Jacqueline, I haven't read the article yet (so maybe I should stay out of this!), but I had the impression that the amount of endogamy among the Acadians made DNA analysis quite difficult.
(Now that I have read the article, I'll just clarify that I was mainly thinking of autosomal DNA; while mtDNA seems to be reliable for the purpose discussed, it can only be used for one part of one's ancestry--the matrilinear line.)