Specimens of B. erythrostoma and P. broderipii were collected in northern Chile’s Atacama Region, at Copiapó–Barranquilla and Copiapó–Totoral, respectively, and preserved in 96% ethanol. Shell morphology and established identification criteria were used by Juan Francisco Araya and Ricardo Catalán-Garrido. DNA was extracted from foot tissue, and paired-end sequencing with 150-bp reads was performed on an Illumina NovaSeq 6000. The B. erythrostoma run generated 63.6 million spots and 19.1 Gb of sequence data, while the P. broderipii run generated 39.2 million spots and 11.8 Gb.

After adapter and low-quality sequence removal, researchers assembled the mitochondrial DNA with multiple workflows, including MEGAHIT, SPAdes and the mitochondrion-targeted GetOrganelle pipeline. One mitochondrial contig was recovered for each species. Read mapping with BWA-MEM showed 100% breadth of coverage for both assemblies, with mean depths of 1,202.9× for B. erythrostoma and 348.2× for P. broderipii. The P. broderipii assembly was treated as complete, whereas one localized region of the B. erythrostoma assembly had reduced coverage and complex soft-clipping. Independent assembly approaches did not resolve that region unequivocally from the short Illumina reads, so the researchers described the B. erythrostoma mitogenome as nearly complete.

The B. erythrostoma mitogenome is 15,525 base pairs long, while the P. broderipii mitogenome is 14,978 base pairs. Both have the standard metazoan complement of 37 genes: 13 protein-coding genes, 22 transfer RNAs and two ribosomal RNAs. A and T together account for 69.75% of the B. erythrostoma genome and 72.08% of the P. broderipii genome. Both species have the same strand distribution for protein-coding and transfer RNA genes, although the magnitudes of their A+T and G+C skews differ. MITOS2 annotations were manually curated and independently assessed with MitoFinder, while transfer RNAs were evaluated with ARAGORN and tRNAscan-SE. The two annotation approaches agreed on gene content, order and strand orientation, with differences confined to boundary refinements of 1–27 base pairs.

Much of the difference in total genome length was associated with non-coding DNA rather than major differences in coding-gene content. B. erythrostoma has 23 intergenic regions totaling 1,489 base pairs, or about 9.59% of its genome; its largest, at 959 base pairs, lies between trnV and trnP. P. broderipii has 21 intergenic regions totaling 949 base pairs, or about 6.34%, with its largest 370-base-pair spacer between trnK and cox1. The B. erythrostoma assembly also has an alternative cox1–rrnL–trnL1–trnV organization. The same arrangement was independently observed in a published Bostryx mitogenome, making a lineage-specific feature more likely than an isolated assembly error, although its distribution across the genus was not established by the limited comparison.

Most transfer RNAs adopted the canonical metazoan cloverleaf structure after manual refinement. A small number, particularly trnS2, retained reduced structural elements, a pattern also documented in animal mitochondrial genomes. In P. broderipii, nad3, cox3 and nad2 contain incomplete stop codons, consistent with post-transcriptional completion via polyadenylation. By contrast, no incomplete stop codons were identified in B. erythrostoma. The researchers cautioned that mitochondrial gene boundaries, especially near transfer RNA genes, remain partly tentative because current annotation methods cannot fully account for post-transcriptional RNA processing.

For the phylogenomic analysis, the researchers extracted and codon-aligned the 13 mitochondrial protein-coding genes, producing a nucleotide supermatrix of 11,829 aligned sites across 19 taxa. The dataset contained 17 ingroup taxa and two Systellommatophora outgroups, Imerinia grandidieri and Eleutherocaulis alte. Model and partition selection used the Bayesian Information Criterion, and the initial 39 codon-position partitions were optimized to 20 for the final maximum-likelihood analysis in IQ-TREE. Branch support was estimated with 1,000 ultrafast bootstrap and 1,000 SH-aLRT replicates.

The maximum-likelihood and Bayesian trees recovered the same focal relationships. B. erythrostoma was sister to a published Bostryx sequence, with an ultrafast bootstrap value of 100 and posterior probability of 1.00. The Rabdotus mooreanus–Naesiotus nux pair was also strongly supported and grouped with the two Bostryx sequences. P. broderipii was recovered as sister to the remaining sampled Orthalicoidea, with support values of 100 and 1.00 at these focal nodes. A separate amino-acid analysis also recovered the focal relationships.

Some deeper relationships among stylommatophoran superfamilies received lower support or varied slightly among inference methods. The authors noted that heterogeneous evolutionary rates and compositional variation among mitochondrial genomes from distantly related lineages can influence phylogenetic inference at deeper scales. Accordingly, the strongest conclusion concerns relationships among the sampled Orthalicoidea rather than a definitive resolution of the entire stylommatophoran tree. The new mitogenomes provide reference resources for comparative and phylogenetic studies of Bulimulidae and Bothriembryontidae, while the limited taxon sampling constrains broader conclusions about the genus and superfamily.

Subject of Research: Comparative mitogenomics and phylogeny of two Atacama Region Orthalicoidea land snails

Article Title: Mitochondrial genomes and phylogenomic analysis of Plectostylus broderipii and Bostryx erythrostoma ( Gastropoda , Stylommatophora , Orthalicoidea ) from the Atacama Desert, Chile

Article References: Contreras-Díaz, R., Barahona-Segovia, R. M., Catalán-Garrido, R., Araya, J. F., Arias-Aburto, M., & Pizarro-Gacitúa, C. (2026). Mitochondrial genomes and phylogenomic analysis of Plectostylus broderipii and Bostryx erythrostoma (Gastropoda, Stylommatophora, Orthalicoidea) from the Atacama Desert, Chile. ZooKeys, 1291, 1-18. https://doi.org/10.3897/zookeys.1291.197983

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DOI: 10.3897/zookeys.1291.197983

Keywords: mitochondrial genomes, phylogenomics, Orthalicoidea, Bostryx erythrostoma, Plectostylus broderipii, land snails, Atacama Desert, Chile, next-generation sequencing, molecular systematics, Mitochondrial, genomes

Leaf samples were collected in spring 2018 from a riparian floodplain forest in central Moravia, Czechia, where Ericales plants were absent. The analyzed trees were Alnus glutinosa, Carpinus betulus, Corylus avellana, Quercus petraea and Q. robur. The investigators also mined the GlobalFungi database for published environmental sequences to assess the occurrence of Exobasidium beyond known host plants.

After filtering, the researchers identified 75 Exobasidium amplicon sequence variants from leaves and insect guts, which clustered into 12 phylotypes. Seven grouped with described species that had publicly available DNA barcodes, including E. arescens, E. bisporum, E. camelliae, E. euryae, E. gracile, E. maculosum and E. miyabei. The other five had less than 94% similarity to sequenced species in the National Center for Biotechnology Information database, indicating possible undescribed or as-yet-unsequenced diversity.

This interpretation remains uncertain because many named Exobasidium species still lack public molecular data. Exobasidium communities differed significantly among host tree species in an analysis of similarity based on Jaccard and Morisita-Horn indices with 9,999 permutations. Quercus petraea had the highest measured alpha diversity, with a mean Shannon index of 0.50 and a mean Simpson index of 0.39, while Q. robur had the lowest values, at 0.32 and 0.17, respectively.

Principal component analysis also separated several tree-associated communities. Phylotype 9 accounted for more than 66% of Exobasidium reads on A. glutinosa and 62% on Q. robur, occurred in more than 30% of leaf samples from every analyzed tree and also dominated several caterpillar-gut communities. Overall, the gut datasets did not differ significantly from one another, and their phylotype proportions broadly reflected those in the corresponding tree phyllospheres.

Phylotype 9 was recovered in pure culture from two Tischeria ekebladella caterpillars and from healthy Tilia cordata leaves collected in Slovakia. All three isolates were genetically identical. Phylogenetic analysis placed them as a sister lineage to E. woronichinii and E. rhododendri.

