Cortinarius species diversity in British Columbia and molecular phylogenetic comparison with European specimen sequences

Botany ◽  
2011 ◽  
Vol 89 (11) ◽  
pp. 799-810 ◽  
Author(s):  
Emma Harrower ◽  
Joseph F. Ammirati ◽  
Adam A. Cappuccino ◽  
Oldriska Ceska ◽  
J.M. Kranabetter ◽  
...  
Keyword(s):  
British Columbia ◽  
Species Diversity ◽  
Sequence Variation ◽  
Reference Sequence ◽  
Herbarium Specimens ◽  
Its Sequence ◽  
Working Definition ◽  
Improve Accuracy ◽  
Molecular Phylogenetic ◽  
European Specimen

Throughout the world, the diversity of fungi remains poorly characterized and Cortinarius is a classical example of a difficult, species-rich, and under-researched mushroom genus. Here, we sequenced and analyzed ribosomal internal transcribed spacer (ITS) sequence barcodes from herbarium specimens to improve understanding of Cortinarius species diversity in British Columbia (B.C.), Canada. Starting with 962 specimen sequences, 617 from B.C. herbaria, we present a maximum likelihood tree showing 179 putative Cortinarius species in British Columbia. As a working definition, we considered a “species” to be a monophyletic clade that included a reliably identified reference sequence, with a maximum of 3% ITS sequence variation. If no reference sequence was available, “species” were groups sharing 97% or more sequence identity. By these criteria, 110 putative B.C. species matched European species and 12 B.C. species matched species exclusively found in the Americas. Of the 56 B.C. species that did not match an identified reference sequence, some may be new to science, while others likely represent described species without available sequences. By depositing sequences from B.C. specimens into GenBank and BOLD, and by providing our alignment to TreeBASE, we have supplied the resources necessary to improve accuracy in identifications of Cortinarius in future systematic and ecological studies.

Systematics and evolution of Lentibulariaceae: III. Utricularia

2018 ◽  
Author(s):  
Richard W. Jobson ◽  
Paulo C. Baleeiro ◽  
Cástor Guisande
Keyword(s):  
Gene Flow ◽  
Species Diversity ◽  
Population Level ◽  
Oceanic Islands ◽  
Vulnerable Species ◽  
Phylogenetic Studies ◽  
Molecular Phylogenetic

Utricularia is a morphologically and ecologically diverse genus currently comprising more than 230 species divided into three subgenera—Polypompholyx, Utricularia, and Bivalvaria—and 35 sections. The genus is distributed worldwide except on the poles and most oceanic islands. The Neotropics has the highest species diversity, followed by Australia. Compared to its sister genera, Utricularia has undergone greater rates of speciation, which are linked to its extreme morphological flexibility that has resulted in the evolution of habitat-specific forms: terrestrial, rheophytic, aquatic, lithophytic, and epiphytic. Molecular phylogenetic studies have resolved relationships for 44% of the species across 80% of the sections. Scant data are available for phylogeography or population-level processes such as gene flow, hybridization, or pollination. Because nearly 90% of the species are endemics, data are urgently needed to determine how to protect vulnerable species and their habitats.

scholarly journals Toward a global reference database of COI barcodes for marine zooplankton

2021 ◽  
Vol 168 (6) ◽  
Author(s):  
Ann Bucklin ◽  
Katja T. C. A. Peijnenburg ◽  
Ksenia N. Kosobokova ◽  
Todd D. O’Brien ◽  
Leocadio Blanco-Bercial ◽  
...  
Keyword(s):  
Species Diversity ◽  
Dna Sequences ◽  
Reference Sequence ◽  
Global Ocean ◽  
Reference Database ◽  
Data Repositories ◽  
Marine Zooplankton ◽  
The North ◽  
Coi Sequences ◽  
Taxonomic Groups

