Author: Bernard Goffinet

Zach’s paper in UCONN news

The publication of the study revealing the presence of (re)introduced lichenized fungi in CT, based on populations present on the university campus (Frye H.A., Z. Muscavitch & B. Goffinet. 2021. Discovery of epiphytic lichens in Connecticut suggests novel introduction and reintroduction via horticultural practices. The Bryologist 124: 191–197. pdf, see post) prompted an article “Ecologists are ‘Lichen’ a Surprising New Find on Campus” in UCONN today.

Antoine Simon awarded BAEF fellowship

Antoine Simon
Welcome back! Dr. Antoine Simon, who has visited UCONN and our lab during his MSc and Ph.D. is coming back! Antoine was awarded a fellowship from the Belgian American Education foundation to spend one year here, and further explore the evolution of lichenized fungi!

Some of the publications emerging from his recent work:

Simon A., B. Goffinet, LS. Wang, T. Spribille, T. Goward, T. Pystina, N. Semenova, N.V. Stepanov, B. Moncada, R. Lücking, N. Magain & E. Sérusiaux. 2021. Global phylogeny and taxonomic reassessment of the genus Dendriscosticta (Ascomycota: Peltigerales). Taxon (accepted, stay tuned!).
Simon A., R. Lücking, B. Moncada, J.A. Mercado-Díaz, F. Bungartz, M. Cáceres, E. Gumboski, S. Maria de Azevedo Martinsi, D. Parker & B. Goffinet. 2020. Emmanuelia, a new genus of lobarioid lichen-forming fungi (lichenized Ascomycota: Peltigerales). Plant and Fungal Systematics 65: 76–94.
Simon A., J. Di Meglio, T. Goward, K. Dillman, T. Spribille & B. Goffinet. 2018. Sticta torii sp. nov., a remarkable lichen of high conservation priority from northwestern North America. Graphis Scripta 30: 105–114.
Simon A., B. Goffinet, N. Magain & E. Sérusiaux. 2018. High diversity, high insular endemism and recent origin in the lichen genus Sticta(lichenized Ascomycota, Peltigerales) in Madagascar and the Mascarene archipelago. Molecular Phylogenetics and Evolution 122: 15–28.
Spjut R., A. Simon, M. Guissard, N. Magain & E. Sérusiaux. 2020. The fruticose genera in the Ramalinaceae (Ascomycota, Lecanoromycetes): their diversity and evolutionary history. MycoKeys, 73: 1.

New publication on lichens

Frye H.A., Z. Muscavitch & B. Goffinet. 2021. Discovery of epiphytic lichens in Connecticut suggests novel introduction and reintroduction via horticultural practices. The Bryologist 124: 191–197. pdf

Abstract readsThe discovery of Teloschistes chrysophthalmus in Connecticut more than one hundred years since its last known occurrence is argued to result from human introduction. The species only occurred on the horticultural tree, Gleditsia triacanthos var. inermis, planted on the University of Connecticut campus. Gleditsia triacanthos is not indigenous to northeastern North America but is widespread in the central United States. Other epiphytic macrolichens also recorded on this phorophyte include Punctelia bolliana and Parmotrema austrosinense, both widespread in the central United States, and new to Connecticut and New England, respectively. This is likely the first reported case of combined introductions of lichenized fungi in North America through the import of ornamental trees.


Congratulations to Zach on NEAS & ASPT awards

Trebouxia and Niebla sample from Western North AmericaDOUBLE congratulations to Zach Muscavitch, co-advised by Drs. Louise Lewis and B. Goffinet for his recent grant of $500 from the Northeast Algal Society to explore the hidden diversity of the green algal genus Trebouxia lichenized with fungi of the Ramalinaceae, AND of $1,200 from the American Society of Plant Taxonomists to explore specificity in the association between the species of fungal symbiont (i.e., Niebla s. lat.) and its algal partner of the genus Trebouxia .

