ModelFinder: fast model selection for accurate phylogenetic estimates

Unique phenomenon of H5 highly pathogenic avian influenza virus in China: co-circulation of Clade 2.3.4.4b H5N1 and H5N6 results in diversity of H5 Virus

Recently, Clade 2.3.4.4b H5N1 virus has been widely prevalent globally. Although no outbreaks of Avian Influenza have occurred in poultry in China recently, Clade 2.3.4.4b H5 virus can still be isolated from wild birds, live poultry markets and environment, indicating the ongoing co-circulation of H5N1 and H5N6 viruses. In this study, phylogenetic analysis of global Clade 2.3.4.4b viruses and 20 laboratory-isolated H5 strains revealed that Chinese H5N1 and H5N6 viruses since 2021 cluster into two distinct groups, G-I and G-II. Bayesian phylodynamic analysis reveals that G-I H5N6 virus has become an endemic virus in China. In contrast, G-II H5N1 virus, with South China as its main epicentre, has been disseminated in China and its surrounding countries, with its transmission more reliant on the connections of wild birds and waterfowl. Reassortment analysis indicates that since 2023, Clade 2.3.4.4b H5 viruses isolated in China have formed seven genotypes. The genome of H5 viruses has undergone changes compared to those previously prevalent in China. Animal experiments have shown that prevalent H5 viruses exhibit significant lethality in chickens. Additionally, certain H5 viruses have shown the capability of systemic replication in mice. It is noted that H5N6 viruses with HA genes derived from H5N1 viruses demonstrate stronger virulence and pathogenicity in chickens and mice compared to G-I H5N6 viruses. Our study indicates that the co-circulation of H5N1 and H5N6 viruses in China has increased the diversity of H5 viruses, making continuous surveillance of H5 viruses essential.

Gut microbes with the gbu genes determine TMAO production from L-carnitine intake and serve as a biomarker for precision nutrition

Gut microbial metabolism of L-carnitine, which leads to the production of detrimental trimethylamine N-oxide (TMAO), offers a plausible link between red meat consumption and cardiovascular risks. Several microbial genes, including cntA/B, the cai operon, and the recently identified gbu gene cluster, have been implicated in the conversion of dietary L-carnitine into TMA(O). However, the key microbial genes and associated gut microbes involved in this pathway have not been fully explored. Utilizing the oral carnitine challenge test (OCCT), which specifically measures TMAO production from L-carnitine intake and identifies TMAO producer phenotypes, we compared the abundance of microbial genes between low- and high-TMAO producers across three independent cohorts. Our findings consistently revealed that the gbu gene cluster, rather than cntA/B or the cai operon, was significantly enriched in high-TMAO producers. We further analyzed 292 paired multi-omic datasets from OCCT and shotgun metagenomic sequencing, which demonstrated a significant positive correlation between the abundance of fecal gbu genes and L-carnitine-induced TMAO production, with gbuB showing the strongest correlation. Interestingly, these fecal gbu genes were found to increase with L-carnitine supplementation and decrease with a plant-based diet. Notably, we verified a previously uncultured gbu-containing bacterium, JAGTTR01 sp018223385, as the major contributor to TMA formation in the human gut. We isolated these gbu-containing gut microbes and confirmed their role in TMA/TMAO production using anaerobic incubation and a gnotobiotic mouse model. Using an in-house collection of gbu-containing isolates, we developed a qPCR-based method to quantify fecal gbuB and validated its correlation with L-carnitine-mediated TMAO production as measured by OCCT. Overall, these findings suggest that gbu-containing gut microbes are crucial for TMAO increases following L-carnitine intake and may serve as biomarkers or targets for personalized nutrition.

Evaluation of global distribution, genetic evolution, and mammalian infectivity and pathogenicity of H13 and H16 avian influenza viruses

H13 and H16 subtype avian influenza viruses (AIVs) typically infect Charadriiformes, are widely distributed throughout coastal regions worldwide, and pose a risk of spill-over to mammals. Systematic research on the epidemiology, transmission dynamics, and biological characteristics of these subtypes remains limited. To address this gap, we analyzed 20 years of wild bird influenza surveillance data from China integrated with global influenza database information to reconstruct the global spatiotemporal distribution, transmission dynamics and public health implications of H13 and H16. During influenza surveillance, 28 H13 and 19 H16 viruses were isolated. The phylogenetic trees for the H13 and H16 viruses revealed that both subtypes could be classified into three distinct groups. Viruses from H13 Group A, H13 Group C, and H16 Group C demonstrated frequent genetic exchanges and intercontinental transmission on a global scale. Mapping host migration revealed overlap between virus spread and host migration pathways. Our results suggest that host migration is a key driver of widespread distribution, cross-regional spread, and gene exchange for some H13 and H16 lineages. Virus isolates exhibit high genetic diversity with rich genotypic variation. Most isolates carry mammalian-adaptive mutations, such as the G228S mutation in the HA protein. H13 and H16 isolates of multiple genotypes infected mice without prior adaptation and exhibited varying tissue tropism. In summary, these findings indicate that host migration patterns are closely associated with the evolution of H13 and H16 AIVs. The potential risk of mammalian infection is highlighted, as viruses carrying mammalian-adaptive mutations may lead to new infection cases.

Development and validation of a new mpox virus sequencing and bioinformatic analysis pipeline

Sequencing and bioinformatic analysis of mpox virus (MPXV) remain challenging in resource-limited settings. We developed and validated a PCR-based sequencing assay that targets a 12.5 kilobase (kb) region that is phylogenetically representative of the whole ∼ 200 kb MPXV genome. We combined this sequencing assay with a lightweight, downloadable, on-and-off-grid-bioinformatics pipeline for rapid phylogenetic analysis. Our findings demonstrate that this simplified sequencing method, and the associated bioinformatics pipeline accurately distinguished clades, subclades, and clusters of MPXV. Therefore, this assay will provide rapid sequence information for understanding transmission patterns and sources of outbreaks in resource-limited settings. In addition, this assay provides a unique opportunity to decentralize mpox molecular surveillance capacities that are needed to contain the ongoing outbreak.

Renal myxosporidiosis by an unknown Bivalvulidan myxozoan parasite in Murray River turtles (Emydura macquarii) in Australia

This case series provides the first published record of a myxozoan parasite in Murray River turtles (Emydura macquarii) in Australia. Thirteen turtles were captured for an eco-toxicology study and underwent postmortem examinations. From these, three were found to have interstitial nephritis and spores within the affected renal tubules. Molecular characterisation was performed with PCR which yielded positive results for myxozoan DNA in the three infected samples. DNA sequencing and phylogenetic analysis of 18S rRNA sequences positioned the unknown species in a distinct clade, closely related to, but separate from, histozoic clades II and III. This discovery contributes significantly to the understanding of myxozoan diversity and ecology, highlighting a potential new threat to the health of Murray River turtle populations and possibly other aquatic reptiles. The discovery of this myxozoan species not only broadens the known host range of myxozoans but also raises concerns about the conservation of affected turtle populations due to its possible pathogenic nature.

Morphology, genetic characterization and molecular phylogeny of Xystrognathus priscus (Nematoda: Rhigonematomorpha)

The infraorder Rhigonematomorpha is a unique group of zooparasitic nematodes commonly occurring in the hindgut of millipedes. Our present knowledge of the composition of the Rhigonematomorpha nematode fauna in China is far from complete. The current genetic data base for Rhigonematomorpha remains very limited, and the molecular phylogeny of Rhigonematomorpha is still in its beginning phase. In the present study, Xystrognathus priscus was redescribed using light microscopy and, for the first time, scanning electron microscopy based on the freshly collected specimens from Litostrophus scaber (Spirobolida: Pachybolidae) in China. SEM observations showed the detailed morphology of some structures for the first time, including cephalic structures bearing 1 pair of peg-like submedian cephalic papillae and 1 pair of amphidial apertures in ventral jaw, cuticular spines (microtrichs) varied from saw-tooth blade-like at anterior of body to tooth-like at posterior of body, excretory pore without cuticular spines surrounded, caudal papillae nipple-shaped, vulva without anterior vulval flap, egg with smooth surface and oval phasmid. The present study is only the second record of X. priscus, and also represents the first record of the species of the genus Xystrognathus and family Ichthyocephalidae in China. The partial 18S, 28S, ITS, cox1 and cox2 sequences of X. priscus were provided for the first time to enrich the genetic data of Rhigonematomorpha, and enabled the molecular identification of Xystrognathus nematodes. Additionally, phylogenetic results based on the partial 18S + 28S sequence data indicated that the families Ichthyocephalidae, Carnoyidae, Rhigonematidae and Xustromatidae in Rhigonematomorpha are all non-monophyletic, but strongly supported the monophyly of the genus Xystrognathus, and suggested a close affinity between Xystrognathus and the genus Obainia belonging to the Xustrostomatidae.

