Plant phylogeography based on organelle genes: an introduction

Plants have unique biological attributes of great interest to researchers investigating population dynamics. Yet, until recently, organelle DNA had been seldom utilized for phylogeographic studies in plants. While cpDNA variation has been used extensively to construct interspecific phylogenies, many researchers have considered that the relatively low levels of intraspecific variation revealed by early studies of plant organelle DNA render these genomes of little use for intraspecific studies. In this review we introduce the field of plant phylogeography based on organelle polymorphisms by providing a detailed discussion of the processes underlying this variation. Progress in molecular organelle genetics has provided insights into the structure, variation, inheritance, vegetative segregation and recombination of organelle genomes. While some of these features (e.g. low substitution rates) may complicate phylogeographic studies, others (e.g. presence of two genomes and frequency of atypical modes of transmission) offer unique opportunities, many of which are virtually unexplored.