Kirbis A., M. Waller, M. Ricca, Z. Bont, A. Neubauer, B. Goffinet & P. Szövényi. 2020. The transcriptomic landscape of differential sporophyte development in two mosses, Physcomitrium (Physcomitrella) patens and Funaria hygrometrica. Frontiers in Plant Sciences11: 747. pdf

Abstract reads: Understanding the molecular basis of morphological shifts is a fundamental question of evolutionary biology. New morphologies may arise through the birth/death of genes (gene gain/loss) or by reutilizing existing gene sets. Yet, the relative contribution of these two processes to radical morphological shifts is still poorly understood. Here, we use the model system of two mosses, Funaria hygrometrica and Physcomitrium (Physcomitrella) patens, to investigate the molecular mechanisms underlying contrasting sporophyte architectures. We used comparative analysis of time-series expression data for four stages of sporophyte development in both species to address this question in detail. We found that large-scale differences in sporophytic architecture are mainly governed by orthologous (i.e., shared) genes frequently experiencing temporal gene expression shifts between the two species. While the absolute number of species-specific genes expressed during sporophyte development is somewhat smaller, we observed a significant increase of their proportion in preferentially sporophyte expressed genes, suggesting a fundamental role in the sporophyte phase. However, further functional studies are necessary to determine their contribution to diverging sporophyte morphologies. Our results add to the growing set of studies suggesting that radical changes in morphology may rely on the heterochronic expression of conserved regulators. 

We propose a new genus to accommodate some species of lichenized fungi from the New World, including the Southeastern United States, in a new genus, as part of the ongoing studies of the evolution of the Lobariaceae.

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. pdf

Abstract reads: The former family Lobariaceae, now included in Peltigeraceae as subfamily Lobarioideae, has undergone substantial changes in its generic classification in recent years, based on phylogenetic inferences highlighting the polyphyly of the speciose genera Lobaria, Pseudocyphellaria and Sticta. Here we introduce the new genus Emmanuelia, named in honor of Prof. Emmanuël Sérusiaux for his extensive work on the Peltigerales. Emmanuelia currently comprises twelve species. It is superficially similar to the lobarioid genus Ricasolia, but differs by its apothecia, rimmed by overarching and often crenulate to lobulate margins, with the parathecium (proper excipulum) and the amphithecium (thalline excipulum formed by the thallus cortex) apically separated and of a different structure. Also, ascospore dimensions and shape differ between the two genera, with the ascospores of Emmanuelia being longer and narrower. Molecular phylogenetic analyses using DNA nucleotide sequences of the internal transcribed spacer region (ITS) and the small subunit of mitochondrial ribosomal DNA (mtSSU) confirm that Emmanuelia belongs to the Lobaria s.lat. clade and forms a monophyletic group sister to the lineage consisting of Dendriscosticta, Lobariella and Yoshimuriella. None of the available generic names of lobarioid lichens can be applied to this group, and consequently a new name is proposed for this new genus, which is typified with E. ravenelii comb. nov. Eleven other species are transferred to Emmanuelia: E. americana comb. nov., E. conformis comb. nov., E. cuprea comb. nov., E. elaeodes comb. nov., E. erosa comb. nov., E. excisa comb. nov., E. lobulifera comb. nov., E. ornata comb. nov., E. patinifera comb. nov., E. pseudolivacea comb. nov. and E. tenuis comb. nov. The genus is represented in North America by three species, including E. lobulifera, which is resurrected from synonymy with E. (Lobaria) tenuis, a South American species, and E. ornata, whose populations were previously treated under E. (Lobaria) ravenelii.

 

Suspected to represent a new species, populations of Peltigera from Papua New Guinea are now recognized as P. serusiauxii: Magain N., B. Goffinet, A. Simon, J. Seelan Sathiya, I. Medeiros, F. Lutzoni & J. Miadlikowska. 2020. Peltigera serusiauxii, a new species in section Polydactylon from Papua New Guinea and Malaysia (Lecanoromycetes, Ascomycota). Plant and Fungal Systematics 65: 139–146. pdf

Abstract reads: Peltigera serusiauxii is proposed here as a new species from Papua New Guinea and Sabah, northern Borneo (Malaysia). The species belongs to the polydactyloid clade of section Polydactylon. Because of its large thalli with a glabrous upper surface, this species was previously identified as P. dolichorhiza, but it differs by its polydactylon-type lower surface and the high amount of dolichorrhizin. It appears to be a strict specialist in its association with Nostoc phylogroup IX throughout its known distribution. This is one of many undescribed species remaining to be formally described within the genus Peltigera,especially in Asia and Australasia.

 

It started with a search for bryophyte fragments in the feces of high Andean birds on Navarino island (see post) when Michael Robertson and Nicholas Russo (former EEB student now at UCLA) discovered tardigrades in the samples. Their observation are now published in Polar Biology.

Robertson M.W., N.J. Russo, S.J. McInnes, B. Goffinet & J.E. Jiménez. 2020. Potential dispersal of tardigrades by birds through endozoochory: evidence from sub-Antarctic White-bellied Seedsnipe (Attagis malouinus). Polar Biology in press.

