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

Vallejo-Trujillo, Adriana; Kebede, Adebabay; Lozano-Jaramillo, Maria; Dessie, Tadelle; Smith, Jacqueline; Hanotte, Olivier; Gheyas, Almas A.

doi:10.3389/fevo.2022.866587

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

Vallejo-Trujillo, Adriana; Kebede, Adebabay; Lozano-Jaramillo, Maria; Dessie, Tadelle; Smith, Jacqueline; Hanotte, Olivier; Gheyas, Almas A.

Authors

Adriana Vallejo-Trujillo

Adebabay Kebede

Maria Lozano-Jaramillo

Tadelle Dessie

Jacqueline Smith

OLIVIER HANOTTE OLIVIER.HANOTTE@NOTTINGHAM.AC.UK
Director of Frozen Ark Project & Professor of Genetics & Conservation

Almas A. Gheyas

Abstract

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

Citation

Vallejo-Trujillo, A., Kebede, A., Lozano-Jaramillo, M., Dessie, T., Smith, J., Hanotte, O., & Gheyas, A. A. (2022). Ecological niche modelling for delineating livestock ecotypes and exploring environmental genomic adaptation: The example of Ethiopian village chicken. Frontiers in Ecology and Evolution, 10, Article 866587. https://doi.org/10.3389/fevo.2022.866587

Journal Article Type	Article
Acceptance Date	Jul 15, 2022
Online Publication Date	Aug 4, 2022
Publication Date	Aug 4, 2022
Deposit Date	Feb 4, 2023
Publicly Available Date	Feb 10, 2023
Journal	Frontiers in Ecology and Evolution
Electronic ISSN	2296-701X
Publisher	Frontiers Media
Peer Reviewed	Peer Reviewed
Volume	10
Article Number	866587
DOI	https://doi.org/10.3389/fevo.2022.866587
Keywords	Ecology and Evolution, environmental adaptation, ecological niche modelling, Ethiopian village chicken, redundancy analysis, selection signature analysis
Public URL	https://nottingham-repository.worktribe.com/output/10358353
Publisher URL	https://www.frontiersin.org/articles/10.3389/fevo.2022.866587/full
Additional Information	Copyright © 2022 Vallejo-Trujillo, Kebede, Lozano-Jaramillo, Dessie, Smith, Hanotte and Gheyas. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.