Antimicrobial resistance poses a major threat to human and wildlife health. Although migratory waterbirds can carry antibiotic resistance genes (ARGs), cross-species ARG sharing and horizontal gene transfer (HGT) risks remain poorly understood under mixed-species overwintering conditions. We combined metagenomic sequencing with analyses of host phylogenetic relationships and species divergence times to characterize the gut resistomes of four mixed-species overwintering waterbirds. We identified 844 ARG subtypes across 24 resistance classes. β-lactam resistance genes exhibited high subtype richness, whereas multidrug resistance genes dominated total ARG abundance. ARG composition differed among host species but did not fully correspond to host phylogeny or divergence history. Among the 225 ARG subtypes shared across all four species, 39 core subtypes accounted for 50.4–61.7% of total ARG abundance in each species. We further identified 39 high-risk ARG subtypes, comprising 28 Rank I and 11 Rank II ARGs across 10 antibiotic classes. Across all samples, we detected 127 mobile genetic element (MGE) subtypes, of which insertion sequences and transposase-associated elements predominated, together accounting for 86.8–97.7% of total MGE abundance in each host species. Colocalization of a subset of ARGs (e.g., sul1 and catB3) with MGE-associated markers (e.g., intI1 and tnpA) suggested the potential for MGE-mediated horizontal transfer of these ARGs. Potential pathogens, including Escherichia coli and Salmonella enterica, were also identified as hosts of potentially mobile ARGs. Overall, this study reveals extensive cross-species ARG sharing and potential HGT risk in mixed-species overwintering waterbirds, highlighting their potential role in mediating ARG dissemination across host species.

The family Scytodidae is known for its unique spitting predatory mechanism, but its fossil record is extremely scarce, with reliable Mesozoic records previously lacking. Based on two male specimens preserved in Kachin amber, we report the first unequivocal Cretaceous record of this family — †Stedotuber gen. nov., with two new species, †S. longitibialis sp. nov. and †S. brevitibialis sp. nov. Maximum parsimony analysis of morphological characters recovers the new genus within the subfamily Scyloxinae, forming a sister-group relationship with the extant genus Stedocys. Tip-dating analyses estimate the crown age of Scytodidae at the Late Jurassic (~150.32 Ma), the crown age of Scyloxinae in the Early Cretaceous (~136.71 Ma), and the split between †Stedotuber gen. nov. and Stedocys in the late Early Cretaceous (~123.68 Ma), all substantially older than previous estimates for comparable nodes based on Cenozoic fossils or molecular clocks alone. Combined with paleogeographic models, our results favour a scenario in which early scyloxine lineages became isolated on the northward-drifting Burma Terrane, consistent with its proposed role as a “biotic ferry” for Gondwanan-derived lineages.

Unlike most plants with localized monocentromeres, some Magnoliales species possess holocentric chromosomes. To investigate the genomic basis of this difference, we generated chromosome-level genomes for the holocentric species Myristica fragrans and the monocentric species Cananga odorata and performed comparative multi-omics analyses. We found that C. odorata shows localized heterochromatin enrichment and clustered transposable elements, whereas M. fragrans exhibits a more dispersed chromatin organization. Despite these differences, centromere-associated regions in both species are positively associated with mCG/mCHG and heterochromatin-related chromatin compartments, while differing in mCHH patterns and repetitive sequence landscapes. Our analyses further suggest that the emergence of holocentricity in Myristica is unlikely to be explained by whole-genome duplication events or major structural changes in core kinetochore proteins. Instead, lineage-specific remodeling of repetitive sequences and epigenetic states may have contributed to centromere reorganization. These results provide new insights into centromere diversification in Magnoliales.

Akodon cursor (Winge, 1887) is widely distributed across more than 2,500 km of the Brazilian Atlantic Forest and shows diploid numbers (2n = 14, 15, 16) associated with the recognized phylogeographic clades (North, Central, and South), but unevenly distributed among populations, suggesting that A. cursor may comprise more than one taxon. We used experimental crosses to investigate how reproductive barriers emerge and accumulate in a geographically structured and chromosomally polymorphic taxon. We estimated reproductive success (RS), litter size (LS), and gestation length (GL) based on 300 intra- and interpopulation crosses founded by 55 wild-caught matrices from three populations: Pernambuco (PE; North clade; 2n = 16), Bahia (BA; North and Central clades; 2n = 14, 15, 16), and Espírito Santo (ES; Central and South clades; 2n = 14). Mean intrapopulation values (RS = 56.06%; LS = 3.7 ± 1.04) were defined as reference parameters for the species. The PE population, geographically distant by at least 1,000 km and isolated for approximately 300,000 years, was reproductively isolated from both ES and BA, supporting its recognition as an Evolutionarily Significant Unit (ESU) for research and conservation. In contrast, BA and ES were not reproductively isolated and produced fertile F₁ hybrids, with heterosis observed in F₁ females. These results show that reproductive isolation in A. cursor is mosaic, direction-dependent, sex-biased, and stage-specific, supporting its value as a model for studying speciation, chromosomal evolution, and conservation-relevant lineage divergence, as well as for understanding how geography and chromosomal architecture interact to generate reproductive isolation.

