A molecular re-examination of phylogenetic relationships among Juniperus, Cupressus, and the Hesperocyparis-Callitropsis-Xanthocyparis clades of Cupressaceae

Previous molecular phylogenetic studies have recovered conflicting hypotheses of relationship among Juniperus (J), Cupressus (C), and Hesperocyparis-Callitropsis-Xanthocyparis (HCX). Conflict between nuclear genes, chloroplast genes, and nuclear and chloroplast data have all been realized in recovering all possible topologies among the three clades. In this study, we use 2.2 kb of aligned sequence from two nuclear loci, and 11.4 kb of sequence from 11 chloroplast regions, in re-examining relationships among J-C-HCX. Unlike previous studies, we find unambiguous support for relationships in the nuclear data, whether the genes are analyzed individually or in combination. In contrast, character conflict between different chloroplast partitions, or even between characters from a single region, results in nearly equally well-supported but conflicting hypotheses of relationship. Statistical tests of likelihood values indicate the chloroplast data always fails to distinguish between two of three competing sister group relationships, and in one instance cannot differentiate between any of the three possible J-C-HCX topologies. Results presented here suggest a complex evolutionary history in which molecular processes in addition to possible ancient hybridization have obscured J-C-HCX relationships. Published on-line www.phytologia.org Phytologia 97(1): 67-75 (Jan 2, 2015). ISSN 030319430.