The Evolution of Gymnosperms Redrawn by Phytochrome Genes: The Gnetatae Appear at the Base of the Gymnosperms

Abstract

Gymnosperms possess two to four phytochrome types which apparently are the result of successive gene duplications in the genomes of their common ancestors. Phytochromes are nuclear-encoded proteins whose genes, contrary to chloroplast, mitochondrion, and rRNA genes, have hitherto rarely been used to examine gymnosperm phylogenies. Since the individual phytochrome gene types implied phylogenies that were not completely congruent to one another, conflicting branching orders were sorted by the number of gene lineages present in a taxon. The Gnetatae (two gene types) branched at the base of all gymnosperms, a position supported by bootstrap sampling (distance and character state trees, maximum likelihood). The Gnetatae were followed by Ginkgo, Cycadatae, and Pinaceae (three gene types) and the remaining conifers (four gene types). Therefore, in phytochrome trees, the most ancient branch of the conifers (Pinatae) seems to be the Pinaceae. The next split appears to have separated Araucariaceae plus Podocarpaceae from the Taxaceae/Taxodiaceae/Cupressaceae group. Structural arrangements in the plastid genomes (Raubeson and Jansen 1992) corroborate the finding that there is no close connection between Pinaceae and Gnetatae as suggested by some publications. The analyses are based on 60 phytochrome genes (579 positions in an alignment of PCR fragments) from 28 species. According to rough divergence time estimates, the last common ancestor of gymnosperms and angiosperms is likely to have existed in the Carboniferous.

Phylogenetics of extant and fossil Pinaceae: methods for increasing topological stability

“…Alignments were generated separately in Geneious version 7.1.7 (Kearse et al 2012) for each gene with MUSCLE (Edgar 2004) on the amino acid translation, back translated to DNA, and further adjusted manually. The PHYP gene was duplicated in Pinaceae into PHYP1 and PHYP2 (Schmidt and Schneider-Poetsch 2002;Mathews et al 2010). Thirtyeight PHYP sequences were included: 23 Pinaceae PHYP1, nine representatives of PHYP2, and six outgroups.…”

Evolutionary Studies Illuminate the Structural-Functional Model of Plant Phytochromes

“…In living gymnosperms, PHYN (PHYA ortholog) is duplicated in cupressophytes (conifer families other than Pinaceae), and PHYP (PHYB ortholog) is duplicated in Pinaceae (Schmidt and Schneider-Poetsch, 2002;Mathews et al, 2010). In Pinus sylvestris, the PHYO (PHYC ortholog) lineage appears to be greatly expanded to include a large number of apparent pseudogenes (García-Gil, 2008).…”

Developmental Evolution of the Sexual Process in Ancient Flowering Plant Lineages

“…Thus, it was most parsimonious to interpret double fertilization in Gnetales and angiosperms as homologous, having been derived from a common seed plant ancestor (Friedman, 1990;Carmichael and Friedman, 1996). Recent seed plant phylogenetic analyses either have rejected a close relationship between Gnetales and angiosperms, or have produced highly conflicting topologies, or have been unable to detect any clear (unambiguous) phylogenetic signal of relationships among extant lineages (Hansen et al, 1999;Winter et al, 1999;Bowe et al, 2000;Chaw et al, 2000;Frohlich and Parker, 2000;Qiu et al, 2000;Sanderson et al, 2000;Magalló n and Sanderson, 2002;Schmidt and Schneider-Poetsch, 2002;Soltis et al, 2002). For the time being, the phylogenetic placement of Gnetales remains a mystery.…”