Population Genomics of Mexican Military Macaws


The iconic but endangered Mexican Green Military Macaw is continuing to decline in numbers. Government and not-for-profit organizations are seeking answers to the causes of decline and effective actions to secure the species future.

The project involves non-invasive extraction and analysis of DNA from molted feathers in five macaw breeding areas in eastern Mexico. It aims to determine whether breeding behavior and loss of genetic diversity within the increasingly isolated macaw populations is contributing to species decline. This will help inform conservation planning and recovery programs for the species. 

Running for 12 months, the project will be conducted by Eldridge Wisely, a University of Arizona PhD student, who has expertise in extracting DNA from non-invasive wildlife samples, and has a research focus on learning how leading-edge genetic analysis methods can improve understanding of the breeding behavior and population dynamics, and how that information can improve conservation outcomes for the northernmost and most at-risk subspecies. 

This project involves multiple collaborations in Mexico. Volunteer citizen scientists will collect naturally-shed feathers, led by United Corridors A.C., a Mexican not-for-profit organization seeking to conserve the macaw. Also, a collaboration with a fisheries genetic lab in Hermosillo, Mexico for training and capacity building in DNA extraction from feathers and advanced genomic DNA analyses techniques for students in that lab. 


Military Macaws (Ara militaris) are large parrots whose size, colorful plumage, intelligence, and social demeanor mean they are highly sought after in the legal and illegal pet trade. They occur as three different subspecies across a massive but fragmented range from Mexico to Argentina. The Mexican Green Military Macaw (A.m. mexicanus) is the northernmost and most endangered subspecies. Once quite common, this subspecies has been displaced and eliminated in many areas. A. militaris is listed as Vulnerable and declining on the IUCN Red List and in Mexico, it is listed as Endangered (NOM-059- SEMARNAT-2010). It is included on Appendix I of CITES1.  

Genetic diversity contain the components for adaptation of species to environmental challenges, thus, conservation of genetic diversity is a main way to facilitate long-term survival of endangered species2. The most recent and detailed genetics study of A. militaris in 2017 utilized microsatellite markers in seven isolated populations in three regions of Mexico: the Sierra Madre Occidental, Oriental, and Sur. The two populations included from the east (Oriental) showed the greatest genetic differentiation from all the other populations and one of them showed high values for inbreeding relative to other populations. That study did not include three of the five eastern populations but the high level of divergence of those populations compared to others studied showed the need to produce high-resolution population genetics information for the eastern populations3. This proposed study will use an advanced genomic technique (ddRAD-seq) to obtain high-resolution data and perform  leading edge analyses genomic analyses.  Beyond resolving gene flow and dispersal patterns among populations, and breeding information (pedigree reconstruction, degree of inbreeding, analyzing if mates originate from same or different populations), we will also assess the degree of local adaptation these macaws may have to their specific environment due to our markers covering the whole genome.  The resulting data from this study will be interpreted and compared to previous studies which covered the full geographic range of the species4,5 and estimates of introgression among subspecies can also be made.

Extracting DNA from molted bird feathers is a well-established, accurate and non-invasive method for analyzing genetic diversity and its distribution among populations of species3.

non-invasively collected military macaw feather

Genetic analyses helps inform conservation planning and programs for endangered species by identifying genetically distinctive groups that can be proposed as conservation units to maintain genetic diversity, potential and real threats that endanger the survival of the species, and the evolutionary processes of natural populations. Understanding and taking conservation action that focuses on maintaining genetic diversity within and between populations is important for the long-term persistence of species. Genetically determined phenotypic variation increases the adaptive potential of populations; and overall genetic variation of natural populations, if reduced, reflects inbreeding and genetic drift, which reduces the viability of individual populations5.            Within endangered species in particular, the loss of individual populations can have a dramatic and negative effect on longer-term survival of the entire species. This project aims to determine whether inbreeding and lowered genetic diversity within any of the increasingly isolated and fragmented Mexican populations is contributing to species decline. Answering this question could assist with conservation planning by identifying genetically distinctive groups that can be proposed as conservation units to maintain genetic diversity, and helping conservation planners determine whether genetic rescue of populations is needed to increase the genetic diversity and resilience of the species, and also to look for specialized adaptations these macaws have evolved in response to the unique environment and climate conditions of eastern Mexico.

1.        BirdLife International. Ara militaris. The IUCN Red List of Threatened Species 2016:e.T22685548A93079238. IUCN Red List(2016).

2.        López-Cortegano, E. et al. Optimal Management of Genetic Diversity in Subdivided Populations. Front. Genet. 10, 1–10 (2019).

3.        Rivera-Ortíz, F. A., Solórzano, S., Arizmendi, M. del C., Dávila-Aranda, P. & Oyama, K. Genetic diversity and structure of the Military Macaw (Ara militaris) in Mexico: Implications for conservation. Trop. Conserv. Sci. 10, (2017).

4.        Gamboa, M. & Watanabe, K. Genome-wide signatures of local adaptation among seven stoneflies species along a nationwide latitudinal gradient in Japan. BMC Genomics 20, 1–12 (2019).

5.        Kahilainen, A., Puurtinen, M. & Kotiaho, J. S. Conservation implications of species-genetic diversity correlations. Glob. Ecol. Conserv. 2, 315–323 (2014).

This project is funded by: T&E, Inc.

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