Unisexual Ambystoma

Unisexual Ambystoma

Tuesday, October 7, 2014

Old Man of the Forest

Our department's graduate students took our fall camping trip over the weekend to southern Ohio, and we were treated to a really special animal:

That's a big timber rattlesnake (Crotalus horridus) hiding out under some fall leaves. This endangered species is both secretive and well camouflaged, so you could easily walk right past one of these bad boys even if you were lucky enough to be near one.

This particular snake is part of a long-term study to understand the movements and behavior of these snakes in Ohio. A radio transmitter guided the volunteers who track these snakes directly to this individual, and we were lucky enough to follow along.

My lab mate Matt Holding was asked to get DNA samples from this snake over the summer, and he remembered this individual fondly. Here is a photo of Matt with this same snake so you can get a sense of scale. The volunteers said that their last measurement of this individual was 54 inches, and it could very well be 15-25 years old.

So next time you are hiking around in timber rattlesnake country, keep an eye out and you may get to appreciate one of these incredible animals for yourself.

I mean really keep an eye out!

Sunday, September 28, 2014

What's Going On in Science, September 2014

Why student evaluations of teaching are worthless
"The paper compared the student evaluations of a particular professor to another measure of teacher quality: how those students performed in a subsequent course. In other words, if I have Dr. Muccio in Microeconomics I, what's my grade next year in Macroeconomics II?
Here's what he found. The better the professors were, as measured by their students' grades in later classes, the lower their ratings from students."

"This class should start an hour later in the morning. Also, the
teacher shouldn't wear sandals."
This NPR article summarizes a new study that tackles a problem that teachers in academia would love to talk your ear off about: teaching evaluations are horribly broken. If you get high scores from students in teaching evaluations, are you a good teacher? Maybe, but probably not. I've noticed the phenomenon of teaching evaluations (like product reviews on Amazon) consisting of only the most extreme opinions resulting in teachers who just don't care about the feedback.

Wildlife is culture, and culture deserves your tax money
"I mostly write about wildlife. So here is how it typically happens for me: A study comes out indicating that species x, y and z are in imminent danger of extinction, or that some major bioregion of the planet is being sucked down into the abyss. And it’s my job to convince people that they should care, even as they are racing to catch the 7:10 train, or wondering if they’ll be able to pay this month’s (or last month’s) rent."

This lovely New York Times Opinion eloquently states why biologists constantly have a lingering pressure to justify their research in terms of benefits to humans. 

Understanding genetics for the future of medicine
"Various efforts are underway to interpret mutations and compile them in publicly available databases; one of the latest is an online registry to which patients can upload their own data. Eventually, they will be able to see how many other people have the same mutation, and how many get cancer."

Genetic testing is becoming a more and more prominent aspect of individualized medicine. Unfortunately, the pace at which genetic tests are increasingly used is racing ahead of the general understanding of genetic tests and how to interpret them. Until better education about traits, alleles, and heritability can permeate into the public, doctors will continue to be limited by their ability to educate their own patients.

Salamanders: forest vacuum cleaners
"On an average day, a salamander eats 20 ants of all sizes, two fly or beetle larvae, one adult beetle and half of an insect called the springtail. And in doing so, they collectively affect the entire course of life in the forest — and perhaps far beyond."

This article is from back in April of this year, but I can't leave a nice salamander study out in the cold on this blog. You may not see them, but in most woodlands in North America, there are salamanders that make big differences in how ecosystems manage nutrients. While they make look cute and cuddly, salamanders are ultra-efficient, insect-seeking torpedoes:

Tuesday, September 23, 2014

How We Work: Dr. Paul Hurtado

Throughout my travels around academia, I've always been very interested in how other scientists work. Scientists in particular make for a great study of working habits for two main reasons: they typically juggle a variety of tasks and they largely determine their own work schedules. This results in a huge variety of work habits: night owls, early birds, multitaskers, focus-taskers, and on and on.

I've been a long-time reader of Lifehacker's "How I Work" series, an interview format in which folks from various organizations detail the secrets behind their work habits. I've always loved this idea: getting a peak into the habits of someone who's work you admire. As I've read more and more "How I Work" articles, I began to think that this format would work really well for scientists. So, in the same vein as the previous "Get to know a grad student" series, I'm bringing you a series of interviews that showcase how scientists get stuff done. I'm calling it "How We Work". 

