For the Taxa field in Data Set content when using an autocomplete (tags style) widget, a comma separated list of names without the entity id number would not be saved. The latest dev version of entity reference has fixed this bug. See https://www.drupal.org/node/1959624
Now a comma separted list of taxa are saved or an error message is displayed if not in the list of taxa. New taxa will have to created before being referenced in a data set.