Genetic characterisation of Military Macaw subspecies and its implication for the ex-situ breeding programme

Military macaws have a discontinuous distribution range, stretching from Mexico to Argentina. Their patchy distribution range corresponds to three described allopatric morpho-subspecies (A.m. militaris, A.m. mexicana and A.m. boliviana) making this species interesting from a phylogeographic point of view. Taking part in the general trends of increased levels of habitat loss and illegal bird trade the species is listed on the IUCN Red List of Threatened Species and called into existence conservation breeding programmes. However due to uncertainties on subspecific variation, ex-situ species determination and/or possible hybridisation, current breeding programmes only include those birds for which initial sample locations are available. The consequence of this conservative strategy is that only a small number of confiscated macaws form the basis of the current A. m. mexicana breeding program, which interferes with the long-term sustainability of this population. As such resolving these taxonomic uncertainties is vital to safeguard the long-term viability of all captive military macaw breeding programs. As the studbook keeper of the European population of the Mexican military macaw (Ara militaris mexicana) we initiated a project on resolving taxonomic uncertainties for the species. To this end we use over 150-year old toe pads from historical collections of the American Museum for Natural History in New York of all described A. militaris ssp and its most closely related sister species (A. ambigua). Targeted enrichment strategies, a relatively novel high throughput sequencing method which already proved its strengths when dealing with highly fragmented DNA, will be used to evaluate genetic differentiation in the wild. In a first phase we aim to reconstruct the full mitochondrial genomes for all described subspecies (which will give us extra insight in the population genetic history of these species). Meanwhile we will scan neutral and coding nuclear regions to counteract maternally induced phylogenetic patterns and to get some first insights in functional adaptations of these different subspecies. One of the final objectives is to design diagnostic tools to characterise the current captive population, including specimens which could be used as potential founders.