The research team, led by scientists working on deep-sea echinoderms, sequenced the mitochondrial genomes of four brittle star species collected from deep-sea environments: Ophioctenella acies, a hydrothermal vent dweller; Ophiura cf. irrorata and Ophiactis profundi, both from non-reduced deep-sea habitats; and Ophiocreas nudusoralis. Notably, the mitochondrial genome of O. acies represents the first ever reported from a hydrothermal vent ophiuroid, filling a significant gap in our understanding of how life thrives at these chemically extreme undersea hot springs.

Mitochondrial genomes are compact circular DNA molecules inherited maternally, making them powerful tools for reconstructing evolutionary relationships. Using next-generation sequencing on an Illumina NovaSeq 6000 platform, the researchers extracted genomic DNA from specimens preserved in ethanol, assembled the circular mitogenomes with the NOVOPlasty assembler, and annotated them with the MITOS2 toolset. The four new genomes ranged in length from 15,850 to 16,326 base pairs and contained the standard set of 37 mitochondrial genes, including 13 protein-coding genes, two ribosomal RNA genes, and 22 transfer RNA genes.

With these new sequences in hand, the team employed maximum likelihood and Bayesian inference approaches to reconstruct the phylogeny of the entire class. The resulting trees, generated independently by three different methods, consistently supported the monophyly of the two major clades within Ophiuroidea, Ophintegrida and Euryophiurida, as well as the four major orders: Ophiurida, Euryalida, Amphilepidida, and Ophiacanthida. This is a significant achievement, as the monophyly of Amphilepidida and Ophiacanthida had remained controversial in previous analyses, with different datasets and methods yielding up to nine distinct topologies among 18 generated trees in earlier work.

The improved phylogenetic resolution also clarified previously unstable family-level relationships. Within Euryalida, the study confirmed that Asteronychidae clusters with Gorgonocephalidae rather than occupying a basal position, consistent with some prior molecular studies. Within Ophiurida, the relationships among species in the families Ophiuridae and Ophiopyrgidae remain complicated, with the genus Ophiura showing some conflicts with earlier classifications. The authors suggest that an integrated review combining morphological and molecular evidence is urgently needed to fully resolve these remaining uncertainties.

Beyond phylogeny, the study delved into the temporal history of brittle star evolution. Using BEAST software with seven fossil-based calibration points and an uncorrelated relaxed molecular clock, the researchers estimated that the common ancestor of all Ophiuroidea originated around the Permian-Triassic boundary, approximately 255 million years ago, coinciding with the most severe mass extinction event in Earth’s history. The four major orders radiated at different times: Ophiacanthida and Amphilepidida emerged during the Triassic, Ophiurida during the Jurassic, and Euryalida more recently in the Cretaceous.

The ancestral state reconstruction revealed a fascinating pattern of bidirectional habitat transitions between shallow and deep waters. Ophiacanthida and Euryalida appear to have originated in the deep sea and repeatedly colonized shallow environments, while Ophioleucida and Ophiurida expanded from shallow waters into the deep. These transitions were particularly concentrated during the Jurassic and Cretaceous periods, coinciding with major geological events such as plate tectonic movements, the formation of new marine basins, rising deep-sea temperatures that reduced the thermal gradient between surface and bottom waters, and significant sea level rise. The mid-Cretaceous divergences may be linked to repeated oceanic anoxic events and warm geological intervals that reshaped ocean chemistry and ecology.

One of the most intriguing findings concerns the colonization of chemosynthetic ecosystems, such as hydrothermal vents and cold seeps, which are oases of life in the otherwise food-scarce deep sea. The study found that among four chemosynthetic species analyzed, three experienced significant fluctuations in marine sulfate levels just prior to their divergence, suggesting a possible link between sulfur chemistry and the evolution of vent and seep fauna. The cold-seep species Histampica haimaensis was the first to diverge in the mid-Jurassic, followed by Amphiura sp. in the early Cretaceous, while Ophiophthalmus serratus and Ophioctenella acies diverged in the early Paleogene.

