Uncovering ancient allopolyploidy through genomic evidence: A case study in Carex subgenus Uncinia

Abstract

The signature of allopolyploidy becomes increasingly blurred through time, hindering evaluation of its evolutionary role, and ancient hybridization remains difficult to detect even with large-scale genomic data. Understanding these processes is critical for reconstructing plant diversification at deep time scales. We focus on the enigmatic Carex subg. Uncinia (Cyperaceae), which shows unusual genomic and morphological traits and whose phylogenetic placement has long been controversial. To address this, we combined phylogenomic reconstruction with genome size estimates, allele divergence and locus heterozygosity analyses, and ploidy-level inference, together with phylogenetic network approaches. Our framework explicitly integrates allele-aware analyses that are often overlooked in plant phylogenomics. We find that genome size in Uncinia is approximately threefold larger than in other Carex lineages, consistent with an ancient polyploidy event. Phylogenetic networks further suggest that subg. Uncinia was originated through a hybridization event between subgenera Euthyceras and Vignea during the Early Miocene. This signal is reinforced by allele phasing and paralog analyses, with Uncinia gene copies clustering with different parental clades and phased alleles frequently segregating into opposite lineages. These complementary approaches reveal that Uncinia originated through ancient hybridization and allopolyploidy, and that its conflicting placement in previous studies reflects a reticulate evolutionary history. More broadly, our study highlights the power of combining genome size, network analyses, and allele phasing to uncover hidden reticulate processes in plants and emphasizes the importance of explicitly accounting for such processes when investigating diversification in complex evolutionary lineages.