There would be a greater loss of genetic diversity if the populations bred separately (1).
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Gene flow refers to the transfer of alleles and genes between different populations, and thus increases genetic diversity amongst populations. If the populations bred separately, gene flow would not occur, and thus the alleles and genes exclusive to the Mediterranean population would be lost upon extinction. If the populations interbred however (Scenario 2), the Mediterranean genes would also be found in the Caribbean population, and thus there would be less loss of genetic diversity upon extinction of the Mediterranean population.