EDIT

  if($tag) {

    $out .= '</' . $tag . '>';

  }

        if(isset($tagged_text[$i + 3])  && $tagged_text[$i + 2]->type == "separator" && $tagged_text[$i + 3]->type == "secMicroReference"){

  $tagged_text = array_values($tagged_text); // re-index array to make it continuous again

function tagged_text_extract(&$tagged_text, $type) {

  if (is_array($tagged_text)) {

    for ($i = 0; $i < count($tagged_text) - 1; $i++) {

      if($tagged_text[$i]->type == $type){

        $matching_elements[] = $tagged_text[$i];

        unset($tagged_text[$i]);

      }

    }

  }

  $tagged_text = array_values($tagged_text); // re-index array to make it continuous again

  return $matching_elements;

}

function find_tagged_text_elements(&$tagged_text, $type){

  $matching_elements = array();

  if (is_array($tagged_text)) {

    for ($i = 0; $i < count($tagged_text) - 1; $i++) {

      if($tagged_text[$i]->type == $type){

        $matching_elements[] = $tagged_text[$i];

          // full name with relation symbol, rel sec as de-dublication key

          $appended_phrase_text = join(' ', cdm_tagged_text_values($taxon_relation->taggedText, array('appendedPhrase')));

          $full_name_key = cdm_tagged_text_to_string($taxon_relation->taggedText, array('symbol', 'appendedPhrase'));

          $full_name_key = $name_text . ' ' . str_replace($name_text, '', $full_name_key) . ' ' . $symbol_text;

          // remove/extract appendedPhrase, secReference, relSecReference and add placeholders if needed

          tagged_text_extract($taxon_relation->taggedText, 'appendedPhrase');

            // for de-dublicationeverything else needs to be equal except for appendedPhrase + MAN.sec + MAN.secDetail. see #7658#note-21

            $appended_phrase_text = $appended_phrase_text . array_shift($sensu_tagged_text)->text; // remove first element which contains the "sensu", this will be added later in this code

            $sensu_citation_detail = trim(join(' ', cdm_tagged_text_values($sensu_tagged_text, array('secMicroReference'))));

            $full_name_key = preg_replace('/\s+/', ' ', $full_name_key); // sanitize multiple whitespace characters

            $misapplied[$full_name_key]['sensu_uuids'][] = array('uuid' => $sensu_uuid, 'prefix' => $appended_phrase_text, 'citation_detail' => $sensu_citation_detail);

            $ref_key = $sensu_uuid .($sensu_citation_detail ? '#' . $sensu_citation_detail : '');

            if (!isset($joined_refs[$ref_key])) {

              $joined_refs[$ref_key] = array(

          } else if($appended_phrase_text) {

            // appended phrase without reference

            $full_name_key = preg_replace('/\s+/', ' ', $full_name_key); // sanitize multiple whitespace characters

            $misapplied[$full_name_key]['sensu_uuids'][] = array('uuid' => null, 'prefix' => $appended_phrase_text);

          }

          if (isset($relsec_tagged_text[1])) {

            array_shift($relsec_tagged_text); // remove first element which contains the "err. sec", this will be added later in this code

            $relsec_citation_detail = trim(join(' ', cdm_tagged_text_values($relsec_tagged_text, array('secMicroReference'))));

            $relsec_citation_short_markup = cdm_tagged_text_to_markup($relsec_tagged_text);

            $relsec_citation_short = cdm_tagged_text_to_string($relsec_tagged_text);

            $relsec_uuid = $relsec_tagged_text[0]->entityReference->uuid;

            $misapplied[$full_name_key]['relsec_uuids'][] = $relsec_uuid;

            $ref_key = $relsec_uuid . ($relsec_citation_detail ? '#' . $relsec_citation_detail : '');

            if (!isset($joined_refs[$ref_key])) {

              $joined_refs[$ref_key] = array(

                'order_by_key' => $relsec_citation_short,

                'markup' => $relsec_citation_short_markup // the footnote key will be appended later

              );

          }

          if (!isset($misapplied[$full_name_key]['out'])) {

            $misapplied[$full_name_key]['out'] = cdm_tagged_text_to_markup($taxon_relation->taggedText);

            // We need to add the anchors for all of the other misapplied names not

            // being rendered explicitly.

            $misapplied[$full_name_key]['out'] = uuid_anchor($taxon_relation->taxonUuid, $misapplied[$full_name_key]['out']);

        } else {

          RenderHints::pushToRenderStack('other_taxon_relationship');

          // All relationship types except misapplied_name_for and invalid_designation_for.

          $taxon_relationships_lines[] = cdm_taxonRelationship($taxon_relation, TRUE, _is_invers_taxonRelationship($taxon_relation, $focusedTaxon));

        RenderHints::popFromRenderStack();

  foreach ($joined_refs as $ref_key => $sensu_strings) {

      $ref_key_tokens = explode('#', $ref_key);

      $sensu_uuid = $ref_key_tokens[0];

        $joined_refs[$ref_key]['markup'] = '<span class="sensu">' . $sensu_strings['markup'] . $footnote_key . '</span>';

  if (count($misapplied) > 0) {

    // create the list entries per misapplied name

      // all sensu and auct. for this MAN

        foreach ($misapplied_name['sensu_uuids'] as $sensu_data) {

          if($sensu_data['uuid']){

            $joined_ref_key = $sensu_data['uuid'] . ($sensu_data['citation_detail'] ? '#' .  $sensu_data['citation_detail'] : '');

            $sensu_refs_with_fkey[$sensu_data['prefix'] . $joined_refs[$joined_ref_key]['order_by_key']] = $sensu_data['prefix'] . $joined_refs[$joined_ref_key]['markup'];

          } else {

            $sensu_refs_with_fkey[$sensu_data['prefix']] = $sensu_data['prefix'];

          }

        $misapplied_name_markup = str_replace('{PLACEHOLDER_secReference}', $sensu_refs_with_fkey_markup, $misapplied_name_markup);

      // append the err. sec. if there is any for this MAN

      // final line

      $out .= '<li class="synonym"><span class="misapplied">' . $misapplied_name_markup . ' </span></li>';

        assertEquals("–\n\"Ossaea glomerata\" sensu A&S1; sensu A&S: 221; sensu A&S: 331; sensu Lem2; sensu Species solaris; auct.; auct. sensu A&S1; auctrs. afr.", p.getMisappliedName(1).getText());

        assertEquals("–\n" + StringConstants.DOUBTFULMARKER_SPACE +"\"Ossaea glomerata\" sensu A&S1", p.getMisappliedName(2).getText());

        assertEquals("–\nOssaea maculata sec. Lem2, err. sec. A&S1", p.getMisappliedName(3).getText());

        // "Species solaris" must not be in the footnotes as it has the same title as the short citation