Robert K. Jansen

Chloroplast DNA evidence on the ancient evolutionary split in vascular land plants.

Two groups of extant plants, lycopsids and psilopsids, alternatively have been suggested to be the living representatives of the earliest diverging lineage in vascular plant evolution. The chloroplast DNA (cpDNA) gene order is known to contain an inversion in bryophytes and tracheophytes relative to one another. Characterization of tracheophyte cpDNAs shows that lycopsids share the gene order with bryophytes, whereas all other vascular plants share the inverted gene order. The distribution of this character provides strong support for the fundamental nature of the phylogenetic separation of lycopsids and marks the ancient evolutionary split in early vascular land plants.

Phylogenetic implications of chloroplast DNA restriction site variation in the Mutisieae (Asteraceae)

Phylogenetic relationships among 13 species in the tribe Mutisieae and a single species from each of three other tribes in the Asteraceae were assessed by chloroplast DNA restriction site mapping. Initially, 211 restriction site mutations were detected among 16 species using 10 restriction enzymes. Examination of 12 of these species using nine more enzymes revealed 179 additional restriction site mutations. Phylogenetic analyses of restriction site mutations were performed using both Dolio and Wagner parsimony, and the resulting monophyletic groups were statistically tested by the bootstrap method. The phylogenetic trees confirm an ancient evolutionary split in the Asteraceae that was previously suggested by the distribution of a chloroplast DNA inversion. The subtribe Barnadesiinae of the tribe Mutisieae is shown to be the ancestral group within the Asteraceae. The molecular phylogenies also confirm the paraphyly of the Mutisieae and provide statistical support for the monophyly of three of its four currently recognized subtribes (Barnadesiinae, Mutisiinae, and Nassauviinae). The fourth subtribe, Gochnatiinae, is shown to be paraphyletic. Within the subtribes, several closely related generic pairs are identified. Chloroplast DNA sequence divergence among genera of the Asteraceae ranges between 0.7 and 5.4%, which is relatively low in comparison to other angiosperm groups. This suggests that the Asteraceae is either a relatively young family or that its chloroplast DNA has evolved at a slower rate than in other families.

A rare chloroplast-DNA structural mutation is shared by all conifers

Abstract We have examined the phylogenetic distribution of a rare structural mutation in the chloroplast genome of conifers. An exception to the otherwise highly conserved basic structure of land plant chloroplast-DNA (cpDNA) was reported previously in two species of the conifer family Pinacease, where one copy of the inverted repeat was shown to be absent. The present study examined a broad taxonomic representation of conifers, including at least one member of each family, plus representatives of each of the other major extant vascular plant lineages. Our results indicate only one copy of the “repeat” is present in all conifers, whereas two copies were found in those pteridophytes and non-coniferous seed plants surveyed. The evidence that the loss is shared throughout the conifers but with none of the extent outgroups strongly supports conifer monophyly.

Chloroplast DNA Variation in the Asteraceae: Phylogenetic and Evolutionary Implications

The sunflower family (Asteraceae) is one of the largest families of flowering plants, consisting of approximately 1,100 genera and 25,000 species (Jeffrey, 1978). The family has been variously divided into two or three subfamilies and 10 to 17 tribes (reviewed in Jansen et al., 1991a; Bremer, 1987). In addition to the disagreement concerning intrafamilial relationships, the phylogenetic affinities of the Asteraceae to other angiosperm families have been the topic of considerable debate (Cronquist, 1955,Cronquist, 1977, 1981; Carlquist, 1976; Wagenitz, 1976; Stebbins, 1977; Turner, 1977a; Jeffrey, 1977; Bremer, 1987). Until recently, systematic studies in the family relied on more traditional taxonomic characters and less rigorous phylogenetic methods. During the past five years we have been examining chloroplast DNA (cpDNA) variation in the Asteraceae to evaluate phylogenetic relationships at a wide range of taxonomic levels using several cladistic methods. We have accumulated restriction site data for approximately 250 genera in the family from all currently recognized tribes. In addition, we have sequenced the gene encoding the large subunit of ribulose-l,5-bisphosphate carboxylase (rbcL) from representative species in the Asteraceae and putatively related families. Our studies, which have produced the largest molecular data set for any plant family, have allowed us to perform phylogenetic comparisons from the intraspecific to the interfamilial levels.