The class Thermoleophilia represents a deep-branching lineage within the phylum Actinomycetota, yet its taxonomic diversity remains incompletely resolved due to the limited availability of cultured representatives and uneven integration of genome-resolved diversity. Here, we performed an integrative phylogenomic and taxonomic analysis of Thermoleophilia using three newly generated genomes derived from desert soils in Xinjiang, China, including two cultured isolate genomes and one metagenome-assembled genome (MAG), together with publicly available MAGs. Phylogenomic reconstruction based on conserved marker genes, overall genome relatedness indices (OGRI), and 16S rRNA gene sequences revealed several well-supported lineages that expand the currently characterized diversity within the order Solirubrobacterales. Strain SYSU D00693^T represents a novel family, genus, and species, for which the names Vescideserticolaceae fam. nov., Vescideserticola gen. nov., and Vescideserticola fastidiosus sp. nov. are proposed. Strain SYSU D01012^T represents a novel species within the genus Patulibacter, designated Patulibacter desertihabitans sp. nov. Genome-based analyses further demonstrated that BS_bin.015, together with BP_457 and BP_458, forms a distinct lineage corresponding to the GTDB placeholder genus AC-38. Phylogenomic and comparative genomic evidence supports the proposal of Candidatus Sabulibiaceae fam. nov. and Candidatus Sabulibium gen. nov., comprising three candidate species-level lineages. Comparative genomic analyses further revealed lineage-associated variation in genomic functional potential among the analyzed genomes. Collectively, this study expands the currently characterized taxonomic diversity of Thermoleophilia and provides genomic insights into the diversity and evolutionary relationships of this underexplored bacterial class.

Serpentine soils are characterized by high levels of heavy metals, low nutrient availability, and water scarcity, presenting significant ecological challenges for plant species. Soil variation associated with serpentine outcrops generates sharp environmental contrasts over short geographic distances, providing an opportunity for study of lineage divergence and population structure across a heterogeneous edaphic landscape. Here, we examine the evolutionary history of three often sympatric plant species, Lavandula stoechas L., Phlomis purpurea L. (both Lamiaceae), and Halimium atriplicifolium (Lam) Spach. (Cistaceae), which inhabit adjacent serpentine and non-serpentine habitat in the southern Iberian Peninsula. Using a comparative population genomic framework, we test whether serpentine populations represent distinct evolutionary lineages or parallel colonizations of this edaphic habitat, and to what degree genomic differentiation reflects both edaphic conditions and geographic isolation. Highly supported, maximum likelihood population phylogenies suggest repeated, parallel colonizations of serpentine habitat by all three species. The degree of isolation-by-distance and the geographic distribution of ancestral group membership in populations differ notably among these sympatric species. Demographic simulations revealed low to intermediate levels of recent, asymmetric gene flow, characterized by a directional genetic contribution from serpentine patches into adjacent non-serpentine populations, while genotype-environment associations identified potential candidate loci under edaphic selection. Significant variation in plant height among populations on differing soils represents environmentally associated phenotypic differentiation and suggests ecotypic differences, while the magnitude of this association varies among the species. Together, our results show that parallel radiation to serpentine habitat, population ancestry, isolation-by-distance and ongoing gene flow contribute differentially to population genomic structure in these three species.

Carya kweichowensis is a critically endangered hickory species endemic to the karst forests of southwestern China. Its survival is threatened by severe habitat fragmentation and extremely small population sizes driven largely by human activities. In this study, we combined population genomic analyses with species distribution modeling to inform the conservation of C. kweichowensis. We sampled 66 individuals from 18 wild populations across its remaining range and generated genome-wide data for single-nucleotide polymorphisms to assess genetic structure, diversity, mutational load, and demographic history. The results revealed clear genetic subdivision of remnant populations into distinct groups corresponding to their geographic isolation. Demographic reconstructions suggested a history of population decline and bottlenecks, emphasizing the prolonged vulnerability of this species. Species distribution models predicted severe contraction and shift of its suitable habitat under future climate change scenarios, which would further imperil its persistence. Based on the genetic differentiation observed, we delineated three conservation units for C. kweichowensis. We recommend immediate conservation action for the marginal central and eastern groups. Our study demonstrates that the integration of population genomics, genetic load assessment, and species distribution modeling contributes profoundly to the development of targeted conservation strategies for endangered species.

