Brant Faircloth, LSU Professor and co-inventor of the protocol for sequencing ultraconserved elements that is now widely used by KU researchers, is in town this week for a seminar and workshop. This afternoon (Wednesday, Oct. 22nd) at 4PM, Rob Moyle will be hosting a workshop by Brant on UCE probe set design. This workshop will be held in the 7th floor conference room of Dyche Hall. If you don't have access to the 7th floor of Dyche Hall, please contact someone in the BI for assistance or meet on the steps to the 7th floor at 4PM.
The sister of KU Herpetology student Karen Olsen took the photograph above at her house in Florida. Anybody know the species of snake that was in her mailbox?
Doctoral student Abdallah M. Samy has just published a paper entitled Mapping the Potential Risk of Mycetoma Infection in Sudan and South Sudan Using Ecological Niche Modeling in the prestigious open access journal PLoS Neglected Tropical Diseases. Mycetoma is a fungal pathogen that infects and cripples far too many people worldwide. This paper represents one of the very few attempts to produce risk maps for this disease, which remains mostly unknown, in terms of geographic distribution, modes of infection, and many other crucial details. Abdallah assembled 4-country, 3-continent team to carry off these analyses, and the paper appears poised to lead to a number of follow-up analyses, the ultimate goal of which is a global risk map for the disease. The paper can be accessed at http://goo.gl/nxwtcl.
A fundamental part of being a scientist is publishing your research. Scientists ask questions, formulate hypotheses, rigorously test these hypotheses, and publish their research and their results. Other people can then read these results and build off of these studies, either to question or refute the findings, or to use the findings to ask other questions. It is how science grows and evolves.
What almost all scientific publications lack, however, is the flair, the backstory, and general behind-the-scenes action that is part of everyday research. Scientific publications are whittled down to the most concentrated version, filled with the jargon of the discipline, and stripped of any extraneous behind-the-scenes anecdotes. So while any given scientific paper can be exciting to a scientist who wants to learn more about the organism or the methods addressed, they can be a bit unfriendly to a general reader.
So for fun, I have decided to tell some behind-the-scenes stories of the research I do, in the context of my published papers. Hopefully I give you a sense of what it is really like to be a paleontologist, and the work that is involved.
I’ll begin with my two solo-authored papers that I published in 2013. The papers can be found here and here, and if you cannot access those journals, please contact me at email@example.com and I will send you a PDF.
These two papers establish a new genus and two new species of fishes within a group called semionotiforms. Semionotiforms are an extinct group of fishes, but are closely related to living gar, and like gar, their bodies were covered with thick enamel scales (ganoid scales). Semionotiforms are found in geologic deposits worldwide, and range in age from Middle Triassic (~237 million years ago) to Early Cretaceous (~145 million years ago). A lot of variety occurs in semionotiforms in the shape of the body, the characteristics of the skull, the teeth, etc., and part of my research is to figure out what makes these particular fishes different from other species that have been described in the literature by other scientists. So you could say that my hypothesis for these studies is that these fishes represent new species, and I am testing that hypothesis by comparing the anatomy and morphology of these fishes to other semionotiform fishes to see if my hypothesis is correct or incorrect.
Some of the fossil specimens I work on are from museum collections, such as the American Museum of Natural History (AMNH) and the Smithsonian and were collected in the 1950s and 1960s, yet remained in these collections unstudied and undescribed for decades. I began working on these fishes in 2006, when I worked at the St. George Dinosaur Discovery Site (SGDS) as an undergraduate student intern and later as the prep lab and collections manager. The crew of staff and volunteers from SGDS had just gone out to a site in southeastern Utah and collected hundreds of fossils (outlined in Milner et al., 2006), but most of these fishes were not identified. So as I started cleaning the fossils (fossil prep—to be discussed in a later blog!), I started looking for characteristics that defined them as either new or belonging to a described species of semionotiform fish. While I worked on the new specimens, I looked at older literature, in particular a (1967) paper by an AMNH paleontologist Bobb Schaeffer, who mentioned collecting many semionotiforms from the same area but didn't describe them or give them names. So, in 2008, I went to the collections of the AMNH to look at those old specimens collected decades before and reexamined them, seeing which of them could be the same species as the new specimens the SGDS crew had just collected. I identified at least two different species, though there are likely more than that.
