New paper out this week led by the multi-talented Fernando Alda. In this paper we look at a very hard problem in phylogenetics: how to accurately determine relationships in groups that rapidly diverged a long time ago. These short branch lengths at deeper nodes in the tree cause a variety of problems when analyzing even the largest genomic datasets. In this paper we used several different filtering methods and recover a novel relationship for gymnotiform fishes (weakly electric knife fishes found in the Neotropics). If you're interested take a look over at the Systematic Biology website and let me know what you think!
I threw together a short animation using one of the scans from my recent trip to Friday Harbor. Hope you like it!
For the past two weeks I spent my time at the picturesque Friday Harbor Labs (picture above) in the San Juan islands of Washington. I was visiting Adam Summers and learning how to scan fishes using a microCT scanner that he has in his lab. Adam has the ambitious goal to CT scan all fishes. However, with approximately 35,000 species of fishes currently described, doing them one by one would simply take too much time. Luckily, he has figured out a brilliant way to get around this: fish burritos. No, not a burrito that you eat, but a bundle of fishes wrapped together in cheese cloth that gets put into a custom 3D printed tube that Adam makes in-house for scanning. By scanning specimens this way, you can pack up to 20 species in a single scan depending on their size; a HUGE time saver. The resourcefulness and creativity in the lab is impressive, and luckily for me, Adam hasn't scanned many flying fishes yet (the focus of my postdoctoral research). So after a couple of emails back and forth with Adam I found myself making the trek out to Friday Harbor (which involved a flight, a bus ride, and a ferry ride to get on island). With the help of Adam and his postdoc Mackenzie Gerringer, I was able to use the CT scanner, and in 12 short days I managed to scan about 150 specimens. The scanner is impressive and runs 24/7, which is probably the only way that you could end up scanning all fish species in a timely manner. Even more impressive are the awesome projects that people are working on in the lab. Now I have an absurd amount of data to move forward with, so look for upcoming images of CT scanned fishes. A huge thanks to Adam, Mackenzie and all of the other fantastic people in the lab for all of the help and the good times while I was there. I certainly would not have been able to finish these scans without their help, and I hope to go out again in the near future. If you have some fishes that you want to scan, I highly encourage you to plan a trip out to Friday Harbor Labs to help Adam achieve his goal of scanning all fishes!
My last post was announcing my dissertation defense, and I have been silent since then. Well, I am happy to report that all went well and that I have successfully finished my PhD! Since that post I have tied up all of my loose ends at LSU, graduated, and moved away from the swamps of Louisiana. Finishing up at LSU came with a mixture of emotions, and I sincerely want to thank everyone at LSU who has been a friend, colleague, or mentor over the past six years. It has been a wonderful ride, and I hope to visit as soon, and as often, as I can. As always, geaux tigers.
What am I up to now? Well, it is with great pleasure that I can announce that I have officially started a postdoctoral fellowship at the Smithsonian National Museum of Natural History. This postdoc is one of a kind, as it was endowed by one of ichthyology's greats: Bruce Collette. I am the first Sara E. and Bruce B. Collette Postdoctoral Fellow in Systematic Ichthyology, and with this fantastic position I will shift the scope of my research for the next several years. My PhD and Master's degrees mainly focused on using molecular approaches to study biogeographic patterns in marine fishes. For my postdoc I plan to examine the morphological adaptations that allow for gliding in flying fishes. Flying fishes as part of the order Beloniformes, which is an order that Bruce personally knows well and has worked on consistently for decades. I am extremely fortunate enough to be able to work with both Bruce, and my postdoctoral advisor, Carole Baldwin, on this new project, and there is absolutely no better place to be than at the National Museum of Natural History. Look for more posts in the future about my progress with this work, and let the new work begin!
I will be defending my doctoral dissertation next Thursday, June 21st in the LSU Museum of Natural Science exhibit hall. If you're around campus, please come by and see what I've been up to these past several years. If not, you can watch a live feed of it on the LSUMNS Facebook page!
The LSU Museum of Natural Science Special Saturdays program is a long-running outreach series that targets young minds. Held once a month throughout the school year, this series aims to teach young children about science and the world around them. These events cover a plethora of topics and are led by researchers in a variety of departments at LSU, and each talk is followed by a fun, hands on arts and crafts activity. Recently I was able to contribute to this series and led a Special Saturday covering coral reefs and the fishes on them. I organized the talk into the theme of Disney's Finding Nemo and Finding Dory, which the kids absolutely loved. They asked fantastic questions, and were really interested in the topic. After the talk, I showed them museum specimens of the fishes we talked about, and then they proceeded to work on their arts and crafts project. The project was to make paper models of different fishes and the kids had some really creative designs. The parents also got involved and made some really cool fishes! Make sure to check out the pictures below to see what they made. A big thanks to Valerie Derouen, the LSUMNS outreach coordinator, who organized this event, and to Jessie Salter and Link Morgan for helping out with it as well. If you'd like to participate in one of these events make sure to contact Valerie Derouen at the LSUMNS.
Happy New Year! It's officially 2018 now and it's time for an update on how I ended 2017 and what I'm looking forward to in 2018. The last part of 2017 was especially kind to Prosanta and I, as we were able to attend the 10th Indo-Pacific Fish Conference in Tahiti, French Polynesia. On our way out to Tahiti, we had a long layover in Los Angeles and so we decided to get a cab over to the LA County Museum and meet up with Rick Feeney who showed us around the collection. It's always fun to visit that collection, so a big thanks to Rick for the great hospitality. From LA it was just one more flight to Tahiti. The IPFC only occurs every four years, and the last one we attended was in Okinawa, Japan right after I joined Prosanta's lab. It is always a great time, and the venue could not have been more beautiful. Tahiti and Moorea provided the perfect setting for a relaxed, fun meeting, with plenty of excursions to do in your free time. Highlights for me include diving with three large tiger sharks, making new collaborations, and seeing old friends. The next meeting will be in 2021, and will be in Auckland, New Zealand, and I really hope that I'll be able to attend.