When the researchers examined adaptive evolution at the molecular level, they found a surprising contrast between the hydrothermal vent species and the cold-seep species. The three cold-seep brittle stars showed clear evidence of mitochondrial gene rearrangements and positive selection on specific genes, including ATP6, ATP8, ND2, COX1, and COX2, consistent with adaptive responses to the toxic, oxygen-poor conditions of their environments. However, the hydrothermal vent species O. acies showed no gene rearrangements and no positive selection signals, instead exhibiting the lowest nucleotide substitution rates among the four species, suggesting it may have adapted through strong purifying selection that minimizes the accumulation of harmful mutations rather than through the evolution of new molecular functions.

This finding challenges the assumption that extreme environments universally drive positive selection in mitochondrial genomes and highlights the diversity of evolutionary strategies that organisms can employ when colonizing harsh habitats. The study also revealed that mitochondrial gene rearrangement patterns and selective pressures varied markedly between lineages rather than correlating with habitat type or depth, with the clade Ophintegrida showing higher structural plasticity than the more conserved Euryophiurida. By establishing the most comprehensive mitochondrial genome framework for brittle stars to date, this research provides a robust foundation for future investigations into echinoderm diversification, biogeographic dispersal, and the molecular mechanisms that enable life to flourish in some of the most extreme environments on our planet.

Subject of Research: Mitochondrial genome phylogenetics and deep-sea adaptive evolution of brittle stars (Ophiuroidea)

Article Title: Mitochondrial genomes resolve phylogenetic conflicts and lineage-specific adaptive dynamics in Ophiuroidea : insights from deep-sea lineages

Article References: Xu, W., Na, J., Gao, K., Gu, X., Zhou, Y., Zhang, R., Sun, J., & Zhang, D. (2026). Mitochondrial genomes resolve phylogenetic conflicts and lineage-specific adaptive dynamics in Ophiuroidea: insights from deep-sea lineages. Zoosystematics and Evolution, 102(2), 687-699. https://doi.org/10.3897/zse.102.163746

Image Credits: AI Generated

DOI: 10.3897/zse.102.163746

Keywords: brittle stars, Ophiuroidea, mitochondrial genomes, deep sea, hydrothermal vents, cold seeps, phylogenetics, adaptive evolution, echinoderms, gene rearrangement, positive selection, divergence time

Finless porpoises of the genus Neophocaena have puzzled taxonomists since the first skull was collected in India in 1829. For much of the twentieth century, porpoises across the Indo-Pacific were lumped into a single species, Neophocaena phocaenoides, subdivided into three subspecies. A three-species arrangement was proposed in the 1970s but never gained wide acceptance. In the past two decades, integrative analyses combining morphology and genetics settled on a two-species framework: the Indo-Pacific finless porpoise and the narrow-ridged finless porpoise, with the Yangtze population treated as a subspecies of the latter. The new review systematically synthesises studies from those foundational taxonomic revisions through to the most recent population genomic analyses, and concludes that the evidence now favours a three-species classification in which the Yangtze finless porpoise stands alone.

The geographic distribution of the genus already hints at deep separation. The Indo-Pacific finless porpoise occupies shallow coastal waters of the Indian Ocean, the South China Sea and the East China Sea, while the East Asian finless porpoise inhabits the Yellow Sea, Bohai Sea and coastal waters off Korea and Japan, with an overlap zone in the Taiwan Strait. The Yangtze finless porpoise, by contrast, is the sole obligate freshwater lineage in the genus, confined to roughly 1,800 kilometres of the middle and lower Yangtze River and its interconnected Poyang and Dongting Lake systems. This spatially restricted, ecologically specialised range underscores the distinctiveness of a lineage now regarded as a critically endangered evolutionarily significant unit.

Visible and skeletal differences reinforce the split. Adult East Asian finless porpoises are the largest of the three taxa, reaching about 2.00 metres and a maximum of 2.27 metres, whereas the Yangtze and Indo-Pacific porpoises measure roughly 1.70 metres. Finless porpoises lack a dorsal fin, carrying instead a dorsal ridge and a tuberculated area whose dimensions vary dramatically: the Indo-Pacific porpoise has a broad ridge with a tubercle area 48 to 120 millimetres wide and more than 10 rows of tubercles, while the Yangtze porpoise shows the most reduced condition, with a width of only 2 to 8 millimetres and 1 to 5 rows. Skull metrics tell a similar story. The Indo-Pacific porpoise has a short, broad rostrum, the East Asian porpoise a narrow, slender one, and the Yangtze porpoise an intermediate form with reduced tooth counts, elongated temporal fossae and widened occipital condyles. Discriminant analyses can reliably separate the Yangtze porpoise from its closest marine relative using braincase length, premaxillary width, orbital width and temporal fossa length.

