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

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

An international consortium of researchers recently announced another milestone in the quest to unravel the genetic makeup of the human species. The project—ENCODE, for Encyclopedia of DNA Elements—is a collaborative effort among 440 researchers in 32 global institutions, coordinated by the National Human Genome Research Institute (NHGRI). The results of this international effort will stand alongside such research breakthroughs as Watson and Crick’s 1953 description of DNA’s double helix structure and the Human Genome Project’s 2003 complete sequencing of humanity’s 3.2 billion nucleotides.

ENCODE mapped more than four million non-coding regions of the genome that regulate and interact with protein-producing DNA. The scientific consortium also confirmed that 80 percent of the genome performs specific biological functions. This upends the previous consensus that long stretches of DNA were no more than “junk DNA.”

“This is one of the most important collections of information the world is trying to decode,” explains Brian Simison, head of the Academy’s Center for Comparative Genomics.

Not only does ENCODE solve a bit more of the human genome puzzle, but it offers the potential to accelerate medical research. “We’ve known for a long time that there is a genetic basis to many diseases,” says Simison. “What we didn’t realize is that the source of many diseases would be found in the vast regions of the genome previously known as junk DNA.”

While others describe the project as having found the on/off switches to our genes, Simison prefers the term ‘regulatory function.’

“We are learning that junk DNA has a regulatory role in dosage, duration, timing and other regulatory functions. Understanding these functions will transform Western medicine,” Simison adds. “ENCODE reveals that Western medicine is in its infancy.”

Simison points out that ENCODE is also altering our vision of the genetic composition of life. “Most people think all genetic material is passed down to us by our direct ancestors. Actually,” Simison explains, “the human species is filled with ‘fossil DNA’ transferred to us from viruses.”

As an example, Simison describes a retrovirus that has inserted its DNA into a person’s genome. These endogenous retroviruses (ERVs) are found throughout the genome and it is now believed that some of these have been repurposed.

Finally, Simison explains that it’s not just what ENCODE found but how they found it that is significant.

“The wow factor is enormous,” Simison laughs. As the National Institute of Health reports, hundreds of international researchers performed more than 1,600 sets of experiments on 147 types of tissue with technologies standardized across the consortium.

“Although technology has improved, no single institution could have analyzed the genome data on its own,” Simison remarks. “You need many people sifting through the many layers of data to decode the human genome.”

“I believe it is a positive development that so many nations are sharing this knowledge,” he said, lauding the consortium for its cooperative methods. “These illustrate how the path towards lofty ambitions is often as fruitful as the objectives themselves. Unlike the U.S. space program, the Human Genome Project and ENCODE were international projects where the benefits that emerge are shared with and benefit the world.”

ENCODE’s results were published last month in a wide range of scientific journals and posted online to ensure transparency and public access. To learn more, review the publications here.

Barbara Tannenbaum is a science writer working with the Academy’s Digital Engagement Studio. Her work has appeared in the New York Times, San Francisco Magazine and many other publications.

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…