Many marine species undertake long migrations to enhance their fitness by moving from optimal reproductive areas to different foraging grounds, which involves utilizing various habitats that are often widely separated geographically. Furthermore, highly migratory species can also be philopatric, implying that they return to their natal region to breed, despite their migratory behavior. Thus, individuals from the same breeding areas can migrate to different foraging sites, and individuals from genetically different breeding areas can feed in the same sites without mixing (Carreras et al., 2011). The combination of migration and philopatry in marine species can produce mixed feeding aggregates and link widely separated environments, while maintaining overall strong population structuring due to philopatry. Consequently, understanding spatio-temporal movements and connectivity between distant habitats and populations is crucial for migratory and philopatric marine species management and conservation, such as marine turtles (Rees et al., 2017).

Marine turtles have a complex life cycle that involves ontogenetic habitat shifts through large migration events (Bolten, 2003), but with a general plasticity of habitat use (Casale et al., 2018). During the first months of life, sea turtle hatchlings have limited swimming capacity, and are assumed to drift passively heading out into the open ocean (Casale and Mariani, 2014). Eventually, oceanographic fronts and major currents are thought to be the primary drivers of their migration towards the foraging grounds at this first life stage (Casale and Mariani, 2014; Spotila, 2004). Sea turtles feed on pelagic preys in the first period of their lives, and as they grow in size, their swimming ability improves (Revelles et al., 2007). These ontogenic shifts can also imply a change in diet depending on the species, such as the loggerhead turtle (Caretta caretta) feeding on benthic prey or the green turtle (Chelonia mydas) on seagrasses and algae (Bjorndal, 1997). The switch between these two phases is not fixed, as some individuals may remain pelagic (Eder et al., 2012), while in other cases it can be reversible since juveniles recruited to neritic foraging grounds might return to the oceanic environment on shorter scales for reasons not yet completely understood (Saied et al., 2012). Despite the swimming capability improvement with size, juvenile and adult sea turtle distribution seems to be also influenced by oceanography (Carreras et al., 2006). To explain these observations, some authors (Hays et al., 2010; Gaspar et al., 2012) proposed the Learned Migration Goal (LMG) theory, suggesting that grown individuals may use the same foraging areas used as hatchlings when their movements were restricted by the prevailing currents, instead of exploring new areas using their improved swimming skills. Although this theory is widely accepted considering adult and juvenile distributions, it has never been statistically tested.

The complexity of marine turtle life cycles and their long migrations increases their vulnerability to anthropogenic threats. The Mediterranean Sea is a biodiversity hotspot (Coll et al., 2010), and hosts nesting populations of two of the seven sea turtle species in the world: the loggerhead turtle Caretta caretta and the green turtle Chelonia mydas (Casale et al., 2018). After a generalized decline in the past century, the Mediterranean loggerhead turtle populations have increased in the past decade (Casale et al., 2018) and have been declared of least concern, but conservation dependent, by the International Union for Conservation of Nature in their last revision (IUCN, 2025). On the contrary, the green turtle population is still considered endangered (IUCN, 2025), even though recent studies suggest that some populations are now increasing (Stokes et al., 2015). Incidental bycatch by fishing activity is still the main threat for both species (Casale et al., 2018; Wallace et al., 2025). The largest sea turtle nesting areas occur in the eastern Mediterranean, although in recent years, due to global warming, sporadic nesting events have been found westwards for both species (Luna-Ortiz et al., 2024; Marín-Capuz et al., 2025). Loggerhead turtles, the most abundant sea turtle in the Mediterranean, reproduce mainly in Greece, Türkiye, Cyprus, and Libya (Casale et al., 2018), while green turtles primarily nest in the east: Türkiye, Cyprus, and the Levant shoreline to eastern North Africa (Egypt). Furthermore, the Mediterranean Sea also hosts foraging grounds for both species, the whole Mediterranean basin for the loggerhead sea turtle, and the eastern Mediterranean for the green sea turtle (Casale et al., 2018).

