Molecular phylogeny of extant gymnosperms and seed plant evolution: analysis of nuclear 18S rRNA sequences

Abstract

To study the evolutionary relationships among the four living gymnosperm orders and the interfamilial relationships in each order, a set of 65 nuclear 18S rRNA sequences from ferns, gymnosperms, and angiosperms was analyzed using the neighbor-joining and maximum-parsimony methods. With Selaginella as the outgroup, the analysis strongly indicates that the seed plants form a monophyletic group with the ferns as a sister group. Within the seed plants the angiosperms are clearly a monophyletic group. Although the bootstrap support for the monophyly of the gymnosperm clade is moderate, the monophyly is further supported by its lack of angiosperm-specific indels. Within the gymnosperms there appear to be three monophyletic clades: Cycadales-Ginkgoales, Gnetales, and Coniferales. The cycad-ginkgo clade is the earliest gymnosperm lineage. Given the strong support for the sister group relationship between Gnetales and Coniferales, it is unlikely that Gnetales is a sister group of the angiosperms, contrary to the view of many plant taxonomists. Within Coniferales, Pinaceae is monophyletic and basal to the remaining conifer families, among which there are three monophyletic clades: Phyllocladaceae-Podocarpaceae, Araucariaceae, and Sciadopityaceae-Taxaceae-Cephalotaxaceae-Taxodiacea e-Cupressaceae. Within the latter clade, Sciadopityaceae may be an outgroup to the other four families. Among the angiosperms, no significant cluster at the level of subclass was found, but there was evidence that Nymphaeaceae branched off first. Within the remaining angiosperms, the monocots included in this study are nested and form a monophyletic group. This study attests to the utility of nuclear 18S rRNA sequences in addressing relationships among living gymnosperms. Considerable variation in substitution rates was observed among the ferns and seed plants.

Phylogenetic Analysis of Araucariaceae: Integrating Molecules, Morphology, and Fossils

“…The phylogenetic relationships among conifer families obtained in the simultaneous analysis and, in particular, the position of Araucariaceae as sister to Podocarpaceae are in agree- ment with previous phylogenetic hypotheses for the group (Chaw et al 1997;Stefanovic et al 1998;Bowe et al 2000;Magalló n and Sanderson 2002;Quinn et al 2002;Rai et al 2008;Leslie et al 2012) and also with the recently proposed classification of Christenhusz et al (2011), in which Araucariaceae and Podocarpaceae belong to the order Araucariales. Today, most of its diversity is restricted to the Southern Hemisphere.…”

“…In this case, as in all the remaining analyses performed, the searches were ended after consensus stabilization. We rooted the trees in the branch leading to Pinaceae because it has been repeatedly obtained as sister of the remaining extant conifer families (Chaw et al 1997;Stefanovic et al 1998;Bowe et al 2000;Quinn et al 2002). mation is also congruent with the combined analysis in terms of relationships within Araucariaceae ( fig.…”

Functional Characterization of Nine Norway Spruce TPS Genes and Evolution of Gymnosperm Terpene Synthases of the TPS-d Subfamily

“…This analysis also indicated that some manifestation of biochemical functions of very similar di-TPS predated not only the separation of firs and spruces within the pine family, but in fact predated the separation of the Ginkgoales and the Coniferales. Since the Ginkgoales and the Coniferales evolved from a common progymnosperm ancestor (Chaw et al, 1997), this finding suggests that di-TPS of secondary metabolism existed prior to the division of these two orders. In this evolutionary model, we should expect to also find di-TPS of secondary metabolism within other gymnosperm orders, such as the Cycadales.…”

Perspective: The Origin of Flowering Plants and Their Reproductive Biology?a Tale of Two Phylogenies

“…Some analyses have placed Gnetales at the base of seed plants (Hamby and Zimmer 1992, Albert et al 1994, Sanderson et al 2000, Rydin et al 2002, but tests using likelihood and other methods suggest that this arrangement is a result of long-branch attraction, particularly affecting third codon positions (Sanderson et al 2000, Magallón and Sanderson 2002, Rydin et al 2002, Burleigh and Mathews 2004. Most analyses, especially those based on combining several genes, have associated Gnetales with conifers, either as their sister group or nested within them, as the sister group of Pinaceae (Goremykin et al 1996, Chaw et al 1997, Hansen et al 1999, Qiu et al 1999, Shindo et al 1999, Winter et al 1999, Bowe et al 2000, Frohlich and Parker 2000, Sanderson et al 2000, Rydin et al 2002, Burleigh and Mathews 2004, Nickerson and Drouin 2004, Kim et al 2004). Trees of this sort offer a more plausible alternative to the anthophyte hypothesis, because many earlier authors pointed out similarities between Gneta-les and conifers, such as linear leaves, elimination of scalariform pitting even in the primary xylem, and compound strobili constructed on a cordaite-like plan (Bailey 1944, 1949, Eames 1952, Bierhorst 1971, Doyle 1978, Carlquist 1996a.…”