AbstractCharacterization of species diversity of zooplankton is key to understanding, assessing, and predicting the function and future of pelagic ecosystems throughout the global ocean. The marine zooplankton assemblage, including only metazoans, is highly diverse and taxonomically complex, with an estimated ~28,000 species of 41 major taxonomic groups. This review provides a comprehensive summary of DNA sequences for the barcode region of mitochondrial cytochrome oxidase I (COI) for identified specimens. The foundation of this summary is the MetaZooGene Barcode Atlas and Database (MZGdb), a new open-access data and metadata portal that is linked to NCBI GenBank and BOLD data repositories. The MZGdb provides enhanced quality control and tools for assembling COI reference sequence databases that are specific to selected taxonomic groups and/or ocean regions, with associated metadata (e.g., collection georeferencing, verification of species identification, molecular protocols), and tools for statistical analysis, mapping, and visualization. To date, over 150,000 COI sequences for ~ 5600 described species of marine metazoan plankton (including holo- and meroplankton) are available via the MZGdb portal. This review uses the MZGdb as a resource for summaries of COI barcode data and metadata for important taxonomic groups of marine zooplankton and selected regions, including the North Atlantic, Arctic, North Pacific, and Southern Oceans. The MZGdb is designed to provide a foundation for analysis of species diversity of marine zooplankton based on DNA barcoding and metabarcoding for assessment of marine ecosystems and rapid detection of the impacts of climate change.

The Biology of Invasive Alien Plants in Canada. 4. Heracleum mantegazzianum Sommier & Levier

2006 ◽  
Vol 86 (2) ◽  
pp. 569-589 ◽  
Author(s):  
Nicholas A. Page ◽  
Ronald E. Wall ◽  
Stephen J. Darbyshire ◽  
Gerald A. Mulligan
Keyword(s):  
British Columbia ◽  
Urban Areas ◽  
Native Species ◽  
Invasive Plant ◽  
Leaf Shape ◽  
Herbarium Specimens ◽  
Natural Ecosystems ◽  
Alien Plant ◽  
Invasive Alien Plant ◽  
Heracleum Mantegazzianum

Heracleum mantegazzianum (giant hogweed) is an invasive alien plant of management concern in southern Canada where it has escaped from horticulture and established and spread in natural, ruderal, and agricultural ecosystems. It poses a threat to natural ecosystems and human health, and is also a weed in agricultural and urban areas. It is a member of the Carrot family (Apiaceae) and is closely related to the native species Heracleum maximum Bartram (cow-parsnip). It is a monocarpic perennial, which generally flowers in its 3rd or 4th year. Large size, leaf shape, dark reddish pigments in patches on stems and petioles, and fruit characteristics readily distinguish H. mantegazzianum from other plants in Canada. It is increasingly common in riparian areas, floodplains, and forest edges in or near urban areas in southwestern British Columbia and southern Ontario. Based on herbarium specimens, H. mantegazzianum was first recorded in Ontario in 1949, British Columbia in 1964, Nova Scotia in 1980, Quebec in 1990, and New Brunswick in 2000. The development of dense stands of H. mantegazzianum can also reduce the richness of native plants. Contact with H. mantegazzianum can cause phytophotodermatitis, a serious skin inflammation caused by UV photo-activation of furanocoumarins present in the sap. Control methods include herbicide application, mechanical cutting, and animal grazing, but strategies to address seed dispersal and re-establishment from dormant seed must also be adopted. Widespread establishment in southern Canada suggests that eradication is unlikely. However, range expansion and rapid population growth can be prevented through strategic management including public education. Key words: Giant hogweed, Heracleum mantegazzianum, Apiaceae, HERMZ, invasive plant, weed biology, furanocoumarins

scholarly journals Introducing ribosomal tandem repeat barcoding for fungi

2018 ◽  
Author(s):  
Christian Wurzbacher ◽  
Ellen Larsson ◽  
Johan Bengtsson-Palme ◽  
Silke Van den Wyngaert ◽  
Sten Svantesson ◽  
...  
Keyword(s):  
Large Scale ◽  
Tandem Repeats ◽  
Reference Data ◽  
Reference Sequence ◽  
Herbarium Specimens ◽  
Nanopore Sequencing ◽  
Desktop Computer ◽  
Third Generation Sequencing ◽  
Ribosomal Operon ◽  
Sequencing Facility