The isolates differed from E. woronichinii by 3.9% of nucleotides in the ITS region and 1.8% in the LSU region, supporting their recognition as Exobasidium phylloplanum. Its name refers to the phylloplane, the leaf surface. The species produces filamentous colonies with fusiform blastoconidia measuring 8.2 ± 3.0 micrometres long and 1.8 ± 0.2 micrometres wide.

Physiological tests found growth from 6 to 25 °C, with optimal growth between 20 and 25 °C. Salinity of 16% or higher prevented growth. The isolates used all 16 tested carbon sources and grew on glucose without fermenting it.

In the GlobalFungi analysis, 17 of 40 examined Exobasidium species or phylotypes appeared in at least one environmental sample. E. phylloplanum was the most frequently detected lineage, occurring in 841 samples from 52 studies, mainly in European forests and in samples from plant shoots and soil. Its records were concentrated in temperate regions, with an absence in the otherwise well-surveyed boreal and Mediterranean areas.

Known parasites E. arescens, E. vaccinii and E. camelliae were also detected in environmental records, while some environmental phylotypes in the E. bisporum and E. miyabei clades occurred more frequently than the available reference sequences. The researchers could not establish that these environmental phylotypes represented the corresponding parasitic species in the sampled regions. They instead proposed that Exobasidium includes a continuum of life histories, ranging from predominantly parasitic species with short saprotrophic phases to lineages with longer environmental phases and possibly predominantly saprotrophic species.

The genome of E. phylloplanum strain CCF 7021 was assembled into five nuclear scaffolds totaling 17.7 megabases. The assembly had an N50 of 5.8 megabases, 95.5% BUSCO completeness and 7,463 annotated proteins. Comparative analyses found broadly similar numbers of carbohydrate-active enzyme genes and genes associated with pathogen–host interactions among E. phylloplanum and other Exobasidium species.

E. phylloplanum was distinguished by an expanded set of type I polyketide synthases, consistent with its production of red-brown gunacin pigments. The comparison did not identify a genomic feature that explained its apparently different lifestyle. A central limitation is that environmental DNA cannot by itself distinguish actively growing cells from dormant or wind-dispersed propagules.

Nevertheless, the non-random association of phylotypes with host trees, their recovery from healthy leaves and their isolation from insect guts support active surface colonization, although they do not prove a complete saprotrophic life cycle. It remains unresolved whether E. phylloplanum has an unrecognized pathogenic stage, a predominantly saprotrophic lifestyle or another form of ecological flexibility; the study establishes neither outcome. Infection experiments would be required to assess its parasitic potential.

Subject of Research: Environmental, cultural and genomic evidence for saprotrophic diversity in the fungal genus Exobasidium

Article Title: The saprotrophic dimension of Exobasidium ( Exobasidiales , Basidiomycota ): evidence for greater diversity and ecological flexibility than previously recognized

Article References: Veselská, T., Ježková, T., Ngubane, N. P., Wennrich, A., Kostovčík, M., Hařovská, D., Šigut, M., Pyszko, P., Bracewell, R., Drozd, P., Begerow, D., & Kolařík, M. (2026). The saprotrophic dimension of Exobasidium (Exobasidiales, Basidiomycota): evidence for greater diversity and ecological flexibility than previously recognized. IMA Fungus, 17, Article e180524. https://doi.org/10.3897/imafungus.17.180524

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DOI: 10.3897/imafungus.17.180524

Keywords: Exobasidium, Exobasidium phylloplanum, saprotroph, environmental DNA, ITS2 metabarcoding, phyllosphere, fungal diversity, phylogenomics, caterpillar gut microbiome, Exobasidiales, saprotrophic, dimension

The chloroplast genomes were highly conserved in structure and gene content, while sequence divergence was concentrated in 16 hypervariable regions, including trnH-psbA, atpF and accD. The authors identified these regions as potential molecular markers for future phylogenetic and population-level studies. In contrast, mitochondrial genomes showed substantial variation in genome size and extensive structural rearrangements, including inversions of up to 322 kilobases and translocations. The mitochondrial comparison also found interspecific differences in the abundance and size distribution of simple sequence repeats and long sequence repeats.

Additional analyses indicated that mitochondrial protein-coding genes were generally under strong purifying selection, and the researchers detected abundant predicted C-to-U RNA-editing sites. The study identified 114 inter-organellar gene-transfer events, mainly representing chloroplast-derived sequences in mitochondrial genomes; three events involved complete transfer of tRNA genes. Chloroplast phylogenomic analysis recovered four major lineages within Sorbus s.l. The more limited mitochondrial dataset produced a broadly similar division of the major lineages but differed in the placement of several European and East Asian simple-leaved taxa. Both S. medogensis and S. thibetica were nested within the East Asian simple-leaved lineage.

These results, as summarized in the article abstract, show contrasting evolutionary patterns between chloroplast and mitochondrial genomes in Sorbus s.l. and clarify the phylogenetic placement of the two focal species within the East Asian simple-leaved lineage. The authors emphasize that broader mitochondrial and nuclear-genomic sampling is needed to resolve the group’s complex evolutionary history, which the abstract describes as involving extensive hybridization, polyploidization and morphological convergence. Because the supplied evidence is the abstract rather than the full methods and results, the sampling scope, analytical procedures and complete data set cannot be assessed here. The publisher notes that the early article version remains subject to further edits and will be replaced by the final version of record.

Subject of Research: Comparative chloroplast and mitochondrial genomics and phylogeny of East Asian simple-leaved Sorbus species

Article Title: Comparative organellar genomics of two East Asian simple-leaved Sorbus species reveals insights into organelle evolution and phylogeny of Sorbus sensu lato

Article References: Li, X., Feng, Y., Liu, C.-W., Qiu, Y.-L., Li, J.-T., Ju, W.-B., & Xu, B. (2026). Comparative organellar genomics of two East Asian simple-leaved Sorbus species reveals insights into organelle evolution and phylogeny of Sorbus sensu lato. BMC Plant Biology. https://doi.org/10.1186/s12870-026-09950-4

Image Credits: AI Generated

DOI: 10.1186/s12870-026-09950-4

Keywords: Sorbus sensu lato, Sorbus medogensis, Sorbus thibetica, organellar genomics, chloroplast genomes, mitochondrial genomes, phylogenomics, gene transfer, Rosaceae, Comparative, organellar, genomics

Desmophyllum pertusum, long known as Lophelia pertusa, is a habitat-forming cold-water coral documented in tropical and temperate waters of the Atlantic, Indian and western Pacific oceans. It occurs at depths of 40–2,775 metres, occupies settings including seamounts, submarine canyons and rocky outcrops, and can form bioherms and three-dimensional frameworks that shelter other organisms. Its colonies are morphologically variable, and the species accounts for approximately 30% of published research on colonial scleractinian cold-water corals. Those broad characteristics, combined with similarities among specimens from different ocean basins, had contributed to its treatment as cosmopolitan.

That interpretation placed several nominal species into D. pertusum on the basis of morphology, but genetic analyses indicate that geographic distribution alone may conceal evolutionary boundaries. Previous studies found substantial genetic structure among western North Atlantic populations of D. pertusum and very low divergence between it and the close relative D. dianthus. The new study asked whether corals assigned to D. pertusum on opposite sides of North America belonged to one broadly distributed lineage or represented separate species. Its authors also evaluated whether the distinction between colonial Lophelia and solitary Desmophyllum remained useful at the genus level.

