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Author Archives: Bernard Goffinet

Army Ant Guest exhibit opened

The exhibit on the life of army ants and their guests has opened in the Biology/Physics building (see UCONN today).  The public opening drew close to 300 visitors on Sunday, who discovered the giant ant and its eight guests, the 100 photographs illustrating the tiny and unique guests, and actual specimens displayed under microscopes and engaged in activities to earn and collect the guest buttons. Many guests toured the Biodiversity Research Collection, guided by EEB graduate students highlighting its richness and scientific value.  Visit the AAGC Facebook book page for more news on the curation of and activities related to the AAGC.

Bob Capers is awarded Fernald Award

Robert S. Capers (CONN’s collection manager) and Nancy G. Slack are being recognized by the New England Botanical Club’s Merritt Lyndon Fernald Award for the Best Paper published in Rhodora Volume 118 (2016) for their paper entitled “A baseline study of alpine snowbed and rill communities on Mount Washington, NH” (Rhodora 118: 345–381). pdf.  CONGRATULATIONS

Official announcement reads: The Fernald Award Committee notes that “Capers and Slack provide a very nice analysis of rill and snowbed communities on Mt. Washington. The authoritative inclusion of both phanerogams and cryptogams, the numerous years of field work, and the multiple observations within a year to get good data on the duration of snowpack on the different sites, exemplify the quality of this study. The statistical analysis is used in a way that enhances the interpretation of the field observations. Capers and Slack have done their work in a way that is designed as a baseline to be built upon in the future, and they have documented a snow melt gradient that suggests predictions of which particular sites may be most vulnerable.” The committee also states that “if more studies were designed this way to become resources or opportunities for future workers, we would all be in a better position to understand the nature of rapid change in time and space.”

The abstract reads: Quantitative data on the abundance and frequency of vascular plants, bryophytes and lichens are lacking for alpine snowbed and rill communities in northeastern North America. Such data are needed to establish whether the communities are changing in response to climate warming, nitrogen deposition or shifts in the timing of precipitation and snowmelt. We surveyed nine sites (five snowbeds and four rills) on Mount Washington (White Mountain National Forest, New Hampshire), recording 54 vascular plant species, 42 bryophytes and 13 lichens. Although vascular plants were most abundant, bryophytes and lichens, which had not been completely surveyed in these communities previously, were important in terms of species richness (as many as eight bryophytes and four lichens in 1 m2 quadrats) and were occasionally abundant, particularly bryophytes in rills. We found that snowbeds and rills are separate communities. Some species are shared, but far higher numbers of vascular plants, bryophytes and lichens were found in one community but not the other. The most frequent vascular plants had been reported as common in snowbeds and rills previously. However, several species that are common in these communities elsewhere occurred less often in our sites because of variation occurring both across the region and within the White Mountains. Our research provides baseline information on snowbeds and rill plant communities so that future studies can determine how they respond to changes in environmental conditions.

New publication: invasive plants

John Silander and colleagues (all EEB alumni) published their research on the effects of climate change on invasive species in New England in the Proceedings of the National Academy of Sciences. Vouchers for their research are deposited in the CONN herbarium.

Citation: Merow, C., S.T. Bois, J.M. Allen, Y. Xie & J.A. Silander. 2017. Climate change both facilitates and inhibits invasive plant ranges in New England. Proceedings of the National Academy of Sciences 114(16): E3276-E3284. pdf

The significance of the study: Invasive species are often expected to benefit from novel conditions encountered with global change. Our range models based on demography show that invasive Alliaria petiolata (garlic mustard) may have much lower establishment in New England under future climate, despite prolific success under current climate, whereas other invasive and native plants may expand their ranges. Forecasts suggest that management should focus on inhibiting northward spread of A. petiolata into unoccupied areas and understanding source–sink population dynamics and how community dynamics might respond to loss of A. petiolata (it modifies soil properties). Our methods illustrate inadequacy of current approaches to forecasting invasions in progress, which are based on correlations between species’ occurrence and environment and illustrate critical need for mechanistic studies.

