Data for: Echoes of ancient introgression punctuate stable genomic lineages in the evolution of figs

Studies investigating the evolution of flowering plants have long focused
on isolating mechanisms such as pollinator specificity. Some recent
studies have proposed a role for introgressive hybridization between
species, recognizing that isolating processes such as pollinator
specialization may not be complete barriers to hybridization. Occasional
hybridization may therefore lead to distinct yet reproductively connected
lineages. We investigate the balance between introgression and
reproductive isolation in a diverse clade using a densely sampled
phylogenomic study of fig trees (Ficus, Moraceae). Co-diversification with
specialized pollinating wasps (Agaonidae) is recognized as a major engine
of fig diversity, leading to about 850 species. Nevertheless, some studies
have focused on the importance of hybridization in Ficus, highlighting the
consequences of pollinator sharing. Here we employ dense taxon sampling
(520 species) throughout Moraceae and 1,858 loci to investigate
phylogenetic relationships and the prevalence of introgression among
species throughout the history of Ficus. We present a well-resolved
phylogenomic backbone for Ficus, providing a solid foundation for an
updated classification. Our results paint a picture of phylogenetically
stable evolution within lineages punctuated by occasional local
introgression events likely mediated by local pollinator sharing,
illustrated by clear cases of cytoplasmic introgression that have been
nearly drowned out of the nuclear genome through subsequent lineage
fidelity. The phylogenetic history of figs thus highlights that while
hybridization is an important process in plant evolution, the mere ability
of species to hybridize locally does not necessarily translate into
ongoing introgression between distant lineages, particularly in the
presence of obligate plant-pollinator relationships.