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Author Archives: Bernard Goffinet

New publication on mosses

Lily Lewis published the last paper from her dissertation as an invited paper in the Special November issue of the American Journal of Botany. All collections from Nepal, Alaska, Norway, Chile and Papua New Guinea are deposited in the CONN herbarium, and will serve further studies to assess species delimitations.

Lewis L.R., S. Carey, K. Holzinger, S.F. McDaniel, R. Rozzi & B. Goffinet. Resolving the source region for the long-distance dispersal event that gave rise to the Magellanic sub-Antarctic endemic dung moss Tetraplodon fuegianus (Bryopsida: Splachnaceae). American Journal of Botany (in press). pdf

Abstract reads: PREMISE OF THE STUDY: American bipolar plant distributions characterize taxa at various taxonomic ranks but are most common in the bryophytes at infra-specifi c and infrageneric levels. A previous study on the bipolar disjunction in the dung moss genus Tetraplodon found that direct long-distance dispersal from North to South in the Miocene–Pleistocene accounted for the origin of the Southern American endemic Tetraplodon fuegianus , congruent with other molecular studies on bipolar bryophytes. The previous study, however, remained inconclusive regarding a specifi c northern hemisphere source region for the transequatorial dispersal event that gave rise to T. fuegianus .

METHODS: To estimate spatial genetic structure and phylogeographic relationships within the bipolar lineage of Tetraplodon , which includes T. fuegianus , we analyzed thousands of restriction-site-associated DNA (RADseq) loci and single nucleotide polymorphisms using Bayesian individual assignment and maximum likelihood and coalescent model based phylogenetic approaches.

KEY RESULTS: Northwestern North America is the most likely source of the recent ancestor to T. fuegianus.

CONCLUSIONS: Tetraplodon fuegianus , which marks the southernmost populations in the bipolar lineage of Tetraplodon , arose following a single long-distance dispersal event involving a T. mnioides lineage that is now rare in the northern hemisphere and potentially restricted to the Pacifi c Northwest of North America. Furthermore, gene fl ow between sympatric lineages of Tetraplodon mnioides in the northern hemisphere is limited, possibly due to high rates of selfi ng or reproductive isolation.

New publications on plants

Two new publications from the Les lab on Elatine, a genus of aquatic plants:

1. Razifard, H., D. H. Les & G. C. Tucker. 2017. Reticulate evolution in Elatine L.(Elatinaceae), a predominantly autogamous genus of aquatic plants. Systematic Botany 42: 87-95. pdf

Abstract reads: The study of hybridization in aquatic plants is complicated by rarity of flower production, absence of roots, and asexuality. Elatine is a cosmopolitan genus of aquatic flowering plants with about 25 species worldwide. Historically, there has been little concern regarding hybridization in the genus due to the prevalence of autogamy (i.e. self-pollination), which potentially limits xenogamous pollen transfer among the species. Two morphologically complex species (Elatine hexandra and E. americana) are the only known polyploids in the genus. In previous phylogenetic analyses, both species resolved incongruently in gene trees obtained from nuclear (ITS) versus plastid (matK/trnK and rbcL) regions. Suspecting that the phylogenetic incongruence might be a consequence of past hybridization events, we tested that hypothesis by conducting an additional phylogenetic analysis of Elatine, which incorporated sequences from a low copy nuclear gene (phyC). Elatine hexandra and E. americana were the only Elatine species exhibiting intraspecific polymorphic sites, i.e. heterozygosity, in phyC. Allele specific amplification enabled us to resolve these polymorphisms for inclusion in a phylogenetic analysis along with the monomorphic phyCsequences within species obtained for the remaining Elatine species. The phyC tree confirmed that both polyploids probably are allopolyploids, in a pattern consistent with the placement of the putative parental taxa in previous phylogenetic analyses of ITS, matK/trnK,and rbcL sequence data. The distributions of E. americana and E. hexandra, along with their potential parental species, are consistent with the proposed hybrid origins for the polyploids and provide additional clues on their geographic regions of origin.

