Large-scale phylogenomics reveals ancient introgression in Asian Hepatica and new insights into the origin of the insular endemic Hepatica maxima

Hepatica maxima is native to Ulleungdo, which is one of the
oceanic islands in Korea, and it likely originated via anagenetic
speciation from the Korean mainland species H. asiatica. However,
the relationships among the Asian lineages remain unresolved.
Phylogenomics based on plant genomes can provide new insights into the
evolutionary history of plants. We first generated plastid, mitochondrial
and transcriptome sequences of the insular endemic species H.
maxima. Using the genomic data for H. maxima, we obtained a
phylogenomic dataset consisting of 76 plastid, 37 mitochondrial and 413
nuclear genes from Asian Hepatica and two outgroups.
Coalescent- and concatenation-based methods revealed cytonuclear and
organellar discordance in the lineage. The presence of gynodioecy with
cytoplasmic male sterility in Asian Hepatica suggests
that the discordance is correlated with potential disruption of linkage
disequilibrium between the organellar genomes. Species network analyses
revealed a deep history of hybridization and introgression in
Asian Hepatica. We discovered that ancient and recent
introgression events occurred throughout the evolutionary history of the
insular endemic species H. maxima. The introgression may serve as
an important source of genetic variation to facilitate adaptation to the
Ulleungdo environment.