Dong S., J.-Y. Xue, S. Zhang, L. Zhang, H. Wu, Z. Chen, B. Goffinet & Yang Liu. 2018. Complete mitochondrial genome sequence of Anthoceros angustus: conservative evolution of mitogenome in hornworts. The Bryologist 121: 14–22. pdf

Abstract reads: The architecture and composition of the mitochondrial genome of bryophytes is currently considered much more stable and invariant than that of vascular plants. For example, liverworts and mosses appear to have nearly static mitochondrial genomes, whereas neither of two vascular plant mitogenomes sequenced to date share the same gene order. By contrast, the two available mitogenomes of hornworts, Nothoceros aenigmaticus and Phaeoceros laevis, show high consistency in gene content but differ in their gene order. To explore the patterns of hornwort mitogenome structure at a broader phylogenetic breadth and provide insights into plant mitogenome evolution, we assembled the complete mitochondrial genome from a third hornwort species, Anthoceros angustus Steph. Its mitogenome comprises 242,410 base pairs, and encodes 21 protein coding genes, three rRNA genes and 20 tRNA genes, with 38 introns disrupting 16 protein-coding genes, including three newly described introns, making it the most intron-rich plant mitochondrial genome determined to date. A total of ten putatively pseudogenized protein coding genes were found in Anthoceros; eight of them are shared with Nothoceros and Phaeoceros. The genic composition of the Anthoceros mitogenome differs from that of the other two hornworts by only one or two gene insertions or losses. The gene order in the Anthoceros mtDNA differs from that in Phaeoceros and Nothoceros by only one and three events of inversion or translocations, respectively. Overall, hornworts appear to have kept a stable mt genome structure, which could have characterized early land plant mt genome evolution.

An assessment of the diversity and relationships of a group of lichenized basidiomycetes, has been completed and resulted in a global circumscription of the Lepidostromatales: Liu D., B. Goffinet, D. Ertz, A. De Kesel, Z.G. Qian, X.Y. Wang, H.X. Shi, Y.Y. Zhang, J.W. Li, X. Ye, J.S. Hur & L.S. Wang. 2017 (2018). Circumscription and phylogeny of the Lepidostromatales (lichenized Basidiomycota) following discovery of new species from China and Africa. Mycologia 109: 730–748. pdf.

Abstract reads: Based on an exhaustive sampling of all known Lepidostromatales, a lineage of clavarioid lichen-forming basidiomycetes, we assess (i) the phylogenetic affinities of the six Chinese species currently accommodated in Multiclavula(Cantharellales) based on inferences from the 18S and 28S subunits of the nuclear ribosomal DNA repeat and (ii) the phylogenetic structure among Chinese populations of Lepidostromatales, based on the nuc rDNA ITS1-5.8S-ITS2 (ITS) regions. Multiclavula fossicola and M. sinensis belong to the Lepidostromatales, and are transferred to Sulzbacheromyces. Chinese reports of M. clara and M. vernalis belong to species of Lepidostromatales and specimens identified as M. mucida belong to the non-lichenized genus Clavaria. Hence, evidence of Multiclavula occurring in China is lacking. Similarly, L. calocerum is excluded from the Chinese flora. The recently described L. asianum should be regarded as conspecific with S. sinensis. Three new species of Sulzbacheromyces are described: S. bicolor and S. yunnanensis from China, and S. miomboensis from the Democratic Republic of Congo. Consequently, Sulzbacheromyces is new to Asia and Africa. A world-wide key to the species of Lepidostromatales is provided.

The recent exploration of the bryophyte and lichen flora of the Diego Ramirez archipelago South of Cape Horn in subantarctic Chile contributed to the development of a proposal for the extension of the Cape Horn Biosphere Reserve, an effort led by Dr. Ricardo Rozzi, a former student in EEB and now Professor at the University of North Texas and the Universidad de Magallanes (Chile). Click on the image for access to the on-line publication.

The bryophyte collections from Gonzalo Island, the first from this island about 100 km SW of Cape Horn, are being studied and the inventory of the tiny, low elevation and treeless island will be shared through a co-authored publication involving Dr. J. Engel and M. von Konrat from the Field Museum and of course our Chilean colleagues. Unicates will be deposited in the herbarium of the University of Concepcion (Chile) and duplicates in CONN and F.

