Deploying population genetics

Variation is the spice of life, especially on the genetic level. Any two humans, for example, differ on average by 20 million nucleotides out of a total of three billion. “There’s tremendous interest in understanding what those differences do,” says Charles F. Aquadro, Molecular Biology and Genetics. “Do they matter? They must matter.” How can the system still function properly with that much change? Why has it occurred? Clearly something has to be driving changes through the population.

A population geneticist, Aquadro looks at changes in genetic variability in populations over time and space. He and his lab work mainly with drosophila, the fruit fly. The researchers seek to pinpoint changes in genes within and between species of drosophila, to infer the function of those differences, and then to understand the evolutionary forces that drove them to occur. They currently focus on the germline stem cell system, which generates gametes, the haploid germ cells that are the building blocks of sexual reproduction. “These are arguably the most important cells in an organism because unless they are regulated properly, the species doesn’t reproduce,” Aquadro says.

What Drives the Rapid Evolution of the Bag of Marbles Gene?

About 10 years ago, the Aquadro group discovered that a gene whose function is critical to the formation of eggs and sperm in drosophila changes very rapidly between fruit fly species. In particular, the researchers have compared the gene—known as Bag of Marbles—between D. melanogaster and a related species, D. simulans, which last shared a common relative 2.5 million years ago.

“Over the time they’ve diverged, the two species have accumulated 60 amino acid differences in a 442-amino-acid protein,” Aquadro explains. “This is a tremendous amount of change when you think about how important this gene is. How can the system still function properly with that much change? Why has it occurred? Clearly something has to be driving changes through the population.”

To answer the questions, Aquadro and his collaborators have been using a new, cutting edge approach combining the study of naturally occurring genetic variation with direct functional studies using CRISPR-Cas9 methodology to engineer mutations in multiple species of drosophila. They first gather fruit flies from orchards and identify genetic variations within populations and between species. Then they compare the differences using population genetic modeling to predict the functional consequences of the genetic variants they find. Using CRISPR-Cas9—a process that employs the CRISPR (clustered regularly interspaced short palindromic repeats) DNA sequence and the nuclease Cas-9 from bacteria to edit genes in living models—they test these predictions by introducing one genetic mutation at a time into individual flies to see the effect of each variation.

How can the system still function properly with that much change? Why has it occurred? Clearly something has to be driving changes through the population.”

“This combined approach in species other than D. melanogaster is new territory,” Aquadro says. “It’s been a challenge, but I’m happy to say we’ve managed to make it work.”

Could It Be the Bacterium, Wolbachia?

Over the course of many projects, Aquadro and his collaborators have sought to discover the driver of the rapid evolution of the Bag of Marbles gene. Their current belief is that an intracellular bacterium called Wolbachia is the culprit. Wolbachia infects up to 70 percent of all insects and is known to manipulate reproduction, although no one understands fully how it does this. It is transmitted cell to cell, from one generation to another, typically through the eggs. To ensure its own success, in many species of drosophila, Wolbachia leads to the successful reproduction of only infected females who produce only infected offspring, thus spreading the bacteria quickly through the population.

“We have genetic evidence that if a D. melanogaster has a certain mutation in the Bag of Marbles gene that causes it to have fewer offspring, and you infect it with Wolbachia, the fly’s reproductive success goes back up, almost to normal,” says Aquadro. “We’re working on trying to understand how the bacteria accomplishes that.”

What Is the Potential Impact of This Research?

There are broader implications for Aquadro’s research. One application could be to control mosquito-born viruses such as the Zika and dengue fever viruses. “If you take Wolbachia from D. melanogaster and infect it into mosquitos, it creates the same phenomenon that it does in the fruit fly,” Aquadro explains. “It leads to all offspring being infected with Wolbachia and so the bacteria spread rapidly through the population and blocks viral replication in the insects. As a result, the mosquitos no longer transmit the Zika or dengue virus, and the diseases no longer spread.”

Aquadro is also starting a new project looking at another species of fruit fly, D. suzukii, which has invaded the United States from Japan, where it is a major pest on cherries. In 2017 the fly hit New York State, attacking tomatoes, pumpkins, and other fruits. Grape growers are especially worried. “We are going to study the Bag of Marbles gene in D. suzukii,” says Aquadro. “As we begin to discover the connection between the gene and Wolbachia, we hope to figure out ways to potentially disrupt reproduction of this invasive insect species and the spread of this agricultural pest.”

Cornell Center for Comparative and Population Genomics

In 2008, Aquadro cofounded the Cornell Center for Comparative and Population Genomics and currently serves as its director. The center pulls together faculty from throughout the university, provides graduate students and postdoctoral fellows with connections to research activities, and brings speakers from around the world to Cornell.

“When I came to the university in 1985, I was the only one doing population genetic approaches to evolution,” Aquadro says. “Now we have 36 faculty in the center, scattered across 10 departments. Cornell is unusual because of the connection between those of us who take a population and evolutionary approach and our colleagues who focus on the hardcore functional analysis of variation. We are seamlessly integrated here. And the center provides intellectual cohesiveness independent of departments. Faculty, graduate students, postdocs, all just walk back and forth across the disciplines.”

Population Genetics, Medicine, Ancestry

About eight years ago, Aquadro took notice of the growing importance of population genetics to medicine as well as the burgeoning interest of society in genetic ancestry and decided to offer a new class for undergraduates on personal genomics and medicine. Students in the class can choose to participate in genetic testing through the company 23andMe, then use the test results to learn what a genome is and why it matters.

Aquadro envisioned the class as a way to expose non-science majors to principles of population genetics. “As a research scientist, I feel it’s really important for people outside the sciences to understand that science is relevant to them and can make a difference in their lives,” he says. “This class is a way for me to infuse the population genetics way of thinking into a much broader group of people—the nonscientists who will play key roles in making laws and implementing policies that affect science in the future.”