The last piece of the puzzle: a broad population genomics study in Globicephala macrorhynchus

The short-finned pilot whale (SFPW), Globicephala macrorhynchus, has a pan-tropical and -temperate distribution. The existence of two morphologically and genetically distinct forms (Naisa and Shiho) suggests a complex speciation process, which remains to be deciphered. Here, we used whole genome data of 56 individuals from three poorly surveyed regions (Macaronesian islands - Eastern central Atlantic, China and Brazil) to assess the patterns of population structure and genetic diversity of the SFPW. We inferred population structure from admixture and principal component analyses. Additionally, we determined patterns of differentiation of the maternally-inherited mitogenomes. We estimated changes in population size through time using the Pairwise Sequentially Markovian Coalescent (PSMC) analysis. Finally, we searched for genomic regions of high differentiation in each assigned population using the population branch statistics and performed a windows-based analysis to uncover the top outliers of genetic differentiation, corresponding to regions that are potentially under selection. Our results provide evidence for three main genetic clusters of SPFW populations across the analysed individuals, emphasizing the genomic distinctiveness of Atlantic individuals compared with other individuals belonging to the Naisa form – known to be present in the western/central Pacific and Indian Oceans. The exception to this pattern is a Naisa mitochondrial and nuclear genotype found in one individual from Brazil. Moreover, PSMC suggests a shared recent evolutionary history in all three assigned populations. Our study provides a significant contribution to the overall understanding of the demographic history and spatial patterns of genetic diversity in SPFW, by complementing data previously described