Pamela S. Soltis

Phylogeny of basal angiosperms: analyses of five genes from three genomes.

DNA sequences of five mitochondrial, plastid, and nuclear genes from 105 species (103 genera and 63 families) representing all major lineages of gymnosperms and basal angiosperms were analyzed using parsimony methods to reconstruct the phylogeny of basal angiosperms. The standard most parsimonious trees search, taxon deletion analyses, and constraint analyses in combination with Kishino‐Hasegawa tests provided a rigorous analytical perspective for identifying Amborella, Nymphaeales, and Illiciales‐Trimeniaceae‐Austrobaileya (ANITA) as the basalmost lineages of extant angiosperms. The parsimony criterion (equal weighting) favored the trees in which Amborella was sister to all other angiosperms, whereas the likelihood measure favored the trees in which the Amborella‐Nymphaeales clade represented the first diverging lineage of angiosperms. However, the Kishino‐Hasegawa test showed that these trees, as well as those in which Nymphaeales were sister to all other angiosperms, were not significantly different from each other. The clade of eumagnoliids, consisting of Winterales, Piperales, Magnoliales, and Laurales, was also consistently recovered in all of the analyses, albeit with low bootstrap support. Two genera of Gnetales, Gnetum and Welwitschia, did not form a sister group to angiosperms but fell into conifers with strong support. This result refutes the anthophyte hypothesis.

Intraspecific Chloroplast DNA Variation: Systematic and Phylogenetic Implications

Systematists have long sought methodologies that would facilitate phylogenetic reconstruction based on at most a few representative collections per species. As a result of their perceived invariance within species, molecular techniques have become popular tools. Further study, however, has often revealed additional intraspecific variation that must be considered in systematic studies. For example, during the 1960s and 1970s, flavonoid chemistry emerged as the tool of choice. Later, detailed investigations of single species proved that, for many plant groups, flavonoids were much more variable than originally thought and were therefore less useful (reviewed in Bohm, 1987). In contrast, the presence of intraspecific protein variation detected by electrophoresis has long been recognized and so has never been used extensively by plant systematists. An insightful discussion of this is given by Crawford (1989).

Concerted evolution of rDNA in recently formed Tragopogon allotetraploids is typically associated with an inverse correlation between gene copy number and expression

We analyzed nuclear ribosomal DNA (rDNA) transcription and chromatin condensation in individuals from several populations of Tragopogon mirus and T. miscellus, allotetraploids that have formed repeatedly within only the last 80 years from T. dubius and T. porrifolius and T. dubius and T. pratensis, respectively. We identified populations with no (2), partial (2), and complete (4) nucleolar dominance. It is probable that epigenetic regulation following allopolyploidization varies between populations, with a tendency toward nucleolar dominance by one parental homeologue. Dominant rDNA loci are largely decondensed at interphase while silent loci formed condensed heterochromatic regions excluded from nucleoli. Those populations where nucleolar dominance is fixed are epigenetically more stable than those with partial or incomplete dominance. Previous studies indicated that concerted evolution has partially homogenized thousands of parental rDNA units typically reducing the copy numbers of those derived from the T. dubius diploid parent. Paradoxically, despite their low copy number, repeats of T. dubius origin dominate rDNA transcription in most populations studied, i.e., rDNA units that are genetic losers (copy numbers) are epigenetic winners (high expression).

Silenced rRNA genes are activated and substitute for partially eliminated active homeologs in the recently formed allotetraploid, Tragopogon mirus (Asteraceae)

To study the relationship between uniparental rDNA (encoding 18S, 5.8S and 26S ribosomal RNA) silencing (nucleolar dominance) and rRNA gene dosage, we studied a recently emerged (within the last 80 years) allotetraploid Tragopogon mirus (2n=24), formed from the diploid progenitors T. dubius (2n=12, D-genome donor) and T. porrifolius (2n=12, P-genome donor). Here, we used molecular, cytogenetic and genomic approaches to analyse rRNA gene activity in two sibling T. mirus plants (33A and 33B) with widely different rRNA gene dosages. Plant 33B had ~400 rRNA genes at the D-genome locus, which is typical for T. mirus, accounting for ~25% of total rDNA. We observed characteristic expression dominance of T. dubius-origin genes in all organs. Its sister plant 33A harboured a homozygous macrodeletion that reduced the number of T. dubius-origin genes to about 70 copies (~4% of total rDNA). It showed biparental rDNA expression in root, flower and callus, but not in leaf where D-genome rDNA dominance was maintained. There was upregulation of minor rDNA variants in some tissues. The RNA polymerase I promoters of reactivated T. porrifolius-origin rRNA genes showed reduced DNA methylation, mainly at symmetrical CG and CHG nucleotide motifs. We hypothesise that active, decondensed rDNA units are most likely to be deleted via recombination. The silenced homeologs could be used as a ‘first reserve’ to ameliorate mutational damage and contribute to evolutionary success of polyploids. Deletion and reactivation cycles may lead to bidirectional homogenisation of rRNA arrays in the long term.