Citation: Rivera-Ortíz, F.A.; Sanabria-Urbán, S.; Prieto-Torres, D.A.; Navarro-Sigüenza, A.G.; Arizmendi, M.d.C.; Oyama, K. Phylogeography of Ara militaris (Military Macaw): Implications for Conservation. Diversity 2023, 15, 1035. https://doi.org/10.3390/d15101035 Academic Editor: Luc Legal Received: 21 July 2023 Revised: 12 September 2023 Accepted: 24 September 2023 Published: 26 September 2023 Copyright: © 2023 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https:// creativecommons.org/licenses/by/ 4.0/). diversity Article Phylogeography of Ara militaris (Military Macaw): Implications for Conservation Francisco A. Rivera-Ortíz 1, * , Salomón Sanabria-Urbán 2, *, David A. Prieto-Torres 3 , Adolfo G. Navarro-Sigüenza 4 , María del C. Arizmendi 2 and Ken Oyama 5 1 Laboratorio de Ecología Molecular y Evolución, Unidad de Biotecnología y Prototipos, FES Iztacala, Universidad Nacional Autónoma de México, Avenida de los Barrios No. 1, Los Reyes Ixtacala, Tlalnepantla 54090, Mexico 2 Laboratorio de Ecología, Unidad de Biotecnología y Prototipos, FES Iztacala, Universidad Nacional Autónoma de México, Avenida de los Barrios No. 1, Los Reyes Ixtacala, Tlalnepantla 54090, Mexico; coro@unam.mx 3 Laboratorio de Biodiversidad y Cambio Global (LABIOCG), FES Iztacala, Universidad Nacional Autónoma de México, Avenida de los Barrios No. 1, Colonia, Los Reyes Ixtacala, Tlalnepantla 54090, Mexico; davidprietorres@iztacala.unam.mx 4 Museo de Zoología “Alfonso L. Herrera”, Facultad de Ciencias, Universidad Nacional Autónoma de México, Coyacán 04510, Mexico; adolfon@ciencias.unam.mx 5 Laboratorio Nacional de Análisis y Síntesis Ecológica, ENES Morelia, Universidad Nacional Autónoma de México, Antigua Carretera a Pátzcuaro No. 8701, Colonia Ex Hacienda de San José de La Huerta, Morelia 58190, Mexico; kenoyama@enesmorelia.unam.mx * Correspondence: francisco.rivera@iztacala.unam.mx (F.A.R.-O.); sanabria_os@comunidad.unam.mx (S.S.-U.) Abstract: The Military Macaw (Ara militaris) is an endangered bird species with disjunct geo- graphic distribution across the Neotropics, consisting of three recognized subspecies: One in Mexico (A. m. mexicanus) and two in South America (A. m. militaris and A. m. bolivianus). However, due to the limited phenotypic differentiation between these allopatric taxa, their taxonomic status has been the subject of debate. In this study, we explored mitochondrial DNA (mtDNA) variability to determine the phylogeographical pattern through phylogenetic and ecological modelling analyses. We also aimed to describe the evolutionary relationships of twelve A. militaris populations. We identified 41 haplotypes in the 300 bp region of the Cytochrome b (Cyt-b) gene of the mtDNA and low nucleotide diversity. The observed phylogeographic structure suggests the existence of two clades: One composed of A. m. militaris and A. m. bolivianus and another consisting solely of A. m. mexicanus. The A. m. mexicanus clade further divides into two recognized subclades: Sierra Madre Oriental and northeastern portion of the Sierra Madre Occidental. Ecological analyses revealed that the niche similarity between these lineages was lower than expected by chance. Additionally, results from low cross-prediction tests indicated that the two lineages have inhabited different environmental spaces since the Late Pleistocene. This divergence may be associated with a steep ecological gradient and contemporary geographical barrier. Based on our results, we suggest that at least the A. m. mexicanus has a divergent evolutionary history; therefore, it should be considered as a different evolutionarily significant and management unit. We recommend that future conservation strategies in Mexico incorporate effective protection measures, including habitat preservation and the reduction of illegal trade, to ensure the preservation of viable populations. Keywords: Ara militaris; conservation genetics; conservation units; Military Macaw; niche divergence; paleodistributions; phylogeography 1. Introduction Phylogeographical studies have held a central role in comprehending various aspects of Neotropical bird species, encompassing gene flow patterns, hybridization, historical range fragmentation and expansion, and speciation [1–5]. These studies have employed Diversity 2023, 15, 1035. https://doi.org/10.3390/d15101035 https://www.mdpi.com/journal/diversity