The global population structure of the swordfish (Xiphias gladius L.) was examined by analyzing the DNA sequence variation contained within the hypervariable left domain of the mitochondrial control region of 247 individuals. A total of 330 base pairs (bp) of sequence from 112 individuals collected in the Pacific (n = 26), the Atlantic (n = 47) and the Mediterranean (n = 39) revealed a total of 69 haplotypes. Extremely high values of haplotypic diversity characterized all samples and all haplotypes occurred at low frequencies. The topology of a neighbor-joining tree was used to establish phylogenetic relationships among the mtDNA lineages. The genotypes could be assigned to 2 highly divergent clades, namely clade I and clade II (net nucleotide difference 3.9%). Furthermore, clade I could be divided into 2 groups designated alpha and beta. The presence of phylogenetically informative differences in the DNA sequence allowed the design of a Restriction Fragment Length Polymorphism (RFLP) assay which could discriminate members of the 3 subgroups. Using this phylogenetically based RFLP assay, an additional 135 individuals from the Atlantic and the Mediterranean were classified as members of the alpha, beta or theta (clade II) subgroups. The inter-oceanic heterogeneity of swordfish haplotype frequencies was tested on the combined data sets using both Monte Carlo distributions of chi-square values and G-tests. The results indicated that haplotype frequencies in the samples from the Pacific Ocean, the North Atlantic Ocean, the South Atlantic Ocean and the Mediterranean Sea were significantly different. Comparisons of haplotype frequencies between samples from the East and the West North Atlantic corroborate previous studies which indicated that extensive mixing has taken place between these regions and is consistent with a hypothesis of no difference. However, this aspect of the analysis is limited by both small sample sizes and the possibility of populations mixing on the feeding grounds.