Internal anatomy reveals adaptations to life in fresh water. The Yangtze porpoise has smaller kidney structures across several indices, including relative medullary thickness and area, and correspondingly weaker urine concentrating capacity than its marine counterpart, consistent with the challenge of excreting excess water in a hypotonic environment. Its visual system is also remodeled: shorter distances from eye centre to snout tip, reduced eye slit height, a smaller lens and fewer optic and eye muscle nerves, adaptations to the turbid, dim waters of the Yangtze. Recent ultrastructural studies of the epidermis add another layer, showing that the freshwater porpoise has a lipid-rich outermost skin layer with fewer cell layers and enlarged neutral lipid droplets that curb passive water influx, while the marine porpoise relies on densely packed keratin filaments and reinforced desmosomes to prevent water loss in salt water.

Life history traits diverge as well. Populations in the South China Sea mature earliest, with males breeding at about three years and females at four, and live up to 21 years. Yellow Sea porpoises mature around four years and can reach 24 years. The Yangtze porpoise shows the most protracted development, maturing at roughly five years with a maximum longevity of only 17 years, parameters that are critical for modelling the viability of a population hovering near extinction.

Molecular markers have documented significant genetic structure for decades. Analyses of the mitochondrial DNA control region, microsatellites, nuclear SNPs, MHC genes and AFLP fingerprints revealed very strong overall population structure in Sino-Japanese waters, with fixation indices as high as 0.61. Even where distributions overlap, gene flow between populations is very limited or absent. Crucially, the Yangtze porpoise shares no haplotypes with any marine population, a signature of long-standing reproductive isolation.

Population genomics has delivered the strongest evidence yet. In a landmark study, researchers sequenced one Yangtze porpoise de novo and re-sequenced 48 finless porpoises from Chinese waters, identifying more than 13 million high-confidence SNPs. Phylogenetic reconstruction resolved the Yangtze porpoise as a distinct clade, and population structure analyses, principal component analysis, linkage disequilibrium decay and demographic modelling all confirmed stable divergence. Bayesian species delimitation statistically favoured the three-species model. The wide-ridged and narrow-ridged lineages split about 100,000 years ago, while the Yangtze porpoise diverged from its marine narrow-ridged relatives between 5,000 and 40,000 years ago, a timing consistent with sea-level fluctuations during the Last Glacial Period that likely isolated the freshwater population. Most notably, the Yangtze porpoise carries significant positive selection signals in genes governing osmoregulation and the renin-angiotensin system, including ADCY1, DYNC2H1, SLC14A2 and ACE2, matching the earlier kidney morphology findings. Telomere-to-telomere gap-free genome assemblies confirmed substantial genomic divergence, with positively selected genes in the Yangtze porpoise linked to DNA damage repair and those in the East Asian porpoise tied to high-salinity tolerance.

The taxonomic stakes are profound. Species are the fundamental unit of biodiversity law, and in China elevation to full species status enables listing under the Wildlife Protection Law and the National List of Key Protected Wild Animals, unlocking legally mandated habitat preservation, captive breeding programmes and enforceable prohibitions on disturbance. Internationally, CITES regulates trade species by species and IUCN Red List assessments of independent species carry far greater weight in mobilising global action. The porpoise is already acknowledged as a species in China, where it has become a genuine flagship: the country established a dedicated Yangtze Finless Porpoise Conservation Day in 2019, the first for any single wildlife species, and a new ten-year action plan jointly issued by eight ministries designates it a flagship and umbrella species. Known popularly as the aquatic giant panda and the smiling angel, the porpoise is the sole surviving apex predator in the Yangtze, and its recovery from 1,012 individuals in 2017 to 1,426 in 2025, an increase of more than 40 percent, has become a headline indicator of the river’s health under the Yangtze River Protection Law and the ten-year fishing ban. A mature conservation infrastructure now integrates eight in-situ reserves, four naturalised ex-situ populations with over 150 managed individuals, and successful captive breeding including second-generation offspring, practices formally proposed as a global framework for endangered small cetaceans.

