The More Social the Shrimp, the Larger Its Genome

A team of researchers from Columbia University has found that eusocial snapping shrimp possess larger genomes compared to their less-social relatives. The larger genome comprises an accumulation of transposable elements – moving DNA sequences – providing new insights on the relationship between social and genome evolution. The research is published in PNAS.¹

Eusociality in marine creatures

Professor Dustin Rubenstein of Columbia University has been studying snapping shrimp for many years. The crustaceans are so-called because of the distinct "snap" sound that their claws makes when they closes quickly. This is a defense mechanism that can deter predators and stun prey. Sometimes, large gatherings of snapping shrimp are so loud that they have been known to disrupt underwater research and communications.

Rubenstein, a professor of ecology, evolution and environmental biology, is particularly interested in the Synalpheus genus of snapping shrimp, as it contains the only known aquatic eusocial species.

If an organism is eusocial, it demonstrates advanced social behaviors including: living together in groups, cooperating to take care of offspring, division of labor and overlap of generations such that younger populations can assist older generations. It is a phenomenon that is well recognized and studied in certain species of insects, such as ants.

Rubenstein and team serendipitously discovered that the shrimp possess another interesting characteristic: the size of their genome varies dramatically and appears to be related to their social organization. This contradicts what is known about eusociality in the insect world. Genomic studies have demonstrated that eusocial insects typically have smaller genomes than their less-social relatives.  

Larger genome, greater accumulation of transposable elements

The researchers – including collaborators from Seattle University and the Bedford Institute of Oceanography – decided to dig deeper to understand the social shrimp's larger genome. Applying novel genomics research techniques, the group analyzed the genomes of Synalpheus snapping shrimp and uncovered that the larger genome size identified in the eusocial shrimp contained an accumulation of transposable elements.

Transposable elements are sometimes referred to as "jumping genes" – they are DNA sequences that move within the genome. This movement can create and/or reverse mutations that alter a cell's genetic identity, thereby contributing to evolution.

"We developed a method for extracting information about transposable elements from low coverage sequencing data. This approach allowed us to compare large numbers of shrimp species in an efficient and cost-effective manner without first having to sequence and assemble the genomes of every species," Rubenstein told Technology Networks.

"We found that eusocial species had more transposable elements in their genomes than non-eusocial species," he added. "We used evolutionary modeling to explore why such a relationship exists and found that they seem to accumulate in the genomes of eusocial species."

The researchers hypothesize that the increased transposable elements in the genome are due to the unique social organization of the shrimp. Being a eusocial species, the majority of the shrimp will never reproduce in their lifetime. The reduced effective population size means that it is difficult to "purge" transposable elements from the genome; consequently, they accumulate over time. "Interestingly, each eusocial species seems to accumulate a different type of transposable element in their genome," Rubenstein added.   

The relationship between genome and social evolution

In the publication, the authors state that their research highlights a fluid relationship between genome and social evolution, demonstrating how social organization might have an influence on the architecture of the genome. "This is one of the first studies to link transposable elements to different forms of social living, opening a whole range of questions about how the unique population demography of social species influences genome evolution," Rubenstein commented.

The incredible size of the shrimp genomes posed a challenge for the researchers – it precluded them from applying next-generation sequencing techniques to the entire shrimp genome, a method known as whole-genome sequencing, or WGS. "We developed a novel way to study transposable elements from limited amounts of sequence data," Rubenstein explained. As a next step, the team hope to go back and sequence the whole genome to gather even more data and learn as much as possible about the relationship between social evolution and genome evolution. They also intend to analyze – in greater detail – where the transposons occur to determine if they play a role in the evolution of eusociality. "We also hope to look at transposable elements in other social organisms, like birds and mammals, to see whether these same relationships hold in vertebrates," Rubenstein concluded.

Dustin Rubenstein was speaking to Molly Campbell, Science Writer for Technology Networks.

Reference: Chak STC, Harris SE, Hultgren KM, Jeffery NW, Rubenstein DR. Eusociality in snapping shrimps is associated with larger genomes and an accumulation of transposable elements. Proc Natl Acad Sci USA. 2021;118(24):e2025051118. doi: 10.1073/pnas.2025051118.