A cladistic study of North AmericanCoreopsis (Asteraceae: Heliantheae)

A cladistic study of all 44 species of North AmericanCoreopsis was performed using 35 characters. The resulting cladogram indicated that all 11 sections are monophyletic. At the intersectional level, two lineages were revealed, one consisting of six sections occurring almost exclusively in Mexico and California, and another comprising five sections restricted largely to the eastern and southeastern United States. The cladogram is similar to phylogenies produced by less explicit methods but it differs in two major respects: the monotypic sect.Silphidium is placed with other sections from the southeastern United States rather than with Mexican sections, and sect.Anathysana from Mexico is more closely allied with the three California sections than with sect.Electra from Mexico.

Chloroplast DNA variation among five species of Ranunculaceae : structure, sequence divergence, and phylogenetic relationships

A restriction site map of the chloroplast genome ofCaltha palustris L. (Ranunculaceae) has been constructed for 13 restriction endonucleases using filter hybridization with cloned tobacco chloroplast DNA fragments. A size of 153.8 kb has been estimated for theCaltha chloroplast genome. Forty-six chloroplast genes and four open reading frames have been mapped using small tobacco chloroplast gene probes. Chloroplast DNA sequence divergence has been estimated for all pairs of five species ofRanunculaceae, Caltha palustris, Ranunculus bulbosus, R. fascicularis, R. recurvatus, andTrollius ledebourii, and ranges between 0.2% and 9.6% for the total genome. Divergence values are much higher in the small and large single copy regions than in the inverted repeat. Phylogenetic relationships between the five species have been hypothesized using chloroplast DNA restriction site mapping. One hundred and six informative restriction site mutations have been detected using eleven restriction endonucleases. Cladistic analyses of the restriction site mutations have been performed using Wagner and Dollo parsimony algorithms, and confidence intervals have been calculated for the resulting monophyletic groups using bootstrapping. It is demonstrated that restriction site comparisons are applicable to theRanunculaceae on intergeneric level, with the exception of groups having extensive genomic rearrangements. Moreover, sequence divergence is low enough at the interspecific level to allow phylogenetic analyses within genera such asRanunculus.

CHLOROPLAST DNA VARIATION IN COREOPSIS NUECENSOIDES AND C. NUECENSIS (ASTERACEAE), A PRESUMED PROGENITOR-DERIVATIVE SPECIES PAIR

Coreopsis nuecensoides andC. nuecensis are narrowly distributed endemics of southeastern Texas. While they overlap in range, they differ in chromosome number, and F1 hybrids exhibit strong sterility barriers. Previous morphological, cytogenetic, and allozyme studies suggested thatC. nuecensoides andC. nuecensis are very closely related members of a progenitor-derivative species pair. The two species differ substantially in terms of their leaf flavonoid chemistry, but the flavonoid data do not address the exact nature of the relationship between them. We have further examined the relationship between the species by analyzing genetic diversity within both species using chloroplast DNA (cpDNA) restriction site data. Sixteen restriction site changes were used to define thirteen distinct cpDNA haplotypes. The pattern of relationships among haplotypes provides some support for the presumed ancestor-descendent relationship, but other interpretations are possible. Only one cpDNA haplotype was shared by the two species; of the remaining twelve, seven were unique to one species and five to the other. This result is consistent with results of flavonoid studies, in which each species exhibited flavonoid compounds not seen in the other, but differs from the allozyme results, in which the vast majority of alleles were shared by both species and only the presumed progenitor exhibited unique alleles. Taken together, the data support a very close relationship between the species, but are equivocal with regard to a progenitor-derivative relationship.