The research, led by Maëlle Daunesse, Eulalie Liorzou, Elise Parey, Diego Villar and Camille Berthelot, tackles a problem that has long frustrated evolutionary biologists: distinguishing adaptive changes in gene expression from the background noise of neutral evolution. Over millions of years, transcriptomes—the complete sets of RNA molecules produced by tissues—accumulated countless random shifts in expression level. Most of these shifts mean nothing for survival. A minority, however, were driven by natural selection because they improved some aspect of physiology. Separating the two categories with confidence has been notoriously difficult, blurring the adaptive signatures written into mammalian genomes.

To cut through that noise, the team built a phylogeny-aware framework for modelling quantitative trait evolution, integrating comparative multiomics data across four rodent species. They generated RNA-sequencing data from liver and heart tissue in two mole-rats—the naked mole-rat (Heterocephalus glaber) and the Damaraland mole-rat (Fukomys damarensis)—and compared these profiles with two rodent outgroups, the guinea pig (Cavia porcellus) and the mouse (Mus musculus). The outgroups matter because they anchor the comparison: by modelling how expression levels should drift along each branch of the evolutionary tree, the researchers could flag genes whose expression had shifted faster in mole-rat lineages than neutral drift alone could plausibly explain.

The analysis, built around the Expression Variance and Evolution approach, revealed hundreds of genes whose expression levels had undergone lineage-specific acceleration consistent with directional selection rather than random walk. After careful normalisation—using variance-stabilising transformation and transcripts-per-million strategies validated through sensitivity analyses—the team confirmed that these shifts were not artefacts of sequencing depth, gene length or transcript annotation. Orthology reannotation and genome assembly quality checks further ensured that the genes being compared across species were true one-to-one counterparts, eliminating a common source of false positives in cross-species transcriptomics.

But identifying shifted genes was only half of the puzzle. To connect expression evolution with its underlying regulatory mechanisms, the researchers layered a second data type onto the transcriptomic map: epigenomic profiles of cis-regulatory elements, the DNA sequences near genes that control when, where and how strongly they are transcribed. Cis-regulatory landscapes are known to turn over rapidly in mammalian evolution, and regulatory changes are widely hypothesised to be a major engine of phenotypic innovation. If a gene’s expression truly evolved under selection in mole-rats, the logic goes, the regulatory elements governing it should show signs of accelerated change as well.

That is precisely what the team found. Genes with lineage-specific expression shifts were surrounded by epigenomic landscapes that also displayed signals of accelerated evolution—a concordance that is difficult to explain by chance or by neutral genomic processes diverging at different rates. The researchers developed a weighted regulatory score, assigning regulatory elements to nearby genes within optimised genomic windows, and showed that genes exhibiting both transcriptomic and regulatory shifts cluster at specific loci. At these candidate loci, the two independent lines of evidence—expression and regulation—point in the same direction, strengthening the case that selection, not drift, drove the change.

The functional identities of these fast-evolving loci are as striking as the methodological rigour behind them. Enrichment analyses showed that genes with evidence of selection at both expression and regulatory levels cluster in pathways central to mole-rat physiology, including metabolism and stress responses. For animals that spend their entire lives underground in hypoxic, carbon dioxide-rich burrows, metabolic rewiring is not a luxury but a necessity. Cellular stress pathways, likewise, must cope with the oxidative and environmental challenges of the subterranean niche. The study’s molecular signatures suggest that selective pressures honed exactly those biological systems a burrowing mammal would need to tune.

Among the genes implicated by the analysis is Pygl, encoding liver glycogen phosphorylase, a key enzyme in glycogen breakdown. RNA-sequencing read coverage across the Pygl locus, presented in the study’s supplementary figures, illustrates how expression and regulatory profiles diverge across the four species in ways consistent with lineage-specific tuning. Genes of this kind offer testable hypotheses for experimental follow-up: if regulatory sequences around Pygl indeed evolved adaptively in mole-rats, they could contribute to the extraordinary metabolic flexibility these animals display when oxygen is scarce.

Beyond the mole-rat findings themselves, the study’s framework carries broader significance for evolutionary genomics. Comparative multiomics studies have often treated gene expression and gene regulation as separate domains, analysed with different toolkits and interpreted in isolation. By jointly modelling both within a single phylogenetic framework, the Berthelot and Villar teams demonstrate that concordant evidence across molecular layers is a far stronger indicator of adaptive evolution than either layer alone. The approach could be applied to any group of organisms with multiple genome assemblies and tissue-specific expression data, from cavefish to high-altitude mammals, wherever convergent adaptation to extreme environments raises similar questions.

The work also underscores how much biology remains hidden in species that were long considered curiosities. Mole-rats have already reshaped research on ageing, cancer suppression and pain insensitivity, and the loci flagged by this study provide a molecular shortlist for understanding traits that could eventually inform human medicine. As the authors note, their results illuminate how gene regulation and expression evolve in concert in this mammalian model, and they highlight genomic loci where multiple lines of evidence converge on a single conclusion: these are the places in the mole-rat genome where natural selection left its clearest fingerprints, shaping a lineage into one of the most unusual mammals on Earth.

