About this Research Topic
Phylogenetics often uncovers contradicting hypotheses regarding the relationships within the same group of organisms, a phenomenon known since the beginning of the molecular systematics era. While, historically, single marker-based analyses produced discordance, nowadays entire cellular genomes or portions of the same genomic compartment conflict with others or the rest, respectively. In contrast to the beginning of the molecular systematics era, when adding markers and taxa offered a way out of systematic errors, genome inference-based incongruences cannot be addressed and explained easily.
Disagreeing phylogenomic hypotheses might originate from various evolutionary processes, including but not limited to hybridization or incomplete lineage sorting, thereby leading to gene tree-versus species tree-associated discrepancies. Today, this can be expanded to genome discordance, where phylogenomic signals of organellar genomes (plastid, mitochondrial) and the nuclear genome disagree due to intrinsically different coalescent paths or phenomena like organelle capture.
Progress in analytical approaches allows comparing hundreds to thousands of loci from all three plant genomes to provide a comprehensive picture of the phylogenomic mosaic of species and gene tree histories. This Research Topic focuses on phylogenomic studies based on high-throughput sequence data that produce discordant phylogenies between, among, or within organellar genomes and the nuclear genome.
Original research and reviews addressing the mechanistic or technical bases of phylogenetic discordance and those focusing on aspects of cytoplasmic coevolution or cross-genomic interaction are preferred. Methodological advances to detect and analyze discordance as well as improved methods for the visualization of discordant tree topologies from hundreds of loci are appreciated. Approaches that fuse microsynteny or other structural genomic analyses with marker-based phylogenomic analysis are encouraged as well. Articles that merely report phylogenetic incongruence between or within cellular genomes are discouraged unless these results are placed and discussed comprehensively in an evolutionary context and regarding the results’ relevance for systematics research of the particular lineage. Single loci approaches or Sanger sequencing-based data will not be considered.
Keywords: plastid genomes, mitochondrial genomes, nuclear genome, phylogenetic signal, discordance, structural genomics, systematics, evolution, genomic coevolution, phylogenomics
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