Unlocking Gene Secrets: How Two Life Forms Evolved

Jim Crocker
21st August, 2025

Unlocking Gene Secrets: How Two Life Forms Evolved

Transcriptome sequencing of head and leg tissues from Pagurus maculosus and P. lanuginosus (a, b) produced high-quality assemblies (c) dominated by protein-coding gene expression (d) and revealed extensive sequence homology between these closely related species (e, f).

Image adapted from: Sultana et al. / CC BY (Source)

Key Findings

  • A study of Japanese hermit crabs, Pagurus lanuginosus and P. maculosus, confirmed they are distinct species that diverged about 6.24 million years ago
  • Gene activity in their legs showed more differences between the species than in their heads, suggesting legs evolved more rapidly
  • Pagurus maculosus legs showed increased activity in genes related to structural components like chitin, while Pagurus lanuginosus legs had more active pigmentation genes
Hermit crabs of the genus Pagurus are known for their wide variety of species and broad geographical spread. Within this diverse group, two species, Pagurus lanuginosus and Pagurus maculosus, have long posed a challenge to scientists due to their striking resemblance. Historically, these “right-handed hermit crabs” were often considered to be mere color variations of the same species, making it difficult to accurately classify and study them. Understanding the true relationships between such closely resembling species is crucial for mapping biodiversity and tracing evolutionary pathways. The advent of powerful genetic tools, such as Next-Generation Sequencing (NGS)[2], has revolutionized our ability to investigate these subtle distinctions. NGS allows researchers to rapidly sequence millions of DNA fragments simultaneously, providing detailed insights into an organism's genetic makeup and how genes are expressed. This technology has been instrumental in recent years for exploring genetic diversity and evolutionary relationships across many species. Indeed, earlier research utilized NGS to examine the molecular phylogeny of Pagurus species found along the Pacific coast of Japan[3]. That study revealed that while Pagurus lanuginosus and Pagurus maculosus share significant morphological similarities, they are in fact distinct species and are genetically the closest relatives among the Japanese Pagurus species studied[3]. This finding set the stage for a deeper investigation into the molecular changes that led to their separation. Building on this foundational understanding, a recent study conducted by researchers from institutions including the Japan International Research Center, Chinese Academy of Sciences, Tokyo Metropolitan University, National Institute of Genetics, SOKENDAI, Kyoto University, and Nanjing Agricultural University[1] aimed to uncover the specific molecular and gene expression changes that occurred as these two species diverged. The team sought to understand not just that they are different, but how they became different at a genetic level. To achieve this, the researchers employed transcriptome sequencing and de novo transcriptome assembly. Transcriptome sequencing involves analyzing all the active genes (those being copied into RNA) in specific tissues, rather than the entire DNA blueprint. This provides a snapshot of gene activity. De novo transcriptome assembly is like piecing together a puzzle without a reference image; it involves reconstructing full gene sequences from short RNA fragments, especially useful for species without a previously mapped genome. For this study, genetic material was collected from the cephalothorax (the fused head and chest region) and pereopods (legs) of both Pagurus lanuginosus and Pagurus maculosus. The findings provided significant insights into the evolutionary journey of these two species. The molecular analysis confirmed their close relationship, estimating that they diverged from a common ancestor approximately 6.24 million years ago. This timeline offers a clearer picture of their evolutionary history. The study also examined how genes were expressed differently in the head and leg tissues. It was found that gene expression in the head regions was more conserved, meaning fewer differences were observed between the two species in this area. However, the legs showed more distinct patterns. Pagurus maculosus exhibited an upregulation of more genes in its legs, while Pagurus lanuginosus showed increased activity in genes related to pigmentation in its legs. Crucially, the research identified specific gene categories that were highly expressed in the legs of Pagurus maculosus. These included genes associated with the extracellular matrix (the network of molecules that provides structural support to cells), chitin binding, and chitin-based larval cuticles. Chitin is a tough, protective substance that forms the exoskeleton of crustaceans. The higher expression of genes related to chitin and larval cuticles in P. maculosus legs suggests these genes play a role in the morphological differences observed between the two species. This aligns with earlier detailed descriptions of Pagurus maculosus's complete larval development[4], which highlighted distinct morphological features throughout its prezoeal, zoeal, and megalopal stages, including the formation of its chitinous exoskeleton. The presence of red-yellowish chromatophores on the maxillipeds of Pagurus maculosus larvae[4] further underscores the species-specific morphological traits that these genetic differences might influence. By combining advanced molecular techniques with a focus on specific tissue expression, this study has significantly advanced our understanding of the evolutionary divergence between Pagurus lanuginosus and Pagurus maculosus. It moves beyond simply identifying them as distinct species, as established by prior phylogenetic work[3], to pinpointing the specific genes and molecular pathways that underpin their unique characteristics and developmental processes[4]. This research offers new perspectives for systematic studies of hermit crabs and provides important information for future population-level research and the identification of variations within these ecologically important, though less studied, decapod species.

GeneticsMarine BiologyEvolution

References

Main Study

1) Transcriptome sequencing reveals the evolutionary histories and gene expression evolution in two related Pagurus species

Published 20th August, 2025

https://doi.org/10.1371/journal.pone.0330170

Related Studies

2) Next-Generation Sequencing Technology: Current Trends and Advancements.

https://doi.org/10.3390/biology12070997

3) Molecular phylogeny of ten intertidal hermit crabs of the genus Pagurus inferred from multiple mitochondrial genes, with special emphasis on the evolutionary relationship of Pagurus lanuginosus and Pagurus maculosus.

https://doi.org/10.1007/s10709-018-0029-8

4) The complete larval development of Pagurus maculosus Komai & Imafuku, 1996 (Decapoda, Anomura, Paguridae) reared in the laboratory, and a comparison with sympatric species.

https://doi.org/10.11646/zootaxa.3947.3.1


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