AbstractSequence analysis of the various ribosomal genetic markers is the dominant molecular method for identification and description of fungi. However, there is little agreement on what ribosomal markers should be used, and research groups utilize different markers depending on what fungal groups are targeted. New environmental fungal lineages known only from DNA data reveal significant gaps in the coverage of the fungal kingdom both in terms of taxonomy and marker coverage in the reference sequence databases. In order to integrate references covering all of the ribosomal markers, we present three sets of general primers that allow the amplification of the complete ribosomal operon from the ribosomal tandem repeats. The primers cover all ribosomal markers (ETS, SSU, ITS1, 5.8S, ITS2, LSU, and IGS) from the 5’ end of the ribosomal operon all the way to the 3’ end. We coupled these primers successfully with third generation sequencing (PacBio and Nanopore sequencing) to showcase our approach on authentic fungal herbarium specimens. In particular, we were able to generate high-quality reference data with Nanopore sequencing in a high-throughput manner, showing that the generation of reference data can be achieved on a regular desktop computer without the need for a large-scale sequencing facility. The quality of the Nanopore generated sequences was 99.85 %, which is comparable with the 99.78 % accuracy described for Sanger sequencing. With this work, we hope to stimulate the generation of a new comprehensive standard of ribosomal reference data with the ultimate aim to close the huge gaps in our reference datasets.

Russula rubricolor sp. nov. from Himalayan forests of Pakistan

Mycotaxon ◽  
2020 ◽  
Vol 135 (4) ◽  
pp. 765-776
Author(s):  
Sana Jabeen ◽  
Arooj Naseer ◽  
Abdul Nasir Khalid
Keyword(s):  
Phylogenetic Analysis ◽  
New Species ◽  
Sequence Data ◽  
Molecular Phylogenetic Analysis ◽  
Its Sequence ◽  
Central Depression ◽  
Molecular Phylogenetic ◽  
A New Species ◽  
Himalayan Forests

A new species, Russula rubricolor, was collected in the Himalayan forests of Pakistan. This species is morphologically characterized by the yellowish hymenium, bright red pileus that is convex to flat with central depression and finally infundibuliform and striate towards margin, becoming blackish red with age. The newly reported species is placed in Russula subsect. Maculatinae based molecular phylogenetic analysis of ITS sequence data and supported by the red pileus color.

Standing Waters, Especially Ancient Lakes

2020 ◽  
pp. 280-302
Author(s):  
Kristina von Rintelen ◽  
Patricio De los Ríos ◽  
Thomas von Rintelen
Keyword(s):  
Species Diversity ◽  
Ancient Lakes ◽  
Ecological Data ◽  
Widespread Species ◽  
Research Priority ◽  
Trophic Morphology ◽  
Molecular Phylogenetic ◽  
Standing Waters ◽  
Species Flocks

Crustacea in standing waters are a diverse taxonomic assemblage with representatives in all available habitats from the benthic zone to the pelagial in larger water bodies. While most higher taxa are widespread and occasionally cosmopolitan, this is only partially true at the genus and species level. The crustacean fauna of geologically young lakes, or ponds, is characterized by widespread species that are not even necessarily restricted to lentic habitats. These species generally have good to excellent dispersal capabilities, especially those dwelling in ephemeral habitats. Small groups such as branchiopods and copepods dominate under these conditions among obligate still-water dwellers. In contrast, endemism and occasional striking adaptations are the hallmarks of crustacean species flocks, especially in the radiations of amphipods, decapods, and ostracods in the fewer than 10 ancient lakes worldwide. These radiations have arisen in situ through the diversification of unspecialized ancestors. All comparatively well-studied radiations for which molecular phylogenetic, taxonomic, and ecological data are available show particular adaptations of trophic morphology correlated to specific habitats. Prime examples are the species flocks of amphipods in Lake Baikal and of atyid shrimps in Lake Tanganyika and in two Indonesian lakes. These groups have most likely evolved through adaptive radiation. A major challenge for research on crustaceans in ancient lakes, and in standing waters generally outside Europe and North America, is the lack of basic data from species diversity to genetics for many, if not most, taxa. Getting a grip on species diversity, distributions, ecology, and, at a different level, genomics will be a research priority for coming decades.