Convergent evolution in nuclear and mitochondrial OXPHOS subunits underlies the phylogenetic discordance in deep lineages of Squamata

The order Squamata is a good candidate for detecting unusual patterns of mitochondrial evolution. The lineages leading to the snake and agamid clades likely experienced convergent evolution in mitochondrial OXidative PHOSphorylation (OXPHOS) genes, which provides strong support for the sister relationship of these two groups. The OXPHOS subunits are encoded by both the nuclear and mitochondrial genomes, which are subject to distinct evolutionary pressures. Nevertheless, the cooperation between OXPHOS subunits is essential for proper OXPHOS function, as incompatibilities between subunits can be highly deleterious. In the present study, we annotated OXPHOS genes of 56 Squamata species. The nuclear OXPHOS subunits that physically interact with mitochondrial proteins also support the clade sister relationship between snakes and agamids. Additionally, we found a significant number of convergent amino acid changes between agamids and snakes, not only in mitochondrial OXPHOS genes, but also in nuclear ones, with a higher rate of convergence in the nuclear OXPHOS subunits that play central roles in the OXPHOS complexes, like COX4 and NDUFA4. Overall, the common selective pressures in two distinct lineages can lead two sets of genes, encoded by two different genomes, to exhibit similar patterns of convergent evolution, as well as similar evolutionary rates. As a consequence, the coevolution of interdependent subunits and their adaptation to specific evolutionary pressures can heavily influence the molecular structure of cytonuclear enzyme complexes and blur phylogenetic signals.

Threshold sensitivity analysis for HIV-1 transmission cluster detection using different genomic regions and subtypes

HIV-1 cluster analysis has been widely used in characterizing HIV-1 transmission and some countries have implemented such molecular epidemiology as part of their prevention strategy. However, HIV-1 sequences derive from varying genome regions, which affects phylogenetic clustering outputs. Here, we apply different tools to run a sensitivity analysis for assessing which threshold give the most cohesive clustering outputs for different data sources. We used a dataset of 174 full-length sequences of subtype B from the Swiss HIV Cohort Study and publicly available subtype C from South Africa. Each dataset was divided into sub-genomic sub-datasets covering gag, pol, and env. pol was further subdivided into regions commonly used in HIV-1 genotyping laboratories (pr-rt, rt-int, and pr-rt-int). Cluster analyses for each sub-genomic region was performed specifying varying distance thresholds of 0.5 %-4.5 % and tree branch support of 70 %, 90 % and 99 % in ClusterPicker. Tree topologies and clustering outputs were compared against each other to assess cluster similarity. Pylogenies using pol, pr-rt-int, or rt-int had more robust tree topologies compared to gag and env. Cluster composition changed with increasing genetic distance threshold but was not affected by branch support. Cluster identity was most similar around genetic distances of 2.5 (±0.5)% for all sub-genomic regions and for both subtype B and C. Our study demonstrated the value of performing a sensitivity analysis before setting a genetic distance threshold for clustering output and that the pol region is appropriate for clustering outputs and can be used for near real-time HIV-1 cluster detection.

Phylogeny of Palicoureeae (Rubiaceae) based on 353 low-copy nuclear genes - with particular focus on Hymenocoleus Robbr

Members of the tribe Palicoureeae of the coffee family (Rubiaceae) have a complex taxonomic history and have been the focus of few modern systematic studies. The tribe comprises about 1,100 tropical species in ten genera. To investigate phylogeny, we used a target capture approach and the angiosperm-wide Angiosperms353 bait set to produce genomic data for a representative taxon sample of Palicoureeae, with particular focus on the African genus Hymenocoleus. Using coalescent-based inference methods, we find that Puffia gerrardii (recently separated from Geophila) is sister to Hymenocoleus. The deepest split in Hymenocoleus is highly affected by incomplete lineage sorting, possibly as a consequence of rapid speciation during the early evolution of the clade. Remaining interspecific relationships in Hymenocoleus could be confidently resolved and while Robbrecht's traditional infrageneric classification scheme based on floral features is not supported as reflecting evolution in the group, we find that several other features do, e.g. characters of pyrenes and involucral cups. Although not free of challenges, a strong advantage with our analytical approach is that gene tree heterogeneity can be taken into account. Including flanking regions yielded data sets that had the strongest power to reject polytomies and produced less gene tree error, resulting in species trees with higher normalised quartet scores and higher average support compared to trees inferred only from exon data. Presumably paralogous loci are often filtered out prior to species tree estimation but we find that they may contribute important phylogenetic information when using an inference method that actively accounts for them.

Phylogenomics provides new insight into the phylogeny and diversification of Asian Lappula (Boraginaceae)

The application of omics data serves as a powerful tool for investigating the roles of incomplete lineage sorting (ILS) and hybridization in shaping genomic diversity, offering deeper insights into complex evolutionary processes. In this study, we utilized deep genome sequencing data from 76 individuals of Lappula and its closely allied genera, collected from China and Central Asia. By employing the HybPiper and Easy353 pipelines, we recovered 262-279 single-copy nuclear genes (SCNs) and 352-353 Angiosperms353 genes, respectively. We analyzed multiple datasets, including complete chloroplast genomes and a filtered set of 475 SCNs, to conduct phylogenetic analyses using both concatenated and coalescent-based methods. Furthermore, we employed Quartet Sampling (QS), coalescent simulations, MSCquartets, HyDe, and reticulate network analyses to investigate the sources of phylogenetic discordance. Our results confirm that Lappula is polyphyletic, with L. mogoltavica clustering with Pseudolappula sinaica and forming a sister relationship with other taxa included in this study. Additionally, three Lepechiniella taxa nested within distinct clades of Lappula. Significant gene tree discordance was observed at several nodes within Lappula. Coalescent simulations and hybrid detection analyses suggest that both ILS and hybridization contribute to these discrepancies. Flow cytometry (FCM) analyses confirmed the presence of both diploid and tetraploid taxa within Lappula. Phylogenetic network analyses further revealed that Clades IV and VII likely originated through hybridization, with the tetraploids in Clade IV arising from two independent hybridization events. Additionally, the "ghost lineage" identified as sister to Lappula redowskii serves as one of the donors in allopolyploidization. In conclusion, our study provides new insights into the deep phylogenetic relationships of Asian Lappula and its closely allied genera, contributing to a more comprehensive understanding of the evolution and diversification of Lappula.

Salmonella Heidelberg isolates from poultry in Brazil and the United States share a large number of resistance and virulence determinants

Salmonella enterica subps. enterica serovar Heidelberg (SH) is one of the most common serovars isolated from poultry and associated with severe infections in humans. Commonly considered multidrug-resistant, it represents a risk to public health. We analyzed 317 SH genomes, including 314 from the Enterobase database from Brazil and the United States (US), and added three recently sequenced Brazilian isolates. In genomes from both countries, the main identified resistance genes were: aac(6')-Iaa, fosA7, sul2, tet(A), and blaCMY-2. Mutations in GyrA (S83Y only from US genomes and S83F and D87N from Brazilian genomes) were observed in 17 % and 90.62 % of genomes from US and Brazil, respectively, and ParC mutation (T57S), was identified in all genomes. The plasmid replicons most identified in both countries were ColpVC, IncC, IncI1-I(Gamma), and IncX1. The core and soft-core genes were utilized as the basis for conducting a phylogenetic analysis, showing seven clusters of strains, of which only one was shared between strains from the US and Brazil. Overall, this study highlights the variation in genomic profiles of SH circulating in poultry production in both countries, emphasizing the need for improved surveillance measures to protect human and animal populations from potential outbreaks worldwide.

Phylogenomics and population genomics of Nothobranchius in lowland Tanzania: species delimitation and comparative genetic structure

Annual killifishes of the genus Nothobranchius are widespread across East Africa, with a particularly high biodiversity in lowland Tanzania. While they are typically found in ephemeral pools, the pools vary greatly in size, connectivity and inundation patterns. It was previously suggested that main river channels formed significant barriers to Nothobranchius dispersal. Here, we study the distribution of genetic lineages in an equatorial part of their range where main river channels that may act as barriers occur and closely related lineages frequently coexist in secondary contact zones. We used single-nucleotide polymorphism (SNP) dataset from double-digest restriction site-associated DNA (ddRAD) sequencing to investigate how genetic diversity is structured in Nothobranchius species from the coastal lowlands of Tanzania. Our analyses resolved some uncertain phylogenetic relationships within the N. melanospilus and N. guentheri species groups and placed N. flammicomantis outside the Coastal clade. Rather than a shared intraspecific genetic diversity pattern across four coexisting and widely distributed species, we found highly diverse patterns of intra-specific genetic structure among N. eggersi, N. janpapi, N. melanospilus and N. ocellatus. Populations of Nothobranchius species from the humid coastal lowlands of Tanzania are therefore structured, but not constrained by barriers formed by river channels or by basins - in contrast to Nothobranchius species from the dry part of their distribution. Some of the genetic relationships determined call for a re-evaluation of taxonomic delimitations.

