Here’s a great idea for a super-power: what if by merely emitting a sound, you could detect nearby friends and enemies in the way the sound echoes? Echoes. Echoes.

For many species of bats and dolphins, echolocation isn’t a super-power but a necessity. It allows these animals to hear predators and prey without seeing them in the dark skies or cloudy oceans. This adaptation evolved separately in these mammals—a great example of convergent evolution.

Scientists at Queen Mary, University of London were curious how this type of convergent evolution looked at the genomic level. So they compared the complete genomes of 22 mammals, including new sequences of four bat species, to look at how echolocation is expressed in the genes.

To perform the analysis, the team had to sift through millions of “letters” of genetic code using a computer program developed to calculate the probability of convergent changes occurring by chance, so they could reliably identify “odd-man-out” genes.

Remarkably, they found genetic signatures consistent with convergence in nearly 200 different genomic regions! “We had expected to find identical changes in maybe a dozen or so genes but to see nearly 200 is incredible,” explains Queen Mary team member Joe Parker. “We know natural selection is a potent driver of gene sequence evolution, but identifying so many examples where it produces nearly identical results in the genetic sequences of totally unrelated animals is astonishing.”

Although many of the gene region similarities are in genes involved in hearing, which the team expected, others are all over the place, reports ScienceNOW:

…some genes with shared changes are important for vision, but most have functions that are unknown.

The team published their findings last week in Nature.

“These results could be the tip of the iceberg,” says group leader Stephen Rossiter. “As the genomes of more species are sequenced and studied, we may well see other striking cases of convergent adaptations being driven by identical genetic changes.”

So perhaps not a super-power, but a regular occurrence…

Image: Greg Hume

Two years ago, we produced a video about the remarkable work that scientists at Mote Marine Laboratory and the Academy are doing on spotted eagle rays. Little is known about these stunning elasmobranchs, but Kim Bassos-Hull of Mote and Anna Sellas from the Academy are continuing their studies to discover more about the rays and perhaps protect them along the way.

Bassos-Hull recently came to the Academy, and she and Sellas took the time to give Science Today an update on their long-term project.

Satellite Tagging & Genetics
They were excited about a satellite tag (a location-only SPOT tag) they deployed on a ray in April. Unlike sharks and marine mammals, rays are hard to tag because they have no prominent fins. The scientists’ colleague, Matt Ajemian of the Harte Research Institute, has had some luck with tagging rays, and he visited Mote to work with Bob Hueter, Mote’s expert on tagging sharks, to give the team some tips and best practices.

Generally, Ajemian has had satellite tags stay on animals for up to a few months, though the batteries last up to six months. Ajemian recently presented these findings at a special symposium on stingrays hosted by the American Elasmobrach Society in Albuquerque, New Mexico. Bassos-Hull says that the tag isn’t too invasive to the ray and that “many of the rays carry remoras larger than these tags.”

The first tag from April was unsuccessful, but in late May, Hueter and the team put a six-month pop-up archival satellite tag on a large female eagle ray.  If all goes well, this tag will pop off as programmed in about six months and give scientists more data on these mysterious rays.

Sellas is hoping the tag reveals information on the spotted eagle rays’ movements. The rays are generally found near Mote, off the coast of Sarasota in the Gulf of Mexico, from March through November. Few of the rays are seen in the summer months, and hardly any in the winter. Spotted eagle rays are also found on the Atlantic side of Florida, as well as off the coasts of Mexico and Cuba, but these rays could come from the same or different populations.

Sellas’ genetic work has revealed little genetic difference between rays found off Mexico and those found off Cuba, suggesting they are likely from the same population. Greater genetic differences seem to exist between rays sampled off Sarasota and those sampled off Mexico, suggesting limited movement across the Gulf. The satellite tagging data could confirm this “weak, but significant, genetic structure,” as Sellas calls it.

