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UW Researcher Contributes to Science Cover Story About Insect Genome Sequencing

May 15, 2014
Green insect
This wingless stick insect was used for genome research conducted by a team that included Alex Buerkle, a UW professor of botany. The work was published as the cover story in this week’s issue of Science. (Moritz Muschick Photo)

While scientists know that natural selection can drive the origin of species, far less is known about the genetics of parallel speciation -- something that has intrigued scientists for decades.

Alex Buerkle, a University of Wyoming professor in the Department of Botany, along with multiple researchers, looked to wingless stick insects (often referred to as walking sticks) out West for answers. The group analyzed genome divergence between replicate pairs of these California insect populations that were adapted to two different host shrub species and undergoing parallel speciation. Parallel speciation is the simultaneous independent origin of species -- in this case, walking sticks living on two different types of shrubs in fairly close proximity.

“This research is getting so much attention. Not only did we sequence the genome of a walking stick, but we then sequenced 160 of them,” Buerkle says. “That scale is highly unusual. That scale has not been done on very many organisms, especially not those in their natural setting.”

A research article on the subject, titled “Stick Insect Genomes Reveal Natural Selection’s Role in Parallel Speciation,” was published today (Thursday) as the cover story in this week’s issue of Science, an international weekly science journal.

The work includes contributions from two others with UW connections. Utah State University Assistant Professor Zach Gompert, co-lead writer of the paper, was a doctoral student in Buerkle’s lab from 2008-2012. University of Nevada-Reno Assistant Professor Tom Parchman, another co-writer of the paper, was a post-doctoral fellow in Buerkle’s lab from 2008-2013. Patrik Nosil, the paper’s senior writer, is in the Department of Animal and Plant Sciences at the University of Sheffield in the United Kingdom. In all, 13 writers contributed to the paper.

Let the insects do the walking

Armed with a grant from the European Union, Nosil performed the study in California. He conducted his observations in nature at four locations near Joshua Tree National Park and Palm Springs. Nosil studied the allele frequencies, or frequency of genetic variants in evolution, of walking insects living on one shrub and compared them to the insects living on a different type of shrub in near proximity, Buerkle explains.

“When we move the insets to a new plant, they have some genetic changes,” Buerkle says. “Any change in the frequency of genetic variants is evolution. Any time a population reproduces, the allele frequency changes. Some changes are due to chance variation. In others, it’s due to natural selection, where certain insects reproduced and survived better than others.”

But Buerkle stresses some genetic variants found in the insects do repeat at multiple locations, which indicate that parallel speciation can involve both repeatable and peculiar divergence at the genetic level, and the repeated component involves many regions affected by divergent selection.

“When we see repeated things, this shows there are potentially rules. It’s not just happenstance,” he says.

According to the study’s results, 83 percent of divergent Single Nucleotide Polymorphisms (SNPs) were divergent in only a single population pair of the insects. The other 17 percent of divergent SNPs were divergent in two or more of the insect population pairs. An SNP is a DNA sequence variation occurring when a single nucleotide in the genome differs between members of a biological species or paired chromosomes.

“This is one of the things that’s striking. A lot of differences were restricted to one locale. They were peculiar, not shared,” Buerkle says. “For most genetic change of this type, if you replayed the tape of life again, it wouldn’t be repeated.”

UW computing plays integral research role

UW’s high-performance computing capabilities played an important role in completing the research. Buerkle and his students used both Buerkle’s computer cluster and Mount Moran, the nickname for UW’s high-performance computing cluster, as resources to conduct the work.

“We did many of the analyses of the genome, for this paper, at UW. This included assembling the genome and doing a lot of the computationally intensive statistics,” Buerkle says. “The way UW contributed is that we have been out front in being able to use computers to analyze the genome sequencing data.”

Buerkle adds the research experience allowed Gompert and Parchman, his former students, to obtain faculty jobs “in a very competitive environment.”

“The work we’re doing isn’t just to understand these insects,” Buerkle says. “It’s to understand how life evolves through the generations and the extent to which the changes are peculiar and esoteric, and wouldn’t be repeated if life did repeat itself.”

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