Species diversity and forest health in northwest British Columbia

2003 ◽  
Vol 79 (5) ◽  
pp. 892-897 ◽  
Author(s):  
Alex J Woods
Keyword(s):  
British Columbia ◽  
Species Diversity ◽  
Lodgepole Pine ◽  
Forest Health ◽  
Root Disease ◽  
Pine Plantations ◽  
Thuja Plicata ◽  
Interior Spruce ◽  
Dothistroma Needle Blight ◽  
Needle Blight

Forest management in the Interior Cedar Hemlock (ICH) zone of the Kispiox TSA in northwest British Columbia has focused on two tree species. Interior spruce (Picea engelmanni Parry ex Engelm. × Picea glauca (Moench) Voss) and lodgepole pine (Pinus contorta var. latifolia Dougl. ex Loud.) have dominated plantations, while historically, western hemlock (Tsuga heterophylla (Raf.) Sarg.), true firs (Abies lasiocarpa (Hook.) Nutt. and (Abies amabilis (Dougl. ex Loud.) Dougl. ex Forbes) and western redcedar (Thuja plicata Donn ex D. Don), have dominated the landscape. Tomentosus root disease (Inonotus tomentosus (Fr.) Teng) and Dothistroma needle blight (Mycosphaerella pini Rostr. in Munk) are the principal diseases affecting interior spruce and lodgepole pine plantations, respectively. Tomentosus root disease was found in 92% of spruce-dominated stands 100 years and older in the study area. The annual recruitment of dead interior spruce and lodgepole pine tree volume due to the disease in those stands is 4.29 m3/ha or 51 990 m3. The incidence of Tomentosus root disease in ten randomly selected spruce leading plantations aged 25–30 years ranged from 0.6% to 10.4% and averaged 5.9% of the host trees. Dothistroma needle blight was the most prevalent pest in a survey of 100 randomly selected lodgepole pine plantations and has caused considerable crop tree mortality. The disease has even caused mortality in 55-year-old lodgepole pine trees. Maintaining species diversity is essential to long-term forest health. Intensive planting of interior spruce and lodge-pole pine in this study area appears to have exacerbated disease problems. Key words: forest health, species diversity, interior spruce, lodgepole pine, Tomentosus root disease, Dothistroma needle blight

New insights on Hygrophorus penarioides and H. penarius (Agaricales, Hygrophoraceae) from Hungary

Phytotaxa ◽  
2019 ◽  
Vol 392 (2) ◽  
pp. 127
Author(s):  
ERIK ZAJTA ◽  
TORDA VARGA ◽  
GÁBOR M KOVÁCS ◽  
BÁLINT DIMA
Keyword(s):  
Sequence Variation ◽  
Geographical Origin ◽  
Phylogenetic Analyses ◽  
Morphological Variability ◽  
Strong Support ◽  
Morphological Evidence ◽  
Its2 Region ◽  
Herbarium Specimens ◽  
Nrdna Its ◽  
Nrdna Its Regions

