A Mitogenomics View of the Genetic Status and Population History of the Basking Shark, Cetorhinus maximus

The basking shark, Cetorhinus maximus , has historically been a target of fisheries exploitation, leading to well-documented declines in parts of its range. Little is known about the genetic status and population history of this CITES Appendix II listed species. Prior analysis of basking sharks based on a single, non-coding, mitochondrial locus (control region (CR); 1,085bp), has suggested an absence of population structure and very low levels of genetic diversity (π = 0.0013) globally. In the present study, we assessed population genetic parameters by completing the first whole mitochondrial genome (~16,669 bp) survey of basking sharks sampled from three widespread geographic regions: the western North Atlantic (n=10), the eastern North Atlantic (n=10) and western South Pacific (n=10). Concordant with CR locus findings, whole mitogenome analyses (despite 15X more sequence data) showed no evidence of population differentiation and even lower genetic diversity (π = 0.0005). However, comparative analyses of individual loci revealed unexpected evolutionary dynamics: the protein coding genes ATP8, CO2, and ND3 contained the highest nucleotide diversity, while commonly utilized loci for population genetic studies (CR, ND2 and Cytb) showed an order of magnitude lower diversity. Bayesian Skyline Plot analyses of mitogenomes indicated a largely stable effective population size with limited growth. Demographic tests for population expansion produced non-significant values. Whole mitogenome findings of exceptionally low genetic diversity and results from population demographic analyses are consistent with a hypothesis of a historical bottleneck with limited population expansion thereafter, adding to conservation concerns for this regionally Endangered (IUCN Red List) species.