Unearthing limestone fungal diversity: Description of seven novel species from Portugal

Stone-built heritages are found worldwide, and despite stony surfaces being considered a stressful environment with challenging conditions to overcome, research has demonstrated that it can support diverse fungal communities, fostering a unique array of peculiar yet crucial species. These species exhibit a dual nature, being both foe and friend. While these fungi play a considerable role in the deterioration of cultural heritage, their mechanisms of adaptation to unfavourable environments hold great promise for biotechnology. Despite their importance, there is limited information available about these stone dwellers in Portugal. During an experimental survey aimed at isolating fungal species thriving in a deteriorated limestone funerary art piece at the Lemos Pantheon, a national monument located in Águeda, Portugal, several fungal specimens were isolated that could not be identified as any currently known species. Through morphological characteristics and multilocus phylogenetic analyses, seven new species (Aspergillus albicolor sp. nov., Banksiophoma dissensa sp. nov., Knufia lusitanica sp. nov., Microascus lausatensis sp. nov., Neodevriesia saximollicula sp. nov., Paramicrodochium filiforme sp. nov. and Talaromyces benedictus sp. nov.) are here proposed, illustrated, and compared to closely related species. These newly discovered fungal taxa form distinct lineages independent of other previously described species and are classified into seven families across six orders within the phylum Ascomycota. This paper also provides additional evidence that stone heritages harbour a diverse range of new species, deserving additional focus in the future. Citation: Paiva DS, Fernandes L, Pereira E, Mesquita N, Tiago I, Trovão J, Portugal A (2025). Unearthing limestone fungal diversity: Description of seven novel species from Portugal Fungal Systematics and Evolution 15: 47-77. doi: 10.3114/fuse.2025.15.02.

Explosion of goby fish diversity at the Eocene-Oligocene transition

A rapid drop of sea level at the Eocene-Oligocene transition (EOT; 34-33 Ma) triggered a marine mass extinction event and the turnover of terrestrial fauna, but its influence on the diversification of nearshore marine fish communities is unclear. Goby fishes (Acanthomorpha: Percomorpha: Gobiiformes) provide an ideal system to investigate the hypothesis that ecological opportunity at the EOT triggered the proliferation of coastal marine fishes. However, despite more than 30 years of molecular evolutionary research, divergence time estimates for gobies are widely variable, incomplete with respect to sampling of taxonomic families and sub-familial lineages, and far older than evident by the modest fossil record. Here we use 1,314 ultraconserved element (UCE) sequences sampled from 121 species, including all gobiiform families and sub-familial goby lineages, to infer phylogeny and node ages under species tree and relaxed molecular clock models. Our time-calibrated phylogenomic hypothesis reconciles molecular clock- and fossil-based estimates for gobiiform diversification, dating the origin of Apogonidae and Gobioidei to the uppermost Late Cretaceous, with lower to middle Paleogene divergence of the gobioid backbone and an explosion of goby lineages at the EOT. Our results support a remarkably recent evolutionary origin of goby families and stimulate new questions on the seemingly exceptional diversity of the group.

Cryptic species, biogeography, and patterns of introgression in the fish genus Mogurnda (Eleotridae) from the Australian wet tropics: A purple patch for purple-spots

Accurately delimiting species is an essential first step towards understanding the true biodiversity of an ecosystem and any subsequent efforts to identify and protect taxa at risk of extinction. Current molecular evidence suggests that purple-spotted gudgeons (genus Mogurnda) harbour high levels of cryptic biodiversity across their broad distributional range. The present study uses a large single nucleotide polymorphism (SNP) dataset plus a companion allozyme dataset to clarify taxonomic uncertainty, patterns of introgression, and biogeographic relationships among Mogurnda populations within the Queensland Wet Tropics (QWT), a known biodiversity hotspot. Both datasets were strongly concordant in identifying a total of seven taxa split among distinct southern, northern, and lowlands groups. No two taxa were found in strict sympatry, but many appear to be parapatric and occur within the same drainage basin. Although clear evidence of introgression was only evident at six sites (∼4%), the genomic signature of modest historic admixture between proximally-distributed taxa was detected at multiple other sites. Nevertheless, all primary genetic and phylogenetic analyses strongly supported the integrity and diagnosability of these seven taxa. We therefore nominate these as novel candidate species for what appears to be yet another hyper-cryptic complex within the Australian freshwater ichthyological fauna. These results offer up intriguing ecological scenarios and conservation implications for multiple candidate species with narrow ranges in specialised habitat. We conclude by exploring the major biogeographic patterns displayed by QWT Mogurnda.

Genome-wide analysis reveals the evolutionary history of TAG intracellular lipases and their roles in different molting stages of Decapods

Intracellular lipases can be broadly divided into two categories: neutral lipases and acid lipases. Adipose triglyceride lipase (ATGL), hormone-sensitive lipase (HSL), and monoacylglycerol lipase (MAGL) are three key neutral lipases responsible for the hydrolysis of triacylglycerol (TAG) in lipid droplets (LDs). Although these three TAG intracellular lipase genes have been identified and characterized in multiple model species, their evolutionary history remains largely unknown. For the TAG intracellular lipase genes in Decapoda, there is also a large knowledge gap. Thus, in this study, we performed a genome-wide identification and investigation of TAG intracellular lipase genes in Decapoda and outgroups, analyzing their phylogenetics, structural features, conserved motifs, and expression patterns. In total, 22 ATGL genes, 23 HSL genes and 21 MAGL genes were identified in 17 selected species. HSL is the oldest and most conserved gene to exist in any species. Furthermore, RNA-seq analysis was conducted on two representative Decapod species, Chinese mitten crab (Eriocheir sinensis) and swimming crab (Portunus trituberculatus), which represent freshwater and marine environments, respectively. The analysis revealed a positive correlation between the expression levels of TAG intracellular lipase genes and the energy demand during different molting stages. Overall, the results of this study provide valuable insights into the evolutionary history of TAG intracellular lipase genes, which could enhance our understanding for the role of these genes during key physiological processes of Decapods.

Phylogeny, species delimitation, and biogeographical history of Bredia

Species delimitation in plants is sometimes challenging due to morphological convergence, interspecific gene flow, and historically limited sampling. Bredia Blume as currently defined comprises 27 species and has been resolved as monophyletic in previous phylogenomic studies. However, relationships among several major lineages in the genus remain elusive, and the species boundaries of some problematic taxa have not been tested. In this study, we employed comprehensive taxon sampling and reconstructed the phylogeny of Bredia using single-copy orthologs (SCOs), genomic single nucleotide polymorphisms (SNPs), and whole plastomes. The species tree derived from SCOs provided the highest resolution, strongly supporting all interspecific relationships. We identified instances of morphological convergence and potential hybridization/introgression within groups of interest and discussed species limits based on monophyly, genetic divergence, and morphological diagnosability. Using this robust phylogeny, we inferred divergence times and biogeographical history for Bredia. The genus originated in the Yunnan-Myanmar-Thailand Border region and the Beibu Gulf region during the middle Miocene, initially adapting to karst habitats. Over time, certain lineages shifted to non-karst environments. One such lineage migrated to the southeastern part of the Eastern Asiatic Kingdom in the late Miocene, where it rapidly diversified forming several major lineages. Subsequently, a mainland lineage reached Taiwan via a land bridge between the late Pliocene and the early Pleistocene and diversified in the region, eventually spreading to the Ryukyu Islands in the middle Pleistocene.

Mixed, not stirred: Genomic data confirm the first case of interspecific hybridization in planarian triclads (Platyhelminthes: Tricladida) and raise questions about a possibly novel form of hybrid speciation

Speciation is a complex process where many evolutionary forces interplay. The Mediterranean is acknowledged as one of the most relevant biodiverse areas in the Palearctic region and researchers have long studied the species inhabiting it to pursue the goals of evolutionary biology. Here, we study a complex of freshwater flatworm species of the genus Dugesia from Corsica and Sardinia using restriction site-associated DNA sequencing (specifically, 3RAD) data to unravel their evolutionary history and tackle the processes driving it. We assess the phylogenetic relationships and population structure within the group and evaluate new species boundaries using multispecies coalescent approaches. Furthermore, we offer insights into the environmental niche model of the group and use said model to guide our sampling efforts and collect and present molecular evidence for the first time of Dugesia leporii specimens, endemic from Sardinia last spotted in 1999. Our results indicate that paleoclimatic conditions rather than microplate tectonic dynamics were likely an important driver of diversification for the Corso-Sardinian group. Furthermore, our results warrant the taxonomic re-evaluation of the group as eight primary species candidates are established based on molecular data. Our study also reveals the first case of interspecific natural hybridization reported in Dugesiidae and, to our knowledge, in Tricladida. Finally, we discuss how this hybridization might constitute a new form of hybrid speciation.

