Data from: Possible involvement of ghost introgressions in the striking diversity of Vomeronasal type 1 receptor genes in East African cichlids

Cichlids that have undergone adaptive radiation are genetically close but
exhibit extreme ecological and morphological diversity, making them useful
for understanding speciation mechanisms. Vomeronasal type 1 receptors
(V1R) are highly conserved among teleost fish at the amino acid sequence
level and believed to play a fundamental role in reproduction. We
previously reported the surprisingly high sequence diversity of V1Rs among
certain cichlid species, suggesting a possible role for V1Rs in their
speciation. In this study, we investigated the process of evolutionary
diversification of all 6 V1Rs (V1R1-6) by using the genome data of 528
cichlid species, encompassing nearly all lineages. In the case of V1R2,
two highly divergent alleles (1.17%: variant sites/coding sequence (CDS)
length) without recombination were preserved and shared among cichlids
found in all of the East African Great Lakes. In the case of V1R6,
numerous highly variable alleles that could be derived from multiple
recombination events between two highly divergent alleles (1.39%: variant
sites/CDS length) were found among the Lake Victoria cichlids.
Additionally, we identified highly divergent alleles of V1R1 within the
tribe Tropheini, and of both V1R3 and V1R6 within Trematocarini and
Ectodini. Because one of the two divergent alleles of these V1Rs emerged
rapidly during cichlid evolution, they are likely to have been derived
from introgression. However, despite extensive investigations, we could
not identify the source lineages for these introgressions, implying that
they may have become extinct. This study revealed the potential role of
introgression in explaining the remarkable diversity of V1Rs in East
African cichlids.