Although microbial isolation techniques have been developed for over a century, conventional methods often fail to capture the vast majority of environmental microbial diversity, largely because slow-growing bacteria are outcompeted by fast-growing taxa. To address this limitation, we developed a simple Liquid-Medium-Dilution (LMD) method that physically isolates single cells in liquid microcultures using limiting dilution and the Poisson distribution, without requiring specialized equipment. Comparative analysis of 787 bacterial strains isolated from estuarine sediments of the Qiantang River, China, showed that LMD recovered 72 putative novel species (19.2%), a significantly higher proportion than the Traditional-Solid-Culture (TSC) method (47 strains, 11.4%; P < 0.01). Importantly, LMD uniquely accessed rare and slow-growing lineages, including members of the phylum Verrucomicrobiota and most notably two novel species, Poseidonivirga lenticrescens gen. nov., sp. nov., and Poseidonivirga cretacea sp. nov. These strains exhibit low 16S rRNA gene sequence similarities (90.37% and 90.51%) to known taxa and represent a novel order, Poseidonivirgales, within the class Alphaproteobacteria. Our findings demonstrate that the LMD method effectively minimizes competitive exclusion, enabling the cultivation of previously unculturable, slow-growing, and phylogenetically deep bacterial lineages using standard laboratory conditions.

Catfishes (order Siluriformes) inhabit diverse aquatic environments worldwide, ranging from tropical lowlands to fast-flowing mountain rivers. However, the contribution of genomic variation to ecological diversification in catfishes, particularly within high-altitude lineages, remains poorly understood. Here, we investigated genome evolution in an extreme environment by focusing on Glyptosternon maculatum, the highest-altitude dwelling catfish known and a basal lineage of Glyptosternoid fishes. We generated a high-quality, haplotype-resolved genome assembly using PacBio HiFi and Hi-C sequencing. The two phased haplotypes span 741.8 Mb and 753.7 Mb, with contig N50 values >4 Mb, representing a substantial improvement in continuity and accuracy over previous assemblies. Comparative genomic analyses revealed significant contraction of gene families associated with G protein–coupled receptor activity, particularly olfactory receptor (OR) and trace amine-associated receptor (TAAR) genes. Water-soluble OR subfamilies exhibited a pronounced reduction relative to other catfishes, suggesting lineage-specific remodeling of chemosensory repertoires that may reflect ecological specialization in high-altitude river systems. Population genetic analyses identified chromosome 11 as the sex chromosome, harboring an ~0.97 Mb sex-determining region (SDR) consistent with an XX/XY system. The X and Y chromosomes are highly similar and lack evolutionary strata, indicating a young, homomorphic pair. Despite limited sequence divergence, the SDR exhibits an enrichment of LINE retrotransposons, with evidence of recent transposable element accumulation extending into adjacent regions. Our results provide a chromosome-level genomic resource for Glyptosternoid fishes and offer new insights into sensory gene evolution and the early dynamics of sex chromosome differentiation in a high-altitude teleost.

Evolutionary relationships of Zanthoxylum L. and Vepris Comm. ex A Juss. remain inadequately resolved due to limited genomic resources and conflicting signals from single markers, hindering efforts to understand their diversification and adaptation across tropical environments. In this study, we generated Angiosperms353 target-capture data for 187 individuals representing 51 Zanthoxylum and Vepris species from East Africa. Using concatenated and multispecies coalescent analyses combined with concordance-factor approaches, we recovered Zanthoxylum and Vepris as monophyletic. However, species-level relationships within each genus exhibited substantial phylogenetic discordance, indicating extensive gene-tree heterogeneity across the dataset. Concordance factor analysis revealed moderate genome-wide site concordance (mean sCF=46.64%) but markedly lower gene concordance (mean gCF=28.77%), indicating widespread gene-tree heterogeneity. Both sCF and gCF exhibited strong positive correlations with branch lengths of r=0.698 and r=0.687, respectively. Discordance patterns showed an almost perfect balance between alternative topologies (sDF1=24.9%, sDF2=24.8%), minimal mean asymmetry (3.5-5.1%), and high proportion of polyphyly (gDFP=59.7%), all consistent with incomplete lineage sorting (ILS) as the primary source of phylogenomic conflict. A small fraction of branches (1.9–4.7%) displayed significant asymmetry, which signals only limited evidence for processes beyond ILS and should be interpreted with caution pending explicit tests of introgression. Generally, our findings offer a comprehensive phylogenomic framework for East African Zanthoxylum and Vepris and demonstrate that ILS has played a major role in shaping genomic variation and phylogenetic discordance within these genera. Further analyses will be required to investigate the extent to which hybridization or other reticulate processes have contributed to their evolutionary history.