Biomedical subjects

S B Hoot

Publications and source records attributed to S B Hoot.

3 recordsLinked to original sources

PubMed2000

Phylogenetics of flowering plants based on combined analysis of plastid atpB and rbcL gene sequences.

Following (1) the large-scale molecular phylogeny of seed plants based on plastid rbcL gene sequences (published in 1993 by Chase et al., Ann. Missouri Bot. Gard. 80:528-580) and (2) the 18S nuclear phylogeny of flowering plants (published in 1997 by Soltis et al., Ann. Missouri Bot. Gard. 84:1-49), we present a phylogenetic analysis of flowering plants based on a second plastid gene, atpB, analyzed separately and in combination with rbcL sequences for 357 taxa. Despite some discrepancies, the atpB-based phylogenetic trees were highly congruent with those derived from the analysis of rbcL and 18S rDNA, and the combination of atpB and rbcL DNA sequences (comprising approximately 3000 base pairs) produced increased bootstrap support for many major sets of taxa. The angiosperms are divided into two major groups: noneudicots with inaperturate or uniaperturate pollen (monocots plus Laurales, Magnoliales, Piperales, Ceratophyllales, and Amborellaceae-Nymphaeaceae-Illiciaceae) and the eudicots with triaperturate pollen (particularly asterids and rosids). Based on rbcL alone and atpB/rbcL combined, the noneudicots (excluding Ceratophyllum) are monophyletic, whereas in the atpB trees they form a grade. Ceratophyllum is sister to the rest of angiosperms with rbcL alone and in the combined atpB/rbcL analysis, whereas with atpB alone, Amborellaceae, Nymphaeaceae, and Illiciaceae/Schisandraceae form a grade at the base of the angiosperms. The phylogenetic information at each codon position and the different types of substitutions (observed transitions and transversions in the trees vs. pairwise comparisons) were examined; taking into account their respective consistency and retention indices, we demonstrate that third-codon positions and transitions are the most useful characters in these phylogenetic reconstructions. This study further demonstrates that phylogenetic analysis of large matrices is feasible.

Base Sequence↗

PubMed1998

Inferring complex phylogenies using parsimony: an empirical approach using three large DNA data sets for angiosperms.

To explore the feasibility of parsimony analysis for large data sets, we conducted heuristic parsimony searches and bootstrap analyses on separate and combined DNA data sets for 190 angiosperms and three outgroups. Separate data sets of 18S rDNA (1,855 bp), rbcL (1,428 bp), and atpB (1,450 bp) sequences were combined into a single matrix 4,733 bp in length. Analyses of the combined data set show great improvements in computer run times compared to those of the separate data sets and of the data sets combined in pairs. Six searches of the 18S rDNA + rbcL + atpB data set were conducted; in all cases TBR branch swapping was completed, generally within a few days. In contrast, TBR branch swapping was not completed for any of the three separate data sets, or for the pairwise combined data sets. These results illustrate that it is possible to conduct a thorough search of tree space with large data sets, given sufficient signal. In this case, and probably most others, sufficient signal for a large number of taxa can only be obtained by combining data sets. The combined data sets also have higher internal support for clades than the separate data sets, and more clades receive bootstrap support of > or = 50% in the combined analysis than in analyses of the separate data sets. These data suggest that one solution to the computational and analytical dilemmas posed by large data sets is the addition of nucleotides, as well as taxa.

Classification↗

PubMed1994

Structural rearrangements, including parallel inversions, within the chloroplast genome of Anemone and related genera.

Chloroplast DNA cleavage sites for 10 restriction enzymes were mapped for 46 species representing all sections of Anemone, four closely related genera (Clematis, Pulsatilla, Hepatica, and Knowltonia), and three more distantly related outgroups (Caltha, Ranunculus, and Adonis). Comparison of the maps revealed that the chloroplast genomes of Anemone and related genera have sustained an unusual number and variety of rearrangements. A single inversion of a 42-kb segment was found in the large single-copy region of Adonis aestivalis. Two types of rearrangements were found in the chloroplast genome of Clematis, Anemone, Pulsatilla, Hepatica, and Knowltonia: An approximately 4-kb expansion of the inverted repeat and four inversions within the large single-copy region. These rearrangements support the monophyletic status of these genera, clearly separating them from Caltha, Ranunculus, and Adonis. Two further inversions were found in two Clematis species and three Anemone species. While appearing to support a monophyletic grouping for these taxa, these two inversions conflict with data from both chloroplast restriction sites and morphology and are better interpreted as having occurred twice independently. These are the first two documented cases of homoplastic inversions in chloroplast DNA. Finally, the second intron of the chloroplast rps 12 gene was shown to have been lost in the common ancestor of the same three Anemone species that feature the two homoplastic inversions.

Base Sequence↗