Pagination on custom query

Add this to your query:

'paged' => get_query_var('paged')

Like so:

$args = array(
    'post_type' => 'species',
    'meta_query' => $meta_query,
    'tax_query' => $tax_query,
    'paged' => get_query_var('paged')
);

Should do the trick.. Using Wp-pageNavi? dont forget to add the
wp-pagenavi tag just after the loop ends

<div class="navigation"><?php wp_pagenavi(); ?></div>

.
Hope This Helps 😉
Cheers, Sagive.