Huang D. Zhou X., S. Dong, W. Sheng, Q. Zuo, L. Zhang, W.-Z. Ma, G. K. Golinski, A. Vanderpoorten, B. Goffinet, Y. Liu, T. Peng. A family-level phylogeny of liverworts (Marchantiophyta): new insights from mitochondrial sequences. Journal of Systematics and Evolution (accepted March 3, 2025)  pdf

Abstract reads: Liverworts, with approximately 7300 species worldwide, exhibit remarkable morphological diversity in terms of growth form, ontogeny, and architecture. Their mitochondrial genome exhibits lower average substitution rates compared to their nuclear and plastid genomes, and shows less structural variation, suggesting its suitability for inferring relationships at higher taxonomic levels. In this study, we substantially expanded mitochondrial sampling in liverworts by adding complete mitochondrial gene sets from 97 species across 25 families, thereby increasing family‐level coverage to 71%. Among these, we newly assembled 23 complete mitochondrial genomes. Although four species with structural variants were newly identified, the overall architecture of liverwort mitochondrial genomes remains highly conserved, with taxa that diverged over 470 million years ago still having collinearity. Phylogenetic inferences from mitochondrial genome sequences confirmed the monophyly of most suprafamilial taxa, with the exceptions of Porellales, Ptilidiales, and Pelliidae. Herzogianthus (Ptilidiales) was well‐supported as a sister group to Jungermanniales sensu lato, rather than forming a monophyletic lineage with Ptilidium (Ptilidiales). This work provides an important resource for future genetic and phylogenetic studies of liverworts.

Milis A., M. Hofmann, P. Mäder, J. Wäldchen, M. De Haan, P. Ballings, I. Van der Beeten, B. Goffinet & A. Vanderpoorten. 2026. Towards the automatized identification of moss species from their spore morphology. Annals of Botany 137(1): 171–180. pdf. Google scholar

Abstract reads: Background and Aims: Automatized species identification tools have massively facilitated plant identification. In mosses, spore ultrastructure appears to be a promising taxonomic character, but has been largely under-exploited. Here, we test artificial intelligence-based approaches to identify species from their spore morphology. In particular, we determine whether the number of spores, their polarity, and variation among populations and capsules affect model accuracy. Methods: Scanning electron microscopy spore images were generated for five capsules of five populations in ten species. Convolutional neural networks with a highly modularized architecture (ResNeXt) were trained to identify the species, population and capsule of origin of a spore. The training set was progressively sub-sampled to test the impact of sample size on model accuracy. To assess whether variation in spore morphology among populations affected model accuracy, one population was successively removed to test a model trained on the four remaining populations. Key Results: Species were correctly identified at average rates of 92 %, regardless of polarity. Model accuracy decreased progressively with decreasing sample size, dropping to about 80 % with 15 % of the initial dataset. The population and capsule of origin of a spore was retrieved at rates >75 %, indicating the presence of diagnostic population and capsule markers on the sporoderm. Strong population structure in some species caused a substantial drop of model accuracy when model training and testing was performed on different populations.
Conclusions: Spore morphology appears to be an extremely promising tool for moss species identification and may usefully complement the suite of morphological characters used so far in moss taxonomy. The presence of spore diagnostic features at the population and capsule level raises substantial questions on the origin of this structure, which are discussed. Substantial infraspecific variation makes it necessary, however, to train an automatized identification tool from a range of populations and capsules.

Buck W.R. & B. Goffinet. 2026. Addendum to the new checklist of the mosses of the continental United States and Canada. The Bryologist 129(1): 1–3. pdf

Introduction reads: The recent checklist of mosses of continental United States and Canada (Buck & Goffinet 2024) included 1565 species, 12 subspecies, 34 varieties and one form for a total of 1612 taxa from 366 (and not 367 as originally reported) genera. Upon its publication, 29 omissions, seven missing or new synonymies, one exclusion from the flora and one duplication were identified, and the checklist is hereby updated. In addition, the authority for one taxon was corrected. Consequently, the moss flora of North America north of Mexico holds 1589 species, 13 subspecies, 36 varieties and one form for a total of 1639 taxa in 367 genera. The original Supplementary Tables have been updated and made available. The checklist is now also available and updated online at https://bryology.eeb. uconn.edu/na-moss-checklist/.

Dirick L., Y. Liu, S. Dong, J. Yu, L. Ouerdane, C. Curie & B. Goffinet. 2025. Multiple independent acquisitions of a metallophore-synthesis gene by plants through horizontal microbial gene transfer. Nature Communications 16: 8339. pdf  Google scholar

Abstract reads: The evolution of land plants is marked by major innovations enhancing their vegetative and reproductive fitness. Despite their extensive adaptations to terrestrial habitats, plants rely on ecological interactions with microbes for various physiological processes. Beyond their role as critical partners in the conquest of, and diversification on land, fungi and bacteria also serve as sources of genetic tools. Analyses of the gene space of land plant model organisms suggest that such transfers are unique and ancient. However here, using genomic data spanning the diversity of mosses, we demonstrate that a metallophore-synthesis gene was acquired independently from distinct microbial donors by at least five plant lineages. Furthermore we find that the first NAS gene acquired by mosses was later replaced by another fungal copy, transferred to another major moss lineage. Such a complex history of acquisition of a gene may reflect a more general pattern of highly dynamic gene exchange across the tree of life.

