Following a recent taxonomic revision, two manta species (Manta alfredi and Manta birostris) have been advocated based on meristic and morphological characteristics (Marshall et al. 2009). Subsequent genetic analyses of the two species using mitochondrial and nuclear markers confirmed two distinguishable genetic groups (Kashiwagi et al. 2012). Using the above taxonomic and genetic criteria, we provide evidence for the first record of a living Manta alfredi × Manta birostris hybrid.

The Manta individual (Fig. 1a, b) was non-lethally sampled from a known manta aggregation site in Dunganab Bay, Sudan, Red Sea, in October 2012. The individual was identified in the field as Manta alfredi based on distinguishing morphological criteria: dorso-ventral colouration/spot patterns, mouth and pectoral fin colouration, and absence of remnant spine (Fig. 1b; Marshall et al. 2009). DNA was recovered from a fin clip using standard molecular genetic protocols. The mitochondrial gene ND5 (1,154 bp) and nuclear gene RAG1 (646 bp) were amplified following Kashiwagi et al. (2012), and sequenced. Recovered sequences (GenBank accession nos. KF574269-KF574270) were aligned with those previously reported (Kashiwagi et al. 2012) and a haplotype network was constructed in TCS 1.21 (Clement et al. 2000).

Fig 1
figure 1

a Hybrid manta individual showing mtDNA ND5 haplogroup membership (based on Kashiwagi et al. 2012, red circle indicates hybrid individual) and chromatogram traces indicate heterozygosity (position 73: A and G; position 507: A and C) for species-specific nDNA RAG1 polymorphisms. b Ventral colouration is consistent with M. alfredi designation following Marshall et al. (2009): (1) blue-grey to black spots of variable sizes across most of ventral surface, (2) no remnant dorsal spine, (3) pale to dark charcoal bands present on the posterior edge of each pectoral fin margin, (4) small dark spots posterior to the fifth gill slits, (5) mouth—white to light grey colouration and (6) ventral surface predominantly black with no defined shoulder patches

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The Manta specimen was confirmed to carry a new Manta alfredi mtDNA haplotype (red in Fig. 1). However, the RAG1 sequence indicates that this individual is an interspecific hybrid. The two Manta species are reciprocally monophyletic at the RAG1 locus, which contains two species-specific single nucleotide polymorphisms (SNPs): at position 73 (M. alfredi: G; M. birostris: A) and position 507 (M. alfredi: A; M. birostris: C) following Kashiwagi et al. (2012). The hybrid individual is heterozygous at both SNPs (see inset chromatograms). Heterozygosity was confirmed by sequencing this individual in triplicate in both forward and reverse directions at RAG1.

Our finding indicates that reproductive isolation among M. alfredi and M. birostris may be less complete than previously thought, or alternatively, that species-specific taxonomic and genetic differentiation is not as unambiguous as currently suggested. Given the designation of the two discrete species as vulnerable on the IUCN Red List and their recent listing on CITES appendix II following concern over increasing global exploitation rates, the occurrence of hybridisation underscores implications for monitoring, conservation and management of threatened species.