The researchers used contemporary specimens collected over ten years from the North Atlantic and eastern North Pacific, together with 13 historical specimens from the Smithsonian National Museum of Natural History. Recent collections came from the Iceland Basin Slope, Anton Dohrn Seamount, Whittard Canyon, the Lofoten Basin Slope, Georges Bank, Norfolk Canyon, Pamlico Canyon, the Blake Plateau and Escarpment, the east Florida Slope, the Texas–Florida Slope, Whiting Bank and several Pacific sites. Contemporary sampling used the human-occupied submersibles Johnson Sea-Link and Alvin and the remotely operated vehicles SuBastian, Jason and Hercules. Museum material extended the geographic coverage to California, British Columbia, Hawaii, New Jersey and the Galápagos region.

Initial population-genomic comparisons used restriction-site-associated DNA sequencing, or RADSeq. After filtering, the analysis included 101 specimens and 2,496 unlinked single-nucleotide polymorphisms, although the figure captions report 2,495 SNPs for the principal component and STRUCTURE analyses. Principal component analysis identified three broad genetic clusters: one containing the Georges Bank Slope, Blake Plateau and Escarpment, and east Florida Slope; another joining Norfolk Canyon with the Texas–Florida Slope; and a distinct North Pacific group. A separate STRUCTURE analysis also supported three clusters. Pairwise F_ST values across six regions ranged from 0.01 to 0.27, with the Pacific samples differing from every Atlantic population by 0.23–0.27. In comparison, differentiation among the Georges Bank, Blake Plateau and east Florida groups remained below 0.06.

The team then used low-coverage whole-genome sequencing, known as genome skimming, to recover nuclear ultraconserved elements, exon loci and complete mitochondrial genomes. The final nuclear matrix contained 1,794 loci across 89 targeted specimens and spanned 2,936,258 base pairs. Maximum-likelihood and species-tree analyses produced the same relationships at deep nodes. Both analyses recovered the eastern Pacific specimens formerly identified as D. pertusum as an early-diverging lineage separate from Atlantic D. pertusum. The reconstructed genus also included both colonial and solitary forms, while the two principal colonial lineages and the two solitary lineages were not each monophyletic.

This broader pattern supports treating Lophelia as a synonym of Desmophyllum, a merger previously proposed on mitochondrial, microsatellite and skeletal evidence and subsequently accepted by World Register of Marine Species editors. Some researchers had maintained that more comprehensive molecular evidence was needed. By recovering thousands of nuclear loci and showing a monophyletic Desmophyllum containing both growth forms, the study provides genome-scale support for that synonymy. The result also illustrates why coloniality alone is an unreliable generic character: the recovered relationships do not divide the species into separate colonial and solitary assemblages.

Mitochondrial genomes independently supported the Pacific–Atlantic split. The seven complete genomes recovered in the study were circular, ranged from 16,098 to 16,150 base pairs and contained 34.8%–34.9% GC. Three D. californicum genomes differed from one another by no more than four base pairs, even though samples came from Hawaii and the continental Pacific coast. Pacific genomes differed from Atlantic D. pertusum by as many as 34 base pairs, corresponding to 99.79% sequence identity. Two Atlantic specimens also shared a 51-base-pair deletion in an intron between the nad5 3-prime region and the cob gene that was absent from the other retrieved genomes, reinforcing evidence of genetic discontinuity within western North Atlantic populations.

Skeletal observations supplied a second line of distinction. Desmophyllum californicum forms bushy colonies with closely spaced corallites, frequent intratentacular circumoral budding and short cylindrical coenosteal bridges connecting adjacent branches. As many as eight corallites can bud from the proximal edge of a single corallite, and corallites are usually 4–6 millimetres in greater calicular diameter, although aberrant larger examples occur. Atlantic D. pertusum has more widely spaced corallites, predominantly sympodial budding, a more open colony form and corallites usually 10–15 millimetres wide, sometimes reaching 20 millimetres. The species otherwise share similar septal arrangements, including 28–36 septa in ordinary corallites, so the distinctions are most evident in colony form, budding pattern and corallite size.

The revision carries implications for research and conservation because much of the existing literature and international conservation activity still uses the name Lophelia pertusa. Updating databases, management documents and legislation to Desmophyllum could help maintain continuity with earlier studies. The authors also caution that the sampled Pacific range may not represent the species’ full distribution: populations in the western Pacific or Indian Ocean that remain assigned to D. pertusum may instead belong to D. californicum or other lineages. Their genomic results also identify a solitary lineage previously assigned to D. dianthus that may represent a new or previously described species, but the available samples were insufficient to resolve its taxonomy conclusively. Further sampling, population genomics, ecological data and quantitative morphology are therefore needed to define the remaining lineages and distributions.

Subject of Research: Integrative genomic and morphological analysis of cold-water corals in the Atlantic and eastern North Pacific

Article Title: Integrative Taxonomy Does Not Support a Cosmopolitan Desmophyllum pertusum: Resurrecting D. californicum and Validating the Genus Desmophyllum

Article References: Vaga, C. F., Weinnig, A. M., Cairns, S. D., Taylor, M. L., Everett, M., Herrera, S., Cordes, E. E., Quattrini, A. M., & Morrison, C. L. (2026). Integrative Taxonomy Does Not Support a Cosmopolitan Desmophyllum pertusum : Resurrecting D. californicum and Validating the Genus Desmophyllum. Ecology and Evolution, 16(10), Article e74485. https://doi.org/10.1002/ece3.74485

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DOI: 10.1002/ece3.74485

Keywords: cold-water corals, deep-sea coral, Desmophyllum californicum, Desmophyllum pertusum, Lophelia, integrative taxonomy, population genomics, phylogenomics, mitochondrial genomes, marine taxonomy, Integrative, Taxonomy

The study examined specimens and population samples from New Guinea’s central, eastern and western regions, including the Bird’s Head Peninsula, and used molecular patterns alongside species-level morphological characters to identify taxonomic boundaries. Philaccolilus is a genus of stream-diving beetles endemic to New Guinea. Its members occupy flowing freshwater habitats, including small mountain creeks, lower-order forest streams, and the edges of larger rivers.

Many carry a strongly contrasting dorsal pattern in yellow, orange and black, although the extent and configuration of the pale markings can vary among individuals and sometimes between the left and right elytron. The beetles can swim over sandy or gravelly bottoms in pools beneath cascades, while in larger waterways they are generally associated with fast-flowing water, vegetated margins and submerged roots. Heavy rainfall can produce downstream drift, as indicated by isolated forest beetles found along river margins after flooding.

For the population-genomic component, the researchers used nextRAD, a genotyping-by-sequencing approach that produced data from 1,726 genomic loci. They extracted 5,609 single-nucleotide polymorphisms for analyses of population structure. Among specimens previously identified as P. ameliae, the nextRAD results separated three well-delineated clades.

One contained seven specimens from Sandaun Province and Waaf in Papua; another contained 17 specimens from the Weyland Mountains and Brazza River; and a third contained 34 specimens from across the Bird’s Head Peninsula. The structure analysis also revealed that geographic position did not always correspond neatly to genetic separation. Specimens from Waaf at the north coast and Sandaun in the central highlands showed a high degree of genetic admixture despite their separation, whereas the analysis identified substructure among some localities in the Arfak and Tamrau Mountains.

The researchers complemented the genome-wide data with PCR-based Sanger sequencing of a 738-base-pair fragment of the mitochondrial cytochrome c oxidase subunit 1 gene, or CO1. An alignment from 98 specimens formerly assigned to P. ameliae recovered the same major clades identified by nextRAD. Divergence among the principal lineages was above 8%, including 64 substitutions between the former P. a. weylandensis material and P. ameliae, and 67 substitutions between those lineages and specimens from the Bird’s Head Peninsula.

Haplotype networks likewise showed structure within the major clades, including differentiation between the Arfak and Tamrau Mountains. The concordance between genome-wide data, mitochondrial sequences and morphology supported the division of the broadly defined P. ameliae into at least three species, although the authors noted that some population relationships remain unresolved. Philaccolilus intania was described from the Tamrau Mountains near Kebar in West Papua.

