Tiny Copepods Illuminate Genetic Adaptation and Natural Selection

A groundbreaking study from the University of Wisconsin–Madison has established a direct link between the chromosomal location of genes and the process of natural selection. Researchers discovered that the arrangement of genes significantly influences a population’s ability to adapt to rapid environmental changes. The findings, published on November 24, 2025, in Nature Communications, shed light on how these tiny aquatic crustaceans, known as copepods, have evolved in response to shifting habitats.

The research team focused on three sibling species within the Eurytemora affinis species complex. By analyzing their genomes, they mapped the impact of specific mutations, known as chromosomal fusions, on gene locations. Surprisingly, the team found that these ancient fusions, which occurred millions of years ago, continue to affect the adaptability of contemporary copepod species.

Historically, copepods thrived in coastal estuarine ecosystems. In recent decades, they have invaded freshwater environments like the Great Lakes due to the transport and discharge of ship ballast water. Professor Carol Eunmi Lee, an expert in integrative biology at UW–Madison, has dedicated over 20 years to studying copepod genetics, aiming to unravel how these creatures adapt and flourish in new ecosystems.

Understanding Chromosomal Changes

The short lifespan and compact genome of copepods make them ideal for genetic research. Despite their suitability, postdoctoral researcher Zhenyong Du spent nearly three years sequencing the genomes and mapping chromosomal fusions to identify patterns of natural selection. The study revealed that each sibling species possesses a distinct number of chromosomes, which is unusual for organisms that can interbreed.

The European clade of copepods has 15 chromosomes, the Gulf clade has seven, while the Atlantic clade, now inhabiting the Great Lakes, has only four. This variation prompted Du and Lee to investigate the evolutionary implications of these differing chromosomal structures.

Implications for Evolutionary Adaptation

The research highlighted how chromosomal fusions play a crucial role in adaptation. These mutations, which merge different chromosomes into one, can physically link genes, creating a potential unit of inheritance during natural selection. Du noted that throughout the evolutionary history of copepods, salinity has been a significant environmental factor influencing their living conditions.

One of the primary mechanisms for coping with salinity changes involves proteins known as ion transporters. The study found that ancient chromosomal fusions had grouped the genes responsible for these transporters closer together. This arrangement moved them away from areas of the chromosome prone to recombination, preserving advantageous gene combinations.

Recombination, the exchange of genetic material during reproduction, enhances genetic diversity and can aid in a species’ survival. However, the fusions observed in copepods are so beneficial that they may have become fixed in the evolutionary process.

The research marks a significant milestone in understanding the architecture of genomes and their role in evolutionary adaptation. The findings suggest that the fusion sites established millions of years ago have remained critical for natural selection, particularly in invasive copepod populations in the Great Lakes.

While the study primarily focuses on copepods, Du and Lee anticipate broader implications for understanding genetic architecture and adaptation mechanisms in other invasive species. Moreover, these insights could help predict which populations are likely to survive and adapt to future climate change.

Lee emphasized the importance of genome architecture in determining how populations respond to natural selection, stating, “It’ll affect the mechanism of natural selection in a population, and determine how quickly it can evolve and respond.”

This pioneering research not only enhances our understanding of copepod evolution but also opens new avenues for studying genetic adaptation across various species in the face of environmental change.