Linda E. Watson

An ITS phylogeny of tribe Senecioneae (Asteraceae) and a new delimitation of Senecio L

Senecioneae is the largest tribe ofAsteraceae, comprised ofca. 150 genera and 3,000 species. Approximately one-third of its species are placed in Senecio, making it one of the largest genera of flowering plants. Despite considerable efforts to classify and understand the striking morphological diversity in Senecioneae, little is known about its intergeneric relationships. This lack ofphylogenetic understanding is predominantly caused by conflicting clues from morphological characters, the large size ofthe tribe, and the absence of a good delimitation of Senecio. Phylogenetic analyses of nrITS and plastid DNA sequence data were used to produce a hypothesis of evolutionary relationships in Senecioneae and a new, monophyletic, delimitation of Senecio. The results of separate and combined phylogenetic analyses of the two datasets were compared to previous taxonomic treatments, morphological and karyological data, and biogeographic patterns. These studies indicate that the subtribal delimitation of Senecioneae needs to be revised to reflect exclusively monophyletic subtribes. This would involve abolishing subtribes Adenostylinae, Blennospermatinae, and Tephroseridinae and recognizing subtribes Abrotanellinae, Othonninae, and Senecioninae. Moreover, Tussilagininae may need to be split into three or four subtribes: Brachyglottidinae, Chersodominae, Tussilagininae, and perhaps Doronicinae. On the intergeneric level, these phylogenies provide new insights into evolutionary relationships, resulting in a first approximation of a comprehensive phylogeny for the tribe. Most species currently assigned to Senecio form a well supported clade. Thus, a new delimitation of Senecio is proposed, which involves transferring the species ofAetheolaena, Culcitium, Hasteola, locenes, Lasiocephalus, and Robinsonia to Senecio and removing several Senecio groups that are only distantly related to the core of Senecio. Area optimization analyses indicate a strong African influence throughout the evolutionary history of Senecioneae, predominantly in subtribes Senecioninae and Othonninae.

Patterns and causes of incongruence between plastid and nuclear Senecioneae (Asteraceae) phylogenies

One of the longstanding questions in phylogenetic systematics is how to address incongruence among phylogenies obtained from multiple markers and how to determine the causes. This study presents a detailed analysis of incongruent patterns between plastid and ITS/ETS phylogenies of Tribe Senecioneae (Asteraceae). This approach revealed widespread and strongly supported incongruence, which complicates conclusions about evolutionary relationships at all taxonomic levels. The patterns of incongruence that were resolved suggest that incomplete lineage sorting (ILS) and/or ancient hybridization are the most likely explanations. These phenomena are, however, extremely difficult to distinguish because they may result in similar phylogenetic patterns. We present a novel approach to evaluate whether ILS can be excluded as an explanation for incongruent patterns. This coalescence-based method uses molecular dating estimates of the duration of the putative ILS events to determine if invoking ILS as an explanation for incongruence would require unrealistically high effective population sizes. For four of the incongruent patterns identified within the Senecioneae, this approach indicates that ILS cannot be invoked to explain the observed incongruence. Alternatively, these patterns are more realistically explained by ancient hybridization events.

Molecular phylogeny of Subtribe Artemisiinae (Asteraceae),including Artemisia and its allied and segregate genera

