Travel Tales of a Worldwide Weed: Genomic Signatures of Plantago major L. Reveal Distinct Genotypic Groups With Links to Colonial Trade Routes.

Retracing pathways of historical species introductions is fundamental to understanding the factors involved in the successful colonization and spread, centuries after a species' establishment in an introduced range. Numerous plants have been introduced to regions outside their native ranges both intentionally and accidentally by European voyagers and early colonists making transoceanic journeys; however, records are scarce to document this. We use genotyping-by-sequencing and genotype-likelihood methods on the selfing, global weed, Plantago major, collected from 50 populations worldwide to investigate how patterns of genomic diversity are distributed among populations of this global weed. Although genomic differentiation among populations is found to be low, we identify six unique genotype groups showing very little sign of admixture and low degree of outcrossing among them. We show that genotype groups are latitudinally restricted, and that more than one successful genotype colonized and spread into the introduced ranges. With the exception of New Zealand, only one genotype group is present in the Southern Hemisphere. Three of the most prevalent genotypes present in the native Eurasian range gave rise to introduced populations in the Americas, Africa, Australia, and New Zealand, which could lend support to the hypothesis that P. major was unknowlingly dispersed by early European colonists. Dispersal of multiple successful genotypes is a likely reason for success. Genomic signatures and phylogeographic methods can provide new perspectives on the drivers behind the historic introductions and the successful colonization of introduced species, contributing to our understanding of the role of genomic variation for successful establishment of introduced taxa.

Molecular and Morphological Data Improve the Classification of Plantagineae (Lamiales).

The tribe Plantagineae (Lamiales) is a group of plants with worldwide distribution, notorious for its complicated taxonomy and still unresolved natural history. We describe the result of a broadly sampled phylogenetic study of tribe. The expanded sampling dataset is based on the trnL-F spacer, rbcL, and ITS2 markers across all three included genera (Aragoa, Littorella and Plantago) and makes this the most comprehensive study to date. The other dataset uses five markers and provides remarkably good resolution throughout the tree, including support for all of the major clades. In addition to the molecular phylogeny, a morphology database of 114 binary characters was assembled to provide comparison with the molecular phylogeny and to develop a means to assign species not sampled in the molecular analysis to their most closely related species that were sampled. Based on the molecular phylogeny and the assignment algorithm to place unsampled species, a key to sections is presented, and a revised classification of the tribe is provided. We also include the description of new species from North America.

Stem and Leaf Anatomy of Aragoa (Plantaginaceae): In Search of Lost Rays.

Aragoa is a shrubby genus endemic to páramo in the northern Andes representing the sister group to Plantago and Limosella. Stem and leaf structure of Aragoa corrugatifolia were studied to clarify the evolutionary pathways and ecological significance of their anatomical traits. Aragoa and Plantago share a non-fascicular primary vascular system, rayless wood and secondary phloem, and anomocytic stomata. Aragoa is distinctive from most Plantaginaceae in the presence of cortical aerenchyma and of helical thickenings in vessels. Its procambium emerges in the primary meristem ring as a continuous cylinder. The view on the ring meristem and procambial strands as developmental stages in the formation of a primary vascular system is not relevant for Aragoa, and probably for other Plantaginaceae. The raylessness is synapomorphic for the crown clade of Plantaginaceae comprising Aragoa, Littorella, Plantago, Veronica, Picrorhiza, Wulfenia, and Veronicastrum. The loss of rays is thought to be predetermined by procambium rather than by the vascular cambium. The extremely narrow vessels with helical thickenings are presumably adaptive to hydric and thermic conditions of páramo. Cortical aerenchyma is thought to be a response to the local hypoxia caused by the water retained by ericoid leaves. Trichomes on juvenile leaves are expected to be the traits of considerable taxonomic importance.

First Phylogeny of Bitterbush Family, Picramniaceae (Picramniales).

