Throughout the last couple of decades substantial progress has been made in optimizing efficient genetic management of both in -and ex-situ populations. Alongside the traditional focus on preserving (genetic) diversity, conservation management programs, such as captive breeding and reintroduction initiatives, recently started to focus on durable consistent characterization of subspecies or taxonomic units. The added value of these recent efforts in conservation are twofold. On the one hand more profound knowledge on the evolutionary history of specific taxa is needed to move from a potential conservative ap-proach (i.e. focus on the smallest described taxonomic entity) towards more biologically appropriate conservation actions, meanwhile preventing unin-tended interspecific mixing. In general this extra layer of information is there-fore suggested to be crucial in minimizing both inbreeding and outbreeding depression.
Except for some iconic species (e.g. orangutan, tiger and chimpanzee), the evolutionary history of many endangered taxa is still incomplete. Alongside more traditional approaches, phylogenetic research is slowly closing the gaps in our current understanding of the dynamic nature of speciation. An often limiting factor in molecular taxonomy reconstructions, especially in endan-gered species, is the availability of DNA samples. The rise of high throughput sequencing in combination with museum collections generates interesting opportunities, especially in non-model species. Here I describe the use of tar-geted enrichment strategies on approx. 150 years old museum samples to re-construct full mitochondrial genomes of all previously described subspecific categories of both military (A. militaris) -and Buffon’s macaws (A. ambiguus).
Although being applicable to a wide range of species, macaws were chosen in this pilot study based on recently raised questions on their taxonomy (e.g. the role of subtle morphological dissimilarities in delineating allopatric subspe-cies). In practice current identifications are often based on geographical loca-tion, as such generating problems in e.g. assigning unknown birds to the cor-rect ex-situ conservation breeding program. Apart from generating insight in: (i) the evolutionary history of these birds and (ii) the phylogeography of the Central American and Andes region as a whole, this study underlines benefits of using museum material in the genomics era (e.g. genotype - phenotype cor-relations). Apart from highlighting the overall advantages of this specific tar-geted enrichment strategy, some of the main issues in using degraded DNA and some preliminary results will be presented.