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Without genetic variation, species cannot cope with changing environments, and evolution does not proceed. In endangered species, adaptive potential may be eroded by decreased population sizes and processes that further reduce gene flow such as philopatry and local adaptations. Here, we focused on the philopatric and endangered loggerhead sea turtle (Caretta caretta) nesting in Cape Verde as a model system to investigate the link between adaptive potential and philopatry. We produced a dataset of three complementary genomic regions to investigate female philopatric behaviour (mitochondrial DNA), male-mediated gene flow (microsatellites) and adaptive potential (major histocompatibility complex, MHC). Results revealed genetically distinct nesting colonies, indicating remarkably small-scale philopatric behaviour of females. Furthermore, these colonies also harboured local pools of MHC alleles, especially at the margins of the population's distribution, which are therefore important reserves of additional diversity for the population. Meanwhile, directional male-mediated gene flow from the margins of distribution sustains the adaptive potential for the entire rookery. We therefore present the first evidence for a positive association between philopatry and locally adapted genomic regions. Contrary to expectation, we propose that philopatry conserves a high adaptive potential at the margins of a distribution, while asymmetric gene flow maintains genetic connectivity with the rest of the population.

Sea turtles can be considered a sentinel species for monitoring the health of marine ecosystems, acting, at the same time, as a carrier of microorganisms. Indeed, sea turtles can acquire the microbiota from their reproductive sites and feeding, contributing to the diffusion of antibiotic-resistant strains to uncontaminated environments. This study aims to unveil the presence of antibiotic-resistant bacteria in (i) loggerhead sea turtles stranded along the coast of Sicily (Mediterranean Sea), (ii) unhatched and/or hatched eggs, (iii) sand from the turtles’ nest and (iv) seawater. Forty-four bacterial strains were isolated and identified by conventional biochemical tests and 16S rDNA sequencing. The Gram-negative Aeromonas and Vibrio species were mainly found in sea turtles and seawater samples, respectively. Conversely, the Gram-positive Bacillus, Streptococcus, and Staphylococcus strains were mostly isolated from eggs and sand. The antimicrobial resistance profile of the isolates revealed that these strains were resistant to cefazolin (95.5%), streptomycin (43.2%), colistin and amoxicillin/clavulanic acid (34.1%). Moreover, metagenome analysis unveiled the presence of both antibiotic and heavy metal resistance genes, as well as the mobile element class 1 integron at an alarming percentage rate. Our results suggest that Caretta caretta could be considered a carrier of antibiotic-resistant genes.

Linking foraging and breeding habitats is key to the understanding of behaviour, ecology and demography of migratory species. Establishing such connections has long been hampered by the logistical problems of following individuals between foraging and breeding areas, especially in the marine realm. We used variation in nitrogen stable isotope patterns between 2 foraging regions of loggerhead sea turtlesCaretta carettadetermined from samples of satellite-tracked individuals to assign untracked turtles to a foraging region. We sought to enhance determination of the relative importance of geographically separated foraging regions and to investigate the relationship between fitness correlates and inferred migratory strategies. Of 18 turtles followed by satellite tracking from Zakynthos (Greece), 10 moved north to foraging areas in the Adriatic Sea and the Gulf of Amvrakikos and 8 moved south to foraging areas off the coast of North Africa. Of 51 untracked individuals sampled for stable isotope analysis, we considered the stable isotope signature of 47 to qualify for assignment to foraging areas in the north (n = 22) and south (n = 25). Females foraging north were significantly larger (curved carapace length), and the former group laid larger clutches (even after correction for body length) than turtles foraging south, a fact that can be interpreted as a carry-over effect. Combining satellite tracking with stable isotope signatures in marine turtles opens new perspectives into how forensic tracking methodologies may be used to scale up knowledge from electronic tracking of a limited number of individuals to sample sizes that are more meaningful from a population perspective.

