Unisexual Ambystoma

Unisexual Ambystoma

Thursday, August 7, 2014

First publication from SciFund support

The reason I started this blog two years ago was to connect to those who helped fund my science through the SciFund Challenge. Crowdfunding has come a long way, even since then, and I hope that my funders have been able to check back time and again to see how my PhD is progressing. However, after the t-shirts were sent and the thank-yous were written, I haven't shown much about the salamander for for which I was so graciously supported by a group of science-loving citizens.

One thing that is difficult to appreciate about science: it takes a long time. Creating new knowledge is tough. From generating new ideas to collecting and analyzing large amounts of data to having your work evaluated by your peers, even small projects can take years until the product of all that work is produced. 

I'm thrilled to finally have the first scientific publication resulting from crowdfunded support officially in press. The paper is titled "Evolutionary basis of mitonuclear discordance between sister species of mole salamanders" appeared in volume 23 (issue 11) of Molecular Ecology. If you take a look at the acknowledgements at the end of the paper, there is a specific sentence where I send my thanks to all of those who funded my work through SciFund. How cool is that!

The data that was collected for this project was done while I was in the field working on the Ambystoma dispersal project, and my Scifund support was much appreciated during the associated travel across the state of Ohio.

So, that sounds nice, but what is the science?
One thing we noticed when looking at the salamander samples that we had from all across Ohio: some of the species of salamander were showing up in weird places. Particularly, these two sweethearts:



The salamander above on the left is only found in the very southwest of Ohio and is mostly located in Eastern Kentucky. The reason? The Streamside Salamander loves to breed in small streams that don't have fish. In contrast, the Smallmouth Salamander, which is found over most of Ohio and across a wide part of the central United States, only lays its eggs in ponds and other wetlands that aren't streams. 

Here are some of the areas we find these two salamanders ("sympatry" just means they are found in the same county):

BUT, when we used DNA to identify the samples we had from across Ohio, we identified many animals as Streamside Salamanders that we were almost sure were actually Smallmouth Salamanders. 


See all that green in the middle of Ohio? That didn't seem right.

We found these animals in ponds (not streams) and they were well outside of the above range of Streamside Salamanders. Since we only had DNA samples, how could we figure out what was going on?

Because we were using tiny pieces of DNA from the salamanders' mitochondria, there were three main explanations for this unexpected pattern:

The kidney bean thing is suppose to be a mitochondria!

So, we could be observing 1) a misidentification of the central Ohio salamanders or 2) the presence of mitochondria from one species inside the other species (weird!) or 3) hybridization between the two species.

We used DNA collected from both the mitochondria and nuclear DNA of salamanders from all across the state to show that mitochondria inside of the Smallmouth Salamanders in central Ohio are invaders from the Streamside Salamanders, a biological process called mitochondrial introgression

Mitochondrial introgression happens when two species hybridize at some point in time and the mitochondria that comes from the female of one species becomes abundant in the other species, either by natural selection or random chance. As strange as it sounds, the phenomenon is well-recognized and has been identified in a diverse group of animals. 


So why is our publication important? 
First, we solve the mystery of finding salamanders with strange DNA by using a bunch of different genetic techniques. Our methods show the pros and cons of the different ways that scientists have tried to study mitochondrial introgression in the past and provides a guide for how to use these techniques.

Yellow-Rumped Warbler
Second, we took a look at all of the locations where we find salamanders with mismatched mitochondrial DNA and found that these wetlands are located in places with significantly higher rainfall during the spring and summer. This could be a sign of an adaptive link between the foreign mitochondria and a wetter environment.

Making the links between patterns of foreign mitochondria and their adaptive advantages is important and finally becoming common. Other recent publications like ours have shown both advantages (in Warblers) and disadvantages (in Long-Toed Salamanders) to having an introgressed mitochondria. Using genetic information, scientists are finding out what evolutionary processes are happening hidden from sight inside the animals of our backyards. Pretty neat.

Long-Toed Salamander






























Thursday, June 26, 2014

Three things from Evolution 2014

I just got back from Evolution 2014, a scientific conference for those who study all aspects of organismal evolution. The conference was held in Raleigh, North Carolina, and I had an absolute blast during my first time at Evolution.