Inside out: New root endophytic Penicillium and Talaromyces species isolated from Cattleya orchids (Orchidaceae) in Brazil

The Orchidaceae family comprises a highly diverse group of flowering plants. The genus Cattleya is restricted to the Neotropics, with approximately 80 % of the species present in Brazil occurring in epiphytic, rupicolous, and terrestrial habitats. During surveys that aimed to investigate root fungal endophytes of two native orchids, C. locatellii and C. violacea, a total of 10 endophytic isolates were identified as belonging to Eurotiales. A polyphasic approach was applied for the identification and characterization of the cultured species, combining morphological and molecular data. Phylogenetic analyses were performed using the internal transcribed spacers (ITS) of the rDNA, beta-tubulin (BenA), calmodulin (CaM), and RNA polymerase second-largest subunit (RPB2) sequences. Two new endophytic species were identified and described from roots of C. locatellii, namely Penicillium endophyticum sp. nov. (section Aspergilloides), and Talaromyces cattleyae sp. nov. (section Purpurei). In addition, P. yuyongnianii (section Lanata-Divaricata), T. amestolkiae, and T. atkinsoniae (section Talaromyces) were reported as endophytes from the genus Cattleya. Citation: Condé TO, Ramos DO, Nogueira PTS, Pereira OL (2025). Inside out: New root endophytic Penicillium and Talaromyces species isolated from Cattleya orchids (Orchidaceae) in Brazil. Fungal Systematics and Evolution 15: 179-200. doi: 10.3114/fuse.2025.15.08.

Phylogenetic Diversity and Geographic Distribution of Atlantic Salmon Calicivirus in Major Salmon Farming Regions

Salovirus is a genus within the family Caliciviridae, which contains a single member species, Salovirus nordlandense, also known as Atlantic salmon calicivirus (ASCV). While previous work has shown that ASCV can replicate in fish cell lines and establish systemic infection in vivo, its exact role in disease remains unclear and very little is known about its geographic distribution and evolution among Atlantic salmon. To expand the phylogenetic range of ASCV and better understand its potential role in disease, we screened publicly available transcriptomes for ASCV-like sequences. Notably, we detected ASCV in sequencing projects of Atlantic salmon (Salmo salar) (n = 40) and wild common whitefish (Coregonus lavaretus) (n = 1), across Chile, Scotland and Norway. Our phylogenetic analysis identified two viral species, which we provisionally name Salovirus nordlandense 1 and 2, each containing distinct genotypes. Both viral species were found in all three countries, with no clear geographic pattern, indicating that saloviruses have spread through the Atlantic salmon trade. It was notable that 88% of these transcriptomes were generated for the study of other pathogens, including infectious salmon anaemia virus, piscine myocarditis virus and Piscirickettsia salmonis, suggesting that saloviruses might be frequently associated with co-infections. Overall, this study indicates that viruses, like ASCV, can silently spread through aquacultural practices, potentially contributing to a variety of fish diseases.

Avian metapneumovirus subtype B in a Northern shoveler (Spatula clypeata) wintering in Italy: implications for the domestic-wild bird interface?

Avian metapneumovirus (aMPV) is an important pathogen in poultry, primarily affecting chickens and turkeys, and it causes acute respiratory disease or reproductive disorders. Considering previous molecular or serological evidence of aMPV in different wild bird species, the role of non-domestic hosts in the virus epidemiology has been called into question. A molecular survey was therefore performed on wild aquatic bird species sampled during the Italian Avian Influenza Surveillance plan from 2021-2023 in the Bologna province. A total of 250 oropharyngeal swabs were collected and screened for all circulating aMPV subtypes through multiplex real-time RT-PCR. An aMPV-B strain, named aMPV/B/Italy/Northern_shoveler/80/21, was detected in an adult Northern shoveler (Spatula clypeata) wintering in Italy in 2021, and it was characterized by partial amplification and sequencing of the attachment glycoprotein gene. Phylogenetic analysis showed close relationships between this strain and those circulating in Italian poultry from 2014-2019. Given the high aMPV-B burden on the Italian poultry sector and the similarity of aMPV/B/Italy/Northern_shoveler/80/21 strain to those circulating in chickens and turkeys, potential virus spillover from domestic to wild birds could have occurred at the livestock-wildlife interface. Considering that aMPV-B is well adapted to gallinaceans, this represents one of the rare molecular detections of this subtype in waterfowl species. Expanding aMPV monitoring and conducting further biological studies on wild hosts are essential for a better understanding of their role in maintaining aMPV circulation.RESEARCH HIGHLIGHTSWild birds sampled in Italy tested for aMPV detection and characterization.aMPV-B found for the first time in a wintering Northern shoveler.Close phylogenetic relationship with aMPV-B strains circulating in Italian poultry.

Morphological and molecular characterization of Myxobolus aculeatus n. sp. (Myxozoa: Myxosporea) from the ovary of Macrognathus aculeatus, Bloch, 1786 (Synbranchiformes: Mastacembelidae) in China

Macrognathus aculeatus is a commercially significant cultured fish in China. However, prior to this study, there had been minimal attention directed towards its myxosporean infection. The present study has identified a previously unrecorded species of Myxobolus found in the ovary of M. aculeatus. The mature spores were elliptical in the frontal view, and fusiform in the sutural view, measuring 13.0 ± 0.2 (11.5-14) μm in length, 6.4 ± 0.3 (6.0-7.2) μm in width, and 5.3 ± 0.2 (4.9-5.6) μm in thickness. The two equal polar capsules were pyriform, with a length of 4.5 ± 0.2 (3.5-4.7) μm and a width of 2.4 ± 0.1 (2.3-2.6) μm, and contained 5-6 polar filament coils. A rigorous morphological comparison revealed that the current species exhibited notable distinctions from the previously documented congeners. Histopathological analysis indicated that the parasite resided between oocytes, yet no discernible host inflammatory response was observed. A comparison of the SSU rDNA gene sequences revealed that the present species exhibited the highest degree of similarity to Myxobolus parasites found in the gills of Tachysurus fulvidraco, with a sequence similarity of 86.54 %. Further phylogenetic analysis demonstrated that the current species exhibited a clustering pattern with several myxobolids infecting Tachysurus (Siluriformes), yet displayed a distinct positioning. The Myxobolus species in question represents a new scientific discovery and has been designated as Myxobolus aculeatus n. sp. on the basis of an integrated analysis of morphological, histopathological and molecular data.

Arcyria and allied genera: taxonomic backbone and character evolution

Arcyria, one of the most diverse genera of bright-spored myxomycetes, has recently been identified as polyphyletic within the paraphyletic family Arcyriaceae sensu lato. However, due to the high variability and inconsistency of morphological traits in Trichiales, no taxonomic decision has yet been proposed to rectify this situation. A thorough revision of the genus is necessary. To address this, we present results of the extensive taxonomic and geographic sampling of the genus by incorporating sequences of two marker genes from 192 specimens of Arcyria spp. from 19 countries and six continents into the existing three gene phylogenetic backbone of Trichiales. Our phylogenies decisively confirm the polyphyletic nature of Arcyria, with a considerable part of the genus forming a sister clade to Hemitrichia. Consequently, we erect here the new family Hemitrichiaceae and resurrect the genus Heterotrichia to accommodate the second major branch of former Arcyria species. Additionally, we describe the new genus Spiromyxa with intermediate phylogenetic position and unique combination of morphological traits. Furthermore, we show that most of the Arcyria morphospecies included into this study are either species complexes or para- or polyphyletic taxa. Traits, previously thought to delimit the genus Arcyria, show little consistency with the phylogeny. In particular, the expanding, net-like capillitium, attached to the cup or stalk, appears to have been present in the ancestor of three families of Trichiales, afterwards mostly persisted in two of them and evolved into something else in the third. Such traits as ornamentation of capillitium, cup and spores retain their taxonomic value primarily at the species level. However, the colour of the spore mass in fresh condition partially aligns with our phylogenetic results: most of the yellow "Arcyria" species cluster within Heterotrichia, while red and grey species sort mostly into separate subclades within the clade incorporating the remaining species of the genus Arcyria. Citation: Yatsiuk I, Leontyev D, Schnittler M, Ehlers T, Mikryukov V, Kõljalg U (2025). Arcyria and allied genera: taxonomic backbone and character evolution. Fungal Systematics and Evolution 15: 97-118. doi: 10.3114/fuse.2025.15.04.

Machine learning models accurately predict clades of proteocephalidean tapeworms (Onchoproteocephalidea) based on host and biogeographical data

Proteocephalids are a cosmopolitan and diverse group of tapeworms (Cestoda) that have colonized vertebrate hosts in freshwater and terrestrial environments. Despite the ubiquity of the group, key macroevolutionary processes that have driven the group's evolution have yet to be identified. Here, we review the phylogenetic relationships of proteocephalid tapeworms using publicly available (671) and newly generated (91) nucleotide sequences of the nuclear RNA28S and the mitochondrial MT-CO1 for 537 terminals. The main tree search was carried out under the parsimony optimality criterion, analysing different gene alignments simultaneously. Interestingly, we were not able to recover monophyly of the Proteocephalidae. Additionally, it was difficult to reconcile the tree with host and biogeographical data using traditional character optimization strategies in two dimensions. Therefore, we investigated if host and biogeographical data can be correlated with the parasite clades in a multidimensional space-thus considering multiple layers of information simultaneously. To that end, we used random forests (a class of machine learning models) to test the predictive potential of combined (not individual) host and biogeographical data in the context of the proteocephalid tree. Our resulting models can correctly place 88.85% (on average) of the terminals into eight representative clades. Moreover, we interactively increased the levels of clade perturbation probability and confirmed the expectation that model accuracy negatively correlates with the degree of clade perturbation. Our results show that host and biogeographical data can accurately predict proteocephalid clades in multidimensional space, even though they are difficult to optimize in the parasite tree. These results agree with the assumption that the evolution of proteocephalids is not independent of host and biogeography, and both may provide external support for our tree.

