Author: Bernard Goffinet

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.

New publication on mosses

Rahmatpour N., N.V. Perera, V. Singh, J.L. Wegrzyn & B. Goffinet. 2021. High gene space divergence contrasts with frozen vegetative architecture in the moss family Funariaceae. Molecular Phylogenetics and Evolution 154: (in press).pdf  Google scholar

Abstract reads: A new paradigm has slowly emerged regarding the diversification of bryophytes, with inferences from molecular data highlighting a dynamic evolution of their genome. However, comparative studies of expressed genes among closely related taxa is so far missing. Here we contrast the dimensions of the vegetative transcriptome of Funaria hygrometrica and Physcomitrium pyriforme against the genome of their relative, Physcomitrium (Physcomitrella) patens. These three species of Funariaceae share highly conserved vegetative bodies, and are partially sympatric, growing on mineral soil in mostly temperate regions. We analyzed the vegetative gametophytic transcriptome of F. hygrometrica and P. pyriforme and mapped short reads, transcripts, and proteins to the genome and gene space of P. patens. Only about half of the transcripts of F. hygrometrica map to their ortholog in P. patens, whereas at least 90% of those of P. pyriforme align to loci in P. patens. Such divergence is unexpected given the high morphological similarity of the gametophyte but reflects the estimated times of divergence of F. hygrometrica and P. pyriforme from P. patens, namely 55 and 20 mya, respectively. The newly sampled transcriptomes bear signatures of at least one, rather ancient, whole genome duplication (WGD), which may be shared with one reported for P. patens. The transcriptomes of F. hygrometrica and P. pyriforme reveal significant contractions or expansions of different gene families. While transcriptomes offer only an incomplete estimate of the gene space, the high number of transcripts obtained suggest a significant divergence in gene sequences, and gene number among the three species, indicative of a rather strong, dynamic genome evolution, shaped in part by whole, partial or localized genome duplication. The gene ontology of their specific and rapidly-evolving protein families, suggests that the evolution of the Funariaceae may have been driven by the diversification of metabolic genes that may optimize the adaptations to environmental conditions, a hypothesis well in line with ecological patterns in the genetic diversity and structure in seed plants.

New publication

Sánchez-Jordón, L., B. Goffinet & R. Rozzi. 2020. Los colonizadores vegetales del estrecho de Magallanes y su función indicadora en el cambio climático. Adumbrationes as Summae Editionem 94: 1–14. (with photographs by J.F. Soza & B. Goffinet). pdf

A miscellaneous work that combines a brief historical account of a series of three discoveries in the southern region extreme of South America, from the last ice age to the present day, with the taxonomic, morphological description and geographical distributions, functions in the ecosystem and utilities for man of 9 representative taxa of colonizing organisms of the Strait of Magellan, with their respective photographs.

(Spanish) Un trabajo misceláneo que combina un breve relato histórico de una serie de tres descubrimientos de la región meridional extrema de Sudamérica, desde la última edad glacial hasta nuestros días, con la descripción taxonómica, morfológica y distribuciones geográficas, funciones en el ecosistema y utilidades para el hombre de 9 taxones representativos de organismos colonizadores del estrecho de Magallanes, con sus respectivas fotografías.)

Lab in the news in Chile

The daily newspaper “Prensa Austral” published out of Punta Arenas, Sub-Antarctic Chile, published an article in its Sunday science section entitled “The ancient plants of the Strait of Magellan: key pieces for investigating climate change”, referring to some of the inventories of the regional bryophyte and lichen flora we have contributed to. See: Prensa_Austral

Below your feet: new exhibit on mosses

Picture of wall with moss picturesAn exhibit of nine high resolution images of mosses from New England and Chile, printed on 5 ft metal sheets is on display at Wilbur Cross, on the UCONN campus. The material was collected and photographed by Bernard Goffinet and Mark Smith using the Macropod technology.

While the exhibit can be visited now, it will formally open after the constraints imposed by the pandemic have eased.