Picramniaceae is the only member of Picramniales which is sister to the clade (Sapindales (Huerteales (Malvales, Brassicales))) in the rosidsmalvids. Not much is known about most aspects of their ecology, geography, and morphology. The family is restricted to American tropics. Picramniaceae representatives are rich in secondary metabolites; some species are known to be important for pharmaceutical purposes. Traditionally, Picramniaceae was classified as a subfamily of Simaroubaceae, but from 1995 on, it has been segregated containing two genera, Picramnia and Alvaradoa, with the recent addition of a third genus, Nothotalisia, described in 2011. Only a few species of the family have been the subject of DNA-related research, and fewer than half of the species have been included in morphological phylogenetic analyses. It is clear that Picramniaceae remains a largely under-researched plant group. Here we present the first molecular phylogenetic tree of the group, based on both chloroplast and nuclear markers, widely adopted in the plant DNA barcoding. The main findings are: The family and its genera are monophyletic and Picramnia is sister to two other genera; some clades corroborate previous assumptions of relationships made on a morphological or geographical basis, while most parts of the molecular topology suggest high levels of homoplasy in the morphological evolution of Picramnia.

The application of high-throughput sequencing for taxonomy: The case of Plantago subg. Plantago (Plantaginaceae).

Plantago is a cosmopolitan genus including over 250 species, concentrated in temperate and high-elevation tropical regions. The taxonomy of Plantago is very difficult, mainly because of its reduced morphology, which features relatively few characters for species classification. Consequently, the infrageneric classification of the genus remains controversial and inadequate. In this study we applied high-throughput plastid genome skimming to provide powerful phylogenetic resolution to clarify the relationships within subg. Plantago, which is the largest, most broadly distributed and poorest understood subgenus of Plantago. Ninety-four samples covering ~56% of all species and representing all sections of subg. Plantago as well as an outgroup were successfully sequenced. The resulting phylogenetic topology was used, complemented by field and herbarium studies, to revise the sectional classification of subg. Plantago and present a complete listing of the accepted species in the subgenus. Our phylogenetic results were also tested for their usefulness in clarifying the taxonomic placement of some taxonomically complicated species in the subgenus. We conclude that a combination of morphological studies and state-of-the art high-throughput DNA data provide a useful toolbox for resolving outstanding taxonomic puzzles exemplified by the genus Plantago.

Changes in the composition of the RNA virome mark evolutionary transitions in green plants.

BACKGROUND: The known plant viruses mostly infect angiosperm hosts and have RNA or small DNA genomes. The only other lineage of green plants with a relatively well-studied virome, unicellular chlorophyte algae, is mostly infected by viruses with large DNA genomes. Thus RNA viruses and small DNA viruses seem to completely displace large DNA virus genomes in late branching angiosperms. To understand better the expansion of RNA viruses in the taxonomic span between algae and angiosperms, we analyzed the transcriptomes of 66 non-angiosperm plants characterized by the 1000 Plants Genomes Project. RESULTS: We found homologs of virus RNA-dependent RNA polymerases in 28 non-angiosperm plant species, including algae, mosses, liverworts (Marchantiophyta), hornworts (Anthocerotophyta), lycophytes, a horsetail Equisetum, and gymnosperms. Polymerase genes in algae were most closely related to homologs from double-stranded RNA viruses leading latent or persistent lifestyles. Land plants, in addition, contained polymerases close to the homologs from single-stranded RNA viruses of angiosperms, capable of productive infection and systemic spread. For several polymerases, a cognate capsid protein was found in the same library. Another virus hallmark gene family, encoding the 30 K movement proteins, was found in lycophytes and monilophytes but not in mosses or algae. CONCLUSIONS: The broadened repertoire of RNA viruses suggests that colonization of land and growth in anatomical complexity in land plants coincided with the acquisition of novel sets of viruses with different strategies of infection and reproduction.

All that is gold does not glitter? Age, taxonomy, and ancient plant DNA quality.

More than 600 herbarium samples from four distantly related groups of flowering plants were used for DNA extraction and subsequent measurements of DNA purity and concentration. We did not find any significant relation between DNA purity and the age of the sample. However, DNA yields were different between plant groups studied. We believe that there there should be no reservations about "old" samples if the goal is to extract more DNA of better purity. We argue that the older herbarium samples are the mine for the future DNA studies, and have the value not less than the "fresh" specimens.

Exclusionary interactions among diverse fungi infecting developing seeds of Centaurea stoebe.