One of my favorite events was Saturday's Evolution film festival. A bunch of short films created by scientists and science educators were screened to a rowdy audience. There were a lot of laughs and nerdery-induced groans. My favorite film ("Dinosaur", below) was catchy and cute, where others varied from humorous explanations of evolutionary principles to fantastic visualizations of scientific studies. You can see all the videos here (some of my favorites include "The Genetics of Mouse Burrowing", "Selfish Gene", and "Drift").


Dinosaur from Lori Henriques on Vimeo.


Here are my biggest takeaways from Evolution 2014:

1. A modern evolutionary biologist needs A LOT of skills. Many presentations I saw described projects that required fieldwork to collect samples (sometimes across continents or the entire globe), laboratory skills to collect huge genetic data sets, bioinformatic techniques to curate and analyze that data,and enough knowledge/perspective to fit conclusions into a rapidly-changing body of knowledge. I tend to perceive a typical PhD student in my field 25 years ago as having a very specific niche, whether that be a certain study organism or a particular technique to collect/analyze data. Based on chatting with other scientists-in-training, a pressure to "do it all" is noticeable, with most students feeling like field, laboratory, and bioinformatic skills were all necessary to get a job.



2. A modern evolutionary biologist needs collaboration. That being said, no one can do it all. That is why I saw (and participated in) so many lunch, dinner, and "quick we have twenty minutes to chat" meetings. Finding other scientists and labs that have experience with what you are interested in isn't hard, and most of the time these folks are thrilled to brainstorm and provide advice. This meeting was a reminder of how much our lab interacts with others around the world and how invigorating these connections can be.


Google "Bad scientific posters" for yourself
3a. Speaking of skills, where are the communication skills? Far and away my biggest complaint about scientific conferences in general is a lack of clarity in communication. At my first few conferences, I struggled to walk through a session of poster presentations and actually learn anything. This caused me to doubt that I was really smart enough to keep up with the rest of science. As I've come to learn, scientists generally have a hard time following some basic rules about communication (for instance, simplify your message and never use comic sans). There is a multitude of potential reasons for this, like a perception that simplicity equals laziness or a lack of understanding. 

Just so you don't think I'm too cocky about visual communication, here is the poster I prepared for Evolution 2014. I've got a lot to learn too!
Even though Evolution showcased some of the most exciting science happening right now, that science was sometimes much to difficult to access (even for other evolutionary biologists!). A 15 minute browse through Dr. Zen's Better Posters blog would have made my brain ache a little less at the end of the night. I will continue to be a proponent for better visual presentation of science, even if at the continued annoyance of my lab mates.



"TWEET"
3b. Speaking of communication skills, some people have them in spades. I saw a lot of great talks from established scientists that demonstrated how powerful good communication skills are when in the hands of gifted minds. For example, Dr. Steve Jones was the recipient of this years' Stephen Jay Gould Award and gave an engaging talk about his career with snails using both art and science. I was inspired by a whole bunch of talks like his.

Also, this meeting was easily the most aware of social media technology of any I have attended. Couldn't make a talk? Need a restaurant recommendation? What posters should I swing by? Just go check the Twitter feed! There was so much Twitter participation at this meeting, and it definitely added something extra for me. I used my own Twitter account to participate, and I look forward to using the spike in blog views and Researchgate publication downloads that resulted as evidence for why tools like Twitter can help you share your work effectively!

Here is a great summary (via The Molecular Ecologist) of the tweeting that was happening and here is a great collection of tweets from the meeting organized by Morgan Ernest (check out her blog, Jabberwocky Ecology too!).


Overall, I can't wait until next time! Now I should get back to making a list of all the new ideas I need to try.








Thursday, June 19, 2014

Small rattles, big personalities

In the dark recesses of Aronoff laboratory, many are surprised to know that our lab has an entire room filled with rattlesnakes. In fact, most visitors don't believe us until we show them. Behind a plain, gray door lives a group of dusky pigmy rattlesnakes (Sistrurus miliarius barbouri). This group of animals has been one of the main sources of data for our lab's efforts in studying pit viper venom and how it relates to these animals diets and behavior. This work is currently being done by our principal investigator, Dr. Lisle Gibbs, and current PhD student Sarah Smiley. 

