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. pumila, D. laticollis, D. 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 polyrhiza. American 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

Given the interest in EEB5500 is being offered for a second time this academic year. The enrollment reached capacity and includes nine undergraduates (juniors and seniors from CLAS and the College of Agriculture), three MS and three PhD students. The course is led by Jane O’Donnell, Sue Hochgraf and Robert Capers, with participation of EEB faculty. Students will be introduced to the management of natural history collection, with discussions on ethics, ownership, mission, etc. and learn also how to mount insects and vascular plants and prepare vertebrates for preservation in our Biodiversity Research Collections.

A study on the evolutionary history of a lineage of bugs, by colleagues from Argentina and the Smithsonian was recently published in Zoological Journal of the Linnean Society. It is based in part on paratypes and other specimens collected by Dr. Jane O’Donnell that are deposited in our insect collection.

Dellapé P.M., M.C. Melo & T.J. Henry. 2016. A phylogenetic revision of the true bug genus Heraeus (Hemiptera: Rhyparochromidae: Myodochini), with the description of two new genera and 30 new species. Zoological Journal of the Linnean Society 177: 29–134. pdf

The abstract reads: Prior to this study, the genus Heraeus Stål, 1862 included 14 species, all of which are restricted to the Western Hemisphere. Three species are known from the Nearctic Region, nine from the Neotropical Region, and two mainly tropical elements are distributed in both regions. In this contribution, we consider Heraeus cincticornis Stål, 1874 a junior synonym of Heraeus elegans (Walker, 1873), select a lectotype for Heraeus coquilletti Barber, 1914, and neotype for Lygaeus triguttatus Guérin-Méneville, 1857, and describe 28 new species. In addition, the two new genera, Baranowskiobius gen. nov., to include H. elegans (Baranowskiobius elegans comb. nov.) and two new species, and Paraheraeus gen. nov., to include Heraeus eximius Distant, 1882 (Paraheraeus eximius comb. nov.), are described. Previously described species and new taxa are (re)described and illustrated, including male genitalia. Scanning electron micrographs, general habitus photographs, and distribution maps are included for all species studied. A phylogenetic analysis comprising 46 terminal taxa and 50 morphological characters was performed, and five species groups were hypothesized, including the coquilletti, caliginosus, guttatus, illitus, and plebejus groups. All known species of Heraeus and the new genera are included in the phylogenetic analysis. The type species of the genera Myodocha Latreille, 1807, Orthaea Dallas, 1852, and Paisana Dellapé, 2008 are used as out-groups.

Recent publications from the Les lab on plant systematics, for which voucher specimens are deposited in the CONN herbarium:

Ross T. G., C. F. Barrett, M. S. Gomez, V. K.-Y. Lam, C. L. Henriquez, D. H. Les, J. I. Davis, A. Cuenca, G. Petersen, O. Seberg, M. Thadeo, T. J. Givnish, J. Conran, D. W. Stevenson & S. W. Graham.  2016. Plastid phylogenomics and molecular evolution of Alismatales.  Cladistics 32: 160–178. pdf

Abstract reads: Past phylogenetic studies of the monocot order Alismatales left several higher-order relationships unresolved. We addressed these uncertainties using a nearly complete genus-level sampling of whole plastid genomes (gene sets representing 83 protein-coding and ribosomal genes) from members of the core alismatid families, Tofieldiaceae and additional taxa (Araceae and other angiosperms). Parsimony and likelihood analyses inferred generally highly congruent phylogenetic relationships within the order, and several alternative likelihood partitioning schemes had little impact on patterns of clade support. All families with multiple genera were resolved as monophyletic, and we inferred strong bootstrap support for most inter- and intrafamilial relationships. The precise placement of Tofieldiaceae in the order was not well supported. Although most analyses inferred Tofieldiaceae to be the sister-group of the rest of the order, one likelihood analysis indicated a contrasting Araceae-sister arrangement. Acorus (Acorales) was not supported as a member of the order. We also investigated the molecular evolution of plastid NADH dehydrogenase, a large enzymatic complex that may play a role in photooxidative stress responses. Ancestral-state reconstructions support four convergent losses of a functional NADH dehydrogenase complex in Alismatales, including a single loss in Tofieldiaceae.

Razifard H., D. H. Les & G. C. Tucker.  2016.  Evidence for the transfer of Elatine rotundifolia to Linderniaceae. Systematic Botany 41: 665–671. pdf

Abstract reads: Elatine rotundifolia was described in 2008 from Ecuador as a new species because of its unique morphology and geographical distribution. However, an examination of type material for E. rotundifolia suggested to us initially that this taxon had been assigned incorrectly to Elatine, despite some superficial similarity to that genus. This possibility was investigated using morphological and molecular data. We found that E. rotundifolia differed from other members of Elatine by several vegetative and reproductive features, which indicated a distant alliance closer to Linderniaceae (Lamiids; Asterids) rather than Elatinaceae (Fabids; Superrosids). We then conducted a phylogenetic analysis of DNA sequences from the internal transcribed spacer region, which included isotype material of E. rotundifolia, as well as various representatives of Elatinaceae, Linderniaceae, and other angiosperm clades. The molecular data resolved E. rotundifolia among several accessions of Micranthemum (Linderniaceae) in a position quite remote phylogenetically from accessions of Bergia and Elatine (Elatinaceae). From these results, we conclude that the name E. rotundifolia refers to a taxon that was misplaced in Elatine, and represents instead a member of Micranthemum (Linderniaceae), and possibly is synonymous with the aquatic species M. umbrosum.

