Population genomics of marine turtles in Singapore and the mycobiome of their nests

Abstract

Marine turtles, comprising of seven globally threatened species, are increasingly imperilled by human activities and climate change. Addressing these threats requires a comprehensive understanding of their genetic diversity, population dynamics, and ecological health. However, our current knowledge is fragmented, constrained by limited genomic resources, and insufficient population-level studies. My research bridges these gaps through an integrative approach on the marine turtle populations in Singapore, focusing on four key areas: 1. Population Genetics: The analysis of mitochondrial DNA (mtDNA) control region revealed six hawksbill and three green turtle haplotypes in Singapore, including one green and three hawksbill haplotypes that are novel. The findings also illustrated the close genetic relationships within the hawksbill and green turtle populations in Singapore and in Southeast Asia, contributing valuable insights into regional population connectivity. 2. Genomics: I developed a de novo genome assembly of the hawksbill turtle using PromethION and Illumina HiseqX technologies. This assembly was compared with other published marine turtle genomes through comparative genomic analysis. This reference genome assembly serves to overcome the limitations of previous studies that relied on short DNA regions like mtDNA control regions and microsatellites. It serves as a foundation for a comprehensive population genomic approach to better understand the population’s genetic diversity and evolutionary history the subsequent study. 3. Population Genomics: Whole genome analysis of 35 hawksbill individuals from Singapore revealed low genetic diversity and high inbreeding, with most individuals identified as first-degree relatives. A multiple-paternity nest with closely related parents was also discovered. Demographic history analysis suggests that climate change has driven a population decline in hawksbill turtles. Furthermore, positive selection in genes associated with environmental sensing, environmental response, and natal behaviour highlights the critical link between turtle survival and climate adaptation. 4. Metagenomics: Focusing on the nesting environment’s microbiome, particularly on the mycobiome, revealed Fusarium fungal pathogens in over half of the samples. These pathogens, identified through both Sanger sequencing of cultured isolates and amplicon metabarcoding, are associated with sea turtle egg fusariosis (STEF) disease, which compromised embryo development and contributed to the mortality of hawksbill turtle eggs. This research offers an in-depth understanding of the genetic diversity, demographic history, and ecological challenges faced by hawksbill turtles in Singapore. By integrating population genetics, genomics, population genomics and metagenomics, my work highlights the population’s susceptibility to climate change and human activities, such as land reclamation at nesting sites. These findings underscore the critical importance of using whole genome data and microbiome studies to inform conservation strategies, providing valuable insights for global marine turtle conservation efforts.