Right now, one of our undergraduate students (Hardy Kern) is finishing a project examining how these snakes, which have been eating the same type of food for months (either mice or frogs), differ in their interest in other food items. Since some of the snakes were born in the lab, the question is pretty simple: do these animals prefer the only food they've ever known or do they have a preference? I'm sure Hardy will come by at some point to write about his project here, but until then I thought I'd share some photos of the pigmy rattlesnakes that we took as part of Hardy's graduation gift from the grad students. 

The photos show these venomous snakes as we see them: beautiful, gentle, and curious animals.



























If seeing snakes in their natural habitat is more your thing, here are some photos of pigmy rattlesnakes we found last summer during a lab trip to Florida:
































Wherever you see one, these reclusive snakes are always a treat.



Friday, February 28, 2014

Scenes from the OSU Museum of Biological Diversity Open House

Earlier this month, I was happy to again participate in the Ohio State Museum of Biological Diversity Open House, our department's biggest outreach event. We had more than 2,200 visitors from all parts of Ohio and elsewhere. This year, Matt Holding and I teamed with two fantastic undergraduates who work in our lab (Meghan Parsley and Paul Hudson) to go even bigger than we did last year. Since this year's theme was all about how scientists use technology to discover and classify biodiversity, we put together a booth that showed visitors how our lab uses technology across all aspects of our science, from catching animals to analyzing their DNA.

We had an absolute blast at this event. Apparently, so did a whole bunch of other people!

Here are some photos I took frantically between showing salamanders to (big and little) kids:


































And here are some photos of our booth, some of our materials, and some of the great visitors we met!





 


























At the end of the tables, we had a few animals on display that showcased some ways that DNA can reveal biological differences between organisms. Included among these animals was the eastern glass lizard that we brought back from Florida last year, and I was astounded at the number of kids that could immediately identify it! The little "flip quizzes" at the end of the booth sparked a lot of discussions with both adults and children.





 

This is a great event and I highly recommend it if you are a local. All the faculty, staff, and students are so excited to meet the citizens of Ohio and share their passion. For more pictures and information, I'd recommend the Museum of Biological Diversity Facebook page here.


Monday, February 17, 2014

Who Works 80 Hours a Week in Academia?

Part of being a graduate student is working hard. Whispers of disappearing faculty positions and decreases in funding percentages are heard at most social gatherings. You have to be in the lab 80 hours per week to stay at the front. Right? In this really good blog post, Dr. Meghan Duffy (follow her on twitter here!) presents her argument for why the myth of the 80 hours/week = success equation is pretty silly. 

When I read Dr. Duffy's post a few weeks ago, I had already been intensely thinking about the way I work for about a month. After reaching doctoral candidate status in the fall, I realized that I had a lot of irons in the fire. I also realized I had no real grip on how I spent my time. I knew I was working and I knew I felt like I was working hard, but I needed some more information about my habits. Ya know, data.

So how does a PhD student spend their time? Well, I've been diligently logging all of my work hours since January 14th. I'm no Steven Wolfram, but I put this app on my phone and set up six categories of my work: 
  • General Work: a catch-all for emailing, running small errands, generally finding journal articles, etc.
  • Meetings: anytime I was sitting in a meeting for the lab, the department, or other research activities went here
  • Thesis Research: any activity related to thesis research
  • Other Research: any research, including educational research, that doesn't directly apply to the ol' thesis
  • Outreach Activities: this included both things outside of the university (giving a public talk, preparing materials for outreach events, etc.) and things within our lab (running undergraduate lab meetings)
  • Teaching: any time spend preparing for teaching or preparing for teaching
There is definitely a lot of subjectivity involved when placing actions in one of these categories, but this is what I rolled with for better or worse. Bottom line: whenever I was really working (not surfing the internet) on one of these categories, I was "clocked-in".

How much am I working?
As of downloading the data on Sunday, I've averaged 45 hours/week of real work. I'm working an average of 6.43 hours per day (including weekends). If I look at when I'm working, I start my Monday-Friday work days on average at 9:04 am and head home at 6:40 pm on average. 

Here is a boxplot of the start times of different activities:


This makes pretty good sense compared to my general thoughts about my schedule. I usually have meetings during the morning or midday, handle little things and email first thing in the morning, and often use larger blocks of time in the afternoon for research in the lab or at my computer. I generally go to the gym early in the morning and take time for lunch with other grad students. 

