Heidi M. Meudt

Piecing together the "new" Plantaginaceae.

Scrophulariaceae is one of the families that has been divided extensively due to the results of DNA sequence studies. One of its segregates is a vastly enlarged Plantaginaceae. In a phylogenetic study of 47 members of Plantaginaceae and seven outgroups based on 3561 aligned characters from four DNA regions (the nuclear ribosomal ITS region and the plastid trnL-F, rps16 intron, and matK-trnK intron regions), the relationships within this clade were analyzed. The results from parsimony and Bayesian analyses support the removal of the Lindernieae from Gratioleae to a position outside Plantaginaceae. A group of mainly New World genera is paraphyletic with respect to a clade of Old World genera. Among the New World taxa, those offering oil as a pollinator reward cluster together. Ourisia is sister to this clade. Gratioleae consist of Gratiola, Otacanthus, Bacopa, Stemodia, Scoparia, and Mecardonia. Cheloneae plus Russelia and Tetranema together constitute the sister group to a clade predominantly composed of Old World taxa. Among the Old World clade, Ellisiophyllum and Lafuentea have been analyzed for the first time in a molecular phylogenetic analysis. The former genus is sister to Sibthorpia and the latter is surprisingly the sister to Antirrhineae.

Optimizing Automated AFLP Scoring Parameters to Improve Phylogenetic Resolution

The amplified fragment length polymorphism (AFLP) technique is an increasingly popular component of the phylogenetic toolbox, particularly for plant species. Technological advances in capillary electrophoresis now allow very precise estimates of DNA fragment mobility and amplitude, and current AFLP software allows greater control of data scoring and the production of the binary character matrix. However, for AFLP to become a useful modern tool for large data sets, improvements to automated scoring are required. We design a procedure that can be used to optimize AFLP scoring parameters to improve phylogenetic resolution and demonstrate it for two AFLP scoring programs (GeneMapper and GeneMarker). In general, we found that there was a trade-off between getting more characters of lower quality and fewer characters of high quality. Conservative settings that gave the least error did not give the best phylogenetic resolution, as too many useful characters were discarded. For example, in GeneMapper, we found that bin width was a crucial parameter, and that although reducing bin width from 1.0 to 0.5 base pairs increased the error rate, it nevertheless improved resolution due to the increased number of informative characters. For our 30-taxon data sets, moving from default to optimized parameter settings gave between 3 and 11 extra internal edges with >50% bootstrap support, in the best case increasing the number of resolved edges from 14 to 25 out of a possible 27. Nevertheless, improvements to current AFLP software packages are needed to (1) make use of replicate profiles to calibrate the data and perform error calculations and (2) perform tests to optimize scoring parameters in a rigorous and automated way. This is true not only when AFLP data are used for phylogenetics, but also for other applications, including linkage mapping and population genetics.

Species delimitation and phylogeny of a New Zealand plant species radiation

BackgroundDelimiting species boundaries and reconstructing the evolutionary relationships of late Tertiary and Quaternary species radiations is difficult. One recent approach emphasizes the use of genome-wide molecular markers, such as amplified fragment length polymorphisms (AFLPs) and single nucleotide polymorphisms (SNPs), to identify distinct metapopulation lineages as taxonomic species. Here we investigate the properties of AFLP data, and the usefulness of tree-based and non-tree-based clustering methods to delimit species and reconstruct evolutionary relationships among high-elevation Ourisia species (Plantaginaceae) in the New Zealand archipelago.ResultsNew Zealand Ourisia are shown to comprise a geologically recent species radiation based on molecular dating analyses of ITS sequences (0.4–1.3 MY). Supernetwork analyses indicate that separate tree-based clustering analyses of four independent AFLP primer combinations and 193 individuals of Ourisia produced similar trees. When combined and analysed using tree building methods, 15 distinct metapopulations could be identified. These clusters corresponded very closely to species and subspecies identified on the basis of diagnostic morphological characters. In contrast, Structure and PCO-MC analyses of the same data identified a maximum of 12 and 8 metapopulations, respectively. All approaches resolved a large-leaved group and a small-leaved group, as well as a lineage of three alpine species within the small-leaved group. We were unable to further resolve relationships within these groups as corrected and uncorrected distances derived from AFLP profiles had limited tree-like properties.ConclusionOurisia radiated into a range of alpine and subalpine habitats in New Zealand during the Pleistocene, resulting in 13 morphologically and ecologically distinct species, including one reinstated from subspecies rank. Analyses of AFLP identified distinct metapopulations consistent with morphological characters allowing species boundaries to be delimited in Ourisia. Importantly, Structure analyses suggest some degree of admixture with most species, which may also explain why the AFLP data do not exhibit sufficient tree-like properties necessary for reconstructing some species relationships. We discuss this feature and highlight the importance of improving models for phylogenetic analyses of species radiations using AFLP and SNP data.

