Publications by authors named "Jeffery M Saarela"

14 Publications

  • Page 1 of 1

Vascular plants of Victoria Island (Northwest Territories and Nunavut, Canada): a specimen-based study of an Arctic flora.

PhytoKeys 2020 6;141:1-330. Epub 2020 Mar 6.

Centre for Arctic Knowledge and Exploration and Botany Section, Research & Collections, Canadian Museum of Nature, Ottawa, Ontario, Canada Canadian Museum of Nature Ottawa Canada.

Victoria Island in Canada's western Arctic is the eighth largest island in the world and the second largest in Canada. Here, we report the results of a floristic study of vascular plant diversity of Victoria Island. The study is based on a specimen-based dataset comprising 7031 unique collections from the island, including some 2870 new collections gathered between 2008 and 2019 by the authors and nearly 1000 specimens variously gathered by N. Polunin (in 1947), M. Oldenburg (1940s-1950s) and S. Edlund (1980s) that, until recently, were part of the unprocessed backlog of the National Herbarium of Canada and unavailable to researchers. Results are presented in an annotated checklist, including keys and distribution maps for all taxa, citation of specimens, comments on taxonomy, distribution and the history of documentation of taxa across the island, and photographs for a subset of taxa. The vascular plant flora of Victoria Island comprises 38 families, 108 genera, 272 species, and 17 additional taxa. Of the 289 taxa known on the island, 237 are recorded from the Northwest Territories portion of the island and 277 from the Nunavut part. Thirty-nine taxa are known on the island from a single collection, seven from two collections and three from three collections. Twenty-one taxa in eight families are newly recorded for the flora of Victoria Island: , , (Asteraceae); , , , , (Brassicaceae); Carex bigelowii subsp. bigelowii, Eriophorum russeolum subsp. albidum (Cyperaceae); Anthoxanthum monticola subsp. monticola, , Deschampsia cespitosa subsp. cespitosa, , Festuca rubra subsp. rubra, , Poa pratensis subsp. pratensis (Poaceae); (Potamogetonaceae); Potentilla × prostrata (Rosaceae); (Rubiaceae); and Salix ovalifolia var. ovalifolia (Salicaceae). Eight of these are new to the flora of the Canadian Arctic Archipelago: , , , Anthoxanthum monticola subsp. monticola, , Deschampsia cespitosa subsp. cespitosa, Poa pratensis subsp. pratensis and Salix ovalifolia var. ovalifolia. One of these, , is newly recorded for the flora of Nunavut. Four first records for Victoria Island are introduced plants discovered in Cambridge Bay in 2017: three grasses (Festuca rubra subsp. rubra, , and Poa pratensis subsp. pratensis) and . One taxon, Juncus arcticus subsp. arcticus, is newly recorded from the Northwest Territories. Of the general areas on Victoria Island that have been botanically explored the most, the greatest diversity of vascular plants is recorded in Ulukhaktok (194 taxa) and the next most diverse area is Cambridge Bay (183 taxa). The floristic data presented here represent a new baseline on which continued exploration of the vascular flora of Victoria Island - particularly the numerous areas of the island that remain unexplored or poorly explored botanically - will build.
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http://dx.doi.org/10.3897/phytokeys.141.48810DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7070024PMC
March 2020

Non-native vascular flora of the Arctic: Taxonomic richness, distribution and pathways.

Ambio 2020 Mar 2;49(3):693-703. Epub 2019 Dec 2.

Botanical Museum, Finnish Museum of Natural History, University of Helsinki, P.O. Box 7, 00014, Helsinki, Finland.

We present a comprehensive list of non-native vascular plants known from the Arctic, explore their geographic distribution, analyze the extent of naturalization and invasion among 23 subregions of the Arctic, and examine pathways of introductions. The presence of 341 non-native taxa in the Arctic was confirmed, of which 188 are naturalized in at least one of the 23 regions. A small number of taxa (11) are considered invasive; these plants are known from just three regions. In several Arctic regions there are no naturalized non-native taxa recorded and the majority of Arctic regions have a low number of naturalized taxa. Analyses of the non-native vascular plant flora identified two main biogeographic clusters within the Arctic: American and Asiatic. Among all pathways, seed contamination and transport by vehicles have contributed the most to non-native plant introduction in the Arctic.
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http://dx.doi.org/10.1007/s13280-019-01296-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6989699PMC
March 2020

A 250 plastome phylogeny of the grass family (Poaceae): topological support under different data partitions.