Subject of Research: Comparative multiomics analysis of gene expression and regulatory evolution in African mole-rats

Article Title: Coordinated shifts in gene expression and regulation identify fast evolving loci linked to unique mole-rat traits

Article References: Daunesse, M., Liorzou, E., Parey, E., Villar, D., & Berthelot, C. (2026). Coordinated shifts in gene expression and regulation identify fast evolving loci linked to unique mole-rat traits. BMC Biology. https://doi.org/10.1186/s12915-026-02713-5

Image Credits: AI Generated

DOI: 10.1186/s12915-026-02713-5

Keywords: mole-rats, evolutionary genomics, gene expression, gene regulation, adaptive evolution, cis-regulatory elements, comparative multiomics, phylogenetic modelling, BMC Biology, naked mole-rat, Damaraland mole-rat, subterranean adaptation

Crustacyanin, a crucial component of the crustacean’s shell pigmentation, plays a pivotal role in the protective coloration that aids in camouflage and survival. The study meticulously maps out the various genes associated with crustacyanin, shedding light on the evolutionary pressures that have shaped these genetic traits. Through genomic analysis, the researchers have identified multiple isoforms of the crustacyanin genes, suggesting a complex regulatory mechanism that underlies their expression and functional diversity.

Delving into the comparative genomics aspect, the team draws on genomic data not only from Neocaridina denticulata sinensis but also from related crustacean species. This comparative analysis elucidates the evolutionary trajectory of the crustacyanin gene family, highlighting conserved regions that suggest a shared ancestor among various taxa. By employing alignment techniques, the study underscores the genetic variations that have emerged and persisted in different lineages, emphasizing the role of natural selection in shaping these vital traits.

Localization analysis emerges as another critical component of this research. The team has employed in situ hybridization techniques to determine the specific tissues in which crustacyanin genes are expressed. This spatial characterization is essential, as it correlates with the functional roles these genes play in pigmentation and environmental adaptability. The findings indicate that crustacyanin expression is not uniform; instead, it varies across different developmental stages and tissue types, suggesting a finely tuned regulatory network that responds to both intrinsic and extrinsic factors.

The implications of this research extend beyond academic curiosity, touching upon significant environmental and ecological themes. Understanding the gene family responsible for pigmentation can provide insights into how crustaceans adapt to changing environments and threats, including predation and climate change. Furthermore, the insights gained could foster better conservation strategies for these species, as key genetic markers can be monitored to assess population health and resilience.

Moreover, the study’s findings could have groundbreaking implications for aquaculture, where Neocaridina species are increasingly favored for their ornamental value. The introduction of specific breeding programs that consider these genomic insights might enhance desirable traits in ornamental shrimp, leading to healthier stocks with vibrant colors that appeal to aquarists worldwide. Indeed, such applications further underscore the potential for genomic research to bridge academic exploration with practical benefits in commercial industries.

In the realm of evolutionary biology, the research prompts a re-evaluation of how pigmentation genes like crustacyanin contribute to speciation and biodiversity. The depth of information uncovered serves as a vital resource for evolutionary biologists examining the adaptive significance of pigment production in various species, four illuminating the genetic mechanisms that foster diversity across ecological niches.

Moreover, the intricate understanding of gene expression regulation revealed through this study can inspire further investigations into analogous systems across different taxa. It draws attention to the broader implications of gene families involved in pigmentation and color change, which may have evolutionary parallels in other animal groups. Identifying these relationships can unravel the complexities of evolutionary adaptations and their genetic foundations.

As the realm of genomics continues to evolve at a rapid pace, studies like this one by Feng et al. highlight the significance of integrating comparative genomics with practical applications. It pushes the boundaries of how we perceive not only crustaceans but also the vast network of genetic interrelations that characterize life on Earth. As future research endeavors build on these findings, the hope is to unravel even more about the genetic tapestry that underlies survivability and adaptability in changing ecosystems.

This extensive exploration of the crustacyanin gene family opens numerous avenues for future research, prompting scholars to delve deeper into the multifaceted aspects of gene function. Possibilities abound for researchers interested in investigating how environmental factors influence gene expression, how these adaptations contribute to overall fitness, and how such knowledge can be translated into the conservation of biodiversity.

In conclusion, the pioneering work presented by Feng et al. sets the stage for further exploration into the crustacyanin gene family and its implications for various fields. The study not only enriches our comprehension of the genetic landscape of Neocaridina denticulata sinensis but also serves as a crucial reminder of the interconnectedness of life at the genomic level. It exemplifies how the intricacies of evolutionary biology and comparative genomics can pave the way for innovations in sustainability, conservation, and aquaculture, blending fundamental research with practical applications that hold the promise for a brighter ecological future.

Through the meticulous efforts of the research team, the crustacyanin gene family is unveiled, not merely as a subject of academic inquiry but as a critical piece in the puzzle of life’s evolutionary narrative. As researchers and practitioners alike reflect on the broader implications of these findings, one can only anticipate the continued revelations that await in the intricate dance of genetics, adaptation, and survival.

Subject of Research: Crustacyanin gene family in Neocaridina denticulata sinensis

Article Title: Genome-wide identification of the crustacyanin gene family in Neocaridina denticulata sinensis based on comparative genomics and localization analysis.

Article References:

Feng, D., Li, H., Liu, Y. et al. Genome-wide identification of the crustacyanin gene family in Neocaridina denticulata sinensis based on comparative genomics and localization analysis.
BMC Genomics (2025). https://doi.org/10.1186/s12864-025-12371-6

Image Credits: AI Generated

DOI: 10.1186/s12864-025-12371-6

Keywords: Crustacyanin, Neocaridina denticulata sinensis, Comparative Genomics, Gene Family, Evolutionary Biology, Pigmentation, Aquaculture.