Goffinet, B. & T. Pócs. 2025. Reporting Rhachithecium perpusillum H. Rob. new to Uganda. In Ellis M. Alataş, Sk. N. Ali, D. J. Alvarez, A. M. Aponte Rojas e, J. J. Atwood f, N. Batan g, H. Bednarek-Ochyra, M. J. Cano, Ž. L. Cimerman, T. Colotti, M. J. F. Costa, E. Enkhjargal, H. Erata, P. Erzberger, B. Espinoza-Prieto, M. Evangelista-dos-Santos, T. Ezer, L. Fatková, V. E. Fedosov ,R. Gabriel, L. Gil, B. Goffinet, A. Graulich, Yu-Chwen Hsu, T. Kiebacher, J. M. Kocjan, S. S. Krajšek, S. Kubešová, J. Kučera, J. Larraín, E. Lavocat-Bernard, Y. Mamontov, P. M. Mir-Rosselló, C. P. Morales, R. Natcheva, M. A. Negritto, Juan D. Ospino-C, M. Paul, B. Papp, T. Pócs, E. Rodríguez-Quiel, M. Rogošić, K. Ramírez-Roncallo, A. A. Roque, A. D. Sabovljević, M. S. Sabovljević, A. Schäfer-Verwimp, V. Šegota, C. Sérgio, P. H. Sette-de-Souza, D. Singh, P. Širka, A. Sotiaux, G. M. Suárez, D. Ya. Tubanova, Kuei-Yu Yao & G. Winter. New national and regional bryophyte records, 79. Journal of Bryology 46: 295–318.

Coca L.F., H.T. Lumbsch, J.A. Mercado-Díaz, T. Widhelm, B. Goffinet, P. Kirika & R. Lücking. 2025. Diversity, phylogeny, and historical biogeography of the genus Coccocarpia (lichenized Ascomycota: Peltigerales) in the tropics. Molecular Phylogenetics and Evolution 206: 108312. pdf  Google Scholar

Abstract reads Coccocarpia Pers. currently comprises 28 mostly broadly distributed tropical species of fungi associated with cyanobacteria. Three of these taxa, C. erythroxyli, C. palmicola, and C. pellita, are presumably pantropical to subcosmopolitan, with broad morphological variation across their range. This study provides the first global phylogeny of the genus, to test current species concepts and infer distribution patterns, based on samples from Colombia, Puerto Rico, Gabon, Kenya, Thailand, Fiji, and Hawaii. We also estimate divergence times within the clade and provide a first reconstruction of its biogeographic history. Based on phylogenetic reconstructions inferred from maximum likelihood and Bayesian approaches of four molecular markers (mtSSU, nuLSU, ITS, RPB2), Coccocarpia was recovered as monophyletic. However, the currently accepted taxa are largely polyphyletic entities and the underlying diversity in this genus is much higher than currently understood. Different methods for species delimitation boundaries came to agree on a scenario involving more than 150 species in the available, albeit still small, dataset. This suggests that with broader sampling, Coccocarpia may indeed represent a hyper-diverse genus, potentially containing over 200 species. The phylogeny is geographically structured: one clade is exclusive to the Paleotropics, one to the Neotropics, and one is pantropical. Coccocarpia likely emerged during the Late Cretaceous (90 ± 10 Mya) in the tropical regions of Australasia-Oceania, initially colonizing Oceania, and Asia and subsequently the Neotropics. The three main clades diverged between the Late Cretaceous and the Paleocene, with significant diversification in the Oligocene, during which the neotropical clade gave rise to morphological novelties, including the epiphylla and stellata clades.

