Biology subjects

Bradshaw, A. J.

Publications and source records attributed to Bradshaw, A. J..

11 recordsLinked to original sources

bioRxiv2026

Genomic Characterization of the Endangered Medicinal Polypore Agarikon (Laricifomes officinalis syn. Fomitopsis officinalis)

Agarikon (Laricifomes officinalis syn. Fomitopsis officinalis) is an endangered fungus belonging to a unique lineage in the Polyporales (Basidiomycota) with a growing body of evidence supporting its medicinal value. In this study, we report the hybrid de novo assembly and annotation of the first L. officinalis nuclear and mitochondrial genome sequences, with a nuclear genome size of 28.76 Mb assembled across 66 scaffolds (51.96% GC content; BUSCO completeness of 99.4%), and a complete core mitochondrial genome size of 197.67 kb. Structural and functional annotation of the nuclear genome yielded 8,717 predicted genes including 8,604 protein-coding genes, with 310 genes in 27 biosynthetic gene clusters. We characterized the mating type loci matA and matB, consistent with a tetrapolar mating system, and identified genes encoding key enzymes involved in triterpenoid and polyketide biosynthetic pathways that lead to the production of a diverse array of secondary metabolites. Additionally, we conducted maximum likelihood phylogenomic analysis to confirm the taxonomic position of L. officinalis among 21 species in Polyporales using protein sequences for 860 shared BUSCO genes. This high-quality annotated genome of L. officinalis will serve as a foundation for further investigations into the evolutionary history of this distinct fungal lineage, provide a reference for future population genomic analyses, and elucidate mechanisms underlying the synthesis of the bioactive compounds responsible for agarikons wide-ranging medicinal benefits.

genomics↗

bioRxiv2026

Draft genome assembly of the green-bronze dung beetle, Onthophagus orpheus

Dung beetles (Coleoptera: Scarabaeinae) are ecologically important insects, yet genomic resources for this diverse lineage remain limited. Here, we present a high-quality genome assembly for Onthophagus orpheus, an understudied species that is abundant in urban forests in the eastern United States. The assembled genome is highly contiguous and exhibits strong completeness, as assessed by Benchmarking Universal Single-Copy Ortholog (BUSCO) analyses, indicating robust representation of conserved protein-coding genes. Structural and functional annotation recovered a comprehensive gene set consistent with expectations for coleopteran genomes. This genome assembly provides an important resource for future work on the behavioral ecology and population genetics of Onthophagus orpheus, specifically, and Scarabaeinae more broadly.

genomics↗

bioRxiv2026

The one that abstained: Psilocybe fuscofulva genome suggests two recent origins of the psilocybin gene cluster in Psilocybe

Production of the psychoactive compound psilocybin is a defining feature of the genus Psilocybe, commonly referred to as "psychedelic mushrooms". However, Psilocybe fuscofulva is a striking exception within Psilocybe sensu stricto as it lacks the stereotypical blue bruising characteristic of the genus, and psilocybin has not been detected in the species.To investigate the evolutionary events leading to differential psilocybin production among Psilocybe species, we produced genome assemblies two P. fuscofulva strains, one Psilocybe polytrichoides strain, and one Psilocybe tampanensis strain, complemented by reannotated public genomes and metagenome-derived assemblies from fungarium specimens. This sample represents both major Psilocybe clades (Clade I and Clade II) and the most closely related genera. Phylogenomic analysis based on 100 single-copy orthologs curated for high branch support strongly placed P. fuscofulva as the earliest-diverging lineage in Psilocybe Clade I. No psilocybin gene cluster (PGC) homologs, whether clustered or dispersed, were identified in P. fuscofulva, whereas a single intact PGC was present in all other examined Psilocybe genomes. The PGC resides in two distinct, clade-specific genomic loci: one conserved in Clade I and another in Clade II, each displaying characteristic gene orders and orientations consistent with rearrangement through circular intermediates. Time-calibrated phylogenies estimated the Psilocybe crown group at approximately 28 million years ago, with major clade divergences occurring in the Miocene. The absence of the PGC in P. fuscofulva, together with clade-specific structural conservation and the lack of remnant sequences at alternate loci, supports two independent origins of the PGC within Psilocybe: one in the ancestor of Clade II and a subsequent origin in Clade I following divergence from P. fuscofulva, most likely via horizontal gene transfer (HGT). Gene phylogenies provide weak support for transfer from Clade I to Clade II, although broader sampling is required for confirmation. These results constrain the timeframe of PGC emergence and dispersal to the Miocene, implying rapid HGT events possibly driven by ecological pressures in expanding grassland ecosystems. This study challenges the assumption of an ancestral psilocybin pathway in Psilocybe and its close relatives and underscores multiple recent acquisitions of the PGC that suggest it is an ecologically important metabolic trait in psychoactive fungi.

