University of Connecticut University of UC Title Fallback Connecticut

Author Archives: Bernard Goffinet

Diego Ramirez trip in Chilean news

Following an interview with the Prensa Austral the following article was published on Sunday December 25, 2016 highlighting the framework for our recent exploration of Isla Gonzalo of the Diego Ramirez islands, a 100 km  SW of Cape Horn (Chile). See also some pictures taken on Isla Gonzalo.


Best dissertation award to Lily


lilyCongratulations to Lily Lewis whose dissertation entitled “Resolving bipolar phylogeographic histories in the common dung moss Tetraplodon (Bryopsida: Splachnaceae)” earned the “Greg and Mona Anderson Ecology and Evolutionary Biology best Ph.D. dissertation award”.  Lily is now Postdoctoral Associate in the Department of Biology at the University of Florida with Dr. Stuart MacDaniel. Well done.

New publication

At last, the systematic consequences of phylogenetic inferences in the genus Orthotrichum are formalized in a publication emerging from a collaboration of colleagues at the University of Madrid (Spain) and our lab.

Lara F., R. Garilleti, B. Goffinet, I. Draper, R. Medina, B. Vigalondo & V. Mazimpaka. Lewinskya, a new genus for the phaneroporous, monoicous taxa previously accommodated in Orthotrichum Hedw. (Bryophyta, Orthotrichaceae). Cryptogamie-Bryologie 37: 361–382. (pdf)

Abstract: Molecular analyses have consistently evidenced the phylogenetic heterogeneity of Orthotrichum Hedw., and suggested the need to segregate the species with superficial stomata in a separate genus. A recent proposal has been made to accommodate the monoicous species with such stomata in the genus Dorcadion Adans. ex Lindb., which is, however, an illegitimate name according to the current Code of nomenclature of algae, fungi and plants. Consequently a new name is required, and the generic name Lewinskya F.Lara, Garilleti & Goffinet is proposed. New combinations are made for all the species included in the new genus. Given the long history of the genus Orthotrichum and the similarities between this genus and Lewinskya, the morphological and geographic circumscriptions of both genera are provided to define them accurately. The taxa remaining in Orthotrichum s.str. are also listed.

New publication: Sphagnum phylogenomics

Our lab contributed to a phylogenomic reconstruction of the Sphagnopsida, which was published this past week: Shaw A.J., N. Devos, Y. Liu, C. J. Cox, B. Goffinet, K.I. Flatberg & B. Shaw. 2016. Organellar phylogenomics of an emerging model system: Sphagnum (peatmoss). Annals of Botany 118: 185–196.

The abstract reads: 

Background and Aims: Sphagnum-dominated peatlands contain approx. 30 % of the terrestrial carbon pool in the form of partially decomposed plant material (peat), and, as a consequence, Sphagnum is currently a focus of studies on biogeochemistry and control of global climate. Sphagnum species differ in ecologically important traits that scale up to impact ecosystem function, and sequencing of the genome from selected Sphagnum species is currently underway. As an emerging model system, these resources for Sphagnum will facilitate linking nucleotide variation to plant functional traits, and through those traits to ecosystem processes. A solid phylogenetic framework for Sphagnum is crucial to comparative analyses of species-specific traits, but relationships among major clades within Sphagnum have been recalcitrant to resolution because the genus underwent a rapid radiation. Herein a well-supported hypothesis for phylogenetic relationships among major clades within Sphagnum based on organellar genome sequences (plastid, mitochondrial) is provided.

Methods: We obtained nucleotide sequences (273 753 nucleotides in total) from the two organellar genomes from 38 species (including three outgroups). Phylogenetic analyses were conducted using a variety of methods applied to nucleotide and amino acid sequences. The Sphagnum phylogeny was rooted with sequences from the related Sphagnopsida genera, Eosphagnum and Flatbergium.

Key Results: Phylogenetic analyses of the data converge on the following subgeneric relationships: (Rigida (((Subsecunda) (Cuspidata)) ((Sphagnum) (Acutifolia))). All relationships were strongly supported. Species in the two major clades (i.e. Subsecunda + Cuspidata and SphagnumAcutifolia), which include >90 % of all Sphagnum species, differ in ecological niches and these differences correlate with other functional traits that impact biogeochemical cycling. Mitochondrial intron presence/absence are variable among species and genera of the Sphagnopsida. Two new nomenclatural combinations are made, in the genera Eosphagnum and Flatbergium.

Conclusions: Newly resolved relationships now permit phylogenetic analyses of morphological, biochemical and ecological traits among Sphagnum species. The results clarify long-standing disagreements about subgeneric relationships and intrageneric classification.

Rafa is hitting the road

Rafa Medina has been an inspiring member of the lab since 2012, and is now moving to new adventures in Illinois at Augustana College. We will miss him and wish him much happiness and success.

