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The commercially important Atlantic bluefin tuna (Thunnus thynnus), a large migratory fish, has experienced notable recovery aided by accurate resource assessment and effective fisheries management efforts. Traditionally, this species has been perceived as consisting of eastern and western populations, spawning respectively in the Mediterranean Sea and the Gulf of Mexico, with mixing occurring throughout the Atlantic. However, recent studies have challenged this assumption by revealing weak genetic differentiation and identifying a previously unknown spawning ground in the Slope Sea used by Atlantic bluefin tuna of uncertain origin. To further understand the current and past population structure and connectivity of Atlantic bluefin tuna, we have assembled a unique dataset including thousands of genome‐wide single‐nucleotide polymorphisms (SNPs) from 500 larvae, young of the year and spawning adult samples covering the three spawning grounds and including individuals of other Thunnus species. Our analyses support two weakly differentiated but demographically connected ancestral populations that interbreed in the Slope Sea. Moreover, we also identified signatures of introgression from albacore (Thunnus alalunga) into the Atlantic bluefin tuna genome, exhibiting varied frequencies across spawning areas, indicating strong gene flow from the Mediterranean Sea towards the Slope Sea. We hypothesize that the observed genetic differentiation may be attributed to increased gene flow caused by a recent intensification of westward migration by the eastern population, which could have implications for the genetic diversity and conservation of western populations. Future conservation efforts should consider these findings to address potential genetic homogenization in the species. [ABSTRACT FROM AUTHOR]

The genetic diversity of the Mediterranean swordfish (Xiphias gladius Linneus) has not been explored extensively at its easternmost range so far. In this study, modern X. gladius samples from the eastern part of the Mediterranean basin, north of the Aegean Sea (Aegean‐2013, n = 26) and the Mediterranean coast of Turkey (N.Levantine‐2013, n = 42) were studied genetically, along with ancient samples from Yenikapı excavation (n = 6). Partial mitochondrial DNA control region sequences (entire sequences, clade I and clade II) were evaluated spatially and temporally together with previously published sequences (Alvarado Bremer et al., Molecular Phylogenetics and Evolution, 2005, 36, 169–187; Viñas et al., ICES Journal of Marine Science, 2010, 67, 1222–1229; Righi et al., Diversity, 2020, 12, 170) from the rest of the Mediterranean Sea. Pair‐wise FST and pair‐wise AMOVA tests showed that, in general, groups of eastern populations and western Mediterranean populations have not genetically differed from each other significantly nearly in the past 20 years. Therefore, the results direct reconsideration of previous descriptions of population sub‐structure within the Mediterranean and support high gene flow throughout the region. On the contrary, the results of this study confirmed the existence of genetic diversity differences between western and eastern Mediterranean, with eastern being low. One‐tailed permutation tests revealed that θ, which is directly proportional to long‐term female effective population size (Ne), decreased significantly (P < 0.05) in both regions over the past two decades. On the Turkish coasts, θ is not significantly different from that of the nearly contemporary eastern Mediterranean population. Nonetheless, θ of the ancient sample was consistently and significantly (P < 0.001) higher than those of the eastern and western Mediterranean populations in clade I and clade II. Furthermore, it contains two mitochondrial haplotypes that are not observed in modern samples, suggesting that the Ne of X. gladius in the eastern was high in Byzantium times. Eight microsatellite loci were also genotyped in modern samples. The microsatellite‐based present Ne estimate of the pooled Aegean‐2013 and N.Levantine‐2013 populations was lower than 1000 according to the upper limit of 95% c.i. and possibly even lower than 100 according to the mean of posterior distribution of the present Ne estimate calculated by the software package MSVAR. These alarming genetic signals for the sustainability of X. gladius on the coasts of Turkey are in agreement with the nearly collapsing X. gladius fisheries as depicted also in the fisheries statistics. Overall, congruent with the previous studies, the data presented here show that sustainability of the X. gladius population in Mediterranean is under major threat. Therefore, X. gladius around the Turkish coasts need an immediate stringent action and management plan. [ABSTRACT FROM AUTHOR]