MASS BARCODING OF CANADIAN VASCULAR PLANTS

Kuzmina et al. 2017. Using herbarium-derived DNAs to assemble a large-scale DNA barcode library for the vascular plants of Canada. Applications in Plants Sciences 2017 5(12):1700079 https://onlinelibrary.wiley.com/doi/pdf/10.3732/apps.1700079

ABSTRACT

Premise of the study: Constructing complete, accurate plant DNA barcode reference libraries can be logistically challenging for large-scale floras. Here we demonstrate the promise and challenges of using herbarium collections for building a DNA barcode reference library for the vascular plant flora of Canada.

Methods: Our study examined 20,816 specimens representing 5076 of 5190 vascular plant species in Canada (98%). For 98% of the specimens, at least one of the DNA barcode regions was recovered from the plastid loci rbcL and matK and from the nuclear ITS2 region. We used beta regression to quantify the effects of age, type of preservation, and taxonomic affiliation (family) on DNA sequence recovery.

Results: Specimen age and method of preservation had significant effects on sequence recovery for all markers, but influenced some families more (e.g., Boraginaceae) than others (e.g., Asteraceae).

Discussion: Our DNA barcode library represents an unparalleled resource for metagenomic and ecological genetic research working on temperate and arctic biomes. An observed decline in sequence recovery with specimen age may be associated with poor primer matches, intragenomic variation (for ITS2), or inhibitory secondary compounds in some taxa.

BEN NOTES BY ADOLF CESKA

Results of this study have been incorporated into the BOLDSYSTEM databases and are available here: http://www.boldsystems.org/index.php/Public_SearchTerms?query=DS-VASCAN

Selection of the herbaria is typical for the "Ottawa" (Federal Government) based studies. The major part of the studied specimens came from Ontario based herbaria: 5537 DAC (Guelph, ON), 4046 CAN (Ottawa, ON), 2833 TRT (Toronto, ON), and 1072 DAO (Ottawa, ON). From the western Canadian herbaria, only two herbaria were substantially represented in this study: 2918 UBC (Vancouver, BC) and 2068 BABY (Whitehorse, YT). I was disappointed that the Royal BC Museum herbarium (V) was totally ignored in this study. That herbarium houses over 19,000 of vascular plant specimens that I had collected while I was employed there and I would have liked to have at least few of "my" collections sequenced. Yukon collections by Bruce Bennett, BABY herbarium, fared much better, thanks to the connections Bruce made with "Ottawa" long time ago. With 2608 BABY (Whitehorse, YT) collections included in this study, BABY may have the highest percentage of its collections sequenced compared with other Canadian herbaria.

The purpose of this study was to get DNA sequences for as many collections as possible in the shortest possible time while fitting into a limited budget. Besides the actual DNA data on 5076 species of Canadian vascular plants, this work provides a nice insight in what DNA segments are the best to use for sequencing when dealing with specimens of various age and various plant families.

I admire this work and I am little bit envious to see what has been done in this study. I am now involved in a long-term mycofloristics study that my wife Oluna has been conducting on Observatory Hill, Saanich Peninsula. From November 2004 till now, Oluna has collected over 1,300 species of macrofungi from an area of about 75 ha. Some older Cortinarius and Inocybe collections were sequenced and studied, and those studies produced several new, up to then undescribed species. Several other mycologists have been working on a few other genera, but the majority of Oluna's collection is still waiting for a closer look. Would somebody have the money for the DNA sequencing of at least a part of that collection? What about "Ottawa"?

SPECIAL HABITATS OF NEWFOUNDLAND & LABRADOR: LIMESTONE BARRENS - MINIREVIEW

Burzynski, Michael, Henry Mann & Anne Marceau. 2016. Exploring the Limestone Barrens of Newfoundland and Labrador. A Photographic Guide ... ISBN 0969950977, 9780969950974 [soft cover] 364 p. Gros Morne Cooperating Association, Rocky Harbour, NL. Price: $26.95.

FULL DISCLOSURE

Book was written by my friends, using a few of my photos, parts vetted by me, about one of my favourite habitats. No pretence at objectivity or impartiality.

