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 because of strong gene-tree species tree discordance. Divergence times estimates 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 and 2.5 Ma. Otaria diverged first, followed by Phocarctos and then four major lineages within Arctocephalus. However, we found Zalophus to be nonmonophyletic, with California (Zalophus californianus) and Steller sea lions (Eumetopias jubatus) grouping closer than the Galapagos sea lion (Zalophus 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. [Hybridization; ILS; phylogenomics; Pleistocene; Pliocene; monophyly.].Fil: Lopes, Fernando. Pontificia Universidade Católica do Rio Grande do Sul; Brasil. Universidad de Vale do Rio dos Sinos; BrasilFil: Oliveira, Larissa R.. Universidad de Vale do Rio dos Sinos; Brasil. Grupo de Estudos de Mamíferos Aquáticos do Rio Grande do Sul; BrasilFil: Kessler, Amanda. Pontificia Universidade Católica do Rio Grande do Sul; BrasilFil: Beux, Yago. Pontificia Universidade Católica do Rio Grande do Sul; BrasilFil: Crespo, Enrique Alberto. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Centro para el Estudio de Sistemas Marinos; ArgentinaFil: Cárdenas-Alayza, Susana. Universidad Peruana Cayetano Heredia; PerúFil: Majluf, Patricia. Universidad Peruana Cayetano Heredia; PerúFil: Sepúlveda, Maritza. Universidad de Valparaiso; ChileFil: Brownell, Robert L.. National Oceanic and Atmospheric Administration; Estados UnidosFil: Franco-Trecu, Valentina. Universidad de la República; UruguayFil: Páez-Rosas, Diego. Universidad San Francisco de Quito; EcuadorFil: Chaves, Jaime. San Francisco State University; Estados Unidos. Universidad San Francisco de Quito; EcuadorFil: Loch, Carolina. University of Otago; Nueva ZelandaFil: Robertson, Bruce C.. University of Otago; Nueva ZelandaFil: Acevedo-Whitehouse, Karina. Universidad Autonoma de Queretaro.; MéxicoFil: Elorriaga-Verplancken, Fernando R.. Instituto Politecnico Nacional; MéxicoFil: Kirkman, Stephen P.. Oceans and Coasts; SudáfricaFil: Peart, Claire R.. Ludwig Maximilians Universitat; AlemaniaFil: Wolf, Jochen B W. Ludwig Maximilians Universitat; AlemaniaFil: Bonatto, Sandro Luis. Pontificia Universidade Católica do Rio Grande do Sul; Brasi