Phylogeography and phylogeny of the epineritic cosmopolitan bonitos of the genus Sarda (Cuvier): inferred patterns of intra‐ and inter‐oceanic connectivity derived from nuclear and mitochondrial DNA data

Aim  To reconstruct the phylogenetic relationships of the four species of the genus Sarda ( Sarda sarda , Sarda orientalis , Sarda australis and Sarda chilensis ) and their phylogeographic history in the context of historical and ecological biogeography. Also, to reconstruct within‐species phylogenetic relationships to test whether the North Atlantic and Mediterranean populations of Atlantic bonito ( S. sarda ) warrant subspecies status, and the validity of the allopatric northern and southern populations of eastern Pacific bonito ( S. chiliensis ), recognized as S. chiliensis lineolata and S. chiliensis chiliensis . Location  Representative samples of all four Sarda species collected world‐wide were analysed. Methods  Phylogenetic inference was carried out with neighbour‐joining, maximum parsimony and maximum likelihood, employing nucleotide sequences of the mitochondrial DNA (mtDNA) control region I (CR‐I) and of the single‐copy nuclear DNA (nDNA) Tmo‐4c4 gene. Analysis of molecular variance was used on the mtDNA data to estimate the extent of geographic population structuring. Results  Gene trees derived from mtDNA and nDNA data yielded concordant phylogenies that support the monophyly of the genus Sarda . The following sibling pairs received strong statistical support: striped bonito ( S. orientalis ) with Australian bonito ( S. australis ), and Atlantic bonito ( S. sarda ) with eastern Pacific bonito ( S. chiliensis ). Furthermore, the origin of S. sarda mtDNA is paraphyletic with respect to S. chiliensis , and these results are indicative of introgression. The analysis of Tmo‐4c4 sequences corroborates the ancestral hybridization between these allopatric species. Comparisons of north‐west Atlantic and Mediterranean populations of S. sarda using mtDNA CR‐I data revealed substantial genetic differentiation. By contrast, no differences between the putative northern and southern allopatric subspecies of S. chiliensis were detected. Main conclusions  The monophyly of the genus Sarda as indicated by morphology is corroborated using both molecular markers. However, molecular phylogenies depicted a paraphyletic relationship between S. sarda and S. chiliensis . This phylogeographical relationship is better explained by an ancestral introgression facilitated by trans‐Arctic contact during the Pleistocene. The pronounced genetic differentiation between S. sarda samples from the north‐west Atlantic and the Mediterranean is consistent with the differentiation of these two regions, but not with the amphi‐Atlantic speciation hypothesis. Finally, the S. chiliensis lineolata and S. chiliensis chiliensis subspecies status is not supported by the molecular data.