Ginkgoes, the cordaites (note here that "ginkgo" and "cordaite" are being used as informal terms, like "conifer"; these informal groups denote relatives of the living genus Ginkgo and the extinct genus Cordaites respectively), and the conifers are seed plants that trace their origins to the late Paleozoic. They produced large, long-lived trees with abundant wood; these trees constituted major components of their respective ecosystems. The ginkgoes first appeared in the Permian and were important elements of the Mesozoic flora. The Cordaites, which are now all extinct, had a variety of growth forms and probably a variety of ecologies to go with them. They were important swamp and "upland" trees in the Pennsylvanian and continuing into the Permian of the Northern Hemisphere. Some Cordaites also occupied the "mangrove" habitat of the Pennsylvanian. True conifers first appear in upland environments during the Pennsylvanian and increased their abundance, dominance, and taxonomic richness during the Permian and into the Mesozoic. Conifers continue to be an important component of the modern vegetation and in some places are ecosystem dominants, such as the boreal forests and some montane tropical forests.

The fossil record has been important in understanding relationships of ancient, as well as modern, taxa of these groups. For example, the conifer family Pinaceae (pines) consists of 10 extant genera; as many as 22 more genera are now extinct, many with character combinations that are different from the ones we see today. If we consider only the modern pines, a fairly well resolved phylogenetic hypothesis emerges. However, when extinct taxa are added to the analysis, novel character combinations produce analyses with many more trees and many more steps. As with the ferns, one wonders whether good synapomorphies for a conifer clade can be found. While frustrating to the systematist, this pattern may have a lot to tell us about underlying evolutionary pattern.

At first glance, Ginkgo, Cordaites and the conifers seem to be very distinct. One of the important characters that supports their phylogenetic connection is the morphology of the female reproductive shoot. In an influential 1951 paper, Rudolf Florin hypothesized that the ovuliferous cone scale with its subtending bract of the modern conifer cone is homologous to the reproductive short shoot and its subtending bract of Cordaites. Ginkgo ovules are also borne on a short shoot that is subtended by a leaf. However, it has been difficult to fully resolve whether the short shoot reproductive morphology of Ginkgo is homologous to that of the conifers and Cordaites. For example, Ginkgo biloba seeds are surrounded by a collar-like structure that is considered by some to be a modified megasporophyll, and by others to be a structure that develops during the growth of the seed. Either interpretation may support a different phylogenetic hypotheses that allies Ginkgo either with the Cordaites and conifers, or alternatively, with the cycads and Medullosa.

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