Anna K. Monfils

Phylogeny of the euglenales based upon combined SSU and LSU rDNA sequence comparisons and description of Discoplastis gen. nov. (Euglenophyta)

A Bayesian analysis, utilizing a combined data set developed from the small subunit (SSU) and large subunit (LSU) rDNA gene sequences, was used to resolve relationships and clarify generic boundaries among 84 strains of plastid‐containing euglenophytes representing 11 genera. The analysis produced a tree with three major clades: a Phacus and Lepocinlis clade, a Discoplastis clade, and a Euglena, Colacium, Trachelomonas, Strombomonas, Monomorphina, and Cryptoglena clade. The majority of the species in the genus Euglena formed a well‐supported clade, but two species formed a separate clade near the base of the tree. A new genus, Discoplastis, was erected to accommodate these taxa, thus making the genus Euglena monophyletic. The analysis also supported the monophyly of Colacium, Trachelomonas, Strombomonas, Monomorphina, and Cryptoglena, which formed two subclades sister to the Euglena clade. Colacium, Trachelomonas, and Strombomonas, all of which produce copious amounts of mucilage to form loricas or mucilaginous stalks, formed a well‐supported lineage. Our analysis supported retaining Strombomonas and Trachelomonas as separate genera. Monomorphina and Cryptoglena formed two well‐supported clades that were sister to the Colacium, Trachelomonas, and Strombomonas clade. Phacus and Lepocinclis, both of which have numerous small discoid chloroplasts without pyrenoids and lack peristaltic euglenoid movement (metaboly), formed a well‐supported monophyletic lineage that was sister to the larger Euglena through Cryptoglena containing clade. This study demonstrated that increased taxon sampling, multiple genes, and combined data sets provided increased support for internal nodes on the euglenoid phylogenetic tree and resolved relationships among the major genera in the photosynthetic euglenoid lineage.

Monophyly and Phylogeny of Monarda (Lamiaceae): Evidence from the Internal Transcribed Spacer (ITS) Region of Nuclear Ribosomal DNA

Abstract The phylogenetic relationships of the 16 species of Monarda (Lamiaceae) were investigated using sequences of the internal transcribed spacer regions of nuclear ribosomal DNA. Thymus and Mentha were used as outgroups, and Blephilia, Clinopodium, Conradina, Hesperozygis, Monardella, Pycnanthemum, and Ziziphora were included in the ingroup to test the monophyly of Monarda. Two parsimony searches were performed after removing redundant sequences from the analysis: one with indels scored as missing and a second with indels treated as binary characters. Both searches yielded congruent results, but the treatment of indels as binary characters resulted in considerably more resolution within Monarda. There was strong support for the monophyly of Monarda and a close relationship was found between Monarda, Blephilia, and Pycnanthemum. The molecular phylogeny was completely congruent with the infrageneric classification of the genus. Our results were consistent with hypotheses of hybridization between M. fistulosa and M. lindheimeri in Texas. Despite considerable morphological variation among many species, especially in floral characters, little molecular diversification was found in those same species groups. Intraspecific polymorphism in ITS sequence was found in over half the species examined, and may be attributable to ancestral polymorphism, hybridization, or detection of paralogous loci. Communicating Editor: Jim Smith

Characterization of paramylon morphological diversity in photosynthetic euglenoids (Euglenales, Euglenophyta)

Monfils A.K., Triemer R.E. and Bellairs E.F. 2011. Characterization of paramylon morphological diversity in photosynthetic euglenoids (Euglenales, Euglenophyta). Phycologia 50: 156–169. DOI: 10.2216/09-112.1 A characteristic feature of euglenoid cells is the presence of a β1–3 glucan storage product called paramylon. The euglenoid lineage is tremendously diverse, with a great deal of variation in paramylon grain morphology. Number, shape, location and external morphology of paramylon have been used as diagnostic features for several euglenoid species. The goals of this study were to examine and characterize the paramylon grains from a variety of different species in vivo and in vitro, provide a consistent, descriptive terminology that can be used to describe paramylon grain types, and discuss the potential phylogenetic utility of paramylon grain morphology. Over 1000 light microscopy images were examined to survey paramylon diversity across the Euglenales, and scanning electron microscopy was used to examine paramylon in 11 representative species (Colacium vesiculosum, Cryptoglena skujae, Discoplastis spathirhyncha, Euglena gracilis, Lepocinclis acus, L. ovum, Monomorphina pyrum, Phacus orbicularis, P. pleuronectes, Strombomonas borystheniensis, and Trachelomonas ellipsoidalis). The various types of paramylon grains were separated into six distinct morphological categories: disk, ellipse, pyrenoid cap, plate, bobbin or rod, with further distinction for varieties found within each category. These categories were then applied to the diversity found in the genera and major lineages. This study was able to determine a high level of distinction among differing paramylon grain morphologies both within a species and among species, and variation was found in both large and small grains. Paramylon can be used at the generic level to support major clades and generic relationships and may provide insight into the taxonomic placement of euglenoids currently unavailable for sequencing.

