ISTS Symposium43 Program/Agenda

In an era of rapidly changing ocean conditions, understanding the evolutionary history and genetic diversity of marine species, such as sea turtles, is crucial for effective conservation strategies. The recent advances in Next-Generation Sequencing (NGS) and availability of reference genomes now allow for deeper investigation of within-species genetic diversity, population structure, and historical changes over time. However, a single genome cannot represent the diversity of a species and structural and sequence polymorphisms across populations may influence conservation strategies in different ways. We performed whole genome sequencing (> 30 Gb output) on 27 individuals of loggerhead sea turtle (Caretta caretta, Linnaeus 1758) from four different Regional Management Units (RMU): North Pacific (Mexico: 2), North-west Atlantic (Mexico: 2; USA: 2), Northeast Atlantic (Cabo Verde: 5) and Mediterranean (Italy: 2; Libya: 5; Greece: 4; Türkiye: 5). We genotyped all samples by mapping their reads against the reference genome (GCA_023653815.1) to produce a set of more than 10 million nuclear single-nucleotide polymorphisms (SNPs) across the individuals, with the number of SNPs per chromosome highly correlated to chromosome size. We conducted a multidimensional scaling analysis, which revealed that all individuals clustered according to their RMU. The genetic distances, measured by Fst values (a metric that quantifies population genetic), confirmed this pattern, showing a high differentiation for the Pacific RMU, while the two Atlantic RMUs appeared less distinct from each other. In our pairwise Fst comparisons across chromosomes, we identified extreme values in certain genomic regions. Notably, we found that the Mediterranean RMUs exhibits common significant high differentiation in several chromosomal regions compared with the two North Atlantic RMUs, suggesting that these regions could be candidates for local adaptation.  This differentiation may be influenced by distinct environmental factors or other selective pressures unique to the Mediterranean and Atlantic regions. We also analyzed Runs of Homozygosity (ROHs), genomic regions where identical haplotypes are inherited from each parent, to assess the level of inbreeding across populations, as inbreeding can generally increase the presence of rare deleterious variants in homozygous form. Our analysis of ROHs showed that the degree of inbreeding was uneven across RMUs. The individuals from the Mediterranean had genomes with longer ROHs and a higher portion of the genome in homozygosity, indicating higher inbreeding. Moreover, the ROHs distribution across the 28 chromosomes was not uniform, as macrochromosomes (chromosomes 1 to 11) had a higher proportion of their content in homozygosis than microchromosomes. Overall, using multiple genomes from different RMUs alongside the reference genome provides a robust framework to uncover the genetic basis of key traits and population differentiation in loggerhead sea turtles. Our findings on inbreeding and ROH distribution emphasize the importance of preserving genetic diversity to enhance population resilience. Whole-genome data provide valuable insights that guide conservation strategies aimed at preserving the genetic integrity and adaptive potential of sea turtles in response to multiple pressures.

The persistence of threatened species relies on successful reproduction, which is dependent on energy acquisition, constrained by access to suitable temperatures and sufficient resources. Leatherback turtles are highly migratory, vulnerable to numerous anthropogenic threats, and subject to dynamic environmental conditions throughout their life history. Leatherback energy acquisition in the wild is poorly understood, as existing knowledge is primarily derived from research on captive individuals. Physiological data derived from captive rearing can be applied to understand energy acquisition in the wild using Dynamic Energy Budget (DEB) theory. Here we apply DEB theory within a mechanistic modeling approach to demonstrate how temperature and food availability impact leatherback growth and reproductive potential – factors essential to population longevity. As hatchlings migrate from nesting beaches through oceanic habitats, their migratory movements may align with optimal temperature and food conditions, maximizing early life growth. We used the Sea Turtle Active Movement Model (STAMM) developed by Mercator Ocean International, to simulate the movements and migrations of individual turtles from emergence to adulthood, recording daily food and temperature conditions along their migratory routes. Here we present the first integration of DEB and STAMM models for East Pacific leatherbacks, revealing that nesting beach origin can result in variations in food and temperature conditions, which influence early life growth rates. These early differences persist into adulthood, with some individuals more likely to encounter sufficient food resources to reproduce earlier in life. In accordance with a recent IUCN-facilitated workshop that highlighted the need for more knowledge to support ex-situ conservation efforts, we hope that these findings offer actionable insights for conservation, with the potential to inform targeted release strategies to enhance early growth and ultimately contribute to the persistence of leatherback populations.