evolutionary biology↗

bioRxiv2025

Characterization of a core fungal community and captivity-induced "mycobiome" change in Fowler's Toad (Anaxyrus fowleri)

Amphibious animals, such as frogs, are found at the intersection of aquatic and terrestrial ecosystems. They often serve as keystone and sentinel species, essential in nutrient cycling and food webs. In recent decades, amphibians have experienced drastic population declines due to habitat loss, climate change, and disease. These declines have prompted investments in ex situ conservation and captive breeding programs, which aim to reduce extinction risk by creating assurance colonies and reintroducing individuals once threats are mitigated. A critical component of these programs is proper husbandry, which ensures the health and longevity of captive populations and their ability to produce offspring that can be reintroduced into the wild. The artificial environment in captivity can profoundly impact animal behavior and health, particularly in relation to diet and nutrition. Diet not only provides nutrients and energy but also shapes the hosts gut microbial community, which in turn impacts digestive health. Complex microbial communities, collectively known as the microbiome, are characterized by the high biodiversity of prokaryotes, microscopic fungi, and viruses. The diet-associated microbiome is increasingly studied for its role in captive animal health and behavior, although research has focused more on bacteria than fungal communities, or the "mycobiome". Here, we investigated the core mycobiome using metabarcoding of fungal communities in 15 wild-caught Anaxyrus fowleri (Fowlers Toad), documenting shifts as toads transitioned from wild to captive settings. We identified a core set of fungal taxa and observed distinct changes in non-core fungi associated with dietary differences. These findings highlight the dynamic nature of the amphibian mycobiome and the significant impact captivity can have on microbial composition, providing a framework for understanding the role of the amphibian mycobiome in future conservation efforts.

microbiology↗

bioRxiv2025

Unraveling the Genomic and Phylogenetic Complexity of the understudied microfungus Basidiobolus: Insights from 19 Newly Sequenced Genomes

Basidiobolus is a globally distributed genus of early-diverging fungi within Zoopagomycota, known for its presence in diverse ecological niches ranging from soil and decaying organic matter to vertebrate gastrointestinal tracts. Despite its ecological and medical relevance, the taxonomy and evolutionary relationships within the genus remain poorly resolved due to limited genomic resources. In this study, we present nineteen newly sequenced Basidiobolus genomes, expanding the available genomic data. Using short-read Illumina sequencing, assembly, and annotation pipelines, we characterize genic content, assess completeness, and explore biosynthetic gene content across isolates. Phylogenomic analysis reveals two major clades corresponding to B. meristosporus and B. ranarum, while B. heterosporus forms a distinct lineage. Several isolate clusters exhibit deep divergence suggestive of cryptic species, underscoring the need for expanded sampling and taxonomic revision. Functional annotations reveal a rich repertoire of biosynthetic gene clusters, including non-ribosomal peptide synthetases, polyketide synthases, and hybrid clusters, pointing to an underexplored reservoir of secondary metabolite diversity. These findings position Basidiobolus as a compelling model for investigating fungal evolution, ecological adaptation, and natural product biosynthesis.

genomics↗

bioRxiv2025

Impacts on the microbial fungal communities across water, sediment, and amphibian hosts across an urbanization gradient waterway in Worcester, Massachusetts