EXECUTIVE SUMMARY

Buy it! With a little searching, you can find a very good bottle of wine for the same price that will give you similar enjoyment for an evening. The difference is that you can open this book night after night for the same enjoyment each time.

Limestone outcroppings occur throughout the world, wherever continental shifts have raised ancient sea bottoms to the surface. In very exposed sites these rocky fields have remained relatively barren, becoming home to some interesting organisms, able to thrive in a habitat both alkaline and exposed to wind, sun and chill. Such organisms, and one such collection of regions, are the subjects of this book. The first third deals with the geology, history, place and impact of the limestone barrens in Newfoundland and Labrador. The second two-thirds is an identification to about 300 organisms living in this habitat, dividing them up into fungi (including lichens) and some algae; ferns, mosses, and allied non-flowering plants; trees and shrubs; flowering plants, divided into sections by flower colour (yellow, white, pink, blue and green).

Naturalists know that if you print flower pictures you cannot fail. The authors have capitalized on this. The entire book is filled with beautiful photos of the subject matter. As is usual in field guide sized books, some photos are small. But small photos are used only to show very specific, magnified details. All other photos are as generous as the size allows: full-page photos abound and two-page spreads are used. All organisms are well shown, with, beautiful, well-focussed, creatively chosen and tastefully arranged photos. To leaf through the book, just looking at the pictures, is a rewarding experience that can be repeated for years. A keen eye and countless hours in the field have contributed many photos that even a seasoned barrens veteran may not have seen.

Not adverse to risk, the authors have chosen to ignore the respected tradition that text in natural history guidebooks must be long, dry and uninteresting. The content is informative, presented in an interesting and original manner. Its biggest strength is that it comes from a wealth of personal experience. "Book knowledge" is not eschewed, but used to supplement personal observation, rather than cover its lack. These are authors who have lived on the barrens, studied them, seen them, scraped their knees, gotten wet and felt the flies (usually not too many, thanks to abundant unbroken wind). Without the attempt at slapstick, humour lies scattered on the pages: for example, one caption describes an endangered Braya next to an extinct Canadian one-cent coin. Also endearing is the overt celebration of scatterbrainedness: the last three pages are out-of-place "Late additions", gems well worth the addition to fill the final signature.

The book is small enough to be a field guide, fitting easily into a backpack, maybe even a large pocket. Its soft covers are durable, thick, near-waterproof, and its thick, glossy pages should shed both water and much grime, ideally constructed for field use. The reproduction quality is excellent, with faithful colours. This is an above average product, whose individual parts share the same high standard.

NEW MOSS GUIDE FOR THE PACIFIC NORTHWEST

Bruce McCunne & M. Hutten. 2018. Common Mosses of Western Oregon and Washington. Wild Blueberry Media, Corvallis, Oregon. iv+148 pages. ISBN 978-0-9987108-2-2 [soft cover] Cosdt: US$40.00 For information on purchasing, please go to the publisher's website, http://www.wildblueberrymedia.net

This is the first introductory all-color guide to mosses for any part of the Pacific Northwest of North America. Written by authors with decades of experience studying and teaching about mosses in the Pacific Northwest, the book provides an entry into the lush, intricate world of mosses. These miniature plants combine to form spectacular carpets on the forest floor, lushly drape trees and shrubs, and create beautiful gardens on rock outcrops. Mosses are an ecologically important and beautiful, but often neglected, part of the biodiversity of western Oregon and Washington.

The book is aimed at serious amateurs, naturalists, and professional botanists at beginning to intermediate levels. It includes 200 species in 100 genera, with keys; 529 micro- and macro-scale color photographs; notes on distribution, abundance, and habitats; and an illustrated glossary. Brief descriptions of each species are embedded in the keys. While the geographic area covered by the book is the area west of the crest of the Cascade Range in Oregon and Washington, the book will also be useful in a much broader area of the western U.S. and Canada, including coastal Alaska, British Columbia, and California. It will also be useful in the inland oceanic forests of northern Idaho and western Montana.

A compound microscope will be necessary to identify many of the species, although some genera - and even species - can be identified without using a compound microscope.

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