Revealing Temporal and Spatial Patterns of Genetic Diversity in Human-harvested Molluscs through High-throughput Sequencing Ancient and Contemporary DNA

Species may respond to climate change and human disturbances by either altering their distribution or adjusting themselves in situ. Comparing ancient and contemporary DNA may detect spatial and temporal changes in genetic diversity and assess their impact on the long-term survival of a species. Yet, concrete examples of adaptative spatial and
temporal genetic modifications remain sparse, especially in invertebrates. Here we propose to compare the ancient and contemporary DNA of two human-harvested molluscs (the veined rapa whelk Rapana venosa and the blood cockle Tegillarca granosa) widely distributed along the coasts of China using high-throughput sequencing. Using ~8,000-year-old subfossil shells collected from Jingtoushan, Zhejiang Province, we will streamline a workflow of extracting ancient DNA (aDNA) from the shells, conduct genome-wide targeted capture genes from the aDNA, and analysing the data for DNA
yield and damage patterns. We will also collect contemporary specimens of the two species across their distribution range along the coasts of China, extract DNA from their tissues, and conduct genome-wide targeted capture. When both the ancient and modern DNA sequences are available, we will conduct demographic analysis and calculate population statistics including effective population size, nucleotide diversity, heterozygosity, and inbreeding coefficient, determine intra- and inter-population genetic differentiation between the ancient and contemporary populations, and among the
contemporary populations. We will also quantify the gene flow, hybridization, and introgression among the populations. Furthermore, we will compile climate data from a public database, determine the relative predictive power of various climatic variables to explain the population genetic structure and determine whether climate change and/or human exploitation over the last ~8,000 years has been responsible for the genetic changes. Our study will be one of the first population genomic studies based on DNA extracted from subfossil shells and contemporary tissues and thus will contribute to the streamlining methods applicable to other ecologically and commercially important molluscs. Conducting this study and similar studies on molluscs will reshape our understanding of the genetic adaptations of this large group of invertebrates to climate change and human activities, contributing towards conserving their genetic resources. Our study contributes to ensuring “genetic diversity of wild and domesticated species is safeguarded” – one of the key objectives of the United Nations Decade of Ocean Science for Sustainable Development (2021–2030).