Spotlight on mud snakes: Study unveils evolut

LAWRENCE — A brand new University of Kansas genomic investigation of a gaggle of unheralded however distinctive “mud snakes” from Southeast Asia is rewriting the evolutionary historical past of this household, named the Homalopsidae. The outcomes simply had been printed within the Bulletin of the Society of Systematic Biologists. 

Species of mud snake can inhabit contemporary, brackish or saltwater coastal and inland areas, principally sleeping by day and munching on fish and crustaceans by night time. Now, they’ve additionally fascinated two generations of KU researchers.

The new DNA-driven investigation by lead creator Justin Bernstein, a KU Center for Genomics postdoctoral researcher, is an instance of systematics: the examine of how species evolve and their relationships via time. It builds on a “monumental” examine of mud snakes carried out with out good thing about DNA evaluation in 1970 by Ko Ko Gyi. Gyi was a promising evolutionary biologist from Myanmar who carried out analysis within the Division of Herpetology of the KU Natural History Museum throughout a three-year fellowship from the United Nations Educational, Scientific and Cultural Organization.

“Our new paper looks at the evolutionary relationships and history of mud snakes, which are found in primarily South Asia, Southeast Asia, Australia and New Guinea — and they’re very poorly studied,” Bernstein mentioned. “We don’t know too much about them, despite decades of effort, including the efforts of Gyi, because they’re kind of hard to find. They’re aquatic snakes who prefer muddy environments. They’re nocturnal. Very few people have studied their evolution.”

Bernstein and his co-authors make clear mud snake evolutionary historical past utilizing genomics by combining genetic analyses of older museum specimens’ mitochondrial DNA with brisker genetic samples from recent area collections (which permit for a lot higher-resolution molecular evaluation — they used information from 4,800 nuclear loci in every genome).

“If you have an animal that’s been dead for days and extract DNA from that tissue, it’s going to be degraded — it’s not going to be high quality, which interferes with our results,” Bernstein mentioned. “That means we either can’t analyze it, or the results might be kind of weird and we can’t trust them. But this idea of getting DNA from old specimens in natural history museums has really been on the rise in the last decade. While the DNA is degraded, there’ve been protocols in the last 10 years to get high-quality DNA out of old specimens that are over 100 years old from natural history collections.”

The researchers used the mitochondrial information from these museum-specimen samples to fill in data gaps for a extra correct biogeographic historical past of Homalopsidae. Combining that with DNA samples from recent specimens, they reconstructed essentially the most complete household tree of Homalopsidae relationships, displaying which species branched from frequent ancestors and roughly when.

Bernstein’s co-authors had been Hugo de Souza and Kartik Shanker of the Indian Institute of Science; John Murphy, Harold Voris and Sara Ruane of the Field Museum in Chicago; Edward Myers of Clemson University and the California Academy of Sciences; Sean Harrington of the University of Wyoming and American Museum of Natural History; and Rafe Brown, curator-in-charge on the KU Biodiversity Institute and Natural History Museum and professor of ecology & evolutionary biology.

“Following up on Gyi’s pioneering and foundational work, Justin has been able to avail of a technological breakthrough, which we refer to now as ‘museumomics’ — the extraction and sequencing of degraded DNA, even from very old formalin-preserved specimens that were preserved dozens to hundreds of years ago,” mentioned Brown, who served as an “outside” member of Bernstein’s doctoral committee at Rutgers. “Obviously, the quality of that highly degraded DNA is variable, but new genomic sequencing technologies, bioinformatic tools, and diligent studies on the part of museum biologists have developed best practices for reconstructing highly fragmented genomes of specimens that were preserved upwards of a century ago. Justin successfully harnessed these new state-of-the-art tools, but also brought his own research ‘full circle,’ historically following up on Gyi’s work.”

The new paper reveals one long-held idea concerning mud snakes was incorrect. For years, scientists (together with Bernstein) thought ice age fluctuations in sea degree may need acted as a “species pump” that drove diversification of the mud snakes. Indeed, a lot regional biodiversity could be traced to sea degree rise and fall. But the brand new paper reveals, “Pleistocene sea level changes and habitat specificity did not primarily lead to the extant species richness of Homalopsidae.”

Instead, Bernstein and his colleagues imagine a extra probably driver of mud snake species richness occurred round 20 million years earlier, through the Oligocene, when sliding tectonic plates and shifting rivers in Southeast Asia may need severed and reestablished gene move repeatedly between mud snake teams, driving diversification.

“Although we can never prove what did happen, exactly, to trigger diversification in mud snakes, we can rule out, or reject, some previously articulated hypotheses,” Bernstein mentioned. “Because we found strong statistical support for diversification pre-dating Pleistocene sea level fluctuations by 15-20 million years, we need to look to alternative explanations, or novel ways of interpreting the production of biodiversity.”

Bernstein and Brown are fast to level to the pioneering work on mud snakes carried out 50 years in the past by Gyi, whose work not solely figured into the brand new paper however had a number of concepts confirmed by later DNA testing.

“Gyi completed a monumental work on this group of snakes, more than 50 years ago, and without the benefit of molecular analysis,” Brown mentioned. “That, in and of itself, is quite an accomplishment — his work was thoroughly comprehensive for the time, he really made the most of the available technologies, such as detailed X-rays of the skulls of all the species in this mysterious group of snakes, and he totally took the study of the evolutionary relationships of mud snakes ‘from zero to 60’ in his 1970 monograph. I know his adviser, the late Bill Duellman, was heartbroken to find out that Gyi passed away unexpectedly back in Myanmar, shortly after he left KU. But, here at KU, we still honor revisit and celebrate Ko Ko Gyi’s unique contributions, even to this day, and his work is continued on by Field Museum of Natural History researchers John Murphy and Harold K. Voris — and now by Justin Bernstein.”