Coast Horned Lizard (P. cerroense)

A coast horned lizard (Phrynosoma cerroense) on Baja California's Vizcaíno Peninsula.

Adam Leaché, a University of California, Berkeley, Ph.D. recipient and a National Science Foundation (NSF) bioinformatics postdoctoral fellow at the University of California, Davis, at the time, and the U.S. Geological Survey released a study in 2009 that showed that over their million-year evolution, when California's coast horned lizards moved north from Baja California and spread throughout the state, they diverged into at least two new species. The species of coast horned lizard pictured here, P. cerroense, was newly identified by the researchers.

The study findings are important for future conservation efforts. Coast horned lizard populations are declining from southern Baja California to northern California for many reasons including loss of lowland habitat from agriculture and urbanization and the introduction of Argentine ants, which displace the more nutritious harvester ants that these lizards feed on.

The study was funded in part by NSF (grant DEB 03-30750). To read more about this study, see the UC-Berkeley news story For horned lizard, horns alone do not make the species.

(Date of Image: July 1991)

Credit: Jimmy A. McGuire, University of California, Berkeley

Mapping the Genomes of Crocodiles and Alligators--It's Not for the Faint of Heart!

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.

Questions About Incredible Sea Turtle Migration Answered by Scientists

New insights by researchers reveal how young loggerhead sea turtles stay on course during one of the longest and most spectacular migrations on Earth

Immediately after emerging from their underground nests on the lush beaches of eastern Florida, loggerhead sea turtles scramble into the sea and embark alone on a migration that takes them around the entire North Atlantic basin. Survivors of this epic migration eventually return to North America's coastal waters.

The most comprehensive perspective to date on precisely how young loggerheads navigate their transoceanic migration was recently published in two complementary papers produced by a research team led by Kenneth J. Lohmann, a marine biologist at the University of North Carolina at Chapel Hill.

How they get there

The team's most recent paper argues that young loggerheads, which begin their migrations as tiny two-inch-long hatchlings, likely advance along their open-sea route through a combination of strategic swimming interspersed with passive drifting on favorable ocean currents. By swimming only in places where they are in danger of being carried off course and drifting passively in other areas where ocean currents move in the same direction that the turtles want to go, young loggerheads can migrate long distances on limited energy stores.

"Young turtles probably rely on a strategy of 'smart swimming' to optimize their energy use during migrations," Lohmann said. "The new results tell us that a surprisingly small amount of directional swimming in just the right places has a profound effect on the migratory paths that turtles follow and on whether they reach habitats favorable for survival."

The research, published in the June 2012 issue of The Journal of Experimental Biology, was partially funded by the National Science Foundation (NSF).

The findings--which were based on computer simulations combining ocean currents and 'virtual turtles' swimming for various period of time--challenge a long-standing belief that young sea turtles drift passively and that their distribution is determined entirely by ocean currents. "Most researchers have assumed that, because ocean currents in some places move faster than young turtles can swim, the turtles cannot control their migratory paths," Lohmann explained. "This study shows otherwise."

"The research team's results have important implications for 'weakly moving animals,' including larval fish, butterflies and ballooning spiderlings," said David Stephens, a program director at NSF. They suggest that even small amounts of effort from these creatures can have big effects on where they end up, and how they get there.

Stephens continued: "All those things that we've thought of as 'just drift along with the current' might, after all, have a lot of control over where they're going, with minimal effort!"

This discovery may be particularly useful in understanding commercially important creatures, such as fish and crab, that have weakly swimming larvae that, like turtles, have often been assumed to drift passively, added Lohmann. An improved understanding of their movements may lead to better fisheries management.

How they steer

A related paper published last month by Lohmann's team explains how young Florida-hatched loggerheads know where they are and in what direction to steer as they migrate around the North Atlantic basin. The paper, which appears in the April 2012 issue of Current Opinion in Neurobiology and describes research funded by NSF, reports that the turtles are guided at least partly by an inherited "magnetic map."

The Earth's magnetic field differs slightly in different geographic areas. The turtles' magnetic map enables them to instinctively and wondrously use differences in these fields as navigational markers that serve as equivalents to road signs for turtles in the open sea. Each change in the magnetic field elicits a change in the turtle's swimming direction, which in turn steers the turtle along its migratory route at each location.

