Phylogenomic discordance in the Eared Seals is best explained by incomplete lineage sorting following explosive radiation in the Southern Hemisphere

The phylogeny and systematics of fur seals and sea lions (Otariidae) have
long been studied with diverse data types, including an increasing amount
of molecular data. However, only a few phylogenetic relationships have
reached acceptance pointing at strong gene-tree species tree discordance.
Divergence times in the group also vary largely between studies. These
uncertainties impeded the understanding of the biogeographical history of
the group, such as when and how trans-equatorial dispersal and subsequent
speciation events occurred. Here we used high-coverage genome-wide
sequencing for 14 of the 15 species of Otariidae to elucidate the
phylogeny of the family and its bearing on the taxonomy and
biogeographical history. Despite extreme topological discordance among
gene trees, we found a fully supported species tree that agrees with the
few well-accepted relationships and establishes monophyly of the genus
Arctocephalus. Our data support a relatively recent trans-hemispheric
dispersal at the base of a southern clade, which rapidly diversified into
six major lineages between 3 to 2.5 Mya. Otaria diverged first, followed
by Phocarctos and then four major lineages within Arctocephalus. However,
we found Zalophus to be non-monophyletic, with California (Z.
californianus) and Steller sea lions (Eumetopias jubatus) grouping closer
than the Galapagos sea lion (Z. wollebaeki) with evidence for
introgression between the two genera. Overall, the high degree of
genealogical discordance was best explained by incomplete lineage sorting
resulting from quasi-simultaneous speciation within the southern clade
with introgresssion playing a subordinate role in explaining the
incongruence among and within prior phylogenetic studies of the family.