Gene tree conflict in chloroplast‐based phylogenies in <i>Pyropia</i> species

Summary Chloroplast genomes are widely used in studying evolutionary relationships and conducting phylogenetic analyses. However, few studies have specifically addressed gene tree conflicts. Using the taxonomically complex seaweed genus Pyropia , comprising a group of red algae in the family Bangiaceae commonly found in intertidal zones worldwide, we analyzed gene tree conflicts within Pyropia species. Traditionally, the classification of Pyropia species has relied on morphological traits and short genetic markers such as the chloroplast RuBisCO large subunit ( rbcL ) and small subunit (SSU) genes. In the present study, we performed phylogenetic analyses using the chloroplast genomes of 15 Pyropia species, including five newly sequenced genomes: Pyropia tanegashimensis , Pyropia acanthophora , Pyropia pseudolinearis , Pyropia kanakaensis and Pyropia kinositae . Notably, P. tanegashimensis and P. acanthophora exhibited structural changes similar to those previously reported in P. vietnamensis . Our analysis revealed that, although previous studies reported conflicting topologies for the phylogenetic relationships among the four major clades of Pyropia , we have resolved these conflicts, at least in terms of the evolution of the chloroplast genome. By contrast to the traditional view of chloroplast genomes as single evolutionary units, our findings suggest that this assumption does not always hold true, leading to different topological patterns across chloroplast genes. Furthermore, we identified several incongruences between individual gene trees and the species tree within clades of Pyropia . These findings highlight the complexities and challenges in resolving phylogenetic relationships within Pyropia , providing valuable insights for future evolutionary studies.