As ikegami and wol hinted at, apply from List::MoreUtils is a good tool to use here.

use List::MoreUtils qw(apply );

my @bad_species = grep { 
    !exists $refspecies{$_} # find undefined names
} apply {
    s/^-//;                 # normalize species names
} @species;

if( @bad_species ) {
    my $bad = join ', ', @bad_species;
    die "These values are not in the species table: $bad\n";
}
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List::MoreUtils has many simple little functions that can make your code much easier to read and maintain.