Research

In what will be the most extensive and comprehensive taxonomic sampling of any major group of organisms ever undertaken, we will construct sequence-based phylogenetic hypotheses within gymnosperms and for seed plants overall, and employ the fossil record to test the resulting hypotheses of phylogenetic pattern.

ALL species of gymnosperms will be included as well as exemplar angiosperms and other representative vascular plants as outgroups. One set of sequences (nine regions from the nuclear and plastid genomes: data set A) will be obtained for all species, while an additional set of sequences (six plastid regions, four nuclear genes, two mitochondrial genes: data set B) will be obtained for 180 core species.

Because most (70-80%) lineages of seed plants are extinct and because placement of extant lineages within extinct clades is essential to understanding the gymnosperm tree of life and seed plant phylogeny, we include a significant morphological component. Fossil plants give us our ONLY means to access the considerable (and considerably important) early diversification of the seed plants, of which the extant clades are only relicts. Ongoing investigation and scoring of characters will be completed for living species (data set C) and extinct taxa (data set D), with a focus on the many available whole plant reconstructions for the fossils. Our different data partitions will be analyzed individually and in combination.

Loci (Data sets A & B)
The plastid, nuclear, and mitochondrial loci comprising regions 10-21 are regions of relatively conservative evolution, and have utility in the inference of relationships in angiosperms, gymnosperms, and among seed plants.    The loci included in our study are: atpB, rbcL, 18S rDNA, psbBTNH, psbDC, psbEFLJ, rpoC2, RPB2, PHYN (PHYA in angiosperms), PHYO (PHYC in angiosperms), and PHYP (PHYB in angiosperms), matR and atp1.

Morphology (Data sets C & D)
Character categories include ovulate cone structure, pollen cone structure, leaf morphology and venation, and wood anatomy.    We will include characters, many likely to be preserved in fossils, which have proven to be systematically informative across seed plants.    The inclusion of living exemplars in morphological analyses is critical. Thus, the extant gymnosperms on our core taxa sampling list also will be scored for the morphological character set.

Analyses of data sets
Our data sets will be analyzed both individually and in the following combinations:

• Global phylogeny of living taxa
  —Data sets A + B
• Backbone phylogeny for core living taxa
  —Data set B
• Generic phylogenies
  —Subsets of Data set A with additional available data
• Molecular and morphological phylogenies for core living taxa
  —Data sets B + C
• Molecular and morphological phylogenies for core living and extinct taxa
  —Data sets B + C + D
• Morphological phylogenies for living and extinct taxa
  —Data sets C + D