Author: Bernard Goffinet

New publication on mosses

The evo-devo model species Physcomitrella patens changes its 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.

Herbaria and the study of effects of climate change

New study integrating CONN herbarium specimens in estimating the effect of climate change on plant behavior. 

Lorieul T., K.D. Pearson, E.R. Ellwood, H. Goëau, J.-F. Molino, P.W. Sweeney, J.M. Yost, J. Sachs, E. Mata-Montero, G. Nelson, P.S. Soltis, P. Bonnet &  A. Joly. 2019. Toward a large-scale and deep phenological stage annotation of herbarium specimens: Case studies from temperate, tropical, and equatorial floras. Applications in Plant Sciences 7(3): e1233. pdf

Abstract reads: Premise of the Study: Phenological annotation models computed on large‐scale herbarium data sets were developed and tested in this study.

Methods: Herbarium specimens represent a significant resource with which to study plant phenology. Nevertheless, phenological annotation of herbarium specimens is time‐consuming, requires substantial human investment, and is difficult to mobilize at large taxonomic scales. We created and evaluated new methods based on deep learning techniques to automate annotation of phenological stages and tested these methods on four herbarium data sets representing temperate, tropical, and equatorial American floras.

Results: Deep learning allowed correct detection of fertile material with an accuracy of 96.3%. Accuracy was slightly decreased for finer‐scale information (84.3% for flower and 80.5% for fruit detection).

Discussion: The method described has the potential to allow fine‐grained phenological annotation of herbarium specimens at large ecological scales. Deeper investigation regarding the taxonomic scalability of this approach is needed.

New publication on Pelargonium

Graphical abstract of studyAnother study from the Jones and Schlichting lab on the diversification of Pelargonium with vouchers deposited in the CONN herbarium.

van de Kerke S.J., B. Shrestha, T.A. Ruhlman, M.L. Weng, R.K. Jansen, C.S. Jones, C.D. Schlichting, S. Hosseini, S. Mohammadin, M.E. Schranz & F.T. Bakker. 2019. Plastome based phylogenetics and younger crown node age in Pelargonium. Molecular Phylogenetics and Evolution 137: 33–43. pdf


Abstract reads: The predominantly South-African plant genus Pelargonium L’Hér. (Geraniaceae) displays remarkable morphological diversity, several basic chromosome numbers as well as high levels of organelle genomic rearrangements, and represents the 7th largest Cape Floristic Region clade. In this study, we reconstructed a phylogenetic tree based on 74 plastome exons and nuclear rDNA ITS regions for 120 species, which represents 43% taxon coverage for Pelargonium. We also performed a dating analysis to examine the timing of the major radiations in the genus.

Phylogenetic analyses of nucleotide, amino acid, and ITS alignments confirmed the previously-documented subgeneric split into five main clades ((C1,C2),(B(A1,A2))) although clade only A1 received low bootstrap support.

Using calibration evidence from a range of sources the Pelargonium crown age was estimated to be 9.7 My old, much younger than previous estimates for the genus but similar to recent studies of other Cape Floristic lineages that are part of both Fynbos and Succulent Karoo biomes.

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 species of moth discovered

The monographic study by Matson et al. reveals a new species in the genus Lactura with type and other specimens held in the BRC: Matson T.A., D.L. Wagner & S.E. Miller. 2019. A revision of North American Lactura (Lepidoptera, Zygaenoidea, Lacturidae). ZooKeys 846: 75–116. pdf

Abstract reads: The Lactura Walker, 1854 fauna north of Mexico is revised. Six species are documented, one new species Lactura nalli Matson & Wagner, sp. n. is described, and two new synonymies are proposed: Lactura psammitis (Zeller, 1872), syn. n. and L. rhodocentra(Meyrick, 1913), syn. n. One new subspecies Lactura subfervens sapeloensis Matson & Wagner, ssp. n. is also described. Adult and larval stages, male and female genitalia, are illustrated, a preliminary phylogeny is presented based on nuclear and mitochondrial data, distribution records provided for verified specimens, and the biology and life history for each species is briefly characterized. Phylogenetic analyses, larval phenotypes, and life history information reveal that much of the historic taxonomic confusion rampant across this group in North America traces to the phenotypic variation in just one species, L. subfervens (Walker, 1854).

Video on Rettenmeyer legacy released

The exhibit “The Legacy of a Lifetime of Collecting: The Carl and Rettenmeyer Story” that focuses on the inspiring lives of Carl and Marian Rettenmeyer, their scientific journey and the unique collection of army ants and their guests, opened to the public last October. The interactive exhibit emerged from the collaboration between Dr. Anna Lindemann and her students in Digital Media & Design (School of Fine Arts), and members of the AntU team in Ecology & Evolutionary Biology and the Connecticut State Museum of Natural History. A video highlighting the exhibit and the interdisciplinary collaboration that gave rise to it, as well as testimonials from students and relatives of Carl and Marian Rettenmeyer, is now released.


Exploring plant diversity at UCONN

Every other spring, Dr. Les teaches EEB 3271 Systematic Botany, covering the vast diversity of vascular plants. With 3,000 species, the EEB Biodiversity Education & Research Greenhouses enable students to explore global plant diversity and examine diagnostic traits of lineages on living samples from throughout the world. The course relies also on the extensive holdings of preserved plants in the George Safford Torrey Herbarium (CONN). Together these resources provide unique experiential learning opportunities to all students interested in biodiversity and plant evolution.

A Special Orchid Event at UConn

A special event celebrating Orchids presented by the Department of Ecology & Evolutionary Biology and the Connecticut State Museum of Natural History. Flyer

This event is FREE and open to the public.

When: Saturday, April , 11:00 am – 3:00 pm

Where: Biology/Physics Building Lobby, 91 North Eagleville Road, Storrs, CT 06269



11:00 am – 12:00 noon: Morning Tea with Charles Darwin—Almost Mad About the Wealth of Orchids

UConn Professor Kenneth Noll portrays history’s most famous biologist and naturalist, Charles Darwin. Charles Darwin’s 1862 book Fertilisation of Orchids explores natural theology and the relationship between insects and plants that resulted in their beautiful and complex forms. Tea and scones will be served.

12:00 — 1.30 pm: Between Talks Visit the EEB Greenhouses (and its orchids)

The greenhouses hold the broadest collection of global plant diversity in the Northeast—including over 200 species of orchids, many of which are not commonly grown. Staff will be on hand to guide visitors.

1:30 pm – 2:30 pm: Understanding Orchids with Renowned Author William Cullina 

William Cullina, President and CEO, Coastal Maine Botanical Gardens, Boothbay, ME

Orchids are the most diverse, mysterious, and exotic plants in the world. Their popularity as houseplants has surged in recent years as advances in nursery production have made them inexpensive and widely available. Drawing from his award-winning Understanding Orchids, Bill will explore the fascinating, challenging, and deeply rewarding world of orchids. You will never see them the same way again! |



New study enabled by the BRC

Physcomitrium pyriforme (Goffinet &  Smith)

The first ordinal phylogenetic study of mosses based on loci from all three genomic compartments was published by Liu et al. Dr. Liu and Medina were former research associates in the Goffinet lab. This study was made possible by the collections held in several herbaria including our CONN collections.

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. pdf

Abstract reads: Mosses are 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.