Unlocking the genetic basis of adaptive evolution: study reveals complex chromosomal rearrangements in a stick insect

Chromosomal rearrangements where large chunks of chromosomes are inverted, moved, deleted or duplicated, provide a possible source for such large-scale “macromutations.” However, characterizing chromosomal rearrangements with commonly tried DNA sequencing methods has been difficult.

Many organisms, including humans, are diploid, meaning they have two sets of chromosomes — one from each parent. The same is true for stick insects. This makes identifying chromosomal rearrangements with species challenging when assembling genomes.

“In the past, we’ve averaged data from each chromosome set, but the limited accuracy of this method doesn’t tell the whole story,” says Utah State University evolutionary biologist Zachariah Gompert. “Using newer, molecular and computational approaches that generate phased genome assemblies, where the two copies of each chromosome are assembled separately, has enabled us to directly show how complex chromosomal rearrangements have allowed stick insects to adapt by being cryptic on different host plants and thereby avoid predation.”

In the April 18, 2025 online issue of the American Association for the Advancement of Science journal Science, Gompert and colleagues report adaptive divergence in cryptic color pattern is underlain by two distinct, complex chromosomal rearrangements, where millions of bases of DNA were flipped backwards and moved from one part of a chromosome to another, independently in populations of stick insects on different mountains. Contributing authors on the paper include Gompert’s long-time collaborator Patrik Nosil and other researchers from the French National Center for Scientific Research (CNRS), along with scientists from the University of Notre Dame, the University of Nevada, Reno, and The Institute of Cancer Research in the United Kingdom. The research is supported by the National Science Foundation and the European Research Council.

The scientists studied Timema cristinae insects with varied color patterns, collected from two mountains near Santa Barbara, California. The wingless, plant-feeding insects are divergently adapted to two different plant species in the coastal chaparral habitats. One stick insect pattern is green, allowing it to blend in with the California lilac, while the other sports a thin, white stripe on its back making it nearly undetectable among the needle-like leaves of the chamise shrub.

Gompert and colleagues showed this adaptive difference in color pattern is almost completely explained by the presence versus absence of these individual complex, chromosomal rearrangements.

“The new phased genomic assembly technology used in this study was a critical piece in helping us examine how color pattern evolved in these insects,” says Gompert, professor in USU’s Department of Biology and the USU Ecology Center. “Our findings suggest chromosomal rearrangements might be more widespread and more complex than we previously thought.”

He says these mutations, despite being large, are easy to miss using traditional DNA sequencing approaches.

“Chromosomal rearrangements can be difficult to detect and characterize using standard approaches,” Gompert says. “We’re essentially exploring the ‘dark matter’ of the genome.”

Structural variation, he says, rather than being rare, may be regularly available to prompt evolution.

“We’re just scratching the surface,” Gompert says. “We’ve lacked the tools to detect structural variation, but with improved technology we hypothesize it plays a more important role in evolution than previously recognized.”