Submitted to: Canadian Journal of Botany
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/18/2007
Publication Date: 6/12/2008
Citation: Rai, H.S., Reeves, P.A., Peakal, R., Olmstead, R.G., Graham, S.W. 2008. Inference of higher-order conifer relationships from a multi-locus plastid data set. Botany 86:658-669. Interpretive Summary: We used DNA sequence data from the chloroplast genome to reconstruct evolutionary relationships among the 7 extant families of conifers. Sequence from 15-17 genes, 3 introns and 8 intergenic spacers (~14,000 base pairs total) were obtained from 22 conifer species. Phylogenetic analyses showed that the Pinaceae (pine tree family) is the oldest conifer family. This is not the same as saying that our present day pine species have persisted unchanged for the longest period of time. This is not the case; other conifer species appear earlier in the fossil record. We did not find a close relationship between pines and Gnetales, contrary to other studies. The southern hemisphere conifer families Araucariaceae and Podocarpaceae appear to be each other’s closest relatives. The recently-discovered “living fossil” Wollemia is most closely related to Agathis, a genus from Oceania used locally for resin and timber. This study provides substantial new empirical evidence in support of accepted taxonomic relationships within the conifers.
Technical Abstract: We reconstructed the broad backbone of conifer phylogeny from a survey of 15–17 plastid loci and associated noncoding regions from exemplar conifer species. Parsimony and likelihood analyses recover the same higher-order relationships, and we find strong support for most of the deep splits in conifer phylogeny, including those within our two most heavily sampled families, Araucariaceae and Cupressaceae. Our findings are broadly congruent with other recent studies, and are inferred with comparable or improved bootstrap support. The deepest phylogenetic split in conifers is inferred to be between Pinaceae and all other conifers (Cupressophyta). Our current gene and taxon sampling does not support a relationship between Pinaceae and Gnetales, observed in some published studies. Within the Cupressophyta clade, we infer well-supported relationships among Cephalotaxaceae, Cupressaceae, Sciadopityaceae, and Taxaceae. Our data support recent moves to recognize Cephalotaxus under Taxaceae, and we find strong support for a sister-group relationship between the two predominantly southern hemisphere conifer families, Araucariaceae and Podocarpaceae. A local hotspot of indel evolution shared by the latter two conifer families is identified in the coding portion of one of the plastid ribosomal protein genes. The removal of the most rapidly evolving plastid characters, as defined using a likelihood-based classification of substitution rates for the taxa considered here, is shown to have little to no effect on our inferences of higher-order conifer relationships.