The database of 9,888 mammal specimens in the Biodiversity Research Collection has now been published for all the research world to see. Our data are now available through the VertNet data portal and also through the Global Biodiversity Information Facility, a.k.a. GBIF and the iDigBio data portal. Publishing our data in these portals enhances the value of our collection, providing data on species occurrences and indicating the availability of specimens for loans to researchers. The database can be continually updated as new specimens are accessioned and as new information is gathered. As we continue to update the mammal database we are also working to complete and publish databases of our fishes, amphibians and reptiles, and birds.

On Thursday 4/14, starting at 3, the Department of Ecology and Evolutionary Biology, and more specifically the Biodiversity Research Collections, is hosting a reception in the Biology Physics atrium, honoring the career of mammalogist Ralph Wetzel, who retired in the mid-1980s after 40 years on faculty here.  Among other things he discovered that the Chacoan peccary was not extinct but was alive and well.  Ralph published an article in the prestigious journal Science in 1975 for this discovery.

The reception will include remarks by one of his former students, still living in the area, and by one of our grad students who set up a new display case in the atrium featuring Wetzel.  Wetzel family members will be present, coming from Florida and Maine.

The reception will be followed by a presentation at 4 pm by Phil Myers, who was a colleague of Wetzel’s and recently retired from the University of Michigan.

The first analysis of transcriptomes of pleurocarpous mosses led by Matt Johnson (postdoc with norman Wickett in Chicago) appeared: Johnson M.G., C. Malle, B. Goffinet, A.J. Shaw & N.J. Wickett. 2016. A phylotranscriptomic analysis of gene family expansion and evolution in the largest order of pleurocarpous mosses (Hypnales, Bryophyta). Molecular Phylogenetics and Evolution 98: 29–40.

Most vouchers for this study are deposited in the CONN herbarium.

The abstract reads: The pleurocarpous mosses (i.e., Hypnanae) are a species-rich group of land plants comprising about 6,000 species that share the development of female sex organs on short lateral branches, a derived trait within mosses. Many of the families within Hypnales, the largest order of pleurocarpous mosses, trace their origin to a rapid radiation less than 100 million years ago, just after the rise of the angiosperms. As a result, the phylogenetic resolution among families of Hypnales, necessary to test evolutionary hypotheses, has proven difficult using one or few loci. We present the first phylogenetic inference from high-throughput sequence data (transcriptome sequences) for pleurocarpous mosses. To test hypotheses of gene family evolution, we built a species tree of 21 pleurocarpous and six acrocarpous mosses using over one million sites from 659 orthologous genes. We used the species tree to investigate the genomic consequences of the shift to pleurocarpy and to identify whether patterns common to other plant radiations (gene family expansion, whole genome duplication, or changes in the molecular signatures of selection) could be observed. We found that roughly six percent of all gene families have expanded in the pleurocarpous mosses, relative to acrocarpous mosses. These gene families are enriched for several gene ontology (GO) terms, including interaction with other organisms. The increase in copy number coincident with the radiation of Hypnales suggests that a process such as whole genome duplication or a burst of small-scale duplications occurred during the diversification. In over 500 gene families we found evidence of a reduction in purifying selection. These gene families are enriched for several terms in the GO hierarchy related to ‘‘tRNA metabolic process.” Our results reveal candidate genes and pathways that may be associated with the transition to pleurocarpy, illustrating the utility of phylotranscriptomics for the study of molecular evolution in non-model species.

 

Drs. Janine N. Caira and Jane O’Donnell spoke on WILI’s Wayne Norman show (AM 1400) about the Biodiversity Research Collection, and in particular the Army Ant Guest Collection and the recent NSF award for the preservation, curation and databasing of the collection. Enjoy the show!

Drs. J.N. Caira,  J. O’Donnell and B. Goffinet were awarded funds by the “Collections in Support of Biological Research” program at the National Science Foundation for transferring ownership and securing the future and accessibility of the Carl W. and Marian E. Rettenmeyer army ant guest collection (AAGC; see abstract below). For more info on the collection and Carl W. and Marian E. Rettenmeyer visit the AAGC website.

