Canadian Flora Research Articles

Metabarcoding Extends the Distribution of Porphyra corallicola (Bangiales) into the Arctic While Revealing Novel Species and Patterns for Conchocelis Stages in the Canadian Flora

Porphyra corallicola was described based on a filamentous red alga inadvertently introduced into culture from a crustose coralline alga. This species is known only in its sporophyte (Conchocelis) stage, being possibly asexual and lacking the charismatic and “collectable” gametophyte stage. Consequently, little is known of its range and distribution. Taxon-targeted metabarcoding was explored as a pathway to gain insights into the vertical (intertidal versus subtidal) and biogeographical distribution of this species, as well as to assess host diversity. We also wanted to ascertain if other species occur in only the Conchocelis stage in the Canadian flora. Primers targeting a short (521 bp) region of the plastid rbcL gene in the Bangiales were used to screen DNA from 285 coralline crusts collected throughout Canada and adjacent waters. In addition to confirming the presence of P. corallicola in the Bay of Fundy, this species was recovered from coralline crusts along the coast of Nova Scotia (n = 1) and in the low Arctic (Labrador; n = 2), greatly extending its range and suggesting it is a cold-water taxon. We have confirmed its presence in both the low intertidal and subtidal (to 10 m), and its occurrence in three different coralline species, suggesting that it lacks host specificity. In total, nine genetic groups of Bangiales were uncovered in our survey, six matching entries currently in GenBank and three apparently novel genetic groups—two from the northeast Pacific and one from the low Arctic. Notable host and ecological patterns are discussed. This method, when further developed, will facilitate the study of Conchocelis stages in nature, which will greatly enhance ecological knowledge of bangialean species.

Even Simple Habitat Ontologies are Hard to Use

An essential component in describing, delimiting, and understanding the evolutionary context of a taxon is characterizing the habitats in which the taxon is found. We report on a simple habitat ontology that we have developed, and on our ongoing experience using volunteers to annotate legacy habitat descriptions with terms from the ontology. Our botanical informatics group is building the Canadian Flora Commons, a knowledge platform to aggregate, integrate and facilitate collaboration on information about Canadian plants. Species pages in the Commons are seeded with structured data extracted from authoritative sources such as the Flora of North America (FNA), Flora of British Columbia, etc. In previous TDWG talks (e.g., Sachs et al. 2019), we described our workflow for extracting and structuring morphological data. To understand why habitat descriptions are different and pose a unique set of challenges, consider the following (from Plectocephalus rothrockii in FNA): “Damp soil near streams, roadsides, open pine-oak woodlands and forests”. Here, the single field “habitat” is used to capture environmental conditions, canopy coverage, and taxonomic associations. We also find it often used for geology, climate, etc. Information in the habitat field is often detailed, but it is presented in free text with little editorial guidance, and comparison between treatments within a given flora and among floras is challenging. Environment ontologies that could aid in the standardization of habitat descriptors exist, notably ENVO (ENVironment Ontology; Buttigieg et al. 2016). However, ENVO’s goals have been primarily focused on describing the biomes, environmental features and environmental materials of molecular datasets, resulting in an ontology that thus far does not serve our needs. To our knowledge, no habitat ontology exists that supports species-level use cases (but see the habitat classification scheme developed by the IUCN). To address this, we developed a small and simple habitat ontology by examining over 3000 habitat descriptions across multiple families, and asked “what is the author trying to tell us?”. In our taxonomic treatment authoring tool, being developed as part of another project, we will use this ontology to replace or supplement the single “habitat” field with multiple habitat dimensions (“soil type”, “canopy coverage”, etc.), some with controlled vocabularies (e.g. {open, closed, partial} for canopy coverage). We are also “translating” legacy habitat descriptions into instance data for the ontology. This is a time-consuming process and has the potential to be dependent on interpretations made by the translator. The crowdsourcing experiment described below is aimed at addressing the first issue and quantifying the second. With our centre's support, we recruited a team of volunteers (6–8 at any given time), and taught them how to annotate habitat descriptions with WebProtegé (Horridge et al. 2014). We divided volunteers into two groups, with each group working with the same dataset, so that we could compare results. While a purpose-built habitat ontology offers advantages over existing environment ontologies and a consensus was reached on habitat class definitions (e.g., moisture, elevation, canopy coverage), we discovered that it is difficult to achieve consensus on the application of habitat classes. Between the two groups, shared annotations represented 57% of the total annotations added to terms and phrases and unique annotations represented 43%. This aligns with previous efforts to build a controlled vocabulary for FNA treatments, where differences between term categorizations represented 49% of the effort (Endara et al. (2017)). Amongst classes in our ontology, unique annotations varied between 11% and 76% (see Fig. 1). Our talk will describe our findings, discuss the subjectivity of habitat classes and other difficulties we’ve encountered while building our ontology, and demonstrate the power of a habitat-driven search interface. This interface will live alongside parsed morphological descriptions (see dev.floranorthamerica.org). We invite collaboration towards increasing the robustness and applicability of the ontology.