The ectomycorrhiza forming basidiomycete Hygrophorus penarius sensu lato was recognized as two species, H. penarioides and H. penarius in 2007 based on molecular and morphological evidence. However, this was based on few collections of restricted geographical origin and no studies have performed molecular analysis on additional specimens to date.To this end we sequenced the nrDNA ITS regions of 29 H. penarius s. l. collections from Hungary and Slovakia and analysed with collections from previous studies. Bayesian and Maximum Likelihood phylogenetic analyses confirmed the separation of H. penarioides and H. penarius in two clades with the majority of the specimens belonging to H. penarioides and only three to H. penarius. Despite the strong support of the lineages, there was no coherent difference in basidiome and spore traits. We also provide the first evidence of an intraspecific nrDNA sequence variation in the ITS2 region of H. penarioides together with morphological variability that has not been reported to date.On the basis of our result, we conclude that the Quercus associated H. penarioides is far more common in Hungary than the Fagus associated H. penarius and we suggest that identification of the two species in the absence of DNA sequence analysis should be handled with caution, especially when herbarium specimens are examined.

scholarly journals Present state of knowledge on the family Begoniaceae CA Agardh (Magnoliopsida) of Bangladesh

2018 ◽  
Vol 4 (1) ◽  
pp. 35-46
Author(s):  
PK Deb ◽  
MA Rahman
Keyword(s):  
Species Diversity ◽  
New Records ◽  
Herbarium Specimens ◽  
Field Investigations ◽  
The Family ◽  
First Time ◽  
Generic Family ◽  
Term Field

The inventory and assessment of species diversity in the mono-generic family Begoniaceae C. A. Agardh of Bangladesh were made through long term field investigations, collections, identification, survey and examination of preserved herbarium specimens and review of relevant taxonomic and floristic literature. The family is recognized to be represented in the flora of Bangladesh by 19 species under the genus Begonia L. Of these, 11 species were known to be previously recorded from the area of Bangladesh, hence additional 8 species of the present account are being reported here for the first time as new records from Bangladesh, these are: Begonia grandis Dryand. ssp. holostylla Irmsch. , B. heracleifolia Cham. and Schltdl. Cult., B. maculata Raddi Cult. B. modestiflora Kurz, B. muliensis T. T. Yu. Cult., B. scintillans Dunn, B. surculigera Kurz and B. thomsonii A. DC. An enumeration of these 19 species is prepared, and each species is cited with detailed taxonomic data. All species of the Begonia L. are herbaceous in nature and possess potential economic values, viz. 11 (52%) medicinal, 5 (24%) ornamental, 3 (14%) beverage, 1 (5%) food and 1 (5%) poisonous. Determination of status of occurrence showed that 2 (10.53%) species are common, 5 (26.32%) cultivated, 9 (47.36%) threatened and 3 (15.79%) possibly extinct in Bangladesh. Field photographs and hand drawings of recorded taxa are provided.J. Biodivers. Conserv. Bioresour. Manag. 2018, 4(1): 35-46

scholarly journals Urocystis cumminsii sp. nov., a smut fungus on Themidaceae from Arizona

Mycotaxon ◽  
2020 ◽  
Vol 134 (4) ◽  
pp. 591-599
Author(s):  
Kyryll G. Savchenko ◽  
Sylena R. Harper ◽  
Lori M. Carris ◽  
Lisa A. Castlebury
Keyword(s):  
United States ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
First Record ◽  
Smut Fungi ◽  
Its Sequence ◽  
Sequence Analyses ◽  
Molecular Phylogenetic ◽  
A New Species ◽  
Basal Position

The morphology and phylogenetic relationships of a species of Urocystis on Dichelostemma capitatum (Themidaceae, Asparagales) collected in the Tucson Mountains in Arizona, United States, were studied using microscopy and ITS rDNA sequence analyses. This is a first record for smut fungi on hosts from Themidaceae. Molecular phylogenetic analyses based on ITS sequence data revealed its basal position in relation to species on Poaceae. As a result, the smut in leaves of Dichelostemma capitatum is described and illustrated here as a new species, Urocystis cumminsii.

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