Sellas also hopes these tags can reveal how deep the rays are swimming and which habitats they frequent. Bassos-Hull says that habitat usage is particularly important off Sarasota, where there is proposed sand dredging in the Big Sarasota Pass Inlet for beach renourishment. But the Mote team knows the rays use this area to feed and that additional data could help protect this habitat for the rays.

Gulf Oil Spill
Since the Gulf Oil Spill, the Mote team has observed the number of spotted eagle rays off their coast decreased by about half. They began measuring and documenting the rays in 2009 and 2010, but in 2011 and 2012 the numbers per unit of measure had decreased. And, while the season isn’t finished this year, the lower population trend seems to have continued into 2013.

In addition, the Mote team has observed species rarely seen in the area—devil rays and whale sharks have started appearing in higher numbers than previously recorded. “It might be that these fish moved away from where the oil contaminated water was,” says Sellas.

Overseas collaborations
Bassos-Hull and Sellas have been working with Mexican scientists to collect tissues of spotted eagle rays for genetic sampling. Unlike the Florida samples, these tissues don’t come from live animals, but rather dead rays sold at local fish markets for consumption. One of their Mexican colleagues, Juan Carlos Perez-Jimenez, visited Mote in May to update them on the catch rates of spotted eagle rays in their fisheries.

Sellas and Bassos-Hull are also excited that this type of collaboration has expanded to Cuba.  A colleague there has similarly collected market samples for Sellas to conduct genetic work on here at the Academy.

Citizen Scientists on the Job
In the meantime, Bassos-Hull has received funding to utilize citizen scientists to learn more about these rays off the Florida Keys. She’s distributed small cards to dive shops there that, like the back of a milk carton, show a picture of one of these beautiful rays and ask, “Have you seen me?” Citizens can then refer to the back of the card which directs them to a website where they can report their sightings.

Mote is hoping that divers might spot these rays and input their sightings into the database, including pictures and location information. The small cards also give divers clues about where on the rays they might find small “spaghetti tags.” These tags indicate whether the ray has been caught before by Mote.

Bassos-Hull says that these citizen scientist sightings can help researchers understand where the hot spots for spotted eagle rays are in the Keys and where researchers should direct their attention for future studies.

Recognition and Recaptures
If you remember the video we produced in 2011, one of the most astonishing aspects of Mote’s work with these rays is the spot recognition software they use to identify the rays. The program, called I³S, is based on star recognition software and allows the researchers to recognize rays they’ve previously captured and released. Like fingerprints, no two rays’ spot patterns are the same.

Based on the data Mote has collected over the past few years, approximately 5% of the rays sampled are recaptures. This suggests that a certain number of rays are either remaining in the same area or returning to that area over time.

Busy Summer
Bassos-Hull and Sellas still have a lot of work ahead of them to understand these charismatic creatures and to share that knowledge with the world. In the meantime, this summer has kept them busy with a recent presentation at a professional conference on stingrays and forthcoming publications on their findings. And with more seasonal captures, they’ll undoubtedly learn more about the rays and their habitats. “We’re documenting the flux of nature,” Bassos-Hull says.

That could take a while.

Bob Hueter of Mote is also a principal investigator on this project. The researchers receive support and funding from the National Aquarium, the Disney Worldwide Conservation Foundation, the PADI Foundation, the Save Our Seas Foundation, and the California Academy of Sciences.

Image: Kim Bassos-Hull, Mote Marine Laboratory

Invasive species often worry scientists—how will native species respond to competition in their ecosystem? The Academy’s Brian Simison shares this concern, but he looks a little deeper. He asks: how does invasive species’ DNA affect that of native species?

Studying slider turtles (Trachemys) is a good way to this address this question. Some species, like the abundant red-eared slider, are invasive all over the world. Others are threatened native species. The invasive and native species often mate with each other, creating offspring. This mixing of two species genomes through crossing, that is, hybridization, can have a profound effect on the evolution of these species and on ecosystem health.

