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Author Archives: Bernard Goffinet

New publication on mosses

Members of the Goffinet lab contributed to this study for which voucher specimens are deposited in the CONN herbarium.

Carvalho-Silva M., M. Stech, L.H. Soares-Silva, W.R. Buck, N. J. Wickett, Y. Liu & P.E.A.S. Câmara. 2017. A molecular phylogeny of the Sematophyllaceae sl (Hypnales) based on plastid, mitochondrial and nuclear markers, and its taxonomic implications. Taxon 66: 811–831.

Abstract reads: The Sematophyllaceae s.l. (Sematophyllaceae + Pylaisiadelphaceae) is a family of pleurocarpous mosses that is widely distributed throughout the globe, with centers of diversity in tropical forests. The circumscriptions of the family and its genera have been unstable, due to reductions in morphological complexity and alternative weightings of discrete morphological traits. Based on a sample spanning much of the generic diversity of the family, we inferred the phylogenetic relationships within the Sematophyllaceae s.l. from the variation in eight molecular markers from all three genomes (nuclear, mitochondrial, chloroplast). The Sematophyllaceae s.l. was resolved as monophyletic, as was the Sematophyllaceae s.str.; whereas the Pylaisiadelphaceae was found to be paraphyletic, although its monophyly could not be rejected. The morphological definition of the Pylaisiadelphaceae remains dubious, in the absence of unambiguous synapomorphies. The relationships of the clades of Pylaisiadelphaceae and Sematophyllaceae are discussed with respect to the circumscription of morphogenera, with a focus on the Sematophyllaceae crown clade (Aptychopsis, Chionostomum, Colobodontium, Donnellia, Macrohymenium, Paranapiacabaea, Pterogoniopsis, Rhaphidorrhynchium, Schroeterella, Sematophyllum, Warburgiella). Most genera of Sematophyllaceae were resolved as polyphyletic (e.g., Acroporium, Donnellia, Schroeterella, Sematophyllum, Trichosteleum) indicative of severe homoplasy in their putative diagnostic traits. We propose 4 new genera (Brittonodoxa, Microcalpe, Pocsia, Vitalia) and 19 new combina- tions (Aptychopsis cylindrothecia, A. estrellae, A. tequendamensis, Brittonodoxa allinckxiorum, B. cataractae, B. lithophila, B. squarrosa, B. steyermarkii, B. subpinnata, Microcalpe subsimplex, Pocsia matutina, Pterogoniopsis paulista, Schroeterella exigua, Trichosteleum amnigenum, T. lonchophyllum, Vitalia caespitosa, V. cuspidifera, V. esmeraldica, V. galipensis).

Endowment sponsored internship

Matt Brandt was offered a short internship this summer in the Biodiversity Collection to measure condylobasal (CB) length, using digital calipers, of about 1,000 of our 1,600 accessioned Fisher (Martes pennanti) skulls. He plans to use these data, in combination with data on CB lengths of skulls of American Pine Martens (Martes americana) for his Honors thesis. In addition, he transferred field measurements and data on reproductive status from original paper files to an excel table, from which they can be added to our specimen database.

New paper in Science Advances

Kevin Burgio and Veronica Bueno, currently graduate students in EEB, joined EEB alumnus Colin Carlson and others in reporting their study “Parasite biodiversity faces extinction and redistribution in a changing climate” in Science Advances. The study rests on data for countless samples preserved in natural history collections including the Biodiversity Research Collection EEB at UCONN.

Carlson, C.J., Burgio, K.R., Dougherty, E.R., Phillips, A.J., Bueno, V.M., Clements, C.F., Castaldo, G., Dallas, T.A., Cizauskas, C.A., Cumming, G.S. and Doña, J., 2017. Parasite biodiversity faces extinction and redistribution in a changing climate. Science Advances 3(9), p.e1602422.

