Incomplete lineage sorting and gene flow within Allium (Amayllidaceae)

Area of Science:

• Genomics
• Phylogenetics
• Evolutionary Biology

Background:

• The genus Allium presents significant challenges for phylogenetic reconstruction due to widespread topological discordance and uncertainty.
• Previous studies utilized diverse data but failed to establish a consistent phylogeny for Allium.

Purpose of the Study:

• To resolve phylogenetic discordance in the genus Allium by assessing the roles of incomplete lineage sorting (ILS), gene flow, and gene tree estimation error.
• To reconstruct a reliable phylogenetic backbone for Allium species.

Main Methods:

• Generated 75 transcriptomes from 38 Allium species across 10 subgenera.
• Estimated phylogenetic trees using whole plastid genomes, single-copy genes, and consensus coding sequences (CDS) via coalescence and concatenation methods.
• Employed multiple analytical approaches, including coalescence simulation and reticulate network inference, to quantify ILS, gene flow, and gene tree estimation error.

Main Results:

• A fully supported species tree for Allium was established, confirming monophyly and agreeing with established relationships.
• Substantial ILS was detected, alongside evidence of two ancient hybridization events and several introgression events.
• Regression analysis identified gene tree inference error and gene flow as the primary factors driving gene tree variation.

Conclusions:

• Incomplete lineage sorting (ILS) and gene flow are the principal causes of phylogenetic heterogeneity in Allium.
• The study provides a well-resolved phylogenetic framework for Allium, demonstrating methods to untangle phylogenetic signal heterogeneity.
• Gene flow and ILS significantly impact the evolutionary history reconstruction of the Allium genus.