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The genetics and evolution of the critically endangered Trinidad Piping Guan Pipile pipile, synonym Aburria pipile.The Trinidad Piping Guan, Pipile pipile synonym Aburria pipile (Jaquin, 1784) is the only endemic Cracid on the island of Trinidad. The species is currently listed as Critically Endangered and is considered to be in ‘on-going decline’ by the IUCN, BirdLife International and Cracid Specialist Group. This study aims to examine aspects of genetic variation and the evolution of the mitochondrial genome in the Trinidad Piping Guan utilising, for the first time, samples collected from individuals in the wild and reference specimens of the genus Pipile sourced from museum collections. In this study the complete mitochondrial genome of the Trinidad Piping Guan was sequenced for the first time. Analysis of intra-specific variation of wild Trinidad Piping Guan individuals using single nucleotide polymorphisms demonstrates extremely limited variation within the genes of the mitochondrial genome and nuclear gene intron sequences. Limited variation within this population is consistent with both historical and contemporary contractions of populations within a restricted island system, which may have serious implications for the future of this species in terms of both genetic diversity and conservation management. Phylogenetic analysis of the complete mitochondrial genome of the Trinidad Piping Guan enabled placement of the genus Pipile within the Galliforme evolutionary tree for the first time, and subsequently places the genus within the broader context of the Aves class. Mito-genomic analysis confirms that the Cracids are one of the basal Galliforme clades, and sister taxa to the Megapodidae. Phylogenetic placement of the Pipile genus is basal to that of the Crax species within the Cracidae family, indicative of an earlier evolutionary origin of the Piping Guans. The inclusion of the Trinidad Piping Guan, in the avian evolutionary tree using the whole mitochondrial genomes expands the current genetic phylogeny of the Cracid family, yielding a better understanding of evolutionary relationships among the Galliforme order and the diversification of modern avian lineages. This study has established novel molecular techniques for the analysis of mitochondrial DNA in historical specimens of the genus Pipile from museum reference collections. The analysis of inter-specific relationships within the genus Pipile has clarified the evolutionary and biogeographic relationships between the Piping Guan species. Additionally, the Trinidad Piping Guan is genetically defined for the first time as an evolutionarily significant unit, which represents a unique evolutionary pathway within this important genus in a closed island system on the island of Trinidad.