Decoding ancient genomes: Genomics approaches and innovative species recognition pipeline for diadromous fish

Abstract

International audienceUnderstanding the evolution of wild species is crucial for developing effective population management strategies and predicting their future trajectories. In my doctoral research, we opted for genomics approaches to explore the demographic history of two iconic diadromous fishes: Anguilla anguilla (European eel) and Salmo salar (Atlantic salmon). We aim to elucidate their adaptive responses to environmental changes. Setting this project apart is the sequencing and genotyping of both archaeological (aDNA) and modern DNAs samples. Our study encompasses archaeological samples from various locations across Europe, spanning a temporal range of 17,000 years – from the Paleolithic to the modern era. To accurately assign species to each sample, we developed DeFiS (Detect Fish Species), a pipeline relying on reference genomes and samples to analyze k-mers: fixed-size nucleotide sub-strings. The list of k-mers and their occurrences from specific dictionaries for both reference genomes and samples. By comparing the dictionaries of the samples with those of the references, we could assign each sample to a specific species. We are currently validating the pipeline using freely available modern samples of all European diadromous fish species found in public databases (NCBI, Essembl, and scientific paper). The aim is to provide a valuable resource for biological scientists. Our method offers a significant advancement in the species identification process for aDNA research. By accelerating and refining this crucial step we aim to contribute to future aDNA-based investigations by facilitating the work of biologists studying wild species evolutions