Most molecular phylogenetic studies indicate that Genetales has a close relationship with conifers. Some of them support the Gnetifer hypothesis. Gnetales sister to conifers, based mainly on analyses of nrDNA and the mitochondrial. However, the Gnepine hypothesis, Gnetales sister to Pinaceae, is supported by many more studies after eliminating bias in data analyses. Interestingly, obtained a tree topology supporting a sister relationship between Gnetales and cupressophytes (the Gnecup hypothesis) when all chloroplast genes were used. However, when they discarded some fast-evolving genes and three genes with many parallel amino acid substitutions between Gnetales and cupressophytes (the Gnecup hypothesis)
When all chloroplast genes were used. However, when they discarded some fast-evolving genes and three genes with many parallel amino acid substitutions between Gnetales and cupressophytes, the topology changed to support the Gnepine hypothesis. Although the nearly complete loss of one of the inverted repeats (IRs) in the conifer chloroplast genomes seemed to support the monophyly of conifers, this structural mutation occurred in different IRs of Pinaceae and Cupressophytes, and thus could not be used as a homologous character or a synapomorphy