Evolutionary history of the porpoises ( Phocoenidae ) across the speciation continuum: a mitogenome phylogeographic perspective

• Main Authors: Chehida, Yacine Ben, Thumloup, Julie, Schumacher, Cassie, Harkins, Timothy, Aguilar, Alex, Borrell, Asunción, Ferreira, Marisa, Rojas-Bracho, Lorenzo, Roberston, Kelly, Taylor, Barbara, Víkingsson, Gísli, Weyna, Arthur, Romiguier, Jonathan, Morin, Phillip, Fontaine, Michael C.
• Other Authors: Groningen Institute for Evolutionary Life Sciences Groningen (GELIFES), University of Groningen Groningen, University of Barcelona, Sociedade Portuguesa de vida Selvagem (SPVS), Universidade do Minho = University of Minho Braga, Centro de Investigacion Científica y de Educacion Superior de Ensenada, NOAA National Marine Fisheries Service (NMFS), National Oceanic and Atmospheric Administration (NOAA), Marine and Freshwater Research Institute (MFRI), Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), Université Paris Sciences et Lettres (PSL)-Université Paris Sciences et Lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement IRD : UR226-Centre National de la Recherche Scientifique (CNRS), Diversity, ecology, evolution & Adaptation of arthropod vectors (MIVEGEC-DEEVA), Evolution des Systèmes Vectoriels (ESV), Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD France-Sud )-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD France-Sud )-Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD France-Sud )-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD France-Sud )
• Format: Report
• Language: English
• Published: HAL CCSD 2020
• Subjects: [SDE.BE]Environmental Sciences/Biodiversity and Ecology; [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE]; toothed whales
• Online Access: https://hal.science/hal-02915433; https://doi.org/10.1101/851469

Historical changes affecting food resources are a major driver of cetacean evolution. Small cetaceans like porpoises (Phocoenidae) are among the most metabolically challenged marine mammals and are particularly sensitive to changes in their food resources. The seven species of this family inhabit mostly temperate waters and constitute a textbook example of antitropical distribution. Yet, their evolutionary history remains poorly known despite major conservation issues threatening the survival of some porpoises (e.g., vaquita and Yangzte finless porpoises). Here, we reconstructed their evolutionary history across the speciation continuum, from intraspecific subdivisions to species divergence. Phylogenetic analyses of 63 mitochondrial genomes suggest that, like other toothed whales, porpoises radiated during the Pliocene in response to deep environmental changes. However, all intra-specific phylogeographic patterns were shaped during the Quaternary Glaciations. We observed analogous evolutionary patterns in both hemispheres associated with convergent adaptations to coastal versus oceanic environments. This result suggests that the mechanism(s) driving species diversification in the relatively well-known species from the northern hemisphere may apply also to the poorly-known southern species. In contrast to previous studies, we showed that the spectacled and Burmeister’s porpoises share a more recent common ancestor than with the vaquita that diverged from southern species during the Pliocene. The low genetic diversity observed in the vaquita carried signatures of a very low population size throughout at least the last 5,000 years, leaving one single relict mitochondrial lineage. Finally, we observed unreported subspecies level divergence within Dall’s, spectacled and Pacific harbor porpoises, suggesting a richer evolutionary history than previously suspected. These results provide a new perspective on the mechanism driving the adaptation and speciation processes involved in the diversification of cetacean species. ...