A big thanks go to the inspiration for these questions, and to Andy Orin for giving me permission to use them. Go read Lifehacker for more neat stuff.

The first subject for How We Work is Dr. Paul Hurtado. I met Paul through OSU's Evolution and Ecology Club, and have since learned he is our resident statistics guru, birding expert, and all-around smart guy. Paul's work focuses on using mathematical models and computational techniques to answer large-scale biological questions (see his research page). In simple terms, Paul is a statistics wiz that thinks of new ways to analyze tricky data.

Location: Mathematical Biosciences Institute (MBI), OSU, Columbus, OH

Current Position: It’s complicated. Technically, I’m unemployed, however I just finished a postdoc at OSU in August and I’m currently negotiating a faculty position at a university out west that would start January, 2015. Fortunately my wife has one more year of funding for her postdoc position, which gave me some flexibility in hunting for jobs.

One word that best describes how you work: Inertia. Hard to get started sometimes, and also hard to stop once I get rolling.

Current mobile devices: Galaxy S4 smartphone

Current computer:
1. Desktop: Windows 8.1 (64-bit) 3.1GHz Intel i7 CPU with 8GB RAM.
2. Laptop: An older Dell Latitude D630 with too little storage capacity and speed.
3. I also have access to a multicore linux server through the MBI which I use occasionally.

What apps/software/tools can’t you live without?
Because I interact with biologists and mathematicians, I prefer to use free (or widely used) software so that licensing issues and/or software costs don’t get in the way of communicating and sharing content.

1. R is my go-to platform for data visualization, stats and model simulation.
2. I occasionally use R Studio – a front-end for R – but I tend to prefer the multi-window configuration of R and use Notepad++ to edit and run R scripts via NppToR.
3. Matlab is usually my second-in-line computing platform
4. MatCont (a Matlab add-on; although I really need to try Auto or XPP-Auto).
5. Maple and sometimes the free software Maxima for computer algebra (i.e., symbolic manipulation of algebraic expressions instead of crunching numbers)
6. I also use Python, Perl, and C from time to time, so access to a Linux command line is a must.
7. PuTTY and WinSCP for connecting to remote servers via SSH.
8. TeXstudio is my new favorite editor for writing manuscripts and other documents in LaTeX
9. Google Calendar is my primary means of scheduling everything.
10. “To Do” lists help me keep my days organized, so I also use apps like Google Keep (or emails to myself) to jot down important ideas and to organize and schedule tasks.
11. Facebook and Twitter have proven to be useful platforms for “crowdsourcing” technical problems, and soliciting advice or other information from friends and colleagues (Facebook) as well as people I've never met (twitter).
12. I can’t seem to go without Microsoft Office, despite my preference for using free software.
13. The internet, so I guess that means my web browser belongs on this list!

You need big screens to display big data

What is your best time-saving shortcut/life hack?
Talk with the right people, at the right time. Sometimes, I need to spend a lot of time wrapping my head around a problem and thinking it through carefully. But more often than not, I’m stuck on something mundane. In those cases, it can really pay off to just seek out someone with the right expertise who can either point me towards an existing solution, or who can help bounce around ideas until we figure it out. Especially when it comes to doing research, it pays to be selective in how you spend you time.

How do you organize all the stuff you have to do?
I should first admit that I've never considered myself to be a well-organized person, and over the past few years I've been spoiled by the flexible schedule that comes with being a graduate student and postdoc. That said, I have found some nice ways of staying somewhat organized:

1. Simple “To Do” lists – either in a smartphone app, a text file on my desktop, in an email, or written out on some scratch paper next to my computer keyboard – are a primary tool I use to prioritize and schedule most of my day-to-day tasks.

2. Software helps immensely with scheduling. I rely on Google Calendar and a note taking app on my phone to help with scheduling.

3. When I comes to organizing my work, a lot of it takes place on my computer, so I have a simple system of keeping work projects in their own folders, and using cloud-based software (e.g. Box, Dropbox, etc.) to sync content across my laptop and other computers. I incorporate “To Do” lists in code comments, text files and emails, etc. as needed. I’ve tried using version control software like Git to manage code revisions and manuscript drafts, however I’ve abandoned them in favor of just saving copies (with the date appended to the file name) and keeping those in their respective project directories. 

