From your description, it sounds like you want something like this (mildly tested):

#!/usr/bin/perl

use strict;

my @animals = ( "bear<1>\n", "camel<0> <2>\n", "<2>horse\n", "duck<3>\
+n" );

my %changemap = (
   "<0>" => 'A',
   "<1>" => 'B',
   "<2>" => 'C',
   "<3>" => 'D',
);

# build a single regular expression to match all of the
# items we're changing from
my $from = join '|', keys %changemap;

for (@animals) {
   s/($from)/$changemap{$1}/g;
}
print @animals;
__END__
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update: removed line in the code that compiled the RE. I don't think it adds anything in the way of understanding.