Complete Mitochondrial Genomes Recovered From Environmental Metagenomics Samples Can Facilitate Non‐Intrusive Population Genetic/Genomics Studies in the South American Sea Lion Otaria byronia

The abundance of many marine mammals is declining due to local, regional, and global climate stressors that characterize the Anthropocene. Long‐term monitoring is crucial for understanding how these declining populations respond to further environmental stress, and developing non‐invasive genetic sampling strategies is needed to guide their recovery effectively. The aim of this study was to test if complete mitochondrial genomes can be assembled from environmental DNA (eDNA) metagenomics scat samples taken non‐invasively using the South American Sea Lion Otaria byronia as a model and examine if the retrieved mitochondrial genomes can facilitate non‐intrusive population genetic studies. Complete mitochondrial genomes of O. byronia were assembled from each of a total of 30 eDNA samples with coverages greater than 40× using a “target‐restricted‐assembly” bioinformatics strategy. The AT‐rich mitochondrial genomes contained 13 protein coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and a control region. Mitochondrial gene order in O. byronia was identical to that reported for all other cofamilial species. An Analysis of Molecular Variance and pairwise Φ ST tests using a 228 bp fragment of the CR demonstrated statistically significant genetic dissimilarity among the sampled population and others in the Pacific and Atlantic basin. This study demonstrates that complete mitochondrial genomes can be assembled from eDNA metagenomics scat samples, with which insights into metapopulation genetics can be achieved. Mitochondrial genomes assembled from eDNA metagenomics scat samples can support non‐disruptive biomonitoring of this iconic marine mammal across its distribution.