For example, for some of those smaller functions, I'd do this:

sub gene_length {
    my @gls = sort map { length } keys %genome;
    die "Invalid genotype" unless $gls[0] == $gls[$#gls];
    return $gls[0];
}
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And this:

use List::Util 'first';
sub check_for_winner {
    return first { get_result($_) == $target } @population
}
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And this;

use List::Util 'sum';
sub get_population_fitness_score {
    return sum map { get_fitness_score($_) } @population;
}
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(Or just inline those statements, if they're only used once.)

In other words, when you can trim it down so that you can actually tell what it's doing at a glance, then it's easier to benchmark!.