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. However, the difference in branch ordering (and consequently the biogeographical reconstruction) between the mt and nu phylogenies could be due to the influence of recombination and gene flow on the nuclear genome upon secondary contact. The BBM analysis has in this example selected an evolutionary history that minimises the changes between different ancestral states as the most likely model, given the data. However, the positioning of the in-group has changed, so that it is now a sister taxa to the North Pacific transients, rather than the Southern Ocean population. The positioning of taxa within the in-group for which the biogeographical history is under debate (i.e., North Atlantic, North Pacific Resident and North Pacific Offshore) does not change between the mt and nu phylogenies in a way that would affect the inference of ancestral distribution ( Figures 1a and b). In Figure 1b we show how their nu phylogeny is also compatible with the matrilineal historical biogeographical scenario suggested by Foote et al. using nuclear (nu) DNA phylogenies inferred that divergence at the specified node most probably occurred in the North Pacific. The phylogeographic reconstruction by Moura et al. (2011) inferred from these results that the matrilineal history of North Pacific ecotypes included a period of allopatry, but acknowledged mtDNA may not fully reflect the underlying pattern of divergence and lineage formation. ![]() The branching order, supported by tests of alternative topologies, suggested a series of dispersal events from the Pacific to the Atlantic and back again, additionally supported by stepwise reductions in genetic diversity with each putative dispersal and founding event. Two North Pacific ecotypes (‘resident’ and ‘offshore’) shared a more recent ancestor with two North Atlantic clades than they did with the third North Pacific ‘transient’ ecotype. (2011) interpreted complete mitochondrial (mt) genome phylogenies as evidence that three North Pacific killer whale ecotypes did not meet the criteria for having diverged in sympatry ( Coyne and Orr, 2004), as they were not sister taxa or a monophyletic endemic species flock. Killer whales are a globally distributed, highly mobile predator, but distinct ecotypes are found in sympatry in a number of locations including the North Pacific. We question whether their data can exclude alternative biogeographical scenarios, and argue that gene flow upon secondary contact could have resulted in the changes in topology of their nuclear phylogeny that ultimately led to the Bayesian binary model (BBM) analysis inferring that divergence of the North Pacific ecotypes had occurred in situ. ![]() We contend that Moura et al.’s inference of divergence within the Pacific Ocean do not equate to divergence in sympatry, but given that the criteria for robustly establishing sympatric divergence have already been much debated and are well established ( Coyne and Orr, 2004 Bolnick and Fitzpatrick, 2007), we focus here on questioning the robustness of their biogeographical inference at the ocean basin level. (2014) claim their phylogenomic analysis of historical biogeography indicates killer whale ecotypes found in the largest ocean basin, the North Pacific, diverged in sympatry. However, in a recent study published in Heredity, Moura et al. Although theoreticians have identified the conditions and evolutionary processes under which sympatric speciation may be possible, empirical support of divergence that initiated and proceeded in sympatry has been limited to studies of monophyletic, geographically isolated ‘island’ populations, such as found in small crater lakes or on small remote oceanic islands, where other historical biogeographical scenarios can be effectively ruled out (see Bolnick and Fitzpatrick, 2007 for a review). Sympatric speciation was long assumed to be a rare, if not impossible, phenomenon.
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