Global warming threatens biodiversity worldwide, with populations forced to either adapt or shift distribution, or otherwise face extinction. Poikilothermic species and those with temperature-dependent sex determination (TSD) are particularly vulnerable due to their direct link with environmental temperature. Sea turtles exemplify this risk, as increasing temperatures can lead to the over production of females at birth. Although the resulting female-biased sex ratios can contribute to population expansion in the short to medium term, they may represent an early warning sign of future population collapse and extinction. In this study, we focused on the rapidly growing loggerhead sea turtle (Caretta caretta) population nesting on Sal Island, in the Cabo Verde Archipelago. To understand the complex link between population dynamics and the environment, we used a multifaceted approach that combines (i) 15 years of monitoring of the reproductive population, (ii) movement tracking to identify key habitat use, (iii) remote sensing to determine the key oceanic variables of those habitats, and (iv) drone surveys to determine adult sex ratios at the breeding site. Our findings suggest that rising incubation temperatures in the past have driven the recent population growth observed in Cabo Verde. This stems from increasing temperatures that have shifted sex ratio, which we confirmed by our drone surveys on the breeding grounds. Neither sea surface temperature, nor chlorophyll-a (used as a proxy for feeding ecology), correlated with population growth. Mechanistic simulations further confirmed that temperature-driven sex ratio shifts can influence population trend in the observed extent in loggerheads from Cabo Verde, hence revealing a strong link between population dynamics and local thermal regime. Building on these findings, we tested our predictions across 27 global loggerhead populations and found that lower latitude populations may face greater risk from global warming and sex ratio shift due to the rapid increase in temperature and reduced fluctuations. This study underscores the urgent need for effective conservation strategies to mitigate the impact of global warming on global sea turtle populations. Our work provides crucial insights into the complex interplay between climate change and population dynamics, offering a foundation for targeted conservation efforts.

Sea turtle populations are especially vulnerable to climate change due to the nest environment inducing hatchling sex via temperature-dependent sex determination (warm female-cool male). The rapid increase of global temperatures risk producing extremely female-biased hatchling sex ratios, potentially leading populations to extinction. The lack of exact quantification of primary sex ratios highlights the need to assess hatchling sex ratios broadly on nesting beaches. Currently, there are only two reliable methods of identifying hatchling sex: gonadal histology and laparoscopic examination of the gonads. The former requires sacrificing hatchlings, which is counterproductive to enhancing hatchling production, and the latter requires specialized surgical skills and aquaculture facilities as hatchlings need to be reared for several months prior to laparoscopy. The need for a non-lethal method to identify sex in hatchlings has led researchers to look for biomarkers in tissues obtained via minimally invasive methods. Because blood transports hundreds of signaling molecules and is nucleated in reptiles, it is an ideal target to search for diverse sex-specific biomarkers. Although sea turtles lack sex chromosomes, the incubation temperature induces sex-specific genetic cascades that determine the fate of the bipotential gonad. Thus, distinctive gene expression patterns occur in the gonads at specific embryonic stages. This dimorphic pattern likely is regulated, in part, by DNA methylation. Until now, it was unknown if sex-specific DNA methylation and gene expression patterns were also present in hatchlings and in non-gonadal tissue. Here, we used a multi-omics approach to examine red blood cells (RBCs) for sex-specific markers at DNA methylation and transcriptional levels in male and female loggerhead (Caretta caretta) hatchlings. Hatchlings were incubated at a male producing temperature (27°C), a mixed sex ratio temperature (30°C), and a female producing temperature (32°C), with sex verified through laparoscopy. Our genome-wide discovery studies identified sex-specific differential methylation at over 700 genomic loci and 11 differentially expressed genes, revealing a set of molecular biomarkers for hatchling sex identification. Next steps are to validate the top sex-specific biomarkers in in situ (natural nest) samples of known sex. Once validated, these biomarkers may be used to develop minimally invasive methods for identifying hatchling sex. Such techniques will enhance our ability to measure sex ratios across nesting beaches worldwide, a crucial step in assessing and mitigating the impacts of climate change on sea turtle populations threatened with extinction. Ultimately, the application of the novel technique will provide the opportunity to make informed management decisions based in science.

