Military macaws (A. militaris) used to range from Mexico all the way down to
Argentina. Recently increased levels of habitat loss and illegal bird trade resulted in dramatic decrease in terms of numbers and available habitat. Currently, their
patchy distribution range matches three allopatric subspecies (A. m. militaris, A. m.mexicana and A. m. boliviana) which are all listed as vulnerable on the IUCN RedList of Threatened Species. Apart from some early morphological descriptions, littleis known about the taxonomy of this species. Resolving these taxonomic uncertainties, would not only be of interest to better understand the
phylogeographic structure of the species (and add extra insights in the
phylogeograpy of the Central American and Andes region as a whole), but this
information will also be crucial in preserving the species on the long-term. Asides conservation actions on the field, breeding programs were created to conserve the species ex-situ. The Royal Zoological Society of Antwerp (RZSA) is European studbook keeper of the Mexican military macaw (A. m. mexicana) and, as such,started a project on resolving these taxonomy uncertainties, aiming at developing molecular diagnostic tools to identify pure subspecies. Therefore, the present work aims to evaluate: (i) the genetic differentiation of Military macaws within their former natural range, (ii) the “pureness” of the current captive breeding program (iii) and the availability of potential extra founders currently excluded from the breeding program due to taxonomic uncertainties. As such, we are making use of targeted enrichment strategies to study the complete mitochondrial genome (through NGS platforms) of 150-year old toe pads belonging to historical collections representing all described subspecies and a closely related sister species (Ara ambigua). Here we will underline the use (and potential pitfalls) of targeted enrichment strategies when dealing with old degraded starting material.