But now that it's the new year, here are some things I'm looking forward to for 2018: First, I have several long-standing projects that are finally coming to fruition and that will hopefully be submitted soon. Second, I'm looking forward to starting new collaborations with several scientists that I met at meetings this last year. Third, I'm excited to see the directions that some of our newer projects will go. We have several exciting projects that are just gaining momentum, from large-scale ordinal level studies, to whole genome sequencing studies (a first for me). Watching these projects develop and seeing the directions they take is very exciting. Last, but certainly not leasat,I look forward to finishing my PhD this year, and hope to find a lab to join as a post-doc. 2017 was an interesting year, but now it's time to move on. Here's to 2018!
The LSUMNS Ichthyology Collection made the front page of LSU's 'The Pursuit' magazine with stunning cleared and stained fishes from Louisiana's coasts. The article in the magazine focuses on the intertwining cultures of art and science and highlights ichthyology postdoc Brandon Ballengée, who combines these two fields in a unique way to engage the public. In addition to an interview with Brandon, there are pictures of his work, as well as images showing a public outreach event last year in Grand Isle, LA. Our own star undergraduate, Link Morgan, even got his own picture in the magazine showing off a fish that he had personally cleared and stained. Great work from Brandon, and all who were involved. If you're on campus, go check out a copy and learn a little bit more about what we do, or stop by the museum and see some of the cleared and stained fishes in our collection!
Members from the Chakrabarty lab attended two main meetings this summer to give presentations on the research we've been doing this past year. Fernando Alda and I started off the summer by attending the Evolution meeting in Portland, OR, from June 23rd to the 27th. Right before that meeting, though, I was able to attend a BAMM workshop led by Dan Rabosky at the Oregon State Campus in Corvallis. The workshop was an immersive two days event, but I walked away with a greater understanding the theory, math, and implementation of BAMM (and other packages, like FISSE). Local host, Brian Sidlauskas, also managed to give some of us a quick tour of the Oregon State Ichthyology Collection as well, which was a real treat. Thanks to Dan, Brian, and all of the others that made that workshop possible. After leaving Corvallis, I headed back up to Portland for the meeting. There were a lot of LSU students, alumni, and faculty at the meeting, and it was great to see everyone give talks and to catch up with old friends. Strangely, there was a Walking Dead event going on at the convention center concurrently, and the center was filled with a strange mixture of scientists, and people dressed up as zombies, Walking Dead characters, or random characters from a number of other series. No zombies interrupted any talks, but it was difficult to tell apart scientists from zombies at times... Evolution is always a good meeting, full of inspiring talks and great people. This meeting was no different, and Portland is a great place to visit, with a lot of good bars, restaurants, and things to do. Thanks to all of the organizers of the meeting for pulling off another great meeting.
Not too long after the Portland meeting, Fernando and I found ourselves at another meeting, this time joined by the entirety of the Chakrabarty lab (AJ Turner, Diego Elias, and Pam Hart). The meeting was the JMIH 2017 annual meeting in Austin, TX, commonly referred to as the ichs and herps meeting in near-Austin, TX. This was because the meeting was in the very northern reaches of the city, and quite far from downtown Austin. Despite this, the meeting was still a blast and there were still enough nearby restaurants and bars to keep people busy and happy. I was blown away by many of the student talks at this meeting, which were the highest caliber I've seen yet. So many good studies, with fantastic visuals provided by the wide-spread adoption of CT scans that many people are doing now. It even got a genomics guy like me excited for fish morphology. Overall it was a busy summer, but a lot of fun. I still have an upcoming meeting this October in Tahiti, so stay tuned for a posting on that.
Over the past three years, my advisor, Prosanta Chakrabarty, and I have traveled to the Middle East to sample fishes from the Persian Gulf (also called the Arabian Gulf there). We have visited Kuwait and the United Arab Emirates twice each and have always had a good time on these trips meeting new friends and learning new fishes. These trips began at the invite of LSU museum associate Jim Bishop, who works at the Kuwait Institute for Scientific Research (KISR). Jim has always been the most gracious host, and KISR has provided excellent facilities for us when we visit Kuwait. During our last visit to Kuwait in 2015, Jim, Prosanta, and I were discussing places we've been, field work we've done, and exchanges funny field stories. While we were talking we began to realize some common themes in the places we've been and experiences we had, and as we talked more we came up with some strange similarities (and differences) between the Red Sea and the Persian Gulf. These two seas were created by the same geological events, but are quite distinct. However, it was when we were discussing this that I began to relate our discussion to field experiences in the Gulf of California that I had as an undergraduate student at the University of Arizona. There are some striking similarities between the Gulf of California; some aspects were more similar to the Red Sea, but certain areas were complementary to the Persian Gulf (especially the northern regions). This eventually led to a publication comparing the marine biodiversity of these three seas that was recently published in the journal Marine Biodiversity. This publication wouldn't have been possible without the initial invitation out to Kuwait by Jim, or without the hard working efforts of my co-authors, including an undergraduate in our lab, Link Morgan, who gathered the majority of the data for this study. It is always a pleasure to publish with friends, and this publication will always remind me of our visits to the Middle East. If you're interested in the article, please click the link below, and if you have any questions or don't have access to the article please don't hesitate to send me an email. Enjoy!
A quantitative and statistical biological comparison of three semi-enclose seas: the Red Sea, the Persian (Arabian) Gulf, and the Gulf of California