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.

Source: National Science Foundation