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Unlocking the secrets of vertebrate evolution

Despite having no limbs and more vertebrae, snake skeletons are just as regionalized as lizards' skeletons. Image courtesy Craig Chandler, Angie Fox and Jason Head, University of Nebraska-Lincoln.

Conventional wisdom holds that snakes evolved a particular form and skeleton by losing regions in their spinal column over time. These losses were previously explained by a disruption in Hox genes responsible for patterning regions of the vertebrae.

Paleobiologists P. David Polly, professor of geological sciences at Indiana University, US, and Jason Head, assistant professor of earth and atmospheric sciences at the University of Nebraska-Lincoln, US, overturned that assumption. Recently published in Nature, their research instead reveals that snake skeletons are just as regionalized as those of limbed vertebrates.

Using Quarry, a supercomputer at Indiana University, Polly and Head arrived at a compelling new explanation for why snake skeletons are so different: Vertebrates like mammals, birds, and crocodiles evolved additional skeletal regions independently from ancestors like snakes and lizards.

“Our study finds that snakes did not require extensive modification to their regulatory gene systems to evolve their elongate bodies,” Head notes.

P. David Polly. Photo courtesy Indiana University.

Polly and Head had to overcome challenges in collection and analysis to arrive at this insight. “If you are sequencing a genome all you really need is a little scrap of tissue, and that's relatively easy to get,” Polly says. “But if you want to do something like we have done, you not only need an entire skeleton, but also one for a whole lot of species.”

To arrive at their conclusion, Head and Polly sampled 56 skeletons from collections worldwide. They began by photographing and digitizing the bones, then chose specific landmarks on each spinal segment. Using the digital coordinates of each vertebra, they then applied a technique called geometric-morphometrics, a multi-variant analysis that plots x and y coordinates to analyze an object's shape.

Armed with shape information, the scientists then fit a series of regressions and tracked each vertebra's gradient over the entire spine. This led to a secondary challenge — with 36,000 landmarks applied to 3,000 digitized vertebrae, the regression analyses required to peer into the snake's past called for a new analytical tool.

“The computations required iteratively fitting four or more segmented regression models, each with 10 to 83 parameters, for every regional permutation of up to 230 vertebrae per skeleton. The amount of computational power required is well beyond any desktop system,” Head observes.

Researchers like Polly and Head increasingly find quantitative analyses of data sets this size require the computational resources to match. With 7.2 million different models making up the data for their study, nothing less than a supercomputer would do.

Jason Head with ball python. Photo courtesy Craig Chandler, University of Nebraska-Lincoln.

“Our supercomputing environments serve a broad base of users and purposes,” says David Hancock, manager of IU's high performance systems. “We often support the research done in the hard sciences and math such as Polly's, but we also see analytics done for business faculty, marketing and modeling for interior design projects, and lighting simulations for theater productions.”

Analyses of the scale Polly and Head needed would have been unapproachable even a decade ago, and without US National Science Foundation support remain beyond the reach of most institutions. “A lot of the big jobs ran on Quarry,” says Polly. “To run one of these exhaustive models on a single snake took about three and a half days. Ten years ago we could barely have scratched the surface.”

As high-performance computing resources reshape the future, scientists like Polly and Head have greater abilities to look into the past and unlock the secrets of evolution.

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