The filtered VCF file containing SNPs detected from the Vitis bryoniifolia clade using RAD-seq.

The grape genus (Vitis L.) is of great agronomic importance and represents
an economically valuable resource. Researchers have explored the
phylogenetic relationships of subgenus Vitis for decades. However, the
evolutionary patterns of many morphological characters of subgenus Vitis
have not yet been explored in the context of a robust phylogenetic
framework. Within the East Asian clade, V. bryoniifolia and its closely
related taxa form the V. bryoniifolia clade, which is taxonomically
complex. The phylogenetic relationships and species delimitation within
this clade remain poorly resolved, due to the limited sampling in prior
studies. We tested morphological trait evolution based on ancestral
character state reconstruction using a phylogenomic framework. With 89
accessions from the East Asian subgenus Vitis sampled, a robust
phylogenetic relationship of the V. bryoniifolia clade is reconstructed
using the restriction-site associated DNA sequencing (RAD-seq) data, which
support the monophyly of most taxa of the V. bryoniifolia clade. Ancestral
character state reconstructions suggest that the weak climbing ability and
simplified tendrils of Vitis each evolved multiple times. This study
provides a reliable phylogenomic framework for the V. bryoniifolia clade.
Coupled with morphological analyses, we discuss the taxonomic status of
some taxa in the V. bryoniifolia clade and untangle a taxonomic dilemma in
the grape genus.