The type locality is a shaded forest stream, and the beetles were observed swimming on a sandy and gravelly bottom in current, including pools behind large rocks and beneath shallow cascades. The male holotype is 4.8 mm long and 2.7 mm wide. Its body is black apart from an orange head, while a narrow dark-orange subbasal band on each elytron does not reach the lateral margin.

Twelve paratypes measured 4.7–5.1 mm in total length and 2.6–2.9 mm in width. In some specimens, the orange subbasal band is broken into isolated dots. The species was distinguished using body size, dorsal coloration, the shape of the median lobe of the male aedeagus and the form of the hind margin of the terminal abdominal ventrite, which differs between males and females.

Philaccolilus kirana was established from Testega in the southern Arfak Mountains, with material also collected at nearby localities. Its holotype, a male, is 5.6 mm long and 3.1 mm wide. Like P. intania, it has an orange head and a black pronotum, but its broad dark-yellow subbasal elytral band reaches the lateral margin and is usually accompanied by a small apical spot.

The size of 27 paratypes ranged from 5.0 to 5.6 mm in total length and 2.9 to 3.2 mm in width. The subbasal band was consistently developed, although the apical spot was not visible in every specimen, and one individual had unusual pale markings on the right elytron. The species was collected from a small lower-order stream concealed in dense montane forest, as well as from a more exposed stream where P. febrina was also present.

The male genital lobe and terminal-ventrite shape completed the combination of characters used to distinguish P. kirana. The third new species, P. febrina, was described from material collected in the Tamrau and Arfak Mountains. Its male holotype, from a forest stream north of Kebar, is 5.0 mm long and 2.7 mm wide.

The head is dark yellow, the anterior half of the pronotum’s lateral margins is dark orange, and the elytra carry dark-yellow spots arranged as a subbasal band, a medio-discal spot, a postmedial band and a small apical spot. The three components of the subbasal band are rarely fused and do not reach the lateral margin. Across 25 paratypes, total length ranged from 4.7 to 5.3 mm and width from 2.5 to 2.8 mm.

P. febrina resembles P. ameliae and P. weylandensis but has a slightly smaller average size and a somewhat broader male genital lobe in ventral view. It was recovered from exposed streams as well as shaded forest water, and a specimen was found swimming in a larger pool behind rocks. The evidence for the two morphologically distinct Bird’s Head lineages was more limited than the nextRAD evidence for the three major clades within the P. ameliae complex.

Four specimens from the two putative lineages were included in the nextRAD population-genomic analysis, whose species-status results were ambiguous, probably because sampling was limited. A separate CO1 analysis included 12 specimens from the two populations and recovered geographic clusters associated with Testega in the southern Arfak Mountains and the Tamrau Mountains, but the divergence between them was only about 0.4%. The researchers nevertheless recognized the lineages as separate species because of their clearly different body sizes, elytral color patterns and separate mountain distributions.

They interpreted them as recently evolved lineages following colonization of the Bird’s Head from the main body of New Guinea, an evolutionary interpretation offered by the authors rather than a result directly measured by the molecular analyses. The taxonomic revision also changed the status of P. weylandensis, which had previously been treated as a subspecies of P. ameliae. The original subspecies was distinguished partly by the slightly narrower curvature of the male genital lobe in ventral view.

The new examination found that this structure varies somewhat among specimens and populations, so the morphological difference is subtle. Molecular analyses nevertheless delineated the lineage clearly. Specimens from the Weyland Mountains had a mean total length of 5.6 mm, compared with 5.4 mm for specimens from the Digul River, although the reported size ranges overlap.

In the Weyland Mountains population, the outer subbasal elytral spot broadly contacted the lateral margin in all specimens; among Digul River specimens, it usually made only vague contact, and the outer spot was rarely fully separated from the margin. The authors therefore retained the Weyland Mountains and Digul River populations under P. weylandensis while noting that they might represent two species. Several limitations remain in the reconstruction of the group’s diversification.

Populations assigned to P. weylandensis from the Weyland Mountains and Digul River are genetically differentiated even though they occur on opposite sides of New Guinea’s central watershed, and the authors did not have enough intervening samples to determine whether they warrant separate recognition. The only locality found between the Digul River and the Weyland Mountains contained a population of P. ameliae, suggesting that the spatial pattern may be more complex than the currently sampled distribution indicates. The study also found unusual connectivity: geographically distant populations from Sandaun and Waaf shared a mitochondrial haplotype, while closer Sandaun and Brazza River populations were more clearly differentiated.

The authors conclude that broader field sampling is needed to distinguish the biotic and abiotic factors behind these patterns and to clarify the evolutionary history of New Guinea’s stream-diving beetles.

Subject of Research: Integrative taxonomy and population genomics of New Guinea diving beetles in the genus Philaccolilus

Article Title: NextRAD phylogenomics, sanger sequencing and morphological data to establish three new species of New Guinea stream beetles

Article References: Balke, M., Panjaitan, R., Surbakti, S., Shaverdo, H., Hendrich, L., Van Dam, M. H., & Lam, A. (2022). NextRAD phylogenomics, sanger sequencing and morphological data to establish three new species of New Guinea stream beetles. Alpine Entomology, 6, 51-64. https://doi.org/10.3897/alpento.6.86665

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DOI: 10.3897/alpento.6.86665

Keywords: Philaccolilus beetles, New Guinea, species delimitation, integrative taxonomy, nextRAD sequencing, Sanger sequencing, mitochondrial CO1, cryptic diversity, population genomics, diving beetles, NextRAD, phylogenomics

Narcine electric rays are small- to medium-sized, bottom-dwelling members of the order Torpediniformes, distinguished by paired electric organs derived from modified branchial musculature. The genus is especially challenging taxonomically because many characters used in conventional identification overlap or vary within species. A major revision proposed that Western Atlantic populations represented Narcine brasiliensis, Narcine bancroftii and a potentially undescribed form ranging from Suriname to northeastern Brazil. The first species was associated with diffuse blotches and broad horizontal, oval or circular markings, whereas the second was characterized by ocelli and incomplete rings. Research has since shown that tooth-row counts and dorsal coloration can vary substantially, undermining simple assignment of individuals to named species.

For the new analysis, the team sampled fresh muscle from seven rays captured as bycatch in artisanal fisheries at seven localities: two in the Gulf of Mexico, one on the Mexican Caribbean, one near Santa Marta in Colombia, and three in Brazil. Initial identifications used pigmentation, ocelli, snout markings and geographic distribution. The selection deliberately included unusual forms, such as a Gulf of Mexico individual with no dorsal spots or ocelli and a Brazilian specimen resembling the putative undescribed Narcine form. DNA was extracted, fragmented, indexed and sequenced as paired-end Illumina reads before complete mitogenomes were assembled and annotated. The seven new sequences, deposited in GenBank as PZ347752–PZ347758, were analysed with five public reference mitogenomes.

Phylogenetic analysis combined all 13 mitochondrial protein-coding genes in both nucleotide and amino acid datasets. Under partitioned maximum-likelihood inference, the two approaches produced broadly congruent trees. Narcine timlei from the Indo-West Pacific formed the deepest branch, while the eastern Pacific species Narcine entemedor was sister to the Western Atlantic group. Within the Atlantic radiation, all seven newly assembled mitogenomes joined a Florida reference sequence in a single lineage. Relationships among individual Atlantic samples received moderate to high support, and differences between nucleotide and amino acid trees were confined to shallow nodes. The agreement across sequence types, tree methods and distance calculations indicates that the central signal was not confined to one marker or analytical model.