PeerJ 2018 2;6:e4299. Epub 2018 Feb 2.

Plant Molecular and Bioinformatics Center, Biological Sciences, Northern Illinois University, DeKalb, IL, USA.

The systematics of grasses has advanced through applications of plastome phylogenomics, although studies have been largely limited to subfamilies or other subgroups of Poaceae. Here we present a plastome phylogenomic analysis of 250 complete plastomes (179 genera) sampled from 44 of the 52 tribes of Poaceae. Plastome sequences were determined from high throughput sequencing libraries and the assemblies represent over 28.7 Mbases of sequence data. Phylogenetic signal was characterized in 14 partitions, including (1) complete plastomes; (2) protein coding regions; (3) noncoding regions; and (4) three loci commonly used in single and multi-gene studies of grasses. Each of the four main partitions was further refined, alternatively including or excluding positively selected codons and also the gaps introduced by the alignment. All 76 protein coding plastome loci were found to be predominantly under purifying selection, but specific codons were found to be under positive selection in 65 loci. The loci that have been widely used in multi-gene phylogenetic studies had among the highest proportions of positively selected codons, suggesting caution in the interpretation of these earlier results. Plastome phylogenomic analyses confirmed the backbone topology for Poaceae with maximum bootstrap support (BP). Among the 14 analyses, 82 clades out of 309 resolved were maximally supported in all trees. Analyses of newly sequenced plastomes were in agreement with current classifications. Five of seven partitions in which alignment gaps were removed retrieved Panicoideae as sister to the remaining PACMAD subfamilies. Alternative topologies were recovered in trees from partitions that included alignment gaps. This suggests that ambiguities in aligning these uncertain regions might introduce a false signal. Resolution of these and other critical branch points in the phylogeny of Poaceae will help to better understand the selective forces that drove the radiation of the BOP and PACMAD clades comprising more than 99.9% of grass diversity.
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http://dx.doi.org/10.7717/peerj.4299DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5798404PMC
February 2018

Using herbarium-derived DNAs to assemble a large-scale DNA barcode library for the vascular plants of Canada.

Appl Plant Sci 2017 Dec 22;5(12). Epub 2017 Dec 22.

Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1, Canada.

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 and 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.
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http://dx.doi.org/10.3732/apps.1700079DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5749818PMC
December 2017

Molecular phylogenetics of cool-season grasses in the subtribes Agrostidinae, Anthoxanthinae, Aveninae, Brizinae, Calothecinae, Koeleriinae and Phalaridinae (Poaceae, Pooideae, Poeae, Poeae chloroplast group 1).

PhytoKeys 2017 9(87):1-139. Epub 2017 Oct 9.

Department of Vascular Plant Systematics and Phytogeography, W. Szafer Institute of Botany, Polish Academy of Sciences, Kraków, Poland.

