UConn rainforest Now Home to Collection of Unique Ginger Relatives

see press release: “UConn rainforest acquires major collection of ginger relatives”

 

One new exhibit at the University of Connecticut’s Ballard Institute and Museum of Puppetry entitled  “Army Ants and their Guests: Works Inspired by the Carl and Marian Rettenmeyer Collection” opened last week and can be visited until February 9th. To read more about the opening, go to the article in the Daily Campus.

The BRC endowment provided opportunities for students to work in the collections during the summer. In the living plant collection, the student attended to essential horticultural task and help with the acquisition of a significant collection of Zingiberales (ginger relatives, over 200 species) which will greatly enhance the UConn living collections and directly support EEB faculty looking at a number of important questions utilizing the ginger family as a model system.  A number of the recently acquired gingers are also new to science and will hopefully be described and published in the near future.

In the vertebrate collection, student completed checking the fluid levels of the spirit preserved collection of fish, reptiles and amphibians, deaccessioning specimens that were dried out, or lacking data. Finally, all peccary skulls are now kept in archival boxes.

Thank you to the supporters of the BRC that make these internships possible.

 

Dr. Stan Malcolm, an UCONN alum in Systematics and Entomology, has volunteered since 2017, to assist in the curation of the insect collection. He has reorganized several families of beetles, and he is shown here with his latest accomplishment: the weevils. The taxonomy of this group is now current, with all specimens transferred to new unit trays, and all trays with new labels. Great Job Dr. Malcolm!

A unique collection of mites associated with hummingbird pollinated flowers, assembled over nearly 50 years by Dr. Robert Colwell, Distinguished Emeritus Professor in EEB, is now housed in the Biodiversity Research Collection. The collection consists of thousands of specimens mounted on slides, with nearly 3000 specimens from about 50 species identified to genus and species, and 578 specimens used in original descriptions of 16 species of hummingbird flower mites.

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.

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.

Another 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.

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.