Inferring Species Networks from Gene Trees in High-Polyploid North American and Hawaiian Violets (Viola, Violaceae)

Abstract

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.

Phylogeny of a Genomically Diverse Group of Elymus (Poaceae) Allopolyploids Reveals Multiple Levels of Reticulation

“…The recognition of an allotetraploid lineage as a separate named genus makes sense in some ways – from a population standpoint, species that arise through diversification from a single polyploid ancestor can be defined as a monophyletic group (e.g., as applied by [6,22]). On the other hand, recognition of an allopolyploid lineage as a taxon renders both of the originating groups paraphyletic [160,161].…”

The Recent Recombinant Evolution of a Major Crop Pathogen, Potato virus Y

“…28 years), which is 35% of the 80 year putative timeframe for the observation of the disease in crops, but is likely to represent a much smaller proportion of the total age of PVY root node (which is unknown). Using the taxon duplication approach, the ages of recombinant isolates contribute to calibration in multiple branches of the tree (similar to the calibration of multiple homeologues in polyploids in [71]). We applied the general time reversible (GTR) substitution model with gamma distributed rates and a proportion of invariable sites.…”

Are polyploids really evolutionary dead‐ends (again)? A critical reappraisal of Mayroseet al. (2011)

“…Other examples of polyploid complexes have only recently been published (e.g. Opuntia , Majure et al ., ; Viola , Marcussen et al ., ; Fragaria , Njuguna et al ., ) and hence could not have been included in Mayrose et al . ().…”