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.

Charophytes (Charales) are benthic algae with a complex morphology. They are vulnerable to ecosystem changes, such as eutrophication, and are red-listed in many countries. Accurate identification of Chara species is critical for understanding their diversity and for documenting changes in species distribution. Species delineation is, however, complicated, because of high phenotypic plasticity. We used barcodes of the ITS2, matK and rbcL regions to test if the distribution of barcode haplotypes among individuals is consistent with species boundaries as they are currently understood. The study included freshly collected and herbarium material of 91 specimens from 10 European countries, Canada and Argentina. Results showed that herbarium specimens are useful as a source of material for genetic analyses for aquatic plants like Chara. rbcL and matK had highest sequence recoverability, but rbcL had a somewhat lower discriminatory power than ITS2 and matK. The tree resulting from the concatenated data matrix grouped the samples into six main groups contrary to a traditional morphological approach that consisted of 14 different taxa. A large unresolved group consisted of C. intermedia, C. hispida, C. horrida, C. baltica, C. polyacantha, C. rudis, C. aculeolata, and C. corfuensis. A second unresolved group consisted of C. virgata and C. strigosa. The taxa within each of the unresolved groups shared identical barcode sequences on the 977 positions of the concatenated data matrix. The morphological differences of taxa within both unresolved groups include the number and length of spine cells, stipulodes, and bract cells. We suggest that these morphological traits have less taxonomic relevance than hitherto assumed.

These microsatellite markers will be useful in obtaining estimates of population-level genetic diversity and in phylogeographic studies of C. americana.

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Premise of research. Understanding how various organisms respond to previous changes in climate could provide insight into how they may respond or adapt to the current changes. Conopholis americana has a broad distribution across eastern North America, covering both previously glaciated and unglaciated regions. In this study, we investigated the postglacial history and phylogeographic structure of this parasitic plant species to characterize its genetic variation and structure and to identify the number and locations of refugia. Methodology. Molecular data from 10 microsatellite markers and DNA sequences from the plastid gene / introns (clpP) were obtained for 281 individuals sampled from 75 populations spanning the current range of the species in eastern North America and analyzed using a variety of phylogeographic methods. Distribution modeling was carried out to determine regions with relatively suitable climate niches for populations at the Last Glacial Maximum (LGM) and present. Pivotal results. We inferred the persistence of a minimum of two glacial refugia for C. americana at the LGM, one in north-central Florida and southern Alabama and another in the Appalachian Mountains near the southern tip of the Blue Ridge Mountains. High levels of genetic diversity were observed across the southern Appalachian Mountains, the region where populations from two refugia come together following recolonization northward. Conclusions. The genetic and geographic patterns revealed by our results provide further evidence of the dynamic nature and phylogeographical history of eastern North American taxa. The discovery of a distinct southern lineage is in agreement with the location of a previously proposed southern glacial refugium spanning across Florida, southern Georgia and Alabama, and the Lower Mississippi Valley. The second lineage is dominant across the present northern range of the species and is hypothesized to have been located in the southern extent of the Blue Ridge mountain range of the Appalachian Mountains at the LGM.

Premise of the study : Little is known of the evolutionary relationships within Conopholis , a small holoparasitic genus belonging to the broomrape family. Presently, Conopholis is described as having two species, C. americana and C. alpina . This classifi cation is based on a combination of presence/absence of morphological characters along with a number of quantitative traits. We assessed the relationships among populations and species of this genus to determine whether the present taxonomic hypothesis is refl ected in molecular phylogenies.• Methods : We conducted the fi rst phylogenetic study of Conopholis using plastid ( trnfM-E intergenic spacer and clpP gene/introns) and nuclear ( PHYA intron 1) sequences from a wide taxonomic sampling covering its entire geographical range in North America. Analyses were carried out using a variety of phylogenetic inference approaches. • Key results : Reciprocal monophyly between the two traditionally accepted species has not yet been achieved. Instead, three distinct genetic clusters were recovered. Conopholis alpina is clearly paraphyletic and shows evidence of belonging to at least two distinct lineages. Specimens found in Costa Rica and Panama form a distinct group from those located in northern Mexico and the southwestern United States. The monophyly of C. americana was also not recovered; however, the possibility of it being monophyletic could not be rejected with confi dence. • Conclusions : These analyses recovered three distinct lineages indicating that there could be a minimum of three species within the genus. A reevaluation of morphological features within Conopholis may reveal shared features that could further corroborate our molecular fi ndings.