Medina R., M. Johnson, Y. Liu, N. Wilding, T. Hedderson, N. Wickett & B. Goffinet. 2018. Evolutionary dynamism in bryophytes: Phylogenomic inferences confirm rapid radiation in the family Funariaceae. Molecular Phylogenetics and Evolution 120: 240–247. pdf

Abstract reads: Rapid diversifications of plants are primarily documented and studied in angiosperms, which are perceived as evolutionarily dynamic. Recent studies have, however, revealed that bryophytes have also undergone periods of rapid radiation. The speciose family Funariaceae, including the model taxon Physcomitrella patens, is one such lineage. Here, we infer relationships among major lineages within the Entosthodon-Physcomitrium complex from virtually complete organellar exomes (i.e., 123 genes) obtained through high throughput sequencing of genomic libraries enriched in these loci via targeted locus capture. Based on these extensive exonic data we (1) reconstructed a robust backbone topology of the Funariaceae, (2) confirmed the monophyly of Funariaand the polyphyly of Entosthodon, Physcomitrella, and Physcomitrium, and (3) argue for the occurrence of a rapid radiation within the Entosthodon-Physcomitrium complex that began 28 mya and gave rise more than half of the species diversity of the family. This diversification may have been triggered by a whole genome duplication and coincides with global Eocene cooling that continued through the Oligocene and Miocene. The Funariaceae join a growing list of bryophyte lineages whose history is marked by at least one burst of diversification, and our study thereby strengthens the view that bryophytes are evolutionarily dynamic lineages and that patterns and processes characterizing the evolution of angiosperms may be universal among land plants.

Lücking R., B. Moncada, B. McCune, E. Farkas, B. Goffinet, D. Parker, J. L. Chaves, L. Lőkös, P. R. Nelson, T. Spribille, S. Stenroos, T. Wheeler, A. Yanez-Ayabaca, K. Dillman, O. T. Gockman, T. Goward, J. Hollinger, E. A. Tripp, J. Villella, W. R. Álvaro-Alba, C. Julio Arango, M. E. S. Cáceres, L. Fernando Coca, C. Printzen, C. Rodríguez, K. Scharnagl, R. Rozzi, E. Soto-Medina & L. S. Yakovchenko. 2017. Pseudocyphellaria crocata (Ascomycota: Lobariaceae) in the Americas reveals to be ten species, and none of them is Pseudocyphellaria crocata. The Bryologist 120: 441–500. pdf

Abstract reads: We provide a phylogenetic revision of the Pseudocyphellaria crocata complex in the Americas. Specimens traditionally identified as P. crocata, based on their cyanobacterial photobiont, yellow pseudocyphellae, at least partially white medulla, and yellow soralia or soralia-like structures, are shown to represent 13 distinct species, forming a monophyletic group divided into four large clades, three comprising one species each and one containing eight species, plus two taxa for which no molecular data are available. Seven species correspond to what was previously recognized as P. crocata and one to P. dozyana, whereas a further one is identified as the sorediate counterpart of the usually apotheciate taxon P. lechleri and another as a pseudosorediate morph of the usually phyllidiate species P. neglecta. Surprisingly, none of the species represents P. crocata s.str., which must therefore be excluded from the American lichen biota. The 13 recognized species include three species new to science and three new combinations: P. citrina (Gyeln.) Lücking, Moncada & S.Stenroos, comb. nov. [bas.: Cyanisticta citrina Gyeln., nom. nov. pro Sticta citrina Pers. nom. illeg.], P. desfontainii (Delise) Vain., P. deyi Lücking, sp. nov., P. dozyana (Mont. & Bosch) D.J.Galloway, P. epiflavoides (Gyeln.) Lücking, Farkas & Lokös, comb. nov. [bas.: Cyanisticta epiflavoides Gyeln.], P. hawaiiensis H.Magn., P. hillii (C.W.Dodge) D.J.Galloway, P. holarctica McCune, Lücking & Moncada, sp. nov., P. lechleri (Müll. Arg.) Du Rietz, P. neglecta (Müll. Arg.) H.Magn., P. punctata Lendemer, Lücking & Moncada sp. nov., P. sandwicensis (Zahlbr.) Moncada & Lücking, comb. nov. [bas.: Sticta crocata f. sandwicensis Zahlbr.], and P. xanthosticta (Pers.) Moncada & Lücking. Based on sequenced specimens, a neotype is selected for P. citrina and epitypes for P. hawaiiensis, P. lechleri, P. sandwicensis and P. xanthosticta. A key to all sorediate or pseudosorediate species of this complex in the Americas is presented, and all species are described, discussed and illustrated. pdf