Kirbis A., N. Rahmatpour, S. Dong, J. Yu, L. Waser, H. Huang, N. van Gessel, M. Waller, R. Reski, D. Lang, S. A. Rensing, E. M. Temsch, J. L. Wegrzyn, B. Goffinet, Y. Liu & P. Szövényi. 2025. Comparative analysis of the Funaria hygrometrica genome suggests greater collinearity in mosses than in seed plants. Communication Biology 8: 330. pdf

Abstract reads: Mosses, the largest lineage of seed-free plants, have smaller and less variable genome sizes than flowering plants. Nevertheless, whether this difference results from divergent genome dynamics is poorly known. Here, we use newly generated chromosome-scale genome assemblies for Funaria hygrometrica and comparative analysis with other moss and seed plant genomes to investigate moss genome dynamics. Although someaspects of moss genome dynamics are seed plant-like, such as the mechanism of genome size change and de novo gain/loss of genes, moss genomes retain higher synteny, and collinearity over evolutionary time than seed plant genomes. Furthermore, transposable elements and genes are more evenly distributed along chromosomes in mosses than in seed plants, a feature shared with other sequenced seed-free plant genomes. Overall, our findings support the hypothesis that large-scale genome structure and dynamics of mosses and seed plants differ. In particular, our data suggest a lower rate of gene order reshuffling along chromosomes in mosses compared to seed plants.Wespeculate that such lower rate of structural genomic variation and unique chromosome structure in mosses may contribute to their relatively smaller and less variable genome sizes.

Crystal Zhu, Zach Muscavitch and Bernard were invited to join the multidisciplinary expedition to parts of the Cape Horn Biosphere Reserve.

Crystal and Bernard focused on various groups of Peltigerales (lichens) whereas Zach explored the whole diversity. Together we came back with ± 700 collections, which will be added to the CONN herbarium, with duplicates in Chile.

Amazing fieldwork. We are grateful to our Chilean hosts and to all who supported Crystal’s and Zach’s participation by acquiring lithographs of Sowerby. Hope to go back soon…

Former postdoc Antoine Simon and honors student Dinah Parker led a study now published on photomorphs of New World Peltigerales:

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

The list is being and will continued to be updated on this site.

Abstract reads:  The checklist includes a listing of the genera and species of North American Bryophyta thought to occur in the continental United States and Canada. The floras of Mexico, Hawaii and Greenland are not included. The current list recognizes 1565 species, 12 subspecies, 34 varieties and one form (for a total of 1612 taxa) in 366 genera and 100 families. As a preface to the list, a systematic arrangement of the families and included genera for North America is presented. Many changes from the previous checklist are documented via footnotes that provide references to where changes were made. Only synonymy since the previous checklist is included. Twenty nomenclatural changes are made. These include 19 new combinations: Bryum brassicoides (≡ Gemmabryum brassicoides), B. pacificum (≡ Ptychostomum pacificum), B. torenii (≡ Imbribryum torenii), B. vinosum (≡ Gemmabryum vinosum), Chionoloma maragniphyllum (≡ Oxystegus maragniphyllus), Lescuraea tribulosa (≡ Pseudoleskea tribulosa), Pterygoneurum ×kieneri (≡ P. subsessile var. kieneri Habeeb), Pylaidiadelpha canadensis (≡ Brotherella canadensis), Streblotrichum convolutum var. eustegium (≡ Barbula eustegia), Streblotrichum convolutum var. gallinula (≡ Barbula convoluta var. gallinula), Voitia angustata (≡ Splachnum angustatum), V. mnioides (≡ Splachnum mnioides), V. pallida (≡ Tetraplodon pallidus), V. paradoxa (≡ Splachnum paradoxum), V. urceolata (≡ Splachnum urceolatum), Warnstorfia badia (≡ Hypnum badium), W. straminea (≡ Hypnum stramineum), W. straminea var. patens (Lindb.) (≡ Amblystegium stramineum var. patens), W. wickesiae (≡ Calliergon wickesiae). A new order is also introduced: Rhizogemmales W.R.Buck & Goffinet (≡ Rhizogemmaceae Bonfim Santos, Siebel & Fedosov).