Evolutionary insights into adaptation of hemocyanins from deep-sea hydrothermal vent shrimps

Deep-sea hydrothermal vent shrimps inhabit environments with low oxygen levels and may even be exposed to hypoxic conditions. In response, their respiratory pigment, hemocyanin (Hc) may undergo molecular adaptations to enable them to survive in such extreme ecosystems. Therefore, we sampled four Alvinocarididae species from hydrothermal vents in the northern Central Indian Ridge and two types of Hc genes (α and γ) were observed. Employing the branch model, we detected positive selection for the deep-sea hydrothermal vent lineage, including 11 Decapoda species. Furthermore, using the branch-site model, we identified a putative mutant residue (Leu226, Ser377, and Ile390) close to the active site of Hc. Moreover, our results suggested potential molecular docking between two α-type Hc proteins. Thus, this study provides valuable and novel perspectives on the functional significance of the Hc gene in deep-sea hydrothermal vent shrimps, laying the foundation for future investigations in this intriguing area of research.

Morphological and molecular characterization of a new microsporidium, Neoflabelliforma leuchtenbergianum n. sp. from the adipose tissue of Diaphanosoma leuchtenbergianum (Crustacea: Sididae) in China

This study describes a new microsporidian species from the adipose tissue of Diaphanosoma leuchtenbergianum collected from a eutrophic water body of Lianyungang city, Jiangsu province, China. Infected cladocerans exhibited opacity due to the accumulation of numerous spores in the adipose tissue. The earliest stages observed were uninucleate meronts which were in direct contact with the host cell cytoplasm. Multinucleate sporogonial plasmodia underwent plasmotomy to form uninucleate sporoblasts. Mature spores were ovoid, monokaryotic, and measured 4.80 ± 0.37 (4.09-5.23) µm in length and 2.64 ± 0.15 (2.34-3.01) µm in width. The polaroplast was bipartite with the tightly packed anterior lamellae and posterior tubules. The isofilar polar filament coiled in 9-10 turns and arranged in 2-3 rows. The exospore was covered with tubular projections and consisted of four layers. Phylogenetic analysis based on the SSU rDNA sequence indicated that the present species clustered with two Neoflabelliforma species (N. dubium from freshwater oligochaetes and N. aurantiae from freshwater daphnia) and an unidentified microsporidium from soil with high support values to form a solitary branch in microsporidia. Based on the morphological characteristics, ultrastructural features, and SSU rDNA-inferred phylogeny, a new species was named as Neoflabelliforma leuchtenbergianum n. sp.

Domestic cat hepadnavirus is detected infrequently in feline blood and liver samples submitted for diagnostic testing in Texas, USA

Domestic cat hepadnavirus (DCH), a novel hepatitis B-like virus, has been detected in cats in several regions but data are fragmented. Investigation of DCH is driven by the societal role of cats as human companions, disease risk to sympatric endangered felids, as well as HBV medicine. This study investigated the molecular epidemiology and sequence diversity of DCH in diagnostic blood or non-paired liver samples submitted in Texas. Patient age, sex, breed, neuter status, and retrovirus serology results were recorded for risk factor analyses. Using qPCR, DCH DNA was amplified from 3/400 blood samples (0.8 % (95 % CI: 0.3-2.2 %) with virus loads of 4.06 × 106, 2.33 × 108, and 27.1 × 109 copies/μL of blood. Feline immunodeficiency virus and feline leukemia virus seroprevalence was 4.3 % (95 % CI: 2.5-7.1 %) and 7.5 % (95 % CI: 5.0-10.8 %), respectively. A low DCH detection rate precluded risk factor analysis. Among liver samples, DCH DNA was amplified by PCR from 4/303 (1.3 % (95 % CI: 0.4-3.4 %), one of which also tested positive by in situ hybridization. Phylogenetic analyses of 3 DCH genomes obtained in this study showed high homology to viruses in Genotype A with no evidence of geographic clustering. This study, only the second in the USA, contributes to data on the worldwide prevalence of DCH viremia and, in the context of accumulating data on this potential feline pathogen, supports that the prevalence of DCH viremia, may vary geographically, as described for hepatitis-B virus and woodchuck hepatitis virus.

The mytilin gene cluster: Shedding light on the enigmatic origin of mussel dispensable genes

Mussels exhibit a sophisticated innate immune response characterized by many highly variable molecules responsible for recognizing and killing potential pathogenic microorganisms. The complexity of this molecular arsenal is marked by the occurrence of gene presence-absence (PAV), a phenomenon that targets numerous expanded lineage-specific gene families. This phenomenon enhances inter-individual sequence variability, further enriching the diversity of the repertoire of molecules involved in the immune response. Until now, the origin of mussel dispensable genes, which, unlike core genes, are not shared by all individuals, has remained elusive. In this study, by analyzing the resequenced genomes of more than 160 individuals in four distinct species of the Mytilus complex, we characterize the repertoire of mytilin genes encoding hemocyte-specific antimicrobial peptides (AMPs). We define a canonical gene architecture comprising four protein-coding genes and two pseudogenes in most haplotypes. However, the organization of the locus displays a marked intra-specific diversity due to the presence of variable alleles, the frequent pseudogenization of mytilin G1 and structural variants associated with additional dispensable mytilin genes, which often retain features that support functional preservation. Molecular phylogeny supports an ancient origin for dispensable mytilin genes, predating the radiation of modern Mytilus species. This suggests that most widespread extant haplotypes derive from a larger and more complex ancestral mytilin gene cluster and that dispensable mytilin genes are vestigial AMPs that have been retained only in a few populations where their presence may have contributed to fitness advantages and local adaptation.

Nectar metabolomes contribute to pollination syndromes

'Pollination syndromes', where convergent floral signals reflect selection from a functional pollinator group, are often characterized by physical features, yet floral rewards such as nectar may also reflect selection from pollinators. We asked whether nectar chemistry shows evidence of convergence across functional pollinator groups, i.e. a 'chemical pollination syndrome'. We used untargeted metabolomics to compare nectar and leaf chemical profiles across 19 bee- and bird-syndrome species, focusing on Salvia spp. (Lamiaceae), selected to maximize switching events between pollination syndromes. We found that independently derived bird-syndrome nectar showed convergence on nectar traits distinct from bee-syndrome nectar, primarily driven by the composition and concentration of alkaloid profiles. We did not find evidence for 'passive leaking' of nectar compounds from leaves since metabolite abundances were uncorrelated across tissues and many nectar metabolites were not present in leaves. Nectar and leaf metabolomes were strongly decoupled from phylogenetic relationships within Salvia. These results suggest that functional pollinator groups may drive the evolution of floral reward chemistry, consistent with our 'chemical pollination syndrome' hypothesis and indicative of selection by pollinators, but we also consider alternative explanations. In addition, our results support the notion that nectar chemistry can be decoupled from that of other tissues.

Repeatome diversity in sea anemone genomics (Cnidaria: Actiniaria) based on the Actiniaria-REPlib library

BACKGROUND

Genomic repetitive DNA sequences (Repeatomes, REPs) are widespread in eukaryotes, influencing biological form and function. In Cnidaria, an early-diverging animal lineage, these sequences remain largely uncharacterized. This study investigates sea anemone REPs (Cnidaria: Actiniaria) in a phylogenetic context. We sequenced and assembled de novo the genome of Actinostella flosculifera and analyzed a total of 38 nuclear genomes to create the first ActiniariaREP library (Actiniaria-REPlib). We compared Actiniaria-REPlib with Repbase and RepeatModeler2 libraries, and used dnaPipeTE to annotate REPs from genomic short-read datasets of 36 species for divergence landscapes.

RESULTS

Our study assembled and annotated the mitochondrial genomes, including 27 newly assembled ones. We re-annotated ~92% of the unknown sequences from the initial nuclear genome library, finding that 6.4-30.6% were DNA transposons, 2.1-11.6% retrotransposons, 1-28.4% tandem repeat sequences, and 1.2-7% unclassifiable sequences. Actiniaria-REPlib recovered 9.4x more REP sequences from actiniarian genomes than Dfam and 10.4x more than Repbase. It yielded 79,903 annotated TE consensus sequences (74,643 known, 5,260 unknown), compared to Dfam with 7,697 (3,742 known, 3,944 unknown) and Repbae (763 known).

CONCLUSIONS

Our study significantly enhances the characterization of sea anemone repetitive DNA, assembling mitochondrial genomes, re-annotating nuclear sequences, and identifying diverse repeat elements. Actiniaria-REPlib vastly outperforms existing databases, recovering significantly more REP sequences and providing a comprehensive resource for future genomic and evolutionary studies in Actiniaria.