2. Razifard, H., A. J. Rosman, G. C. Tucker & D. H. Les. 2017. Systematics of the cosmopolitan aquatic genus Elatine. Systematic Botany 42: 73–86. pdf

Abstract reads: The cosmopolitan genus Elatine (Elatinaceae) includes about 25 aquatic species of mostly diminutive aquatic plants, whose relationships have not been evaluated using a phylogenetic approach. The taxonomic study of this group has been complicated by the small stature of the plants, their minute reproductive structures, and their cosmopolitan distribution. Consequently, much uncertainty exists with respect to species delimitations, their geographical distributions, and interspecific relationships. To clarify the infrageneric classification of Elatine and to provide insights on interspecific relationships within the genus, we conducted a phylogenetic study of nearly all (24) of the currently recognized species using both morphological and molecular data. The tree topology obtained based on morphological data (including vegetative and reproductive characters) was less-resolved than the trees based on molecular data, derived from either nuclear (ITS) or two plastid regions (matK/trnK and rbcL). However, the tree topology obtained from combined morphological and molecular data was well resolved and placed the morphologically distinctive E. alsinastrum as the sister group of the remaining species, which fell within two major clades: a clade of 4-merous-flowered species and a clade of 3-merous species, within which was embedded a subclade of 2-merous species. Although a number of topological differences occurred between the ITS and plastid tree topologies, significant incongruence was observed only for the placements of E. americana and E. hexandra, possibly resulting from reticulate evolution. Bergia, the sister genus of Elatine, comprises larger species, which often are mostly helophytic but never truly aquatic. Ancestral state reconstructions based on the ITS tree indicated that a morphological reduction series (in stature and floral merosity) exists among Elatine species, which is best explained as a consequence of adaptation to their aquatic life. These phylogenetic analyses also have helped to clarify the infrageneric classification of the genus and to provide a better understanding of the natural and nonindigenous distributions of the species. The new monotypic section Elatine sect. Cymifera , including E. brochonii, is described.

New publications on parasites

Three new studies were published by the Caira lab in EEB that further highlight the diversity and evolution of parasites.

1. Bueno V. M.  & J. N. Caira. 2017. Redescription and molecular assessment of relationships among three species of Echeneibothrium (Rhinebothriidea: Echeneibothriidae) parasitizing the Yellownose Skate, Dipturus chilensis, in Chile. Journal of Parasitology 103: 268–284. pdf

Abstract reads: Much progress has recently been made in revising the taxonomic assignments of genera originally classified in the polyphyletic “Tetraphyllidea.” Many of these genera, including Echeneibothrium, were accommodated in the order Rhinebothriidea. However, beyond this larger taxonomic action, little work has been conducted on this genus over the past 50 yr. Consequently, the criteria used for characterizing species of Echeneibothrium have lagged behind those typically used in more modern descriptions of elasmobranch-hosted cestode taxa. A series of collecting trips to Chile to obtain cestodes from the yellownose skate, Dipturus chilensis, provided a unique opportunity to apply modern morphological and molecular methods to investigate the 3 species of Echeneibothrium reported parasitizing this skate, specifically Echeneibothrium megalosoma, Echeneibothrium multiloculatum, and Echeneibothrium williamsi. In addition to redescribing all 3 species, using morphological data from light and scanning electron microscopy, maximum likelihood and bayesian inference phylogenetic analyses of the D1–D3 regions of the 28S rDNA gene were conducted to assess their relationships among other echeneibothriids for which comparable data are available. Sequencing of 59 specimens representing these 3 species of Echeneibothrium allowed us to assess the intra- and interspecific variation in the 28S rDNA gene. The redescriptions use standardized terminology for scolex morphology, proglottid anatomy, and microthrix forms and pattern; they also expand on the original descriptions to include data on scolex size, ovary size, vas deferens and vaginal configurations, testes arrangement, and genital pore position. Our morphological work led to a major reinterpretation of the scolex morphology with the recognition that all 3 species bear an apical bothridial sucker, rather than an apical loculus, prompting emendation of the diagnosis for the family Echeneibothriidae. The presence of a band of spinitriches at the apex of the apical modification of the scolex proper seems to represent an important feature for distinguishing the 2 portions of the myzorhynchus across species. Intraspecific variation ranged from 0 to 7 bp across species and interspecific variation ranged from a low of 39–46 bp between E. williamsi and E. multiloculatum to a high of 61–66 bp between E. multiloculatum and E. megalosoma. Phylogenetic analyses indicate that the 3 species of Echeneibothrium hosted by the yellownose skate are not each other’s closest relatives, suggesting multiple colonization events of D. chilensis have occurred. Further phylogenetic investigation is also likely to confirm the status of the genus Pseudanthobothrium as a synonym of Echeneibothrium because its species generally group among members of Echeneibothrium.