This exhibit was designed and installed by Collin Harty and funded by the Connecticut State Museum of Natural History, with additional support from a National Science Foundation grant entitled Collaborative research: Diversity of the moss Physcomitrium pyriforme: significance of autopolyploidy within a phylogenomic and experimental framework, awarded to Bernard Goffinet in the Department of Ecology & Evolutionary Biology (No. DEB-1753811).

Special thanks are extended to the Universidad de Magallanes, Instituto de Ecología & Biodiversidad, and Omora Ethnobotanical Park for facilitating collection of species in Chile.

New publication on lichens

Graphical abstractComplementing the study of the diversity of lichenized fungi of the Lobariaceae, is the study by Lindgren et al. exploring the patterns in the association in the two symbionts.

Lindgren H., B. Moncada, R. Lücking, N. Magain, A. Simon, B. Goffinet, E. Sérusiaux, M.P. Nelsen, J. Mercado-Díaz, T. Widhelm & T. Lumbsch. 2020. Cophylogenetic patterns in algal symbionts correlate with repeated symbiont switches during diversification and geographic expansion of lichen-forming fungi in the genus Sticta (Ascomycota, Peltigeraceae). Molecular Phylogenetics and Evolution 150: (in press). pdf  Google scholar


Abstract reads: Species in the fungal genus Sticta form symbiotic associations primarily with either green algae or cyanobacteria, but tripartite associations or photosymbiodemes involving both types of photobionts occur in some species. Sticta is known to associate with green algae in the genus Symbiochloris. However, previous studies have shown that algae from other genera, such as Heveochlorella, may also be suitable partners for Sticta. We examined the diversity of green algal partners in the genus Sticta and assessed the patterns of association between the host fungus and its algal symbiont. We used multi-locus sequence data from multiple individuals collected in Australia, Cuba, Madagascar, Mauritius, New Zealand, Reunion and South America to infer phylogenies for fungal and algal partners and performed tests of congruence to assess coevolution between the partners. In addition, event-based methods were implemented to examine which cophylogenetic processes have led to the observed association patterns in Sticta and its green algal symbionts. Our results show that in addition to Symbiochloris, Sticta associates with green algae from the genera Chloroidium, Coccomyxa, Elliptochloris and Heveochlorella, the latter being the most common algal symbiont associated with Sticta in this study. Geography plays a strong role in shaping fungal-algal association patterns in Sticta as mycobionts associate with different algal lineages in different geographic locations. While fungal and algal phylogenies were mostly congruent, event-based methods did not find any evidence for cospeciation between the partners. Instead, the association patterns observed in Sticta and associated algae, were largely explained by other cophylogenetic events such as host-switches, losses of symbiont and failure of the symbiont to diverge with its host. Our results also show that tripartite associations with green algae evolved multiple times in Sticta.

The lab at Botany 2020

Logo for Botany 2020 conferenceThe annual meeting of the Botanical Society of America starts tomorrow. Initially planned to take place in Alaska, it was converted into a virtual conference. The lab is contributing (to) four presentations:

Regular talk:

Patel, N., R. Medina, M.G. Johnson & B. Goffinet. 2020. Autopolyploidy contributes to cryptic speciation in mosses. Abstract 738.

Lightning talks:

Williams L.,N. Patel, R. Medina, B. Goffinet& M. Johnson. 2020. Methods to delimit speciation and determine population parameters of the moss Physcomitrium pyriforme using target capture sequencing. Abstract 400.

Buckowing, K., Y. Liu, A.J. Shaw, B.Goffinet, N.J. Wickett & M.G. Johnson. 2020. Expanded phylotranscriptomic sampling reveals gene family expansion in pleurocarpous mosses. Abstract 523.


Anguloa J., M.G. Johnson, L. Pokorny, R. Medina, Y. Liu, B. Goffinet, A.J. Shaw & N.J. Wickett. 2020. Reconstructing the rapid radiation of pleurocarpous mosses using 802 nuclear genes. Abstract 605.