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

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…

Enter Caenorhabditis elegans, or C. elegans, scientists’ favorite worm. C. elegans has traveled on many spaceflights, making it the perfect study for aging and space travel.

Lifespan and aging rates in animals are influenced by numerous environmental factors, such as temperature, oxygen, and food intake. The effect of microgravitational space environments on aging remains poorly understood, in part because scientists must disentangle it from many other influences.

To address the question of spacefaring worms’ longevity, Yoko Honda of the Tokyo Metropolitan Institute of Gerontology examined ISS-flown C. elegans and compared them to earth-bound worms.

During the International C. elegans Experimental First project, scientists incubated worms and flew them for two days to the ISS. The worms resided on-board for nine days, and then returned to Earth to be flash frozen in liquid nitrogen. Control animals underwent the same procedures at the same time on the ground.

First off, the team noted that spaceflight suppressed the formation of particular compounds that normally accumulate with increasing age.

Secondly, the team looked at how spaceflight affected specific genes’ expression (not whether the genes smiled or frowned, but how efficiently the genes transfered the information they encode into actual proteins). The space travel downregulated seven of the worms’ genes: these genes encode proteins linked to neuronal or endocrine signaling. Honda and his colleagues observed that the inactivation of each of these genes led to an extension of the worms’ lifespan on the ground. So when the scientists “turned off” the genes that slowed down in space, the worms lived longer.

Space travel leads to longevity? Well, perhaps in worms. Further research is required, but the present study suggests that space-flown worms age more slowly compared with the control group, and hints that spaceflight may extend worm lifespan. Can astronauts hope for similar results? Far too early to tell…

The research appears in the current edition of Scientific Reports.

Image: Bob Goldstein, UNC Chapel Hill, Wikipedia

The Riverside flies are not alone. Scientists have known about flies’ love of beer since the 1920s. But Anupama Dahanukar, an entomologist at UC Riverside, wanted to know why so she headed to the lab.

She and her colleagues examined the feeding preference of the common fruit fly for the pale ale (the least sweet beer) and other products of yeast fermentation. They found that a receptor (a protein that serves as a gatekeeper) associated with neurons located in the fly’s mouth-parts is instrumental in signaling a good taste for beer.

The receptor in question is Gr64e.  When a fly settles on beer, Gr64e detects glycerol and transmits this information to the fly’s neurons, which then influences the fly’s behavioral response.

Once the group identified the receptor, NPR reports,

Dahanukar and [colleague Zev] Wisotsky even found the particular gene responsible for flies’ ability to detect glycerol. When they created flies missing that gene, and gave them the sugar water-beer choice, the flies went for the sugar water.

“Taste becomes important only after the fly makes physical contact with food,” says Dahanukar. “A fly first locates food sources using its odor receptors—crucial for its long-range attraction to food. Then, after landing on food, the fly uses its taste system to sample the food for suitability in terms of nutrition and toxicity.”

As often happens in science, Dahanukar’s discovery has left her with more questions than when she started this research. Her lab will work to answer them.]

“How do you get information from the chemical environment to the brain—not just in flies but other insects as well?” Dahanukar asks. “How is that information processed to give rise to appropriate behavior? How does feeding behavior change with hunger? These are some questions we would like to pursue.”

The research was published earlier this month in Nature Neuroscience.

Image: UCR Strategic Communications

Researchers out of the University of Wisconsin Madison published an article in Nature this week with the possible answer, at least for fruit flies: the Wingless morphogen.

Wingless what?

In studying wing patterns of certain North American spotted fruit flies, the scientists discovered a morphogen (a substance that determines the development of cells and the position of those cells within a tissue) encoded with the Wingless gene (a specific gene that affects wing and limb development during the embryonic and metamorphosis stages).

Late in wing development, the Wingless morphogen diffuses through tissue where it prompts cells in certain areas of the wing to make pigment. “It acts by triggering responding cells to do things, in this case make color,” explains Sean Carroll, the senior author of the report.

“The Wingless molecule is deployed in this species at specific points in time and in specific places — the places where the spots are going to be.”

So the team began experimenting. Three years and thousands of fruit fly embryos later, they found that by inserting the Wingless gene into different parts of the fly’s genome, they were able to successfully manipulate the decoration of the fly’s wing, creating stripes instead of spots, and patterns not seen in nature. “We can make custom flies,” notes Carroll. By manipulating the gene, “we can make striped flies out of spotted flies.”

Although the study was conducted in teeny fruit flies, the principles uncovered by Carroll’s group, he argues, very likely apply to many animals, everything from butterflies to boa constrictors. “This is animal color patterning, how they are generated, how they evolved.”

Creative Commons image by photoholic1