New publication on liverwort organellar genomes

Graphical abstract Dong S., S. Zhang, L. Zhang, H. Wu, B. Goffinet & Y. Liu. 2021. Plastid genomes and phylogenomics of the early land plant liverworts (Marchantiophyta): conserved genome structure and highest plastid substitution rates among three genetic compartments. Molecular Phylogenetics and Evolution 161: 107171.  pdf  Google Scholar.


  • We newly generated 42 complete liverwort plastomes spreading 13 out of 15 liverwort orders.This study confirmed the conserved structural evolution of liverwort plastomes despite characterization of two structural variants in simple thalloid liverworts, including one newly reported structural variant of Pallavicinia lyellii.
  • Our plastid phylogenomic reconstruction cemented the backbone phylogeny of liverwort and consistently supported the sister relationship of Ptilidium with Porellales.
  • In liverworts, plastid protein-coding genes have the highest substitution rates, they are on average 1.5-fold, 15-fold that of their nuclear, and mitochondrial counterparts.

Storrs L. Olson supporter of bryology at UCONN passed away

Storrs L. Olson and B. Goffinet examining Dillenius' 1741 book "History Muscorum"
Storrs L. Olson and B. Goffinet examining Dillenius’ 1741 book “History Muscorum”

Storrs L. Olson, an international renowned ornithologist and emeritus curator of birds at The National Museum of Natural History, Smithsonian Institution, passed away on January 20, 2020 in Fredericksburg, VA. Storrs Olson was also a passionate bryologist, inspired by a bryology course taught by Ruth Breen (author of the Mosses of Florida, 1963, University of Florida Press Gainesville) at Florida State University.

Storrs had acquired a comprehensive library of bryological literature that included one of 250 copies of John Dillenius’ 1741 Historia Muscorum, Hedwig’s 1801 Species Muscorum Frondosorum and Schwägrichen’s 1830 Species Muscorum Frondosorum.

In 2008, Storrs donated his entire library to the University of Connecticut in support of bryological research, and the collection of books and reprints is housed in the library of the Biodiversity Research Collection as the Storrs L. Olson bryological library. Through financial support from Storrs, his mother and various donors, the library continues to grow, and currently holds close to 1800 publications.

We remain grateful for his support. Our sincere condolences to his family. Obituary

New publication on mosses: Fontinalis genome

Fontinalis antipyreticaYu J., L. Li, S. Wang, S. Dong, Z. Chen, N. Patel, B. Goffinet, H. Chen, H. Liu & Y. Liu. 2021. Draft genome of the aquatic moss Fontinalis antipyretica (Fontinalaceae, Bryophyta). Gigabyte (online November 2020). pdf

Abstract readMosses comprise one of three lineages forming a sister group to extant vascular plants. Having emerged from an early split in the diversification of embryophytes, mosses may offer complementary insights into the evolution of traits following the transition to, and colonization of, land. Here, we report the draft nuclear genome of Fontinalis antipyretica  (Fontinalaceae, Hypnales), a charismatic aquatic moss that is widespread in temperate regions of the Northern Hemisphere. We sequenced and de novo-assembled its genome using the 10X Genomics method. The genome comprises 385.2 Mbp, with a scaffold N50 of 45.8 Kbp. The assembly captured 87.2% of the 430 genes in the BUSCO Viridiplantae odb10 dataset. The newly generated F. antipyretica genome is the third moss genome, and the second seedless aquatic plant genome, to be sequenced and assembled to date.


New publications: “first” exploration of Diego Ramirez (subantarctic Chile)

view from stationOutcomes of our expedition of 2018 to the subantarctic Chilean island of Diego Ramirez have now been published in this issue of Anales del Instituto de la Patagonia.