Considering that sea turtles are species of conservation concern, it is essential to establish connections between all these foraging grounds and putative nesting areas of origin to link threats at sea with the affected populations. During the last years, several genetic studies have assessed the origin of loggerhead and green sea turtles foraging in multiple Mediterranean areas (Figure 1, Clusa et al., 2013, Clusa et al., 2014; Garofalo et al., 2009; Karaman et al., 2022; Rees et al., 2017; Saied et al., 2012; Tikochinski et al., 2012; Turkozan et al., 2018; Yilmaz et al., 2011). However, connectivity analyses are particularly sensitive to gaps in knowledge, as missing key populations or foraging areas may lead to undiagnosed population sinks to otherwise protected stocks (Carreras et al., 2013). In this context, the Aegean Sea in the eastern Mediterranean has not been addressed and remains a significant knowledge gap (Figure 1) despite hosting relevant foraging grounds for both species. In particular, Kuşadası Bay is an important foraging aggregation site of loggerhead and green turtles. Therefore, it is crucial to investigate the origins of turtles foraging in this area for a complete regional assessment. Since bycatch of individuals at their foraging grounds is one of the most significant anthropogenic threats for sea turtles, fine-scale information on the contribution from the different nesting areas to the principal foraging grounds and the assessment of sea turtle’s migratory foraging routes at regional scale is essential for an effective management and conservation of these two species in the Mediterranean Sea.

There are a wide variety of methodologies to assess connectivity and population structure among reproductive areas and developmental and foraging areas for marine species, such as mark and recapture techniques, stable isotope analysis (SIA) (Cardona et al., 2024), satellite telemetry, and genetics (Rees et al., 2017). Genetic tools have been demonstrated to be effective in inferring connectivity in migrating marine animals (Clusa et al., 2014; Clusa et al., 2018), providing information of the relative contribution of each breeding area to specific foraging grounds, which can be assessed through mixed-stock analysis (MSA; (Grant et al., 1980). Selecting the appropriate genetic marker is crucial when planning an MSA project (Karl et al., 2012). Population genetic studies with marine turtles in the last two decades have used short (380 bp) or long (800 bp) fragments of the control region D-loop of the mitochondrial DNA (mtDNA) sequences, a non-coding region of the mtDNA expected to evolve neutrally (Moritz et al., 1987). The haplotypes of the long fragments of the control region provided better genetic resolution for the loggerhead turtles (Yilmaz et al., 2011; Carreras et al., 2006; Clusa et al., 2013) than for Mediterranean green turtles, since 97% of the Mediterranean green turtles have the same CM-A13 haplotype (Bagda et al., 2012). Subsequently, Tikochinski et al., 2012 sequenced four consecutive mitochondrial short tandem repeats (mtSTR) at the 3’ end of the control region and subdivided the CM-A13 haplotype into 33 variants, revealing high polymorphism. This new haplotyping system for Chelonia mydas turtles involves AT-rich mtDNA STRs that are polymorphic enough to provide a much better resolution in mixed-stock analysis (Karaman et al., 2022; Tikochinski et al., 2018). In this study, we genetically characterize the foraging area of Kuşadası Bay for a better understanding of the migratory pathways for Caretta caretta and Chelonia mydas in the Mediterranean Sea. To do so, we sequenced 92 samples from C. caretta and C. mydas from Kuşadası Bay, with the long D-loop and STR sequences, respectively, which allowed us to infer the nesting populations of origin using MSA. We then combined our results with the available information on other nesting grounds and foraging areas to perform a regional assessment of migratory routes in the Mediterranean Sea. In addition, we compared the origin assignment based on genetic tools with the one inferred from particle dispersal model simulations to unveil the extent of the Learned Migration Goal theory in both species. Our results highlight the importance of compiling region-wide datasets of both nesting and foraging areas to have a comprehensive understanding of global patterns of connectivity in highly migratory and philopatric species.

