Phylogenomic analysis reveals persistent gene tree discordance across the Chenopodium album aggregate, indicating complex evolutionary histories shaped by hybridisation and polyploidy.
Key Points
To determine whether gene-tree discordance persists when subgenome lineages are evaluated separately in the polyploid Chenopodium album aggregate and whether unresolved relationships reflect reticulate evolution.
Analyzed 2,298 conserved nuclear BUSCO families across 27 assembly-level plant terminals using tree- and network-based phylogenetic methods.
Conducted lineage-aware analyses across 2,156 gene families by partitioning polyploid Chenopodium genomes into A through H components, with Dysphania ambrosioides as an outgroup.
Assessed hybridization and site-pattern asymmetry across loci using HyDe with global false-discovery-rate correction.
Lineage-aware analyses successfully recovered expected B-, C-, and D-affinity groupings, but extensive gene-family heterogeneity remained widespread across loci.
Reticulate phylogenetic networks provided a superior fit to the genomic data compared to bifurcating tree models, although inferred topologies differed across analytical approaches.
HyDe detected significant site-pattern asymmetry in a small subset of loci, reflecting shared evolutionary signals rather than pinpointing direct ancestral hybrid progenitors.