Despite, or perhaps because of (Patterson 1981), an excellent fossil record, the relationships of the conifers to other seed plants are still not entirely clear. Whilst conifers have usually been accepted as a monophyletic group (Chaw et al. 1997; Stefanovic et al. 1998), some recent phylogenetic studies have suggested that extant conifers are paraphyletic, with the Gnetales as sister to Pinus L. (Bowe, Coat & dePamphilis 2000). This result appears to be especially strongly supported by mitochondrial and chloroplast sequences (Chaw et al. 2000). However, in the absence of any morphological evidence for such a relationship, and with the great depth of branching events within the gymnosperms (>300 Ma), other workers (e.g. Graham, S. W. et al. 2002) have suggested that conifer paraphyly is a statistical artefact of long branch attraction sensu Felsenstein (1978). Graham et al. considered that substitutions are unlikely to provide useful phylogenetic resolution in such an ancient group, and instead sought evidence of major genomic rearrangements to support hypotheses of phylogenetic relationships (Graham, S. W. et al. 2002).
Within the conifers, evidence is growing for a sister-group relationship between the Araucariaceae and a clade consisting of the Podocarpaceae and the Phyllocladaceae (Chaw et al. 1997; Stefanovíc et al. 1998; Chaw et al. 2000). Recently, Graham et al. (2002) reported that a unique triplication of the rps7 gene on the chloroplast genome defines a clade containing all members of the Podocarpaceae (including Phyllocladaceae) and Araucariaceae. This group of families is often referred to as the ‘southern conifers’ (e.g. Enright & Hill 1995; Enright & Ogden 1995; Hill & Brodribb 1999).
Within the Araucariaceae itself, phylogenetic relationships are not at well understood. Different studies of different genes have resolved different relationships between the three genera Wollemia, Agathis and Araucaria (including Eutassa Salisb. sensu de Laubenfels (2002)) (Gilmore & Hill 1997; Setoguchi et al. 1998; Codrington et al. 2002), although all studies to date have supported the monophyly of each of the larger genera. Setoguchi et al. (1998) provided the most comprehensive treatment so far of the phylogeny of the family, based on the rbcL gene, but their tree is poorly resolved, and much of the phylogenetic structure within Agathis is poorly supported, with almost all of it collapsing in the strict consensus tree. Additionally, many of the taxa in their study cannot be identified confidently as the voucher material they cite is of uncertain provenance or dubious geographical locality. However, their study does show support for Jaffré’s (1995) hypothesis that the diversity of the Araucariaceae in New Caledonia is the result of rapid post-Eocene speciation of neo-endemic lineages, rather than the persistence of relictual palaeo-endemics.
Recent efforts at a phylogeny of Agathis have not sampled densely among the Malesian species (Ryan & Whiffin 2002). Beyond increased support for the Jaffré hypothesis of the monophyly of the New Caledonian species of Agathis (Ryan & Whiffin 2002), contrary to the taxonomic schemes of Page and Whitmore (Page 1980; Whitmore 1980; Whitmore & Page 1980) and de Laubenfels (1988), no study has yet recovered robust phylogenetic structure within the genus: indeed, within both the New Caledonian species of Araucaria and the genus Agathis there is remarkably little genetic differentiation in the rbcL gene (Setoguchi et al. 1998), although for one Australian species of Araucaria the 18S rRNA sequence, highly conserved in many eukaryotes, provides a useful marker for population level studies (Graham, G. C. et al. 1996).
Almost all the phylogenetic studies that have so far been carried out on Agathis sequence data have been conducted using only a single specimen for each species examined, with the notable exception of that of Ryan & Whiffin (2002). Consequently, there has been very little examination of the issue of paraphyletic species (sensu Crisp & Chandler 1996) in the genus or the possible polyphyly of some of the questionably distinct montane species of Western Malesia (Waters & Farjon 2002). Ryan & Whiffin (2002) suggested, on the basis of sampling primarily cultivated material, that Agathis montana de Laub. was paraphyletic with respect to Agathis moorei (Lindl.) Mast. Further phylogenetic studies, with denser sampling both across the genus and within species, will be necessary to address these questions and understand the relationships of the Malesian species, as well as Agathis macrophylla (Lindl.) Mast. and Agathis silbae de Laub., on geologically young islands, to those on the Gondwanan fragments of New Caledonia, New Zealand, and Queensland, given that the explanation offered by Whitmore & Page (1980) lacks evidential support.
Bowe, L. M., Coat, G. & dePamphilis, C. W. (2000). Phylogeny of seed plants based on all three genomic compartments: extant gymnosperms are monophyletic and Gnetales’ closest relatives are conifers. Proceedings of the National Acdemy of Sciences of the United States of America 97: 4092-4097.
Chaw, S.-M., Parkinson, C. L., Cheng, Y., Vincent, T. M. & Palmer, J. D. (2000). Seed plant phylogeny inferred from all three plant genomes: monophyly of extant gymnosperms and origin of Gnetales from conifers. Proceedings of the National Acdemy of Sciences of the United States of America 97: 4086-4091.
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