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Genotyping-by-Sequencing Study Uncovers Evolutionary Event in a Common Apple Tree Pest

Rhagoletis pomonella

NEW YORK (GenomeWeb) – Researchers from Rice University have used a genotyping-by-sequencing strategy to piece together genomic changes of a fruit fly Rhagoletis pomonella that allowed it to infect apple trees.

Reporting their results in Ecology Letters this week, the team found that the fly underwent extensive, genome-wide changes in a single generation that caused the divergence of two forms of the fly — an ancestral population with a life cycle timed to hawthorn trees and the population that diverged around 1850 with a life cycle timed to apple trees.

The flies lay their eggs once a year in either apples or hawthorns, depending on the population. Because apple trees fruit three to four weeks before hawthorn trees, the population that infests apple trees had to significantly adjust their life cycle. The researchers wanted to identify the genetic changes and how those changes evolved to enable the flies to lay eggs in apples. In addition, although the two populations currently continue to mate, there is evidence suggesting that they are diverging with the potential to become two separate species.

"These two forms have evolved very distinct differences and are on the path to evolving into two new species," lead author Scott Egan, an evolutionary biologist at Rice, said in a statement." In addition, "because they have a single generation per year, we know that all of the differences between the two has happened in no more than 170 generations."

The researchers collected hawthorn fly pupae and grew them under different environmental conditions to simulate both the apple tree environment and the hawthorn tree environment.

They then compared the genomic differences from one generation of environmental selection to the genomic differences seen between the two populations in nature.

For each of the groups of flies, researchers from the National Center for Genome Research performed reduced representation sequencing. The technique uses restriction enzymes and PCR to generate a library of fragments that focus in on regions of interest. For large numbers of samples, it can be more cost-effective than whole-genome sequencing approaches.

In the experimental group, the researchers identified over 32,000 SNPs that differed between the flies grown under hawthorn conditions and flies grown under apple conditions. When comparing those SNPs to the genomes of each fly population, the researchers found that the majority of the changes that were seen after just one generation of growing under a different lifecycle condition were the same changes that have evolved since the populations first split.

"Overall, we found that the genetic changes undergone by this first generation accounted for up to 70 percent of all the genetic changes that had occurred between the two populations since the 1850s," Egan said in a statement.

In addition, the changes that the researchers identified were widespread across the genome, impacting "numerous independent gene regions," the authors wrote. While it may seem unusual for such dramatic changes to be seen after just one generation, the authors attribute it in part to the nature of the specific condition. An ecological adaption like when and where a fly lays its eggs and its dormant stage likely impacts many different genes, so "selection may more often have genome-wide consequences," the authors wrote.