Adventurous
field work expands knowledge of evolution and could help save endangered
species
David Ray never turns his back on his
research, and with good reason! "If it can't bite you, it's not
interesting," he jokes.
Ray and his team study alligators,
crocodiles, bats and flies, among other creatures. There's no handbook for
learning how to capture an alligator or a crocodile. "Oh, it's great. I
mean, there's just a thrill," says Ray, an evolutionary biologist at
Mississippi State University (MSU).
With support from the National Science
Foundation (NSF), this multidisciplinary team from several universities is
mapping crocodile and alligator genomes. Reptiles resembling these animals have
existed for around 80 million years and they are among the first reptiles to
have their DNA sequenced. The research could expand our knowledge well beyond
crocodilians to other reptiles, birds, and even dinosaurs.
"Birds and crocodiles, though you
wouldn't think it from looking at them, are each other's closest existing
relative," notes Ray.
"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," explains Lou
Densmore, chair of the Biological Sciences Department at Texas Tech University.
"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."
Catching a 'croc' or 'gator' is usually
done at night from a boat or a canoe. These animals have a layer of tissue in
their eyes called tapetum lucidum, which reflects back red. So, when a
researcher's headlamp spots that red color, the team heads 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," says Ray. "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," he warns.
The Crocodilian Genomes Project has
benefited from the input of a bona fide movie star. Errol, the Australian
saltwater crocodile whose genome is being sequenced by the group, has been
featured in a number of films--most notably the 2007 thriller Black Water.
"I never thought I'd get the opportunity to work with crocodiles or
celebrities," jokes project co-investigator Daniel Peterson, associate
director of Genomics at MSU's Institute for Genomics, Biocomputing &
Biotechnology. "Now I can say that I have had the rare privilege of
working with a celebrity crocodile."
Learning more about the genetic makeup
of crocodilians could help efforts to save some endangered species, such as the
very odd-looking Indian gharial (Gavialis gangeticus), which is now down to
just a few hundred animals. Scientists could possibly identify the most diverse
animals in the gene pool and then breed them. "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," says Ray.
That is one of the most exciting aspects
of the research for Lou Densmore. "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," explains Densmore.
Two other team members, biologist Fiona
McCarthy, who teaches in the College of Veterinary Medicine at MSU, and Carl
Schmidt, an associate professor in the College of Agriculture and Natural
Resources at the University of Delaware, take the assembled sequences, identify
genes, and provide 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," says
McCarthy. "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."
"Incorporating some of these
insights into my teaching ensures that I have examples that students won't soon
forget," she adds.
At the University of Florida, team
member and associate professor of biology Ed Braun is also a co-investigator,
along with microbiology professor Eric Triplett, on a separate NSF grant to
create a curriculum that is based on the research.
"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," says Braun.
Up to now, most of the vertebrate
genomes sequenced and analyzed have been from mammals. "Thus, most of what
we know about genome evolution is very mammalian-centric," notes Ed Green,
assistant professor of biomolecular engineering at University of California,
Santa Cruz. "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."
When they're not fishing for 'crocs' and
'gators,' Ray's team might be tracking down bats for their research on
transposable elements or so-called 'jumping genes.' These genes can copy
themselves and literally jump around in a DNA sequence. Better understanding of
them could lead to improved genetic therapies.
"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," explains Richard
Stevens, associate professor of biology at Louisiana State University.
"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."
"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," adds Ray.
The team is also investigating 'jumping
genes' in flies and the group's research may contribute to a new tool for
medical examiners and crime scene investigators. Those experts have long used
blowfly eggs and larvae to help determine time of death, but a lot of fly
species and their young look alike.
"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," says Ray.
Miles
O'Brien, Science Nation Correspondent
Marsha
Walton, Science Nation Producer.
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