The authors close with a warning drawn from history. The extinction of the baiji, the Yangtze River dolphin, showed that conservation operates within a closing window: once a population collapses, the chance for recovery may vanish entirely. Recognising the Yangtze finless porpoise as a full species would affirm millions of years of unique freshwater evolution and trigger the most robust protections available, ensuring that the porpoise does not follow the baiji’s trajectory. Its umbrella effect means that measures taken on its behalf simultaneously promote the restoration of the entire riverine environment, making its formal recognition a decisive test of whether science-driven taxonomy can still outrun decline.

Subject of Research: Taxonomic review of the Yangtze finless porpoise's species status based on multidisciplinary evidence

Article Title: Evolutionary differentiation and adaptive divergence support the Yangtze finless porpoise as an independent species, a flagship of conservation value: A review

Article References: Lu, Y., Zhou, K., & Yang, G. (2026). Evolutionary differentiation and adaptive divergence support the Yangtze finless porpoise as an independent species, a flagship of conservation value: A review. Nature Conservation, 64, 77-92. https://doi.org/10.3897/natureconservation.64.193600

Image Credits: AI Generated

DOI: 10.3897/natureconservation.64.193600

Keywords: Yangtze finless porpoise, Neophocaena asiaeorientalis, species delimitation, taxonomy, population genomics, osmoregulation, adaptive evolution, freshwater cetacean, conservation policy, critically endangered, Yangtze River, flagship species

The framing matters because much of biodiversity science has historically been fragmented. Studies of speciation often focus on a single region or a single group of organisms, and the same is true of work on adaptation, community ecology, and biogeography. The editors of the special issue argue that explaining Earth’s biological richness requires connecting these threads into a single mechanistic chain, from the origin of genetic variation through lineage diversification and trait evolution to the assembly of communities and the long-term persistence of diversity. The call explicitly welcomes contributions that cross-compare across the tree of life, across levels of biological organization, and across timescales, from deep-time macroevolution to contemporary eco-evolutionary feedbacks.

Guest editing the issue is Professor Pat Heslop-Harrison of the University of Leicester in the United Kingdom, an evolutionary biologist known for work on plant genomes and genome evolution. According to the announcement, the special issue aims to build a unified evolutionary framework for understanding biodiversity, and the editors welcome rigorous approaches of every kind: theoretical modelling, experimental work, field observation, comparative analysis, data synthesis, and the development of new methods that unpack the evolutionary foundations of diversity and inform the conservation of adaptive potential. That methodological openness is one of the issue’s defining features, since the organizers have deliberately avoided restricting submissions to any particular technique, taxon, or region.

The timing of such a call is no accident. A wave of technological advances has transformed what is possible in evolutionary and biodiversity research. Phylogenomics now allows researchers to reconstruct the branching history of lineages with unprecedented resolution using genome-scale data. Pangenomics captures the full spectrum of genetic variation within a species rather than relying on a single reference genome, revealing how variable genomes really are. Metagenomics extends this power to entire microbial communities, experimental evolution lets scientists watch adaptation unfold in real time, and ancient DNA recovers genetic information from organisms that lived thousands of years ago. Digitized natural-history collections, long-term ecological monitoring programs, and artificial intelligence tools for analyzing massive ecological and genomic datasets round out a toolkit that previous generations of biologists could scarcely have imagined.

Together, these methods make it feasible, for the first time, to test general rules about how biodiversity is generated and maintained across animals, plants, fungi, microbes, and viruses. The special issue’s thematic scope reflects that breadth. Listed topics include speciation and lineage diversification; genomic variation and adaptive phenotypic change; hybridization, introgression, and reticulate evolution; functional-trait and niche evolution; biotic interactions and co-evolution; community assembly and the persistence of rare species; eco-evolutionary feedback; deep-time biogeography; multi-evidence cross-taxon comparisons; and evolutionary responses under global change that can inform conservation practice.

Several of these themes deserve particular attention because they represent areas where evolutionary thinking is actively reshaping established views. Reticulate evolution, for example, acknowledges that lineages do not always diverge cleanly along a branching tree. Hybridization and introgression, in which species exchange genes after splitting, can transfer adaptations between lineages, blur species boundaries, and even generate new evolutionary trajectories. Similarly, eco-evolutionary feedback describes the loop in which ecological conditions drive evolutionary change, and evolved traits in turn alter ecological dynamics, a coupling that challenges the traditional separation of ecology and evolution into separate timescales and separate disciplines.