Species-delimitation analyses produced different numbers of mitochondrial operational taxonomic units, illustrating the difficulty of applying generic thresholds to shallow genetic variation. Automatic Barcode Gap Discovery returned between three and eight units depending on its assumed level of within-species divergence, while Assemble Species by Automatic Partitioning favoured three primary clusters. A multi-rate Poisson tree process identified four. Despite these methodological differences, all three approaches placed the newly sampled Atlantic rays and the Florida reference together, separated them from the two Colombian reference mitogenomes and recognised the external species as distinct lineages. The authors interpret these outputs as hypotheses about mitochondrial diversity rather than formal species diagnoses because every analysis used mitochondrial rather than nuclear DNA.

The mitogenomes themselves were highly stable in structure. Each of the seven new sequences was about 17,071 base pairs long and contained the canonical vertebrate complement of 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes and a noncoding control region. Gene order and strand orientation were conserved, with ND6 and eight tRNAs on the light strand and the remaining components arranged conventionally. Base composition was also nearly uniform: adenine averaged 36.23%, thymine 29.99%, cytosine 21.94% and guanine 11.84%, giving an overall A+T content of about 66.2%. Positive AT skew and negative GC skew were consistent across the new Atlantic genomes, matching the compositional asymmetry widely observed in vertebrate mitochondria.

Selection appears to have constrained the functional parts of these genomes. Comparisons of nonsynonymous and synonymous substitution rates produced Ka/Ks values well below one for every protein-coding gene, a pattern consistent with strong purifying selection. The cytochrome c oxidase genes COX1–COX3 were among the most constrained, while ATP8 and several NADH dehydrogenase subunits generally had higher values but remained below unity. Codon usage was non-random and closely followed the genomes’ A+T bias, with A- or T-ending codons generally favoured. The 22 tRNAs ranged from 58 to 72 base pairs and usually folded into the classic cloverleaf structure; tRNA-Ser (AGN) was the standard exception, lacking the D-arm. In the control region, newly assembled genomes contained mainly 46-base-pair tandem repeats, sometimes accompanied by 23-base-pair units.

A striking anomaly emerged from two Colombian reference mitogenomes. Although identified in GenBank as different nominal species—N. brasiliensis and N. bancroftii—they differed from each other by only about 1.74–1.76%. Conversely, their divergence from the newly sampled Atlantic lineage reached 12.93–13.94% in uncorrected protein-gene distances and 14.32–15.56% with Kimura two-parameter correction. Those values were greater than the 6.82–7.22% separation between the Western Atlantic lineage and N. entemedor. Their exclusion from the main Atlantic cluster was stable across every phylogeny, delimitation method and distance analysis. The pattern could reflect misidentification, an unrecognised lineage or another taxonomic problem, but it also makes the reference sequences a warning against the uncritical reuse of database identifications without voucher support.

For now, the results support mitochondrial continuity among the newly analysed Western Atlantic Narcine populations and provide no mitochondrial evidence for multiple evolutionary lineages corresponding to their contrasting dorsal patterns. That conclusion is important because coloration has long been central to numbfish identification, and the analysis suggests that at least some visually distinct forms may represent phenotypic variation within a common mitochondrial population. The sample nevertheless remains small, and mitochondrial ancestry records history rather than necessarily reflecting recent species boundaries. Low elasmobranch mutation rates, incomplete lineage sorting, past demographic events or historical introgression could also obscure recent divergence. Expanded geographic sampling, direct morphological reassessment, nuclear genomic evidence and carefully curated voucher-linked sequences will therefore be essential for an integrative taxonomy of the Narcine complex.

Subject of Research: Mitochondrial lineage structure and species delimitation in Western Atlantic Narcine electric rays

Article Title: Mitogenomic and phylogenomic analyses identify a cohesive Western Atlantic lineage within the Narcine complex (Torpediniformes: Narcinidae)

Article References: Palacios-Barreto, P., Boza, B. R., da Cruz, V. P., da Silva Ferrette, B. L., Oliveira, C., Rotundo, M. M., Sandoval-Laurrabaquio-Alvarado, N., Adams, D. H., & Díaz-Jaimes, P. (2026). Mitogenomic and phylogenomic analyses identify a cohesive Western Atlantic lineage within the Narcine complex (Torpediniformes: Narcinidae). Molecular Biology Reports, 53(1), Article 1530. https://doi.org/10.1007/s11033-026-12694-x

Image Credits: AI Generated

DOI: 10.1007/s11033-026-12694-x

Keywords: Narcine electric rays, Western Atlantic, mitochondrial genomes, mitogenomics, phylogenomics, species delimitation, taxonomy, morphological variation, colombian references, elasmobranch evolution, Mitogenomic, phylogenomic

The project combined publicly available RNA sequencing data with the reference genome of Cycas panzhihuaensis. Paired-end Illumina reads were assembled into transcriptomes, from which protein-coding regions were predicted and orthologous gene families were identified. The researchers applied a relaxed single-copy strategy, retaining loci present in at least 75% of the 346 cycad accessions and allowing no more than 10% to carry a second copy. This produced 1,409 nuclear loci with average taxon occupancy of 94.9%, compared with only 115 loci under a strictly single-copy approach.

Each locus was aligned independently, and regions that were poorly aligned or rich in gaps were removed. IQ-TREE then inferred a gene tree for every locus, with phylogenetic pruning used where accessions contained multiple copies. A partitioned maximum-likelihood analysis treated all 1,409 loci as independent partitions, each with its own best-fit substitution model. The concatenated alignment contained 411,345 amino-acid sites. Support was assessed with 1,000 ultrafast bootstrap replicates, while gene and site concordance factors measured how individual gene trees and alignment sites supported each branch.

The resulting backbone placed Dioon as sister to the remaining Zamiaceae. The other zamiads formed two principal clades: Encephalartos, Lepidozamia and Macrozamia in one, and Bowenia, Stangeria, Ceratozamia, Microcycas and Zamia in the other. Every genus had 100% ultrafast bootstrap support and crown-node gene concordance factors of 62% to 81%. The Microcycas–Zamia relationship had the strongest genomic support among the intergeneric nodes, with a gene concordance factor of 66.7% and a site concordance factor of 85.5%.

Support was less uniform for other relationships. Although 240 of 344 scored internal branches, or 69.8%, had bootstrap support of at least 95%, and the median bootstrap value was 100%, the median gene concordance factor was only 3.2%. A total of 272 nodes, or 79.1% of the scored internal branches, had gene concordance below 10%. Site concordance was generally higher, averaging 40.3%, and approximately 71% of scored nodes exceeded the 33.3% expectation under random quartet resolution. The placements of Bowenia and Stangeria were comparatively weak, with gene concordance factors of 11.6% and 16.1% and site concordance factors of 33.8% and 36.8%.

The study links the contrast between high bootstrap values and low gene concordance to the kind of signal contained in the individual loci. The dominant pattern of discordance was polyphyly, with a mean gene-tree failure proportion of 89.0%, rather than strong support for an alternative resolution, whose mean values were 1.6% for the first alternative and 1.7% for the second. The authors note that slow molecular evolution characteristic of gymnosperms, together with recent diversification within cycad genera, can leave short internal branches with too few substitutions for individual loci to resolve confidently. Concatenation across 1,409 loci can still provide strong support for the overall topology.

Divergence times were estimated by penalized likelihood in TreePL after Ginkgo was pruned from the tree, with 12 minimum–maximum age constraints. Five constraints were derived from a fossil-calibrated total-evidence analysis, while seven were secondary genus-level calibrations taken from confidence intervals in recent molecular dating studies. Gene-wise bootstrap resampling was performed 100 times, with the 1,409 loci resampled with replacement and branch lengths re-optimized on the fixed maximum-likelihood topology, to calculate 95% confidence intervals for all 345 internal nodes. The mean width of these intervals was 3.97 million years.

