Global phylogeography of ridley sea turtles (Lepidochelys spp.): evolution, demography, connectivity, and conservation

Genomic insights into marine environment adaptation and conservation of the threatened olive ridley turtle (Lepidochelys olivacea)

Sea turtles are marine flagship species and most of them are currently in a threatened state. Long-term surviving in the ocean has driven significant morphological and physiological changes for this group, which makes them an ideal model for studying adaptive evolution of marine environments. Herein, we present a chromosome-scale genome of Lepidochelys olivacea with a genome size of 2.22 Gb and a contig N50 of 97.3 Mb. Comparative genomic analyses uncovered a suite of adaptive changes in genes related to olfaction, vision, virus defense, and longevity, which may help explain the genetic underpinnings of its marine environment adaptation. We also observed that the genome-wide heterozygosity of L. olivacea was low (6.45e-4), consistent with its prolonged population decline. Overall, our study provides valuable genetic resources for understanding evolutionary adaptations to aquatic environment and for the conservation of this threatened species.

Taking advantage of reference-guided assembly in a slowly-evolving lineage: Application to Testudo graeca

BACKGROUND

Obtaining de novo chromosome-level genome assemblies greatly enhances conservation and evolutionary biology studies. For many research teams, long-read sequencing technologies (that produce highly contiguous assemblies) remain unaffordable or unpractical. For the groups that display high synteny conservation, these limitations can be overcome by a reference-guided assembly using a close relative genome. Among chelonians, tortoises (Testudinidae) are considered one of the most endangered taxa, which calls for more genomic resources. Here we make the most of high synteny conservation in chelonians to produce the first chromosome-level genome assembly of the genus Testudo with one of the most iconic tortoise species in the Mediterranean basin: Testudo graeca.

RESULTS

We used high-quality, paired-end Illumina sequences to build a reference-guided assembly with the chromosome-level reference of Gopherus evgoodei. We reconstructed a 2.29 Gb haploid genome with a scaffold N50 of 107.598 Mb and 5.37% gaps. We sequenced 25,998 protein-coding genes, and identified 41.2% of the assembly as repeats. Demographic history reconstruction based on the genome revealed two events (population decline and recovery) that were consistent with previously suggested phylogeographic patterns for the species. This outlines the value of such reference-guided assemblies for phylogeographic studies.

CONCLUSIONS

Our results highlight the value of using close relatives to produce de novo draft assemblies in species where such resources are unavailable. Our annotated genome of T. graeca paves the way to delve deeper into the species' evolutionary history and provides a valuable resource to enhance direct conservation efforts on their threatened populations.

Unusual Patterns of Lateral Scutes in Two Olive Ridley Turtles and Their Genetic Assignment to the Thai Andaman Sea Populations of Lepidochelys olivacea Eschscholtz, 1829

Two stranded Lepidochelys-like sea turtles were rescued from the Thai Andaman Sea coastline by veterinarians of the Phuket Marine Biological Center (PMBC), one in May of 2019 and another in July of 2021. They were first identified as olive ridley turtles (Lepidochelys olivacea), as the external appearance of both turtles was closer to that species than the other four species found in the Thai Andaman Sea. In fact, when carefully examined, an unusual pattern of the lateral scutes on each turtle was observed, specifically symmetric 5/5 and asymmetric 5/6, both of which are considered rare for L. olivacea and had never been reported in the Thai Andaman Sea. In contrast, this characteristic was more common for the closely related species, Kemp's ridley (L. kempii), although this species is not distributed in the Indo-Pacific Ocean. Thus, we further investigated their genetic information to confirm species identification using two molecular markers, namely the mtDNA control region and nDNA RAG2. The results from the mtDNA control region sequences using the Basic Local Alignment Search Tool (BLAST) indicated that both individuals exhibited a higher percent identity with L. olivacea (99.81-100.00%) rather than L. kempii (94.29-95.41%) or any other species. A phylogenetic tree confirmed that these two turtles belonged to the L. olivacea clade. Moreover, the results of RAG2 also supported the mtDNA result, as both individuals shared the same RAG2 haplotype with L. olivacea. Thus, we have concluded that the two turtles with unusual lateral scute patterns exhibited genetic consistency with their original species, L. olivacea, which has brought attention to the importance of exploring rare phenotypes in sea turtle populations residing in Thai Seas.

Dynamic shoreline alterations and their impacts on Olive Ridley Turtle (Lepidochelys olivacea) nesting sites in Gahirmatha Marine Wildlife Sanctuary, Odisha (India)

Currently, sea turtle habitats are being altered by climate change and human activities, with habitat loss posing an urgent threat to Indian sea turtles. Thus, the objective of this study is to analyze the dynamic shoreline alterations and their impacts on Olive Ridley Sea Turtle (ORT) nesting sites in Gahirmatha Marine Wildlife Sanctuary from 1990 to 2022. Landsat satellite images served as input datasets to assess dynamic shoreline changes. This study assessed shoreline alterations and their rates across 929 transects divided into four zones using the Digital Shoreline Analysis System (DSAS) software. The results revealed a significant 14-km northward shift in the nesting site due to substantial coastal erosion, threatening the turtles' Arribada. This study underscores the need for conservation efforts to preserve nesting environments amidst changing coastal landscapes, offering novel insights into the interaction between coastal processes and marine turtle nesting behaviors.

Nesting Ecology of Lepidochelys olivacea in Lobito, Angola

The scarcity on the Atlantic coast of the African sea turtle population and its dynamics data is well known. This article discusses the nesting ecology methods and analysis of a nascent Angolan project aimed at preserving the nesting female population of the Olive Ridley turtle (Lepidochelys olivacea) on the coast of Lobito. This study examines the nesting ecology of this species from 2020 to 2023. Females had an average CCL of 70.2 cm and CCW of 68.5 cm. These females laid 127 eggs in nests that averaged 47.0 cm deep. The ex situ nest incubation period averaged 60 days, and the hatchling success was 82.1%. Some techniques used in this project require modifications and enhancements. The utilization of photo identification did not yield the anticipated outcomes, prompting the adoption of passive integrated transponders (PITs) in the last season. However, due to limited funding, the success of this method is contingent upon an augmented field effort, allowing for the recapture of a larger number of females. The continuity of this project hinges upon collaboration between higher authorities and the local community. Together, it is possible to deepen the understanding of the nesting ecology of this species and address pivotal issues for its conservation, thereby implementing the most effective preservation measures.

Genetic Evidence for Indo-Western Pacific Olive Ridley Sea Turtles in Mexican Waters

The olive ridley sea turtle is predominantly an epipelagic species with no apparent migration corridors. Research in feeding areas in other sea turtle species has identified aggregations of individuals from diverse backgrounds; however, no specific feeding areas have been identified for the olive ridley. We used mtDNA control region sequencing to identify the haplotype composition of 85 olive ridley turtles (adult and immature turtles from both sexes) captured and released in Central Mexican Pacific waters. Amplified fragments of the control region (751 bp) revealed the presence of 17 haplotypes (h = 0.5877 ± 0.0622 and π = 0.001698 ± 0.001185), and 16 of them were phylogenetically grouped within the lineage of the Eastern Pacific, but the haplotype Lo37 showed close evolutionary relationships with the lineage of the East Coast of India. Lagrangian drifter data showed that West–East transport from the Indo-Pacific to the tropical Eastern Pacific might be possible through passive drift. These results highlight the importance of more genetic studies offshore and the role of the ocean currents in the migratory behavior of olive ridleys, as well as the need to establish multinational strategies for the conservation and management of the species in international waters.