There are several things to consider.
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The lava flows are relatively recent, within the last few millions years, and are like little black islands in a sea of light brown desert. The species is older than the black basalt lava flows.
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The dark coat color allele is dominant.
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As you move away from the lava flows you don’t find the dominant black allele, even though there is free interbreeding between the brown and black populations. This demonstrates strong negative selection against the black allele outside of the basalt islands.
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There is more than one basalt island with black mice. Interestingly, the genetics of their adaptations are different. That is, each black population of mice has a unique mutation for that population.
All of this added together demonstrates that the black allele emerged as a mutation within the brown population.