Taxonomy and molecular phylogeny of a new species of black fly (Diptera: Simuliidae) in the Simulium striatum species-group from central Thailand

Generally, the DNA barcode relying on a short fragment of the cytochrome c oxidase I (COI) gene is a powerful tool for facilitating species discovery and taxonomic resolution in Diptera, including black flies. However, the COI barcode lacks sufficient resolution to identify several species or infer phylogenetic relationships of black flies in the Simulium striatum species-group, whereas the fast-evolving nuclear big zinc finger (BZF) gene has been suggested as a key marker for identifying the species. In this study, a new species of black fly in the S. striatum species-group from Kamphaeng Phet province, central Thailand, was discovered and characterized through an integrated method combining morphological analysis and molecular data based on the BZF gene. The new species, Simulium (Simulium) concitatum sp. nov., was morphologically described for all life stages, excluding the egg. It shares many morphological similarities with other species of the S. striatum species-group, particularly S. thilorsuense Takaoka, Srisuka & Saeung, 2022 described from Tak province, western Thailand. Sequence analysis and phylogeny inferred from the BZF gene further confirmed that S. concitatum sp. nov. is a distinct species of the S. striatum species-group and revealed its close genetic relationship to S. wangkwaiense Takaoka, Srisuka & Saeung, 2020. The morphological differences between the new species and all known species of the S. striatum species-group documented in Thailand and other countries are provided to assist in species identification. Furthermore, this study underscores the BZF gene as an effective genetic marker to differentiate the species.

Insights into infraspecific differentiation of the medicinally important species Bupleurum Chinense revealed by morphological and molecular evidence

BACKGROUND

Radix Bupleuri, derived from the dried roots of Bupleurum chinense DC., is a well-documented phytomedicine in global pharmacopoeias and a common constituent in herbal formulations. While previous studies have hinted at regional variations in the chemical composition of B. chinense, a comprehensive understanding of its morphological, genetic, and chemical diversity across China remains incomplete.

OBJECTIVE

This study aims to investigate the infraspecific variation of B. chinense by analyzing its morphological, genetic, and chemical phenotypes.

METHODS

Wild B. chinense specimens were collected from 31 locations spanning nine Chinese provinces/municipalities, representing a wide range of its natural distribution. A multi-faceted approach combining 21 morphological traits, plastid genome sequencing, and chemical analysis was employed to explore infraspecific variation and clustering patterns.

RESULTS

Distinct infraspecific variation was revealed through integrated morphological and molecular data. Morphological clustering analysis identified two geographically associated clusters, roughly corresponding to coastal and inland regions. Although plastid genome sequencing of 40 specimens showed high sequence identity, population structure analysis detected variable hotspots. Both maximum likelihood (ML) tree and population structure results consistently identified three distinct clades, which mirrored the patterns observed in morphological clustering. Quantitative analysis of saikosaponins content in 10 representative specimens across the three clades demonstrated significant chemotype variation. Notably, samples from Anhui Province exhibited the highest saikosaponins content, while those from Shanxi Province showed the lowest levels. This chemotype variation, coupled with observed genetic diversity, suggests that B. chinense germplasm from Clade I (particularly from Anhui Province) represents a promising wild resource for further development.

Genomic insights into novel extremotolerant bacteria isolated from the NASA Phoenix mission spacecraft assembly cleanrooms

BACKGROUND

Human-designed oligotrophic environments, such as cleanrooms, harbor unique microbial communities shaped by selective pressures like temperature, humidity, nutrient availability, cleaning reagents, and radiation. Maintaining the biological cleanliness of NASA's mission-associated cleanrooms, where spacecraft are assembled and tested, is critical for planetary protection. Even with stringent controls such as regulated airflow, temperature management, and rigorous cleaning, resilient microorganisms can persist in these environments, posing potential risks for space missions.

RESULTS

During the Phoenix spacecraft mission, genomes of 215 bacterial isolates were sequenced and based on overall genome-related indices, 53 strains belonging to 26 novel species were recognized. Metagenome mapping indicated less than 0.1% of the reads associated with novel species, suggesting their rarity. Genes responsible for biofilm formation, such as BolA (COG0271) and CvpA (COG1286), were predominantly found in proteobacterial members but were absent in other non-spore-forming and spore-forming species. YqgA (COG1811) was detected in most spore-forming members but was absent in Paenibacillus and non-spore-forming species. Cell fate regulators, COG1774 (YaaT), COG3679 (YlbF, YheA/YmcA), and COG4550 (YmcA, YheA/YmcA), controlling sporulation, competence, and biofilm development processes, were observed in all spore-formers but were missing in non-spore-forming species. COG analyses further revealed resistance-conferring proteins in all spore-formers (n = 13 species) and eight actinobacterial species, responsible for enhanced membrane transport and signaling under radiation (COG3253), transcription regulation under radiation stress (COG1108), and DNA repair and stress responses (COG2318). Additional functional analysis revealed that Agrococcus phoenicis, Microbacterium canaveralium, and Microbacterium jpeli contained biosynthetic gene clusters (BGCs) for ε-poly-L-lysine, beneficial in food preservation and biomedical applications. Two novel Sphingomonas species exhibited for zeaxanthin, an antioxidant beneficial for eye health. Paenibacillus canaveralius harbored genes for bacillibactin, crucial for iron acquisition. Georgenia phoenicis had BGCs for alkylresorcinols, compounds with antimicrobial and anticancer properties used in food preservation and pharmaceuticals.

CONCLUSION

Despite stringent decontamination and controlled environmental conditions, cleanrooms harbor unique bacterial species that form biofilms, resist various stressors, and produce valuable biotechnological compounds. The reduced microbial competition in these environments enhances the discovery of novel microbial diversity, contributing to the mitigation of microbial contamination and fostering biotechnological innovation. Video Abstract.

Genetic insights for enhancing conservation strategies in captive and wild Asian elephants through improved non-invasive DNA-based individual identification

Asian elephant is a key umbrella species that plays a crucial role in maintaining biodiversity and ecological balance. As an iconic symbol of Thailand, it also significantly contributes to the nation's tourism industry. However, human activities pose serious threats to their long-term survival and population health. To tackle these challenges and develop effective conservation strategies, extensive genetic reference data were collected to enhance both captive and wild elephant conservation, improve non-invasive DNA-based individual identification, and assess genetic diversity using 18 microsatellite markers. High genetic diversity was observed across all populations; however, high levels of inbreeding were evident in NEI, EKS, BCEP, and wild elephant populations, except for the MEP population, which recorded low inbreeding levels. Significant variation in the gene pool estimates was observed across different populations, with three maternal haplogroups (α, β1, and a tentative β3) identified. A reduced panel of six microsatellite markers proved highly efficient for individual identification. Additionally, non-invasive DNA samples were tested using 18 microsatellite loci for individual identification. Using only 7 out of the 18 microsatellite loci tested, individuals were successfully identified, demonstrating enough discriminatory power to distinguish between individuals. Among these, four loci (LaT08, LaT13, FH19, and FH67) were both effective and efficient for reliable individual identification in fecal samples. These findings offer valuable insights for optimizing conservation efforts, including the design of tailored strategies to protect Asian elephants in Thailand and ensure the long-term viability of their populations.

A chromosome-level genome assembly of the aphid Semiaphis heraclei (Takahashi)

The S. heraclei (Takahashi) (Hemiptera: Aphididae) is a destructive pest of cultivated insectary plant Cnidium monnieri (L.) Cuss. However, to date, no S. heraclei-related genomic information has been reported. Here, we present the first chromosomal-scale genome assembly of S. heraclei approximately 440.3 Mb with contig N50 of 81.7 Mb. Using PacBio long-read sequencing, Illumina sequencing, and Hi-C scaffolding techniques, 94.24% of the assembled sequences were successfully anchored to the four pseudochromosomes. BUSCO assessment showed a completeness score of 95.4%. The S. heraclei genome consisted of 32.02% repetitive elements and 13,983 predicted protein-coding genes. Phylogenetic analysis showed that S. heraclei was closely related to Diuraphis noxia. This high-quality genome assembly of S. heraclei will serve as a genomic resource for aphid evolution and pave the way for deciphering the tri-trophic interaction mechanisms between plants, herbivores, and natural enemies.

Comparative analysis of chloroplast genomes and phylogenetic relationships of different pitaya cultivars

BACKGROUND

Pitaya is an important tropical fruit highly favoured by consumers owing to its good and juicy characteristics. It contains a large amount of betacyanin, which is a natural food-colouring agent, in the peel and pulp. However, few studies have focused on the pitaya chloroplast (cp) genomes.

