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Stick Insect Study Reveals Reproducible Aspects of Parallel Speciation

NEW YORK (GenomeWeb) – A study appearing online today in Science suggests that natural selection prompts changes affecting at least some reproducible genetic regions in related organisms adapting to new environments.

By sequencing and comparing the genomes of more than 150 Timema cristinae stick insects from two different host plants at four sampling sites in California, researchers from the University of Sheffield and elsewhere narrowed in on thousands of genome regions that have diverged between ecotypes of the insect that have become adapted to the alternative plant hosts.

The team saw that some of these divergent regions in the genomes of stick insects from those two ecotypes also overlapped with areas showing genetic shifts in insects experimentally forced to adapt to new host plants in the field.

Together, the findings are consistent with the notion that some parts of the genome are prone to change during speciation events associated with particular selective pressures, while other adaptations are more malleable.

That suggests that the general reproducibility and repeatability of evolution "is really a quantitative question," according to Patrik Nosil, the study's senior author and an animal and plant sciences researcher at the University of Sheffield.

"Sometimes it's painted as black-or-white," Nosil told GenomeWeb Daily News, "but what our paper shows is something in between."

The stick insect has found favor as a model system for studying adaptation and speciation, Nosil noted, since it's easy to swap the wingless insects to different host plants — manipulations that sometimes start the bugs on the road to reproductive isolation and speciation.

Past studies suggest that stick insects that reside on distinct host plants, known as ecotypes, are somewhat more prone to such reproductive isolation than those from different locations, regardless of the degree of genetic relatedness.

To look at this in more detail, Nosil and his colleagues began by assembling, ordering, and annotating a stick insect draft genome that had been described in an Ecology Letters paper earlier this year.

From there, they used Illumina instruments to re-sequence the genomes of 160 T. cristinae insects adapted to Adenostoma fasciculatum or Ceanothus spinosus host plants, looking at around 20 insects per ecotype at four sampling locations representing insects.

Those experiments highlighted several regions of the genomes where ecotype pairs had divergent sequences regardless of the sampling site.

"Somewhere in the range of 15 to 20 percent of the time, you'd see these repeated areas of genomic divergence," Nosil said. "If you went to one hillside, the ecotypes would be different in that genomic region and if you went to another hillside they'd also be different in that same region."

Given the malleability of the model system, the researchers were able to take this observation a step further, testing the consequences of placing stick insects onto new host plants.

"We transplanted the insect ecotypes onto the different host plants in a new area and then measured allele frequency changes in real time," Nosil said.

The insects selected for the transplantation experiments came from a hybrid region where interbreeding between the T. cristinae ecotypes still occurred, he explained, and were transplanted onto both Adenostoma and Ceanothus plants.

After letting the insects adapt for one generation, the researchers re-captured hundreds of stick insects, which were re-sequenced and compared with pre-transplantation insects — again with the goal of seeing genomic areas prone to change in insects from both plant hosts.

Not only did such areas turn up, but many coincided with parts of the genomes with sequence divergence in the original ecotype genome comparison, suggesting at least some of the genetic changes involved in speciation are reproducible.

The field studies "provided experimental validation that those regions of divergence evolved by natural selection," according to Nosil.

He noted that such allele frequency changes were particularly common within protein-coding portions of the genome and amongst genes involved in metal-binding pathways, though potential reasons for the over-representation of such processes have not yet been explored.

The researchers are in the process of using genetic mapping to try to learn more about the variants behind various physical, biological, and behavioral features that differ between insects from the T. cristinae ecotypes included in the study. They are also doing similar experiments in species from other Timema species found in California, including some at early stages of reproductive isolation and speciation.