Community assembly and species coexistence form another conceptual frontier. Why some species become rare and others abundant, and how diverse communities persist without collapsing into dominance by a few competitors, are questions that increasingly draw on evolutionary explanations, including the history of trait divergence among co-occurring lineages. Deep-time biogeography adds a historical dimension, using phylogenetic and fossil evidence to reconstruct how lineages dispersed, diversified, and went extinct as continents shifted and climates changed. By encouraging cross-taxon comparisons that integrate multiple lines of evidence, the special issue is positioned to showcase work that treats these questions as interconnected rather than isolated.

The practical stakes are considerable. Under global environmental change, species are shifting ranges, communities are reorganizing, and adaptive potential has become a central concept in conservation planning. Evolutionary-informed conservation asks not only which species are threatened but which populations carry the genetic and phenotypic variation needed to persist under future conditions. The special issue’s inclusion of evolutionary responses under global change as an explicit theme underscores the organizers’ intent that the collection speak to conservation practice as well as to fundamental theory, bridging a gap that has often separated academic evolutionary biology from on-the-ground biodiversity management.

For prospective authors, the logistics are straightforward. Manuscripts should follow the journal’s author guidelines and be designated for the special issue during online submission, using the dropdown menu that responds to the question of whether a submission is for a special issue. Article processing charges are fully waived for this issue, removing a common financial barrier for researchers, particularly those working in institutions with limited publication funds. The journal, which carries the ISSN 2994-4139, is sponsored by the South China Botanical Garden of the Chinese Academy of Sciences and published in partnership with John Wiley & Sons Australia, Ltd. It is indexed in Chemical Abstracts Service and the Directory of Open Access Journals, and it welcomes original research, reviews, commentaries, and short communications spanning botany, zoology, microbiology, taxonomy, phylogenetics, genomics, ecology, climatology, and related disciplines.

Whether the special issue succeeds in its unifying ambition will depend on the community’s response, but the call arrives at a moment when the intellectual ingredients for synthesis are unusually well aligned. Genomic and ecological data streams are richer than ever, computational tools can integrate them at scale, and there is growing recognition across subfields that biodiversity’s origin, change, and persistence form a single evolutionary narrative. Researchers with theoretical models, long-term field datasets, comparative genomic analyses, or novel methods relevant to any stage of that narrative now have until 31 August 2027 to contribute to what the editors hope will become a landmark reference point for understanding how evolution builds and sustains the living world.

Subject of Research: A special issue of the journal Biological Diversity inviting research on evolutionary mechanisms underlying biodiversity formation, evolution, and maintenance

Article Title: New special issue of Biological Diversity call for papers decoding biodiversity through evolutionary mechanisms

Article References: New special issue of Biological Diversity call for papers decoding biodiversity through evolutionary mechanisms. (n.d.). Original publication

Image Credits: AI Generated

DOI: Not provided

Keywords: biodiversity, evolution, speciation, phylogenomics, reticulate evolution, community assembly, eco-evolutionary feedback, biogeography, adaptive evolution, conservation, Biological Diversity journal, call for papers

Treeshrews are small, agile mammals that inhabit the forests of South and Southeast Asia, with some species extending into southwestern China. Despite their name, they are neither true shrews nor particularly arboreal in all cases; they occupy a bewildering middle ground in mammalian classification that has fascinated evolutionary biologists for more than a century. Their most celebrated claim to scientific fame is their phylogenetic position within Euarchonta, the grand clade that also contains primates, colugos, and rodents and rabbits in the broader Euarchontoglires grouping. This placement makes treeshrews a living reference point for understanding what the ancestors of primates may have been like, and it underpins their growing status as biomedical models in studies of vision, immunity, and metabolism.

The review’s authors emphasize that treeshrews offer a rare combination of features that make them unusually informative for studying mammalian evolution. They are phylogenetically distinctive, meaning that their lineage separated early and retains a mosaic of ancestral and derived traits. Their history of diversification is heterogeneous, with island species in maritime Southeast Asia following very different evolutionary trajectories from their mainland relatives, producing natural experiments in isolation, dwarfism, and speciation. And the recent explosion of genomic resources for the group means that researchers can now move beyond morphology-based trees to test hypotheses about relationships and adaptation with genome-scale data.

