Wednesday, November 12, 2014

At the iDigBio Summit IV, Gainsville, Florida

Rafe, Robin and Matt at iDigBio Summit 

The Integrated Digitized Biocollections (iDigBio; is the national resource for digitization of vouchered natural history collections and was established by the community strategic plan for the Network Integrated Biocollections Alliance (NIBA). iDigBio is supported through funds from the NSF’s Advancing Digitization of Biodiversity Collections (ADBC) program. The vision of the ADBC is a permanent database of digitized information from all biological collections in the United States. It is anticipated that this effort will lead to new discoveries through research, a better understanding and appreciation of biodiversity through improved education and outreach, and subsequent improved environmental and economic policies. Key partners in this effort are the Thematic Collections Networks (TCNs), which form a national grid of institutions that are digitizing specimens and associated resources. Within this context, animal vocalizations (like that of birds and anurans) and electrical signals (such as by fishes), which also form vital specimen-associated resources for research, are currently being digitized and archived by the Macaulay Library at the Cornell Lab of Ornithology ( and other institutions around the country. Avian and anuran calls recorded by researchers at KU have been being digitized and contributed to this repository, with a substantial part of the collection already accessible to the public. 

Exhibit at the Florida Museum of Natural History

The 2 day iDigBio IV summit, which was held in Gainsville between October 27–28, 2014 saw Rafe and I, along with Matthew Medler (who represented Mike Webster, Director of the Macaulay Library) as the attending members of the fledgling TCN devoted to digitizing animal vocalizations and electric signals. Eighty-four on-site attendees and nine remote attendees from TCNs, iDigBio, NSF, USGS and other biodiversity informatics initiatives convened for the summit. A series of brief presentations and demonstrations were made by representatives of the various TCNs and Matthew made a presentation of the basic components of our TCN and the progress made so far. One of the more inspired demonstrations was that of John La Salle, who showcased the Atlas of Living Australia portal (, which was supported by a $45 million investment by the Australian Government. I guess I would be very inspired too, had I had that kind of money backing me. Another interesting demo was that of augmented reality for public outreach, education and research purposes, where digitized 3D images of specimens can be viewed through a device such as a mobile phone, iPad, or a desktop webcam; the following video illustrates the point: Following the talks and demos, we then spread out between a set of four breakout discussion groups. The afternoon saw a poster session that was offered in a unique format, where posters were displayed on 55-inch high-definition flat screen televisions instead of the traditional posters printed on paper. The day culminated in a reception at the Florida Museum of Natural History at Powell Hall on the University of Florida campus, where a sensational Megalodon exhibition had just opened to the public. Overall, the Summit offered valuable insight into the ongoing multi-dimensional digitization and archival processes and the efforts to make them openly accessible, along with networking opportunities in this respect.

A few interesting webpages that were highlighted at the Summit:

  1. The Society For The Preservation of Natural History Collections:
  2.  Digital Morphology library:
  3.  Photosynth, a software application that analyzes digital photographs and generates a three-dimensional model of the photos and a point cloud of a photographed object:



Wednesday, November 12, 2014

Antarctica Research Team Heads to the Ice

Although most people think of Antarctica as a barren, cold environment, 200 million years ago it was a lush forest – a forest that now permineralized can yield clues to the climate change of the past, and how plants today may react to current climate change as well.

An international research team headed by KU scientists will head to Antarctica this week as part of a project aimed at understanding floral changes during the Jurassic in the Transantarctic Mountains of Antarctica. The group, departing on Tuesday, Nov. 11, will be on the ground for about one month and plans to blog and post to social media about the experience. The public is invited to follow the team’s work through the Biodiversity Institute blog

As part of this research, the group will examine the Early Jurassic fossil flora and the corresponding paleoenvironments from southern Victoria Land using a combination of geology, geochemistry and paleobotany. Learn more about the research on our news page.

Thursday, November 6, 2014

Is This Treefrog a Long Way from Home?

Treefrog found on a farm in eastern Kansas.

We recently received the photograph above from Steven Hallstrom, who owns and operates a sustainable farm just north of Tonganoxie. These photographs are of a frog that Steven observed in abundance earlier this season. Steven notes this frogs apparent similarity with the Pine Barrens Treefrog (Hyla andersonii) and is wondering if this identification could be correct given that this species isn't known from anywhere even close to Kansas (it occurs only in a few isolated patches of pine barren habitat along the Gulf and eastern coasts of the United States). 

Wednesday, October 22, 2014

Visit from Brant Faircloth

Herpetologists and ornithologists unite
over beers at a reception for
visiting LSU professor Brant Faircloth.

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.

Thursday, October 16, 2014

BI Grad Student Published Mycetoma Risk Maps

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 

Wednesday, October 15, 2014

Behind the Research: Identifying a New Species of Fossil Fish

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 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!!


Gibson, S.Z. 2013a. A new hump-backed ginglymodian fish (Neopterygii, Semionotiformes) from the Upper Triassic Chinle Formation of southeastern Utah. Journal of Vertebrate Paleontology 33: 1037–1050. 

Gibson, S.Z. 2013b. Biodiversity and evolutionary history of †Lophionotus (Neopterygii: †Semionotiformes) from the western United States. Copeia 2013: 582–603.

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.

Schaeffer, B. 1967. Late Triassic fishes from the western United States. Bulletin of the American Museum of Natural History 135: 289–342.