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Rey-Iglesia, Alba, Gaubert, Philippe, Espregueira Themudo, Gonçalo, Pires, Rosa, de la Fuente, Constanza, Freitas, Luís, Aguilar, Alex, Borrell, Asunción, Krakhmalnaya, Tatiana, Vasconcelos, Raquel, Campos, Paula F (2021): Mitogenomics of the endangered Mediterranean monk seal (Monachus monachus) reveals dramatic loss of diversity and supports historical gene-flow between Atlantic and eastern Mediterranean populations. Zoological Journal of the Linnean Society 191 (4): 1147-1159, DOI: 10.1093/zoolinnean/zlaa084, URL: https://academic.oup.com/zoolinnean/article/191/4/1147/5897344

The porpoise family (Phocoenidae) has seven species that inhabit mostly temperate waters and display a textbook example of anti-tropical distribution. Their evolutionary history remained poorly known, and some species face major conservation issues (e.g., critically endangered vaquita and Yangzte finless porpoises). Here, we used a comparative genomic approach to reconstruct the evolutionary history of porpoises across the entire speciation continuum, from the intraspecific level to species divergence in relation to past climatic changes. We assembled the mitochondrial genomes and resequenced at low coverage the entire nuclear genome of 63 porpoises. Phylogenetic reconstructions suggest that, like other toothed whales, porpoises radiated during the late Miocene-Pliocene but their current intraspecific subdivisions were shaped by environmental variations during the Quaternary Glaciations. We highlighted a parallel evolution in both hemispheres associated with symmetric adaptations to different environments (coastal versus pelagic) exhibiting convergent patterns of coloration and genetic diversity. This result suggests that the mechanism driving diversification of the well-known species of the Northern Hemisphere may apply also to the poorly-known southern species. In contrast to previous results, our results showed that spectacled and Burmeister’s porpoises share a more recent common ancestor than with the vaquita. The vaquita diverged from southern species during the Pliocene but has low diversity, possibly due to long-term small population size, population bottleneck(s), or small founding population in the Gulf of California. We also observed divergent lineages within Dall’s, spectacled and North Pacific harbor porpoises, suggesting a richer evolutionary history than previously thought. Genetic inferences of demographic trends from mitochondrial and nuclear genomes for each species and sub-species shed light on the dynamics of population size fluctuations and subdivisions. These results provide a new perspective on the divergence, adaptation and speciation processes of the porpoises. We will discuss how this knowledge can provide an evolutionary context for their conservation.

Heteroplasmy is defined as the presence of two or more different mitochondrial DNA (mtDNA) genomes in one individual. Heteroplasmy can arise from insertions or deletions (length heteroplasmy) or single nucleotide substitutions (point heteroplasmy). The phenomenon has been widely studied in humans and model species; however, reports from non-model species are rare, possibly because heteroplasmy was undetected or ignored during sequencing. Among cetaceans, a few studies have reported heteroplasmy and speculated on its possible effects, suggesting that heteroplasmy could be rare or simply ignored. The aim of the present study was to assess and confirm point heteroplasmies, as well as to determine their frequency in five baleen whale species. We analyzed 10,748 mtDNA sequence electropherograms of the mitochondrial control region obtained by Sanger sequencing. A pipeline was developed to detect potential heteroplasmy by analyzing chromatogram peak heights. Potential heteroplasmies were subsequently verified experimentally. A total of 7,882 samples were assessed, among which 326 (4,1%) presented potential point heteroplasmy at more than 35 different nucleotide positions. These results indicated that heteroplasmy is more frequent than previously reported. Several heteroplasmies were tracked across multiple generations, providing insights into the introduction of new mtDNA haplotypes. Ignoring heteroplasmy might bias relatedness analyses as well as estimates of genetic diversity and mtDNA mutation rates. Thus, it is extremely important to develop efficient ways to detect and verify heteroplasmy.