Speciation due to rapid genetic divergence in coding and noncoding regions accompanied by phenotypic differences in the tabular coral Acropora

Abstract

The reef-building coral genus Acropora is essential for coral reefs due to its role in the reef, as a habitat for other marine organisms. The diversity of coral species might have arisen explosively, accompanied by hybridization in response to historical climate change, Pleistocene, with sea level changes. Here, we aimed from integrative approaches (morphology, genetics, and reproduction) to evaluate the speciation history of the four tabular Acropora species (Acropora aff hyacinthus, A. cf bifurcata, A. cf cytherea, and A. cf subulata). Here, we show that introgression might have a minor role in specifying the four tabular Acropora spp. Instead, rapid genetic divergence occurred, accompanied by morphological differences and gamete incompatibility. Furthermore, extensive morphological analyses showed that these four species were distinguishable from morphology, and their gamete incompatibility was sufficiently high to prevent hybridization. Population structure and principal component analyses with the SNPs (>60,000) indicated these four species were also distinctive, and the ABBA-BABA test did not support introgression among these species. In addition, many coding and noncoding RNA sequences were in the high genetic variances among four species with high Fst loci along the genome. Comparing these orthologs among other Acropora species suggests that many of these genes were under positive selection, which could be associated with their divergence at spawning time, gamete incompatibility, and morphological differences. These results show that the speciation of the tabular Acropora occurred without hybridization, and divergence accompanying the genes’ rapid evolution could be associated with specifying in the species-rich Acropora.