Besides your phone and computer, what gadget can’t you live without and why?
For work, my phone and computer are pretty much all I need! I suppose my coffee mug is the next most essential gadget in my arsenal. Outside of work, however, I am a fairly serious bird watcher (Rob: Paul is probably being modest here. Check out his birding resources page and note that he is one of the top 50 birders in Ohio). I rarely venture outside or do any traveling without bringing along a pair of binoculars. Especially during spring and fall migration! 

The first Kirtland's Warbler in central Ohio. Spotted by Paul in 2011.

What do you listen to while you work?
It depends. My musical interests are pretty broad, so if I want music I’ll just leave Pandora on and let it play from a mix of different channels. But, I can get pretty distracted by music. I’m usually better off with a lot of silence or a lot of ambient noise that won’t draw my attention away. For example, I used to be most effective at getting my math homework done as an undergraduate by bringing it with me to the Biology Club’s weekly bowling night and working on it one or two problems at a time. It was pretty effective, but definitely a compromise between getting my homework done and hanging out with friends.

What are you currently reading?
I've most recently been trying to finish up Writing Science by Schimel, which was the book the Aquatic Ecology Lab chose to read for the summer.

Are you more of an introvert or an extrovert?
I’m closer to the extrovert side of the spectrum, but definitely somewhere in the middle.

What is your sleep routine like?
I have a two and a half year old who loves to sneak into bed with us in the middle of the night, so lately my sleep has been pretty variable. I probably average around 8 hours a night but often with at least one interruption during late morning, which takes a toll. Now that I’m a parent, I definitely go to bed earlier (and probably sleep about the same or slightly more on average) although the interruptions definitely take their toll.

I’d love to see _____________ answer these same questions.
Libby Marschall (Ohio State), Liza Comita (Yale), Amy Downing (Ohio Wesleyan)

What’s the best advice you've ever received?
Work hard, play harder.

Monday, September 1, 2014

Salamander Snapchats

With the school year starting up again, it means that the undergraduate crew that I work with in the laboratory at Ohio State are back on campus. They are great to work with. Really great. One of my favorite things about them, aside from their work ethic and trustworthiness, is that they have a fantastic collective sense of humor. Because levity is a big part of my own personal work environment, I encourage joking around extensively while doing scientific work. 

One of our salamander caretakers, Paul, is particularly fond of updating me regularly about how the captive salamanders are doing. However, instead of coming to my office or sending me an email, Paul chooses to accomplish this through funny snapchats. If you don't know what Snapchat is, it is a messaging app for phones that allows the sender to create picture messages that are only viewable for a few seconds.

I thought I'd share some of Paul's work (with his permission). These messages are irreverent and silly and very funny to me. I hope you think so too.

Sunday, August 24, 2014

Apps for Academia: Let's Talk Tech

A big part of training to be a scientist is training to be productive. Grad students and faculty do a lot of different things in a set amount of time, and that amount of time always stubbornly stays the same or reduces. Improving efficiency not only allows you to have more time for non-work things, but also allows you to devote valuable time to tasks that need creativity instead of efficiency. My advisor often tells us that we are too busy and need more time to sit around and think

As much as technology can be a rabbit-hole of wasted time, I love using tech for helping me stay on task. I thoroughly enjoy talking to other grad students and faculty about what programs, devices, and apps they use to organize their work lives, and I've cherry-picked from them extensively.

Here is a summary of the nine apps that I would be lost in academia without, organized from most essential to most expendable. As a warning, most of these are based on Microsoft Windows, Google Chrome, and Android platforms. Have additions or suggestions? Let me know.

Here is my number one productivity tool and secret weapon against wasted hours, and it is the simplest thing to do. I keep track of how much time I spend doing things. I've written about my experience before, and I have continued to keep track of my hours ever since. In fact, I've gotten so used to it, I can't start working on anything until I glance at my timesheet and decide "Ok, what am I doing right now?".

There are a million apps that keep track of time spent on various projects. I use this one, but they all seem similar.