Dong S., S. Wang, L. Li, J. Yu, Y. Zhang, J.-Y. Xue, H. Chen, J. Ma, Y. Zeng, Y. Cai, W. Huang, J. Li, Y. Yao, R. Hu, T. Zhao, J.C. Villarreal A., L. Dirick, L. Liu, M. Ignatov, J. Ruan, Y. He, H. Wang, B. Xu, J. Wegrzyn, D. W. Stevenson, K. S. Renzaglia, H. Chen, L. Zhang, S. Zhang, R. Mackenzie, J. Moreno, M. Melkonian, T. Wei, Y. Gu, X. Xu, M. Long, J. Huang, S. Rensing, B. Goffinet, J. L. Bowman, Y. Van de Peer, H. Liu, and Y. Liu. 2025. Bryophytes hold a larger gene family space than vascular plants. Nature Genetics 2025. pdf

(See also commentary: The dawn of bryophyte genomics is here by Potente, G., Yue, Y. & Szövényi, P. )

Abstract reads: After 500 million years of evolution, extant land plants compose the following two sister groups: the bryophytes and the vascular plants. Despite their small size and simple structure, bryophytes thrive in a wide variety of habitats, including extreme conditions. However, the genetic basis for their ecological adaptability and long-term survival is not well understood. A comprehensive super-pangenome analysis, incorporating 123 newly sequenced bryophyte genomes, reveals that bryophytes possess a substantially greater diversity of gene families than vascular plants. This includes a higher number of unique and lineage-specific gene families, originating from extensive new gene formation and continuous horizontal transfer of microbial genes over their long evolutionary history. The evolution of bryophytes’ rich and diverse genetic toolkit, which includes new physiological innovations like unique immune receptors, likely facilitated their spread across different biomes. These newly sequenced bryophyte genomes offer a valuable resource for exploring alternative evolutionary strategies for terrestrial success.

 

 

The American Bryological and Lichenological Society announced the awards for the best papers published in The Bryologist in 2024 (Volume 127) and awarded the SULLIVANT AWARD (for the best bryological paper) to our checklist: Buck W.R. & B. Goffinet. 2024. A new checklist of the mosses of the continental United States and Canada. The Bryologist 127: 484–549.  pdf  Google Scholar

Atwood, J., WR. Buck & B. Goffinet. 2025. Bryomyces, a genus described from foliar moss gemmae, is an earlier name for Plenogemma (Orthotrichaceae). Novon 33: 115–121.

Abstract reads: Bryomyces Miq. and Phragmidiolum Müll. Hal., originally described as genera of endophytic bryophilous ascomycetes, refer instead to foliar moss gemmae based on a comparative assessment of their published illustrations with bryophyte specimens and relevant bryological literature. Phragmidiolum and Plenogemma Plášek, Sawicki & Ochyra are morphologically congeneric with Bryomyces, the latter of which has priority. The new combination B. phyllanthus (Brid.) J. J. Atwood, W. R. Buck & Goffinet is proposed. Bryomyces elegans Miq., Phragmidiolum apicale Müll. Hal., and Ulota phyllantha Brid. [≡ Plenogemma phyllantha (Brid.) Sawicki, Plášek & Ochyra] are new synonyms of that species. Bryomyces montagneanus Miq. is a new synonym of Calymperes androgynum Mont. [= Syrrhopodon rigidus Hook. & Grev.], whereas B. muelleri Miq., Phragmidiolum ramosum Müll. Hal., and Phragmidiolum sparsum Müll. Hal. are new synonyms of Orthotrichum lyellii Hook. & Taylor [≡ Pulvigera lyellii (Hook. & Taylor) Plášek, Sawicki & Ochyra]. Lectotypes are designated for B. montagneanus, Phragmidiolum, Phragmidiolum apicale, and Phragmidiolum ramosum, while a neotype is designated for B. elegans.

Milis A., P. Mäder, M. De Haan, P. Ballings, I. Van Der Beeten, B. Goffinet & A. Vanderpoorten. 2025. Time to spice-up paleoecological records with bryophyte spores. Trends in Plant Sciences in press

Abstract reads: Paleovegetation reconstructions rely virtually exclusively on inferences from vascular plants, particularly pollen grains, ignoring other components of the land flora. Artificial intelligence (AI) opens the door to the identification of other microfossils, particularly bryophyte spores, which offer a new, higher magnification lens to characterize past climatic environments.

Finally, the study first completed by Nasim Rahmatpour for her Ph.D. and then picked up by former postdoc Niki Patel and current Ph.D. student Vidya Vuruputoor is now published in the New Phytologist! Amazing study highlighting the “Immediate premeiotic transcriptomic effects following nonchemically induced whole genome duplication in the moss Funaria hygrometrica” pdf  Congratulations to all and thank you to our collaborators, Drs. Yang Liu, Shanshan Dong and Peter Szövényi.

 

Patel N.*, V. Vuruputoor*, N. Rahmatpour, Y. Liu, P. Szövényi, B. Goffinet & J. Wegrzyn. 2025. Induced whole genome duplication triggers immediate shifts in gene expression in an emerging moss model. New Phytologist 247: 24–32.

Brenden Thomson earned his MSc degree having completed his thesis on the phylogenetic diversity of Physcomitrium (Bryopsida) win North America. Well done and congratulations.