Periodic Reporting for period 1 - SeaTGen (Conservation genomics of endangered green sea turtles)
Período documentado: 2021-04-22 hasta 2023-04-21
The Southwest Indian Ocean (SWIO) is known as a biodiversity hotspot. It has diverse marine ecosystems, including coral reefs, rocky shores, and mangroves. These habitats are home to diverse marine life, including five species of marine turtles. The green turtle (Chelonia mydas) plays a vital role in these habitats by maintaining the ecological balance in these environments. However, conservation and management of marine turtle populations is challenging because they face many threats, including direct harvesting and bycatch in fisheries, habitat degradation, pollution, and the effects of climate change. In addition, their mainly aquatic life history and the large distances they travel make them difficult to study. The SeaTGen project aims to improve our understanding of the spatial structure and genetic makeup of green turtles in the SWIO. We do this using the turtles' DNA to 1) understand how turtle populations are related and 2) to trace marine turtles in the ocean back to their nesting origins. The information gathered through this project can help us to link turtles to their population origins more accurately, which is crucial for developing conservation efforts that target the specific needs of each turtle population. Furthermore, this data can be used to identify and establish efficient conservation units, such as Regional Management Units.
The SeaTGen project aims to update and improve the genetic resolution of green turtles in the SWIO. Working with various partners, we have collected and analysed genetic samples from multiple populations of green turtles. Using the portable Oxford nanopore MinION for sequencing entire mitochondrial genomes, we can map the genetic diversity and structure of these turtles at a higher resolution than before. This helps shed light on complex patterns of connectivity and migration.
In the initial phase of the project, we focused on developing and testing primers to amplify the entire mitochondrial genome into smaller, overlapping fragments. This led to the identification of four fragments, ranging from 2.5 to 5 kilobases in size, that when put together, amplify the entire mitochondrial genome. These fragments were then sequenced using the MinION. Early findings from significant nesting sites like the Chagos archipelago and Seychelles have shown that whole mitochondrial genomes offer much higher resolution than traditional methods like the control region (also known as the d-loop). This increased resolution is crucial for understanding how marine turtles are genetically linked to their places of origin.
We are currently analysing all the mitochondrial genomes we have sequenced with the aim of providing a more detailed understanding of the population structure across the SWIO. This will create a better tool that can be used to accurately trace turtles in foraging areas or those captured in fisheries back to their original populations. We are preparing a comprehensive scientific publication manuscript that will present these findings.
The SeaTGen project faced initial challenges due to the global pandemic, mainly impacting sample collection and constraining some of the planned data production. We also faced sample quality issues with older samples, which provided additional challenges. During this period, we conducted an extensive regional meta-analysis of all available genetic data for foraging and nesting green turtles across the Indian and Pacific Oceans. This dataset includes data from over 150 green turtle nesting and foraging locations and provides a first-of-its-kind comprehensive overview of the regional connectivity of green turtle nesting and foraging habitats and is currently being prepared for publication. Furthermore, these data form an important base layer in the recent update of Regional Management Units (RMU) in the final stages of publication.
In the initial phase of the project, we focused on developing and testing primers to amplify the entire mitochondrial genome into smaller, overlapping fragments. This led to the identification of four fragments, ranging from 2.5 to 5 kilobases in size, that when put together, amplify the entire mitochondrial genome. These fragments were then sequenced using the MinION. Early findings from significant nesting sites like the Chagos archipelago and Seychelles have shown that whole mitochondrial genomes offer much higher resolution than traditional methods like the control region (also known as the d-loop). This increased resolution is crucial for understanding how marine turtles are genetically linked to their places of origin.
We are currently analysing all the mitochondrial genomes we have sequenced with the aim of providing a more detailed understanding of the population structure across the SWIO. This will create a better tool that can be used to accurately trace turtles in foraging areas or those captured in fisheries back to their original populations. We are preparing a comprehensive scientific publication manuscript that will present these findings.
The SeaTGen project faced initial challenges due to the global pandemic, mainly impacting sample collection and constraining some of the planned data production. We also faced sample quality issues with older samples, which provided additional challenges. During this period, we conducted an extensive regional meta-analysis of all available genetic data for foraging and nesting green turtles across the Indian and Pacific Oceans. This dataset includes data from over 150 green turtle nesting and foraging locations and provides a first-of-its-kind comprehensive overview of the regional connectivity of green turtle nesting and foraging habitats and is currently being prepared for publication. Furthermore, these data form an important base layer in the recent update of Regional Management Units (RMU) in the final stages of publication.
The SeaTGen project is the first project to use the Oxford nanopore MinION for whole mitochondrial genome sequencing of marine turtles. This portable technology is transformative as it makes advanced genetic research accessible in regions without extensive laboratory setups. Our methodology is promising as it provides a detailed and comprehensive view of the genetic structure and connectivity among green turtle populations that surpass the capabilities of traditional methods. As the SeaTGen project concludes, we expect to uncover more fine-scale details about the genetic makeup of green turtle populations across the SWIO. Our ongoing analysis of mitochondrial genomes will provide a clearer understanding of regional population structures. This will allow us to more precisely track turtles back to their original populations, whether in foraging areas or those caught in fisheries bycatch.