Phylogenetic relationships between Southern pines (genus Pinus, subsection Australes)

Background/Question/Methods

Pines are keystone species playing critical role as the backbone of pine forest ecosystems and providing habitat for numerous other species.  They are also one of the most important crops in the USA.  The phylogenetic relationships within Southern pines (genus Pinus, section Trifoliae, subsection Australes), native to the Southeastern United States, have not been unambiguously classified.   Shared habitat and adaptive challenges, as well as common history that spans recent ice age similarly affected the species within this evolutionarily young group.

We analyzed phylogenetic relationships between four major Southern pines, Pinus echinata Mill., P. elliottii Engelm., P. palustris Mill., and P. taeda L. with respect to the outgroup pine species (P. radiata, P. pinaster and P. sylvestris), for which the orthologous nucleotide sequence data were available in the NCBI GenBank.  We applied Maximum Parsimony, Maximum Likelihood and Bayesian Inference methods to nucleotide data from twelve nuclear loci.

Results/Conclusions

Our results confirmed very tight phylogenetic relationships within the subsection Australes.  However, different subsets of genes generated conflicting phylogenies. The observed phylogenetic reconstructions can be linked with ecological information, and the inconsistencies may be explained by differences in ecological functions of these genes.

Our results demonstrated that interpretation of phylogenetic relationships between the Southern pines depends heavily on the subset of genes selected.  Moreover, conclusions about “species” trees based on “gene” trees need to be interpreted with caution as they may be misleading, especially for closely related species.