Tuesday, January 05, 2010

Story behind the science: #PLoS Biology paper on cichlid vision evolution

I am continuing on a new theme here in trying to get author feedback on recent PLOS publications.  Today I write about a recent paper on PLoS Biology "The Eyes Have It: Regulatory and Structural Changes Both Underlie Cichlid Visual Pigment Diversity" by Christopher Hofmann, Kelly O'Quin, N. Justin Marshall, Thomas Cronin, Ole Seehausen and Karen L. Carleton

This paper discusses "how changes in gene regulation and coding sequence contribute to sensory diversification in two replicate radiations of cichlid fishes." A good overview of the paper is in an accompanying article "Visual Tuning May Boost African Cichlid Diversity" by Robin Meadows:
"African cichlid fish form new species faster than any other vertebrates, with hundreds of species evolving within the last 2 million years in Lake Malawi and within the last 120,000 years in Lake Victoria. This rapid speciation makes cichlids good models for elucidating the genetic mechanisms behind biodiversity. Vision may play a key role in cichlid evolution, adapting them to forage for new foods or colonize new habitats. Vertebrate retinas have two groups of light-sensitive proteins called opsins: those in rod photoreceptors, which are sensitive to dim light, and those in cone photoreceptors, which are sensitive to color. Changes in the visual system could be due to differences either in the expression of opsin genes or in their DNA sequences. A Research Article in this issue of PLoS Biology by Christopher Hofmann and colleagues suggests that both mechanisms underlie changes in visual sensitivity in cichlids."
For more on the science, see her summary and see the article itself. Additional information can be found in the press release from U. MD

But what I wanted to cover here was some of the story behind the science.  So I emailed the authors some questions which they were kind enough to answer and I post the details here. There are some really interesting tidbits in these answers in my opinion, including how they dealt with merging two papers into one, and how difficult (but fun) it is to do this field work in Lake Malawi.

1. What led you to do the study reported in the paper?

From Karen Carlton:
This study was a long time in the making.  We started studying the visual system of cichlids in the 1990’s.  We learned quickly that there was a lot of variation in opsin expression within the Lake Malawi species.  However, we had only examined a few species.  In 2005, Tom Cronin and Justin Marshall (world experts on aquatic visual systems) agree to come to Lake Malawi with us and help examine a greater number of species.  Justin brought his underwater spectrometer and characterized the light environment.  Tom and I measured fish colors (that paper is under review) and I extracted retina for quantifying gene expression.
Because Lake Malawi and Lake Victoria both contain large cichlid radiations and had such different light environments, Ole Seehausen and I started working together in 2000 to compare visual systems in Malawi and Victoria.  (Ole is the world expert on Lake Victoria cichlids, having helped discover the large rock dwelling species flock that escaped the devastation of the Nile perch). We concentrated on opsin sequences in our previous publications.  However, we wanted to look at gene expression as well.
I was fortunate in 2006 to move to U Maryland where Chris Hofmann and Kelly O’Quin joined in our efforts.  Chris took on the Victoria cichlid gene expression based on samples that Ole had collected.  Kelly became our statistical wizard and analyzed the Malawi data we had gathered.  (He has also been working on the visual system of Tanganyikan cichlids, which are the ancestors of the Malawi and Victoria flock.  This work has recently been submitted).
From Kelly:
I see Karen gave you a nice review of how this paper was started.  As she said, the work was started before I joined her lab.  At that time, we were primarily concerned with moving into the new lab at UMCP, so no one was actively working on the data set.  I initially analyzed the data to practice for a similar study of Tanganyikan cichlids.  But, as I learned more about the power (and pitfalls) of the comparative analysis, I became more and more involved with the actual analysis and discussions, and after about 6 months Karen asked me to write up the paper for the Lake Malawi data set.  At the same time Chris was working on a manuscript for the Victorian data.  After seeing the overlap in the two papers -- really the similarities and differences -- Karen and Chris and I decided it would be useful to put the two together.
2. How did this group come together, with people from Australia, Switzerland and Maryland?

From Karen:
Vision science is a small international community that is wonderfully supportive.  The cichlid community is also small and makes for excellent collaborations.  This is what makes research great – combining expertise from such a diverse group of people.  This enables us to think across many disciplines from physics to biology and integrate light measurements, ecology, molecular biology and genetics to try and understand what drives cichlid visual communication and determine how it plays a role in speciation.
From Christopher
I would add that both Europe and Australia have some top people in the field of visual ecology.  Also, I don't think we could have had a paper with such a broad scope without our collaborators.  Once we all got together things just kept building and was very exciting.
3. A question for Kelly -- how do you feel about the "joint contribution" statement.  Do you think there needs to be a system to truly list two first authors or do you think this statement will suffice? 

