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The Spermatophyta are more commonly known as the seed plants. The most obvious characteristic shared by all seed plants is the production of seeds. There are five groups that together constitute the extant seed plants:
(1) the angiosperms (=flowering plants)
(2) the conifers
(3) the gnetophytes (Ephedra, Gnetum, and Welwitschia)
(4) the cycads
(5) Ginkgo biloba
The last four of these groups are often referred to together as the gymnosperms (and a number of additional gymnosperm lineages are known only from the fossil record).
Inferring the phylogenetic relationships among the five clades of seed plants has been difficult (Burleigh and Mathews 2004; Mathews 2009). A particular challenge has been the placement of the gnetophytes on the seed plant tree. The gnetophytes have been variously placed as (1) sister to the angiosperms (the "Anthophyte" hypothesis, based on morphological analyses in the 1980s and early 1990s), (2) sister to all the conifers (the "Gnetifer" hypothesis), (3) falling within the conifer clade and sister to Pinaceae (the "Gnepine hypothesis), and (4) falling within the conifers but sister to the non-Pinaceae conifers (the "Gnecup" hypothesis) (these last three hypothese have been based largely on various molecular analyses). Similarly, various molecular studies have supported at least half a dozen different positions on the seed plant tree for the Ginkgo lineage, ranging from being sister to the cycads to sister to all the other gymnosperms. One point on which there now seems to be broad consensus, however, is that the Anthophyte hypothesis is probably false, making the extant gymnosperms a monophyletic group (with the ferns sensu lato [i.e., the monilophytes] sister to all seed plants).(Zhong et al. 2010 and references therein; Wu et al. 2013 and references therein)
Investigations of seed plant relationships have utilized increasingly large data sets and sophisticated analyses. With regard to the placement of the gnetophytes, Zhong et al. (2010) argued that available molecular data support hypothesis (3), above, placing the gnetophytes as sister to the Pinaceae. However, the debate was not over. Lee et al. (2011) used novel nuclear genome-scale analyses to infer the phylogenetic relationships of the major groups of seed plants. From their analysis, they concluded (in contrast to Zhong et al. 2010) that the gnetophytes are basal (and sister to) the other extant gymnosperms. With regard to the placement of Ginkgo, based on their chloroplast phylogenomic analyses, Wu et al. (2013) concluded that Ginkgo is sister to the cycads. Although, as of 2013, key questions about the relationships among the major groups of seed plants may not yet be settled, great progress has been made with the advent of large-scale genomic studies and consensus among researchers seems possible in the not-too-distant future.