Editorial: Phylogenomic discordance in plant systematics

Topic Phylogenomic discordance in plant systematicsIn the omics-age of molecular systematics, entire genomes or genomic segments often contradict each other or the broader consensus of organismal relationships.Furthermore, this potentially conflicts with pre-omics phylogenetics, where true conflicts often remained undiscovered due to data limitations.Unlike earlier times when adding markers and taxa might have helped to address or even (superficially) resolve conflicts around phylogenetic hypotheses, incongruences arising from genome inferences remain challenging.Phylogenetic discordance can result from various evolutionary processes that lead to disparities between gene trees and species trees.This extends to genomic discordance, where organellar and nuclear genomes exhibit different coalescent paths or phenomena such as organelle capture.Advances in analytical methods enable the comparison of hundreds to thousands of loci across all plant genomes, offering a comprehensive view of phylogenomic complexity.This Research Topic explores high-throughput sequence-based phylogenomic studies that uncover discordant phylogenies.A total of 79 authors present a rich array of 14 original research articles focusing on phylogenomic studies based on highthroughput sequence data.These studies delve into the discordant phylogenies between, among, or within organellar genomes and the nuclear genome.Through large-scale comparative analysis of over 3,600 plant plastomes, Yang et al. contribute to the growing body of studies that find potential issues with phylogenetic inference using plastid-only data, which suffer from saturation at third codon positions.Similarly, organellar phylogenomic analysis by Wu et al. of Poales, one of the largest monocot orders, attribute phylogenetic conflicts to potential ancient rapid radiation, advocating the integration of nuclear data to fully resolve relationships.In fact, a set of articles caution against overreliance on organellar genomes in resolving evolutionary relationships, due to their intrinsic limitations.Low mutation rates, extensive homoplasy, and lack of taxonomic coherence limit the utility of plastid genomes, for example in Salix spp.(Salicaceae), as Wagner et al. demonstrate through their analysis of shrub willow plastomes and comparing these to RAD sequencing-based data.They suggest nuclear data may better resolve biogeographical questions, as these reflect not just one coalescence line.