New publication on plant radiation

Nora Mitchell, who defended her dissertation this week, lead a study on the radiation of the charismatic South African genus Protea L., which appeared in the American Journal of Botany.

Mitchell N., P.O. Lewis, E.M. Lemmon, A.R. Lemmon & K.E. Holsinger. 2017. Anchored phylogenomics improves the resolution of evolutionary relationships in the rapid radiation of Protea L. American Journal of Botany 104: 102–115. pdf

The abstract reads: PREMISE OF THE STUDY: Estimating phylogenetic relationships in relatively recent evolutionary radiations is challenging, especially if short branches associated with recent divergence result in multiple gene tree histories. We combine anchored enrichment next-generation sequencing with species tree analyses to produce a robust estimate of phylogenetic relationships in the genus Protea (Proteaceae), an iconic radiation in South Africa.

METHODS: We sampled multiple individuals within 59 out of 112 species of Protea and 6 outgroup species for a total of 163 individuals, and obtained sequences for 498 low-copy, orthologous nuclear loci using anchored phylogenomics. We compare several approaches for building species trees, and explore gene tree–species tree discrepancies to determine whether poor phylogenetic resolution reflects a lack of informative sites, incomplete lineage sorting, or hybridization.

KEY RESULTS: Phylogenetic estimates from species tree approaches are similar to one another and recover previously well-supported clades within Protea, in addition to providing well-supported phylogenetic hypotheses for previously poorly resolved intrageneric relationships. Individual gene trees are markedly different from one another and from species trees. Nonetheless, analyses indicate that differences among gene trees occur primarily concerning clades supported by short branches.

CONCLUSIONS: Species tree methods using hundreds of nuclear loci provided strong support for many previously unresolved relationships in the radiation of the genus Protea. In cases where support for particular relationships remains low, these appear to arise from few informative sites and lack of information rather than strongly supported disagreement among gene trees.

New type specimens added to CONN

Colleagues in California described a new species of moss, and several types (i.e., specimen upon which the original description is based) are deposited in the CONN herbarium, further enhancing its significance as a biodiversity repository.

Toren, D. R., K. M. Kellman, and J. R. Shevock. Archidium crassicostatum (Archidiaceae), a new and long-overlooked species from California, USA. Madroño 63: 348–352. pdf

AbstractArchidium crassicostatum D.R. Toren, Kellman & Shevock is described and illustrated, and is currently known from two counties from California. It appears to be the sole species of the genus from the state and is well marked by its exceptionally wide costa, which can occupy as much as one third the width of the leaf base. Previous reports of Archidium alternifolium (Dicks. ex Hedw.) Schimp. and A. donnellii Austin from California are actually A. crassicostatum. Details of habitat, ecology, and distribution are given and morphological distinctions among similar-looking but unrelated taxa are discussed.


Historical plant collections databased

Undergraduate students working in the G.S. Torrey Herbarium have finished a 3-year project that involved creating high-resolution digital images of nearly 33,000 specimens donated by the Delta Institute in Maine. Most of the specimens were collected by members of the Hadwen Botanical Club at Clark University in Worcester, Massachusetts, in the 1930s and 1940s. The botanists at the time were attempting to collect one specimen of every species in every town in Worcester County, which is the largest county in Massachusetts. Now that all of the images have been created, the UConn students have begun using the images to enter information about the specimens – when and where they were collected, for instance – into a database that already contains information on all other specimens in the herbarium (about 210,000 specimens in all). The database makes specimen information available online to botanists all over the world so the information can be used in research on plant systematics, variation within plant species, changes in flowering time and other subjects

New publications: parasitology

Two new publications from the Caira lab on parasites, with vouchers deposited in the BRC collections:

1. Bernot J. P., J.N. Caira & M. Pickering. 2016. Diversity, phylogenetic relationships and host associations of Calliobothrium and Symcallio (Cestoda:‘Tetraphyllidea’) parasitising triakid sharks. Invertebrate Systematics 30: 616–634. pdf