The new paper summarizes a decade of research in which scientists investigated the turtles' magnetic map, using laboratory experiments in which young loggerheads were exposed to magnetic fields that exist along the natural migratory route. Amazingly, the direction that turtles swam in the lab in response to various magnetic fields matched observations of the steering decisions made by turtles when swimming through comparable magnetic fields in the ocean. The results indicate the turtles' brains are hard-wired to navigate their migratory routes from birth.

"The results also indicate that turtles obtain both latitude and longitude-like information from the oceanic magnetic field," said Stephens. "They may thereby obtain much richer spatial representations from magnetic fields than do humans with their compasses."

Why migrate?

Tiny loggerhead hatchings are born small and defenseless, said Dr. Lohmann. Unable yet to make deep dives, they can only swim slowly along the ocean's surface. Their limitations make them easy targets for predatory fish swimming below them and for hungry birds searching out their next meals from above. Such turtle predators are particularly abundant in shallow, coastal areas.

Scientists believe that loggerhead hatchlings attempt to dash from danger-filled coastal zones--in nature's version of a football maneuver known as a "Hail Mary pass"--into the relative safety of the open sea largely to avoid their enemies. Eating and growing in the open ocean where predators are less abundant, the turtles migrate slowly and wait until their larger size reduces their chances of being attacked by coastal predators, before they return to coastal North American waters.

Nevertheless, the odds are still stacked against the survival of any particular loggerhead hatchling. Estimates suggest that only about one in four thousand hatchlings from Florida survives to adulthood.

Conservation implications

All species of sea turtles are listed as threatened or endangered. The new research may provide insights that are helpful in conservation, Lohmann said.

For example, different populations of loggerheads around the world are likely to have different magnetic maps, Lohmann explained, with each map specific to a particular migratory pathway in one part of the world. If loggerheads in one geographic area go extinct, it will probably be impossible to replace them with turtles from another area, because the new arrivals will lack the inherited instructions needed to navigate within and from their transplanted homes.

In addition, conditions that impair the functioning of turtles' magnetic sense may jeopardize survival. Lohmann says that in Florida and elsewhere, a common conservation practice is to surround turtle nests on the beach with wire cages to protect the turtle eggs from raccoons. But such cages also distort the local magnetic field, and may thereby compromise the ability of hatchlings to navigate after they emerge from their nests.

 -NSF-

Spotted Salamander Eggs With Developing Larvae

Spotted salamander eggs with developing larvae are green from the presence of symbiotic algae. The algae provide oxygen that helps the salamander embryos develop and the embryos provide nutrients that facilitate growth of the algae.

(Date of Image: March 2007)

Credit: Roger Hangarter, Indiana University Department of Biology

Fossil Snake Fed on Hatchling Dinosaurs

This life size reconstruction shows a moment captured in time through a fossil, when a snake coiled around a recently hatched, crushed dinosaur egg adjacent to a hatchling sauropod. The remains of the fossil, unearthed in 67-million-year-old sediments from Gujarat in western India, has given scientists a rare glimpse of an unusual feeding behavior in ancient snakes.

The nearly complete snake was found preserved in the nest of a sauropod dinosaur. The 11.5 foot-long snake, which represents a new species (Sanajeh indicus), was no match for the 1.6 foot-long baby dinosaur that was probably defenseless. Remains of other snake individuals associated with egg clutches at the same site indicate that the newly described snake survived by feeding on young dinosaurs. The arrangement of the bones and delicate structures, such as eggshells and the snake's skull, point to quick entombment.

The discovery was made by an international paleontology team led by Jeff Wilson of the University of Michigan (U-M) and Dhananjay Mohabey of the Geological Survey of India.

"We think that the hatchling had just exited its egg, and that activity attracted the snake," said Mohabey. "The eggs were lain in the loose sands near a small drainage and covered by a thin layer of sediment."

The decade long odyssey required preparation and study of the fossil at U-M's Museum of Paleontology, weeks of museum study in India, and field reconnaissance at the original location in Gujarat by a team that included Wilson, Mohabey, snake expert Jason Head of the University of Toronto-Mississaugua and geologist Shanan Peters of the University of Wisconsin. (Date of Image: 2008)

Credit: Sculpture by Tyler Keillor; original photography by Ximena Erickson; image modified by Bonnie Miljour