On the phylogenetic front, the review organizes treeshrew evolutionary history across three nested levels. At the interordinal level, the question is where Scandentia sits relative to primates and colugos within Euarchonta, a problem that has oscillated across decades of molecular and morphological analyses. At the intraordinal level, the review traces the diversification of treeshrew families and genera, including the split between the largely terrestrial, plains-dwelling tupaiids and the more scansorial ptilocercids, exemplified by the pen-tailed treeshrew, as well as the subsequent radiations that produced the species richness seen today. At the intraspecific level, the authors examine population differentiation within widespread species, where geography, altitude, and habitat fragmentation have carved genetic structure into populations that often look deceptively uniform in the field.

Biogeography emerges as a central theme of the synthesis. The islands of Southeast Asia, from the Sunda Shelf to the Philippines and Sulawesi, have repeatedly acted as both cradles and traps for treeshrew lineages. Sea-level fluctuations during Pleistocene glacial cycles alternately connected and severed land bridges, allowing populations to mix and then isolate in pulses. The review highlights that mainland and island treeshrews have followed qualitatively different diversification histories, with island populations frequently showing deep genetic divergence over small geographic distances, particularly on ecologically complex islands such as Borneo and Sulawesi. Disentangling these patterns requires explicit testing of alternative biogeographic models, something the authors flag as a major priority rather than an afterthought.

The genetic diversity section of the review underscores how much remains unknown about treeshrew species boundaries. Morphology alone has historically underestimated diversity in the group, and mitochondrial genetic studies have revealed cryptic lineages within what were once considered single widespread species. The authors argue for integrative taxonomic revision, combining genome-wide markers, acoustic and ecological data, and museum specimens to redraw the species map of Scandentia. This matters not only for evolutionary theory but for conservation, since several treeshrew species are restricted to narrow island ranges or threatened forest habitats, and mislabeled species boundaries can hide endangered lineages within seemingly common ones.

Perhaps the most technically rich portion of the review concerns the molecular mechanisms underlying adaptive evolution in treeshrews. The authors survey evidence for the genetic basis of specialized sensory, immune, and metabolic traits that set treeshrews apart. Treeshrews possess remarkable visual acuity among small mammals, and studies have identified signatures of selection in phototransduction and cone-related genes consistent with their diurnal, color-rich lifestyles. Their immune systems have drawn attention because treeshrews tolerate certain pathogens differently than laboratory rodents, making comparative immunogenomics both medically relevant and evolutionarily revealing. Metabolic adaptations, including the famous ability of some treeshrews to consume large quantities of fermented nectar rich in ethanol without apparent intoxication, point to accelerated evolution in alcohol-metabolizing enzymes and related pathways, a trait that has made them a favorite case study in debates about the evolutionary origins of ethanol metabolism in primates.

The review does not stop at cataloguing these adaptations; it frames them as candidate systems demanding experimental validation. Genome scans and comparative analyses can identify genes with signatures of positive selection, but the authors stress that demonstrating function requires experimental work, from gene expression studies to physiological assays and, ultimately, functional validation of candidate adaptive genes. This call for mechanistic rigor reflects a broader shift in evolutionary biology from correlation to causation, and treeshrews, with their emerging genomic resources and established laboratory husbandry protocols, are well positioned to make that transition.

Looking forward, the authors lay out a clear set of research priorities. Comprehensive taxon sampling remains fundamental, since many species and populations have never been included in molecular analyses. Chromosome-level genome assemblies and population resequencing across the full geographic range would provide the resolution needed to reconstruct demographic history, detect local adaptation, and settle long-standing phylogenetic disputes. Integrative taxonomy should be applied systematically to resolve species boundaries. Biogeographic hypotheses need to be tested formally against explicit models rather than accepted by narrative plausibility. And candidate adaptive genes emerging from comparative genomics must be validated experimentally. Each of these priorities, the review argues, is now technically feasible given advances in long-read sequencing, computational phylogenetics, and genome editing.

The broader significance of the review lies in its insistence on integration. Genomic data alone, the authors contend, cannot resolve the evolutionary history of Scandentia; it must be woven together with morphological, ecological, and functional evidence. Treeshrews sit at a phylogenetic crossroads that illuminates the deep history of Euarchonta, yet their species-level diversity remains incompletely described, their biogeography only partly modeled, and their adaptive biology only beginning to be understood at the molecular level. By consolidating what is known and specifying what must be done next, Gu and colleagues have effectively set the agenda for a field that is small in numbers of researchers but outsized in evolutionary importance. For anyone watching the intersection of genomics, biogeography, and mammalian diversity in tropical Asia, treeshrews are no longer a footnote; they are fast becoming a textbook example of how modern evolutionary biology dissects the origins of a lineage.