Monophyly and Phylogeny of Schoenoplectus and Schoenoplectiella (Cyperaceae): Evidence from Chloroplast and Nuclear DNA Sequences

Abstract Relationships within Schoenoplectus and Schoenoplectiella are largely unknown and the phylogenetic positions of these genera relative to the other four genera in Fuireneae and clade of Cypereae are unclear. A few studies with sparse or localized sampling have added valuable insights, but a North American sampling and a broad global perspective are needed. To generate a more robust phylogenetic hypothesis, we increased the number and breadth of taxon sampling in Schoenoplectus and Schoenoplectiella, including all constituent species in North America, all genera in Fuireneae, and strategically sampled genera in Cypereae. Phylogenetic relationships were estimated using DNA sequences from the nuclear ribosomal ITS region, chloroplast DNA trnL intron and trnL-trnF intergenic spacer region, and partial chloroplast DNA ndhF coding region and parsimony, likelihood, and Bayesian analyses. The proposed phylogeny reveals Pseudoschoenus, Schoenoplectiella, and Cypereae are supported as a clade, and Schoenoplectiella is paraphyletic and sister to Pseudoschoenus. Schoenoplectus is monophyletic, sister to Actinoscirpus. Schoenoplectus sections Schoenoplectus and Malacogeton were resolved; comprehensive sampling in Schoenoplectus section Schoenoplectus and unclear placement of S. californicus suggests the need to examine formerly recognized section Pterolepis. The proposed phylogeny supports the erection of sections in Schoenoplectiella, but indicates further morphological and molecular data is needed for section diagnoses. Two Cypereae taxa previously resolved in a Schoenoplectiella clade were included in this analysis: Scirpoides varia resolved in a clade with Cypereae taxa, and Isolepis humillima resolved within Schoenoplectiella. Results from the phylogenetic hypotheses support a need to revisit the generic placement of Isolepis humillima and revise Fuireneae to resolve tribal paraphyly.

Testing the spectral diversity hypothesis using spectroscopy data in a simulated wetland community

Abstract The spectral diversity hypothesis proposes that as the number of plant species increases for a given area, the diversity of spectra observed from that area should also increase. This approach could be very useful as an assessment and monitoring tool to help ecologists understand the spatial and temporal patterns of biodiversity without relying on consistently detecting individual species. While the spectral diversity hypothesis has been examined for a wide range of ecosystems using a variety of remote sensing data, it has not been tested using spectroscopy (i.e. hyperspectral) data for wetlands. Previous studies have not explicitly considered the impact that flowers may have on spectral diversity and how this may impact the spectral diversity hypothesis. To test the spectral diversity hypothesis and the potential impact on flowers, we used a simulation approach to combine leaf and flower spectra collected from a diverse prairie fen wetland ecosystem into datasets of virtual plots with varying levels of species diversity and different combination of species. To address the high dimensionality of the data, we compared spectral diversity and floristic diversity using partial least squares regression. Our results found that defining floristic diversity using the Shannons diversity index, which accounts for plant abundance in each plot, produced the best predictive models where the predicted values had a RMSE less than 40% of the mean observed value. We also found that the inclusion of flower spectra with leaf spectra did increase the RMSE of the best model, but across all models, correlation increased. Our results indicate that spectral diversity could be used as an initial biodiversity assessment tool for wetlands, especially with on-going advancements in unmanned aerial vehicle technology that can provide a low altitude platform for imaging spectroscopy.

A Five Gene Phylogenetic Study of Fuireneae (Cyperaceae) with a Revision of Isolepis humillima

Abstract Cyperaceae tribe Fuireneae consists of six genera (Actinoscirpus, Pseudoschoenus, Fuirena, Bolboschoenus, Schoenoplectus, and Schoenoplectiella) and approximately 155 species distributed widely across all continents except Antarctica. Recent molecular analyses suggest that Fuireneae is paraphyletic with respect to Cypereae, but limited taxonomic sampling and low branch support have resulted in unresolved relationships among key genera. To address the potential paraphyly of Fuireneae as well as intratribal and intertribal relationships, thirty taxa representing major lineages from the six Fuireneae genera within Cypereae were sequenced for five coding and non-coding regions from the nuclear (internal transcribed spacer, ITS) and chloroplast (trnL intron/ trnL-trnF spacer; partial ndhF, rbcL and matK genes) genomes. Maximum parsimony, maximum likelihood and Bayesian analyses of the dataset strongly support Fuireneae as a grade of three clades: (1) Fuirena, (2) Bolboschoenus and (3) a group composed of Cypereae and the four remaining Fuireneae genera (Schoenoplectus, Schoenoplectiella, Actinoscirpus, and Pseudoschoenus). Individual and combined gene trees consistently position Isolepis humillima within a well supported clade consisting of species in Schoenoplectiella sect. Schoenoplectiella. Based on molecular evidence, we transfer Isolepis humillima to Schoenoplectiella humillima, and suggest that a large-scale revision of tribal limits is required to reflect the natural relationships of the genera currently treated in Fuireneae.