Razifard H., G. C. Tucker, L. Ahart & D. H. Les.  2016.  Noteworthy collections. California. Elatine americana. Madroño 63: 3–4.

King U. M. & D. H. Les.  2016.  A significant new record for Hydrilla verticillata (Hydrocharitaceae) in central Connecticut.  Rhodora 118: 306–309. pdf

The Elphick lab published further results from their ongoing studies on tidal marsh sparrows. Feathers collected as part of this study are deposited in the collection.

Reference: Borowske A.C., C. Gjerdrum & C.S. Elphick. 2017. Timing of migration and prebasic molt in tidal marsh sparrows with different breeding strategies: comparisons among sexes and species. Auk: Ornithological Advances 134:51–64. pdf

The abstract reads: Breeding strategies can shape the timing of other events and processes, including arrival on the breeding grounds, prebasic molt, and departure for fall migration. We studied these relationships in sympatric Saltmarsh Sparrows (Ammodramus caudacutus) and Seaside Sparrows (A. maritimus), 2 closely related species with notably different breeding strategies. On average, females of both species arrived on the breeding grounds later, initiated molt later, and departed from the breeding grounds later than did conspecific males. Furthermore, we found that female Saltmarsh Sparrows—which mate with multiple males and care for nests, eggs, and chicks alone—were last to arrive on the breeding grounds and last to initiate molt, had the shortest molt duration, and were last to depart for the nonbreeding grounds. Both species exhibited protandry, but Seaside Sparrows averaged earlier arrival on the breeding grounds than Saltmarsh Sparrows. Molt and departure timing also differed between the species, with Seaside Sparrows initiating molt and departing before same-sex Saltmarsh Sparrows. These observations support the hypotheses that breeding strategies can influence arrival timing and that reproductive investment can have carryover effects on molt and departure.

This past summer earnings from the collection endowment allowed us to offer internships to several undergraduates who acquired skills in specimen curation, databasing and communicating about their findings. See a brief description of their work here.

EEB5500 has once again a full enrollment of undergraduate and graduate students who will be introduced to the management of natural history collection. The course is led by Jane O’Donnell, Sue Hochgraf and Robert Capers, with participation of EEB faculty. Student learn among other thing how to mount insects and vascular plants and prepare vertebrates for preservation in our Biodiversity Research Collections.

The Goffinet lab  contributed to a phylogenomic reconstruction of the Sphagnopsida, and some of the vouchers are deposited in the CONN herbarium.

Shaw A.J., N. Devos, Y. Liu, C. J. Cox, B. Goffinet, K.I. Flatberg & B. Shaw. 2016. Organellar phylogenomics of an emerging model system: Sphagnum (peatmoss). Annals of Botany 118: 185–196.

The abstract reads:

Background and Aims: Sphagnum-dominated peatlands contain approx. 30 % of the terrestrial carbon pool in the form of partially decomposed plant material (peat), and, as a consequence, Sphagnum is currently a focus of studies on biogeochemistry and control of global climate. Sphagnum species differ in ecologically important traits that scale up to impact ecosystem function, and sequencing of the genome from selected Sphagnum species is currently underway. As an emerging model system, these resources for Sphagnum will facilitate linking nucleotide variation to plant functional traits, and through those traits to ecosystem processes. A solid phylogenetic framework for Sphagnum is crucial to comparative analyses of species-specific traits, but relationships among major clades within Sphagnum have been recalcitrant to resolution because the genus underwent a rapid radiation. Herein a well-supported hypothesis for phylogenetic relationships among major clades within Sphagnum based on organellar genome sequences (plastid, mitochondrial) is provided.

Methods: We obtained nucleotide sequences (273 753 nucleotides in total) from the two organellar genomes from 38 species (including three outgroups). Phylogenetic analyses were conducted using a variety of methods applied to nucleotide and amino acid sequences. The Sphagnum phylogeny was rooted with sequences from the related Sphagnopsida genera, Eosphagnum and Flatbergium.

Key Results: Phylogenetic analyses of the data converge on the following subgeneric relationships: (Rigida (((Subsecunda) (Cuspidata)) ((Sphagnum) (Acutifolia))). All relationships were strongly supported. Species in the two major clades (i.e. Subsecunda + Cuspidata and Sphagnum + Acutifolia), which include >90 % of all Sphagnum species, differ in ecological niches and these differences correlate with other functional traits that impact biogeochemical cycling. Mitochondrial intron presence/absence are variable among species and genera of the Sphagnopsida. Two new nomenclatural combinations are made, in the genera Eosphagnum and Flatbergium.

Conclusions: Newly resolved relationships now permit phylogenetic analyses of morphological, biochemical and ecological traits among Sphagnum species. The results clarify long-standing disagreements about subgeneric relationships and intrageneric classification.

Two studies citing plant specimens deposited in the CONN herbarium were published recently:

Connolly B.A. & I.L. Hale. 2016. Lepidium latifolium (Brassicaceae): Invasive perennial pepperweed observed in Rhode Island. Rhodora 118: 229–231.

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