2. Caira, J. N., C. J. Healy, F. P. Marques & K. Jensen. 2017. Three new genera of rhinebothriidean cestodes from stingrays in Southeast Asia. Folia parasitologica 64: 008. pdf

Abstract reads: Three genera of rhinebothriideans, previously referred to as New genus 1, New genus 2 and New genus 4, are erected in the the Anthocephaliidae. New genus 1 is established as Divaricobothrium gen. n., with Divaricobothrium tribelum sp. n. as its type species; Echeneibothrium trifidum Shipley et Hornell, 1906 is transferred to the genus as Divaricobothrium trifidum (Shipley et Hornell, 1906) comb. n. This genus is unique among rhinebothriidean genera in bearing bothridia that are posteriorly deeply divided into two lobes with facial loculi but no apical sucker, and a vagina that extends to near the anterior margin of the proglottid. Its species parasitise Indo-Pacific members of the genera Brevitrygon Last, Naylor et Manjaji-Matsumoto, Maculabatis Last, Naylor et Manjaji-Matsumoto and Pateobatis Last, Naylor et Manjaji-Matsumoto. New genus 2 is established as Barbeaucestus gen. n., with Barbeaucestus jockuschae sp. n. as its type species; Barbeaucestus ralickiae sp. n. is also described. Anthobothrium sexorchidum Williams, 1964 and Rhinebothrium shipleyi Southwell, 1912 are transferred to the genus as Barbeaucestus sexorchidus (Williams, 1964) comb. n. and Barbeaucestus shipleyi (Southwell, 1912) comb. n., respectively. This genus is unique among rhinebothriidean genera in that its bothridia are substantially wider than long, bear an apical sucker and at least one row of two or more facial loculi in their anterior half. Its species parasitise the genera Neotrygon Castelnau and Taeniura Müller et Henle. New genus 4 is established as Sungaicestus gen. n. with transfer of Rhinebothrium kinabatanganensis Healy, 2006, as Sungaicestus kinabatanganensis (Healy, 2006) comb. n., as its type species. Among the genera of its order, this genus most closely resembles Rhinebothrium Linton, 1890, however, despite the original description, the bothridia were found to bear, rather than lack, apical suckers. This monotypic genus is known only from the freshwater stingray Urogymnus polylepis (Müller et Henle). The familial diagnosis of the Anthocephaliidae Ruhnke, Caira et Cox, 2015 is emended. The family now houses five genera.

3. Gallagher K., J. N. Caira & M. Cantino. 2017. Ultrastructure of cell types within the scolex and cephalic peduncle of the litobothriidean tapeworm, Litobothrium aenigmaticum. Invertebrate Biology 136: 243–259. pdf

