The swordfish (Xiphias gladius) is of special economic importance in the Indian Ocean.
At present, the Indian Ocean Tuna Commission (IOTC) considers the swordfish to be a single
panmictic population in the Indian Ocean. Over the last few years, however, several population
studies have contested this tenet, and through the implementation of different approaches, have
provided conflicting results, including emerging evidence that population structuring exists
within this species. Namely, Muths et al (2013) based their examination on the ND2 region of the
mitochondrial locus and failed to identify multiple distinct populations within the Indian Ocean,
while Grewe et al (2020) applied Single Nucleotide Polymorphic loci (SNPs) to highlight two
subpopulations on either side of the equator. These past studies provided ambiguous results
regarding the structure of this species and consequently, called into question the guidelines for
management to be adopted for the IOTC. In the present study, we have investigated the structure
of the swordfish population in the Indian Ocean using a large number of samples spread over the
Indian Ocean. We used a dataset of 1 990 SNPs loci for 1 694 swordfish from 23 distinct
locations across the Indian Ocean, generating one of the most extensive datasets for the Indian
Ocean swordfish to date. We implemented the Discriminant Analysis of Principal Components
(DAPC) statistical technique, which is advantageous for analyzing overlapping or closely related
groups. Our findings revealed a low genetic differentiation among swordfish in the Indian Ocean,
rather than multiple genetically distinct stocks, further supporting that only one population
should be considered for future stock assessment measures. The analysis shows the impact of
gene under selection on the estimates of genetic differentiations, i.e. a much lower FST value
was found when removing these specific genes.