The time-calibrated tree placed the Cycadales crown at approximately 359 million years, with a 95% confidence interval of 320–359 million years. This estimate reached the upper calibration bound and was consistent with the Carboniferous–Permian age inferred from the fossil record. The Zamiaceae crown was estimated at approximately 194 million years, with a 95% confidence interval of 165–196 million years. Backbone divergence estimates generally occupied 28% to 66% of their permitted calibration intervals, indicating that molecular branch lengths contributed to those ages rather than the bounds alone determining them.

Estimates for the crowns of individual genera were less independent of their constraints. Six of the seven genera with crown calibrations converged on the maximum permitted age: Dioon at 57 million years, Cycas at 40 million years, Lepidozamia at 34 million years, Zamia at 33 million years, Macrozamia at 29 million years and Encephalartos at 27 million years. Ceratozamia was the exception. Its estimated crown age of 32 million years, with a 95% confidence interval of 25–33 million years, fell within its 13–36 million-year calibration range and was interpreted as more directly informed by the molecular data. The authors caution that rate smoothing can push ages toward older values across short branches associated with recent radiations.

All trees and supporting data have been archived in Zenodo and linked to the World List of Cycads, where the phylogram and timetree can be explored through an interactive display. The public resources include the maximum-likelihood tree with branch lengths, bootstrap and concordance values; the dated tree with confidence intervals; 1,409 individual gene trees; and the concatenated alignment, partition definitions, support values and calibration data. Tip labels use accepted taxonomic names, allowing tree tips to be connected directly to the World List’s species records. The framework can support taxonomic evaluation, identification of species groups needing denser population sampling, trait mapping, biogeographic analysis and conservation calculations based on phylogenetic diversity or evolutionary distinctiveness.

Subject of Research: Species-level phylogenomic relationships and divergence times of the 10 extant cycad genera

Article Title: A comprehensive phylogenomic framework for cycads ( Cycadales )

Article References: Calonje, M., Clugston, J. A. R., & Coiro, M. (2026). A comprehensive phylogenomic framework for cycads (Cycadales). PhytoKeys, 275, 81-95. https://doi.org/10.3897/phytokeys.275.194283

Image Credits: AI Generated

DOI: 10.3897/phytokeys.275.194283

Keywords: cycads, Cycadales, phylogenomics, phylotranscriptomics, molecular dating, gene concordance, Zamiaceae, Cycadaceae, plant evolution, open genomic data, comprehensive, phylogenomic

The focal mushroom was originally described from Pennsylvania in 1822 as Boletus alboater. It was later moved among Suillus, Porphyrellus and Tylopilus as mycologists revised its classification. For decades, its identification rested heavily on the form and colour of the fruiting body, especially the dark cap, pinkish pore surface, pale flesh and the dramatic transformation from red to black after bruising. Yet fungal morphology can be highly conserved and also variable with age, weather and environment. The apparent similarity of mushrooms collected in China, Indonesia, Thailand, Australia and the United States therefore concealed lineages that the researchers found to be only distantly related within Boletaceae.

To establish the broad evolutionary position of the complex, the researchers generated three new genomes using Illumina HiSeq technology and combined them with 45 previously available genomes representing all eight subfamilies of Boletaceae. Two Suillus and two Paxillus genomes served as outgroups. An assessment of gene completeness identified 259 single-copy orthologous genes shared by all 52 genomes, and their aligned amino-acid sequences formed a matrix of 89,095 sites. Maximum-likelihood analysis strongly recovered the family’s eight-subfamily framework and showed that fungi labelled as T. alboater were polyphyletic, despite all falling within the subfamily Boletoideae.

The researchers then focused on 13 specimens: 11 identified as T. alboater from Australia, China, Indonesia, Thailand and the United States, along with two North American specimens of T. atronicotianus. A concatenated dataset of the nuclear ribosomal large subunit region, translation elongation factor 1-alpha, and the two largest RNA polymerase II subunits produced 3,056 aligned nucleotides. Maximum-likelihood and Bayesian analyses gave nearly identical topologies, placing the fungi in five generic lineages. The multi-locus tree supported many terminal relationships strongly, although some deeper branches received limited support, reflecting the smaller number of genes compared with the genome-scale analysis.

One of the most decisive results was a strongly supported lineage containing fungi from New York and China. It was unlike any previously recognized genus in the family and became Neoporphyrellus, a name that refers to its similarity in colour to Porphyrellus. The new genus contains three species: Neoporphyrellus alboater, N. atronicotianus and the newly described N. sinoalboater. Its members share dark fruiting bodies, a white-to-cream pore surface that becomes pinkish or gray, smooth spores, a trichoderm-type cap cuticle and flesh that turns reddish before eventually blackening when injured.

The revised identity of N. alboater also resolves a long-standing nomenclatural problem. Although Lewis David von Schweinitz assigned the number 864 to the specimen associated with his 1822 description, the researchers could not locate the presumed original material in several major fungal herbaria. Another specimen in Philadelphia had been collected by Persoon, who was not known to have collected in the United States, and the species has no verified European record. They therefore designated a North American specimen as a neotype, with a duplicate isoneotype, to give the name a stable modern reference point. The selected mushroom was collected at the New York Botanical Garden, about 150 kilometres from the later-cited type locality in Pennsylvania.

Beyond the new genus, the study expanded the known range of Abtylopilus, a genus previously represented by two species from China. Abtylopilus australiensis was described from a specimen collected in Queensland, Australia, and A. indonesiensis from Java, Indonesia. Both resemble the other members of their genus by producing a pale pore surface that becomes red and then black after damage. The Australian species has a reddish-brown, finely pruinose cap and stem, while the Indonesian fungus has a chocolate-brown to black cap and a pinkish-orange stem that turns deep purple or black toward the base. These records suggest that the genus is more geographically widespread than its known catalogue previously indicated.

Not every member of the old complex required a new name. Thai specimens were identified as the previously described Anthracoporus cystidiatus and Indoporus squamulosus, while a North American sample represented Tylopilus rubrobrunneus. Across the eight species, the most conspicuous field characteristic is the bruising reaction, but that feature cannot safely identify a specimen on its own. Cap colour, pore dimensions, tissue structure, cystidia and spore measurements all differ among the lineages. The new Chinese species N. sinoalboater, for example, has a gray to brownish-gray cap and a stipe that stains reddish brown before becoming black, while N. alboater has a much darker cap that becomes finely cracked with age.

The result is both a taxonomic correction and a warning for field guides, food-safety systems and biodiversity surveys. The old name T. alboater functioned as a broad label for mushrooms that looked sufficiently alike to be treated as one geographically dispersed species, but molecular evidence shows that the label united four previously recognized genera and one newly established genus. For science, the episode illustrates why fungal systematics increasingly depends on converging evidence: complete genomes establish deep relationships, targeted genes resolve nearer lineages, and microscopy supplies the structural details needed to name and diagnose species. The researchers also note that further sampling may reveal additional members of Neoporphyrellus and extend the newly documented distribution of Abtylopilus, suggesting that the true diversity of these dark, bruise-stained boletes is still only partly mapped.

