Author: Bernard Goffinet

New publication on bryophytes

Dong S., J. Yu, L. Zhang, B. Goffinet & Y. Liu. Phylotranscriptomics of liverworts: revisiting the backbone phylogeny and ancestral gene duplications. Annals of Botany accepted.

Abstract reads: Background and Aims — With some 7,300 extant species, liverworts (Marchantiophyta) represent one of the major land plant lineages. The backbone relationships, such as the phylogenetic position of Ptilidiales, and the occurrence and timing of whole genome duplications, are still contentious. Methods – Based on analyses of the newly generated transcriptome data for 38 liverworts and complemented with those publicly available, we reconstructed the evolutionary history of liverworts and inferred gene duplication events along the 55-taxon liverwort species tree. Key Results – Our phylogenomic study provided an ordinal-level liverwort nuclear phylogeny and identified extensive gene tree conflicts and cyto-nuclear incongruences. Gene duplication analyses based on integrated phylogenomics and Ks distributions indicated no evidence of whole genome duplication events along the backbone phylogeny of liverworts. Conclusions – With a broadened sampling of liverwort transcriptomes, we re-evaluated the backbone phylogeny of liverworts, and provided evidence for ancient hybridizations followed by incomplete lineage sorting that shaped the deep evolutionary history of liverworts. The lack of whole genome duplication along the deep evolution of liverworts indicates that liverworts might represent one of the few major embryophyte lineages whose evolution was not driven by whole genome duplications.

New publication (on new bird species!)

Rozzi R., C. S. Quilodrán, E. Botero-Delgadillo, R.D. Crego, C. Napolitano, O. Barroso, R. MacKenzie, J.C. Torres-Mura, C. Bravo, S. Ippi, V. Quirici, J. Rivero-de-Aguilar, C.G. Suazo, B. Goffinet, B. Kempenaers, E. Poulin & R.A. Vásquez. 2022. Aphrastura subantarctica: the Subantarctic Rayadito, a new bird species on the Southernmost islands of the Americas. Scientific Reports 12: 13957. pdf

In the news: FoxNews Daily Mail

Abstract reads: We describe a new taxon of terrestrial bird of the genus Aphrastura (rayaditos) inhabiting the Diego Ramírez Archipelago, the southernmost point of the American continent. This archipelago is geographically isolated and lacks terrestrial mammalian predators as well as woody plants, providing a contrasted habitat to the forests inhabited by the other two Aphrastura spp. Individuals of Diego Ramírez differ morphologically from Aphrastura spinicauda, the taxonomic group they were originally attributed to, by their larger beaks, longer tarsi, shorter tails, and larger body mass. These birds move at shorter distances from ground level, and instead of nesting in cavities in trees, they breed in cavities in the ground, reflecting different life-histories. Both taxa are genetically differentiated based on mitochondrial and autosomal markers, with no evidence of current gene flow. Although further research is required to define how far divergence has proceeded along the speciation continuum, we propose A. subantarctica as a new taxonomic unit, given its unique morphological, genetic, and behavioral attributes in a non-forested habitat. The discovery of this endemic passerine highlights the need to monitor and conserve this still-pristine archipelago devoid of exotic species, which is now protected by the recently created Diego Ramírez Islands-Drake Passage Marine Park.

Congratulations to Zach for $5,000 Lewis & Clark grant

Zach Muscavitch was awarded a grant from the American Philosophical Society for his project entitled “Resolving symbiont specificity for endemic lichens on the Channel Islands of California.” This project aims to collect Niebla lichens from the Channel Islands and characterize their fungal and algal symbionts applying a novel DNA sampling method: Target Capture. Results will complement those from the mainland to test patterns of isolation and reciprocal specificity between symbionts.


Congratulations to Olivia for Margaret F. Ertman Award

Olivia Lemieux, a graduating honors student who has been in the lab, mentoring by Niki and myself, has been awarded the Margaret F. Ertman Award in recognition of her significant accomplishments at University of Connecticut. Her project is entitled “Whole-range study reveals consistent hybrid nature and conserved progenitors of the North American endemic moss, Physcomitrium immersum.”

Each year, the Margaret F. Ertman Award is awarded to the outstanding senior across all four biology degree programs: Biological Sciences, EEB, MCB, and PNB. The student will have distinguished themselves both through outstanding scholarship in EEB, MCB, and PNB during their undergraduate career, and through original research conducted in biology (broadly defined) at UConn.

