Something like this should help:
<?php
$post_type="animals";
$tax = 'vertebrate';
$tax_terms = get_terms($tax);
if ( $tax_terms ) {
foreach ($tax_terms as $tax_term) {
$args = array(
'post_type' => $post_type,
"$tax" => $tax_term->slug,
'post_status' => 'publish',
'posts_per_page' => -1,
'caller_get_posts' => 1,
'orderby' => 'title',
'order' => 'ASC'
);
// $my_query = null; <- REMOVE THIS, YOU DON'T NEED TO NULL VARIABLE BEFORE ASSIGNING IT'S VALUE
$my_query = new WP_Query($args);
?>
<?php if ( $my_query->have_posts() ) : ?>
<h2><?php echo esc_html($tax_term->name); ?></h2>'; <?php // <- YOU SHOULD ESCAPE PRINTED VALUES ?>
<ol>
<?php while ($my_query->have_posts()) : ?>
$my_query->the_post(); ?>
<li>
<a href="https://wordpress.stackexchange.com/questions/158329/<?php the_permalink() ?>" rel="bookmark" title="Permanent Link to <?php the_title_attribute(); ?>"><?php the_title(); ?></a>
<?php
// setup_postdata( $post ); <- THERE IS NO NEED TO SETUP_POSTDATA HERE (YOU'VE ALREADY CALLED the_post() ON QUERY
$type_terms = wp_get_post_terms( $post->ID, 'type');
if ( $type_terms ) {
echo '<span>('. esc_html($terms[0]->name) .')</span>';
}
?>
</li>
<?php endwhile; ?>
</ol>
<?php endif; ?>
<?php
// wp_reset_query(); <- YOU DON'T CHANGE GLOBAL $wp_query, SO THERE IS NO NEED TO RESET QUERY (ESPECIALLY DON'T DO THIS FOR EACH $tax_term
}
}
// BUT YOU DO CHANGE GLOBAL $post, SO YOU SHOULD RESET IT'S VALUE TO BE COMPATIBLE WITH PLUGINS AND SO ON
wp_reset_postdata();
?>
Ordered lists (OLs) would be much better than paragraphs (P) in this case (since these are LISTS of animals ORDERED BY name).