Time-calibrated phylogeny and full mitogenome sequence of the Galapagos sea lion ( Zalophus wollebaeki ) from scat DNA

• Published in: PeerJ (San Francisco, CA) Vol. 11; p. e16047
• Main Authors: Asadobay, Pacarina, Urquía, Diego O., Künzel, Sven, Espinoza-Ulloa, Sebastian A., Vences, Miguel, Páez-Rosas, Diego
• Format: Journal Article
• Language: English
• Published: United States PeerJ. Ltd 28.09.2023; PeerJ Inc
• Subjects: Animal behavior; Animals; Bioinformatics; DNA sequencing; DNA, Mitochondrial - genetics; Ecosystem; Ecosystems; Galapagos archipelago; Genes; Genome, Mitochondrial - genetics; Genomes; Genomics; Marine mammals; Mitochondrial DNA; Mitochondrial genome; Molecular Biology; Molecular clock; Nucleotide sequencing; Otariid; Phylogeny; Scat; Sea Lions - genetics; Taxonomy; Transfer RNA; Zoology; Galapagos archipelago; Phylogeny; Otariid; Scat; Mitochondrial genome; Molecular clock
• ISSN: 2167-8359; 2167-8359
• DOI: 10.7717/peerj.16047

The Galapagos sea lion, , is an endemic and endangered otariid, which is considered as a sentinel species of ecosystem dynamics in the Galapagos archipelago. Mitochondrial DNA is an important tool in phylogenetic and population genetic inference. In this work we use Illumina sequencing to complement the mitogenomic resources for genus-the other two species employed Sanger sequencing-by a complete mitochondrial genome and a molecular clock of this species, which is not present in any case. We used DNA obtained from a fresh scat sample of a Galapagos sea lion and shotgun-sequenced it on the Illumina NextSeq platform. The obtained raw reads were processed using the GetOrganelle software to filter the mitochondrial DNA reads (∼16% survive the filtration), assemble them, and set up a molecular clock. From the obtained 3,511,116 raw reads, we were able to assemble a full mitogenome of a length of 16,676 bp, consisting of 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNA), and two ribosomal RNAs (rRNA). A time-calibrated phylogeny confirmed the phylogenetic position of in a clade with , and , and sister to ; as well as establishing the divergence time for 0.65 million years ago. Our study illustrates the possibility of seamlessly sequencing full mitochondrial genomes from fresh scat samples of marine mammals.