The Margaret F. Ertman Award was established in 1983 by Irvin L. Ertman (class of 1939) and Ronnie Ertman (class of 1941) in honor of their daughter Margaret F. Ertman (class of 1974). The award is based not only on your excellent presentation at the research colloquium but also on your superb academic performance throughout your UConn career.

New publications on bryophytes

Patiño J., I. Bisang, B. Goffinet, L. Hedenäs, S. McDaniel, S. Pressler, M. Stech, C. Ah-Peng, A. Bergamini, R.T. Caners, C. Cargill, N. Cronberg, J. Duckett, S. Eppley, N. Fenton, K. Fisher, J. M. González-Mancebo, M. Hasebe, J. Heinrichs†, K. Hylander, M.S. Ignatov, J. Martínez-Abaigar, N. Medina, R. Medina, D. Quandt, S. Rensing, K. Renzaglia, M. Renner, R. M. Ros, A. Schäfer-Verwimp, J. Carlos Villarreal & A. Vanderpoorten. 2022. Unveiling the nature of a miniature world: A horizon scan of fundamental questions in bryology. Journal of Bryology 41: 1–34. pdf

Abstract reads: INTRODUCTION Half a century since the creation of the International Association of Bryologists, we carried out a review to identify outstanding challenges and future perspectives in bryology. Specifically, we have identified 50 fundamental questions that are critical in advancing the discipline.
METHODS We have adapted a deep-rooted methodology of horizon scanning to identify key research foci. An initial pool of 258 questions was prepared by a multidisciplinary and international working group of 32 bryologists. A series of online surveys completed by a broader community of researchers in bryology, followed by quality-control steps implemented by the working group, were used to create a list of top-priority questions. This final list was restricted to 50 questions with a broad conceptual scope and answerable through realistic research approaches.
KEY RESULTS The top list of 50 fundamental questions was organised into four general topics: Bryophyte Biodiversity and Biogeography; Bryophyte Ecology, Physiology and Reproductive Biology; Bryophyte Conservation and Management; and Bryophyte Evolution and Systematics. These topics included 9, 19, 14 and 8 questions, respectively.
CONCLUSIONS Although many of the research challenges identified are not newly conceived, our horizon-scanning exercise has established a significant foundation for future bryological research. We suggest analytical and conceptual strategies and novel developments for potential use in advancing the research agenda for bryology.

New publication

Cycas circinalis
Cycas circinalis in the Plant Biodiversity Conservatory and Research Core

Liu Y., S. Wang, L. Li, T. Yang, S. Dong, T. Wei, S. Wu, Y. Liu, Y. Gong, X. Feng, J. Ma, G. Chang, J. Huang, Y. Yang, H. Wang, M. Liu, Y. Xu, H. Liang, J. Yu, Y. Cai, Z. Zhang, Y. Fan, W. Mu, S. Kumar Sahu, S. Liu, X. Lang, L. Yang, N. Li, S. Habib, Y. Yang, A.J. Lindstrom, P. Liang, B. Goffinet, S. Zaman, Jill. L. Wegrzyn, D. Li, J. Liu, J. Cui, E.C. Sonnenschein, X. Wang, J. Ruan, J.-Y. Xue, Z.-Q. Shao, C. Song, G. Fan, Z. Li, L. Zhang, J. Liu, Z.-J. Liu, Y. Jiao, X.-Q. Wang, H. Wu, E. Wang, M. Lisby, H. Yang, J. Wang, X. Liu, X. Xu, N. Li, P.S. Soltis, Y. Van de Peer, D.E. Soltis, X. Gong, H. Liu, S. Zhang. 2022. The cycad genome and the early evolution of seed plants. Nature Plants 8: 389–401.  pdf  Google Scholar


Abstract readsCycads represent one of the most ancient lineages of living seed plants. Identifying genomic features uniquely shared by cycads and other extant seed plants, but not non-seed-producing plants, may shed light on the origin of key innovations, as well as the early diversification of seed plants. Here, we report the 10.5-Gb reference genome of Cycas panzhihuaensis, complemented by the transcriptomes of 339 cycad species. Nuclear and plastid phylogenomic analyses strongly suggest that cycads and Ginkgo form a clade sister to all other living gymnosperms, in contrast to mitochondrial data, which place cycads alone in this posi- tion. We found evidence for an ancient whole-genome duplication in the common ancestor of extant gymnosperms. The Cycas genome contains four homologues of the fitD gene family that were likely acquired via horizontal gene transfer from fungi, and these genes confer herbivore resistance in cycads. The male-specific region of the Y chromosome of C. panzhihuaensis contains a MADS-box transcription factor expressed exclusively in male cones that is similar to a system reported in Ginkgo, suggesting that a sex determination mechanism controlled by MADS-box genes may have originated in the common ancestor of cycads and Ginkgo. The C. panzhihuaensis genome provides an important new resource of broad utility for biologists.