The abstract reads: Climate change is a well-documented driver of both wildlife extinction and disease emergence, but the negative impacts of climate change on parasite diversity are undocumented. We compiled the most comprehensive spatially explicit data set available for parasites, projected range shifts in a changing climate, and estimated extinction rates for eight major parasite clades. On the basis of 53,133 occurrences capturing the geographic ranges of 457 parasite species, conservative model projections suggest that 5 to 10% of these species are committed to extinction by 2070 from climate-driven habitat loss alone. We find no evidence that parasites with zoonotic potential have a significantly higher potential to gain range in a changing climate, but we do find that ectoparasites (especially ticks) fare disproportionately worse than endoparasites. Accounting for host-driven coextinctions, models predict that up to 30% of parasitic worms are committed to extinction, driven by a combination of direct and indirect pressures. Despite high local extinction rates, parasite richness could still increase by an order of magnitude in some places, because species successfully tracking climate change invade temperate ecosystems and replace native species with unpredictable ecological consequences.

The book on tapeworms of the world

Drs. Janine Caira and Kirsten Jensen edited a special volume of the University of Kansas, Museum of Natural History publication entitled “Tapeworms from the vertebrate bowels of the earth” presenting the outcome of their NSF funded Planetary Biodiversity Inventory project. This publication is open source (available through the above link).

The preface reads: This document is organized into 22 peer-reviewed chapters. Each of the chapters focuses on an individual cestode group, begins with the status of knowledge of the group prior to the inception of the PBI project, and ends with an assessment of the current understanding of the group. In each case, diversity, classification, morphology, phylogenetic relationships, host associations, and geographic distribution are addressed. In all but one case, each chapter includes a list of valid taxa. Synonyms have not generally been listed; this was determined to be beyond the scope of the project given the immensity of such lists for some groups.  With over 3,000 valid species, the generation of a list of species for the Cyclophyllidea was also determined to be beyond the scope of this project. However, a list of valid higher taxa is provided. Each of the 19 cestode orders is addressed alphabetically in separate chapters with two exceptions. The Mesocestoididae are treated as a family in the Cyclophyllidea. Although evidence supporting recognition of the former as an independent order is mounting, the case remains to be formally made based on more detailed investigations of this enigmatic group of mammal parasites. The Onchoproteocephalidea are the second exception. So as to emphasize the dual nature of the host associations and scolex morphology of its members, the freshwater fish-parasitizing taxa (formerly assigned to the order Proteocephalidea) are treated in a chapter as the Onchoproteocephalidea I separately from the taxa that parasitize elasmobranchs, which are treated as the Onchoproteocephalidea II. Use of quotation marks around taxon names (e.g., the order “Tetraphyllidea”) is to remind readers of the definitively non-monophyletic nature of these groups. The first and last chapters are more synthetic in nature. The first chapter provides an overview of the results of the project both in terms of its Intellectual Merit and Broader Impact elements (to use NSF terminology). The final chapter provides a molecular framework for the phylogenetic relationships among the cestodes as they are understood at the end of the PBI project. The final chapter also describes the molecular methods and taxon sampling employed to achieve that framework. This Special Issue concludes with an Appendix listing the more than 220 publications directly resulting from project efforts, all of which cite the PBI award (NSF DEB Nos. 0818696 and 0818823).

The book on aquatic plants

Dr. Don Les, director of the CONN herbarium published his first treatment of the aquatic plants of North America: Aquatic Dicotyledons of North America: Ecology, Life History, and Systematics. Congratulations.

Summary: Aquatic Dicotyledons of North America: Ecology, Life History, and Systematics brings together a wealth of information on the natural history, ecology, and systematics of North American aquatic plants. Most books on aquatic plants have a taxonomic focus and are intended primarily for identification. Instead, this book provides a comprehensive overview of the biology of major aquatic species by compiling information from numerous sources that lie scattered among the primary literature, herbarium databases, and other reference materials. Included dicotyledon species are those having an obligate (OBL) wetland status, a designation used in the USACE National Wetland Plant List. Recent phylogenetic analyses are incorporated and rationale is provided for interpreting this information with respect to species relationships. This diverse assemblage of information will be useful to a wide range of interests including academic researchers, wildlife managers, students, and virtually anyone interested in the natural history of aquatic and wetland plants. Although focusing specifically on North America, the cosmopolitan distribution of many aquatic plants should make this an attractive text to people working virtually anywhere outside of the region as well. This book is an essential resource for assisting with wetland delineation.


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.