Subject of Research: Phylogenomic and taxonomic revision of the global Tylopilus alboater mushroom complex

Article Title: Global diversity of the Tylopilus alboater complex ( Boletaceae , Boletales ): new genus and species, and typification of the name Boletus alboater

Article References: Li, J., Halling, R. E., Osmundson, T. W., Yang, Z. L., & Li, Y.-C. (2025). Global diversity of the Tylopilus alboater complex (Boletaceae, Boletales): new genus and species, and typification of the name Boletus alboater. IMA Fungus, 16, Article e159676. https://doi.org/10.3897/imafungus.16.159676

Image Credits: AI Generated

DOI: 10.3897/imafungus.16.159676

Keywords: fungal taxonomy, mushroom diversity, phylogenomics, Boletaceae, Neoporphyrellus, Abtylopilus, species delimitation, molecular evolution, mycology, Global, diversity, Tylopilus

The research team, led by biogeographers working at the intersection of plate tectonics and genomics, constructed a new palaeogeographic framework spanning the last 35 million years. Rather than relying on broad regional tectonic models, the authors stitched together high-resolution reconstructions of Indonesian New Guinea and Papua New Guinea, which track the movement of crustal fragments in one to two million year time slices. These reconstructions draw on multibeam sonar, seismic surveys, isotopic dating, thermochronology and sedimentary records. The result is a dynamic map of what the team calls proto-New Guinea, the shifting mosaic of continental and oceanic crust along the northern margin of the Australian Plate that would eventually fuse into the world’s largest tropical island.

The model reveals something unexpected. For decades, some biogeographers argued that New Guinea was essentially submerged until about 15 million years ago, while others proposed it emerged far earlier. The new reconstruction shows that substantial land was present surprisingly early: roughly 330,000 square kilometres of emergent terrain existed by 35 million years ago, following the Peninsular Orogeny, when a volcanic arc called the Sepik Terrane slammed into the Australian Plate. Even during high sea-level episodes, proto-New Guinea persisted as an archipelago of large islands that periodically coalesced as sea levels fell, with emergent land fluctuating between roughly 210,000 and 320,000 square kilometres through the Oligocene and Miocene. For comparison, today’s island covers about 790,000 square kilometres.

Sea level proved to be the critical accomplice. When Antarctica first glaciated 34 million years ago, global sea level dropped by at least 50 metres, exposing vast shallow carbonate reef platforms that had built up along the Australian margin. The researchers reason that corals kept pace with rising seas for most of the Cenozoic, generating atolls and reef flats that repeatedly emerged during sea-level falls of more than 20 metres, forming temporary land bridges and stepping stones. Only during extreme highstands, such as the Mid Miocene Climatic Optimum, when seas stood more than 50 metres above the present, did the platforms stay drowned, and during the Pliocene a phenomenon the authors describe as the Pliocene Reef Gap meant that even later lowstands could not re-expose them, because coral growth had collapsed permanently in those areas.

Armed with this geological scaffold, the team quantified the changing distances between micro-tectonic landmasses, the coherent crustal blocks that drifted independently before merging into modern islands. Using GPlates and geographic information software, they measured pairwise distances every million years across 20 million years of history, applying a 10 kilometre uncertainty buffer. The analysis identified two golden windows for dispersal between New Guinea and Halmahera, an island now lying roughly 250 kilometres to the west. The first came around 13.8 million years ago, when tectonic transport along the Sorong Fault Zone brought Halmahera within 20 kilometres of proto-New Guinea while the Middle Miocene Climate Transition dropped seas by up to 50 metres. The second came around 8.2 million years ago, when a dramatic Milankovitch-driven lowstand exposed carbonate platforms and shrank water gaps of 60 to 70 kilometres to something far more crossable.

Enter the birds. The team built new dated phylogenies of the Paradisaeidae using randomly subsampled 10 kilobase genomic window alignments analysed in BEAST2, calibrated against the geological windows. Their enigmatic focus was the distribution of three species on Halmahera and nearby Obi: the dusky and Obi paradise-crows, Lycocorax pyrrhopterus and L. obiensis, and Wallace’s standard-wing, Semioptera wallacii. Two independent lineages on the same remote islands demanded an explanation. When the tree was calibrated to the older 13.8 million year window, the resulting divergence for Waigeo and Batanta endemics, Paradisaea rubra and Diphyllodes respublica, landed around 3.3 to 3.8 million years ago, during the high seas of the Pliocene Climatic Optimum, when those islands were more than 100 kilometres from New Guinea. Geologically, the researchers judged this scenario very unlikely.

The younger calibration told a far more coherent story. Under the 8.2 million year anchor point, both the paradise-crow ancestor and Wallace’s standard-wing lineage reached Halmahera within the same narrow window between 8.2 and 7.4 million years ago, plausibly hopping across emergent platforms via Obi and Bacan. The separation of the Obi paradise-crow from its Halmahera relative then falls around 1.9 million years ago, when Pleistocene cooling pushed seas 60 metres below present levels, allowing intermittent contact. The red bird-of-paradise and Wilson’s bird-of-paradise, endemic to Waigeo and Batanta, diverged from mainland relatives around 2.0 to 2.3 million years ago, precisely when the Sorong Fault had carried Waigeo closer than ever to the Bird’s Head Peninsula and when glacial lowstands repeatedly exposed land bridges. Every event in this scenario matches the geological record, whereas the older scenario fails on nearly every count.

The implications stretch far beyond birds-of-paradise. Songbirds, or oscine passerines, make up half of all bird species on Earth, and genomic evidence places their origin in the Australo-Papuan region before their worldwide radiation. Whether New Guinea could have hosted that early diversification has been fiercely debated. The new model shows that extensive, intermittently connected land existed on the northern Australian Plate from 35 million years ago, complete with wet forest refugia as Australia itself dried out. Independent evidence from lizards, insects, monotremes and pigeons is consistent with early colonisation of proto-New Guinea, suggesting the emerging archipelago served as an engine of avian diversity long before the modern island took shape.

What makes the study methodologically distinctive is its iterative, mutualistic logic. Geological reconstructions generated hypotheses about when dispersal was physically possible; phylogenetic divergence times then tested those hypotheses and, where they clashed, flagged which geological scenarios were most plausible. The same trick has previously clarified the amalgamation history of Sulawesi, and the authors argue that molecular clocks can serve as a genuine constraint on tectonic models, not merely a downstream beneficiary of them. Biology and geology, treated as partners, turn out to be more powerful than either discipline alone.

The study also carries a cautionary note for future biogeographic work across the Indo-Pacific, the largest expanse of tropical islands on the planet. Shallow marine carbonate platforms, often invisible in simple tectonic maps, acted as critical corridors that appeared and vanished with orbital-scale sea-level swings. Understanding their emergence history, the authors conclude, is essential for decoding the distribution of virtually any weakly dispersing terrestrial organism in the region. For now, the flamboyant birds-of-paradise have done what their forebears could not have imagined: carried rocks, reefs and shifting plates along on their wings, and helped geologists redraw the map of a vanished world.

Subject of Research: Palaeo-tectonic reconstruction of New Guinea and its role in shaping Indo-Pacific avian diversification

Article Title: A new palaeo-tectonic model of New Guinea and its consequences for understanding Indo-Pacific avian diversity in space and through time

Article References: Jønsson, K. A., Webb, M., Fotheringham, J., Gunawan, I., Haryoko, T., Iova, B., Melia, S., Nagombi, E., Reeve, A. H., Blom, M. P. K., Irestedt, M., & Rijsdijk, K. F. (2026). A new palaeo-tectonic model of New Guinea and its consequences for understanding Indo-Pacific avian diversity in space and through time. Frontiers of Biogeography, 19, Article e200936. https://doi.org/10.21425/fob.19.200936

Image Credits: AI Generated

DOI: 10.21425/fob.19.200936

Keywords: biogeography, New Guinea, birds-of-paradise, plate tectonics, sea-level change, phylogenomics, dispersal, vicariance, passerines, Halmahera, palaeogeography, Sorong Fault Zone

The Chaetothyriales are a fascinating order of ascomycete fungi, characterized by their dark, melanin-rich cell walls and their remarkable ability to colonize extreme environments. Ancestral state reconstructions suggest the order originated from melanized, slow-growing rock-inhabiting fungi or lichen-associated ancestors, and today its members occupy a striking diversity of niches: some live on bare rock exposed to punishing ultraviolet radiation, others associate with ants, lichens, or plants, and a few have evolved as opportunistic pathogens of humans. The order is currently divided into at least seven families, including the Herpotrichiellaceae, which contains thermophilic human pathogens such as Cladophialophora carrionii, the agent of chromoblastomycosis. The Epibryaceae, first formally described in 2014, sit near the base of this evolutionary tree, making them a key lineage for understanding how the ecological diversity of the entire order came to be.

