbarium’s (or museum’s) collections and are content specialists that are responsible for species identification and the species’ geographical data. This interview was, therefore, a good opportunity to learn more about their job.

Dr Charlotte Taylor is a curator of the Missouri Botanical Garden (MOBOT). Photo by Kate Lawless, MOBOT.

Dr Charlotte Taylor is a curator of the Missouri Botanical Garden (MOBOT). Photo by Kate Lawless, MOBOT.

Can you walk us through a typical day as a curator? For example, the percentage of time spent in the field, in the office, or in educational outreach.

” I first start by taking my morning coffee, this is essential. My main duties are the identification of plant specimens, description of new species and taxonomy.”

Dr. Taylor also assists people from the different places in the tropics with specimen identification and verification. For instance, she recently received 150 boxes from a “blank area on the map” (a place that has been poorly explored), in this case the MOBOT Peru Project, filled with plant specimens that need to be identified. After identification, the next step is to compile the species data in a database for analysis. Geographical, community diversity and composition analysis are a few things that can be done with the data obtained. Dr. Taylor works closely with different personnel to perform these analyses, such as ecologists and conservationists working at the MOBOT. She also does field work, which can be either mind numbing or exciting, depending on the project and the location.

She explained that the main output of the work as a curator highly depends on the mission statement of the institution you work with. In the case of the Missouri Botanical Garden (MOBOT), it relates to field exploration, research and conservation. Other museums allow curators to do their own independent research.

We previously had a talk given by Dr. Kellogg regarding project funding. How does the gathering research funds process work when you are a curator?

A MOBOT curator is responsible for a project, such as organizing flora or doing surveys of an ecological area, which is funded by the Institution. Yet sometimes curators can be responsible for the funding of the project, which means writing up proposals. Depending on the institution, curators will run projects in which they are interested. This is indeed very important, because institution-wide projects often have large grants or institutional funding, but smaller personal projects require curators to obtain their own funding through grants. At the MOBOT, Dr. Taylor has a specific set of duties that do not require her to apply for grants, but she has the option to apply for grants for her own research. She usually spends 10-20% of her time writing up grant proposals. However, there is much more pressure for grant writing in other museums, where the primary mission is cutting edge research and publications. Dr. Taylor has applied for and received her own funding in the past, and this has allowed her to manage her projects as she likes.

QuotesCover-pic78

How about fieldwork and traveling as a curator?

 According to Dr. Taylor, young scientists working in the country where the samples are being collected primarily do the majority of fieldwork. Scientists and curators from the museum will occasionally travel and work alongside other field workers.

 In your job, how do you share your findings of new species and their locations?

 She writes as many papers as possible for publication in scientific journals, regarding the new species found. The MOBOT does a great job in terms of sharing information: TROPICOS is the MOBOT’s database that is used to upload project data on specimen information, literature references, and images. TROPICOS used to be an internal database, but has now become publicly available (you can access it at www.tropicos.org), and it is also used within the MOBOT to verify information from outside sources and ensure data accuracy.

How about innovations in the type of Museum work you do?

 Dr. Taylor expressed the need to integrate new technology into the museum work. Currently they use high-resolution scans, which are magnified, copied and printed, and then are used as reference in the museum. New positions are occasionally created for database work, data analysis, GIS work, and predictive modeling. These types of positions require plant/biological knowledge, as well as specific technical skills.

 Does one need a MS or a PhD degree to become an entry or senior level curator?

 Entry-level personnel are usually assigned specific topics consistent with their expertise, typically from their graduate research. A Ph.D. is required as a tool for projects that require heavy outside funding, even though people holding MS or BS degrees also work in other capacities in these projects. For example, individual projects have research assistants that help in data processing, specimen handling and identification and some may even have smaller projects; these assistants may have BS or MS degrees.

 What are the criteria for advancement?

 She explained that unlike other jobs, in Museums there is not much competition, and likewise little room for advancement. There are assistant curators, then associate curators and finally [full] curators, and in some institutions, senior curators. Advancing to the next level typically happens with time and may not always come with a salary increase. Other people can also switch to more administrative roles or take a position at a University.

What is the typical salary range (entry and senior level)?

 Salary can range from about US$30,000 to as high as US$250,000, with an average of US$40,000-60,000 per year. Some museums offer tenure positions, and generally administrative positions are higher up on the pay scale than curators.

QuotesCover-pic82What is the job security like as a curator?

Many people stay within the museum for life, and because of this, there is generally a low turnover rate in these positions. However, this depends on the institution. For example, in a sister organization, personnel in the molecular section have been denied tenure for not securing grants and publishing. Publishing may not always be mandatory, but Dr. Taylor views publications as her form of success and tries to publish as often as possible.

 How do you determine a curator’s productivity?

 Productivity is mainly in the form of publications: such as floras, identification guides and papers in scientific journals. In her job, the samples she receives are mainly from previously unexplored areas; this allows her to publish papers on approximately eight or more new species per year. However, Dr. Taylor estimates that she discovers 20-30 new species each year, but the publications associated with those sometimes require more time than what she has available.

 

How long does it take you to become an expert in the field?

 This is not something that happens quickly. It took her about 20 years before she got a handle on her area of expertise. She started out with relevant knowledge, and slowly learned more throughout her career and gradually became more comfortable and confident with her results, and identifying specimens quickly.

 How demanding is your job?

 She believes it is not as high pressure as a University setting. However, you have to learn to pace yourself because there is a lot of work, and there are no large breaks such as spring and summer vacation. Many curators work on weekends and devote extra time to their personal research, but you can limit yourself to 40 hours a week if you want.

Finally, to all readers out there, if you find yourself interested in pursuing this career and want to get some hands-on experience, Dr. Taylor shared information regarding volunteering at the Missouri Botanical Garden.

First of all, she explained that this requires a commitment of regular work, from two hours up to a full workday in the museum once a week. Interested persons can contact the volunteers’ office and they are matched with personnel according to their interests. Another possibility is to directly contact Dr. Peter Hoch, MOBOT Graduate Director, and he will spread the word to people who are looking for a volunteer. Another option for you is to directly contact a curator by finding their information on the MOBOT website. http://www.missouribotanicalgarden.org/

I hope this has provided you with useful details into the life of herbarium and museum curators. As you read, one of their main duties is species identification, but they are also able to do their own research, and although they do not travel much, they can visit the sites where the species come from and collaborate with other professionals such as ecologists and conservationists. What do you think about this choice of career? Is it for you?

me

 

About Haydée Hernández: I am a PhD student at the University of Missouri-St. Louis in Dr. Robert Marquis Lab. My main interests are ecological interactions and their role in community structure. I believe that pollination and herbivory are fascinating processes that are able to change ecological communities. I also enjoy reading and delving into the fascinating worlds that books can provide.