I tried to insert some debugging code between the $mech->get() and $mech->select() lines, as following:

my $f = 0;
for my $form ($mech->forms) {
    printf "Find form #%d: %s\n", ++$f, $form->attr('name');
    my $i = 0;
    for my $input ($form->inputs) {
        printf "Input #%d: %s (type: %s), values: [%s]\n",
               ++$i,
               $input->name,
               $input->type,
               join(', ', $input->possible_values);
    }
}
[download]

I also add a debugging line after the $mech->select() line to print the value set for the field ("S. cerevisiae").

print 'Selected species: ', $mech->value('species'), "\n";
[download]

When I run it, I got this result:

Find form #1: paramForm
Input #1: paramFile (type: hidden), values: []
Input #2: upstream (type: hidden), values: []
Input #3: runBeam (type: hidden), values: []
Input #4: runAmbiguizer (type: hidden), values: []
Input #5: runBipartites (type: hidden), values: []
Input #6: upstreamType (type: radio), values: [intergenic, fixed]
Input #7: group (type: textarea), values: []
Input #8: groupFile (type: file), values: []
Input #9: emailAddress (type: text), values: []
Input #10: emailSubject (type: text), values: []
Input #11: selectParamsButton (type: submit), values: []
Input "species" not found at monkfan.pl line 31
No such field 'species' at /usr/lib/perl5/site_perl/5.8.8/WWW/Mechaniz
+e.pm line 1324
[download]

Somehow the 'species' field isn't found and an error is issued instead. There are 11 fields. I can't figure out why the 'species' field isn't recognized. I think there's something went along the way to the remote server. So I download the html code and put it on my local web server. What I get is even more suprising, increasing my curiosity level:

Find form #1: paramForm
Input #1: paramFile (type: hidden), values: []
Input #2: upstream (type: hidden), values: []
Input #3: runBeam (type: hidden), values: []
Input #4: runAmbiguizer (type: hidden), values: []
Input #5: runBipartites (type: hidden), values: []
Input #6: species (type: option), values: [init, A. fumigatus Af293, A
+. gossypii, A. nidulans, A. thaliana, A. tumefaciens C58, B. subtilis
+, C. elegans, C. tetani E88, C. trachomatis, Candida albicans, Candid
+a glubrata, Candida lusitaniae, Candida tropicalis, Cryptococcus neof
+ormans, D. melanogaster, D. rerio, E. coli K12-MG1655, Fusarium verti
+cillioides, H. influenzae, H. pylori, H. sapiens, Histoplasma capsula
+tum, Kluyveromyces lactis, M. jannaschii, M. tuberculosis CDC1551, M.
+ tuberculosis H37Rv, Magnaporthe grisea, N. crassa, Neurospora crassa
+#2, P. aeruginosa PA01, P. falciparum 3D7, R. norvegicus, Rhizopus or
+yzae, S. aureus MW2, S. cerevisiae, S. pombe, S. typhimurium LT2 SGSC
+1412, V. cholerae El Tor N16961, Y. pestis CO92, Yarrowia lipolytica]
Input #7: upstreamType (type: radio), values: [intergenic, fixed]
Input #8: group (type: textarea), values: []
Input #9: groupFile (type: file), values: []
Input #10: emailAddress (type: text), values: []
Input #11: emailSubject (type: text), values: []
Input #12: selectParamsButton (type: submit), values: []
Selected species: S. cerevisiae
[download]

First, there are 12 fields. Second, the 'species' field is there at #6 (as type 'option') along with the possible values for the select. Third, the selected option is confirmed, and it's "S. cerevisiae".

Frankly, I haven't find anything why the difference. I'm not even sure whether this has something to do with the internal of WWW::Mechanize although I tend to think "no".