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The phylogenies of allopolyploids take the shape of networks and cannot be adequately represented as bifurcating trees. Especially for high polyploids (i.e., organisms with more than six sets of nuclear chromosomes), the signatures of gene homoeolog loss, deep coalescence, and polyploidy may become confounded, with the result that gene trees may be congruent with more than one species network. Herein, we obtained the most parsimonious species network by objective comparison of competing scenarios involving polyploidization and homoeolog loss in a high-polyploid lineage of violets (Viola, Violaceae) mostly or entirely restricted to North America, Central America, or Hawaii. We amplified homoeologs of the low-copy nuclear gene, glucose-6-phosphate isomerase (GPI), by single-molecule polymerase chain reaction (PCR) and the chloroplast trnL-F region by conventional PCR for 51 species and subspecies. Topological incongruence among GPI homoeolog subclades, owing to deep coalescence and two instances of putative loss (or lack of detection) of homoeologs, were reconciled by applying the maximum tree topology for each subclade. The most parsimonious species network and the fossil-based calibration of the homoeolog tree favored monophyly of the high polyploids, which has resulted from allodecaploidization 9-14 Ma, involving sympatric ancestors from the extant Viola sections Chamaemelanium (diploid), Plagiostigma (paleotetraploid), and Viola (paleotetraploid). Although two of the high-polyploid lineages (Boreali-Americanae, Pedatae) remained decaploid, recurrent polyploidization with tetraploids of section Plagiostigma within the last 5 Ma has resulted in two 14-ploid lineages (Mexicanae, Nosphinium) and one 18-ploid lineage (Langsdorffianae). This implies a more complex phylogenetic and biogeographic origin of the Hawaiian violets (Nosphinium) than that previously inferred from rDNA data and illustrates the necessity of considering polyploidy in phylogenetic and biogeographic reconstruction.

Premise of the Study: Climate change and shifts in land use are two major threats to biodiversity and are likely to disproportionately impact narrow endemics. Understanding their origins and the extent of their genetic diversity will enable land managers to better conserve these unique, highly localized gene pools. Viola guadalupensis is a narrow endemic of the Guadalupe Mountains (west Texas, USA). Its affinities within Viola section Chamaemelanium have been the subject of some debate. Furthermore, the polyploid and presumably reticulate relationships within this section remain largely unknown., Methods: We counted chromosomes for V. guadalupensis. Phylogenies for the chloroplast trnL-F region and the low-copy nuclear gene GPI for 24 Viola taxa were generated and used to produce a polyploid phylogenetic network. Divergence dates were obtained by fossil calibration., Key Results: Meiotic chromosome counts revealed that V. guadalupensis is tetraploid (n = 12), and the presence of two GPI homoeologs further suggested allotetraploidy. Phylogenetic reconstructions showed that it originated through hybridization between unidentified members of subsection Canadenses (paternal parent) and subsection Nuttallianae (maternal parent). A fossil-calibrated relaxed clock dating analysis of GPI estimated the maximum age of V. guadalupensis to be 8.6 (5.7-11.6) Myr, suggesting the species evolved after the Guadalupe Mountains formed 12-13 Ma., Conclusions: Viola guadalupensis originated by intersubsectional hybridization followed by polyploidization. Within section Chamaemelanium, this phenomenon has occurred repeatedly in the last 9 Myr (at least for V. bakeri, V. douglasii, V. glabella, and V. sempervirens). Consequences for the systematics of the section are discussed.