Phylogenomics of the genus Tursiops and closely related Delphininae reveals extensive reticulation among lineages and provides inference about eco-evolutionary drivers

Andre E. Moura*, Kypher Shreves, Małgorzata Pilot, Kimberly R. Andrews, Daniel M. Moore, Takushi Kishida, Luciana Möller, Ada Natoli, Stefania Gaspari, Michael McGowen, Ing Chen, Howard Gray, Mauvis Gore, Ross M. Culloch, Muhammad S. Kiani, Maia Sarrouf Willson, Asma Bulushi, Tim Collins, Robert Baldwin, Andrew WillsonGianna Minton, Louisa Ponnampalam, A. Rus Hoelzel

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

30 Citations (Scopus)
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Phylogeographic inference has provided extensive insight into the relative roles of geographical isolation and ecological processes during evolutionary radiations. However, the importance of cross-lineage admixture in facilitating adaptive radiations is increasingly being recognised, and suggested as a main cause of phylogenetic uncertainty. In this study, we used a double digest RADseq protocol to provide a high resolution (~4 Million bp) nuclear phylogeny of the Delphininae. Phylogenetic resolution of this group has been especially intractable, likely because it has experienced a recent species radiation. We carried out cross-lineage reticulation analyses, and tested for several sources of potential bias in determining phylogenies from genome sampling data. We assessed the divergence time and historical demography of T. truncatus and T. aduncus by sequencing the T. aduncus genome and comparing it with the T. truncatus reference genome. Our results suggest monophyly for the genus Tursiops, with the recently proposed T. australis species falling within the T. aduncus lineage. We also show the presence of extensive cross-lineage gene flow between pelagic and European coastal ecotypes of T. truncatus, as well as in the early stages of diversification between spotted (Stenella frontalis; Stenella attenuata), spinner (Stenella longirostris), striped (Stenella coeruleoalba), common (Delphinus delphis), and Fraser's (Lagenodelphis hosei) dolphins. Our study suggests that cross-lineage gene flow in this group has been more extensive and complex than previously thought. In the context of biogeography and local habitat dependence, these results improve our understanding of the evolutionary processes determining the history of this lineage.

Original languageEnglish
Article number106756
Number of pages12
JournalMolecular Phylogenetics and Evolution
Early online date3 Feb 2020
Publication statusPublished - May 2020

Bibliographical note

Funding Information:
The authors would like to acknowledge Karis Baker, Michelle Gaither for help with laboratory work, and Menno de Jong for help with handling large raw files between servers. We also acknowledge Dr. Rupert Ormond, Umer Waqas and Babar Hussain for support in obtaining samples from Pakistan. For the Steno bredanensis and Stenella attenuata samples, we would like to thank P. Morin and K. Robertson (Southwest Fisheries Science Center ? SWFSC) for approval and extractions, as well as L. Balance (SWFSC), E. Oleson (PIFSC), and C. Potter (Smithsonian NMNH) for use of these samples. This work was supported by a pump-priming grant awarded by the University of Lincoln School of Life Sciences. M. Pilot was supported by a grant from the Polish National Agency for Academic Exchange (NAWA; Polish Returns Fellowship PPN/PPO/2018/1/00037).


  • Cetacea
  • Delphininae
  • Phylogeny
  • Phylogeography
  • Radseq
  • Tursiops


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