In a world of increasingly urbanized environments, it is critical to understand the impact of urbanization on microbial communities, including fungal communities, as a measure of ecosystem health, and to document how these environments are changing. Aquatic environments, in particular, can be highly sensitive to urbanization with removal of local habitat and inputs of wastewater and contaminants, leading to displacement or extinction of natural flora, fauna, and funga. Aquatic microbial communities, especially fungal communities, are extremely complex and far less characterized compared to their macro counterparts. Here, we characterized the fungal microbiome, i.e. "mycobiome", across multiple habitats-- water, sediment, and frog fecal matter from three species (American bullfrog (Lithobates catesbeianus), Green frog (Lithobates clamitans), and Pickerel frog (Lithobates palustris)) -- within the Tatnuck Brook waterway in Worcester, MA. The Tatnuck Brook waterway is a connected group of streams, ponds, and lakes that transition from protected areas at its headwaters, below the citys drinking water reservoir, to highly urbanized regions within Worcester. Using metabarcode sequencing, we found that water, sediment, and frog gut habitats harbor distinct fungal communities, but all exhibit parallel shifts in diversity along an urbanization gradient. In particular, we identified fungal taxa from the amphibian mycobiome and environmental samples that exhibited a range of sensitivities to urbanization. These taxa, including Basidiobolus, Cladosporium, and Lemonniera in fecal and sediment samples, as well as Candida, which was found in all habitats, are potential indicators of shifts in aquatic ecosystems due to urbanization. Their responses to urban stressors may serve as a baseline for further studies of aquatic fungal communities. IMPORTANCEAs cities grow, they can change nearby rivers, streams, and ponds in ways that affect plants, animals, and even tiny microbes. Fungi are an important part of these ecosystems because they help break down materials and can affect the health of animals like frogs. However, we still know very little about how fungi respond to urban environments. In this study, we looked at fungi living in water, sediment, and frog guts along a range of places from natural to highly developed areas in Worcester, Massachusetts. We found that some fungi were more common in cleaner, less developed sites, while others were more common in urban ones. These patterns suggest that fungi could be useful indicators of environmental health. Our work helps scientists better understand how urbanization affects nature and offers a new way to monitor and protect freshwater ecosystems.

ecology↗

bioRxiv2024

Discovery of the closest free-living relative of the domesticated "magic mushroom" Psilocybe cubensis in Africa

The "magic mushroom" Psilocybe cubensis is cultivated worldwide for recreational and medicinal uses. Described initially from Cuba in 1904, there has been substantial debate about its origin and diversification. The prevailing view, first proposed by the Psilocybe expert Gaston Guzman in 1983, is that P. cubensis was inadvertently introduced to the Americas when cattle were introduced to the continents from Africa and Europe ([~]1500 CE), but that its progenitor was endemic to Africa. This hypothesis has never been tested. Here, we report the discovery of the closest wild relative of P. cubensis from sub-Saharan Africa, P. ochraceocentrata nom. prov. Using DNA sequences from type specimens of all known and accessable African species of Psilocybe, multi-locus phylogenetic and molecular clock analysis strongly support recognizing the African samples as a new species that last shared a common ancestor with P. cubensis [~]1.5 million years ago ([~]710k - 2.55M years ago 95% HPD). Even at the latest estimated time of divergence, this long predates cattle domestication and the origin of modern humans. Both species are associated with herbivore dung, suggesting this habit likely predisposed P. cubensis to its present specialization on domesticated cattle dung. Ecological niche modeling using bioclimatic variables for global records of these species indicates historical presence across Africa, Asia, and the Americas over the last 3 million years. This discovery sheds light on the wild origins of domesticated P. cubensis and provides new genetic resources for research on psychedelic mushrooms.

evolutionary biology↗

bioRxiv2023

From populations to pan-genomes: investigating the role of ecology and genomic architecture in maintaining species boundaries in the porcini mushroom, Boletus edulis

Hybridization among diverged species is common across all domains of eukaryotic life, but appears to be particularly common in fungi. However, some fungi exhibit a greater tendency for hybridization than others and it is unclear what mechanisms facilitate or prevent hybridization. Here, we generated 253 whole genome sequences and 22 reference genomes within the globally distributed ectomycorrhizal species complex Boletus edulis Bull. and use a multi-faceted genomic approach to identify patterns of ongoing hybridization and determine whether hybridization is mediated by changes in genome structure, ecology, or both. We found that hybridization is common among species of B. edulis despite 2.1 million years of divergence. However, not all lineages that hybridize today exhibit patterns of introgression, indicating the presence of strong reproductive boundaries among some species. Using a pan-genomic approach we find that genome structural variation is abundant within B. edulis, but that the presence of ongoing introgression does not correlate with genome structural similarity or overall gene content. Instead, we find that the composition of ecologically relevant gene families more accurately predicts the presence of introgression among lineages and B. edulis as a group may specialize on chitin decomposition. Altogether, we show that ecological preferences are likely the primary driver of reproductive barriers in B. edulis.

