First Mitochondrial Genome of the Critically Endangered Madagascar Pochard (Aythya innotata)

The Madagascar pochard (Aythya innotata) is one of the world’s rarest birds, with fewer than 50 mature individuals remaining in the wild. Despite its critically endangered status, genetic resources for this species remain extremely limited. In this study, we assembled and annotated the complete mitochondrial genome of A. innotata for the first time. The mitogenome is 16,620 bp in length and contains 13 protein-coding genes (PCGs), 22 transfer RNA genes, two ribosomal RNA genes, and a single control region. The overall nucleotide composition exhibits a significant AT bias (51.81%), with a positive AT-skew (0.14) and a negative GC-skew (–0.36), consistent with other Aythya species. Comparative analysis across eight Aythya species revealed highly conserved genomic features, including gene order, nucleotide composition, and codon usage patterns. Selection pressure analysis indicated that all PCGs have evolved under strong purifying selection (Ka/Ks < 1), with ND3 displaying the highest nucleotide diversity and ATP8 the lowest. Phylogenetic reconstruction based on 13 PCGs indicates that A. innotata, A. baeri, and A. nyroca were most closely related. This newly assembled mitogenome provides essential genetic information for conservation planning, population genetics, and evolutionary studies of this critically endangered species.