Abstract readsLitobothrium aenigmaticum Caira, Jensen, Waeschenbach, & Littlewood 2014 is a cestode species that parasitizes pelagic thresher sharks in Taiwan and the Gulf of California. A previous study using light microscopy suggested the scolex contains four types of unusual tissues, one of which was considered to aid in adhesion of the worm to the mucosa of the spiral intestine. The function of the other tissues was unknown. Also unknown was the function of two laterally paired ducts found extending throughout the length of the worm. The goal of the present study was to use transmission electron microscopy (TEM) to examine the internal anatomy of the scolex and cephalic peduncle of this tapeworm in more detail. Three specimens from Taiwan were examined with TEM and two with light microscopy. Transmission electron microscopy revealed that the laterally paired ducts were excretory, since they were closely associated with numerous protonephridia. The number of cell types, previously referred to as tissues, in the scolex was expanded to 11 based on a combination of features including cell size, nucleus size, ratio of the maximum diameter of the nucleus to maximum diameter of the whole cell, and types of observed organelles, as well as the presence or absence of cytoplasmic electron-dense and electron-lucent vesicles. The cytoplasm of all 11 cell types was found to include electron-dense vesicles, and all types were periodic acid-Schiff (PAS) positive. This suggests that the electron-dense vesicles may contain glycoproteins and/or mucoproteins. As all 11 cell types occurred within the region of the scolex that is surrounded by a papilla of host mucosa at the site of tapeworm attachment, we hypothesize that one or more of these cell types may produce a substance that induces this inflammatory reaction. The specific products in the secretory vesicles and how those products are released are still unclear, as are any relationships between or among the cell types in terms of products produced. Further research will be necessary to fully understand the complexity of this organism.

New publication on algae

Simona Augyte who completed her Ph.D. dissertation in EEB with Dr. C. Yarish, lead-authored a publication focused on the brown alga Saccharina angustissima. Specimens studied are deposited in the CONN herbarium. The reference of the publication is: Augyte, S., L. Lewis, S. Lin, C. D. Neefus and C. Yarish. 2018. Speciation in the exposed intertidal zone: the case of Saccharina angustissima comb. nov. & stat. nov. (Laminariales, Phaeophyceae). Phycologia 57: 100–112. pdf

The abstract reads: Saccharina latissima is a perennial kelp with a circumboreal distribution from the North Pacific to the North Atlantic coasts. Our study clarified the taxonomy of the morphologically distinct Saccharina latissima forma angustissima (Collins) A.Mathieson from the low intertidal zone on exposed islands and ledges of Casco Bay, Maine, USA. To identify genetic divergence between the two morphotypes, S. latissima and S. latissima f. angustissima, we used a multilocus phylogenetic approach including nuclear-encoded internal transcribed spacer, mitochondrial cox1 and cox3, and plastid-encoded rbcL gene sequences. Genetic analysis of the individual markers and combined data set using SVDquartets resulted in p-distance values for all markers of , 1%, suggesting low divergence between the two forms. However, there was as much or more genetic divergence between S. latissima and S. latissima f. angustissima as there were between other taxonomically accepted species of Saccharina. To investigate sexual compatibility between the two forms, we made reciprocal crosses of the gametophytes and observed sporophyte formation. All crosses were successfully grown to the juvenile sporophyte stage, suggesting that the two are reproductively compatible in vitro. It is unknown if the two populations freely hybridize in the field. Last, we compared wave action, the ecological factor most likely driving the unique morphology, at exposed sites with S. latissima f. angustissima and protected sites with S. latissima. The mean wave force at the exposed site was over 30 times higher in magnitude than at the protected site at 160.04 6 32.58 N and 4.75 6 6.75 N, respectively, during the summer. The significant differences in morphology, the lack of specimens with intermediate morphologies, and the results of a common garden experiment suggest that the morphological differences in S. latissima f. angustissima are heritable with a genetic basis. Therefore, on the basis of our molecular evidence coupled with ecological studies, we are elevating S. latissima f. angustissima (Collins) A.Mathieson to specific rank as S. angustissima (Collins) Augyte, Yarish & Neefus comb. nov.& stat. nov.

Biases in herbarium collections

Dr. Daru (Harvard) and collaborators are presenting a study of holdings of herbaria in three regions with complete digitized floras, including New England, and thus based on CONN specimens. Their study, entitled “Widespread sampling biases in herbaria revealed from large-scale digitization” is to appear in the New Phytologist.