A molecular assessment of species diversity and generic boundaries in the red algal tribes Polysiphonieae and Streblocladieae (Rhodomelaceae, Rhodophyta) in Canada

ABSTRACTSequence data generated during a Canadian barcode survey (COI-5P) of the tribes Polysiphonieae and Streblocladieae, a large and taxonomically challenging group of red algae, revealed significant taxonomic confusion and hidden species diversity. Polysiphonia pacifica Hollenberg, P. paniculata Montagne, P. stricta (Dillwyn) Greville and Vertebrata fucoides (Hudson) Kuntze were all complexes of two or more genetically distinct yet overlooked species. One variety of P. pacifica was elevated to the rank of species as P. determinata (Hollenberg) Savoie & Saunders, stat. nov. Several new additions to the Canadian flora were recorded including P. kapraunii Stuercke & Freshwater and P. morrowii Harvey. Subsequent multi-gene (COI-5P, LSU and rbcL) phylogenetic analyses confirmed that the genus Polysiphonia Greville was polyphyletic, and currently assigned species resolved with many other genera. Polysiphonia sensu stricto was restricted to a group of species that formed a monophyletic lineage with the type, Polysiphonia stricta. Carradoriella P.C.Silva was resurrected based on the South African species Carradoriella virgata (C.Agardh) P.C.Silva. Species previously attributed to Polysiphonia were transferred to Carradoriella, Leptosiphonia and Vertebrata as well as to three new genera described here: Acanthosiphonia gen. nov., based on A. echinata (Harvey) comb. nov.; Eutrichosiphonia gen. nov. for E. confusa (Hollenberg) comb. nov. and E. sabulosia (B.Kim & M.S.Kim) comb. nov.; and Kapraunia gen. nov., which includes K. schneideri (Stuercke & Freshwater) comb. nov. and three additional species.

Resolving species diversity in the red algal genus Callophyllis (Kallymeniaceae, Gigartinales) in Canada using molecular assisted alpha taxonomy

The COI-5P DNA barcode (the 5′ region of the mitochondrial cytochrome c oxidase I gene) has proven an effective tool for quickly screening large numbers of biological specimens and assigning them to genetic species groups for subsequent examination in an approach known as molecular-assisted alpha taxonomy (MAAT). In the present study, we applied MAAT to Canadian species of the red algal genus Callophyllis in order to resolve confusion surrounding this taxonomically perplexing group. A total of 563 Callophyllis specimens were examined (either molecularly, morphologically or both) – 504 from British Columbia along the Pacific coast of Canada and 59 from the U.S.A., Australia and Chile. In total, 16 genetic species groups were resolved including 12 in Canada although only nine species are reported in the flora. Here we report range extensions of C. beringensis and C. radula from the NW Pacific, C. dissecta from California, U.S.A. and the Chilean species C. variegata (the type species) into the Canadian flora. Our results also uncovered cryptic diversity in the genus necessitating the description of C. schneideri Clarkston & G.W. Saunders sp. nov. Subsequent analyses of a subset of specimens using the internal transcribed spacer of the ribosomal cistron (ITS) resolved the same groups as COI-5P while the universal plastid amplicon (UPA, domain V of theplastid 23S rRNA gene) had poor resolution at the species level and in one case underestimated species diversity. Finally, large-subunit ribosomal DNA (LSU), nuclear elongation factor 2 (EF2), COI-5P and a combined LSU, EF2 and COI-5P alignment were subjected to phylogenetic analyses in order to investigate relationships among Canadian species of Callophyllis. A significant outcome was the resolution of two well-supported lineages for the monocarpogonial versus polycarpogonial species of this genus, as had been posited in the literature.

