Critically endangered hawksbill turtles nest in Singapore, and they preserve coral reef ecosystems with its dietary niche on sponges that compete with corals for space. However, rising sea levels and global warming are threatening turtle populations by reducing nesting habitats and hatchling success rates. Population genetic studies contribute to conservation strategies and reveal their population history in response to environmental changes. Previous genetic studies of hawksbill populations used limited data including maternal lineages using mitochondrial DNA (mtDNA), which cannot fully represent the genetic diversity in populations. We produced the first de novo genome assembly of the hawksbill turtle and population genome sequencing datasets to examine the genetic diversity of the population nesting in Singapore. We collected dead hatchlings and eggs from hawksbill nests on Singapore beaches from 2018 to 2022. DNA was extracted from whole eggs and liver tissues of hatchlings. We sequenced 69 samples by Sanger sequencing for the mitochondrial (mt) DNA control region and 40 samples using Illumina HiSeq X for whole genomes. Our results revealed five mtDNA haplotypes, and three are endemic to Singapore while, most haplotypes are identical. Using whole genome sequencing datasets, we estimated the degree of genetic diversity and homogeneity within the population. The analysis shows a small genetic diversity with close relationships between individuals, indicating inbreeding within the population. Furthermore, the inferred effective population size using multiple sequentially Markovian coalescence (MSMC) shows a sharp decline of population, coinciding with the last deglaciation period, suggesting the impact of past climate change on sea turtles. This study highlights the vulnerability of endangered populations and emphasizes the importance of population genomics studies for the conservation of endangered wildlife.
Inbred hawksbill turtle nesting population in Singapore