New publication: HybPiper

The bioinformatic pipeline central to our ATOL pleurocarp and Funariaceae diversification studies is out:

Johnson M.G., E.M. Gardner, Y. Liu, R. Medina, B. Goffinet, A.J. Shaw, N.J.C. Zerega & N.J. Wickett. 2016. HybPiper: extracting coding sequence and introns for phylogenetics from high-throughput sequencing reads using target enrichment. Applications in Plant Sciences 4(7):1600016 (DOI: pdf

The abstract reads: Premise of the study: Using sequence data generated via target enrichment for phylogenetics requires reassembly of high- throughput sequence reads into loci, presenting a number of bioinformatics challenges. We developed HybPiper as a user- friendly platform for assembly of gene regions, extraction of exon and intron sequences, and identification of paralogous gene copies. We test HybPiper using baits designed to target 333 phylogenetic markers and 125 genes of functional significance in Artocarpus (Moraceae).
Methods and Results: HybPiper implements parallel execution of sequence assembly in three phases: read mapping, contig as- sembly, and target sequence extraction. The pipeline was able to recover nearly complete gene sequences for all genes in 22 species of Artocarpus. HybPiper also recovered more than 500 bp of nontargeted intron sequence in over half of the phylogenetic markers and identified paralogous gene copies in Artocarpus.
Conclusions: HybPiper was designed for Linux and Mac OS X and is freely available at

New publication

The latest paper from the lab, highlighting Jessica’s work from her postdoc here was published in Frontiers in Plant Sciences: Budke J.M. & B. Goffinet. 2016. Comparative cuticle development in morphologically divergent mosses of the Funariaceae. Frontiers in Plant Sciences 7: 832. pdf (open access).

The abstract reads: The calyptra is a maternal structure that protects the sporophyte offspring from dehydration, and positively impacts sporophyte survival and fitness in mosses. We explore the relationship between cuticle protection and sporophyte height as a proxy for dehydration stress in Funariaceae species with sporophytes across a range of sizes. Calyptrae and sporophytes from four species were collected from laboratory-grown populations at two developmental stages. Tissues were embedded, sectioned, and examined using transmission electron microscopy. Cuticle thickness was measured from three epidermal cells per organ for each individual and compared statistically. All four species have cuticles consisting of a cuticle proper and a cuticular layer on the calyptra and sporophyte at both developmental stages. Across species, shorter sporophytes are associated with smaller calyptra and thinner calyptra cuticles, whereas taller sporophytes are associated with larger calyptra and thicker calyptra cuticles. Independent of size, young sporophytes have a thin cuticle that thickens later during development, while calyptrae have a mature cuticle produced early during development that persists throughout development. This study adds to our knowledge of maternal effects influencing offspring survival in plants. Released from the pressures to invest in protection for their sporophyte offspring, maternal resources can be allocated to other processes that support sporophyte reproductive success. Using a comparative developmental framework enables us to broaden our understanding of cuticle development across species and provides structural evidence supporting the waterproofing role of the moss calyptra.

New publication

In a new paper that came out today we report the cyanomorph of Ricasolia virens, and how this may shape our understanding of the evolution of photosymbiodemes in the Lobariaceae.

Tønsberg T., H. Blom, B. Goffinet, J. Holtan-Hartwig & L. Lindblom. 2016. The cyanomorph of Ricasolia virens comb. nov. (Lobariaceae, lichenized Ascomycetes). Opuscula Philolichenum 15: 12–21. The pdf should be available here.

The abstract reads: The cyanomorph and photosymbiodemes are here reported for the first time for Ricasolia virens (With.) H.H. Blom & Tønsberg comb. nov. (≡ Lobaria virens (With.) J.R. Laundon). The cyanomorph of R. virens is dendriscocauloid. The observed early developmental stages involve (1) a free-living cyanomorph and (2) a photosymbiodeme composed of the cyanomorph supporting small, foliose, chloromorphic lobes. Whereas the chloromorph continues to grow, the cyanomorph decays and disappears leading to the final stage (3), the free-living chloromorph. Secondary cyanomorphs emerging from the chloromorph are not known.

New publication

Laenen B., A. Machac, S.R. Gradstein, B. Shaw, J. Patiño, A. Désamoré, B. Goffinet, C.J. Cox, J. Shaw & A. Vanderpoorten. 2016. Increased diversification rates follow shifts to bisexuality in liverworts. New Phytologist 210: 1121–1129. pdf

The abstract reads: Shifts in sexual systems are one of the key drivers of species diversification. In contrast to angiosperms, unisexuality prevails in bryophytes. Here, we test the hypotheses that bisexuality evolved from an ancestral unisexual condition and is a key innovation in liverworts.
We investigate whether shifts in sexual systems influence diversification using hidden state speciation and extinction analysis (HiSSE). This new method compares the effects of the variable of interest to the best-fitting latent variable, yielding robust and conservative tests.
We find that the transitions in sexual systems are significantly biased toward unisexuality, even though bisexuality is coupled with increased diversification. Sexual systems are strongly conserved deep within the liverwort tree but become much more labile toward the present.
Bisexuality appears to be a key innovation in liverworts. Its effects on diversification are presumably mediated by the interplay of high fertilization rates, massive spore production and long-distance dispersal, which may separately or together have facilitated liverwort speciation, suppressed their extinction, or both. Importantly, shifts in liverwort sexual systems have the opposite effect when compared to angiosperms, leading to contrasting diversification patterns between the two groups. The high prevalence of unisexuality among liverworts suggests, however, a strong selection for sexual dimorphism.

Rafa Medina moves to Illinois

RafaelEarlier this winter, Rafael Medina was offered a tenure-track position at Augustana College. Rafa completed his dissertation at the Universidad Autónoma de Madrid in Spain, in Evolutionary Biology and Biodiversity. His dissertation was entitled: “Estudios de taxonomía integrativa en el género Orthotrichum Hedw., subgénero Pulchella” (Integrative taxonomy studies on the genus Orthotrichum, subgen. Pulchella). Apto Cum Laude. He then joined our lab to lead the phylogenomic reconstruction of the Funariales. Congratulations!