Circumscriptions of and relationships among many genera and suprageneric taxa of the diverse grass tribe Poeae remain controversial. In an attempt to clarify these, we conducted phylogenetic analyses of >2400 new DNA sequences from two nuclear ribosomal regions (ITS, including internal transcribed spacers 1 and 2 and the 5.8S gene, and the 3'-end of the external transcribed spacer (ETS)) and five plastid regions (, , , , ), and of more than 1000 new and previously published ITS sequences, focused particularly on Poeae chloroplast group 1 and including broad and increased species sampling compared to previous studies. Deep branches in the combined plastid and combined ITS+ETS trees are generally well resolved, the trees are congruent in most aspects, branch support across the trees is stronger than in trees based on only ITS and fewer plastid regions, and there is evidence of conflict between data partitions in some taxa. In plastid trees, a strongly supported clade corresponds to Poeae chloroplast group 1 and includes Agrostidinae p.p., Anthoxanthinae, Aveninae s.str., Brizinae, Koeleriinae (sometimes included in Aveninae s.l.), Phalaridinae and Torreyochloinae. In the ITS+ETS tree, a supported clade includes these same tribes as well as Sesleriinae and Scolochloinae. Aveninae s.str. and Sesleriinae are sister taxa and form a clade with Koeleriinae in the ITS+ETS tree whereas Aveninae s.str. and Koeleriinae form a clade and Sesleriinae is part of Poeae chloroplast group 2 in the plastid tree. All species of are part of Koeleriinae, but the genus is polyphyletic. Koeleriinae is divided into two major subclades: one comprises , , , , and subg. Trisetum, and the other / p.p. (multiple species from Mexico to South America), , , , and subg. , , and fall in different clades of Koeleriinae in plastid vs. nuclear ribosomal trees, and are likely of hybrid origin. ITS and trees identify a third lineage of Koeleriinae corresponding to Trisetum subsect. Sibirica, and affinities of with respect to Aveninae s.str. and Koeleriinae are incongruent in nuclear ribosomal and plastid trees, supporting recognition of in its own subtribe. A large clade comprises taxa of Agrostidinae, Brizinae and Calothecinae, but neither Agrostidinae nor Calothecinae are monophyletic as currently circumscribed and affinities of Brizinae differ in plastid and nuclear ribosomal trees. Within this clade, one newly identified lineage comprises , , (Agrostidinae p.p.) and (Calothecinae p.p.), and another comprises (Calothecinae p.p.) and (Agrostidinae p.p.). Within Agrostidinae p.p., the type species of and s.str. are closely related, supporting classification of as a synonym of s.str. Furthermore, the two species of are not sister taxa and are nested among different groups of s.str., supporting their classification in . , and form a clade and species of each are variously intermixed in plastid and nuclear ribosomal trees. Additionally, all but one species from South America classified in Deyeuxia sect. Stylagrostis resolve in Holcinae p.p. (). The current phylogenetic results support recognition of the latter species in , and we also demonstrate is part of this clade. Moreover, Holcinae is not monophyletic in its current circumscription because does not form a clade with and , which are sister taxa. The results support recognition of in its own subtribe Aristaveninae. Substantial further changes to the classification of these grasses will be needed to produce generic circumscriptions consistent with phylogenetic evidence. The following 15 new combinations are made: Calamagrostis × calammophila, , C. breviligulata subsp. champlainensis, C. × don-hensonii, , , , D. chrysantha var. phalaroides, , D. eminens var. fulva, D. eminens var. inclusa, , , and var. ; the new name is proposed; the new subtribe Lagurinae is described; and a second-step lectotype is designated for the name .
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http://dx.doi.org/10.3897/phytokeys.87.12774DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5672130PMC
October 2017

Vascular plant biodiversity of the lower Coppermine River valley and vicinity (Nunavut, Canada): an annotated checklist of an Arctic flora.

PeerJ 2017 31;5:e2835. Epub 2017 Jan 31.

Botany Section and Centre for Arctic Knowledge & Exploration, Research and Collections, Canadian Museum of Nature , Ottawa, ON , Canada.

The Coppermine River in western Nunavut is one of Canada's great Arctic rivers, yet its vascular plant flora is poorly known. Here, we report the results of a floristic inventory of the lower Coppermine River valley and vicinity, including Kugluk (Bloody Falls) Territorial Park and the hamlet of Kugluktuk. The study area is approximately 1,200 km, extending from the forest-tundra south of the treeline to the Arctic coast. Vascular plant floristic data are based on a review of all previous collections from the area and more than 1,200 new collections made in 2014. Results are presented in an annotated checklist, including citation of all specimens examined, comments on taxonomy and distribution, and photographs for a subset of taxa. The vascular plant flora comprises 300 species (311 taxa), a 36.6% increase from the 190 species documented by previous collections made in the area over the last century, and is considerably more diverse than other local floras on mainland Nunavut. We document 207 taxa for Kugluk (Bloody Falls) Territorial Park, an important protected area for plants on mainland Nunavut. A total of 190 taxa are newly recorded for the study area. Of these, 14 taxa (13 species and one additional variety) are newly recorded for Nunavut (, , , subsp. , , , cf. , , , , , var. , var. and ), seven species are newly recorded for mainland Nunavut (, , , , subsp. , subsp. and ) and 56 range extensions are reported. The and DNA sequence data were used to help identify the three taxa recorded in the study area. Three new combinations are proposed: subsp. (Banks ex Pursh) Saarela, subsp. (Fernald) Saarela and subsp. (T. V. Egorova) Saarela.
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http://dx.doi.org/10.7717/peerj.2835DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5300018PMC
January 2017

The "Martian" flora: new collections of vascular plants, lichens, fungi, algae, and cyanobacteria from the Mars Desert Research Station, Utah.