A taxonomic revision ofAllium(Alliaceae) in the Canadian prairie provinces

The taxonomy, rarity, and conservation status of Allium L. is revised for the Canadian prairie provinces, based on analyses of herbarium specimens and fieldwork. Five species are recognized: Allium schoenoprasum L., A. geyeri S. Watson var. tenerum M.E. Jones, A. textile A. Nelson & J.F. Macbride, A. cernuum Roth, and A. stellatum Ker Gawler. Distribution maps and a key to species are provided, as well as complete descriptions of the species examined, including new illustrations, information on nomenclatural types, synonymies, and chromosomal and ecological data. A lectotype is designated for A. geyeri var. tenerum. In this study, A. geyeri var. geyeri reported from Alberta and Saskatchewan and ranked in these provinces as having rarity levels S2 and S1, respectively, by the Nature Conservancy, is excluded from the Canadian flora and the rare list of these provinces because it was misidentified from a herbarium specimen of A. textile. Allium tricoccum Solander in W. Aiton is regarded as a non-native species to Manitoba. The rarity and conservation status of Allium in the Canadian prairie provinces is as follows: (i) A. schoenoprasum, listed as S2 in Saskatchewan, is rare in Manitoba, although its rarity status has not been formally assessed in the province; (ii) A. geyeri var. tenerum is the rarest Allium taxon, with distribution restricted to the Waterton Lakes National Park areas of Alberta, and is currently listed as S2; and (iii) A. cernuum was re-evaluated and a rarity level of S1S2 was recommended for the species in Saskatchewan, particularly in its southwestern distributional habitat.

DNA BARCODING IS A POWERFUL TOOL TO UNCOVER ALGAL DIVERSITY: A CASE STUDY OF THE PHYLLOPHORACEAE (GIGARTINALES, RHODOPHYTA) IN THE CANADIAN FLORA

Previous studies have established that the 5′ end of the mitochondrial gene COI (cytochrome oxidase subunit I) is useful for rapid and reliable identification of red algal species and have demonstrated that our understanding of red algal biodiversity and biogeography is fragmentary. In this context, we are completing a thorough sampling along the Canadian coast and using the DNA barcode for the assignment of collections to genetic species to explore algal diversity in the Canadian flora. In the present study, we provide results regarding diversity of members of the red algal family Phyllophoraceae. We have analyzed 354 individuals from the Arctic, Atlantic, and Pacific coasts of Canada, as well as 26 specimens from the USA, Europe, and Australia, resolving 29 species based on the analyses of the DNA barcode. Twenty-three of these genetic species were present in Canada where only 18 species are currently recognized, including Ceratocolax hartzii Rosenv., which was in the same genetic species group as its host Coccotylus truncatus (Pall.) M. J. Wynne et N. J. Heine and is thus transferred to Coccotylus, C. hartzii (Rosenv.) comb. nov., but retained as a distinct species owing to its unique habit and phenology. Our results revealed the presence of cryptic diversity within the genera Coccotylus, Mastocarpus, Ozophora, and Stenogramme, for which we resurrect Coccotylus brodiei (Turner) Kutz. and describe Mastocarpus pachenicus sp. nov., Ozophora lanceolata sp. nov., and Stenogramme bamfieldiensis sp. nov., leaving a multitude of unnamed Mastocarpus spp. in need of further taxonomic study. In addition, we report range extensions into British Columbia of Besa papillaeformis Setch., previously known only from its type and nearby localities in California; Gymnogongrus crenulatus (Turner) J. Agardh, recorded only from the Atlantic; and Stenogramme cf. rhodymenioides Joly et Alveal, previously only known from South America. Finally, the phylogenetic affinities of the Canadian species of Phyllophoraceae characterized in this study were investigated using LSU rDNA, RUBISCO LSU (rbcL), and combined analyses.

