High and Variable Rates of Repeat-Mediated Mitochondrial Genome Rearrangement in a Genus of Plants.

For 30 years, it has been clear that angiosperm mitochondrial genomes evolve rapidly in sequence arrangement (i.e., synteny), yet absolute rates of rearrangement have not been measured in any plant group, nor is it known how much these rates vary. To investigate these issues, we sequenced and reconstructed the rearrangement history of seven mitochondrial genomes in Monsonia (Geraniaceae). We show that rearrangements (occurring mostly as inversions) not only take place at generally high rates in these genomes but also uncover significant variation in rearrangement rates. For example, the hyperactive mitochondrial genome of Monsonia ciliata has accumulated at least 30 rearrangements over the last million years, whereas the branch leading to M. ciliata and its sister species has sustained rearrangement at a rate that is at least ten times lower. Furthermore, our analysis of published data shows that rates of mitochondrial genome rearrangement in seed plants vary by at least 600-fold. We find that sites of rearrangement are highly preferentially located in very close proximity to repeated sequences in Monsonia. This provides strong support for the hypothesis that rearrangement in angiosperm mitochondrial genomes occurs largely through repeat-mediated recombination. Because there is little variation in the amount of repeat sequence among Monsonia genomes, the variable rates of rearrangement in Monsonia probably reflect variable rates of mitochondrial recombination itself. Finally, we show that mitochondrial synonymous substitutions occur in a clock-like manner in Monsonia; rates of mitochondrial substitutions and rearrangements are therefore highly uncoupled in this group.

The Evolution of Per-cell Organelle Number.

Organelles with their own distinct genomes, such as plastids and mitochondria, are found in most eukaryotic cells. As these organelles and their host cells have evolved, the partitioning of metabolic processes and the encoding of interacting gene products have created an obligate codependence. This relationship has played a role in shaping the number of organelles in cells through evolution. Factors such as stochastic evolutionary forces acting on genes involved in organelle biogenesis, organelle-nuclear gene interactions, and physical limitations may, to varying degrees, dictate the selective constraint that per-cell organelle number is under. In particular, coordination between nuclear and organellar gene expression may be important in maintaining gene product stoichiometry, which may have a significant role in constraining the evolution of this trait.

Untangling reticulate evolutionary relationships among New World and Hawaiian mints (Stachydeae, Lamiaceae).

The phenomenon of polyploidy and hybridization usually results in novel genetic combinations, leading to complex, reticulate evolution and incongruence among gene trees, which in turn may show different phylogenetic histories than the inherent species tree. The largest tribe within the subfamily Lamioideae (Lamiaceae), Stachydeae, which includes the globally distributed Stachys, and one of the largest Hawaiian angiosperm radiations, the endemic mints, is a widespread and taxonomically challenging lineage displaying a wide spectrum of morphological and chromosomal diversity. Previous molecular phylogenetic studies have showed that while the Hawaiian mints group with Mexican-South American Stachys based on chloroplast DNA sequence data, nuclear ribosomal DNA (nrDNA) sequences suggest that they are most closely related to temperate North American Stachys. Here, we have utilized five independently inherited, low-copy nuclear loci, and a variety of phylogenetic methods, including multi-locus coalescence-based tree reconstructions, to provide insight into the complex origins and evolutionary relationships between the New World Stachys and the Hawaiian mints. Our results demonstrate incongruence between individual gene trees, grouping the Hawaiian mints with both temperate North American and Meso-South American Stachys clades. However, our multi-locus coalescence tree is concurrent with previous nrDNA results placing them within the temperate North American Stachys clade. Our results point toward a possible allopolyploid hybrid origin of the Hawaiian mints arising from temperate North American and Meso-South American ancestors, as well as a reticulate origin for South American Stachys. As such, our study is another significant step toward further understanding the putative parentage and the potential influence of hybridization and incomplete lineage sorting in giving rise to this insular plant lineage, which following colonization underwent rapid morphological and ecological diversification.