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Abstract PremiseThe agaricomycete order Cantharellales contains approximately 1000 species of fungi characterized by diverse morphological forms, ecological guilds, and nutritional modes. Examples include coralloid lichens that form symbioses with unicellular green algae, bulbil‐forming lichenicolous species, corticioid free‐living fungi that degrade dead sources of organic carbon, pathogens that cause plant disease, orchid root endosymbionts, and ectomycorrhizal fungi including popular edible mushrooms. However, evolutionary relationships in the Cantharellales remain poorly understood due to conflicting estimates based on ribosomal DNA loci. MethodsWe constructed a five‐gene phylogeny of the Cantharellales using data from 301 specimens to evaluate family‐level relationships. We used penalized likelihood to estimate divergence times and ancestral state reconstruction to test the hypothesis of multiple independent origins of biotrophic ecologies in the order and whether those transitions are younger than the divergence times of associated plant or lichen hosts. ResultsFour monophyletic families were recovered with strong support: Botryobasidiaceae, Ceratobasidiaceae, Hydnaceae s.l., and Tulasnellaceae, with Hydnaceae containing the greatest species richness and morphological diversity. Our results suggest the Cantharellales diverged during the Carboniferous period with subsequent diversification following the Permian‐Triassic extinction. Ancestral state reconstruction supports a saprotrophic most recent common ancestor with at least three transitions to an ectomycorrhizal ecology, multiple transitions to a lichenicolous habit with one or more subsequent transitions to mutualistic nutritional modes, four transitions to an orchid mycorrhizal ecology, and two transitions to a lichenized lifestyle. ConclusionsThis study represents the first comprehensive examination of the evolution of form and function across this ecologically and morphologically diverse order of fungi.
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Genome-wide phylogeny reshapes our understanding of the evolution of deep-sea dragonfishes, bristlemouths, viperfishes, and allies (Stomiiformes)
Abstract BackgroundThe evolutionary relationships within Stomiiformes, a diverse order of deep-sea fishes dominating the mesopelagic and bathypelagic zones, remain contentious due to conflicting morphological and molecular evidence. These fishes, comprising 464 species across four traditionally recognized families (Gonostomatidae, Sternoptychidae, Phosichthyidae, and Stomiidae), exhibit remarkable adaptations such as bioluminescence, ultra-black pigmentation, and extreme jaw morphologies. Their global abundance and ecological significance, including contributions to the biological carbon pump, underscores the need to resolve their phylogeny amid escalating threats from climate change and human activities. ResultsWe conducted the most comprehensive phylogenomic analysis of Stomiiformes to date, integrating 936 nuclear loci from 60 species and an expanded dataset of 135 species with mitochondrial sequences from publicly available repositories such as the Barcode of Life Data Systems (BOLD) database. We used maximum likelihood and coalescent-based approaches to assess family monophyly and relationships, including extensive quality control to address contamination in public databases. Our analyses reveal unstable tree topologies and complex evolutionary histories that challenge traditional classifications, while our quality control analyses identified 29% of BOLD sequences as misidentified or contaminated, emphasizing rigorous curation for deep-sea taxa. Congruent with a recent taxonomic treatment of Stomiiformes, the families Phosichthyidae and Gonostomatidae exhibit polyphyly and paraphyly, respectively, while subfamilies within Stomiidae are extensively non-monophyletic, leading us to recommend their abandonment. We propose the recognition of eight monophyletic families: Vinciguerriidae, Diplophidae, Gonostomatidae, Yarrellidae, Ichthyococcidae, Phosichthyidae, Sternoptychidae, and Stomiidae, supported by robust molecular and morphological evidence. ConclusionsThis revised classification reflects the morphological and ecological diversity of Stomiiformes, aligning with their evolutionary diversification in the deep sea. Our phylogenomic framework resolves longstanding systematic uncertainties and highlights the power of genome-wide data in tackling taxonomically challenging clades. These findings provide a foundation for understanding deep-sea fish diversification and assessing the potential ecological drivers for their evolutionary diversity.
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- Award ID(s):
- 2225130
- PAR ID:
- 10664047
- Publisher / Repository:
- BioMed Central
- Date Published:
- Journal Name:
- BMC Ecology and Evolution
- Volume:
- 25
- Issue:
- 1
- ISSN:
- 2730-7182
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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- Free Publicly Accessible Full Text
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Accepted Manuscript
- Journal Article:
- https://doi.org/10.1186/s12862-025-02453-0
