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We investigated intra- and inter-colony sequence variation in a population of the dominant Hawaiian coral  Montipora capitata  by analyzing marker gene and genomic data. Ribosomal ITS1 regions showed evidence of a reticulate history among the colonies, suggesting incomplete rDNA repeat homogenization. Analysis of the mitochondrial genome identified a major ( M. capitata ) and a minor ( M. flabellata ) haplotype in single polyp-derived sperm bundle DNA with some colonies containing 2–3 different mtDNA haplotypes. In contrast,  Pax-C  and newly identified single-copy nuclear genes showed either no sequence differences or minor variations in SNP frequencies segregating among the colonies. Our data suggest past mitochondrial introgression in  M. capitata , whereas nuclear single-copy loci show limited variation, highlighting the divergent evolutionary histories of these coral DNA markers.

Divergent evolutionary histories of DNA markers in a Hawaiian population of the coral Montipora capitata