Abstract of proposal at time of award: Army ants live in highly complex societies, accompanied by legions of tiny, intimate associates (primarily mites and insects). The study of these host/symbiont systems is precluded by a lack of access to basic information and knowledge about their biology, including physical collections. Resulting from 50 years of fieldwork, the Rettenmeyer Army Ant Guest Collection (AAGC) at the University of Connecticut (UConn) is an unparalleled resource for studying complex systems of social insects. The AAGC comprises more than two million specimens of New World army ants and their associated guests: Hundreds of species of mites, beetles, flies, wasps, springtails, and bristletails. Extensive field notes and numerous photographs complement the biological specimens, detailing intricacies of species interactions. This project will stabilize this collection, addressing critical issues. This project aims to address basic physical storage issues and to make all data publicly available via an on-line database so as to maximize its potential as a source of information on social behavior in insects. A two-part exhibit will engage the campus community. One part will highlight the Rettenmeyers’ collecting activities. Across campus, the second part will include a large ant model complete with an array of mites attached all to scale.

This project is motivated by the recent donation of the Rettenmeyer Army Ant Guest Collection (AAGC) to the UConn Department of Ecology & Evolutionary Biology Biodiversity Research Collection Facility. The AAGC comprises more than 2 million specimens of New World army ants and their associated arthropods. It includes ca. 1,000 types representing 200 species, ca. 16,000 pinned specimens, ca. 5,000 microscope slides, more than 15,000 vials and jars, complemented by detailed field data and 5,000 Kodachrome transparencies. The collection is in dire need of stabilization – fluid levels are low, stoppers are deteriorating, specimens are overcrowded and disorganized. The project’s two primary goals are specimen curation (e.g., replacing fluid, re-vialing, labeling, attaching barcodes, and reorganization) and establishing an on-line presence by modifying an existing MySQL database to accommodate the AAGC in four related Tables. Type specimens and colony exemplars will be image and linked to database records. Data will be shared with iDigBio and the Global Biodiversity Information Facility. High school students will work with graduate students to hone their writing and observation skills as they interpret slide labels to populate the database.

 

New publication referring to specimens deposited in the CONN herbarium:

Bellemare J. & C. Deeg. 2015. Horticultural escape and naturalization of Magnolia tripetala in western Massachusetts: Biogeographic context and possible relationship to recent climate chanage. Rhodora 117: 371–383. pdf

Davis C.C., C.G. Willis, B. Connolly, C. Kelly & A.M. Ellison. 2015. Herbarium records are reliable sources of phenological change driven by climate and provide novel insights into species’ phenological cueing mechanisms. American Journal of Botany 102: 1599–1609. pdf

Fučíková K. 2015. A new record of the rare freshwater red alga Tuomeya americana(Batrachospermaceae, Rhodophyta) from Connecticut. Rhodora 117: 342–353. pdf

Gerke J.M., E.J. Farnsworth & W.E. Brumback. 2015. Fifteen years of change: What a comparison of the two Flora Conservanda lists can tell us about rare plant species in the New England landscape. Rhodora 116:428–493. pdf

Hale I.L., B.A. Connolly & R. Bartaula. 2015. The occurrence of hybrid barberry, Berberis X ottawensis (Berberidaceae) in New Hampshire and Rhode Island. Rhodora 117: 384–387. pdf

New algae from Antarctica!

Sciuto, K., L.A. Lewis, E. Verleyen, I. Moro & N. LaRocca (2015) Chodatodesmus australis sp. nov. (Scenedesmaceae, Chlorophyta) from Antarctica, with the emended description of the genus Chodatodesmus, and circumscription of Flechtneria rotunda gen. et sp. nov.  Journal of Phycology 51: 1172-1188. doi: 10.1111/jpy.12355

Abstract: The family Scenedesmaceae is a taxonomically complicated group due to its simple morphology, high phenotypic plasticity, and the presence of cryptic taxa. Over the years several taxonomic revisions, based on molecular data, affected the family. Here, we describe a new scenedesmacean species from Antarctica, Chodatodesmus australis, based on phylogenetic analyses of data from nuclear (ITS2 spacer, 18S rDNA), and plastid (rbcL, tufA) markers. Morphological (LM and SEM) and ultrastructural (TEM) observations, carried out both on the holotype of C. australis and on the generitype of Chodatodesmus, allow us to emend the original generic description of this genus. Our molecular and phylogenetic data also reveal the existence of a new monotypic genus, Flechtneria, inside the family Scenedesmaceae and lead to the taxonomic reassignment of some microalgal strains available in International Culture Collections to new taxa. Of the considered genomic regions, the tufA gene was the easiest to amplify and sequence and it showed the highest phylogenetic signal, even if the number of sequences already available for this marker in the public databases was considerably lower than for the other chosen loci. The rbcL gene also provided good phylogenetic signal, but its amplification and sequencing were generally more problematic. The nuclear markers gave lower phylogenetic signals, but the 18S rDNA allowed distinction at the genus level and the ITS2 spacer had the advantage that secondary structures could be considered in the analyses. The use of more than one molecular locus is suggested to obtain reliable results in the characterization of scenedesmacean strains.