RESULTS

To explore the genetic differences and phylogenetic relationships among the cp genomes of the six pitaya cultivars, we assembled, annotated, and performed a comparative genomic analysis. The cp genomes of the six cultivars exhibited a typical circular structure, ranging in length from 133,146 to 133,617 bp, with a GC content of 36.4%. All individual cp genomes were annotated with 123 genes, including 80 protein-coding genes, 38 tRNA genes, four rRNA genes, and one pseudogene (ycf68). Six mutated hotspot regions (trnF-GAA-rbcL, trnM-CAU-accD, rpl20-psbB, accD, rpl22, ycf1) were detected, which could be considered potential molecular markers for population genetics and molecular phylogeny studies. Phylogenetic analysis showed that pitaya cultivars clustered into a single branch in the phylogenetic tree of the Cactaceae family. Furthermore, the observed phylogenetic patterns suggest a complex genetic basis for colour variation among pitaya cultivars.

CONCLUSIONS

The study findings expand our understanding of the cp genome of pitaya and the phylogenetic relationships among different cultivars. The genomic data obtained provide important information for the breeding and genetic improvement of pitaya.

Phylogenomics establishes an Early Miocene reconstruction of reef vertebrate diversity

Oceans blanket more than two-thirds of Earth's surface, yet marine biodiversity is disproportionately concentrated in coral reefs. Investigating the origins of this exceptional diversity is crucial for predicting how reefs will respond to anthropogenic disturbances. Here, we use a genome-scale dataset to reconstruct the evolutionary history of the wrasses and parrotfishes (Labridae), which rank among the most species-rich and ecologically diverse lineages of reef fishes. We show that major labrid clades experienced pulses of evolutionary innovation and accelerated diversification during the Miocene approximately 20 to 15 million years ago that the origin of no single phenotypic trait can explain. These results draw parallels to the evolutionary histories of many clades after mass extinctions and corroborate recent fossil evidence for an Early Miocene extinction event in oceanic vertebrates and changes in coral reef faunal composition. Our data provide genomic evidence for a major Early Miocene reassembly of reef faunas.

Genome of the enigmatic watering-pot shell and morphological adaptations for anchoring in sediment

BACKGROUND

In this study, we present the first chromosome-scale genome of Verpa penis (Linnaeus, 1758), and the first for the bivalve clade Anomalodesmata. The present study has two separate foci. Primarily, we provide the genetic resource to bridge further studies from genome to phenome and propose hypotheses to guide future empirical investigations. Secondarily, based on morphology, we outline a conceptual exploration to address their adaptation. Watering-pot shells have been called "the weirdest bivalves" for their fused tubular shell resembling the spout of a watering can. This adventitious tube arose twice convergently in clavagelloidean bivalves. However, previous literature has never provided a convincing adaptive pathway.

RESULTS

The genome assembly of V. penis was about 507 Mb, with contig N50 of 5.33 Mb, and has 96.5% of sequences anchored onto 19 pseudochromosomes. Phylogenomic analyses of this new genome in context of other bivalves confirms the placement for Anomalodesmata as sister to the clade Imparidentia. Contrary to expectations from its highly modified body plan, there is no evidence of chromosome reduction compared to the ancestral karyotype of heterodont bivalves (1 N = 19). Drawing on established principles from engineering as well as morphology, the thought experiment about the adventitious tube seeks to extend current understanding by exploring parallels with other built structures. A new hypothesis explains one possible interpretation of the adaptive significance of this body form: it is potentially structurally optimised for vertical stability in relatively soft sediments, with parallels to the engineering principles of a suction anchor.

CONCLUSIONS

While the conclusions presented here on morphological interpretations are theoretical, this serves as a foundation for further empirical validation and refinement. Our study offers new insights to a long-standing mystery in molluscan body forms and provides genomic resources that are relevant to understanding molluscan evolution, biomineralisation, and biomimetic design.

The ecological niche and population history shape mosquito population genetics on a group of three Caribbean islands

BACKGROUND

While studies on mosquito population genetics have primarily focused on medically relevant species, fewer have examined the genetic population structure of mosquitoes from a diverse range of species within a single geographical area. The limited comparison between native and non-native species, as well as ecologically divergent species from the same region, hampers our ability to generalise previously described patterns in mosquito population genetics. This study uses the mosquito fauna of the Caribbean islands of Aruba, Curaçao and Bonaire as a case study to explore population genetic variation among both native and non-native mosquito species, as well as among native species occupying different ecological niches. We examine how genetic patterns relate to their population history and species-specific ecologies.

METHODS

Mitochondrial COII sequences were obtained from 258 mosquito specimens belonging to six species, occurring on all three islands. Sequences were used in haplotype network analysis to assess the genetic variation between mosquito populations of each of the six ecologically diverse species, which vary in both their population history and ecological niche.

RESULTS

Both the genetic diversity and population genetic structure were found to differ strongly between sets of species, leading to a subdivision into three species groups: (1) non-native species with low genetic diversity across all three investigated islands, (2) locally native species with high genetic diversity and closely related haplotypes occurring on different islands and (3) locally native species with high genetic diversity and locally restricted haplotypes.

CONCLUSIONS

Our results show that the population genetics of non-native and native species strongly differ, likely as a result of population history. Furthermore, the results suggest that mosquito species sharing the same area may display distinct population genetic structure, likely related to differences in their ecology and dispersal capacity. We suggest that addressing a broader range of species within a single area will benefit future research on mosquito population genetics to place observed patterns into a broader historical, ecological and evolutionary context.

A BRASSINOSTEROID INSENSISTIVE 1 receptor kinase ortholog is required for sex determination in Ceratopteris richardii

Most ferns, unlike all seed plants, are homosporous and produce sexually undifferentiated spores. Sex ratio in many homosporous species is environmentally established by the secretion of antheridiogen from female/hermaphrodite gametophytes. Nearby undetermined gametophytes perceive antheridiogen, which induces male development. In the fern Ceratopteris richardii (Ceratopteris), hermaphroditic (her) mutants develop as hermaphrodites even in the presence of antheridiogen. Modern sequencing and genomic tools make the molecular identification of mutants in the 11-Gbp genome of this fern possible. We mapped 2 linked mutants, her7-14 and her7-19, to the same 16-Mbp interval on chromosome 29 of the Ceratopteris genome. An ortholog of the receptor kinase gene BRASSINOSTEROID INSENSITIVE 1 (BRI1) within this interval encoded a deletion mutation in her7-14 and a missense mutation in her7-19. Three other linked her mutants encoded missense mutations in the same gene, which we name HER7. Consistent with a function as a receptor kinase, HER7-GFP fusion protein localized to the plasma membrane and cytoplasm. Analysis of gene expression showed that brassinosteroid biosynthesis was upregulated in hermaphrodites compared with male gametophytes. Our work demonstrates that HER7 is required for sex determination in Ceratopteris and opens avenues for studying the evolution of antheridiogen systems.

Reconstruction of the X and Y haplotypes in the genetically improved Abbassa nile tilapia genome assembly

The success of the Nile tilapia (Oreochromis niloticus) as an aquaculture species is partly the result of continuous selective breeding leading to high performing strains. These elite strains have been derived from breeding populations of diverse origins and crosses with other Oreochromis species. Owing to the complex and unique evolutionary histories of each strain, existing reference genomes of wild populations are unsuitable to implement genomic selection for beneficial traits such as growth or environmental resilience in aquaculture programmes. Here we generated a high-quality genome assembly and annotation of the WorldFish Genetically Improved Abbassa Nile tilapia (GIANT) elite strain using a combination of PacBio HiFi, and Omni-C Illumina sequencing. As a male Abbassa Nile tilapia was used for the generation of the genome assembly, we reconstructed both X and Y haplotypes, identifying both amhY and amhΔy on LG23 indicating that Abbassa likely shares the same sex determination system as GIFT, and thereby differs from the existing reference genome, whose sex determination loci are located on LG1.

Scale dependent niche conservatism in fish communities of the largest freshwater lake in China

Two major theoretical concepts of niche evolution lead to conflicting predictions in ecological studies: the competitive exclusion principle (CEP) predicts that closely-related species should be sufficiently divergent to coexist, whereas niche conservatism (NC) suggests that closely-related species should be more ecologically similar. Here, we test this conundrum by employing stable isotope ratios (δ13C, δ15N) to estimate trophic niches and test niche evolution in fish communities of Poyang Lake, central China. At a broad phylogenetic scale involving 57 species, we examined the relationships between trophic niche differences along genetic distances and tested phylogenetic signals. We found that trophic differences were positively associated with genetic distances when genetic distances were less than 0.24, showing strong phylogenetic signal, but not when larger than 0.24. We then focused on seven Cultrinae species coexisting at a local scale and compared trophic niche differences within and between sister species, closely-related species, and distantly-related species. We found that trophic differences between distantly-related species were significantly larger than those between closely-related species at a broad spatial scale, supporting NC. However, trophic differences between sister species were larger than those between closely-related species at a small local scale (individual sampling sites), suggesting the importance of CEP not NC. Hence, our findings suggest that niche evolution operates in a scale-dependent manner: in a phylogenetic scale (time scale), NC predictions were met well below a certain range, not above that range; at a spatial scale, CEP predictions were met for coexisting sister species, however the other species followed the NC predictions.

