Exploration reveals complex phylogenetic signals in Glycine, indicating challenges in species tree reconstruction.
Key Points
This research aims to investigate the discordance in phylogenetic signals within the Glycine genus, particularly due to polyploidy and cytoplasmic factors.
Analyzed 2389 nuclear genes from 61 Glycine accessions and constructed gene trees for nuclear and organellar genomes.
Utilized ASTRAL for species tree reconstruction and maximum likelihood for concatenation analyses.
Reduced datasets of 6 complete genomes to explore gene tree topology space more comprehensively.
Species trees from nuclear data were congruent but discordant with organellar trees.
No individual gene locus consistently tracked the species tree topology across larger datasets.
In a reduced dataset with complete genomes, most loci aligned with the species tree, revealing complex and scattered phylogenetic signals.