Subject of Research: Phylogenetic relationships and adaptive evolution of treeshrews (order Scandentia)

Article Title: Phylogenetic and adaptive evolution of treeshrews (Scandentia)

Article References: Gu, T., Zhang, H., Mu, R., Qi, H., Lin, Z., & Zhu, W. (2026). Phylogenetic and adaptive evolution of treeshrews (Scandentia). Frontiers in Zoology. https://doi.org/10.1186/s12983-026-00633-2

Image Credits: AI Generated

DOI: 10.1186/s12983-026-00633-2

Keywords: treeshrews, Scandentia, phylogenetics, biogeography, genetic diversity, adaptive evolution, Euarchonta, molecular evolution, species boundaries, genomics, Southeast Asia, mammalian evolution

The team, led by Le Minh Bui of Nguyen Tat Thanh University and Anh Duy Do of HUTECH University, set out to test a question that goes to the heart of antimicrobial stewardship. When bacteria are exposed to antibiotics at doses too low to kill them, they adapt. That adaptation is not limited to surviving the drug in question; it often spills over into cross-resistance against unrelated compounds and, troublingly, into heightened virulence. Sub-inhibitory concentrations of antibiotics have been shown in earlier studies to crank up the expression of quorum-sensing regulators and toxin genes in staphylococci, meaning that the very conditions that breed resistance can also make the surviving cells more dangerous. Whether a natural product could sidestep this double hazard was the central hypothesis of the new study.

To find out, the researchers subjected a standard laboratory strain of S. aureus, ATCC 25923, to thirty days of adaptive evolution under sub-inhibitory pressure from either Piper betle essential oil or three conventional antibiotics: chloramphenicol, streptomycin, and kanamycin. This kind of prolonged exposure experiment is a demanding test. It mimics, in simplified form, the sustained low-dose drug environments that occur in treated tissues and biofilms, and it gives the bacterial populations ample opportunity to select for resistant variants. The design allowed direct comparison of how the pathogen responds evolutionarily to a multicomponent plant oil versus single-target antibiotics.

The contrast between the two trajectories was stark. Populations evolved under chloramphenicol, streptomycin, or kanamycin developed high-level resistance to their selecting drug and displayed extensive cross-resistance, consistent with the well-documented tendency of single-molecule antibiotics to drive rapid resistance evolution. At the same time, quantitative analysis of gene expression revealed that these antibiotic-adapted populations had upregulated a suite of quorum-sensing and virulence-associated genes, including agrA, a core component of the staphylococcal quorum-sensing circuit; luxS, the gene responsible for producing the signalling molecule autoinducer-2; and hla and hlb, which encode the alpha- and beta-toxins that damage host cells. In other words, a month of antibiotic pressure produced bacteria that were harder to kill and, on the genetic evidence, potentially more aggressive.

The populations evolved under Piper betle essential oil told a different story. Over the same thirty days, the minimum inhibitory concentration of the oil did not measurably increase, indicating that no detectable resistance had emerged, and the adapted populations showed no cross-resistance to the tested antibiotics. Instead, antibiotic susceptibility was maintained or even enhanced. Gene expression profiling of the oil-adapted populations showed increased transcription of rot, a repressor of toxins in S. aureus, together with reduced expression of genes tied to quorum sensing, toxin production, and biofilm formation. The overall picture is of a bacterial population that, under continuous oil pressure, becomes less rather than more virulent, a pattern that runs counter to what conventional antibiotics produced in the same experiment.

The most clinically striking result came when the researchers tested how the oil-adapted and antibiotic-adapted populations responded to antibiotics in the presence of the oil. In both wild-type and antibiotic-adapted backgrounds, supplementation with Piper betle essential oil enhanced antibiotic susceptibility, with the minimum inhibitory and minimum bactericidal concentrations of the antibiotics dropping by factors of four to thirty-two in the antibiotic-adapted populations. For bacteria that had spent a month becoming resistant to chloramphenicol, streptomycin, or kanamycin, the oil effectively pulled them back toward sensitivity. This potentiating effect, sometimes described as antibiotic re-sensitisation, is precisely the kind of activity sought in adjunctive therapies designed to extend the useful life of existing drugs rather than replace them.