Biodivers Data J 2016 9(4):e8176. Epub 2016 Jun 9.

Canadian Museum of Nature, Ottawa, Canada.

The Mars Desert Research Station is a Mars analog research site located in the desert outside of Hanksville, Utah, U.S.A. Here we present a preliminary checklist of the vascular plant and lichen flora for the station, based on collections made primarily during a two-week simulated Mars mission in November, 2014. Additionally, we present notes on the endolithic chlorophytes and cyanobacteria, and the identification of a fungal genus also based on these collections. Altogether, we recorded 38 vascular plant species from 14 families, 13 lichen species from seven families, six algae taxa including both chlorophytes and cyanobacteria, and one fungal genus from the station and surrounding area. We discuss this floristic diversity in the context of the ecology of the nearby San Rafael Swell and the desert areas of Wayne and Emery counties in southeastern Utah.
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http://dx.doi.org/10.3897/BDJ.4.e8176DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4911540PMC
June 2016

New vascular plant records for the Canadian Arctic Archipelago.

PhytoKeys 2015 25(52):23-79. Epub 2015 Jun 25.

Botany Section & Centre for Arctic Knowledge and Exploration, Research and Collections, Canadian Museum of Nature, P.O. Box 3443 Stn. D, Ottawa, Ontario K1P 6P4, Canada.

The Canadian Arctic Archipelago is a vast region of approximately 1,420,000 km(2), with a flora characterized by low species diversity, low endemicity, and little influence by alien species. New records of vascular plant species are documented here based on recent fieldwork on Victoria and Baffin Islands; additional records based on recent literature sources are mentioned. This paper serves as an update to the 2007 publication Flora of the Canadian Arctic Archipelago, and brings the total number of vascular plants for the region to 375 species and infraspecific taxa, an increase of 7.7%. Three families (Amaranthaceae, Juncaginaceae, Pteridaceae) and seven genera (Cherleria L., Cryptogramma R. Br., Platanthera Rich., Sabulina Rchb., Suaeda Forssk. ex J.F. Gmel., Triglochin L., Utricularia L.) are added to the flora, and one genus is deleted (Minuartia L.). Five species are first records for Nunavut (Arenarialongipedunculata Hultén, Cryptogrammastelleri (S.G. Gmel.) Prantl, Puccinelliabanksiensis Consaul, Saxifragaeschscholtzii Sternb., Utriculariaochroleuca R.W. Hartm.).
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http://dx.doi.org/10.3897/phytokeys.52.8721DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4549883PMC
August 2015

Plastid phylogenomics of the cool-season grass subfamily: clarification of relationships among early-diverging tribes.

AoB Plants 2015 May 4;7. Epub 2015 May 4.

Biological Sciences, Northern Illinois University, 1425 W. Lincoln Hwy, DeKalb, IL 60115-2861, USA

Whole plastid genomes are being sequenced rapidly from across the green plant tree of life, and phylogenetic analyses of these are increasing resolution and support for relationships that have varied among or been unresolved in earlier single- and multi-gene studies. Pooideae, the cool-season grass lineage, is the largest of the 12 grass subfamilies and includes important temperate cereals, turf grasses and forage species. Although numerous studies of the phylogeny of the subfamily have been undertaken, relationships among some 'early-diverging' tribes conflict among studies, and some relationships among subtribes of Poeae have not yet been resolved. To address these issues, we newly sequenced 25 whole plastomes, which showed rearrangements typical of Poaceae. These plastomes represent 9 tribes and 11 subtribes of Pooideae, and were analysed with 20 existing plastomes for the subfamily. Maximum likelihood (ML), maximum parsimony (MP) and Bayesian inference (BI) robustly resolve most deep relationships in the subfamily. Complete plastome data provide increased nodal support compared with protein-coding data alone at nodes that are not maximally supported. Following the divergence of Brachyelytrum, Phaenospermateae, Brylkinieae-Meliceae and Ampelodesmeae-Stipeae are the successive sister groups of the rest of the subfamily. Ampelodesmeae are nested within Stipeae in the plastome trees, consistent with its hybrid origin between a phaenospermatoid and a stipoid grass (the maternal parent). The core Pooideae are strongly supported and include Brachypodieae, a Bromeae-Triticeae clade and Poeae. Within Poeae, a novel sister group relationship between Phalaridinae and Torreyochloinae is found, and the relative branching order of this clade and Aveninae, with respect to an Agrostidinae-Brizinae clade, are discordant between MP and ML/BI trees. Maximum likelihood and Bayesian analyses strongly support Airinae and Holcinae as the successive sister groups of a Dactylidinae-Loliinae clade.
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http://dx.doi.org/10.1093/aobpla/plv046DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4480051PMC
May 2015

DNA barcoding the Canadian Arctic flora: core plastid barcodes (rbcL + matK) for 490 vascular plant species.