Mackenzie R., O. Vidal, S. Rosenfeld, T. Contador, O. Barroso, B. Goffinet, F. Massardo, P. Arce-Johnson & R. Rozzi. 2020. Flora vascular y ausencia de especies exóticas en el archipiélago Diego Ramírez (56°31’S), Chile. Anales del Instituto de la Patagonia 48(3): 138–148. pdf

Goffinet B., J.J. Engel, M. von Konrat, R. MacKenzie, T. Contador, S. Rosenfeld, O. Barroso & R. Rozzi. 2020. Bryophyte records from Isla Gonzalo, Diego Ramirez Islands, Americas’ deep southern ocean archipelago. Anales del Instituto de la Patagonia 48(3): 127–138. pdf

Marambio J., S. Rosenfeld, J. P. Rodríguez, F. Méndez, T. Contador, R. Mackenzie, B. Goffinet, R. Rozzi & A. Mansilla. 2020. Siete nuevos registros de macroalgas para el archipiélago Diego Ramírez (56°31’S): el valor del nuevo parque marino como sumidero de carbono y conservación de la biodiversidad subantártica. Anales del Instituto de la Patagonia 48(3): 99–111. pdf

Contador T., J. Rendoll, R. Mackenzie, S. Rosenfeld, O. Barroso, R. Rozzi, B. Goffinet, J. Kennedy & P. Convey, P. 2020. Comunidades de Invertebrados Terrestres en el Archipiélago Diego Ramírez (56°, 31’s) y sus Afinidades con las Islas Sub-Antárticas del Océano Austral. Anales del Instituto de la Patagonia 48(3): 83–98. pdf

Rozzi R., R.D. Credo, T. Contador, E. Schüttler, S. Rosenfeld, R. MacKenzie, O. Barroso, E.A. Silva-Rodríguez, X. Álvarez Bustos, A. Silva, I. Ramírez, J. Mella, J. Herreros, J. Rendoll-Cárcamo, J. Marambio, J. Ojeda, F. Méndez, K.P. Moses, J. Kennedy, S. Russell, B. Goffinet, F. Aguirre, L. Sánchez-Jardón, E. Barros, R.A. Vásquez, E. Poulin, F. Squeo, J.J. Armesto, A. Mansilla & F. Massardo. 2020. Extensión de la Red de Estudios Socio-Ecológicos a Largo Plazo (LTSER-Chile) en la Reserva de la Biosfera Cabo de Hornos y el Nuevo Parque Marino Islas Diego Ramírez-Paso Drake (Extension of the long term socio-ecological research network (LTSER-Chile) in the Cape Horn Biosphere Reserve and the new marine park Diego Ramirez Islands Drake passage). Anales del Instituto de la Patagonia 48(3): 45–81. pdf

New publication on bryophytes

Dong S., H.-L. Li, B. Goffinet & Y. Liu. 2021. Exploring the impact of RNA editing on mitochondrial phylogenetic analyses in liverworts, an early land plant lineage. Journal of Systematics and Evolution in press.
Abstract: Plant mitochondrial protein-coding genes are slow evolving, and therefore are less subject to substitution saturation, and therefore perhaps more suitable for resolving deep relationships of high taxonomic categories. Plant mitochondrial genes hold, however, hundreds of RNA editing sites, involving mostly non-synonymous substitutions in the first and second codon positions, which has been reported to affect phylogenetic reconstructions. We have previously identified ca. 4700 mitochondrial RNA editing sites within a group of liverworts representing the ordinal diversity of liverworts, allowing us to critically evaluate the impacts of RNA editing sites on phylogenetic reconstructions in liverworts. Our phylogenetic inferences are mostly congruent on topology inferred from the original mitochondrial gene dataset, dataset with RNA editing sites corrected, and dataset with RNA editing sites excluded. The RNA editing site excluded dataset recovered a topology identical to that of the RNA editing site corrected dataset, supporting the sister relationship of Ptilidium and Jungermanniales, whereas the original dataset supported the sister relationship of Ptilidium and Jungermanniidae. The controversial placements of Ptilidium coulbe explained by site-wise log-likelihood analysis, as the majority of liverwort RNA editing sites supported the sister relationship of Ptilidium and Jungermanniidae, hence the correction or exclusion of the RNA editing sites changethe tree topology and supported the sister relationship of Ptilidium and Jungermanniales. Our study shows that RNA editing sites potentially impact phylogenetic analyses, suggesting that both genome and transcriptome derived data should be used with caution for phylogenetic reconstruction with genes hosting vast numbers of RNA editing sites such as plant organellar genes.