The summary reads: 

  • Nonrandom collecting practices may bias conclusions drawn from analyses of herbarium records. Recent efforts to fully digitize and mobilize regional floras online offer a timely opportunity to assess commonalities and differences in herbarium sampling biases.
  • We determined spatial, temporal, trait, phylogenetic, and collector biases in c. 5 million herbarium records, representing three of the most complete digitized floras of the world: Australia (AU), South Africa (SA), and New England, USA (NE).
  • We identified numerous shared and unique biases among these regions. Shared biases included specimens collected close to roads and herbaria; specimens collected more frequently during biological spring and summer; specimens of threatened species collected less frequently; and specimens of close relatives collected in similar numbers. Regional differences included overrepresentation of graminoids in SA and AU and of annuals in AU; and peak collection during the 1910s in NE, 1980s in SA, and 1990s in AU. Finally, in all regions, a disproportionately large percentage of specimens were collected by very few individuals. We hypothesize that these mega-collectors, with their associated preferences and idiosyncrasies, shaped patterns of collection bias via ‘founder effects’.
  • Studies using herbarium collections should account for sampling biases, and future collecting efforts should avoid compounding these biases to the extent possible.

New publication on lichens

Antoine Simon, now a Ph.D. student at the University of Liège, Belgium, published his assembly and study of the structure of the mitochondrial genome in a lichen forming fungus: Simon, A., Y. Liu, E. Sérusiaux & B. Goffinet. 2017. Complete mitogenome sequence of Ricasolia amplissima (Lobariaceae) reveals extensive mitochondrial DNA rearrangement within the Peltigerales (lichenized ascomycetes). The Bryologist 120(3): 335–339. pdf

Antoine initiated this study while visiting UConn in 2015, and completed it during his stay last spring. The voucher and other collections made by Antoine are deposited in the CONN herbarium.

Abstract reads: The structure of mitochondrial genomes varies among non-lichenized fungi in terms of their genic and intronic content and genic order. Whether lichenized fungal mitogenomes are equally labile is unknown due to the paucity of available mitogenomes. We assembled the mitogenome of Ricasolia amplissima (Peltigerales, Lobariaceae), using massive parallel sequencing, and compared its structure to that of two species of Peltigera (Peltigeraceae). The mitochondrial genome of R. amplissima comprised 82,333 bp, with a 29.8% G+C content, and holds 15 unique protein-coding genes, 29 tRNA genes, two rRNA genes, and one non-coding RNA gene. Although the protein-coding gene content in the mitogenome of Peltigera and Ricasolia was identical, the relative gene order differed substantially, revealing that significant gene rearrangements also characterize the evolution of mitogenomes of lichenized ascomycetes at a relatively shallow phylogenetic depth, such as within the order Peltigerales.

The BRC featured in UCONN today

The significance of the Biodiversity Research Collection to undergraduate and graduate education, its role in a global community of institutions in recording changes in biodiversity through time and its critical contribution to the discovery of new species have been highlighted and shared with the UConn community through an article published in UConn today.

Collection in UCONN magazine

In a recent article entitled “Flocking to Storrs. A birder’s tour of campus” in the UCONN magazine the value of the collection of starlings in the Biodiversity Research Collection is highlighted.

New herbarium manager

Dr. Sarah Taylor will join EEB as the new herbarium collection manager in early November.

Sarah is a Connecticut native who became passionate about plants as an undergraduate. She has spent the last 15 years exploring some of North America’s diverse botanical habitats, from remote gypsum outcrops of the Chihuahuan Desert, to the awe-inspiring vistas of the alpine tundra of the Rocky Mountains, to the sandhills, blackwater swamps, and inner coastal plain of South Carolina.  At the University of Texas at Austin, she examined the evolution of edaphic endemism in Nama (Hydrophyllaceae) using morphological and molecular systematics methods to investigate what patterns we can observe to explain how approximately 20% of the species in this group became partially or totally restricted to gypsum deposits. Most recently, Sarah has been the Collections Manager at the A.C. Moore Herbarium at the University of South Carolina (USCH), where her focus was on databasing incoming accessions and preserving the herbarium of Henry William Ravenel, a prominent South Carolina botanist active during the Civil War.

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).