PLoS One 2013 22;8(10):e77982. Epub 2013 Oct 22.

Botany Section, Research and Collections Services, Canadian Museum of Nature, Ottawa, Ontario, Canada.

Accurate identification of Arctic plant species is critical for understanding potential climate-induced changes in their diversity and distributions. To facilitate rapid identification we generated DNA barcodes for the core plastid barcode loci (rbcL and matK) for 490 vascular plant species, representing nearly half of the Canadian Arctic flora and 93% of the flora of the Canadian Arctic Archipelago. Sequence recovery was higher for rbcL than matK (93% and 81%), and rbcL was easier to recover than matK from herbarium specimens (92% and 77%). Distance-based and sequence-similarity analyses of combined rbcL + matK data discriminate 97% of genera, 56% of species, and 7% of infraspecific taxa. There is a significant negative correlation between the number of species sampled per genus and the percent species resolution per genus. We characterize barcode variation in detail in the ten largest genera sampled (Carex, Draba, Festuca, Pedicularis, Poa, Potentilla, Puccinellia, Ranunculus, Salix, and Saxifraga) in the context of their phylogenetic relationships and taxonomy. Discrimination with the core barcode loci in these genera ranges from 0% in Salix to 85% in Carex. Haplotype variation in multiple genera does not correspond to species boundaries, including Taraxacum, in which the distribution of plastid haplotypes among Arctic species is consistent with plastid variation documented in non-Arctic species. Introgression of Poa glauca plastid DNA into multiple individuals of P. hartzii is problematic for identification of these species with DNA barcodes. Of three supplementary barcode loci (psbA-trnH, psbK-psbI, atpF-atpH) collected for a subset of Poa and Puccinellia species, only atpF-atpH improved discrimination in Puccinellia, compared with rbcL and matK. Variation in matK in Vaccinium uliginosum and rbcL in Saxifraga oppositifolia corresponds to variation in other loci used to characterize the phylogeographic histories of these Arctic-alpine species.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0077982PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3865322PMC
February 2015

Taxonomic synopsis of invasive and native Spartina (Poaceae, Chloridoideae) in the Pacific Northwest (British Columbia, Washington and Oregon), including the first report of Spartina ×townsendii for British Columbia, Canada.

PhytoKeys 2012 21(10):25-82. Epub 2012 Mar 21.

Research & Collections, Canadian Museum of Nature, P.O. Box 3443 Stn. D, Ottawa, Ontario K1P 6P4, Canada.

Five species of the grass genus Spartina are invading salt marshes along the Pacific coast of North America, of which three have been documented in British Columbia, Canada, in only the last decade. A taxonomic synopsis of the two native (Spartina gracilis, Spartina pectinata) and five introduced Spartina taxa (Spartina anglica, Spartina alterniflora, Spartina densiflora, Spartina patens, Spartina ×townsendii) in the Pacific Northwest is presented to facilitate their identification, including nomenclature, a new taxonomic key, new descriptions for a subset of taxa, and representative specimens. Spartina ×townsendii is newly reported for the flora of British Columbia. The non-coastal species Spartina pectinata is reported from an urban site in British Columbia, the first confirmed report of the taxon for the province. Lectotypes are newly designated for Spartina anglica C.E. Hubb., Spartina maritima subvar. fallax St.-Yves, and Spartina cynosuroides f. major St.-Yves.
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http://dx.doi.org/10.3897/phytokeys.10.2734DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3310194PMC
August 2012

The origins of C4 grasslands: integrating evolutionary and ecosystem science.

Science 2010 Apr;328(5978):587-91

Department of Ecology and Evolutionary Biology, Brown University, Providence, RI 02912, USA.