Draft genome of the endemic alpine ground beetle Carabus (Platycarabus) depressus (Coleoptera: Carabidae) from long-read sequencing of a frozen archived specimen

The rapid advancement of genomic technologies has enabled the production of highly contiguous reference genomes for nonmodel organisms. However, these methods often require exceptionally fresh material containing unfragmented high-molecular-weight nucleic acids. Researchers who preserve field-collected specimens in ethanol at ambient temperatures, prior to transferring them to long-term frozen archives, face challenges in applying advanced genomic approaches due to DNA and RNA fragmentation under suboptimal preservation conditions. To explore the potential of such preserved specimens as sources of reference genomes, we utilized Nanopore MinION technology to generate genomic data from a frozen archived specimen of the endemic alpine ground beetle Carabus (Platycarabus) depressus. Using a rapid in-house protocol for high-molecular-weight DNA extraction, followed by sequencing on a single flow cell, we produced 8.75 million raw reads with an N50 of 2.8 kb. The resulting assembly achieved remarkable completeness, recovering up to 98% of Benchmarking Universal Single-Copy Orthologs genes, despite a moderate N50 of 945 kb. This genome is only the second available for the taxonomically diverse genus Carabus, demonstrating the feasibility of using short-to-long-read sequencing on frozen archived specimens commonly housed in natural history collections. These findings open new avenues for advancing nonmodel organism genomics and its downstream applications.

Complete mitochondrial genome of the Korean endemic earthworm Amynthas bubonis (Clitellata: Megascolecidae): mitogenome characterization and phylogenetic positioning

Amynthas bubonis Hong & James, 2001 is an earthworm species endemic to Korea. This species is typically found in mountainous forests at low altitudes. Specimens were collected from Mt. Deogyu in South Korea, and the complete A. bubonis mitogenome was sequenced, assembled, and annotated. The A. bubonic mitogenome is a 15,095 bp circular DNA molecule with 64.85% A + T content. It contains 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and 1 non-coding region (control region). Phylogenetic analysis revealed that A. bubonis clustered with A. jiriensis, A. yunoshimensis, and M. hilgendorfi in the well-supported Megascolecidae family.

Phylogenomic insights into West Nile virus lineage 2 circulating in Croatia

West Nile Virus (WNV) has been circulating in Croatia for over a decade, as well as in numerous countries across the Mediterranean Basin and Central Europe. Using high-throughput Illumina sequencing, we successfully sequenced the WNV genome from serum and urine samples of three Croatian patients infected in 2016, 2023 and 2024. We employed an amplicon-based approach, with optimized primers designed using previously published WNV lineage 2 sequences. This work represents the first report of complete WNV genome sequences from Croatia. Sequenced genomes from 2023 to 2024 exhibited 99% sequence identity with Hungarian genomic sequences, while the genome from 2016 showed 99% identity with genomic sequences from Austria and Czech Republic. Phylogenetic analysis supported these findings, placing the genomes from 2023 to 2024 in subclade D.2.1 and the genome from 2016 in subclade E.2, thereby providing evidence for potential viral dissemination routes. The approach employed in this study performed well in whole-genome assembly of WNV and in identifying nucleotide changes specific for WNV subtypes circulating in Croatia. This study offers deeper genomic insights into the phylogenetic position of WNV in Croatia, bridging a significant knowledge gap and contributing to future studies on WNV transmission dynamics.

Evolution-guided protein design of IscB for persistent epigenome editing in vivo

Naturally existing enzymes have been adapted for a variety of molecular technologies, with enhancements or modifications to the enzymes introduced to improve the desired function; however, it is difficult to engineer variants with enhanced activity while maintaining specificity. Here we engineer the compact Obligate Mobile Element Guided Activity (OMEGA) RNA-guided endonuclease IscB and its guiding RNA (ωRNA) by combining ortholog screening, structure-guided protein domain design and RNA engineering, and deep learning-based structure prediction to generate an improved variant, NovaIscB. We show that the compact NovaIscB achieves up to 40% indel activity (~100-fold improvement over wild-type OgeuIscB) on the human genome with improved specificity relative to existing IscBs. We further show that NovaIscB can be fused with a methyltransferase to create a programmable transcriptional repressor, OMEGAoff, that is compact enough to be packaged in a single adeno-associated virus vector for persistent in vivo gene repression. This study highlights the power of combining natural diversity with protein engineering to design enhanced enzymes for molecular biology applications.

Comparative and evolutionary analysis of chloroplast genomes from five rare Styrax species

BACKGROUND

Styrax, a vital raw material for shipbuilding, construction, perfumes, and drugs, represents the largest and most diverse genus in the Styracaceae. However, there is a relative scarcity of research on Styrax, particularly in evolution and genetics. Therefore, this study conducted comparative and evolutionary analyses of the chloroplast genomes of five rare Styrax species (S. argentifolius, S. buchananii, S. chrysocarpus, S. finlaysonianus, and S. rhytidocarpus).

RESULTS

The results indicated that, despite high levels of conservation in chloroplast genome structure among these species, specific mutation hotspot regions exist, particularly involving the expansion and contraction of the IR region. Additionally, evidence of positive selection was detected in eight genes (atpB, ccsA, ndhD, petA, rbcL, rpoC1, ycf1, and ycf2), which may be associated with adaptive evolution in response to environmental changes. Phylogenetic analysis revealed conflicts between trees constructed based on coding sequences and complete chloroplast genomes for several species, which were similar to previous phylogenetic studies.

CONCLUSION

This study underscores the importance of increasing sample sizes to enhance the accuracy of phylogenetic analyses and provides a new perspective on understanding the adaptive evolution of Styrax species. These findings are not only important for the conservation and sustainable use of Styrax, but also provide valuable insights for research in plant evolution and ecology within the genus.

An atlas of bacterial serine-threonine kinases reveals functional diversity and key distinctions from eukaryotic kinases

Bacterial serine-threonine kinases (STKs) regulate diverse cellular processes associated with cell growth, virulence, and pathogenicity and are evolutionarily related to the druggable eukaryotic STKs. A deeper understanding of how bacterial STKs differ from their eukaryotic counterparts and how they have evolved to regulate diverse bacterial signaling functions is crucial for advancing the discovery and development of new antibiotic therapies. Here, we classified more than 300,000 bacterial STK sequences from the NCBI RefSeq nonredundant and UniProt protein databases into 35 canonical and seven pseudokinase families on the basis of the patterns of evolutionary constraints in the conserved catalytic domain and flanking regulatory domains. Through statistical comparisons, we identified features distinguishing bacterial STKs from eukaryotic STKs, including an arginine residue in a regulatory helix (C helix) that dynamically couples the ATP- and substrate-binding lobes of the kinase domain. Biochemical and peptide library screens demonstrated that evolutionarily constrained residues contributed to substrate specificity and kinase activation in the Mycobacterium tuberculosis kinase PknB. Together, these findings open previously unidentified avenues for investigating bacterial STK functions in cellular signaling and for developing selective bacterial STK inhibitors.

Mitogenomic characterization and phylogenetic positioning of Acropora lutkeni (Scleractinia, Acroporidae)

The complete mitochondrial genome of Acropora lutkeni (Crossland, 1952) (18,480 bp) was assembled and annotated using high-throughput sequencing, revealing 13 PCGs, 2 tRNAs, and 2 rRNAs with AT bias and strand-specific distribution. This study enriches genomic resources and supports research on genetic variation, taxonomy, and evolution within Acropora.

Genome-wide diversity and MHC characterisation in a critically endangered freshwater turtle susceptible to disease

Small, isolated populations are often vulnerable to increased inbreeding and genetic drift, both of which elevate the risk of extinction. The Bellinger River turtle (Myuchelys georgesi) is a critically endangered species endemic to a single river catchment in New South Wales, Australia. The only extant wild population, along with the breeding program, face significant threats from viral outbreaks, most notably a nidovirus outbreak in 2015 that led to a 90% population decline. To enhance our understanding of genomic characteristics in the species, including genome-wide and functional gene diversity, we re-sequenced, assembled, and analysed 31 re-sequenced genomes for pure M. georgesi (N = 31). We manually annotated the major histocompatibility complex (MHC), identifying five MHC class I and ten MHC class II genes and investigated genetic diversity across both classes in M. georgesi. Our results showed that genome-wide diversity is critically low in pure M. georgesi, contexualised through comparison with opportunistically sampled backcross animals-offspring of F1 hybrids (M. georgesi × Emydura macquarii) backcrossed to pure M. georgesi (N = 4). However, the variation observed within the core MHC region of pure M. georgesi, extending across scaffold 10, exceeded that of all other macrochromosomes. Additionally, no significant short-term changes in either genome-wide or immunogenetic diversity were detected following the 2015 nidovirus outbreak (before; N = 19, after; N = 12). Demographic history reconstructions indicated a sustained, long-term decline in effective population size since the last interglacial period, accompanied by more recent steep declines. These patterns suggested that prolonged isolation and reduced population size have significantly influenced the dynamics of genome-wide diversity. It is likely that contemporary stressors, including the recent nidovirus outbreak, are acting on an already genetically depleted population. This study offers new insights into genome-wide and immune gene diversity, including immune gene annotation data with broader implications for testudines. These findings provide crucial information to support future management strategies for the species.