Highly migratory marine species can travel long distances and across entire ocean basins to reach foraging and breeding grounds, yet gaps persist in our knowledge of oceanic dispersal and habitat use. This is especially true for sea turtles, whose complex life history and lengthy pelagic stage present unique conservation challenges. Few studies have explored how these young at-sea turtles navigate their environment, but advancements in satellite technology and numerical models have shown that active and passive movements are used in relation to open ocean features. Here, we provide the first study, to the best of our knowledge, to simultaneously combine a high-resolution physical forcing ocean circulation model with long-term multi-year tracking data of young, trans-oceanic North Pacific loggerhead sea turtles during their ‘lost years’ at sea. From 2010 to 2014, we compare simulated trajectories of passive transport with empirical data of 1–3 year old turtles released off Japan (29.7–37.5 straight carapace length cm). After several years, the at-sea distribution of simulated current-driven trajectories significantly differed from that of the observed turtle tracks. These results underscore current theories on active dispersal by young oceanic-stage sea turtles and give further weight to hypotheses of juvenile foraging strategies for this species. Such information can also provide critical geographical information for spatially explicit conservation approaches to this endangered population.

The northern Adriatic Sea is an important foraging ground for the loggerhead sea turtle Caretta caretta (Linnaeus, 1758) within the Mediterranean Sea. Here, stranding patterns of loggerhead sea turtles were examined over a four-year period (2019–2022) along a short (17 km) stretch of the Italian coast south of the Po River delta. A total of 355 records (alive, n = 24; dead, n = 331) were analysed, and the curved carapace lengths (CCL, notch to tip, cm) mainly reflected large juveniles and sub-adults (average CCL = 57.2 cm; 95% CI = 55.6–58.7). The month of July was identified as the critical month with the highest number of strandings, mirroring migratory processes towards this area during warmer months. The number of stranded turtles•km−1 as well as the absolute number of strandings along the short stretch of the coast might suggest this area as the most impacted in the Mediterranean Sea. This research emphasizes that human activities in the waters south of the Po River delta, particularly trawl fishing, are the primary cause of loggerhead sea turtle strandings and that tracking stranding patterns can offer valuable information about the geographic ranges, seasonal movements, and life cycles of this species.

We present a genome assembly of Caretta caretta (the Loggerhead sea turtle; Chordata, Testudines, Cheloniidae), generated from genomic data from two unrelated females. The genome sequence is 2.13 gigabases in size. The assembly has a busco completion score of 96.1% and N50 of 130.95 Mb. The majority of the assembly is scaffolded into 28 chromosomal representations with a remaining 2% of the assembly being excluded from these.

The Loggerhead sea turtle (Caretta caretta) is a marine reptile belonging to a monophyletic group of chelonians. As these animals are long-lived, they have the ability to accumulate pollutants. To collect epidemiological data on toxic metals in marine Loggerhead sea turtles. Forty Loggerhead sea turtles comprising 25 males and 15 females stranded freshly dead between 2013 and 2018 along the coasts of Sicily, Southern Italy, were examined for arsenic, cadmium, and lead accumulation in muscle and adipose tissues by means of a validated ICP-MS method. A modified K index as a growth condition factor, namely Fulton's K index, was used. Samples were tested in duplicate. A Wilcoxon rank sum test was carried out to evaluate metal contents differences between muscle and adipose tissues and between genders. The Fulton's K index suggested a good body condition of the C. caretta recovered with mean values of 5.34 ± 3.40 (n = 40; ±SD). Detectable concentrations of lead were found in 70% of the samples analysed with mean values of 0.65 ± 1.67 mg/kg wet weight and 0.51 ± 1.29 mg/kg wet weight in muscle and adipose tissues, respectively. No significant differences in arsenic, cadmium, and lead were detected between genders. In addition, no significant correlation was found between modified K index and concentrations of arsenic, cadmium, and lead. Findings on muscle and adipose tissues suggest chronic exposure of Caretta caretta to high concentrations of especially lead which might negatively affect health and welfare of these marine turtles although body condition was good.