Now, identifying a new species is more than just a “Eureka!” moment. A scientist cannot know what is new unless he/she knows what already exists, and so scientists have to be very familiar with other scientists’ work in the field. An inordinate amount of any scientist’s time is spent reading books and papers, and I spent months pouring over scientific literature, some as old as 1820, to find the characteristics of other semionotiforms. As I looked at each bone on the fossil fishes from the AMNH and those newly collected from SGDS, I compared it to the same bones in other semionotiform fishes, and I had to look for similarities and differences. Eventually, I found a suite of anatomical and morphological characters that distinguished these fishes from all other semionotiform fishes, and I had enough to publish two papers on two distinct species. In these papers, I had to give an exhaustively detailed description of every single bone, and I mean EVERY bone (these fishes have hundreds of bones, dozens in their skull alone!) that I could see on the specimens, because other scientists, when trying to identify new species of their own, may turn to my work for comparison, and so my papers have to be provide as much anatomical detail as possible!
Next time….naming a new species!!
Milner, A.R.C., Mickelson, D.L., Kirkland, J.I., and Harris, J.D. 2006. Reinvestigation of Late Triassic fish sites in the Chinle Group, San Juan County, Utah: new discoveries. In: A Century of Research at Petrified Forest National Park: Geology and Paleontology (Eds. Parker, W.G., Ash, S.R., and Irmis, R.B.). Museum of Northern Arizona Bulletin 62: 163–165.
We just received this report from undergraduate herper Kyle Atkins-Weltman about a recent snake encounter in Lawrence: "As I came back to my apartment from campus, someone from the maintenance crew saw me and asked me if I was the "snake guy," and when I said yes they told me they had found a snake while cleaning an empty apartment and asked if I could identify it. It turned out to be an absolutely BEAUTIFUL Pantherophis emoryi - cute little bugger, too! My guess is that it got in there to escape cold nights or perhaps there were some tasty vittles lying around. I'm going to release it back to the wild in a minute."
PhD student Scott Travers just reported back from the Solomon Islands, where he is in the midst of a National Geographic funded expedition. As you can see from the image above, Scott has already seen one of earth's most amazing lizards - the prehensile tailed skink (Corucia zebrata). Because it is so unusual, Corucia is one of those species that just about every herpetologist knows about. They have amazing tails capable of movement in nearly any dimension, a topic that was the focus of one of my first scientific papers. To the right of Scott, you can see Rafe trying to recreate Scott's moment using a plastic lizard.
KU Biodiversity Institute postdoctoral researcher Carlos Yañez-Arenas recently published a paper entitled "Predicting Species' Abundances from Occurrence Data: Effects of Sample Size and Bias" in the prestigious journal Ecological Modelling. Carlos' work was developed in collaboration with four co-authors, including KU BI alumnus Enrique Martínez-Meyer, now a professor in the Instituto de Biología of the Universidad Nacional Autónoma de México in Mexico City. The paper provides important new detail into methods under development for understanding geographic abundance patterns of species.
This week, Town Peterson's Biodiversity Informatics Training Curriculum project holds its first online course, which will focus on Public Health Applications of Biodiversity Informatics. The course is being carried out on Google+, and can be followed via its "event" page: https://plus.google.com/events/ctcg214mb5hmje4fjhi5s00nm5k. The course covers conceptual and practical aspects of biodiversity informatics as it can inform disease risk mapping, a crucial priority in public health initiatives worldwide. KU participants include Lindsay Campbell, Abdallah Samy, and Kate Ingenloff, as well as KU BI alumnus Yoshi Nakazawa.
The 8-10" long snake pictured above was just found in a basement in rural Johnson County, Kansas. Anybody know what it is?
We are having a great start with our Friday Herpetology Lunch meetings for the Fall term. Our lunch on Friday, August 29th included 18 individuals representing seven countries (USA, Brazil, India, Malaysia, China/Tibet, Ecuador, Taiwan). Curator Rich Glor discussed how to assist with development of the division's new website and curatorial assistant Matt Buehler shared some examples of problematic specimens recovered during an assessment of the snake collection.