Until now, genomic information on the Epibryaceae was almost entirely absent, which hindered any serious attempt to understand the molecular basis of their apparent preference for cold. The genus Epibryon comprises roughly fifty described species, most of them tiny fungi that form small, dark, bristly fruiting bodies measuring just 40 to 150 micrometers across. They typically grow on the older, dying, or dead leaves of mosses and leafy liverworts, sometimes showing remarkable specificity for particular host species or even particular microsites such as leaf nerves or individual cells. A few species have been reported from rock surfaces, soil, or as epiphytes, and several were described from high-latitude regions, hinting at a link between the lineage and low temperatures long before genomic tools could test that idea.

To close this gap, the researchers selected six reference strains spanning the diversity of the family: Epibryon bryophilum, E. humicola, E. interlamellare, E. minutissimum, E. sylvestris, and E. turfosorum. The fungi were cultured on Sabouraud’s Glucose Agar at 28 degrees Celsius for a week, and DNA was extracted using the classic CTAB method with chloroform and isoamyl alcohol. Sequencing was carried out on Illumina platforms, including the NovaSeq 6000, MiSeq, and BGI-Seq500, generating 150-base-pair paired-end reads. The team then assembled the genomes de novo using SPAdes with multiple k-mer sizes, filtered out non-eukaryotic contamination with the deep-learning tool Tiara, and assessed completeness with BUSCO against a Chaetothyriales-specific database. Gene prediction and annotation were performed with the Funannotate pipeline, drawing on databases such as InterPro, PFAM, dbCAN, MEROPS, UniProt, and EggNOG to assign functions to the predicted proteins.

The resulting genomes averaged 29.09 megabase pairs in size, ranging from 26.20 to 34.97 Mbp, and contained an average of 10,495 predicted genes. BUSCO completeness averaged 85.8 percent using a set of 6,265 conserved fungal genes, a respectable figure for these fragmented assemblies. The researchers then compared these new genomes with publicly available references across the subclass Chaetothyriomycetidae, including 62 genomes from the Chaetothyriales itself, plus representatives of the Phaeomoniellales, Pyrenulales, and Verrucariales. Orthology analysis with OrthoFinder2 classified genes into orthogroups, and a phylogenomic tree built from 296 single-copy orthogroups confirmed that all Epibryon species share a common ancestor and that the family forms a distinct, early-diverging branch within the order.

One of the most striking taxonomic outcomes concerns Cladophialophora brunneola, a fungus isolated from karst rock at 2,220 meters altitude in Guizhou, China. Previously described as an early-diverging lineage within the Chaetothyriales, this species clearly clusters within the Epibryaceae in both the phylogenomic and multilocus analyses, which were based on the ribosomal genes SSU, ITS, and LSU together with the protein-coding RPB2 gene. The authors therefore formally reclassified it as Epibryon brunneolum comb. nov. Interestingly, this rock-dwelling species showed the highest proportion of orthogroups containing two genes, suggesting greater protein diversity, and it also possesses the highest number of carbohydrate-active enzymes in the family—features that may reflect the severe fluctuations in temperature and humidity experienced by fungi living on sun-exposed rock surfaces.

The functional comparisons revealed a distinctive enzymatic toolkit that sets the Epibryaceae apart from their relatives. On average, family members carry 297 genes assigned to the CAZyme database, spanning 106 families, and 345.7 genes in the MEROPS peptidase database, spanning 89 families. Crucially, the Epibryaceae show a reduced set of enzymes associated with lignin degradation, including contractions in the auxiliary activity families AA7 and AA9 and the glycoside hydrolase family GH12. They also uniquely possess the carbohydrate-binding module CBM52, which binds to endo-1,3-beta-glucanase and enhances its activity during cell septation, though its precise ecological role remains to be elucidated. On the peptidase side, the family uniquely harbors the enzyme U74, which has a nonspecific catalytic site capable of digesting proteins without any restriction on substrate size, and shows expansions in the S53 and T02 families alongside contractions in C26 and C85.

The most compelling evidence for cold adaptation comes from the analysis of stress-response genes. All Epibryaceae species possess the cold shock protein CspA, an RNA-binding enzyme that stabilizes ribosomal structures and maintains protein translation under cold stress. No other family in the Chaetothyriales carries this protein, although it is known to be expanded among black fungi isolated from Antarctic environments in the class Dothideomycetes, underscoring its importance for fungal survival at low temperatures. At the same time, the Epibryaceae lack the ClpA/B conserved site 2, a domain associated with protecting cellular structures during heat stress, suggesting a reduced tolerance for high temperatures. The family also shows a duplication of 5-formyltetrahydrofolate cyclo-ligase in its last common ancestor and an expansion of the DNA recombination and repair protein Rad51, which has five copies compared with four in the ancestral Chaetothyriales and only two in several Herpotrichiellaceae. Rad51 repairs DNA damage caused by ultraviolet light, and its expansion may help these fungi withstand the intense radiation of glacial and high-altitude environments.

These genomic signatures align neatly with the ecological record. Mapping the isolation sites of Epibryaceae strains onto the Köppen climate classification shows that most known isolates come from polar regions and cold or temperate continental zones, with precipitation distributed throughout the year. The family’s reduced capacity for lignin and complex polysaccharide breakdown fits its saprobic lifestyle on mosses and liverworts, which offer readily accessible carbon sources in nutrient-poor, cold environments where lignin-rich plant material is scarce. The authors suggest that this combination of traits—a psychrophilic preference, a saprobic ecology on bryophytes, and occasional associations with lichens, soil, and the phyllosphere—distinguishes the Epibryaceae from all other chaetothyrialean lineages and may reflect an ancestral ecological state shared with closely related orders such as the Verrucariales, many of which are lichen-associated.

The study also highlights how much remains to be discovered. Despite extensive herbarium records, molecularly characterized isolates of Epibryon remain scarce, and the true breadth of the family’s ecological distribution is only beginning to emerge. The finding that a genus once defined by its moss-dwelling habit also includes rock-inhabiting and soil-dwelling species suggests that future sampling from underexplored cold regions will likely reveal further diversity and refine our understanding of its specialization. For now, the genomes of these six strains provide the first molecular window into a lineage that traded heat tolerance for cold resilience, and they demonstrate how comparative genomics can transform a little-known family of moss-inhabiting microfungi into a model for studying fungal adaptation to some of the planet’s most demanding environments.

Subject of Research: Genomics and cold-adaptation mechanisms of the psychrophilic fungal family Epibryaceae in the order Chaetothyriales

Article Title: Genomics and ecology of Epibryaceae , a psychrophilic family in Chaetothyriales

Article References: Lustosa, B. P. R., Belmonte-Lopes, R., de Hoog, S., Costa, F. D. F., Jacomel, B., dos Santos, G. D., Razzolini, E., Li, Y., Xue, R., Baura, V. A., Souza, E. M. D., Gomes, R. R., Ahmed, S. A., Selbmann, L., Song, Y., & Vicente, V. A. (2025). Genomics and ecology of Epibryaceae, a psychrophilic family in Chaetothyriales. IMA Fungus, 16, Article e170120. https://doi.org/10.3897/imafungus.16.170120

Image Credits: AI Generated

DOI: 10.3897/imafungus.16.170120

Keywords: Epibryaceae, Epibryon, Chaetothyriales, psychrophilic fungi, comparative genomics, cold shock protein CspA, CAZymes, MEROPS peptidases, phylogenomics, bryophytes, black fungi, genome annotation