Recently Brian and Academy Research Associate James Parham of CSU Fullerton published a paper on slider populations in the Caribbean. The native sliders there “are endangered, largely because of habitat destruction, and being harvested for food,” Brian explains.

In some places, natives are also threatened by invasive species like the Cuban slider on Jamaica or the red-eared slider in Puerto Rico. “It appears that people have been moving turtles around for hundreds of years, and for some islands there may have been different sources of the introductions,” Brian says.

The recent study reveals a lot of hybridization among the invasive and native species. “We used genetic data to show that there are multiple hybridization events, both recent and ancient, both from natural contact and because of human activities,” Brian describes. “This pattern also shows that the past and ongoing movement of turtles by humans is impacting their DNA.”

But Brian suspects that human impacts may not be the only reason for hybridization. “In addition to the genetic pollution caused by people moving turtles into the range of other turtles, different species also contact each other naturally. So hybridization may be an important part of the natural evolution of these turtles. We have to keep this in mind when reconstructing their evolutionary history. We also need to be very careful determining whether evolution is the result of unnatural (human) or natural processes.”

If hybridization is due to unnatural, human causes, conservation efforts are a top priority in protecting the native turtles from the invasive species. Brian and his colleagues are also confronting these hybridization and conservation issues in the US. “The turtle project is a long-term multi-component project that will last for decades. This publication about Caribbean turtles is a small piece of the entire slider puzzle, which we are unraveling piece by piece.”

And the project goes beyond turtles. “Another facet of the current study addresses how we study genomic data in species that are hybridizing. In other words, we demonstrate how the presence of hybridization confounds certain methods that people are using to reconstruct how different species are related.”

These turtles get to the root of Brian’s work. “Asking, testing and answering evolutionary questions is why I became a scientist,” he explains. “Turtles are one of the few vertebrates that hybridize across deep historical divisions, which provides my colleagues and me the opportunity to test some of the most fundamental questions about the processes of speciation, the engine generating biodiversity.”

Image: James Parham

One way gene expression is altered through epigenetics is called DNA methylation. These are chemical tags that can regulate how genes function. Ed Yong puts it this way in his Discover blog:

These marks, known as methyl groups, are like Post-It notes that dictate how a piece of text should be read, without altering the actual words.

Epigeneticist Andy Feinberg, of John Hopkins, wanted to understand how DNA methylation might be identified in changes in behavior so he teamed up with Gro Amdam, of Arizona State University, a bee behavior expert.

Honeybees make excellent study subjects for this purpose because they are social creatures with very compartmentalized behavior. Female bees are either queens or worker bees, and once the path is chosen, there’s no turning back.

Within the worker bees, however, there are behavior distinctions that are a bit more transient. Workers begin as nurses—tending to the larvae. After two to three weeks, they become foragers, leaving the hive to gather pollen.

The researchers decided to study the chemical tags, DNA methylation, of the two groups—nurses and foragers. “Genes themselves weren’t going to tell us what is responsible for the two types of behavior,” Feinberg says. “But epigenetics—and how it controls genes—could.”

Analyzing the patterns of DNA methylation in the brains of 21 nurses and 21 foragers, the team found 155 regions of DNA that had different tag patterns in the two types of bees. The genes associated with the methylation differences were mostly regulatory genes known to affect the status of other genes.

Then the scientists got tricky. They removed some of the nurses from the hive. When this happens in nature, some of the foragers are able to revert to nursing to fill the gap. Sure enough, the same thing happened in Feinberg’s and Amdam’s experiment—several of the foragers went back to being nurses.

This time, 107 DNA regions showed different tags between the foragers and the reverted nurses, suggesting that the epigenetic marks were not permanent but reversible and connected to the bees’ behavior and the facts of life in the hive.

“It’s like one of those pictures that portray two different images depending on your angle of view,” Amdam says. “The bee genome contains images of both nurses and foragers. The tags on the DNA give the brain its coordinates so that it knows what kind of behavior to project.”