Connecting foraging grounds with nesting areas is essential for conserving highly migratory marine organisms, such as sea turtles, since hazards in foraging aggregations can impact distant nesting populations. This work provides crucial information about the habitat use of loggerhead and green sea turtles by analyzing Kuşadası Bay in the Aegean Sea, a key foraging ground for both species in the eastern Mediterranean. Furthermore, we integrated this novel genetic data into all previously studied foraging aggregations and nesting sites to create a Mediterranean habitat usage map for both species. Additionally, we compared genetic results in adult and juvenile foraging grounds with particle dispersal studies to infer migratory trends when choosing foraging grounds in relation to the Learned Migration Goal theory. The Aegean Sea, and particularly Kuşadası Bay, has been an important gap of knowledge for both species to date. Our results indicate that Kuşadası Bay is used as foraging area by juveniles and subadults, with very few adult individuals for green turtles, while it is mainly inhabited by subadults and adults for loggerhead turtles. We observed seasonality as both species were more abundant in spring, followed by summer for green and autumn for loggerhead turtles (Figure 2). The greater abundance observed during warmer periods may be linked to heightened maritime traffic and intensified fishing activities, which may increase the sightings of turtles and the number of stranded individuals. However, this seasonal pattern could also reflect variations in the availability of food resources and thus an increase of the number of turtles arriving to the area. Whether the observed seasonality is real, or an artifact of the human activity should be evaluated in the future using census methods not related to this activity, such as the use of aerial surveys (Gómez de Segura et al., 2006).

The genetic analysis of individuals feeding in Kuşadası Bay revealed that this is an aggregation of turtles from several distant locations, highlighting its importance as foraging ground within the Mediterranean for both species. However, the highest contribution corresponds to Turkish nesting populations, (such as Sugözü and Davultepe) in green turtles or West Türkiye in loggerhead turtles (Figure 4). This result is not surprising for the green turtles, as this foraging area is located in the westernmost edge of this species distribution within the Mediterranean along the Turkish coast. However, nesting populations of the loggerhead turtles exist along the Greek coast, including Crete, that could potentially have a significant contribution to Kuşadası Bay. Multiple elements could explain the differential contribution of nesting areas to the foraging grounds, including population size of the putative nesting beaches of origin, proximity to the foraging ground, or the pattern of surface currents (Clusa et al., 2014). In this case, sea currents might explain the prevalence of Türkiye nesting turtles in the Aegean Sea for both species, as hatchling movements are mainly driven by the currents because, even with some swimming activity, they cannot swim against them, considering that the potential to swim against currents in sea turtles is related to size (Revelles et al., 2007). The northwestern vein flows along the Turkish slope most of the year, and the prevailing northerly summer winds cause the main surface current to penetrate the Aegean (Millot and Taupier-Letage, 2004), allowing hatchlings to flow towards this area (Figure 1B).

Adding Kuşadası Bay results to previous studies allowed us to obtain a regional assessment of the Mediterranean migration routes to foraging grounds for the two species. This is particularly relevant for the green turtle, due general lack of knowledge on nesting population genetic structure and foraging grounds composition until very recently. The almost nil polymorphism of the D-loop control region within the Mediterranean (Bagda et al., 2012) limited the potential to detect population differentiation, and thus to perform MSA. The development of primers to amplify the mitochondrial STRs of the D-loop (Tikochinski et al., 2012) indicated a deep structuring within the Mediterranean, but only one foraging area has been analyzed to date (Karaman et al., 2022; Tikochinski et al., 2018). Our study is the first to test the potential heterogeneity of different green turtle foraging areas within the Mediterranean. Globally, the Turkish nesting areas are the major contributing locations to the two studied foraging grounds, with 74.99% of Turkish-originated individuals in Kuşadası Bay and 85.49% in Israel, and a reduced presence of individuals from Israel or Cyprus. This result is consistent with several lines of evidence. Firstly, the currents system, inferred by particle dispersal, already predicted a high proportion of turtles from these two areas coming from Türkiye (Casale and Mariani, 2014). Satellite telemetry studies on turtles from Cyprus suggested that the majority of the individuals from Cypriot populations migrate to the African shores, from Egypt to Libya (Bradshaw et al., 2017; Stokes et al., 2015), with a small proportion of tracks passing in front of Israel without stopping to feed there, and no track reaching the Aegean Sea. Finally, Türkiye concentrates more than 80% of the Mediterranean nesting population, and consequently, it is expected to have a higher overall contribution. Besides the general high contribution from Türkiye, the fine scale analysis revealed, for the first time, a clear heterogeneity across different green turtles foraging areas. Thus, Kuşadası Bay would be visited mainly by turtles from the populations of Sugözü and Davultepe, while Israel would be visited by turtles from the easternmost Turkish populations, such as Samandağ, which is consistent with this population being the closest to Israel along the coast. Future studies should focus on foraging grounds discovered by satellite telemetry and isotope stable analysis, but not yet genotyped for STRs, such as Egypt or Libya foraging areas (Bradshaw et al., 2017; Stokes et al., 2015), in order to complete the regional migration assessment for the species.

