Author: Bernard Goffinet

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


Subject line: bryology position

The Goffinet Lab (see

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.

New publication on lichens

Widhelm T.J., F. Grewe, J. P. Huang, J. Mercado, B. Goffinet, R. Lücking, I. Schmitt, B. Moncada, R. Mason-Gamer & H. T. Lumbsch. 2019. Multiple historical processes obscure phylogenetic relationships in a taxonomically difficult group (Lobariaceae, Ascomycota). Scientific Reports 9: 8968. pdf

Abstract reads: In the age of next-generation sequencing, the number of loci available for phylogenetic analyses has increased by orders of magnitude. But despite this dramatic increase in the amount of data, some phylogenomic studies have revealed rampant gene-tree discordance that can be caused by many historical processes, such as rapid diversification, gene duplication, or reticulate evolution. We used a target enrichment approach to sample 400 single-copy nuclear genes and estimate the phylogenetic relationships of 13 genera in the lichen-forming family Lobariaceae to address the effect of data type (nucleotides and amino acids) and phylogenetic reconstruction method (concatenation and species tree approaches). Furthermore, we examined datasets for evidence of historical processes, such as rapid diversification and reticulate evolution. We found incongruence associated with sequence data types (nucleotide vs. amino acid sequences) and with different methods of phylogenetic reconstruction (species tree vs. concatenation). The resulting phylogenetic trees provided evidence for rapid and reticulate evolution based on extremely short branches in the backbone of the phylogenies. The observed rapid and reticulate diversifications may explain conflicts among gene trees and the challenges to resolving evolutionary relationships. Based on divergence times, the diversification at the backbone occurred near the Cretaceous-Paleogene (K-Pg) boundary (65 Mya) which is consistent with other rapid diversifications in the tree of life. Although some phylogenetic relationships within the Lobariaceae family remain with low support, even with our powerful phylogenomic dataset of up to 376 genes, our use of target-capturing data allowed for the novel exploration of the mechanisms underlying phylogenetic and systematic incongruence.

New publication on liverworts

Dong S., Q. He, S. Zhang, H. Wu, B. Goffinet& Y. Liu. 2019. The mitochondrial genomes of Bazzania tridens and Riccardia planiflora further confirms conservative evolution of mitogenomes in liverworts. The Bryologist 122: 130–139.

Abstract reads: The mitochondrial genomes of vascular plants are highly liable in both gene content and genome structure. In contrast, those of hornworts, liverworts, and mosses appear relatively stable over millions of years of evolution. All sequenced liverwort mitogenomes possess similar gene content and exactly the same gene order, except for that of Gymnomitrion concinnatum (Gymnomitriaceae, Jungermanniales), which is characterized by two rearrangements. To further explore the structural characteristic of liverworts mitogenomes, we sequenced and assembled the mitogenomes of representatives of two additional genera of liverworts, namely Bazzania tridens (Lepidoziaceae, Jungermanniales) and Riccardia planiflora (Metzgeriaceae, Metzgeriales). The two mitogenomes comprise 162,643 and 149,371 base pairs, respectively, and encoded the set of 72 genes present in all other liverwort mitochondrial genomes. The mitogenome of Bazzania tridens contains seven fewer introns than that of Marchantia, and the simple thalloid Riccardia planiflora contains one additional intron. A total of 370 and 471 C to U RNA editing sites were predicted from the 42 mitochondrial protein-coding genes of B.tridens and R.planiflora, respectively. The phylogenetic placement of the two taxa based on the mitochondrial protein-coding genes of thirteen liverwort species is consistent with former studies. Although the two sampled taxa are only distantly related, their mitogenomes share a same gene order, which is, moreover, shared by the majority of liverworts, thereby strengthening the hypothesis of overall stasis of the liverwort mitogenomes.

New publication in Nat. Com.

The first publication from our collaborative Assembling the [pleurocarpous moss] Tree of Life project, presenting the first phylogenetic reconstruction of mosses based complete organellar exomes and equivalent set of nuclear markers sampled for exemplars of all but one order, is now published:

Liu Y., M. G. Johnson, C. J. Cox, R. Medina, N. Devos, A. Vanderpoorten, L. Hedenäs, N. E. Bell, J. R. Shevock, B. Aguero, D. Quandt, N. J. Wickett, A. J. Shaw & B. Goffinet. 2019. Resolution of the backbone phylogeny of mosses using targeted exons from organellar and nuclear genomes. Nature Communications 10: 1485. DOI: 10.1038/s41467-019-09454-w pdf

The publication of this study was featured in UConn today.

Abstract reads: Mosses compose a highly diverse lineage of land plants, whose diversification, spanning at least 400 million years, remains phylogenetically ambiguous due to the lack of fossils, massive early extinctions, late radiations, limited morphological variation, and conflicting signal among previously used markers. Here, we present phylogenetic reconstructions based on complete organellar exomes and a comparable set of nuclear genes for this major lineage of land plants. Our analysis of 142 species representing 29 of the 30 moss orders reveals that relative average rates of non-synonymous substitutions in nuclear versus plastid genes are much higher in mosses than in seed plants, consistent with the emerging concept of evolutionary dynamism in mosses. Our results highlight the evolutionary significance of taxa with reduced morphologies, shed light on the relative tempo and mechanisms underlying major cladogenic events, and suggest hypotheses for the relationships and delineation of moss orders.

Chile: new lichen project, colleagues and province visited

Bernard Goffinet spent a week in the Province of Aysén, surveying the
diversity of Lobariales, and in particular of the genus Peltigera with Dr. Julieta Orlando and her student Diego Leiva Cáceres, two microbiologists exploring the diversity and function of the microbiomes of two Peltigera species. Also joining us for a day was Yanira Pía Vega Belmar, a beginning Master student at the University of Magallanes, focusing on public education in the Miniature Forests. Wonderful landscapes, many collections and exciting collaborations developing.

New publication on mosses

Medina R., F. Lara, B. Goffinet, R. Garilleti & V. Mazimpaka. 2019. On the priority of Orthotrichum cylindrocarpum Lesq. over O. coulteri Mitt. and Lesquereux’s early vindication of an autonomous American bryology. Taxon (in press). pdf

Abstract reads: In a recent revision of the Orthotrichum tenellum complex, the authors erroneously concluded that the name O. coulteri predated the supposed synonym O. cylindrocarpum. This confusion was due to incongruent publication dates reported in the literature and lack of evidence of effective publication of the latter. Here, we demonstrate that the name O. cylindrocarpum was indeed published a few months before O. coulteri based on correspondence by the authorities and dated reprints. The almost simultaneous publication of both names occurred during a period in which some early American bryologists advocated that the discovery of new species from North America should be reported by them and not by their European colleagues.