Author: Bernard Goffinet

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.

Poster:

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.

New publication on HGT from fungi to mosses

Sun G., S. Bai, Y. Guan, Q. Wang, S. Wang, Y. Liu, H. Liu, B. Goffinet, Y. Zhou, M. Paoletti, X. Hu, F. Haas, N. Fernendez-Pozo, A. Czyrt, H. Sun, S. Rensing & J. Huang. 2020. Are fungi-derived genomic regions related to antagonism toward fungi in mosses? New Phytologist 228: 1169–1175. pdf

In this article the authors “report two genomic regions in the nuclear genome of the moss Physcomitrium patens, previously Physcomitrella patens (Medina et al., 2019; Rensing et al., 2020), that contain mostly fungi-specific genes and mobile genetic elements. These two regions were identified in our genome screening for horizontally acquired genes in P. patens. Available evidence indicates that these fungi-specific genes are likely involved in the interaction between mosses and fungi. We discuss how these fungi-specific genes might have contributed to the defense against fungal and other microbial pathogens, as well as the loss of MFAs in mosses.”

On-line article on Sub-Antarctic bryophytes and lichens

View of region of Aysen, Sub-Antarctic ChileIntroduction to article “Los pioneros vegetales del Estrecho de Magallanes” published on-line by the NGO Laderasur reads (google translation): Thousands of years ago, the Strait of Magellan was not what we know now, but rather an ice field. Thanks to the deglaciation, large lakes originated and the soils were covered with the pioneering organisms of the place: liquids, bryophytes and fungi. In this article, the scientists Laura Sánchez-Jardón, Bernard Goffinet, Ricardo Rozzi and the photographer Felipe Soza describe some representatives of these pioneers from the subantarctic region of Chile, relating them to the process of human colonization, recounting three successive discoveries that were made in the Strait of Magellan.

 

Visit article for nice pictures! Below is an English translation:

Thousands of years ago, the Strait of Magellan was not what we know now, but rather an ice field. Thanks to the deglaciation, large lakes originated and the soils were covered with the pioneering organisms of the place: liquids, bryophytes and fungi. In this article, scientists Laura Sánchez-Jardón, Bernard Goffinet, Ricardo Rozzi and photographer Felipe Soza describe some of the representatives of these pioneers from the region where they were made in the Strait of Magellan.

 

Twenty thousand years ago the Strait of Magellan was not such, but a vast field of ice. During the deglaciation started some sixteen thousand years ago, the retreat of the ice in its central part and surrounding areas gave rise to large lakes and terrestrial ecosystems whose rocks and soils were progressively covered by pioneering organisms: lichens, bryophytes and fungi.

 

This first discovery of the Strait of Magellan, associated with the melting of the ice cover, was producing unique processes of ecological succession led by small colonizing organisms, plant pioneers that generated the first ecosystems with a unique biota whose exuberance at the “end of the world” it is greater than in any other region of the planet.

 

When Hernando de Magallanes arrived at the southern tip of America five hundred years ago, there was a second discovery of the biota of the strait that today bears his name. The promise of riches offered by the New World, Terra Incognita, motivated scientists to explore the region, who were surprised by the abundance and diversity of lichens, mosses and fungi that grew on the ground and the trunks of subantarctic forests.

 

Some of these unique species are Ganoderma australe, which grows on coigües, lengas and ñires and is striking for its tongue or ear shape; in fact, they are known as “stick ears”; Cortinarius magellanicus, whose surprising color (bright purple) awakens the imaginations of scientists, tourists, and various Magellan co-inhabitants; some are even associated with algae and form lichens: Peltigera patagonica, one of the few species that appears on the tree line in the upper part of the mountain range and whose endemic distribution in the subantarctic region makes this species characteristic of it; Protousnea magellanica or “old man’s beard”, as this lichen is commonly called, abundant and widely distributed in subantarctic forests; along with Pseudocyphellaria berberina, they are endemic to the Southern Cone of South America.

 

In February 1834, Charles Darwin continued his navigation through the strait towards Puerto del Hambre aboard the Beagle, exploring the Shoal cove sector along the way. The British noted that this landscape represents a transition zone between aridity and humidity, between «Patagonia and Tierra del Fuego; many plants from these regions grow here ». The next day they arrived in Puerto del Hambre and on February 6 of that year, the young naturalist made his memorable ascent to Mount Tarn, recording in his Diary: I found a second species in other beech species in Chile; and Dr. Hooker informs me that a third species has recently been discovered in Van Diemen’s Land [Tasmania]. How unique is this relationship between parasitic fungi and the trees on which they grow, in the farthest parts of the world! In Tierra del Fuego, the fungus in its smooth and mature state is collected in large quantities by women and children, and is eaten without cooking.

 

The young naturalist was referring here to the digueñes or dihueñes (Cyttaria spp.), Also recognized in other scientific expeditions by the southern hemisphere during the 19th century. These endemic fungi, metaphorically called “Indian bread”, that grew on the trunks and branches of the coigüe and lenga, both trees of the dominant Nothofagus genus in the region, were already discovered by the first human populations that reached the strait and other areas from the Magellan subantarctic ecoregion, who found in them a unique food source.

 

Indeed, little by little, the extreme richness of fungi was revealed, as well as the exceptional diversity of small plants in the sub-Antarctic region of the Strait of Magellan: mosses, liverworts and hornworts, which together are called bryophytes. These small organisms facilitated the recolonization of life once the ice was removed in the Strait of Magellan, sheltering in the neighboring territories the original peoples that arrived more than ten thousand years ago.

 

Just twenty years ago, a third discovery of the Magallanes region south of the strait, in the Cape Horn archipelagos, happened fortuitously, leading to the identification of this sub-Antarctic region as a world center of diversity of bryophytes and lichens. The unique biodiversity that inhabits these archipelagos is of great value for life on the planet and we must jointly take care of this biota and ecosystems that contribute to planetary health.

 

Among these species are the Dendroligotrichum dendroides or “pinito moss”, with the appearance of a miniature tree – up to 20 centimeters the largest -; Bartramia mossmaniana; Sphagnum magellanicum, an endemic species of the southern hemisphere that proliferates locally on accumulations of dead organic matter, forming a particular type of ecosystem called «peatland», extraordinarily important in carbon fixation and in the retention of water and nutrients; in especially humid and shady places are also found hornwort like Phaeomegaceros chiloensis.

 

These miniature forests of fungi, lichens and bryophytes, in addition to all the associated fauna of invertebrates, have accompanied the three discoveries of the Strait of Magellan. From an ethical point of view, they can be considered as Magellanic co-inhabitants: literally, they have shared the habitats of the strait with humans since the first settlement and have had a leading role in their food, health, fire source, water, culture and , lately, in the scientific vanguard. From the south of the world, the knowledge of the great Magellanic flora will contribute to its conservation and the sustainability of the planet in the scenario of global socio-environmental change. About the authors: Laura Sanchez-Jardón, is a Doctor in ecology and environment at the Complutense University of Madrid; Ricardo Rozzi is a Doctor in Ecology and a Master in Philosophy from the University of Connecticut; Bernard Goffinet is a Doctor in Botany University of Connecticut and Jorge Felipe Soza Soza (Instagram: @felipesozaphotography)