Phylogeographic patterns in the Australasian genus Chionohebe (Veronica s.l., Plantaginaceae) based on AFLP and chloroplast DNA sequences

The alpine genus Chionohebe is one of seven genera in the southern hemisphere Hebe complex. The main aims of this study were to infer the evolutionary relationships and assess phylogeographic patterns among the six species of Chionohebe, determine the origin of the two species with trans-Tasman distributions, and test species delimitations and specimen identifications based on morphology. Analyses of AFLP data recovered five major lineages within Chionohebe, some of which corresponded to species and varieties as currently circumscribed. Although the cushion chionohebes were strongly supported as monophyletic, the sole non-cushion species, C. densifolia, was sister to Parahebe trifida, and thus the AFLP data do not support a monophyletic Chionohebe as usually circumscribed. Strong north/south and west/east phylogeographic patterns were found among and within the main AFLP lineages in New Zealand. Analyses of chloroplast DNA (cpDNA) revealed eight haplotypes in Chionohebe, but these did not correspond to current taxonomy or geography due to widespread interspecific haplotype sharing. Based on both AFLP and cpDNA results, the two trans-Tasman species are shown to have originated in New Zealand and dispersed to Australia independently.

DNA sequences from three genomes reveal multiple long-distance dispersals and non-monophyly of sections in Australasian Plantago (Plantaginaceae)

We examined the geographic origins and taxonomic placements of New Zealand and Australian Plantago (Plantaginaceae) by using molecular phylogenetic data. Plantago comprises over 200 species distributed worldwide. Analyses of three markers from the nuclear (ITS), chloroplast (ndhF–rpl32) and mitochondrial (coxI) genomes showed that the New Zealand species form three distinct, well supported clades that are not each others’ closest relatives, and were each derived relative to the sampled Australian species. Therefore, at least three long-distance directional dispersal events into New Zealand can be inferred for Plantago, likely from Australian ancestors. This result differs from the biogeographic pattern often reported for New Zealand plant genera of a single dispersal event followed by rapid radiation, and may be attributed to ready biotic dispersal of mucilaginous seeds and habitat similarities of the Australasian species. Molecular dating placed the arrival time and diversification of the New Zealand species between 2.291 and 0.5 million years ago, which coincides with the geological dates for the uplift of mountain ranges in New Zealand. The mitochondrial DNA substitution rate of the Australasian clade relative to the rest of the genus is discussed, as well as implications of the non-monophyly of sections Oliganthos, Mesembrynia and Plantago within subgenus Plantago.

Phylogeny of Veronica in the Southern and Northern Hemispheres based on plastid, nuclear ribosomal and nuclear low-copy DNA

The cosmopolitan and ecologically diverse genus Veronica with approximately 450 species is the largest genus of the newly circumscribed Plantaginaceae. Previous analyses of Veronica DNA sequences were in stark contrast to traditional systematics. However, analyses did not allow many inferences regarding the relationship between major groups identified, hindering further analysis of diversification and evolutionary trends in the genus. To resolve the backbone relationships of Veronica, we added sequences from additional plastid DNA regions to existing data and analyzed matching data sets for 78 taxa and more than 5000 aligned characters from nuclear ribosomal DNA and plastid DNA regions. The results provide the best resolved and supported estimate of relationships among major groups in the Northern (Veronica s. str.) and Southern Hemisphere (hebes). We present new informal names for the five main species groups within the Southern Hemisphere sect. Hebe. Furthermore, in two instances we provide morphological and karyological characters supporting these relationships. Finally, we present the first evidence from nuclear low-copy CYCLOIDEA2-region to compare results from the plastid genome with the nuclear genome.

First phylogenetic and biogeographical study of the southern bluebells (Wahlenbergia, Campanulaceae).

