Study Links Gene Location to Rapid Adaptation in Copepods

A groundbreaking study from the University of Wisconsin-Madison has established the first empirical link between the chromosomal location of genes and natural selection. This research indicates that the arrangement of genes can significantly influence how swiftly populations adapt to rapid environmental changes. Published in the journal Nature Communications on November 24, 2025, this study sheds light on the evolutionary mechanisms of three closely related copepod species, collectively known as the Eurytemora affinis species complex.

The research team, led by Professor Carol Eunmi Lee, conducted an extensive analysis of the genomes of these tiny aquatic crustaceans. They focused on mutations known as chromosomal fusions, which have shifted the locations of genes throughout the copepods’ evolutionary history. Surprisingly, despite these fusions occurring millions of years ago, they continue to impact the adaptability of contemporary copepod species.

Historically, these copepods thrived in coastal estuarine ecosystems. In the last eight decades, however, they have expanded into freshwater environments such as the Great Lakes, largely due to the transport and discharge of ship ballast water. Professor Lee, who has spent over two decades investigating copepod genetics, aims to uncover how these organisms manage to adapt and flourish in new habitats.

Uncovering Genetic Mysteries

The short lifespan and compact genome of copepods make them ideal subjects for genetic research. Postdoctoral researcher Zhenyong Du dedicated nearly three years to sequencing their genomes and mapping chromosomal fusions that have influenced natural selection patterns. The findings revealed that each sibling species in the complex possesses a distinct number of chromosomes.

Du explains, “We were absolutely shocked,” as they discovered that the European clade has 15 chromosomes, the Gulf clade has seven, and the Atlantic clade, which now inhabits the Great Lakes, has only four chromosomes. This significant variation prompted the researchers to delve deeper into why these species exhibit such different genomic architectures.

The study examined the evolutionary history of these chromosomes and found that chromosomal fusions—where different chromosomes merge into one—are common mutations that can enhance survival. This phenomenon allows genes from various chromosomes to be physically linked, making them more likely to be inherited together during natural selection.

Adaptation Through Chromosomal Fusions

The researchers hypothesized that the chromosomal fusions leading to different chromosome counts might confer advantages for survival. Du noted that salinity has historically been a critical factor in the copepods’ living conditions. To adapt to varying salinity levels, these organisms rely on proteins known as ion transporters.

The study revealed that ancient chromosomal fusions caused genes coding for vital ion transporters to cluster together. This grouping moved these genes closer to the chromosome’s center, a region less prone to recombination. Such positioning helps maintain beneficial gene combinations, essential for adaptation.

Recombination, the exchange of DNA during reproduction, typically enhances genetic diversity, which is advantageous for species survival. Yet, the study indicates that some fusions are so beneficial they become permanent fixtures in the evolutionary process.

The implications of this research extend beyond copepods. The findings provide empirical evidence supporting the idea that genomic architecture, particularly chromosomal fusions, plays a crucial role in evolutionary adaptation. As copepods evolved, natural selection appeared to favor fusions that positioned key ion-transporter genes centrally on chromosomes.

The research suggests that ancient fusion sites remain significant for natural selection, particularly in invasive populations like those in the Great Lakes. While the focus is on copepods, the insights gained may inform understanding of genetic architecture evolution and adaptation mechanisms in other invasive species.

These findings are also vital for predicting how various populations may survive and adapt to future climate challenges. Professor Lee emphasized, “Genome architecture likely has profound impacts on how populations respond to natural selection. It will affect the mechanism of natural selection in a population and determine how quickly it can evolve and respond.”

This study marks a significant advancement in our understanding of evolutionary biology, offering fresh perspectives on the intricate relationship between genetic structure and natural selection.