This is my checklist app of choice, and it nicely integrates across my web browser and phone. If I have any task to do, it gets quickly jotted down in Any.do and given a priority. I naturally think of tasks in the same way that they are categorized in Any.do: do this "today", "tomorrow", "upcoming (next week", or "someday". Additionally, I really like the daily reminder function of this app. Every morning when I start my work day (usually 8am), Any.do asks me to prioritize what I'm doing that day. Just a few minutes of considering what is important and what can wait can be super helpful when things get busy.

I used to just write down a to-do list on paper at my desk, but going digital allows me to jot something down anytime. What do you carry with you more often, a notebook or a phone?

Google Calendar
When I was an undergrad, I carried a planner everywhere I went. If you tried to schedule something with me, odds are I was going to forget if I didn't write it down. I'm still the same, except now I don't have to carry the planner and I can share my schedule with ease. Important meeting? "Google, remind me 15 minutes before this meeting starts." 

Mendeley + Scholarley
One of the worst parts of writing scientific manuscripts is controlling the references to other papers. There are different formatting guidelines for each journal, and managing huge libraries of PDFs can be a supremely annoying task. The time I was allotting to formatting citations and finding relevant papers was cut down significantly through the use of a citation management software (Endnote, Papers, Zotero are some examples). 

I prefer the free program Mendeley for a few reasons. One, it is free. Two, it is pretty good at finding information about my PDFs on its own. Three, it plays really nicely with a companion mobile app, Scholarley. Scholarley lets me access all of my Mendeley library on my phone, which is helpful when I'd like to read a journal paper away from the computer. Now I just find an interesting paper online and dump the PDF into a folder on my laptop. Mendeley takes that new file, fills in the details about the paper, and organizes it in another directory.

Maybe the most helpful aspect of Mendeley is using the citation plugin for Microsoft Word. When I'm writing and want to insert a citation, I just click Alt+M, search for topic or author keywords, and press enter. Mendeley adds the citation in whatever journal style I specify and builds a literature cited section for me. Easy.

Cloud Storage (Drive + Dropbox)
Sharing files is necessary for any level of collaboration between scientists, and the cloud storage revolution has been a welcome addition to being scientifically productive. Almost all projects I'm working on have an associated folder in Dropbox or Google Drive, where I can add/view/change content in real time. 

Pocket is an app for your phone or internet browser that acts as a glorified bookmarks folder. I had no idea why this would be helpful, but I kept seeing it pop up on websites like lifehacker and decided to give it a try. 

The main advantage of Pocket is the ability to store all the things that I don't have time to read on the internet (blog posts, science articles, discussion boards) into a centralized place. Then when I have time, I can go through and quickly figure out what is worth reading and what's not. Very simple and surprisingly efficient. 

Twitter + Tweetdeck + Plume
I'll tell you what scientists are talking a lot about: using social media. "Uggh, do I have to tweet?" say many. No you don't, but it sure can be helpful. For scientists, Twitter can help your work reach farther, let you know what new science is being talked about, and help you connect to other scientists extremely quickly. Here is an example from my experience where I was trying to find someone who has a treadmill for salamanders. The correspondence below would have taken me at least a few emails and plenty of internet searching. Instead, in five minutes I have two prominent scientists volunteering to help little 'ol me out. How cool is that?

In terms of social media, Twitter hits the time-to-benefit ratio perfectly for me. Part of using Twitter effectively is being a little bit organized. To do this, I use a combination of Tweetdeck on my computer and Plume on my phone. I create columns for groups of people that I follow ("OSU scientists", "Herpetologists") and columns for relative hashtags ("#scicomm", hashtags from conferences). 

Spreed is a plugin available for the Chrome internet browser that serves a very simple function. It helps me read much, much faster. Spreed works by taking the text on a page, feeding it to you one word at a time, and eliminating all the extra noise in your head when you usually read.

Now, I would never spreed a scientific journal article. I take my time doing things like looking up words and glancing back and forth at figures. However, Spreed is exceptionally useful when reading news articles, blog posts, and other internet text. 

Another potential downside is how strange you look when someones walks into your office as you are staring a words quickly flash one-by-one on the screen.

Google dictionary
Speaking of looking words up, Google Dictionary is my favorite way to look up word definitions while I'm browsing. Double click a word to see the definition. Simple.

So there you have it. Everybody's different, so what I find essential, you may find laughable. What really matters is that I get this paper done in time to watch the hockey game. 

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