Ecological Genomics

Benefit description

Ecological genomics integrates genomics and ecology to understand how genetic variation influences the way organisms interact with and adapt to their environment. It uses genome-scale information to study the ecological and evolutionary processes occurring in natural populations. This service provides: i) Ecological genomics techniques for the monitoring, characterization, and assessment of the status of marine and coastal ecosystems. These methodologies enable accurate estimation of biodiversity, taxonomic identification of species, early detection of exotic and invasive species, as well as monitoring of biological communities and assessment of ecological changes associated with environmental pressures or human activities. ii) Genomic techniques applied to the conservation and sustainable management of fisheries resources. These tools allow the delineation of fish stocks, inference of population connectivity and structure, identification of management and conservation units, and estimation of effective population size, abundance, and other demographic parameters of interest. The service integrates technologies based on environmental DNA (eDNA), DNA barcoding, metabarcoding, quantitative PCR (qPCR), genetic kinship approaches such as Close-Kin Mark-Recapture (CKMR), and other high-resolution next-generation sequencing methods, including RADseq. These tools provide rapid, sensitive, and non-invasive solutions for environmental monitoring programs, biodiversity conservation, protected area assessment, and marine resource management. Our capabilities cover the entire workflow, from experimental design and sampling strategy to final interpretation of results. The process begins with the extraction and quality assessment of DNA, RNA, or environmental DNA, followed by the preparation of application-specific sequencing libraries. These libraries are generated through controlled fragmentation of genetic material, incorporation of molecular adapters, and subsequent amplification and purification, ensuring maximum data quality and reproducibility. Samples are subsequently analyzed using high-throughput sequencing platforms capable of generating millions of reads, enabling highly accurate characterization of genetic diversity, biological community composition, population structure, and genomic variation in target species. Depending on the objectives of the study, tailored protocols are applied for population genomics, metabarcoding, transcriptomics, targeted amplicon sequencing, or genetic marker discovery. The service also includes comprehensive processing of sequencing data, from initial quality control to the generation of biologically meaningful results. This is achieved through standardized and reproducible bioinformatics workflows that include sequence filtering and curation, taxonomic assignment, genetic diversity analyses, kinship and connectivity studies, population structure inference, phylogenetic analyses, genetic variant detection, and functional characterization of genes and metabolic pathways. Finally, we provide specialized scientific and technical consultancy for the interpretation of results and their application to research programs, environmental monitoring, conservation initiatives, and fisheries management. This integrated approach, combining laboratory procedures, high-throughput sequencing, and advanced bioinformatics analyses, transforms large genomic datasets into actionable knowledge that supports decision-making and contributes to biodiversity conservation and the sustainable use of marine ecosystems and resources.