Joanne L. Birch

Libertia and Orthrosanthus are sister genera and the only members of the Iridaceae to occur in both Australasia and the Americas. The ‘Out of Australasia’ hypothesis suggests that the Iridaceae moved from Australasia to South America via Antarctica early in their evolution. To assess whether Antarctica may also have been involved in the distributional history of Libertia and Orthrosanthus, we comprehensively sampled both genera and carried out family-wide phylogenetic, divergence time, and ancestral range estimation analyses, the last explicitly including Antarctica. We conducted analyses using maximum likelihood and Bayesian methods with paleogeographic models that made different assumptions about the connectivity of areas over time. Our analyses suggest that following an initial shift out of Australasia by the Iridoideae, the Libertia–Orthrosanthus lineage originated as a result of vicariance associated with formation of the Drake Passage and again moved via Antarctica, this time back to Australia. Disjunctions within Libertia and Orthrosanthus arose as a result of recent direct long-distance dispersal. Consequently, the distributions of these genera, unique among irises, probably reflect a combination of both vicariance and dispersal. Our study highlights the importance of, and challenges associated with, considering Antarctica when attempting to infer floristic assembly in the Southern Hemisphere.

Peziza echinospora P. Karst. (Ascomycota, Pezizomycetes, Pezizaceae) is a species of cup-forming fungi that is typically found on burnt ground in Europe and North America (Hansen et al. 2002; Van V...

Specimen-associated biodiversity data are crucial for biological, environmental, and conservation sciences. A rate shift is needed to extract data from specimen images efficiently, moving beyond human-mediated transcription. We developed Hespi (for herbarium specimen sheet pipeline) using advanced computer vision techniques to extract authoritative data applicable for a range of research purposes from primary specimen labels on herbarium specimens. Hespi integrates two object detection models: one for detecting the components of the sheet and another for fields on the primary specimen label. It classifies labels as printed, typed, handwritten, or mixed and uses optical character recognition and handwritten text recognition for extraction. The text is then corrected against authoritative taxon databases and refined using a multimodal large language model. Hespi accurately detects and extracts text from specimen sheets across international herbaria, and its modular design allows users to train and integrate custom models.

Summary: Grasses (Poaceae) comprise around 11,800 species and are central for human livelihoods and terrestrial ecosystems. Knowing their relationships and evolutionary history is key to comparative research and crop breeding. Advances in genome-scale sequencing allow for increased breadth and depth of phylogenomic analyses, making it possible to infer a new reference species tree of the family. We inferred a comprehensive species tree of grasses by combining new and published sequences for 331 nuclear genes from genome, transcriptome, target enrichment and shotgun data. Our 1,153-tip tree covers 79% of grass genera (including 21 genera sequenced for the first time) and all but two small tribes. We compared it to a 910-tip plastome tree. The nuclear phylogeny matches that of the plastome at most deep branches, with only a few instances of incongruence. Gene tree–species tree reconciliation suggests that reticulation events occurred repeatedly in the history of grasses. We provide a robust framework for the grass tree of life to support research on grass evolution, including modes of reticulation, and genetic diversity for sustainable agriculture.

Angiosperms are the cornerstone of most terrestrial ecosystems and human livelihoods^1,2. A robust understanding of angiosperm evolution is required to explain their rise to ecological dominance. So far, the angiosperm tree of life has been determined primarily by means of analyses of the plastid genome^3,4. Many studies have drawn on this foundational work, such as classification and first insights into angiosperm diversification since their Mesozoic origins^5–7. However, the limited and biased sampling of both taxa and genomes undermines confidence in the tree and its implications. Here, we build the tree of life for almost 8,000 (about 60%) angiosperm genera using a standardized set of 353 nuclear genes⁸. This 15-fold increase in genus-level sampling relative to comparable nuclear studies⁹ provides a critical test of earlier results and brings notable change to key groups, especially in rosids, while substantiating many previously predicted relationships. Scaling this tree to time using 200 fossils, we discovered that early angiosperm evolution was characterized by high gene tree conflict and explosive diversification, giving rise to more than 80% of extant angiosperm orders. Steady diversification ensued through the remaining Mesozoic Era until rates resurged in the Cenozoic Era, concurrent with decreasing global temperatures and tightly linked with gene tree conflict. Taken together, our extensive sampling combined with advanced phylogenomic methods shows the deep history and full complexity in the evolution of a megadiverse clade.

Species trees, which depict the evolutionary relationships among organisms, underlie many evolutionary studies. Phylogenomics, the use of genome-scale datasets for phylogenetic inference, is the current gold standard for species tree inference. The development, maintenance, and execution of phylogenomic workflows is challenging, requiring programming, data management skills, and familiarity with changing best practices. We introduce Orthoflow, a software wherein a single command automatically conducts end-to-end phylogenomic analysis—orthology inference and identification of phylogenomic markers, quality control, data matrix construction, diagnostics, and tree inference using supermatrix and supertree methods from multiple input data formats. To demonstrate the utility of Orthoflow, we successfully recapitulate the evolutionary relationships among 24 yeast species. Orthoflow increases the accessibility of researchers to conduct rigorous phylogenomic analysis flexibly. Orthoflow is freely available from PyPI (https://pypi.org/project/orthoflow/), Bioconda (https://anaconda.org/bioconda/orthoflow) and GitHub (https://github.com/rbturnbull/orthoflow) under the Apache License 2.0.

Agaricus xanthodermus and other species of the yellow-staining section Xanthodermatei are responsible for mushroom-related poisoning cases that require treatment. However, longstanding anecdotal evidence indicates that this species appears to exhibit considerable variation in toxicity, resulting in gastrointestinal irritation of varying severity in most cases. We quantified the amount of phenol, hydroquinone, and catechol in mushrooms using a novel protocol for gas chromatography–mass spectrometry (GC-MS) and investigated their levels in different basidiomatal structures, different developmental stages, and on different nutritional substrates. Phenol concentration was greater in the pileus than the stipe, in mature compared with immature basidiomata, and in basidiomata occurring in woody mulch versus lawns. Variation in toxicity is suggested to be due in part to variation in phenol concentration, developmental stage and tissue type consumed, and substrate. Variation in human sensitivity to simple phenols may also play a role but was not formally investigated in this study.

PREMISE: Universal target enrichment kits maximize utility across wide evolutionary breadth while minimizing the number of baits required to create a cost‐efficient kit. The Angiosperms353 kit has been successfully used to capture loci throughout the angiosperms, but the default target reference file includes sequence information from only 6–18 taxa per locus. Consequently, reads sequenced from on‐target DNA molecules may fail to map to references, resulting in fewer on‐target reads for assembly, and reducing locus recovery.METHODS: We expanded the Angiosperms353 target file, incorporating sequences from 566 transcriptomes to produce a ‘mega353’ target file, with each locus represented by 17–373 taxa. This mega353 file is a drop‐in replacement for the original Angiosperms353 file in HybPiper analyses. We provide tools to subsample the file based on user‐selected taxon groups, and to incorporate other transcriptome or protein‐coding gene data sets.RESULTS: Compared to the default Angiosperms353 file, the mega353 file increased the percentage of on‐target reads by an average of 32%, increased locus recovery at 75% length by 49%, and increased the total length of the concatenated loci by 29%.DISCUSSION: Increasing the phylogenetic density of the target reference file results in improved recovery of target capture loci. The mega353 file and associated scripts are available at: https://github.com/chrisjackson‐pellicle/NewTargets.