Developing seeds are expected to be strongly defended against microbial attack. In keeping with this, only 26% of seeds of Centaurea stoebe from its native and invaded ranges in Eurasia and North America were infected with fungi, and 92.2% of those were infected with a single fungus per seed. Even when developing seeds in flower heads were inoculated under conducive conditions for infection with 14 of these seed-infecting fungi, re-isolation of inoculants was only 16% overall, and again limited to the particular inoculant. Environmental fungi (i.e. those not isolated from seed of C. stoebe) were present in control flower heads under conditions conducive to infection but they were never re-isolated from fully developed seeds in any experiments. When two or three seed isolates were co-inoculated to compete in flower heads, only one inoculant, and always the same one, was re-isolated from all matured seeds, regardless of maternal plant genotype. PCR-based detection methods confirmed that these fungal interactions were exclusionary rather than suppressive. In these strongly defended, developing seeds, we had expected the plant to control not only the overall level of infection but also the outcome of co-inoculations. Consequences for the next plant generation of this exclusionary competition among seed-infecting fungi included effects on seedling emergence, growth and fecundity.

Haptanthus story: rediscovery of enigmatic flowering plant from Honduras.

PREMISE OF THE STUDY: Finding a plant or animal that was previously considered extinct is a fortunate (but rare) event in biology. Haptanthus hazlettii was collected from Honduras (Central America) in 1980, but numerous attempts to re-collect it have failed. Reproductive organs of Haptanthus are unique among angiosperms and make the search for phylogenetic relations difficult. Unfortunately, all attempts to extract DNA from the existing sample were unsuccessful. METHODS: In 2010, we organized a small expedition to Honduras and were able to re-collect this plant, extract DNA from dried samples, and sequence the barcoding region of rbcL. KEY RESULTS AND CONCLUSIONS: We obtained phylogenetic trees with reliable support for the placement of Haptanthus as a new member of Buxaceae (boxwood family).

Endophytes influence protection and growth of an invasive plant.

We investigated the symbiotic activities of fungal endophytes isolated from spotted knapweed, Centaurea stoebe. Previously, an analysis of community similarity had demonstrated differences in the endophyte communities of C. stoebe in its native and invaded ranges. Here, we found that specific endophytes can exert positive effects on their host, whereas others exert negative effects. Endophytes produced metabolites that inhibited germination of a competitor of C. stoebe. Endophytes also repelled a specialist insect herbivore, perhaps by producing biologically active volatiles. Yet other endophytes acted as cryptic pathogens of C. stoebe, suppressing its germination, reducing its growth, increasing the abundance of a generalist insect herbivore, and delaying or suppressing its flowering. Since, as reported here, endophytes are not functionally interchangeable, previously reported community differences could be contributing to the invasiveness of C. stoebe.

Hidden diversity of endophytic fungi in an invasive plant.

Fungal endophytes are important in plant ecology and common in plants. We attempted to test cointroduction and host-jumping hypotheses on a community basis by comparing endophytes isolated from invasive spotted knapweed (Centaurea stoebe, Asteraceae) in its native and invaded ranges. Of 92 combined, sequence-based haplotypes representing eight classes of Fungi, 78 occurred in only one of the two ranges. In the native range of C. stoebe, one haplotype of Alternaria alternata was clearly dominant, whereas in the invaded range, no haplotype was dominant. Many haplotypes were closely related to one another and novel. For example, six putative, new species of Botrytis were discovered as endophytes of C. stoebe, which has never been reported to have Botrytis spp.. Apparent differences between the two communities of endophytes were significant according to an analysis of similarity, but phylogenetic community structure did not differ significantly between the ranges. Both host-jumping and cointroduction of fungal endophytes likely took place during the spotted knapweed invasion.

Dactylorhiza (Orchidaceae) in European Russia: combined molecular and morphological analysis.

Four plastid and two nuclear (internal transcribed spacer [ITS] ribosomal DNA) markers were used in this study of the Dactylorhiza maculata and D. incarnata complexes (Orchidaceae: Orchidinae) to determine diversity and taxonomic distribution of haplotypes, hybridization frequencies, and maternal parentage of hybrids in 125 samples from 78 populations from European Russia and the Caucasus. A morphometric study of all populations revealed significant correspondence between morphological and plastid DNA data. Most D. maculata sensu stricto (s.s.) specimens from Russia have D. fuchsii haplotypes; this could be evidence for introgression or widespread hybridization between these species in northern Russia. Heterogeneity within populations is much higher for ITS data and is strongly correlated with latitude. Both plastid and nuclear data are significantly correlated with distribution along a south-north axis. Several haplotypes and ITS alleles uncommon in western Europe are more widely distributed in Russia, whereas some frequent haplotypes from western Europe are absent.