Figure 1

Schematic diagrams of the topology of (a) the mitochondrial phylogeny, illustrating the dispersal events of maternal lineages from the North Pacific to the North Atlantic via the Southern Ocean and dispersal back to the North Pacific as inferred by Foote et al. (2011); (b) the nuclear phylogeny based on the full data set partitioned for GC content, illustrating the dispersal events inferred by the BBM analysis of Moura et al. (in black) and an alternative biogeographical scenario that is consistent with the inferences from the mt tree, but which requires an additional dispersal event (in grey) and is less well supported under the BBM model; (c) the nuclear phylogeny based on the AT-rich (low recombination) contigs produced by Moura et al. (d) A hypothetical scenario in which the mitochondrial phylogeny represents the true species tree and historical biogeography, but in which gene flow upon secondary contact could result in the clustering of the offshore and transient ecotypes in a nuclear phylogeny. Tip labels indicate lineage (Transient, Offshore, Resident, Atlantic and Southern Ocean). d1, d2, d3 and so on, are derived alleles/shifts in allele frequency that have occurred along different branches of the phylogeny. If upon secondary contact, gene flow occurred between the offshore and transient ecotypes, either directly or via an intermediate population (i), then some alleles derived following sequential splits from the Southern Ocean, North Atlantic and resident lineages would be shared with the transients. In addition, the alleles derived in the transients would be shared with the offshores, but not the other lineages. Allele frequencies at shared ancestral polymorphisms would also become more correlated between the offshore and transient lineages. The relative phylogenetic signal from introgressed versus shared ancestral alleles would depend upon the demographic history and the level of gene flow and would likely vary between genomic regions with different GC content owing to the differences in recombination rates, consistent with the pattern of different topologies being observed in the different nuclear phylogenies generated by Moura et al.