Analysis of Acorus calamus Chloroplast Genome and Its Phylogenetic Implications
Goremykin, V and Holland, BR and Hirsch-Ernst, KI and Hellwig, FH, Analysis of Acorus calamus Chloroplast Genome and Its Phylogenetic Implications, Molecular Biology and Evolution, 22, (9) pp. 1813-1822. ISSN 0737-4038 (2005) [Refereed Article]
Determining the phylogenetic relationships among the major lines of angiosperms is a long-standing problem, yet the
uncertainty as to the phylogenetic affinity of these lines persists. While a number of studies have suggested that the ANITA
(Amborella-Nymphaeales-Illiciales-Trimeniales-Aristolochiales) grade is basal within angiosperms, studies of complete
chloroplast genome sequences also suggested an alternative tree, wherein the line leading to the grasses branches first among
the angiosperms. To improve taxon sampling in the existing chloroplast genome data, we sequenced the chloroplast genome
of the monocot Acorus calamus. We generated a concatenated alignment (89,436 positions for 15 taxa), encompassing
almost all sequences usable for phylogeny reconstruction within spermatophytes. The data still contain support for both
the ANITA-basal and grasses-basal hypotheses. Using simulations we can show that were the ANITA-basal hypothesis
true, parsimony (and distance-based methods with many models) would be expected to fail to recover it. The self-evident
explanation for this failure appears to be a long-branch attraction (LBA) between the clade of grasses and the out-group.
However, this LBA cannot explain the discrepancies observed between tree topology recovered using the maximum likelihood
(ML) method and the topologies recovered using the parsimony and distance-based methods when grasses are deleted.
Furthermore, the fact that neither maximum parsimony nor distance methods consistently recover the ML tree, when
according to the simulations they would be expected to, when the out-group (Pinus) is deleted, suggests that either the
generating tree is not correct or the best symmetric model is misspecified (or both). We demonstrate that the tree recovered
under ML is extremely sensitive to model specification and that the best symmetric model is misspecified. Hence, we
remain agnostic regarding phylogenetic relationships among basal angiosperm lineages.