Abstract reads: The laciniate, relatively large-bodied tetraphyllidean tapeworm genus Calliobothrium van Beneden, 1850 parasitises triakid sharks with all but one species found parasitising sharks of the genus Mustelus Linck, 1790. Historically, species of this genus were thought to exhibit a relaxed degree of host specificity relative to species of their sister genus Symcallio Bernot, Caira, & Pickering, 2015. However, several more recent studies have begun to question this difference and, in particular, the conspecificity of specimens identified as the types species, C. verticillatum (Rudolphi, 1819) van Beneden, 1850, from multiple host species. Our results suggest that diversity in the genus Calliobothrium has been under-reported. To explore this situation, specimens previously identified as C. verticillatum were collected from Mustelus asterias Cloquet, 1819 off the United Kingdom and Mustelus canis (Mitchell, 1815) off Connecticut, USA; these sharks each were found to host distinct species both of which are described here. Mustelus asterias was also confirmed to host Symcallio leuckarti (van Beneden, 1850) Bernot, Caira & Pickering, 2015, which is redescribed. In combination with newly collected material from Mustelus palumbes Smith, 1957 off South Africa and data available from GenBank, molecular phylogenetic analyses based on 28S rDNA data for four of the seven known species of Calliobothrium, including both new species and five of the 11 known species of Symcallio, were conducted. The resulting phylogeny supports the mutual monophyly of the two genera, which are readily distinguished based on whether they exhibit proglottid laciniations, and supports subclades of Symcallio with and without hook accessory pieces. These subclades of Symcallio appear to exhibit an intriguing congruence with two known subclades of their host genus, Mustelus.


2. Koontz A. & J.N. Caira. 2016. Emendation of Carpobothrium (“Tetraphyllidea”) from Bamboosharks (Orectolobiformes: Hemiscyliidae) with redescription of Carpobothrium chiloscyllii and description of a new species from Borneo. Comparative Parasitology 83: 149–161. pdf

Abstract reads: Collection of new material from the bamboosharks Chiloscyllium indicum (Gmelin, 1789) and Chiloscyllium hasseltii Bleeker, 1852, from Indonesian and Malaysian Borneo prompted reevalutation of the identity and host associations of the cestode genus Carpobothrium Shipley and Hornell, 1906. Light microscopical examination of whole mounts, histological sections, and egg preparations, in combination with scanning electron microscopy of scoleces, led to redescription of the type species Carpobothrium chiloscyllii Shipley and Hornell, 1906, from Ch. indicum, as well as description of a new species from Ch. hasseltii. The proglottid anatomy of C. chiloscyllii is described for the first time. The genus was confirmed to exhibit pouch-like bothridia with relatively small anterior and posterior flaps that have a tendency to retract into the bothridial pouches, testes that are entirely pre‐poral, a uterus that extends only to the cirrus sac, and a vas deferens that coils posterior to the cirrus sac. Although not previously reported for the genus, both species were determined to possess an apical sucker on the anterior margin of the anterior bothridial flap. The posterior coiling of the vas deferens allowed free gravid proglottids of the new Carpobothrium species to be distinguished from those of Yorkeria Southwell, 1927, and to determine that, while eggs of the former are spherical with bipolar filaments, those of the latter are spindle-shaped with unipolar filaments. Examination of some of Southwell’s material identified as C. chiloscyllii from the batoid hosts Urogymnus asperrimus Bloch and Schneider, 1801 and Rhynchobatus djeddensis Forsskål, 1775, in Sri Lanka, confirmed evidence from molecular work suggesting that these cestodes, which also bear pouch-like bothridia, represent a distinct group of cestodes from those parasitizing bamboosharks. This work both confirms the association of Carpobothrium species with sharks of the genus Chiloscyllium Müller and Henle, 1837, and paves the way for establishment of a novel genus for the taxa parasitizing batoids

New publication: lichenology

Nicolas Magain who visited UCONN while working on his Master’s thesis (via the uNiversity of Liège, Belgium) and then completed his dissertation project on symbiotic associations within the lichen forming fungal genus Peltigera, published his main chapter:  Magain N., J. Miadlikowska, B. Goffinet, E. Sérusiaux, & F. Lutzoni. 2017. Macroevolution of specificity in cyanolichens of the genus Peltigera Section Polydactylon (Lecanoromycetes, Ascomycota). Systematic Biology 66: 74–99. pdf

The study is based on numerous specimens from the CONN herbarium.