What am I working on?
Since I am not teaching this semester and am being paid through a research assitantship, the data shows that I am (thankfully) working mostly on research projects. The teaching category isn't presented here for the same reason. 

Category: Duration (% of total across 33 days)
General Work: 47.46 hours (22.4% of total)
Meetings: 23.67 hours (11.2% of total)
Thesis Research: 81.28 hours (38.3% of total)
Other Research: 14.76 hours (7.0% of total)
Outreach Activities: 44.99 hours (21.2% of total)

Here is a bar chart showing how I spend each work day on different activities:






I love this view because it primarily demonstrates what I think is so great about being a graduate student: few days are ever the same. Sometimes I can spend the day devoted to a single project and some days I run from place to place doing very different things. For example, on January 30th I spent the whole morning getting some things in the lab organized, had a committee meeting late-morning, ate lunch with the departmental seminar speaker, went to the seminar in the afternoon, worked in the lab for the rest of the day, and then drove to Crawford County in the evening to give a public talk for the Parks District. The following Thursday I spend the majority of the day at my computer writing. Different days produce very different paces and styles of work.

Other observations:
I don't work that much on the weekends. I use the weekends as re-charge time and predominantly spend them with my wife and friends or working on hobbies. I think this is a good use of my time so that's what I do.

Some days are long days and some days are short days. Fridays are generally short days while Mondays/Thursdays are generally long days away from home. I'm not a robot that can work long hours day after day, so long days are usually followed by less work the next day. I can see the sense in this, but definitely see room for improvement. 

How efficient am I?
I wish I had better data to answer this question. Since I didn't log the amount of time I was "trying" to work, it is hard for me to know how many of those hours I was actually working on one of the above categories. 

One thing I was interested in is how long I spend doing each activity. For example, I am extremely fatigued by reading journal articles for more than an hour, but I feel like I can infinitely chip away at a seemingly endless "small things to do list".

Here is another boxplot showing the duration of each activity:


So, generally, I spend an average of about an hour on any given activity, but the duration is awfully variable. The extreme outliers shown here can be explained by the Museum of Biological Diversity Open House (Outreach) and the Ohio Biodiversity Conservation Partnership annual meeting (Meetings). 

But have these been a productive few weeks? I think so. I believe that I spent each of those ~45 hours to get things done. But my whole point here is to quantify what the daily life of a scientist is actually like without the posturing or the caricatures of overworked grad students pulling out their hair.

Haha, yep, there I am.

Besides the obvious benefit of having sweet, sweet data to play with, logging these hours had an entirely unpredicted psychological outcome. It turns out that taking the time to click on my phone and think "Ok, what am I actually going to do right now" is a great exercise in focusing my mind.

I'm now going to click "end outreach activity" and go watch Downton Abbey. See ya.

Wednesday, November 20, 2013

A research lab that herps together, works together

Back in August before the semester began, a good portion of the Gibbs lab headed down to Florida for a week of science and reptiles/amphibians. We were visiting some colleagues/collaborators at Florida State University as well as helping Sarah Smiley catch pigmy rattlesnakes for her thesis research.

Believe it or not, I've just recently downloaded the photos from my camera. Here are some of the interesting things we did and interesting creatures we found:

I almost ordered two slices because I didn't believe that they were "as big as your head".
David and Lisle appreciating the alligators
Sarah took us swimming at Wakulla Springs. We were all brave enough to high dive. 
There I was, expecting a honky-tonk. What a disappointment.
A lifer for me: Pig Frog (Lithobates Grylio)

A handsome juvenile Cottonmouth (Agkistrodon piscivorus)



Matt demonstrating the art form of laying out "rock snakes" to trick other cars searching for snakes at night. Classic.
The snake we were after: The Pigmy Rattlesnake (Sistrurus miliarius)
Sarah studies how these snakes' venom is locally adapted to their prey

Pigmy is a good descriptor. Here are four adult snakes at the bottom of a 5 gallon bucket.
Another lifer for me: Little Grass Frog (Pseudacris ocularis). I thought the first one I saw was an insect jumping through the grass.
Sarah gets the royal treatment during the half of the year she spends in Florida at Stetson University.
It was hot and humid, but we found snakes. Left to right: David Salazar, Sarah Smiley, Terry Farrell, Lisle Gibbs, Matt Holding, Rob Denton