Plastid phylogenomics of the Gynoxoid group (Senecioneae, Asteraceae) highlights the importance of motif‐based sequence alignment amid low genetic distances

Abstract

The concatenation and combined analysis of all plastid genome partitions and the construction of manually-curated, motif-based DNA sequence alignments are found to be instrumental in the recovery of well-supported relationships of the Gynoxoid group. We demonstrate that the correct assessment of homology in genome-level plastid sequence data sets is crucial for subsequent phylogeny reconstruction and that the manual post-processing of multiple sequence alignments improves the reliability of such reconstructions amid low genetic distances between taxa.