Abstract reads: Patterns of specificity among symbiotic partners are key to a comprehensive understanding of the evolution of symbiotic systems. Specificity of mutualistic partners, within a widespread monophyletic group for which all species are sampled has rarely been explored. Here, we assess the level of specificity between the cosmopolitan lichen-forming fungus (mycobiont) from the genus Peltigera, section Polydactylon, and its cyanobacterial partner Nostoc (cyanobiont). The mycobiont and cyanobiont phylogenies are inferred fromfive nuclear loci and the rbcLX region, respectively. These sequences were obtained from 206 lichen thalli, representing ca. 40 closely related Peltigera species sampled worldwide, doubling the number of known species in this group. We found a broad spectrum of specificity for both partners ranging from strict specialists to generalists. Overall, mycobionts aremore specialized than cyanobionts by associating mostly with one or a few Nostoc phylogroups, whereas most cyanobionts associate frequently with several Peltigera species. Specialist mycobionts are older than generalists, supporting the hypothesis that specialization of mycobionts to one or few cyanobionts, is favored through time in geographic areas where species have been established for long periods of time. The relatively recent colonization of a new geographic area (Central and South America) by members of section Polydactylon is associated with a switch to a generalist pattern of association and an increased diversification rate by the fungal partner, suggesting that switches to generalism are rare events that are advantageous in new environments. We detected higher genetic diversity in generalist mycobionts. We also found that Peltigera species specialized on a single Nostoc phylogroup have narrower geographical distributionscompared with generalist species.

Emily Meineke: collections, herbivory and climate change

MeinekeDr. Emily Meineke, a former Ph.D. student of EEB alum Rob Dunn and now a NSF postdoctoral fellow at Harvard, is visiting the BRC to study our vast collection of New England plant specimens deposited in the CONN herbarium. She screens specimens for evidence of herbivory as part of her research focused on changes in incidences of herbivory through time, and hence changing climates (more info on this project).

New publications: phycology

Three new publications from the lab of Louise Lewis:

1. Khan-Bureau D.A., E.A. Morales, L. Ector, M.S. Beauchene & L.A. Lewis. 2016. Characterization of a new species in the genus Didymosphenia and of Cymbella janischii (Bacillariophyta) from Connecticut, USA. European Journal of Phycology 51: 203–216.  pdf

Abstract reads:Two non-native stalk-forming diatoms that were recently observed in the West Branch of the Farmington River, a tributary of the Connecticut River in Connecticut (USA), are characterized morphologically and barcode marker sequences were obtained for each of them. Cymbella janischii, the dominant stalk-forming species during the summer of 2012, previously had not been found in the northeastern USA. Samples of C. janischii were examined microscopically and used to obtain four sequences of the barcode marker, the V4 region of the 18S rDNA gene. Phylogenetic analysis indicated that the four independent sequences of C. janischiiwere distinct from, but most closely related to, published sequences of C. janischii from Idaho and C. mexicana from Texas, USA. A second non-native stalk-producing diatom, resembling Didymosphenia geminata, was found in November 2012 – June 2013 and first reported as Didymosphenia sp. Over this period, the observed cells had a compressed morphology and were consistently small compared with D. geminata. Sequences of the V4 region, obtained from three independent direct polymerase chain reactions (PCR) of single cells isolated from the Connecticut samples, indicated a close relationship to three published sequences of D. geminata from Italy, New Zealand and the USA, and to D. siberica and D. dentatafrom Russia. Frustules of the cells used in the PCR reactions were recovered and examined using scanning electron microscopy, providing a direct link between the observed morphology and sequence data. The morphology of the novel Connecticut Didymosphenia taxon was compared with that of other Didymosphenia taxa, being most similar to D. pumilaD. laticollisD. grunowii and smaller cells of D. geminata. Didymosphenia sp. had a triundulate morphology with a consistent length of 40–60 µm. Given the unique morphological features of this diatom, it is proposed as a new species, Didymosphenia hullii Khan-Bureau, sp. nov.

