Southeast Asia is a biodiversity hotspot characterized by a complex
paleogeography, and its Polypodiopsida flora is particularly diverse.
While hybridization is recognized as common in ferns, investigations
into the relationship between hybridization events and fern diversity
are notably lacking. Lecanopteris s.s., an ant-associated fern, has been
subject to debate regarding species delimitations primarily due to
limited DNA markers and species sampling. Our study integrates 22 newly
generated plastomes, 22 transcriptomes, and flow cytometry of all native
species along with two cultivated hybrids. Our objective is to elucidate
the reticulate evolutionary history within Lecanopteris through the
integration of phylo-biogeography reconstruction, gene flow inference,
and genome size estimation. Key findings of our study include: (1) An
enlarged plastome size in Lecanopteris, attributed to extreme expansion
of the Inverted Repeat (IR) regions; (2) The traditional ‘pumila’ and
‘crustacea’ groups are paraphyletic; (3) Significant cytonuclear
discordance attributed to gene flow; (4) Natural hybridization and
introgression in the ‘pumila’ and ‘darnaedii’ groups; (5) L. luzonensis
is the maternal parent of L. ‘Yellow Tip’, with L. pumila suggested as a
possible paternal parent; (6) L. ‘Tatsuta’ is a hybrid between L.
luzonensis and L. crustacea; (7) Lecanopteris first diverged during the
Neogene and then during the middle Miocene climatic optimum in Indochina
and Sundaic regions. In conclusion, the biogeographic history and
speciation of Lecanopteris have been profoundly shaped by past climate
changes and geodynamics of Southeast Asia. Dispersals, hybridization and
introgression between species act as pivotal factors in the evolutionary
trajectory of Lecanopteris.