Genic evidence that gnetophytes are sister to all other seed plants

Gnetophytes, comprising three relict genera, and , are a morphologically diverse and enigmatic assemblage among seed plants. Despite recent progress on phylogenomic analyses or the insights from the recently decoded genome, the relationship between gnetophytes and other seed plant lineages is still one of the outstanding, unresolved questions in plant sciences. Here, we showed that phylogenetic studies from nuclear genes support the hypothesis that places gnetophytes as sister to all other extant seed plants and so this hypothesis should not be ruled out according to phylogenetic inference based on nuclear genes. However, this extraordinarily difficult phylogenetic problem might never be solved by phylogenetic inference based gene tree under various artificial selection. Hence, we adopted a novel approach, comparing gene divergence among different lineages, to solve the conflicts by showing that gnetophytes actually did not gained a set of genes like the most recent common ancestor (MRCA) of other seed plants. This distinct gene evolution pattern could not be explained by random gene lost as in other seed plants but should be interpreted by the early divergence of gnetophytes from rest of seed plants. With such a placement, the gymnosperms are paraphyletic and there should be three distinct groups of living seed plants: gnetophytes, non-gnetophytes gymnosperms and angiosperms.