Now, an international team of researchers has sequenced the genome of one of the two living species of coelacanths. The results are published in this week’s Nature.

The endangered African coelacanth (Latimeria chalumnae) has more up its sleeve than just the living fossil thing. Scientists have long thought that this group of fishes gave rise to the first four-legged amphibious creatures to climb out of the water and up on land. Lobe-finned fishes (with fins like limbs) are genealogically placed in-between the ray-finned fishes, such as goldfish and guppies, and the tetrapods—the first four-limbed vertebrates and their descendants, including living and extinct amphibians, reptiles, birds, and mammals.

Results from the genomic study place the coelacanths behind lungfish, another lobe-finned living fossil, as the closest fishy relative to tetrapods. But other data from the study still make coelacanths incredibly interesting.

These prehistoric-looking fish are evolving at a very leisurely pace. “We found that the genes overall are evolving significantly slower than in every other fish and land vertebrate that we looked at,” says co-author Jessica Alföldi, of the Broad Institute of MIT and Harvard.

“We often talk about how species have changed over time,” says Kerstin Lindblad-Toh, another co-author from the Broad Institute. “But there are still a few places on Earth where organisms don’t have to change, and this is one of them. Coelacanths are likely very specialized to such a specific, non-changing, extreme environment—it is ideally suited to the deep sea just the way it is.”

Researchers also found several key genetic regions that may have been “evolutionarily recruited” to form tetrapod innovations such as limbs, fingers, and toes, and the mammalian placenta. One of these regions, known as HoxD, harbors a particular sequence that is shared across coelacanths and tetrapods. Tetrapods likely co-opted this sequence from the coelacanth to help form hands and feet.

“This is just the beginning of many analyses on what the coelacanth can teach us about the emergence of land vertebrates, including humans, and, combined with modern empirical approaches, can lend insights into the mechanisms that have contributed to major evolutionary innovations,” says the paper’s lead author, Chris Amemiya of the Benaroya Research Institute.

Image: Ballista/Wikipedia

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.

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

As slight as these finds are, scientists know quite a bit about these ancient hominins. In 2010, a team of scientists isolated and sequenced DNA from that finger bone fragment and discovered that it belonged to a young girl of an extinct Homo species described as Denisovan—after the Denisova cave in Siberia where the remains were found.

Unfortunately, the sequencing wasn’t reliable enough to do further studies. ScienceNOW explains:

But these genomes were too low quality to produce a reliable catalog of differences. Part of the problem was that ancient DNA is fragmentary, and most of it breaks down into single strands after it is extracted from bone.

Enter Matthias Meyer, a postdoc from Germany who developed a new way of sequencing. His novel technique splits the DNA double helix so that each of its two strands can be used for sequencing. This allowed the same team of scientists to sequence every position in the Denisovan genome about 30 times over ensuring that each nucleotide was in the correct spot.

The technique provides 99.9% accuracy—a quality similar to genomes that have been determined from present-day humans!

The much-improved genome furthers our understanding of the 50,000 year-old individual and population. The young girl had brown hair, eyes and skin and the genetic variation of Denisovans was extremely low—suggesting their population was never very large for long periods of time.

In addition, studies of the genome enhance our comprehension of human evolution. They describe the divergence between Denisovans and modern-day humans and confirm that modern populations from the islands of southeastern Asia (like Papua New Guinea) share genes with the Denisovans.

“This research will help determine how it was that modern human populations came to expand dramatically in size as well as cultural complexity while archaic humans eventually dwindled in numbers and became physically extinct,” says study co-author Svante Pääbo.

The findings were published last week in Science.

Image: Max Planck Institute for Evolutionary Anthropology

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…

These particular butterflies have never visited the site in Michoacan before—in fact, their grandparents were likely the last generation there—but somehow the orange and black beauties know exactly where to go.

Circadian clocks in the monarchs’ antennae and brain direct the butterflies in their migration, but researchers at UMass Medical Center wanted to dive deeper. “There must be a genetic program underlying the butterflies’ migratory behavior. We want to know what that program is, and how it works,” explains Steven M. Reppert, MD, chair of neurobiology.

So he and his colleagues sequenced the monarch’s genome. Nature’s newsblog reports:

The 273-million basepair genome is the first of any butterfly and is considerably smaller than—and quite different from—that of the commercial silk moth (Bombyx mori), which has 432 million basepairs, suggesting rapid evolution in the Lepidoptera group, which includes both butterflies and moths.

The entire study is published in a recent edition of the journal Cell.

Within those 273 million basepairs, an estimated set of 16,866 protein-coding genes, comprising several gene families, are likely involved in major aspects of the monarch’s seasonal migration, according to the UMass researchers. These genes influence all of the monarchs’ senses in order to navigate: visual input gathers clues from the sun; monarch-specific expansions of odorant receptors exist for long-distance migration; a full repertoire of molecular components exist solely to support the monarch circadian clock; additional molecular signatures orient flight behavior; and a variant of the sodium/potassium pump underlies a valuable chemical defense mechanism to fend off predators during the migration.

“Dissecting the genetic basis of long-distance migration in the monarch may help us understand these mechanisms not only in monarchs but more generally in other migrants, including migratory birds and sea turtles,” Reppert says.

Image: Sonia Carolina Madrigal Loyola/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