A further contribution from the team working on the genus of lichenized fungi Peltigera, revealing 22 species new to science in a clade comprising 29 species total!

Magain N., J. Miadlikowska, O. Mueller, M. Gajdeczka, C. Truong, A. Salamov, I. Grigoriev, I. Dubchak, B. Goffinet, E. Sérusiaux & F. Lutzoni.  Conserved genomic collinearity as a source of broadly applicable, fast evolving, markers to resolve species complexes: a case study using the lichen-forming genus Peltigera section Polydactylon. Molecular Phylogenetics and Evolution 117: 10–29. pdf

Abstract reads: Synteny can be maintained for certain genomic regions across broad phylogenetic groups. In these homologous genomic regions, sites that are under relaxed purifying selection, such as intergenic regions, could be used broadly as markers for population genetic and phylogenetic studies on species complexes. To explore the potential of this approach, we found 125 Collinear Orthologous Regions (COR) ranging from 1 to >10 kb across nine genomes representing the Lecanoromycetes and Eurotiomycetes (Pezizomycotina, Ascomycota). Twenty-six of these COR were found in all 24 eurotiomycete genomes surveyed for this study. Given the high abundance and availability of fungal genomes we believe this approach could be adopted for other large groups of fungi outside the Pezizomycotina. As a proof of concept, we selected three Collinear Orthologous Regions (COR1b, COR3, and COR16), based on synteny analyses of several genomes representing three classes of Ascomycota: Eurotiomycetes, Lecanoromycetes, and Lichinomycetes. COR16, for example, was found across these three classes of fungi. Here we compare the resolving power of these three new markers with five loci commonly used in phylogenetic studies of fungi, using section Polydactylon of the cyanolichen-forming genus Peltigera (Lecanoromycetes) – a clade with several challenging species complexes. Sequence data were subjected to three species discovery and two validating methods. COR markers substantially increased phylogenetic resolution and confidence, and highly contributed to species delimitation. The level of phylogenetic signal provided by each of the COR markers was higher than the commonly used fungal barcode ITS. High cryptic diversity was revealed by all methods. As redefined here, most species represent lineages that have relatively narrower, and more homogeneous biogeographical ranges than previously understood. The scabrosoid clade consists of ten species, seven of which are new. For the dolichorhizoid clade, twenty-two new species were discovered for a total of twenty-nine species in this clade.

Lily Lewis published the last paper from her dissertation as an invited paper in the Special November issue of the American Journal of Botany:

Lewis L.R., E.M. Biersma, S. Carey, K. Holzinger, S.F. McDaniel, R. Rozzi & B. Goffinet. 2017. Resolving the source region for the long-distance dispersal event that gave rise to the Magellanic sub-Antarctic endemic dung moss Tetraplodon fuegianus (Bryopsida: Splachnaceae). American Journal of Botany 104: 1651–1659. pdf

 

Abstract reads: 

PREMISE OF THE STUDY: American bipolar plant distributions characterize taxa at various taxonomic ranks but are most common in the bryophytes at infra-specifi c and infrageneric levels. A previous study on the bipolar disjunction in the dung moss genus Tetraplodon found that direct long-distance dispersal from North to South in the Miocene–Pleistocene accounted for the origin of the Southern American endemic Tetraplodon fuegianus , congruent with other molecular studies on bipolar bryophytes. The previous study, however, remained inconclusive regarding a specifi c northern hemisphere source region for the transequatorial dispersal event that gave rise to T. fuegianus .