The loggerhead sea turtle (Caretta caretta) is a cosmopolitan sea turtle species and is listed by IUCN as Vulnerable globally. The Southwest Atlantic is an important regional management unit of C. caretta worldwide due to the distinctive mitochondrial DNA (mtDNA) lineage promoted by recent radiation within the Atlantic-Mediterranean region. However, due to the low resolution of mtDNA, the population structure of C. caretta SWA has not been well understood in the previous studies using only mtDNA. Our study encloses data from literature and a long-term genetic survey (1999 to 2021) distributed through four great nesting areas for the Southwest Atlantic to assess the genetic diversity and the population structure of the C. caretta, using both mtDNA and 15 microsatellite loci. The results demonstrate that the genetic diversity indexes of the Southwest Atlantic C. caretta reflect distinct compositions at a population level due to variation at an individual level. The SSRs results identified well-established and significant spatial population structure between nesting areas. Unique genetic patterns were identified for those females from studied areas of the Southwest Atlantic, and it may be related to their philopatric behavior and high relatedness. Thus, this study deeply evaluated the molecular ecology of Southwest Atlantic C. caretta and provides, for the first time, a fine-scale and long-term resolution of the genetic diversity and population structure due to the use of microsatellite data that must be considered for further studies.

One of the largest nesting colonies of the Vulnerable loggerhead sea turtle Caretta caretta is in Cabo Verde. Here we present the first comprehensive study of loggerhead turtle nesting on the island of Maio in Cabo Verde. During 2016–2019 we monitored 38 km of undeveloped sandy beaches that have minimal artificial lighting and where all nesting on Maio takes place. We counted 4,063 nests in 2016, 5,429 in 2017, 14,364 in 2018 and 7,937 in 2019. The estimated total number of females was 1,016, 1,357, 3,591 and 1,984 in each of these years, respectively. Our findings suggest there are more loggerhead turtles nesting in Cabo Verde than previously estimated, and that this could be the species’ largest nesting subpopulation (followed by Florida, USA and Oman). The inter-annual hatching success (the proportion of eggs producing hatchlings) was 29–38% for the whole island but varied between sites. Our study of 250 clutches showed that flooding affected 38–61% and predation by crabs 40–42%, with hatching success on different beaches in the range of 1–59%. Poaching of eggs was rare (< 2% of clutches), but dogs predated 68.4% of all clutches on the beach nearest the largest human settlement. We evaluated different nest management strategies at multiple sites and estimated productivity of hatchlings (the number of hatchlings that would reach the sea for each management strategy), finding that hatcheries are not always the best option for nest management. As the beaches on Maio are relatively undisturbed, and there is a high abundance and density of turtle nests, the island should be protected as a globally important site for the conservation of the loggerhead turtle, and of coastal biodiversity more broadly.

In migratory marine species, demographic estimates are often generated from capture-mark-recapture (CMR) studies conducted at terrestrial breeding sites. However, when logistical difficulties limit the geographic area of these surveys, demographic estimates are vulnerable to biases. We compared demographic rates generated from CMR data of nesting loggerhead turtles (Caretta caretta) collected between 2010 and 2017 at one focal site (Wassaw Island, Georgia, USA; 31.89° N, 80.97° W) with estimates generated from the same group of turtles but including all other nesting events from adjacent sites in Georgia, South Carolina, and North Carolina. We found that estimates of annual recruitment at the focal site were overestimated: each year, 29–45% putative first-time nesters at the focal beach had, in fact, nested on a different beach in a previous season. Estimates of clutch frequency and breeding frequency generated at the focal site were biased low and skewed towards values of one, while estimates for remigration interval were not significantly over- or underestimated. Additionally, estimates of annual and total population productivity in terms of clutches, eggs, and hatchlings were underestimated by more than half at the focal site. Our results show how weak fidelity to a focal nesting/tagging site can affect demographic estimates in marine turtle populations and highlight the need to reconsider estimates from other populations that might be vulnerable to similar biases.