For the loggerhead turtle up to eleven foraging areas were previously studied in the Mediterranean (Clusa et al., 2014; Rees et al., 2017; Turkozan et al., 2018), the Aegean Sea being a notable omission, despite its importance, as this area is located between the Turkish and Greek nesting areas. Our study revealed that in Kuşadası Bay, most of the turtles originated from Turkish beaches, consistent with hatchling movements inferred by particle dispersal analysis (Casale and Mariani, 2014). By combining all data, clear origin differences arise between individuals foraging in the eastern and western Mediterranean basins, as already indicated in previous studies. Turtles of Atlantic origin are found mainly in the western Mediterranean foraging grounds, the Algerian Basin, the Catalano-Balearic Sea, and the Tyrrhenian Sea (Figure 4D; Clusa et al., 2014). This distribution can be explained by a permanent eastward flow of Atlantic water entering through the Gibraltar Straits, generated by a negative water balance of the Mediterranean Sea (Figure 4; Millot and Taupier-Letage, 2004). Once in the Mediterranean, the Atlantic current splits in two branches, one flowing eastwards along the coast of Libya to the southern Levantine Sea, drifting hatchlings to this area, and the other leading Atlantic-origin hatchlings to the Tyrrhenian Sea, Algerian Basin, and the Catalano-Balearic Sea (Figure 1B; Clusa et al., 2014; Millot and Taupier-Letage, 2004). Apart from the Atlantic contribution, the three foraging grounds of the western Mediterranean show clear differences in the contribution from the Mediterranean nesting sites. The Tyrrhenian Sea has a clear contribution from Calabrian nesting turtles, likely due to its proximity, its small population size (only 15 nests per year on average (Casale and Mariani, 2014)), and the influence of the Sicily Channel westward current flow, which may direct hatchlings from Calabria beaches almost exclusively into the Tyrrhenian Sea (Figure 1; Millot and Taupier-Letage, 2004). This Sicily current could also explain the high percentage of Misrata turtles in the Algerian Basin, the Catalano-Balearic, and the Tyrrhenian Sea foraging grounds, allowing hatchlings to drift towards the western foraging areas following the European coast Millot and Taupier-Letage, 2004). The eddies (i. e. circular movements of water) in the central Mediterranean are probably responsible for the high abundance of Misrata and Sirte (Libya) nesting turtles in the Ionian Sea foraging ground. These results are consistent with previous tagging and satellite-tracking studies identifying the Ionian Sea as the main foraging ground for adult loggerhead turtles nesting in Libya (Hochscheid et al., 2012).

The foraging areas of the Adriatic Sea, Amvrakikos Gulf, and Drini Bay are mainly used by turtles from western Greece (Figure 4D), probably due to its proximity, but also because of the current patterns in this zone. This result is consistent with stable isotope (Cardona et al., 2014; Haywood et al., 2020) and telemetry data from the Greek nesting sites (Zbinden et al., 2011) highlighting the importance of these foraging areas for these nesting populations. The principal surface circulation in Greece enters the Adriatic Sea and drifts hatchlings nested in western Greece into the northern Ionian and the Adriatic Sea (Figure 1). These are the most productive habitats of the western Mediterranean Sea. Therefore, access to the Adriatic Sea by turtles from western Greece is likely to promote their fitness and may explain why females nesting there are larger and lay more eggs than females foraging elsewhere in the Mediterranean Sea (Cardona et al., 2014). However, turtles from other origins can also be found in the Adriatic Sea, including Crete and Cyprus, mainly in Drini Bay or different Turkish populations along the Adriatic. To support these alternative origins, satellite tracking of individuals departing Amvrakikos foraging area indicated that a small portion of the turtles using this area could originate in the nesting populations in Türkiye (Rees et al., 2017).