METHODS: To estimate spatial genetic structure and phylogeographic relationships within the bipolar lineage of Tetraplodon , which includes T. fuegianus , we analyzed thousands of restriction-site-associated DNA (RADseq) loci and single nucleotide polymorphisms using Bayesian individual assignment and maximum likelihood and coalescent model based phylogenetic approaches.

KEY RESULTS: Northwestern North America is the most likely source of the recent ancestor to T. fuegianus.

CONCLUSIONS: Tetraplodon fuegianus , which marks the southernmost populations in the bipolar lineage of Tetraplodon , arose following a single long-distance dispersal event involving a T. mnioides lineage that is now rare in the northern hemisphere and potentially restricted to the Pacifi c Northwest of North America. Furthermore, gene fl ow between sympatric lineages of Tetraplodon mnioides in the northern hemisphere is limited, possibly due to high rates of selfi ng or reproductive isolation.

Antoine Simon, now a Ph.D. student at the University of Liège, Belgium, published his assembly and study of the structure of the mitochondrial genome in a lichen forming fungus: Simon, A., Y. Liu, E. Sérusiaux & B. Goffinet. 2017. Complete mitogenome sequence of Ricasolia amplissima (Lobariaceae) reveals extensive mitochondrial DNA rearrangement within the Peltigerales (lichenized ascomycetes). The Bryologist 120(3): 335–339. pdf Google Scholar

Abstract reads: The structure of mitochondrial genomes varies among non-lichenized fungi in terms of their genic and intronic content and genic order. Whether lichenized fungal mitogenomes are equally labile is unknown due to the paucity of available mitogenomes. We assembled the mitogenome of Ricasolia amplissima (Peltigerales, Lobariaceae), using massive parallel sequencing, and compared its structure to that of two species of Peltigera (Peltigeraceae). The mitochondrial genome of R. amplissima comprised 82,333 bp, with a 29.8% G+C content, and holds 15 unique protein-coding genes, 29 tRNA genes, two rRNA genes, and one non-coding RNA gene. Although the protein-coding gene content in the mitogenome of Peltigera and Ricasolia was identical, the relative gene order differed substantially, revealing that significant gene rearrangements also characterize the evolution of mitogenomes of lichenized ascomycetes at a relatively shallow phylogenetic depth, such as within the order Peltigerales.

 

Lily Lewis (formerly in our lab and now at the University of Florida) lead-authored a paper outlining needs of and for bryological research in the Arctic.  Lewis L.R., S.M. Ickert-Bond, E.M. Biersma, P. Convey, B. Goffinet, K. Hassel, H.J.D. Kruijer, C. La Farge, J. Metzgar, M. Stech, J.C. Villarreal & S.F. McDaniel. Future directions and priorities for Arctic bryophyte research. Arctic Science 3: 475–497. pdf (open) Google Scholar

Abstract reads: The development of evidence-based international strategies for the conservation and management of Arctic ecosystems in the face of climate change is hindered by critical knowledge gaps in Arctic floristic diversity and evolution. Particularly poorly studied are the bryophytes, which dominate the vegetation across vast areas of the Arctic and consequently play an important role in global biogeochemical cycles. Currently, much of what is known about Arctic floristic evolution is based on studies of vascular plants. Bryophytes, however, possess a number of features, such as poikilohydry, totipotency, several reproductive strategies, and the ability to disperse through microscopic diaspores, that may cause their responses to Arctic environments to differ from those of the vascular plants. Here we discuss several priority areas identified in the Arctic Council’s “Arctic Biodiversity Assessment” that are necessary to illuminate patterns of Arctic bryophyte evolution and diversity, including dispersal, glacial refugia, local adaptation, and ecological interactions with bryophyte- associated microbiomes. A survey of digitally available herbarium data archived in the largest online aggregate, GBIF, across the Arctic to boreal zones indicates that sampling coverage of mosses is heterogeneous and relatively sparse in the Arctic sensu stricto. A coordinated international effort across the Arctic will be necessary to address knowledge gaps in Arctic bryophyte diversity and evolution in the context of ongoing climate change.