BackgroundSubtribe Artemisiinae of Tribe Anthemideae (Asteraceae) is composed of 18 largely Asian genera that include the sagebrushes and mugworts. The subtribe includes the large cosmopolitan, wind-pollinated genus Artemisia, as well as several smaller genera and Seriphidium, that altogether comprise the Artemisia-group. Circumscription and taxonomic boundaries of Artemisia and the placements of these small segregate genera is currently unresolved.ResultsWe constructed a molecular phylogeny for the subtribe using the internal transcribed spacers (ITS) of nuclear ribosomal DNA analyzed with parsimony, likelihood, and Bayesian criteria. The resulting tree is comprised of three major clades that correspond to the radiate genera (e.g., Arctanthemum and Dendranthema), and two clades of Artemisia species. All three clades have allied and segregate genera embedded within each.ConclusionsThe data support a broad concept of Artemisia s.l. that includes Neopallasia, Crossostephium, Filifolium, Seriphidium, and Sphaeromeria. However, the phylogeny excludes Elachanthemum, Kaschgaria, and Stilnolepis from the Artemisia-group. Additionally, the monophyly of the four subgenera of Artemisia is also not supported, with the exception of subg. Dracunculus. Homogamous, discoid capitula appear to have arisen in parallel four to seven times, with the loss of ray florets. Thus capitular morphology is not a reliable taxonomic character, which traditionally has been one of the defining characters.

Phylogenetic analysis of Artemisia section Tridentatae (Asteraceae) based on sequences from the internal transcribed spacers (ITS) of nuclear ribosomal DNA

Artemisia sect. Tridentatae is composed of 11 species of xerophytic shrubs, which dominate much of western North America. Sequences of the internal transcribed spacers (ITS) of nuclear ribosomal DNA were used to construct a phylogeny, examine circumscription of the section, resolve interspecific relationships, and test competing hypotheses on the origin of the section. The data support the monophyly of sect. Tridentatae, with the exclusion of A. bigelovii and A. palmeri-two historically, anomolous species. However, the ITS data provide insufficient variation to fully resolve interspecific relationships or to support major lineages within the Tridentata clade. Nuclear and chloroplast DNA phylogenies are discordant, which may be a result of interspecific gene flow and subsequent chloroplast capture, particularly related to the placement of A. filifolia and A. californica, in addition to A. bigelovii. Furthermore, the ITS data are in conflict with cpDNA data, providing equivocal evidence for competing hypotheses on the Old World vs. New World origin for the section and do not provide support for definitive subgeneric placement.

Molecular differentiation of the heterocystous cyanobacteria, Nostoc and Anabaena, based on complete NifD sequences.

The segregation of Nostoc and Anabaena into separate genera has been debated for some time. The nitrogen fixation gene nifD was completely sequenced from representatives of these genera and analyzed phylogenetically, by using the representatives of other genera of the heterocystous cyanobacteria as outgroups. We were clearly able to differentiate between Nostoc and Anabaena in all analyses used. Our data suggest that Nostoc and Anabaena should remain as separate genera.

Ancestors of white clover (Trifolium repens L.), as revealed by isozyme polymorphisms

Abstract.Isozymes were used to study the putative ancestors of white clover (Trifolium repens L.). Ten enzymes were examined, and 18 loci were resolved via starch-gel electrophoresis for accessions representing T. repens, Trifolium isthmocarpum, Trifolium nigrescens, Trifolium occidentale and Trifolium uniflorum, in addition to two more distantly related species, Trifolium alpinum and Trifolium purseglovei. Neis genetic identities indicate that T. uniflorum and T. nigrescens are the closest relatives of T. repens. The isozyme data thus support a hypothesis that the two genomes of the tetraploid T. repens could have been derived from hybridization between T. nigrescens and T. uniflorum. This conclusion is further supported by shared alleles between T. repens, T. nigrescens and T. uniflorum. However, the origin of T. repens is somewhat obscured by the presence of shared alleles between T. repens and both T. occidentale and T. isthmocarpum, suggesting that introgression of genes from the latter two species into T. repens may also have taken place. High values of genetic identity are shared between T. occidentale with T. nigrescens and T. uniflorum, also indicative of introgression. Alternatively the presence of shared alleles among the five species may reflect their recent common ancestry.