Two new studies  on bryophytes and for which vouchers are deposited in the BRC  have been published:

The first is part of Lily Lewis’s dissertation and focuses on comparisons of entire organellar genomes and the nuclear rDNA repeat among populations of Tetraplodon fuegianus in the Cape Horn Region:  Lewis, L., Y. Liu, R. Rozzi & B. Goffinet. 2016. Infraspecific variation within and across complete organellar genomes and nuclear ribosomal repeats in a moss. Molecular Phylogenetics and Evolution 96: 195–199. doi:10.1016/j.ympev.2015.12.005  pdf

The abstract reads: Bryophytes (mosses, liverworts, and hornworts) are diverse and ecologically and evolutionarily significant yet genome scale data sets and analyses remain extremely sparse relative to other groups of plants, and are completely lacking at the infraspecific level. By sequencing the complete organellar genomes and nuclear ribosomal repeat from seven patches of a South American sub-Antarctic neo-endemic non-model moss, we present the first characterization of infraspecific polymorphism within and across the three genomic compartments for a bryophyte. Diversity within patches is accounted for by both intraindividual and interindividual variation for the nuclear ribosomal repeat and plastid genome, respectively. This represents the most extensive infraspecific genomic dataset generated for an early land plant lineage thus far and provides insight into relative rates of substitution between organellar genomes, including high rates of nonsynonymous to synonymous substitutions.

The other studies is a phylogegraphic analysis of Bryoxiphium, a genus of scattered distribution in the Northern Hemisphere, with disjunct occurrences on Mauritius: Patiño, J., B. Goffinet, M. Sim-Sim & A. Vanderpoorten. 2016. Is the sword moss (Bryoxiphium) a preglacial Tertiary relict? Molecular Phylogenetics and Evolution 96: 200–206. doi:10.1016/j.ympev.2015.12.004 pdf

The abstract reads: The disjunction of floras between East Asia, Southeast North America, West North America, and Southwest Eurasia has been interpreted in terms of the fragmentation of a once continuous mixed mesophytic forest that occurred throughout the Northern Hemisphere due to the climatic and geological changes during the late Tertiary. The sword moss, Bryoxiphium, exhibits a distribution that strikingly resembles that of the mesophytic forest elements such as Liriodendron and is considered as the only living member of an early Tertiary flora in Iceland. These hypotheses are tested here using molecular dating analyses and ancestral area estimations. The results suggest that the extant range of Bryoxiphium results from the fragmentation of a formerly wider range encompassing North America and Southeast Asia about 10 million years ago. The split of continental ancestral populations is too recent to match with a continental drift scenario but is spatially and temporally remarkably congruent with that observed in Tertiary angiosperm relict species. The timing of the colonization of Iceland from Macaronesian ancestors, about two million years ago, is, however, incompatible with the hypothesis that Bryoxiphium is the only living member of an early Tertiary flora of the island. Alaska was recurrently colonized from East Asia. The ability of Bryoxiphium to overcome large oceanic barriers is further evidenced by its occurrence on remote oceanic archipelagos. In particular, Madeira was colonized twice independently from American and East Asian ancestors, respectively. The striking range disjunction of Bryoxiphium is interpreted in terms of its mating system, as the taxon exhibits a very singular pattern of spatial segregation of the sexes.

Greenhouse Fridays: join a tour of the greenhouse collection of approximately 3000 plant species (that is ±1% of the world diversity!) from around the world

January 29: Professor Terry Webster on January 29; 12:15 pm – 1.30 pm.

The collections are featured in UCONN magazine, and follow the link to this video about biological illustrations.