Why does the oil behave this way? The authors probed one candidate mechanism by supplementing cultures with exogenous AI-2, the autoinducer molecule produced by the LuxS enzyme. Adding AI-2 partially restored antibiotic resistance in the presence of the oil, an observation that implicates modulation of the LuxS/AI-2 signalling system in the re-sensitisation effect. The LuxS/AI-2 pathway, best known as a universal quorum-sensing signal across bacterial species, has previously been linked in S. aureus to antibiotic susceptibility and autolysis, and disrupting it has been proposed as a route to weakening biofilms and restoring drug activity. The partial nature of the restoration, however, is an important caveat: AI-2 signalling appears to contribute to the oil’s effect, but the researchers are careful to note that it may not be the sole or even the predominant mechanism. Essential oils are complex multicomponent mixtures, and their biological activity typically arises from multiple compounds acting on multiple cellular targets, from membrane disruption to interference with regulatory networks.

That multicomponent character may also explain the absence of resistance development. Single-molecule antibiotics present bacteria with a well-defined target, and a single mutation that alters that target or pumps the drug out can confer substantial protection. Plant essential oils, by contrast, present a shifting constellation of weakly acting compounds, few of which exert enough selective pressure on any one target to favour a simple resistance mutation. Prior work on Piper betle supports this framing: the oil and its constituents, including the phenolic compound hydroxychavicol, have been shown to damage bacterial DNA, inhibit cell division, and disrupt membranes, while eugenol, another prominent constituent, provokes reactive oxygen species-mediated membrane damage. Recent studies have also reported synergy between Piper betle oil and antibiotics against methicillin-resistant S. aureus clinical isolates, including computational evidence pointing at the resistance determinant PBP2a.

The context for this work is sobering. Staphylococcus aureus remains one of the world’s most consequential pathogens, colonising roughly a third of the human population in the nose and causing illnesses that range from skin abscesses to fulminant bloodstream infections, bone and joint disease, and endocarditis. Global surveillance reports document rising resistance across clinical isolates, and methicillin-resistant strains continue to limit treatment options. Beyond resistance, the bacterium’s reliance on quorum-sensing circuits such as the agr system and on biofilm formation makes chronic infections, including those associated with implanted devices and chronic rhinosinusitis, particularly difficult to eradicate. Antivirulence strategies, which aim to disarm the pathogen rather than kill it outright, are attractive in principle because they may impose less selective pressure for resistance, and the new study suggests that a traditional medicinal plant can deliver both antivirulence and resistance-reversing activity in a single preparation.

The authors are appropriately measured about what the findings do and do not establish. All experiments were conducted in vitro with a single reference strain, and the study’s own data show that the AI-2 mechanism is only partially responsible for the observed effects. Before any broader therapeutic conclusions can be drawn, the oil’s activity must be validated against methicillin-resistant S. aureus and against genetically diverse clinical isolates, which often behave quite differently from laboratory strains. Dosing, toxicity, and formulation questions, particularly for potential applications such as intranasal treatment of colonisation or biofilm-associated sinus disease, remain entirely open. Nevertheless, the combination of results reported here, no resistance emergence over a month of exposure, reversal of antibiotic resistance in adapted populations, and coordinated downregulation of virulence and biofilm genes, marks Piper betle essential oil as a candidate worthy of the deeper investigation that must now follow.

Subject of Research: Evaluation of Piper betle essential oil as an antivirulence agent and antibiotic potentiator against Staphylococcus aureus in vitro

Article Title: Piper betle essential oil enhances antibiotic susceptibility and attenuates quorum-sensing-associated virulence in Staphylococcus aureus in vitro

Article References: Bui, L. M., Dao, M. D., Nguyen, N. T., Le, X.-T., & Do, A. D. (2026). Piper betle essential oil enhances antibiotic susceptibility and attenuates quorum-sensing-associated virulence in Staphylococcus aureus in vitro. 3 Biotech, 16(10), Article 441. https://doi.org/10.1007/s13205-026-05077-3

Image Credits: AI Generated

DOI: 10.1007/s13205-026-05077-3

Keywords: Piper betle, essential oil, Staphylococcus aureus, antibiotic resistance, quorum sensing, LuxS/AI-2, antivirulence, biofilm, antibiotic potentiation, agrA, adaptive evolution, natural products

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