This study was conducted to determine population structure and genetic origin of green turtles in nearshore waters of Qeshm Island, Iran. Despite its extreme climate, the Persian Gulf host substantial sea turtle populations, which are unique due to their ability to survive in the hot, climate-challenged environment. Along the sandy and muddy shores of Qeshm Island fishers set arrow-head fish traps, locally known as moshta. We collected green turtles (Chelonia mydas) from these moshta during 2016, 2017 and 2018 to investigate population structure and genetic origin. Curved carapace length was measured, and sex and age class were determined via laparoscopy. Tissue samples for genetic analysis were sequenced to identify unique mtDNA haplotypes of each turtle. An ~800 bp fragment of the mtDNA control region (d-loop) was amplified using primers LCM15382 and H950. PCR samples were sent to the Cardiogenetic Center in Iran (https://rhc.ac.ir) for clean-up and sequencing in both forward and reverse directions. Haplotypes were identified by running a search against the ShellBank haplotype database or the GenBank database (http://blast.ncbi.nlm.nih.gov/ Blast.cgi). If no matching haplotypes were found, the sequence was identified as unique and given a new haplotype name. A Bayesian approach using the program BAYES was used to estimate the contribution of the baseline rookeries to the Qeshm foraging ground turtles. Uniform (or flat) priors were applied, assuming an equal likelihood for all rookeries to contribute to the foraging aggregation.

We captured 338 green turtles, which were predominantly juvenile (326, or 96.4%) with only ten subadult (3.0%) and two adult turtles (0.6%). The overall sex ratio was 66% Female : 33% Male (2F : 1M). This finding suggests climate is not leading to undue feminisation and that these turtles may be acclimated to the warmer Arabian region temperatures. A subset of 211 turtles were sampled for genetics. Unfortunately, some samples were not identifiable, resulting in 118 turtles for which sex and age class were known, and 93 samples from individuals of unknown sex and age-class. There were no significant differences between male and female stock origin and these were combined for an overall genetic stock determination. The MSA estimated that the majority (96.36% ± 0.048) of all green turtles originated from the Oman nesting stock located just outside of the Persian Gulf, with negligible contributions from Kuwait or Saudi Arabia which lie within the Gulf – a surprising finding given the proximity of these rookeries.

Despite regional climate extremes, this population appears resilient to climate change and is not overtly feminised. This study underscores the critical role of the Oman nesting stock in sustaining the juvenile green turtle population in Qeshm, highlighting the importance of regional conservation efforts, and the protection of sea turtles on Oman's nesting beaches. These data contribute to our understanding of the population structure and connectivity of sea turtles in a particularly data-sparse and yet important (climate-wise) sea turtle habitat in the NW Indian Ocean.

Loggerhead sea turtle (Caretta caretta) nesting activity on the Spanish Mediterranean coast seems to have stabilized, with events recorded yearly since 2014, although still in low numbers. Western Mediterranean countries, with Spain included, can be considered an emerging nesting area for this species nowadays. In Spain, nesting events have been recorded in all regions, but the Valencia region (eastern Spain) stood out in the last two years with 17 nests (9 in 2023 and 8 in 2024) and several unsuccessful events. From 2014 to 2021, only one nest and/or few unsuccessful events per year were detected. In 2022 the Valencian Region recorded the only two nests laid in Spain. Nevertheless, the number of nests and nesting attempts in the latter years suggests an increasing trend and highlights the importance of this region for loggerhead turtle nesting activity, with 33% of the total number of nests recorded in Spain since 2001 and 40% of the nests recorded in the last 2 years. However, although some beaches are beginning to record nests in consecutive years, nesting is still scattered and nest detection is vital for their protection, as many of these events occur on anthropized beaches with multiple threats to nesting females, clutches, and hatchlings. The success of nest detection in the Valencia Region probably lies in the existence of a cetacean and sea turtle stranding network that has been well-established for more than 30 years and covers over 470 km of coastline in the region. This network, coordinated through a hotline by the University of Valencia in collaboration with the regional government, has facilitated effective coordination between universities, public and private institutions, and NGOs. All this has allowed the effective detection of nests, as well as the tagging of 15 nesting turtles with satellite transmitters, and therefore the detection and protection of some of the turtles’ second and third clutches, both in the Valencian Region and in other regions of the Spanish Mediterranean. The various research and conservation projects carried out by the institutions involved in the latter years have also enabled to carry out many conferences and training workshops held for local authorities and other stakeholders. This has contributed to an increase in the number of nests found on beaches, particularly by local authorities, passers-by, and beach cleaning services. The protection of nests in this region has resulted in the release of more than 1,000 hatchlings into the sea or into a head-starting program for subsequent release one year after hatching. Furthermore, the protection of these nests has enabled the organization of volunteer camps (with almost 1700 volunteers involved) to disseminate information on the conservation of this species to beach visitors and tourists. This has had a significant impact on raising awareness of the nesting activity of loggerhead turtles on these coasts.