The evolution of grasses using C4 photosynthesis and their sudden rise to ecological dominance 3 to 8 million years ago is among the most dramatic examples of biome assembly in the geological record. A growing body of work suggests that the patterns and drivers of C4 grassland expansion were considerably more complex than originally assumed. Previous research has benefited substantially from dialog between geologists and ecologists, but current research must now integrate fully with phylogenetics. A synthesis of grass evolutionary biology with grassland ecosystem science will further our knowledge of the evolution of traits that promote dominance in grassland systems and will provide a new context in which to evaluate the relative importance of C4 photosynthesis in transforming ecosystems across large regions of Earth.
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http://dx.doi.org/10.1126/science.1177216DOI Listing
April 2010

A regional approach to plant DNA barcoding provides high species resolution of sedges (Carex and Kobresia, Cyperaceae) in the Canadian Arctic Archipelago.

Mol Ecol Resour 2010 Jan 22;10(1):69-91. Epub 2009 Jun 22.

Department of Biology, Gendron Hall, Room 160, 30 Marie Curie, University of Ottawa, Ottawa, ON, K1N 6N5, Canada Canadian Museum of Nature, PO Box 3443 Stn "D", Ottawa, ON, Canada K1P 6P4.

Previous research on barcoding sedges (Carex) suggested that basic searches within a global barcoding database would probably not resolve more than 60% of the world's some 2000 species. In this study, we take an alternative approach and explore the performance of plant DNA barcoding in the Carex lineage from an explicitly regional perspective. We characterize the utility of a subset of the proposed protein-coding and noncoding plastid barcoding regions (matK, rpoB, rpoC1, rbcL, atpF-atpH, psbK-psbI) for distinguishing species of Carex and Kobresia in the Canadian Arctic Archipelago, a clearly defined eco-geographical region representing 1% of the Earth's landmass. Our results show that matK resolves the greatest number of species of any single-locus (95%), and when combined in a two-locus barcode, it provides 100% species resolution in all but one combination (matK + atpFH) during unweighted pair-group method with arithmetic mean averages (UPGMA) analyses. Noncoding regions were equally or more variable than matK, but as single markers they resolve substantially fewer taxa than matK alone. When difficulties with sequencing and alignment due to microstructural variation in noncoding regions are also considered, our results support other studies in suggesting that protein-coding regions are more practical as barcoding markers. Plastid DNA barcodes are an effective identification tool for species of Carex and Kobresia in the Canadian Arctic Archipelago, a region where the number of co-existing closely related species is limited. We suggest that if a regional approach to plant DNA barcoding was applied on a global scale, it could provide a solution to the generally poor species resolution seen in previous barcoding studies.
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http://dx.doi.org/10.1111/j.1755-0998.2009.02725.xDOI Listing
January 2010

Hydatellaceae identified as a new branch near the base of the angiosperm phylogenetic tree.

Nature 2007 Mar;446(7133):312-5

UBC Botanical Garden and Centre for Plant Research (Faculty of Land and Food Systems), Centre for Biodiversity Research, and Department of Botany, 2357 Main Mall, The University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada.

Although the relationship of angiosperms to other seed plants remains controversial, great progress has been made in identifying the earliest extant splits in flowering-plant phylogeny, with the discovery that the New Caledonian shrub Amborella trichopoda, the water lilies (Nymphaeales), and the woody Austrobaileyales constitute a basal grade of lines that diverged before the main radiation in the clade. By focusing attention on these ancient lines, this finding has re-written our understanding of angiosperm structural and reproductive biology, physiology, ecology and taxonomy. The discovery of a new basal lineage would lead to further re-evaluation of the initial angiosperm radiation, but would also be unexpected, as nearly all of the approximately 460 flowering-plant families have been surveyed in molecular studies. Here we show that Hydatellaceae, a small family of dwarf aquatics that were formerly interpreted as monocots, are instead a highly modified and previously unrecognized ancient lineage of angiosperms. Molecular phylogenetic analyses of multiple plastid genes and associated noncoding regions from the two genera of Hydatellaceae identify this overlooked family as the sister group of Nymphaeales. This surprising result is further corroborated by evidence from the nuclear gene phytochrome C (PHYC), and by numerous morphological characters. This indicates that water lilies are part of a larger lineage that evolved more extreme and diverse modifications for life in an aquatic habitat than previously recognized.
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http://dx.doi.org/10.1038/nature05612DOI Listing
March 2007
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