Natural selection’s fingerprint identified on fruit fly evolution

Researchers at the University of Rochester have produced compelling evidence of how the hand of natural selection caused one species of fruit fly to split into two more than 2 million years ago. The study, appearing in today’s issue of Nature, answers one of evolutionary biologists’ most basic questions–how do species divide–by looking at the very DNA responsible for the division. Understanding why certain genes evolve the way they do during speciation can shed light on some of the least understood aspects of evolution.

“The study of speciation has a reputation for wild speculation because every time we find a curious genetic element, we suspect it of causing speciation,” says Daven Presgraves, lead author on the study and postdoctoral fellow at the University. “We know embarrassingly little about a core process in evolutionary biology, but now we’ve nailed down the exact sequence of a gene that we know was involved in keeping two species separated. We can see that it was natural selection that made the gene the way it is.”

The study breaks ground in two ways: First, it’s the first time that a gene known to be involved in speciation has had its DNA fully revealed.

Presgraves and colleagues found 20 regions that differed on the chromosomes of two species of fruit flies that were estimated to have diverged in evolution 2.5 million years ago–fairly recently in evolutionary terms. He then needed to find a gene in one of those regions that was responsible for preventing successful reproduction between the two species. If the species could reproduce, then they could swap genes back and forth and thus would not be truly separate species. Something would have to prevent the transfer of genes, and in the case of Presgraves’ fruit flies, that something was the proclivity for hybrid larvae to die before maturing into adults.

He found his gene, called Nup 96, that always prevented a hybrid of the two species from living to reproduce, and he sequenced its DNA.

“We’re seeing a gene responsible for speciation at the maximum possible resolution,” says Presgraves. “It’s as if we had a map and could once zoom in on a city, but now we’ve zoomed in on the exact address.”

Nup 96 turned out to code for a certain kind of protein that was part of an essential pore in the nucleus of every cell in the fly. If one member of one species of fly mated with a member of the other, this pore would not properly form and the hybrid fly would die. Even though this was an unprecedented finding in itself, it posed a new question that came wholly unexpectedly: Nuclear pores are found in every cell in the world that has a nucleus, so it was labeled as “highly conserved,” meaning it was always assumed that it was so important to the survival of an organism that evolution would never tamper with it. Further study will be needed to understand why altering this pore was seen as useful in the evolution of this particular species of fruit fly.

The second groundbreaking result of the study is that Presgraves looked at the DNA of Nup 96 and worked to determine whether these two species simply drifted apart, or whether evolution forcefully took them down their separate paths.

Natural selection, Darwin’s hypothesized tool to explain the development of complexity in species, appeared to have been responsible in moving the species further apart, Presgraves found. He used statistical means to compare the amount of genetic divergence in Nup 96 that existed between the two species to the amount of divergence among individual members of the same species. Members of one species, which readily exchange genes, would indicate what the normal generation-to-generation rate of random genetic mutation would be. The difference between species, however, would show if any of the new randomly acquired traits were useful enough to be “selected for,” and passed on to successive generations. While natural selection appeared to evidently play a major role in the development of Nup 96, Presgraves plans to investigate the other 20 or so genes that keep the two species separate, in order to have a full genetic picture of the species’ divergence.

Additional authors of the study are Lakshmi Balagopalan and Susan M. Abmayr of Pennsylvania State University, and H. Allen Orr of the University of Rochester. The research was funded by the National Institutes of Health and the National Science Foundation.