Fig. S1 Networks of the five nuclear genes sequenced in this study.

Fig. S2 Estimation of the number of groups (K) using the program <SMALLCAPS>STRUCTURE</SMALLCAPS> (Pritchard et  al. 2000).

Fig. S3 Factorial Correspondence Analysis on the first three axes produced with Genetix (Belkhir et  al. 1996–2004) using microsatellite and sequence data for individuals of ‘pure’ species and different hybrid classes.

Fig. S4 Diagrams illustrating the different interspecific crossings investigated in this study: (A) C.  caretta × E.  imbricata, (B) C.  caretta × L.  olivacea, (C) E.  imbricata × L.  olivacea, and (D) C.  caretta × E.  imbricata ×  C.  mydas.

Fig. S5 Output chart from the introgression analysis (admixture) in the program <SMALLCAPS>STRUCTURE</SMALLCAPS> using four microsatellite loci.

Table S1 Primers used to generate autosomal sequence data that are described in detail in the Methods section and Appendix S1.

Table S2 Description of samples used on the complete and filtered data set.

Table S3 Detailed genotype of the filtered data set generated in this study.

Appendix S1 Detailed protocols for genotyping RFLPs, autosomal sequences, and microsatellites.

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