Natural History Collections: Teaching About Biodiversity Across Time, Space, and Digital Platforms

Abstract Natural history collections offer unique physical and virtual opportunities for formal and informal progressive learning. Collections are unique data in that they each represent a biological record at a single place and time that cannot be obtained by any other method. Collections-based experiences lead to an increased understanding of and substantive interaction with the living world. Global biological diversity and changes in that diversity are directly tracked through specimens in collections, regardless of whether changes are ancient or recent. We discuss how collections, specimens, and the data associated with them, can be critical components linking nature and scientific inquiry. Specimens are the basic tools for educating students and interested citizens through direct or virtual contact with the diversity of collections. Such interactions include instruction in a formal classroom setting, volunteering to gather and curate collections, and informal presentations at coffee shops. We emphasize how the recent surge in specimen-based digitization initiatives has resulted in unprecedented access to a wealth of biodiversity information and how this availability vastly expands the reach of natural history collections. The emergence of online databases enables scientists and the public to utilize the specimens and associated data contained in natural history collections to address global, regional, and local issues related to biodiversity in a way that was unachievable a decade ago.

The conserved nature and taxonomic utility of pollen morphology in Cantua (Polemoniaceae)

Pollen exine morphology of nine of the ten species of Cantua (Polemoniaceae) is examined using light and scanning electron microscopy. A total of 28 specimens of C. bicolor, C. buxifolia, C. candelilla, C. cuzcoensis, C. flexuosa, C. pyrifolia, C. quercifolia, C. volcanica, and an as yet undescribed species (Cantua sp. nov.) are examined using either fresh or herbarium material. Pollen grains are found to be spheroidal, pantoporate, and quite large; mean diameter varies from 62 to 87 μm. Mean number of pores varies from 4.5 to 21.2 and mean pore size varies from 4.86 to 12.40 μm. Pollen grains of all species have insulate semitectate sexines. This feature distinguishes the pollen of Cantua species from the remainder of the Polemoniaceae. Insulae are evenly distributed over the surface of the pollen grain, with the exception of C. flexuosa and occasionally C. buxifolia, where insulae are more sparsely and haphazardly distributed. The majority of the species examined have irregularly shaped tectal insulae, with the exception of the large rounded insulae in C. quercifolia and the elongated narrow insulae in C. volcanica. Cantua quercifolia and C. volcanica have supratectal verrucae, a possible synapomorphy. In comparison to close relatives, the pollen grains of Cantua are evolutionarily conserved, and show little variation among species.

Climate change, collections and the classroom: using big data to tackle big problems

Preparing students to explore, understand, and resolve societal challenges such as global climate change is an important task for evolutionary and ecological biologists that will require novel and innovative pedagogical approaches. Recent calls to reform undergraduate science education emphasize the importance of engaging students in inquiry-driven, active, and authentic learning experiences. We believe that the vast digital resources (i.e., “big data”) associated with natural history collections provide invaluable but underutilized opportunities to create such experiences for undergraduates in biology. Here, we describe an online, open-access educational module that we have developed that harnesses the power of collections-based information to introduce students to multiple conceptual and analytical elements of climate change, evolutionary, and ecological biology research. The module builds upon natural history specimens and data collected over the span of nearly a century in Yosemite National Park, California, to guide students through a series of exercises aimed at testing hypotheses regarding observed differences in response to climate change by two closely related and partially co-occurring species of chipmunks. The content of the module can readily be modified to meet the pedagogical goals and instructional levels of different courses while the analytical strategies outlined can be adapted to address a wide array of questions in evolutionary and ecological biology. In sum, we believe that specimen-based natural history data represent a powerful platform for reforming undergraduate instruction in biology. Because these efforts will result in citizens who are better prepared to understand complex biological relationships, the benefits of this approach to undergraduate education will have widespread benefits to society.

Completing the Data Pipeline: Collections Data Use in Research, Education and Outreach

Type of Submission: Symposium and Educational Share Fair Themes: Digitisation and Collections Data, Collections Access and Use, Education, and Science Communications Full Title: Completing the Data Pipeline: Collections Data Use in Research, Education and Outreach Short Title: Joint SCNet/BLUE/iDigBio Symposium at SPNHC 2018 Organizers: Gil Nelson, Molly Phillips, Bruce MacFadden, Gabriela Hogue, and Anna Monfils Sponsors: iDigBio, Small Collections Network (SCNet), and Biodiversity Literacy Litercy in Undergraduate Education (BLUE) Contact information: Molly Phillips mphillips@flmnh.ufl.edu 352-672-2664 and Gil Nelson gnelson@bio.fsu.edu 850-766-2649 ‡ § | § ¶