Mitochondrial phylogeography of the ponderosa pines: widespread gene capture, interspecific sharing, and two unique lineages
The mitochondrial phylogeography of some conifers shows evidence of introgression from sympatric congeners, with mitochondrial lineages not always refecting species. This suggests that unique mitochondrial haplotypes previously reported in the ponderosa pines (Pinus subsection Ponderosae) from the USA might be more widespread in taxa not yet sampled. Recent nuclear and plastome phylogenies placed Pinus ponderosa paraphyletic in relation to Ponderosae in Mexico and Central America and confrmed that sympatric Pinus jefreyi is more closely related to the California big-cone pines (Pinus subsection Sabinianae). We describe a broad survey of the repeated motifs in nad1 intron 2 of Ponderosae and Sabinianae, which revealed that most of the 27 mitochondrial haplotypes were not exclusive to a taxon but showed strong geographic patterns. In surprising contrast to nuclear and plastid phylogenies that resolve a monophyletic P. jefreyi, unidirectional mitochondrial capture by P. jefreyi (Sabinianae) from P. ponderosa was observed in all 28 samples of Jefrey pine. Confrming the paraphyly of P. ponderosa sensu lato, mitochondrial haplotypes found mostly west and those found mostly east of the Great Basin each have more similarity to haplotypes found in Mexican taxa than they have to each other. Two distinctive haplotypes that were terminal nodes on the network were confrmed to be endemic to the Great Basin, USA, suggesting that they arose in place and have been maintained in isolation. Altogether, our results indicate a history of complex and intriguing mitochondrial relationships among the ponderosa pine species, especially between P. ponderosa and P. jefreyi.