Crocodiles and alligators, while not exactly native to West Texas, have been the focus of a Texas Tech biologist's recently published study that mapped the genomes of crocodilian reptiles worldwide.
David Ray, an associate professor of biology at Texas Tech and crocodilian expert, led a group of 55 researchers who sequenced the DNA of alligators and crocodiles to understand more about birds, who are descendants, along with crocodilians and dinosaurs, from an ancient creature called an archosaur.
"There’s a lot more birds out there than there are crocodilians, and if we really want to understand what’s happening with bird evolution, we have to compare it to something," Ray said. "And since we don’t have any dinosaurs - which would be the closest relatives to birds - the next best thing that we have is to look at the crocodilians."
Lou Densmore, chair of Texas Tech's biology department and a former mentor of Ray's, said the biology of crocodilians is an important research area in the understanding of bird biology and evolution.
“If you look at birds, they’re probably the direct descendants of at least one group of dinosaurs. Clearly they share that common ancestor. For over 250 million years, there has been a crocodilian-looking organism that has lived around the world, because it is such a successful phenotype.
The team's research discovered that crocodiles and alligators diverged on the evolutionary path approximately 90 million years ago - but remain so identical-looking that Ray said if you "cut the head off, you can barely tell the difference."
According to Ray's research, the genomes in crocodiles and alligators are 93 percent identical, yet the two types of reptiles diverged approximately 90 million years ago - the mid-Cretaceous period, when Texas and much of North America was submerged under a shallow inland sea. To compare, Ray and his researchers found a species that shared 93 percent DNA with humans - a small monkey called a macaque that diverged from humans about 23 million years ago.
"If you think about it, that’s 90 million years of divergence between crocodiles and alligators, whereas it’s about only 23 million years of divergence between humans and macaques," Ray said. "So we’re dealing with a rate of change in primate genomes that’s about four times what you see in the crocodilians. So crocodilian genomes are changing very slowly, or primate genomes and mammal genomes are changing very rapidly."
Ray said 90 million years ago, crocodilians settled on something that worked for them, eliminating the need to evolve beyond that.
"Everything we’ve seen about the crocodilians that we’ve seen so far seems to suggest that they’ve found something that they like and they’re sticking with it," Ray said.
Densmore said uncovering more and more information about the crocodilian genome has confirmed the biology community's suspicions that crocodilians, while evolving unhurriedly in the past 90 million years, evolved much more rapidly in the millions of year prior to that.
"That’s really the other side of understanding more and more about the genome will really bring to light, Densmore said. "Because there’s speculation by lots of people that perhaps earlier on in their evolutionary history, crocodilians did evolve rapidly. But then they settled on both the phenotype and the genotype, as it were, that was almost ideal. And because of that, they hung with that, and they really haven’t changed a lot."
The major advances made by Ray and his team were possible thanks to a evolution - pun intended - in genome-mapping technology, sending prices per million base pairs plunging in the last few years.
When Ray's team began assembling a budget in 2009, they only anticipated to map about 1 percent of the genome. Thanks to the price drop, they were able to map an entire genome.
"We got some funding to do a little bit of genomic sequencing in crocodilians, [but] it was only going to be about 1 percent of the genome," Ray said. "But between the time that we made the budget and the time that we actually got the funding, sequencing costs plummeted. They went down from about $10,000 per million base pairs to about a buck."
Considering the money and time it took to previously map genomes - mapping the human genome took 13 years and $3 billion - Ray said the speed and ease at which crocodilian genomes were mapped was remarkable.
"Nowadays, you can sequence a genome – you can get the sequence in a week, you can assemble it in a month, and then do the annotation work within a few months. And do everything they did with the human genome that took 10 years and $3 billion dollars – you can do it for about 10,000 bucks."
With the improvement of technology, Ray said just sequencing a genome isn't enough for researchers anymore.
"It’s becoming much more common to sequence an entire genome," he said. "Several years ago, you could get into Nature or Science by sequencing a genome – just sequencing it and saying, this is what it looks like. But that day is no longer with us. Nowadays, you get these high-profile papers, not simply by just sequencing a genome, but by asking a specific question. You have a reason to sequence a genome, because it’s relatively easy now."
While technology has drastically improved research opportunities like the crocodilian genome project, it remains a job that requires a lot of effort. Ray's team included 55 researchers, compiled from some of the nation's top research universities like the University of Arizona and the University of California, Santa Cruz.
Texas Tech had a lot to offer the study as well, Ray said, who earned his PhD in zoology at Tech.
“One of the reasons I wanted to come back here as a faculty member is because the evolutionary biology group at this university is one of the best in the country, if not one of the best in the world.”
Along with the serious, scientific aspects of the study – mapping the genome, writing and publishing a paper in national peer-review – Ray said crocodilian research rarely affords a dull moment.
“They’re fun to work with. I mean, you don’t know what fun is until you got a 10-foot animal on the end of a rope that wants to bite your head off.”
