Genome Mapping Of Crocodiles Could Aid In Species Conservation
May 22, 2012

Genome Mapping Of Crocodiles Could Aid In Species Conservation

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"If it can't bite you, it's not interesting,” jokes David Ray an evolutionary biologist at Mississippi State University (MSU). Ray and his team of researchers study alligators, crocodiles, flies, bats and other animals. Ray stated of the risky work, "Oh, it's great. I mean, there's just a thrill.”

The team, comprised of researchers from many different universities, is undergoing studies on genome mapping of alligators and crocodiles, funded by the National Science Foundation (NSF). Their objective is to find more information on the possible evolution and DNA coding of these reptiles. The findings could increase knowledge of other reptiles, mammals and possibly dinosaurs. Ray states, "Birds and crocodiles, though you wouldn't think it from looking at them, are each others closest existing relative.”

"The group currently assembled by David Ray and others includes scientists with expertise ranging from crocodilian systematics and population genetics to pure molecular biology to the fields of bioinformatics and comparative genomics," Lou Densmore, chair of the Biological Sciences Department at Texas Tech University, states. He also notes, "Although just 10 years ago, the thought of such a study was beyond the wildest dreams of any of us, we are now sitting on the threshold of the most ambitious crocodilian genetics and genomics research ever attempted."

Typically done at night on a boat or canoe, crocodile or alligator catching begins with researches using a headlamp to scan the water. Due to a membrane within the animal´s eyes that reflects red, a researcher can spot a croc simply by moving the light around. Once the creature is spotted, the team moves in that direction.

“You approach the animal as quietly as you can, and preferably from the front so that you can just basically get the breakaway snare to go over the snout,” Ray states. “Of course, the animal doesn't like that, so it thrashes and then you've got potentially a 10-foot animal that wants to eat you on a rope!”

“When they've exhausted all their energy, you can handle them relatively easily. Then, we will go to a sinus on the back of the neck and draw however much blood we need, and then it's time for release. The key is to keep control of the head. That skull is like a brick and if it whips around and knocks you, it can hurt you pretty badly. Always keep a hand on it,” Ray cautions.

Errol, a “celebrity” Australian crocodile featured in movies including Black Water, is aiding researchers, who are mapping his genome. Daniel Peterson, a co-researcher and associate director of Genomics at MSU's Institute for Genomics, Biocomputing & Biotechnology, jokes, “I never thought I'd get the opportunity to work with crocodiles or celebrities. Now I can say that I have had the rare privilege of working with a celebrity crocodile.”

Research on the genome of crocodilians could help in conservation efforts that help save creatures like the Indian gharial (Gavialis gangeticus), a strange looking crocodile whose population has dwindled to a few hundred in number. Findings from the current study could help scientists identify the most genetically diverse Indian gharials and breed them in order to bolster their numbers. "The more we can understand how their DNA is put together, the more likely we are to understand how to keep them from going extinct," states Ray.

For Lou Densmore, this is one of the most thrilling features of the research. Densmore states, “By the time the next genetic sequence analysis of this genome is complete, we will not only know exactly how the gharial fits into the evolutionary history of the Crocodylia, but we will also have the data needed to pursue a 'comparative -omics' approach that will help explain the remarkable cranial morphology that has caused such controversy in interpreting its phylogenetic placement in the order.”

Two researchers on the team, biologist Fiona McCarthy who teaches at the College of Veterinary Medicine at MSU, and associate professor Carl Schmidt of the College of Agriculture and Natural Resources at the University of Delaware, use the compiled gene sequences to identify genes and create standardized gene nomenclature and functional annotation.

"My main research focus is providing functional annotation so that researchers are able to more easily get from data to knowledge, and it is wonderful to work on a sequencing project where functional information is factored in from the start," McCarthy states. "Add on top of that, all the really interesting biology, such as temperature regulation of sex determination, tooth development in crocs and birds, linking reptiles and birds together in an evolutionary sense, and you get a lot of very interesting insights into fundamental biology." She notes,” Incorporating some of these insights into my teaching ensures that I have examples that students won't soon forget.”

“Crocodilians really have the potential to capture the imagination of students since they look like living dinosaurs. Involving students in the annotation and analysis will open their eyes when they see the similarities to and differences from the real living dinosaurs--birds. Understanding crocodilians is critical for understanding birds. Despite their obvious differences, reconstructing their common ancestor will require information from both groups of organisms,” states Braun, a co-author and associate professor of biology at the University of Florida . Together with microbiology professor Eric Triplett, Braun creates a curriculum from the research that is funded separately by the NSF.

Until recently, the majority of vertebrate genome mapping research and sequencing has been comprised of mammals. Ed Green, assistant professor of biomolecular engineering at University of California, Santa Cruz, states of this, “Thus, most of what we know about genome evolution is very mammalian-centric.” He continues, “We're now coming to learn that the reptilian world has evolved more slowly, from the rate of divergence at the level of chromosome rearrangements to how fast individual bases change. On the one hand, this makes things easier for genome assembly, but it also requires that we revisit a lot of assumptions and models that were made when we only had data from mammals.”

Ray´s team, when not searching for or catching crocodilians for research, may be capturing bats for further research on “jumping genes”, or transposable elements. These genes are commonly known to “jump around” the genome of a bat, replicating themselves within the DNA sequence. Further research could create an understanding of this phenomenon that could lead to enhanced genetic therapies.

Richard Stevens, associate professor of biology at Louisiana State University states, “"Bats are the second largest group of mammals in terms of number of species. Transposable elements, which are very common in some groups of bats, alter composition, but perhaps more importantly, regulation of genes when they insert themselves,” he explains. “These genetic changes could be important in the diversification process and may provide key insights especially in terms of understanding mechanisms that generate diversity of species-rich groups, such as bats.”

Ray also speaks of the “jumping gene”, stating, “These transposable elements contributed many of the regulatory elements that tell a gene when to turn on and turn off. So, the fact that these things can move from place to place lets us understand better how genes are regulated.”

Also investigated by the research team are flies. The “jumping gene” could aid crime scene investigators and medical examiners in determining the time of death of a person. Some use blowfly eggs to help identify the time of death, but this technique is difficult because species of flies and their young look very similar.

Ray states, “It's critical that you actually know which species you're dealing with or you're going to get the time of death wrong. Our idea is that we use these transposable elements as genetic markers. Then we can narrow down which species we're dealing with and, therefore, get an accurate time of death.”