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.

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

Abstract: Archidium 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.

 

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

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

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.

Dr. 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).

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