A Mother’s Story, Mitogenome Relationships in the Genus Rupicapra

Abstract

Although the two species of chamois (Rupicapra rupicapra and R. pyrenaica) are currently classified as least-concern by the IUCN (International Union for Conservation of Nature), inconsistencies on the subspecies classification reported in literature make it challenging to assess the conservation status of the single subspecies. Previous studies relying on mitochondrial genes, sometimes in combination with nuclear or Y-chromosome markers, reported the presence of clusters corresponding to the geographic distribution but highlighting ambiguities in the genus phylogeny. Here we report novel de novo assembled sequences of the mitochondrial genome from nine individuals, including previously unpublished R. r. balcanica and R. r. tatrica subspecies, and use them to untangle the genus phylogeny. Our results based on the full mitogenome inferred phylogeny confirm the previously reported genus subdivision in three clades and its monophyletic positioning within the Caprinae. Phylogeny and taxonomy of Rupicapra species thus remain controversial prompting for the inclusion of archeological remains to solve the controversy.

Past, present and future of chamois science

“…Pérez et al (2017) suggested that the patterns of differentiation for various molecular markers in chamois are best explained as reticulate evolution. Recent analyses of complete mitochondrial genomes (Iacolina et al 2021) supported the subdivision into three clades: two corresponding to the classical species R. pyrenaica and R. rupicapra, and a third including the subspecies R. p. ornata and R. r cartusiana.…”

Complete Mitochondrial Genome and Phylogenetic Analysis of Tarsiger indicus (Aves: Passeriformes: Muscicapidae)

“…Vertebrate mitochondrial genomes (mitogenomes) are circular, typically 14,000-20,000 bp, and contain 13 protein-coding genes (PCGs), two ribosomal RNA (rRNAs), 22 transfer RNA genes (tRNAs), and one large non-coding D-loop region [10,11]. The mitogenome has been extensively used in population genetics, population dynamics, and adaptive evolution studies of various animal groups [12][13][14][15][16], particularly in phylogenetic reconstruction among animal species [14,[16][17][18][19]. It is worth emphasizing that mitochondrial genomes are more reliable in phylogenetic reconstruction than a single mitochondrial gene [20][21][22].…”