Goffinet, B. 2024. Reporting Rutenbergia madagassa Geheeb & Hampe new to the Comoros. In Ellis L.T., O.M. Afonina, M. Alataş, H.B. M. Alia, J. Alvarez, A.M. Aponte Rojas, J.J. Atwood, G. Bacilliere, N. Batan, V. Biberdžić, M.A. Bruggeman-Nannenga, L.V. Campos, M.J. Cano, L.F. Coca, I.V. Czernyadjeva, S. de Faria Lopes, Q. Dejonghe, S. Dragićević, H. Erata, B. Espinoza-Prieto, P. Erzberger, T. Ezer, L.L. Forrest, B. Goffinet, O.A. Gonçalves, A. Graulich, V. Hugonnot, S. Huttunen, M.S. Ignatov, E.A. Ignatova, J.A. Jiménez, S. Kumara, I. Kuusisto, E. Yu Kuzminac, D.G. Longt, X-Y. Ma, A.S. Maciel-Silva, C.N. Manju, B. Mufeed, F. Müller, M.B. Nosova, R. Ochyra, M. F. Oliveira, M.S. Özkaya, F. Pépin, V. Plášek, M. Puglisi, C. Reeb, R. Romanov, M.S. Sajitha, T. Saha, P.O. Santos, C.Shakira, Y.-M. Shu, J. B. Silvaa, D. Singh, G.M. Suáre, N. Taşçi, M. Tossou, D. Ya. Tubanova, J. Uribe-M, A. Schäfer-Verwimp, P.M. Vineesha, R. Virtanen, Y.-H. Wu & T.-X. Zheng. 2024. New national and regional bryophyte records, 76. Journal of Bryology 46: 51–74. pdf

Vuruputoor V.S., A. Starovoitov, Y. Cai, Y. Liu, N. Rahmatpour, T. Hedderson, N. Wilding, J.L. Wegrzyn & B. Goffinet. Crossroads of assembling a moss genome: navigating contaminants and horizontal gene transfer in the moss Physcomitrellopsis africana. G3: Genes, Genomes, Genetics 14(7): jkae104. pdf  Google Scholar

Abstract reads:  The first chromosome-scale reference genome of the rare narrow-endemic African moss Physcomitrellopsis africana (P. africana) is presented here. Assembled from 73 × Oxford Nanopore Technologies (ONT) long reads and 163 × Beijing Genomics Institute (BGI)-seq short reads, the 414 Mb reference comprises 26 chromosomes and 22,925 protein-coding genes [Benchmarking Universal Single- Copy Ortholog (BUSCO) scores: C:94.8% (D:13.9%)]. This genome holds 2 genes that withstood rigorous filtration of microbial contaminants, have no homolog in other land plants, and are thus interpreted as resulting from 2 unique horizontal gene transfers (HGTs) from microbes. Further, P. africana shares 176 of the 273 published HGT candidates identified in Physcomitrium patens (P. patens), but lacks 98 of these, highlighting that perhaps as many as 91 genes were acquired in P. patens in the last 40 million years following its divergence from its common ancestor with P. africana. These observations suggest rather continuous gene gains via HGT followed by potential losses during the diversification of the Funariaceae. Our findings showcase both dynamic flux in plant HGTs over evolutionarily “short” timescales, alongside enduring impacts of successful integrations, like those still functionally maintained in extant P. africana. Furthermore, this study describes the informatic processes employed to distinguish contaminants from candidate HGT events. 

Zach has received a 2024 Evolutionary, Ecological, and Conservation Genomics (EECG) Research Award ($6,000) from the American Genetics Association for his project “Unveiling the mysteries of fog lichens: Phylogenomic insights into the phenotypic diversity of a niche-specific radiation. Congratulations!

Crystal (Zhu) was awarded a Summer Undergraduate Research Fellowship from the UConn Office of Undergraduate Research for her project “More than meets the eye: Unveiling the diversity of lichen-forming fungal species in Chile using DNA barcoding”.  The project focuses on Lobarioideae (Peltigerales) and primarily the genus Pseudocyphellaria. The award consists of a stipend and funds to cover research expenses. Congratulations. 

The SURF program is jointly sponsored by the Office of Undergraduate Research, the Provost’s Office, the Office of the Vice President for Research, the Honors Program, donors to the university, and the Deans of the Schools and Colleges.

Crystal will be traveling to subantarctic Chile in May to see the various species in the Nothofagus forests on Navarino Island and near Punta Arenas.