Ecological niche modelling for delineating livestock ecotypes and exploring environmental genomic adaptation: The example of Ethiopian village chicken

In evolutionary ecology, an “ecotype” is a population that genetically adapted to specific environmental conditions. Environmental and genetic characterisation of livestock ecotypes can play crucial role in conservation breeding improvement, particularly achieve climate resilience. However, are often arbitrarily defined without detailed their agro-ecologies. this study, we employ novel integrated approach, combining ecological niche modelling (ENM) with genomics, delineate based on habitats unravel the signatures adaptive selection ecotype genomes. The method was applied 25 Ethiopian village chicken populations representing diverse agro-climatic ENM identified six key drivers adaptation delineated 12 ecotypes. Within-ecotype signature analyses (using Hp iHS methods) 1,056 candidate sweep regions (SRs) associated biological processes. While most SRs ecotype-specific, pathways perturbed by overlapping genes largely shared among A few were amongst involved showed functions important for scavenging chickens, e.g., neuronal development/processes, immune response, vision development, learning. Genotype-environment association using redundancy analysis (RDA) allowed correlating ∼33% major drivers. Inspection some strong from RDA highly relevant relation corresponding This approach offers powerful tool gain insight into complex processes evolution including genotype × environment (G E) interactions.