Wahlenbergia is a largely southern hemisphere genus of at least 260 species; within Campanulaceae only Campanula is larger. This first phylogeny of Wahlenbergia was reconstructed using about 20% of the 260 species in the genus based on the nuclear ribosomal ITS marker and the chloroplast trnL-F marker with samples from South Africa, Europe, Australia and New Zealand. Wahlenbergia was confirmed to be non-monophyletic, though most of the species form a clade. Our tree topology and date estimates indicate that Wahlenbergia diverged in South Africa about 29.6 mya, then dispersed to Australasia about 4.8 mya, thus indicating the radiation of Wahlenbergia occurred relatively recently. Radiations occurred in both of these main centres; there are currently about 170 species in South Africa and 45 species and subspecies in Australasia. New Zealand species comprise two clades, both rooted within the Australasian clade. We thus propose two dispersals from Australia to New Zealand, one leading to a radiation of species with the rhizomatous herbaceous growth form ca. 1.6 mya, and the other leading to a radiation of species with the radicate growth form 0.7 mya. Dispersals from Australia to New Zealand match the expected direction, following the west wind drift and ocean currents. The herbaceous growth form was shown to be ancestral for the genus as a whole, and polyploidy has been a mechanism of the evolution of the genus in Australasia.

A taxonomic revision of native New Zealand Plantago (Plantaginaceae)

Species delimitation is challenging in New Zealand Plantago because of a complex polyploid evolutionary history, few taxonomically useful characters due to reduced habit and wind-pollinated flowers, and phenotypic plasticity. To clarify species limits and revise the taxonomy of this group, analyses of novel morphological data were undertaken and evaluated alongside previously published studies of chromosome number, amplified fragment length polymorphisms, molecular phylogenetics, molecular cytogenetics and morphology. All 11 native species of Plantago recognised here are endemic to New Zealand, except Plantago triantha which is also native to Tasmania, Australia. In contrast to previous treatments, Plantago picta is recognised here at the species rank, Plantago masoniae is treated as a synonym of Plantago triandra, and one new 16-ploid species, Plantago udicola Meudt & Garn.-Jones, is formally described. Seed number and shape, scape, bract and sepal vestiture, and number of flowers and spikes are particularly important characters for species delimitation.

Amplified Fragment Length Polymorphism Data Reveal a History of Auto- and Allopolyploidy in New Zealand Endemic Species of Plantago (Plantaginaceae): New Perspectives on a Taxonomically Challenging Group

Amplified fragment length polymorphism (AFLP) data were generated for most of the ∼12 species and subspecies of endemic New Zealand Plantago (Plantaginaceae) to test species boundaries and interpret polyploid origins. Phylogenetic, network, principal-coordinates, structure, and quantitative analyses of the AFLP data were generally congruent and complementary regarding the main lineages, and the incongruences allowed some inferences of alloploidy and hybridization. Within the largely diploid group III, P. novae-zelandiae, P. lanigera, P. obconica, and P. aucklandica were genetically distinct. Within group II, there was little genetic differentiation between octoploids P. masoniae and P. triandra, and multiple alloploid origins were inferred for decaploid and dodecaploid cytotypes of P. unibracteata. Within group I, the 16-ploid P. sp. “Sylvester” is suggested to be an autoploid of octoploid P. raoulii, octoploid P. picta is clearly a genetically distinct entity, and species boundaries of octoploids P. raoulii, P. spathulata, and P. aff. spathulata are unclear. Additional genetic and molecular cytogenetic studies on New Zealand species and their close relatives from Australia and southern South America are needed to further investigate polyploid origins. AFLP is a useful tool for elucidating the origins and evolutionary history of closely related polyploid species in taxonomically challenging groups such as endemic New Zealand Plantago.

PHYLOGENETIC ANALYSIS OF MORPHOLOGICAL CHARACTERS IN OURISIA (PLANTAGINACEAE): TAXONOMIC AND EVOLUTIONARY IMPLICATIONS 1

Abstract Ourisia Comm. ex Juss. (Plantaginaceae; Scrophulariaceae s.l.) is a genus of herbaceous or suffruticose species that occur largely in high-elevation habitats of Andean South America, New Zealand, and Tasmania. Recent molecular phylogenetic data have clarified evolutionary relationships within Ourisia and provided high support for the recognition of two subgenera based primarily on habit, i.e., Ourisia subg. Ourisia (25 herbaceous species) and Ourisia subg. Suffruticosae Meudt (three suffruticose species). To investigate the utility of morphological data in comparison to molecular data for phylogeny and subgeneric taxonomy, phylogenetic hypotheses were generated using 20 morphological characters for all 33 taxa of Ourisia using Melosperma Benth. as an outgroup. Additional phylogenetic hypotheses were generated by combining the morphological data with molecular data for the 29 species (plus Melosperma) for which the latter were available. With respect to phylogeny, morphological data are congruent with molecular data but generally provide less resolution. Morphological data are informative regarding infrageneric taxonomy and show that at least six morphological characters in addition to habit support the delimitation of the two subgenera. Finally, morphological characters of interest were traced onto the molecular phylogeny. Evolution of these and other characters are discussed in light of the various phylogenetic results.