New publication on lichens

DendriscostictaSimon A., B. Goffinet, L.S. Wang, T. Spribille, T. Goward, T. Pystina, N. Semenova, N.V. Stepanov, B. Moncada, R. Lücking, N. Magain & E. Sérusiaux. 2022. Global phylogeny and taxonomic reassessment of the genus Dendriscosticta (Ascomycota: Peltigerales). Taxon 71: 256–287.  pdf  Google Scholar

Abstract reads: The genus Dendriscosticta (Ascomycota: Peltigerales) encompasses several distinctive lichen-forming fungal species restricted to the Northern Hemisphere. Most are flagship species of old-growth forests with good air quality. A global phylogeny ofthe genus based on multilocus sequence data (ITS,RPB1,EF-1α,MCM7), model-based phylogenetic methods, and morphologicaland chemical assessments, reveals a high level of cryptic speciation often associated with restricted geographical distribution and/orchemical characters. Using sequence-based species delimitation approaches, we circumscribe two main clades referred to as the D. wrightii clade, with five unequivocal species, including D. gelida sp. nov., and the D. praetextata clade, with eight putative species, including D. phyllidiata sp. nov. The absence of recently collected material of D. hookeri comb. nov. from the type locality unfortunately prevents assignment of this epithet to one of the five supported lineages sharing this morphotype. Three new combinations are proposed: D. hookeriD. insinuans comb. nov. and D. yatabeana comb. nov. Epitypes are designated for D. wrightii and D. yatabeanaSpecies diversity within the genus increased from four to nine. Our morphological assessment confirmed that Sticta and Dendriscosticta can be readily distinguished by the presence of excipular algae whereas the structure of the lower surface pores is not a reliable diagnostic feature.

Antoine awarded Marie Curie Fellowship

Antoine SimonAntoine Simon, currently a BAEF fellow with us has been awarded a highly competitive two year Marie Skłodowska-Curie Postdoctoral Fellowship from the European Union, for his project entitled “FRAME – Fungal Research in the Age of Museomic Exploration: revisiting historical lichen collections”.
Antoine will move this summer to the Natural History Museum, University of Oslo to work with Prof. Einar Timdal on genomic approaches applied to historical herbarium specimens.
His project aims at generating informative genetic data from ancient lichen collections, providing a cost-effective and labor-saving strategy to integrate relevant museum collections in biodiversity research.
Congrats to Antoine.

New publication on mosses

Yu J., Y. Cai, Y. Zhu, Y. Zeng, S. Dong, K. Zhang, S. Wang, L. Li, B. Goffinet, H. Liu & Y. Liu. 2022. Chromosome-level genome assemblies of two Hypnales mosses reveal high intergeneric synteny. Genome Biology and Evolution 14: evac020. pdf  Google scholar

Abstract reads: Mosses compose one of the three lineages of bryophytes. Today, about 13,000 species of mosses are recognized from across the globe, and at least a third of this diversity composes the Hypnales, a lineage characterized by an early rapid radiation. We sequenced and de novo assembled the genomes of two hypnalean mosses, namely Entodon seductrix and Hypnum curvifolium, based on the 10x genomics and Hi-C data. The genome assemblies of E. seductrix and H. curvifolium comprise 348.4 Mb and 262.0 Mb, respectively, estimated by k-mer analyses to represent 93.3% and 97.2% of their total genome size. Both genomes were assembled at the chromosome-level, with scaffold N50 of 30.0 Mb and 20.7 Mb, respectively. The annotated genome of E. seductrix comprises 25,801 protein-coding genes and that of H. curvifolium 29,077, estimated to represent 96.8% and 97.2%, respectively, of the total gene spaces based on BUSCO assessment. For both genomes, most contigs were anchored to the largest 11 pseudomolecules, corresponding to the 11 chromosomes of the two species, and each with a putative sex-related chromosome characterized by low gene density. The chromosomes of E. seductrix and H. curvifolium are highly syntenic, suggests limited architectural shifts occurred following the rapid radiation of the Hypnales. We compared their genomic features to the model moss Physcomitrium patens. The hypnalean moss genomes lack signatures of recent whole genome duplication (WGD). The presented high-quality moss genomes provide new resources for comparative genomics to potentially unveil the genomic evolution of derived moss lineages.