From Karen
I feel like I should chime in here.  We originally had written two separate papers with Chris as lead author on the Victoria data and Kelly on the Malawi data.  However, we all felt a combined paper could be more powerful.  I asked Kelly and Chris to combine these papers, though that was a very difficult thing to ask, particularly in these times of first author is best.  However, this paper is truly the joint effort of these two as well as the rest of the authors and would not be the paper that it is without everyone’s contributions and perspectives.
From Kelly
It is nice to be recognized for the work and effort given, and presumably this is accomplished in the 'Author Contributions' statement as well as the order in which authors are listed in.  For this paper, Chris and I each authored manuscripts that Chris had to painstakingly combine.  After a lot of debate over the meaning and limits of our comparative results, we each wrote a new drafts of the combined study that Karen then resolved into a single manuscript.  Tom, Justin, and Ole provided lots of  comments and additional text throughout this process as well.  This truly was a collaborative effort, with plenty of contribution and compromise on everyone's part.  Although the order in which the author's are listed cannot possibly communicate all of the nuances involved (though I am certainly happy with the order given), I hope we were able to addressed them with the 'joint contribution' statement you mention, as well as our 'Author contributions' statement (which lists just about every author under each category).
In short, I don't think a simple change to the way that we list authors will ever capture all of the individual and combined efforts that go into a study.  Instead, I think we need to change the way we read and interpret that list.
4. How did you end up choosing PLoS Biology as a place to submit the paper to? Were there any debates among the group about publishing there?

From Karen:
Online journals, such as PLoS Biology, give us a lot of flexibility to include all the supporting data without limiting the length of the paper.
From Kelly:
Since we had essentially two large studies here, the generous space and supplemental information limits allowed by PLoS made it a natural choice to publish in.
5. Do you have any good stories about the field work?  

From Karen:
Field work in Malawi is never dull.  Getting there is the first problem.  It is a 24 hr plane ride if all goes well (which it never does) plus a 5 hr drive down to the lake, partly on Malawi dirt roads.  Once you get there, however, the lake is a beautiful place.  The diving is about the best in the world and it is wonderful to immerse yourself in your organism’s habitat.  Underwater, it is wall to wall fish, with 50 or more species in a single location so it is perfect for observing and collecting a wide diversity of species.
The field station is run by the University of Malawi. It is right next to Chembe village and the people there are incredibly warm and friendly.  The research station has electricity and cold running water.  This is very high living for the village and makes for an interesting dichotomy.  Several of the villagers are experts on cichlid fish, including Richard Zatha, and they dive with us.  They can catch fish far faster than we can. There is considerable wildlife including the baboons which like to come into the house and steal bread off the table.  We were fortunate in not having to deal with hippos or crocodiles on either of our recent trips.
It is quite expensive to take a group to Malawi.  However, it is essential for everyone to see their organism in its natural habitat.  It also takes a lot of preparation as well to get a group of scuba divers certified and ready to do this kind of field work.
I’m sure Ole has comparable stories for his work in Lake Victoria.
From Christopher:
To build on what Karen said.  Going to Lake Malawi and actually diving with the fish is an incredible experience.  When we work in our aquaculture facility we have maybe a handful of fish from a few different species in a single tank.  In the field, once you drop below the surface it is an entirely different world.  There are literally hundreds if not thousands of fish from many different species all doing their own thing.  Some are eating algae, others plankton and even other fish.  Many of these species are ones that are impossible to keep or breed in captivity, which makes the challenges of getting there worthwhile.
From Kelly:
Not really other than to say that it is a lot of hard work.  But if you like SCUBA diving in remarkably clear water with beautiful, colorful fish, I can't think of a better place to work than Lake Malawi.
6. Can you provide links to web sites of the authors and or other links of interest such as videos of the fish, twitter pages, etc?
7. Anything else you want to add:
From Christopher:
I would also add that its not easy to catch fish in Malawi.  There is a definite art to scuba diving and handling a net.  Having local cichlid experts was invaluable.
Cichlid picture by Christopher Hofmann doi:10.1371/journal.pbio.1000267.g001


Meadows, R. (2009). Visual Tuning May Boost African Cichlid Diversity PLoS Biology, 7 (12) DOI: 10.1371/journal.pbio.1000267

Hofmann, C., O'Quin, K., Marshall, N., Cronin, T., Seehausen, O., & Carleton, K. (2009). The Eyes Have It: Regulatory and Structural Changes Both Underlie Cichlid Visual Pigment Diversity PLoS Biology, 7 (12) DOI: 10.1371/journal.pbio.1000266


  1. Hi Jonathan. Thanks for this. Often it seems like scientific publications can be a bit lifeless. It's good to see how a study and a publication developed over time.

    I hope you can continue this.


  2. Laura -- am hoping to figure out a way to formalize this and start a system where we could do this for all papers easily ---

  3. That's a great idea. I always wished for a bit more context to publications when I was reading them as a graduate student. In fact, I don't see that changing just because I'm now a postdoc! This seems like a good use of journals' online resources.

    Not sure if I can help, but I'm glad to do so.


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