The Evolutionary History of Nitrogen Fixation, as Assessed by NifD

The evolutionary history of nitrogen fixation has been vigorously debated for almost two decades. Previous phylogenetic analyses of nitrogen fixation genes (nif) have shown support for either evolution by vertical descent or lateral transfer, depending on the specific nif gene examined and the method of analyses used. The debate centers on the placement and monophyly of the cyanobacteria, proteobacteria, and Gram-positive bacteria (actinobacteria and firmicutes). Some analyses place the cyanobacteria and actinobacteria within the proteobacteria, which suggests that the nif genes have been laterally transferred since this topology is incongruent with ribosomal phylogenies, the standard marker for comparison. Other nif analyses resolve and support the monophyly of the cyanobacteria, proteobacteria, and actinobacteria, supporting vertical descent. We have revisited these conflicting scenarios by analyzing nifD from an increased number of cyanobacteria, proteobacteria, and Gram-positive bacteria. Parsimony analyses of amino acid sequences and maximum likelihood analysis of nucleic acid sequences support the monophyly of the cyanobacteria and actinobacteria but not the proteobacteria, lending support for vertical descent. However, distance analysis of nucleic acid sequences placed the actinobacteria within the proteobacteria, supporting lateral transfer. We discuss evidence for both vertical descent and lateral transfer of nitrogen fixation.

Molecular phylogeny of Old WorldTrifolium (Fabaceae), based on plastid and nuclear markers

Phylogenies of Old WorldTrifolium species were constructed using nucleotide sequence data of the internal transcribed spacers (ITS) of nuclear ribosomal DNA and chloroplast DNA restriction site data from PCR-amplified genes and genic regions (rbcL,trnK, andrpoC1–C2). Biogeography, morphological evolution, and the existing classification forTrifolium were examined. The genusTrifolium is strongly supported as monophyletic, however, only one small section (Chronosemium) is monophyletic, although the data are in conflict regarding its placement. The two largest sections of the genus, Sects.Lotoidea andTrifolium, are not supported as monophyletic, as currently circumscribed. Many members of Sect.Lotoidea are basal within the genus, supporting previously-proposed hypotheses concerning plesiomorphic morphological characters and a Mediterranean-Mideast biogeographic origin of the genus.

Molecular phylogeny and biogeography of Erithalis (Rubiaceae), an endemic of the Caribbean Basin

Abstract. Erithalis consists of 8–10 species endemic to the Caribbean Basin. DNA sequences of chloroplast (trnF-trnL) and nuclear non-coding spacers (ITS and ETS) indicate that Erithalis is monophyletic. ETS was the most informative marker, resolving some interspecific relationships. Analyses of the combined data revealed two weakly supported clades: one composed of E. fruticosa and E. nk;harrisii, and a sister clade of the remaining species. Since fossil records indicate the presence of Erithalis-like pollen from the Eocene Gatuncillo Formation of Panama, it is possible that an initial colonization may have been from Central America. Through trans-oceanic dispersal, most likely by birds, Erithalis colonized the Caribbean islands. Some of the inter-island colonizations were accompanied by speciation and low molecular divergence, supporting a recent radiation across these islands.

Using restriction-site variation of PCR-amplified cpDNA genes for phylogenetic analysis of tribe Cheloneae (Scrophulariaceae).

Data from restriction-site variation of three PCR-amplified chloroplast genic regions (trnK, rps2, and rbcL) were used to assess the utility of PCR-based methodology for phylogenetic reconstruction. Seventeen genera from tribe Cheloneae s.l. (Scrophulariaceae), and one genus each from Solanaceae, Acanthaceae, and Bignoniaceae, representing 32 taxa, were sampled. Phylogenetic reconstruction, based on a combined data set of 138 variable restriction sites, revealed a monophyletic clade of North American Cheloneae, which were not inconsistent with a polyphyletic Scrophulariaceae. Separate analyses of individual genie regions were unable to completely resolve the phylogeny, but were adequate for resolving relationships of major clades among the taxa sampled. We suggest that analysis of PCR-product restriction-site variation is useful for phylogenetic reconstruction above the species level.