Everywhere we look, we find plants that seem to be perfectly fit for their environment. This is due to a process known as local adaptation. Some species of plant are found in many different environments, and so different individuals from the same species develop characteristics to better suit them within their environment. Groups of these individuals with special characteristics are called ecotypes.

Sometimes the environment can change drastically over short distances and we can find many different ecotypes of the same plant species living in close proximity. Surprisingly, even though these ecotypes are likely interbreeding, they manage to maintain their differences. How is this possible?

In a great collaborative effort, an international research team sought to answer this question using some of the most prolific and resourceful plant species of them all: sunflowers.

The researchers collected samples from 151 different sunflower populations across North America. These represented three different species, each with multiple ecotypes. They then sequenced the genomes of over 1,500 individual sunflowers from these 151 populations to uncover the genetic mysteries underlying ecotypic differentiation in sunflowers.

One of the specific traits that varies between sunflower ecotypes they investigated was flowering time. Some ecotypes flower early to avoid the heat of the summer while others flower later because they live in cooler conditions. The consortium conducted a genome-wide association study to find out where the genes controlling flowering time, along with the genes controlling over 90 other traits, are located on the sunflower genome.

The researchers discovered that the genes controlling flowering in the early flowering ecotype were completely absent from the late flowering ecotype. And, overall, each sunflower ecotype had unique, non-recombining regions of the genome that contained genes contributing to local adaption. 

These “massive haplotypes” aren't exchanged during interbreeding because they simply don’t exist in the other ecotypes. This explains why sunflower ecotypes can coexist in close proximity, but also raises further questions about how the new species within the sunflower family might develop.