The composition of the easternmost Mediterranean foraging grounds is highly variable. Although the global contribution of Turkish nesting beaches is predominant, fine-scale analysis shows differential roles from the distinct Turkish nesting populations in the eastern foraging areas, which can produce differences among foraging grounds even at relatively small scales (Turkozan et al., 2018). The eastern Mediterranean is characterized by a complex pattern of ocean circulation, including the South-to-North surface currents (Hecht et al., 1988) and the western circulation of eddies at the surface in that area (Figure 1B; Millot and Taupier-Letage, 2004). Consequently, turtles from a certain origin could be directed towards certain foraging areas, while avoiding others. As an example, from all the foraging areas analyzed in the eastern part of the Mediterranean, turtles from Cyprus are detected almost exclusively in the nearby western Turkey foraging area, in agreement with telemetry data that suggests a limited and localized use of Turkish foraging areas (Snape et al., 2016), although turtles from this nesting area are known to mainly use foraging areas along the eastern and African coasts of the Mediterranean (Haywood et al., 2020). In addition, Israel’s nesting area contribution is limited to the Southern Levantine Sea foraging area (Figure 4D). As in the case of Calabria, this small localized presence could be explained by its lower nesting activity (only 57 nests per year on average (Casale and Mariani, 2014)), its proximity to this foraging area, and the presence of mesoscale anticyclonic eddies all year in the southern Levantine Sea (Figure 4; Millot and Taupier-Letage, 2004). Finally, most loggerhead turtles hatching in Lebanon forage in the Southern Levantine Sea, probably due to the anticyclonic eddies leading to the eastern Mediterranean (Figure 4; Millot and Taupier-Letage, 2004). Yet, some individuals follow the northern Middle East slope to forage on Türkiye’s coast and Kuşadası Bay in the Aegean Sea (Figure 4D).

Globally, our results showed a high heterogeneity in the composition of the different foraging grounds in the Mediterranean for both species, that are consistent with the major current patterns and uneven nesting population sizes. However, our analyses detected significant differences between the observed composition, as inferred using genetic analyses, and the expected composition if turtles followed the trajectories dictated by currents as hatchlings, considering particle simulations (Casale and Mariani, 2014). Previous studies comparing genetics with particle simulations and Lagrangian drifters concluded that sea turtles in the Mediterranean showed a pattern of passive drift from nesting to foraging areas (Cardona and Hays, 2018), in agreement with the Learned Migration Goal theory, which postulates that grown individuals tend to use the same foraging areas used as hatchlings (Hays et al., 2010; Gaspar et al., 2012). Hence, in addition to passive juvenile migrations, our results indicate that other factors may influence how individuals recruit to foraging grounds as adults. For example, magnetic orientation plays a significant role in sea turtle movements. Hatchlings can detect the intensity and inclination of the magnetic field, and eventually, develop a large-scale coordinate magnetic map to use in long-distance migrations that result in directed hatchling movements that can be tested empirically (Lohmann and Lohmann, 1996). The fact that hatchlings can develop a magnetic map and swim accordingly may have two potential implications. On one side, hatchlings can contribute with some active swimming while migrating, which can slightly modify their trajectories even with their limited swimming capability due to their small sizes (Revelles et al., 2007). On the second hand, turtles could potentially remember the sites visited, while constrained by the current system as hatchlings, but swim actively to select the optimal sites visited when maturing. Several authors have indicated that adults nesting in the same area may have very different foraging strategies and destinations (e.g. Ceriani et al., 2012; Eder et al., 2012; Mansfield et al., 2009; Zbinden et al., 2011). These differences may arise from individual differences in the knowledge of the heterogeneity of habitats, resulting in differences in key fitness parameters, such as the reproductive output, even within populations (Cardona et al., 2014). Consequently, a combination of passive drifting (following the Learned Migration Goal Theory) and active swimming is the most likely explanation of the observed composition of sea turtle foraging grounds in the Mediterranean.

In summary, the present study has revealed the previously unknown composition of the Mediterranean loggerhead and green sea turtles foraging in the Aegean Sea using genetics. By integrating all the available information from foraging grounds, we have also delineated the regional migratory routes from breeding to foraging grounds in the Mediterranean, highlighting the importance of complete datasets to perform global analyses comprising vast sampling areas. By incorporating particle modelling data, we have assessed the role of passive drifting in sea turtle distribution. This study represents the most complete overview of sea turtle distribution within the Mediterranean to date, and thus of paramount importance to include connectivity in management and conservation plans for both species.