Chloroplast phylogenomics of the New World grape species (Vitis, Vitaceae)

Abstract

Vitis L. (the grape genus) is the economically most important fruit crop, as the source of grapes and wine. Phylogenetic relationships within the genus have been highly controversial. Herein, we employ sequence data from whole plastomes to attempt to enhance Vitis phylogenetic resolution. The results support the New World Vitis subgenus Vitis as monophyletic. Within the clade, V. californica is sister to the remaining New World Vitis subgenus Vitis. Furthermore, within subgenus Vitis, a Eurasian clade is robustly supported and is sister to the New World clade. The clade of Vitis vinifera ssp. vinifera and V. vinifera ssp. sylvestris is sister to the core Asian clade of Vitis. Several widespread species in North America are found to be non‐monophyletic in the plastome tree, for example, the broadly defined Vitis cinerea and V. aestivalis each needs to be split into several species. The non‐monophyly of some species may also be due to common occurrences of hybridizations in North American Vitis. The classification of North American Vitis by Munson into nine series is discussed based on the phylogenetic results. Analyses of divergence times and lineage diversification support a rapid radiation of Vitis in North America beginning in the Neogene.

A detailed study of leaf micromorphology and anatomy of New World Vitis L. subgenus Vitis within a phylogenetic and ecological framework reveals evolutionary convergence

“…cinerea and var. baileyana are sisters in the plastome phylogeny (Wen et al, ) but were resolved in different clusters in our PCA analysis (Fig. A).…”

“…A summary of the BBM (Bayesian Binary MCMC) analyses implemented in RASP of New World Vitis subgenus Vitis . The tree is a majority rule consensus of 1200 trees derived from Bayesian Inference of the chloroplast genome (Wen et al, ) with reduced taxon sampling of the New World Vitis subgenus Vitis . Pie charts at internal nodes represent the marginal probabilities for each alternative ancestral character state.…”

“…Here, we have provided new data on leaf anatomical and micromorphological characters in Vitis subgenus Vitis and discuss below their relationships to phylogeny (i.e., Wen et al, ), environment, and their taxonomic utility. We focus our discussion on the characters that we feel may most considerably enhance understanding of trait evolution and environmental interactions in New World Vitis .…”

“…BBM requires a set of phylogenetic trees and a consensus topology. We obtained the set of trees representing the taxa examined in this study by pruning trees of Vitis subgenus Vitis and outgroups resulting from a Bayesian phylogenetic analysis in BEAST 2.4.5 (Drummond & Rambaut, ; Bouckaert et al, ) using plastome sequences (Wen et al, ). Initially, the trees comprised 300 000 posterior topologies.…”

“…We performed the pruning in PAUP* (Swofford, ) and saved 1200 pruned trees, effectively consisting of a random sample. We generated a majority rule consensus tree in RASP with compatible groupings with below 50% support allowed, largely congruent with the topology used in the plastome phylogeny generated by Wen et al (), but we restricted the OTUs to one per taxon. We ran BBM for 50 000 generations, using 9 hot chains and 1 cold chain, with a sampling frequency of 100 from the cold chain.…”