Abstract reads: Tardigrades are potentially dispersed by birds, but the extent of the interactions between birds and tardigrades is virtually unknown. We discovered nine tardigrades within feces of White-bellied Seedsnipe (Attagis malouinus) collected from high Andean tundra on Navarino Island, Chile. Eight of the tardigrade specimens began moving once rehydrated. Two specimens belonged to the genus Adropion (Hypsibiidae), one to the Macrobiotus (Macrobiotidae), and five could not be identified. A ninth specimen was a species of Isohypsibius in an embryonic egg state. These tardigrades could have passed through the avian digestive tract after incidental ingestion or burrowed into the feces post-defecation to feed on microorganisms and undigested plant matter present in the feces. To our knowledge, this is the first discovery of tardigrades in bird feces and may have implications for tardigrade distributions if birds transport tardigrades endogenously.

Juan Carlos Villarreal published the last chapter of his dissertation, focused on the population genetic study of Nothoceros aenigmaticus, a clonal hornwort with allopatric sexual populations. The study was picked up and completed by Juan Carlos’ postdoc, Marta Alonso Garcia, who had visited our lab when she was finishing her Ph.D. in Murcia, Spain. Alonso Garcia M., Villarreal J.C., K. McFarland & B. Goffinet. 2020. Population genomics confirms extreme sex ratio of a clonal bryophyte. Frontiers in Plant Science 11: 495. pdf

 

Abstract reads: The southern Appalachian (SA) is one of the most biodiversity−rich areas in North America and has been considered a refugium for many disjunct plant species, from the last glacial period to the present. Our study focuses on the SA clonal hornwort, Nothoceros aenigmaticus J.C. Villarreal & K.D. McFarland. This hornwort was described from North Carolina and is widespread in the SA, growing on rocks near or submerged in streams in six and one watersheds of the Tennessee (TR) and Alabama (AR) Rivers, respectively. Males and female populations occur in different watersheds, except in the Little Tennessee (TN) River where an isolated male population exists ca. 48 km upstream from the female populations. The sex ratio of 1:0 seems extreme in each population. In this study, we use nuclear and organellar microsatellites from 250 individuals from six watersheds (seven populations) in the SA region and two populations from Mexico (23 individuals). We, then, selected 86 individuals from seven populations and used genotyping by sequencing to sample over 600 bi-allelic markers. Our results suggest that the SA N. aenigmaticus and Mexican plants are a nested within a clade of sexual tropical populations. In the US populations, we confirm an extreme sex ratio and only contiguous US watersheds share genotypes. The phylogenetic analysis of SNP data resolves four clusters: Mexican populations, male plants (Little Pigeon and Pigeon river watersheds) and two clusters of female plants; one from the Little Tennessee and Hiwassee Rivers (TR) and the other from the Ocoee (TR) and Coosa (AR) Rivers. All clusters are highly differentiated (Fst values over 0.9). In addition, our individual assignment analyses and PCAs reflect the phylogenetic results grouping the SA samples in three clades and recovering males and female plants with high genetic differentiation (Fst values between 0.5 and 0.9 using microsatellites and bi-allelic markers). Our results point to Pleistocene events shaping the biogeographical pattern seen in US populations. The extreme sex ratio reflects isolation and highlights the high vulnerability of the populations in the SA.

Zachary Muscavitch joined the Lewis and Goffinet lab to pursue his interests in the lichen symbiosis, with a focus on both symbionts, the green alga and the fungus. By December he designed a project focused on Niebla and Vermilacinia, endemic to Western North America, conducted preliminary fieldwork in California and generated encouraging data to further develop his project. He is planning on sampling populations in Baja California, Mexico. His project is now supported by the American Bryological and Lichenological Society. Congratulations Zach, and let’s hope you can travel to this Niebla and Vermilacinia hotspot.

Olivia Lemieux, who joined the lab last fall to conduct an independent study was awarded a Summer Undergraduate Research Fellowship from UCONN for her project entitled “Hybridization in the Physcomitrium pyriforme complex: Identifying maternal and paternal progenitors of hybrid species” Congratulations and let’s hope you can pursue this project this summer!

Rensing S.A., B. Goffinet, R. Meyberg, S.-Z. Wu & M. Bezanilla. 2020. The moss Physcomitrium(Physcomitrella) patens: a model organism for non-seed plants. The Plant Cell 32: 1361–1376. pdf

Abstract reads: Since the discovery two decades ago that transgenes are efficiently integrated into the genome of Physcomitrella patens by homologous recombination, this moss has been a premier model system to study evolutionary developmental biology (evo-devo) questions, stem cell reprogramming, and the biology of non-vascular plants. P. patens was the first non-seed plant to have its genome sequenced. With this level of genomic information together with increasing molecular genetic tools, a large number of reverse genetic studies have propelled the use of this model system. A number of technological advances have recently opened the door to forward genetics as well as extremely efficient and precise genome editing in P. patens. Additionally, careful phylogenetic studies with increased resolution have suggested that P. patens emerged from within Physcomitrium. Thus, rather than Physcomitrella patens, the species should be named Physcomitrium patens. Here we review these advances and describe the areas where P. patens has had the most impact on plant biology.

