[MARMAM] New publication: Beaked whale genomics

Aubrie Onoufriou aubrieonoufriou at gmail.com
Wed Oct 26 00:43:11 PDT 2022


Hi all,

My co-authors and I are excited to share our new publication in Global Ecology and Conservation, where we have investigated the hierarchical genomic population structure of Cuvier’s and Blainville’s beaked whales using ddRAD and whole mitogenome sequencing. Our paper is available open-access at:  https://doi.org/10.1016/j.gecco.2022.e02308.

Kind regards,
Aubrie Onoufriou
aubrieonoufriou at gmail.com


Title: “Biogeography in the deep: Hierarchical population genomic structure of two beaked whale species”

Authors:
Aubrie B. Onoufriou, Oscar E. Gaggiotti, Natacha Aguilar de Soto, Morten T. Olsen, Morgan L. McCarthy, Phillip A. Morin, Massimiliano Rosso, Merel Dalebout, Nicholas Davison, Robin W. Baird, C. Scott Baker, Simon Berrow, Andrew Brownlow, Daniel Burns, Florence Caurant, Diane Claridge, Rochelle Constantine, Fabien Demaret, Sascha Dreyer, Martina Ðuras, John Durban, Alexandros Frantzis, Luis Freitas, Gabrielle Genty, Ana Galov, Sabine S. Hansen, Andrew C. Kitchener, Vidal Martin, Antonio A. Mignucci-Giannoni, Valeria Montano, Aurelie Moulins, Carlos Olavarría, M. Michael Poole, Cristel Reyes Suárez, Emer Rogan, Conor Ryan, Agustina Schiavi, Paola Tepsich, Jorge Urban, Kristi West, & Emma L. Carroll

Abstract:
The deep sea is the largest ecosystem on Earth, yet little is known about the processes driving patterns of genetic diversity in its inhabitants. Here, we investigated the macro- and microevolutionary processes shaping genomic population structure and diversity in two poorly understood, globally distributed, deep-sea predators: Cuvier’s beaked whale (Ziphius cavirostris) and Blainville’s beaked whale (Mesoplodon densirostris). We used double-digest restriction associated DNA (ddRAD) and whole mitochondrial genome (mitogenome) sequencing to characterise genetic patterns using phylogenetic trees, cluster analysis, isolation-by-distance, genetic diversity and differentiation statistics. Single nucleotide polymorphisms (SNPs; Blainville’s n = 43 samples, SNPs=13988; Cuvier’s n = 123, SNPs= 30479) and mitogenomes (Blainville’s n = 27; Cuvier’s n = 35) revealed substantial hierarchical structure at a global scale. Both species display significant genetic structure between the Atlantic, Indo-Pacific and in Cuvier’s, the Mediterranean Sea. Within major ocean basins, clear differentiation is found between genetic clusters on the east and west sides of the North Atlantic, and some distinct patterns of structure in the Indo-Pacific and Southern Hemisphere. We infer that macroevolutionary processes shaping patterns of genetic diversity include biogeographical barriers, highlighting the importance of such barriers even to highly mobile, deep-diving taxa. The barriers likely differ between the species due to their thermal tolerances and evolutionary histories. On a microevolutionary scale, it seems likely that the balance between resident populations displaying site fidelity, and transient individuals facilitating gene flow, shapes patterns of connectivity and genetic drift in beaked whales. Based on these results, we propose management units to facilitate improved conservation measures for these elusive species.

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