Author: Bernard Goffinet

Chapter on Ecotourism with a hand-lens is out!

Cover of book 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.

New publication: first hornwort genome out!

Cover of Nature Plant issue holding this articleThe 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.

New publication on birds consuming mosses

Notoligotrichum trichodon: one of the mosses eaten by geese 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 xx: xxx–xxx.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.

New publication on liverwort mitochondrial genomes

Dong S., C. Zhao, S. Zhang, L. Zhang, H. Wu, R. Zhu, Y. Jia, B. Goffinet & Y. Liu. 2020. Mitochondrial genomes of the early land plant lineage liverworts (Marchantiophyta): conserved genome structure, and ongoing low frequency recombination. BMC Genomics 20: 953. pdf

Abstract readsBackground: In contrast to the highly labile mitochondrial (mt) genomes of vascular plants, the architecture and composition of mt genomes within the main lineages of bryophytes appear stable and invariant. The available mt genomes of 18 liverwort accessions representing nine genera and five orders are syntenous except for Gymnomitrion concinnatum whose genome is characterized by two rearrangements. Here, we expanded the number of assembled liverwort mt genomes to 47, broadening the sampling to 31 genera and 10 orders spanning much of the phylogenetic breadth of liverworts to further test whether the evolution of the liverwort mitogenome is overall static. Results: Liverwort mt genomes range in size from 147 Kb in Jungermanniales (clade B) to 185 Kb in Marchantiopsida, mainly due to the size variation of intergenic spacers and number of introns. All newly assembled liverwort mt genomes hold a conserved set of genes, but vary considerably in their intron content. The loss of introns in liverwort mt genomes might be explained by localized retroprocessing events. Liverwort mt genomes are strictly syntenous in genome structure with no structural variant detected in our newly assembled mt genomes. However, by screening the paired-end reads, we do find rare cases of recombination, which means multiple concurrent genome structures may exist in the vegetative tissues of liverworts. Our phylogenetic analyses of the nuclear encoded double stand break repair protein families revealed liverwort-specific subfamilies expansions. Conclusions: The low repeat recombination level, selection, along with the intensified nuclear surveillance, might together shape the structural evolution of liverwort mt genomes.

New publication on liverwort organellar genomes

Dong S., C. Zhao, S. Zhang, H. Wu, W. Mu, T. Wei, N. Li, H. Liu, J. Cui, R. Zhu, B. Goffinet & Y. Liu. 2020. The amount of RNA editing sites in liverwort organellar genes is correlated with GC content and nuclear PPR protein diversity. Genome Biology and Evolution 11: 3233–3239. pdf

Abstract reads: RNA editing occurs in the organellar mRNAs of all land plants but the marchantioid liverworts, making liverworts a perfect group for studying the evolution of RNA editing. Here, we profiled the RNA editing of 42 exemplars spanning the ordinal phylogenetic diversity of liverworts, and screened for the nuclear-encoded pentatricopeptide repeat (PPR) proteins in the transcriptome assemblies of these taxa.We identified 7,428 RNA editing sites in 128 organellar genes from 31 non-marchantioid liverwort species, and characterized 25,059 PPR protein sequences. The abundance of organellar RNA editing sites varies greatly among liverwort lineages, genes, and codon positions, and shows strong positive correlations with the GC content of protein-coding genes, and the diversity of the PLS class of nuclear PPR proteins.