Rozzi R., M.T. La Valle, S. Russell, B. Goffinet & F. Massardo. 2020. Ecotourism with a hand-lens: a field environmental philosophy experience from the South of the world. Pages: 222–239. In R. Frodeman & E. Brister (eds.), A Guide to Field Philosophy. Case Studies and Practical Strategies (1st edition). Routledge, a Taylor and Francis Group. Link to book

 

The chapters starts with: Earth is not only a biophysical entity; it is also a word that influences the way we understand and relate to the biophysical reality of the planet. Scientists often forget the gravity of words and focus on the biophysical reality. Conversely, philosophers often focus on examining the language of cultural reality, ignoring the biophysical realm. Biocultural ethics unites biological and cultural realities in one conceptual framework (Rozzi, 2001). In addition, it promotes a contextual and systemic approach that shows consideration for the vast biophysical and cultural diversity found in different regions of the world.

In this chapter, we focus on a transdisciplinary endeavor launched in 1999. This long-term project advocates for a biocultural perspective at the southern end of the American continent, in the Cape Horn County of Chile. A team of philosophers, scientists, artists, members of the Yahgan indigenous community, government authorities, Navy officers, schoolteachers, and members of the local community in the world’s southernmost city, Puerto Williams, created the Omora Ethnobotanical Park.1 This endeavor has resulted in changes in the local sciences, arts, and humanities curricula and educational activities at all levels of formal education, as well as with tourists, members of the public, and policymakers from inside and outside Chile.

The first hornwort genome is now published, filling a major gap in the survey of genomes of major lineages of land  plants. This project was led by collaborators of the Chinese Academy of Sciences, Beijing, China.

Zhang J., X.-X. Fu, R.-Q. Li, X. Zhao, Y. Liu, M.-H. Li, A. Zwaenepoel, H. Ma, B. Goffinet, Y.-L. Guan, J.-Y. Xue, Y.-Y. Liao, Q.-F. Wang, Q.-H. Wang,Q.-H. Wang, J.-Y. Wang, G.-Q. Zhang, Z.-W. Wang, Y. Jia, M.-Z. Wang, S.-S. Dong, J.-F. Yang, Y.-N. Jiao, Y.-L. Guo, H.-Z. Kong, A.-M. Lu, S.-Z. Zhang, Y. Van de Peer, Z.-J. Liu & Z.-D. Chen. 2020. The hornwort genome and early land plant evolution. Nature Plants (2020). pdf  or here.

 

Abstract reads: Hornworts, liverworts and mosses are three early diverging clades of land plants, and together comprise the bryophytes. Here, we report the draft genome sequence of the hornwort. Phylogenomic inferences confirm the monophyly of bryophytes, with hornworts sister to liverworts and mosses. The simple morphology of hornworts correlates with low genetic redundancy in plant body plan, while the basic transcriptional regulation toolkit for plant development has already been established in this early land plant lineage. Although the Anthoceros genome is small and characterized by minimal redundancy, expansions are observed in gene families related to RNA editing, UV protection and desiccation tolerance. The genome of A. angustus bears the signatures of horizontally transferred genes from bacteria and fungi, in particular of genes operating in stress-response and metabolic pathways. Our study provides insight into the unique features of hornworts and their molecular adaptations to live on land.

Former EEB undergraduate Nicholas Russo, now a graduate student at UCLA, published his study of birds eating mosses in sub-Antarctic  Chile: Russo N.J., M. Robertson, R. MacKenzie, B. Goffinet & J.E. Jimenez. 2020. Evidence of targeted consumption of mosses by birds in sub-Antarctic South America. Austral Ecology 45: 399–403.pdf

Abstract reads: Bryophyte consumption is uncommon among bird species globally and is often presumed incidental. We sought to determine whether herbivorous bird species of the high Andes, including the white-bellied seedsnipe (Attagis malouinus) and Chloephaga geese (C. picta and C. poliocephala), consume bryophytes, and if so, how frequently. We collected 26 seedsnipe and 22 goose droppings from alpine and sub-alpine habitats of Navarino Island, Chile and examined their contents for bryophyte diaspores. We detected bryophyte fragments in 84.6% and 90.9% of seedsnipe and Chloephaga goose faecal samples, respectively. We also extracted DNA from three bryophyte fragments isolated from goose droppings and sequenced three chloroplast loci for each sample. We inferred through a barcoding analysis that at least one species of Chloephaga goose consumes Polytrichum strictum and Notoligotrichum trichodon. The composition of 11 collected goose droppings was >50% Polytrichaceae bryophyte fragments, suggesting that at least one Chloephaga goose species foraged deliberately on moss species of this family. These new observations suggest that bryophytes are part of the diet of some high Andean birds and that birds might disperse bryophytes internally – via endozoochory – in the sub-Antarctic.