evolutionary biology↗

bioRxiv2022

Phylogenomics of the psychoactive mushroom genus Psilocybe and evolution of the psilocybin biosynthetic gene cluster

Psychoactive mushrooms in the genus Psilocybe have immense cultural value and have been used for centuries in Mesoamerica. Despite a recent surge in interest in these mushrooms due to emerging evidence that psilocybin, the main psychoactive compound, is a promising therapeutic for a variety of mental illnesses, their phylogeny and taxonomy remain substantially incomplete. Moreover, the recent elucidation of the psilocybin biosynthetic gene cluster is known for only five species of Psilocybe, four of which belong to only one of two major clades. We set out to improve the phylogeny for Psilocybe using shotgun sequencing of 71 fungarium specimens, including 23 types, and conducting phylogenomic analysis using 2,983 single-copy gene families to generate a fully supported phylogeny. Molecular clock analysis suggests the stem lineage arose [~]66 mya and diversified [~]53 mya. We also show that psilocybin biosynthesis first arose in Psilocybe, with 4-5 possible horizontal transfers to other mushrooms between 40 and 22 mya. Moreover, predicted orthologs of the psilocybin biosynthetic genes revealed two distinct gene orders within the cluster that corresponds to a deep split within the genus, possibly consistent with the independent acquisition of the cluster. This novel insight may predict differences in chemistry between the two major clades of the genus, providing further resources for the development of novel therapeutics.

evolutionary biology↗

bioRxiv2021

On the Origin of Feces: Fungal diversity, distribution, and conservation implications from feces of small mammals

Fungi are extremely diverse, but only a small fraction of the total estimated species have been characterized. Often, the extent of diversity and distribution of fungal communities is difficult or near impossible to assess. This is due to the fact that many Fungi are cryptic and persist predominantly hidden within substrates such as soil or plant material. This is particularly true for hypogeous sporocarps, including truffles, which are extremely difficult to survey in a systematic manner. However, fungi with hypogeous sporocarps have evolved traits that make them highly attractive to animals, such as small mammals, which ingest and disperse fungal spores through defecation. Here, samples of feces from 138 small mammals collected in the western United States were assessed for total fungal diversity using a dual-index metabarcoding, high-throughput Illumina sequencing approach. Our findings exhibit many identifications within Agaricomycetidae, with 65 of the 138 samples containing sequences belonging to several species of the hypogeous truffle genus Rhizopogon. Metadata, such as geospatial coordinates, for each captured small mammal can be used as a proxy for the presence or absence of Rhizopogon species identified in their feces. Utilizing these proxy data, along with publicly available data on observation and occurrence from data repositories such as GBIF and MycoPortal, it is possible to augment our current knowledge of the extent of occurrence and area of occupancy of cryptic hypogeous fungi without direct observation, further enhancing our ability to assess their conservation status.

ecology↗

bioRxiv2018

Convergent evolution of psilocybin biosynthesis by psychedelic mushrooms

Psilocybin is a psychoactive compound with clinical applications produced by dozens of mushroom species1. There has been a longstanding interest in psilocybin research with regard to treatment for addiction2, depression3, and end-of-life suffering4. However, until recently very little was known about psilocybin biosynthesis and its ecological role. Here we confirm and refine recent findings5 about the genes underpinning psilocybin biosynthesis, discover that there is more than one psilocybin biosynthesis cluster in mushrooms, and we provide the first data directly addressing psilocybins ecological role. By analysing independent genome assemblies for the hallucinogenic mushrooms Psilocybe cyanescens and Pluteus salicinus we recapture the recently discovered psilocybin biosynthesis cluster5,6 and show that a transcription factor previously implicated in its regulation is actually not part of the cluster. Further, we show that the mushroom Inocybe corydalina produces psilocybin but does not contain the established biosynthetic cluster, and we present an alternative cluster. Finally, a meta-transcriptome analysis of wild-collected mushrooms provides evidence for intra-mushroom insect gene expression of flies whose larvae grow inside Psilocybe cyanescens. These larvae were successfully reared into adults. Our results show that psilocybin does not confer complete protection against insect mycophagy, and the hypothesis that it is produced as an adaptive defense compound may need to be reconsidered.

evolutionary biology↗