Introduction

The genus Carex includes the sedges that dominate wetlands, pastures, prairies, tundra, and the herb layer of temperate forests. These plants are not only frequently dominant in terms of biomass in plant communities, but they are also prominent in terms of numbers of species. Carex is one of the largest genera in the Canadian flora with approximately 300 species, and consequently almost one-tenth of the native vascular plants of Canada are sedges. In North America there are about 500 species. Worldwide, there may be as many as 2000 species.The results of the recently increasing interest in Carex include regional taxonomic treatments, simplified identification, and many improvements to classification. Basic taxonomic work was supported through the application of chemical, anatomical, and cytological techniques. The first detailed ecological studies of Carex have been completed, and much general ecological information has accumulated. Many scientists are now actively involved in research concerning Carex, and the recent and rapid growth of this research area suggests that a review of the subject will be of value, not only to the researchers involved, but also to the general botanist.On 16 June 1987, the Systematics and Phytogeography section of the Canadian Botanical Association/l'Association botanique du Canada hosted a symposium to review major aspects of Carex research and outline appropriate directions for future study in each area. We are pleased to offer the presented papers to a wider audience as a record of the first international symposium on the systematics and ecology of one of the largest and least well known genera of plants in the temperate regions of the world.

Some rare plant collections, including three new records for Canada, from Cathedral Provincial Park, southern British Columbia

Three new vascular plant records for the Canadian flora are reported. In addition, three other species of interest are discussed

THE CONTRAST IN THE FLORAS OF EASTERN AND WESTERN NEWFOUNDLAND

The island of Newfoundland, with an area of more than 42,000 square miles, has a flora as yet only partially worked out, but sufficiently known to indicate a surprising degree of complexity in its makeup. The first impression gained by a casual observer in crossing Newfoundland is that the flora, as one visiting botanist has said, is an attenuated Canadian flora; but further study of the details and a careful daily record of observations on the plants of the island through several seasons of exploration has clearly emphasized that the attenuation of the Canadian element is one of the most conspicuous features of the Newfoundland flora. For, although lying in the latitudes of eastern Canada, Newfoundland has an almost negligible strictly Canadian element in its flora. The number of species characteristic of eastern Canada (Nova Scotia, New Brunswick, and the Gaspe Peninsula) and also found upon Newfoundland is made up primarily of such plants as extend their northeastern ranges along the north shore of the St. Lawrence quite to the Straits of Belle Isle and have obviously reached Newfoundland by crossing the narrow Straits. Besides this meager Canadian flora which has been derived chiefly by way of its northeastern extension to the Straits of Belle Isle, the essential elements of the Newfoundland flora are three: (i) the arcticalpine and Hudsonian elements, of somewhat broad distribution in the arctic regions or in Labrador; (2) the coastal plain element, a group of species abundant to the southwest of Newfoundland, chiefly in coastwise New England, Long Island and New Jersey; (3) the Atlantic European element, species characteristic of the region from the Baltic or the English Channel to the Mediterranean; while the endemic species and varieties are all closely related to members of the other four groups and should, in point of origin, be classed with them. As I have elsewhere shown,2 the essential absence of the plants one

The Age of the Present Canadian Flora

PROF. D. P. PENHALLOW has recently identified some fragments of wood found in the Leda clays of Montreal, as Picea nigra, the common black spruce. This is another addition to the group of plants which represent our present knowledge of the flora of Canada in Pleistocene times. This Pleistocene flora may now be taken to include not merely the plants found in these Leda clays and in the clays believed to be equivalent to them in age in Ontario, but also the ancestors of the present inland maritime flora found on the shores of the Great Lakes, hundreds of miles from the sea-coast, and of the plants which are common to Europe and America, and which include so many arctic and sub-arctic, as well as northern temperate species. The inland maritime plants, and probably also the sub-arctic species now found so far south as the headlands of Lake Superior, made their way to their present localities during the deposit of the Leda clays when a considerable part of Eastern Canada was submerged. Six of the species which occur in the Leda clays at Ottawa and Montreal, and thirteen of the inland maritime plants, as well as several of the Lake Superior subarctic species, are also European, showing that at that period the intermingling of the American and European floras was well established, but leaving open the possibility of these plants common to the two continents being even older than the period of the Leda clays.