2. Watanabe S., K. Fučíková, P.O. Lewis & L.A. Lewis. 2016. Hiding in plain sight:  Koshicola spirodelophila gen. et sp. nov. (Chaetopeltidales, Chlorophyceae), a novel green alga associated with the aquatic angiosperm Spirodela polyrhizaAmerican Journal of Botany 103: 865–875. pdf

The abstract reads: Discovery and morphological characterization of a novel epiphytic aquatic green alga increases our understanding of Chaetopeltidales, a poorly known order in Chlorophyceae. Chloroplast genomic data from this taxon reveals an unusual architecture previously unknown in green algae. Using light and electron microscopy, we characterized the morphology and ultrastructure of a novel taxon of green algae. Bayesian phylogenetic analyses of nuclear and plastid genes were used to test the hypothesized membership of this taxon in order Chaetopeltidales. With next-generation sequence data, we assembled the plastid genome of this novel taxon and compared its gene content and architecture to that of related species to further investigate plastid genome traits. The morphology and ultrastructure of this alga are consistent with placement in Chaetopeltidales (Chlorophyceae), but a distinct trait combination supports recognition of this alga as a new genus and species—Koshicola spirodelophila gen. et sp. nov. Its placement in the phylogeny as a descendant of a deep division in the Chaetopeltidales is supported by analysis of molecular data sets. The chloroplast genome is among the largest reported in green algae and the genes are distributed on three large (rather than a single) chromosome, in contrast to other studied green algae. The discovery of Koshicola spirodelophila gen. et sp. nov. highlights the importance of investigating even commonplace habitats to explore new microalgal diversity. This work expands our understanding of the morphological and chloroplast genomic features of green algae, and in particular those of the poorly studied Chaetopeltidales.

The abstract reads: On the basis of prior phylogenetic analyses placing Gloeomonas as a lineage within the very diverse genus Chloromonas, it was hypothesized that the morphologically distinct Gloeomonas, bearing widely spaced basal bodies, evolved from ancestral organisms like Chloromonas. In addition, the phylogenetically related Chloromonas (Cr.rubrifilum, was expected to possess traits intermediate to the two forms. To test these hypotheses, we performed detailed transmission electron microscope analysis on nine species of these genera. The species were divided into two categories on the basis of ultrastructural features: group 1, consisting of four diverse species of Chloromonas and Ixipapillifera, had a V-shaped basal body arrangement, and group 2, of Cr. rubrifilum and four Gloeomonas species, forming a single clade possessing widely spaced basal bodies. Members of group 1 commonly had a simple, flat plate-like distal connecting fiber (dcf), three or sometimes two microtubules in the sinister root, continuous dexter and sinister striated microtubule-associated fibers (SMAFs), and a coarsely striated proximal fiber (CSPF) at the posterior-most regions of the basal bodies and probasal bodies, but lacked proximal and median proximal connecting fibers. Group 2 inherited these features, but had novel traits including the elongation and modification of the dcf, SMAFs, and CSPF that occurred with separation of basal bodies during growth, a dcf-associated layered structure, as well as protruding flagellar collars. The ultrastructural traits of Gloeomonas are interpreted as being evolutionarily modified from an ancestral Chloromonas morphology. Specific ultrastructural features were determined to be useful in characterizing these genera. Cr. rubrifilum of group 2 was not intermediate morphologically, but possessed the traits of Gloeomonas; thus G. rubrifilum comb. nov. was proposed.

3. Watanabe S., H. Nozaki, T. Nakada & L.A. Lewis. 2016. Comparative ultrastructural analysis of Chloromonas and Gloeomonas: Tracing the origin of Gloeomonas-specific flagellar apparatus traits and a proposal for Gloeomonas rubrifilum comb. nov. Phycologia 55: 585–601. pdf