Filogenômica de Otariidae e história evolutiva de lobos-marinhos da América do Sul

Abstract

The systematics and phylogeny of Otariidae have been extensively studied for over two centuries since the first species descriptions by the European explorers. Yet, several relationships, particularly the monophyly within Arctocephalus, remain unclear. Recent molecular phylogenies only used few concatenated mitochondrial or nuclear genes. Similarly, the relationships within the clade that encompasses the Galapagos (A. galapagoensis), New Zealand (A. forsteri), South American and Peruvian-Chilean fur seals (A. australis subpopulations) are also debated. Although currently recognized as full species, the studies that assessed more than one individual per taxon showed the group paraphyly. In two manuscripts presented in this thesis, we applied a genomic approach to clarify conflicting Otariidae relationships and to shed light on the evolutionary processes of South American, Peruvian-Chilean, Galapagos and New Zealand fur seals. Here, we assessed 15 genomes (12 sequenced by our group and three retrieved from GenBank) and sequenced a reduced representation library composed by 47 individuals of the South American and Peruvian-Chilean fur seals (n= 15/13), Galapagos fur seals (n=10) and New Zealand fur seals (n=9). Our phylogenies showed a high-level of genealogical discordances that we assigned mainly to the incomplete lineage sorting promoted by an explosive adaptive-radiation at ~3Mya in the Plio-Pleistocene transition, potentially induced by the eastern Pacific sea surface cooling. We also found a strong support for the Arctocephalus monophyly, suggesting the maintenance of the current taxonomic nomenclature. Whole-genome and reduced representation libraries analyses showed well-delimited species for the clade encompassing South American, Peruvian-Chilean, Galapagos and New Zealand fur seal. Additionally, Peruvian-Chilean fur seals showing shared genomic components with Galapagos and South American fur seals. Posterior analyses supported that this admixture reflected the hybrid origin of the Peruvian-Chilean fur seals and the ancient evolutionary history of this taxa. We also detected two pure individuals of Galapagos fur seals in Isla Foca, a remote rookery located ~1,000 km from the main distributions of the Peruvian-Chilean and Galapagos fur seals. Besides that, we found a secondary contact of the Peruvian-Chilean with Galapagos fur seals in this locality and in Punta San Juan, southern coast of Peru. These findings highlight that new studies are needed to understand the role of Isla Foca in the population dynamics, distribution and conservation of the Peruvian-Chilean and Galapagos fur seals. The manuscripts presented in this thesis untangled the complex evolutionary history of the fur seals and sea lions by illuminating internal Otariidae relationships and showing the importance of the interspecific gene flow in the biodiversity promotion.