 

Two awards for recent publications

The American Bryological and Lichenological Society awarded Dong S., J.-Y. Xue, S. Zhang, L. Zhang, H. Wu, Z. Chen, B. Goffinet & Yang Liu the Sullivan award for best paper on bryology published in the Bryologist in 2018 (volume 121) for their article entitled “Complete mitochondrial genome sequence of Anthoceros angustus: conservative evolution of mitogenome in hornworts” and published in The Bryologist 121: 14–22. https://doi.org/10.1639/0007-2745-122.1.130

The editors of the Journal of Systematics and Evolution awarded the Special Issue Paper Award to Medina, R., M. G. Johnson, Y. Liu, N.J. Wickett, A.J. Shaw & B. Goffinet for their article entitled “Phylogenomic delineation of Physcomitrium (Bryophyta: Funariaceae) based on targeted sequencing of nuclear exons and their flanking regions rejects the retention of Physcomitrella, Physcomitridium and Aphanorrhegma” and published in the Journal of Systematics and Evolution 57: 404–417 in 2019. https://doi.org/10.1111/jse.12516

Two positions for undergraduates

Undergraduate research and work opportunities

In Evolutionary Biology Fall 2019

As part of a study funded by the National Science Foundation focused on the evolutionary significance of whole genome duplication in plants (we use mosses as model systems) we seek to fill TWO POSITIONS with BIO or EEB majors interested in evolutionary biology (see advertisement: Undergraduate research and work opportunities):

  1. Maintain cultures of mosses: we establish and propagate cultures of mosses for genome analysis, reproduction biology experiments and morphological study
  2. Process DNA sample (extraction, amplification and sequencing) for phylogenetic analysis

Prerequisites: BIOL 1108 or BIOL 1110

Number of hours weekly: 6-8

Open for credit (1 credit = 3 hours) or compensation 

Deadline for application: Sept 6, 2019

Contact bernard.goffinet@uconn.edu.

Subject line: bryology position

The Goffinet Lab (see http://bryology.uconn.edu):

We study the evolution and systematics of plants with a focus on mosses, liverworts, and hornworts, and also of fungi, namely those establishing permanent symbiotic associations, called lichens. Past undergrads have done projects addressing a variety of questions and acquiring experience in DNA extraction, amplification and sequencing, estimating genome size via flow cytometry, analysis of morphological traits, assessing phenotypic signatures following genome duplication, sterile cultures techniques for moss propagation, and lichen barcoding.

New publication on mosses: bye bye Physco

Physcomitrium pyriformeThe evo-devo model species Physcomitrella patens has a new name!

Medina, R., M. G. Johnson, Y. Liu, N.J. Wickett, A.J. Shaw & B. Goffinet. 2019. Phylogenomic delineation of Physcomitrium (Bryophyta: Funariaceae) based on nuclear targeted exons and their flanking regions rejects the retention of Physcomitrella, Physcomitridium and Aphanorrhegma. Journal of Systematics and Evolution 57: 404–417. pdf

Abstract reads: Selection on spore dispersal mechanisms in mosses is thought to shape the transformation of the sporophyte. The majority of extant mosses develop a sporangium that dehisces through the loss of an operculum, and regulates spore release through the movement of articulate teeth, the peristome, lining the capsule mouth. Such complexity was acquired by the Mesozoic Era, but was lost in some groups during subsequent diversification events, challenging the resolution of the affinities for taxa with reduced architectures. The Funariaceae are a cosmopolitan and diverse lineage of mostly annual mosses, and exhibit variable sporophyte complexities, spanning from long, exerted, operculate capsules with two rings of well‐developed teeth, to capsules immersed among maternal leaves, lacking a differentiated line of dehiscence (i.e., inoperculate) and without peristomes. The family underwent a rapid diversification, and the relationships of taxa with reduced sporophytes remain ambiguous. Here, we infer the relationships of five taxa with highly reduced sporophytes based on 648 nuclear loci (exons complemented by their flanking regions), based on inferences from concatenated data and concordance analysis of single gene trees. Physcomitrellopsis is resolved as nested within one clade of Entosthodon. Physcomitrella s. l., is resolved as a polyphyletic assemblage and, along with its putative relative Aphanorrhegma, nested within Physcomitrium. We propose a new monophyletic delineation of Physcomitrium, which accommodates species of Physcomitrella and Aphanorrhegma. The monophyly of Physcomitrium s. l. is supported by a small plurality of exons, but a majority of trees inferred from exons and their adjacent non‐coding regions.