The researchers say they hope their results may begin to shed light on complex behavioral issues in humans, such as learning, memory, stress response and mood disorders, which all involve interactions between genetic and epigenetic components similar to those in the study.

The study is published this week in Nature Neuroscience.

Image: Louise Docker/Wikipedia

The authors of the paper sequenced the entire genomes of five members of each of the following hunter-gatherer populations: forest-dwelling, short-statured Pygmies from Cameroon, and click-speaking Hadza and Sandawe individuals from Tanzania.

The fascinating findings tell us more about human origins and prove to be a bit controversial, so I wanted to get more information from the Academy’s expert in human evolution, Zeray Alemseged. Zeray’s studies of early human remains have been published in prominent journals and garnered him worldwide attention. (PBS’s NOVA filmed an extensive interview with him here last spring, in addition to being on the covers of Nature and National Geographic.)

Zeray says these populations are not well studied and their isolation offers a new view on the human genome. Their unique diets, stature and culture also enable scientists to potentially link specific attributes to genetic markers, he adds.

The researchers used an in-depth method that involves sequencing each strand of DNA more than 60 times on average. This redundancy makes the sequencing highly accurate, giving the geneticists confidence that any mutations they identify are real and not errors.

Their results suggest that different human populations evolved distinctly in order to reap nutrition from local foods and defend against infectious disease. They also identify new candidate genes that likely play a major role in making Pygmies short in stature.

Scanning these sequences, the researchers found 13.4 million genetic variants or mutations—locations in the genome where a single nucleotide differed from other human sequences—and astonishingly, 3 million are new to science.

These new variants can represent the gene expressions unique to these populations, Zeray explains. This study is quite significant in making these genetic links to function and attributes that are phenotypic.

Zeray reminds us that these genetic studies aren’t just for mapping our ancestry, but also for mapping our future. He offers two separate examples—first, personalized medicine could tailor to specific gene regions. Second, “If we can link variants to diet, isolation and environment,” Zeray says, citing this current study’s examples, “then we can also understand what future climate change might look like for our species and how to prepare for it.”

Finally, the study finds genetic evidence that these direct ancestors of modern humans may have interbred with members of an unknown ancestral group of hominins. Zeray remarks that this particular finding—of a potential new species—reminds us why, in this technological age, paleoanthropology is a transdisciplinary endeavor requiring both fossil discovery AND genetic research.

So he’ll wait for more evidence, along with the rest of us…

That’s what Stephanie Venn-Watson announced at the AAAS Meeting today.

Dr. Venn-Watson of the National Marine Mammal Foundation is the vet for a large group of naval dolphins here in San Diego. These dolphins “work” for the US Navy, detecting objects in the oceans—from missing persons to mines.

Several years ago, she was conducting routine blood tests on her subjects. As she compared the blood values of dolphins who fasted overnight to dolphins that were recently fed, she discovered something truly amazing. “Fasted dolphins had a series of changes in serum chemistries that matched those of people with diabetes. Interestingly, these same dolphins switched back to a non-diabetic profile after eating. There appears to be a switch that dolphins use to turn a diabetes-like state on and off.”

Diabetes seems to be a naturally healthy state for dolphins—probably as an adaptation to their diets. As big-brained mammals, they need sugar, but their diet consists entirely of fish—high in protein, but low in sugar. According to Dr. Venn-Watson, “The dolphins have found a way to use fish-protein diets to generate and control the glucose they need.”

Can this new understanding help people who have diabetes? It’s comparative genomics time! (To learn more about the Academy’s involvement in the comparative genomics field, click here.) Dr. Venn-Watson is hoping to take what she’s learned and apply it to humans. “Gene-based dolphin research could lead to a better understanding of how a fasting switch, which may be uncontrolled in some people with diabetes, can be controlled using the dolphin model. Its potential application to treat diabetes is enticing.”

Creative Commons image by Cayusa