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

Adriana  Vallejo Trujillo; Adebabay  Kabede; Maria Lozano-Jaramillo; Tadelle Dessie; Jacqueline Smith; Olivier Hanotte; Almas Gheyas

doi:10.3389/fevo.2022.866587

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

Adriana Vallejo Trujillo
, Adebabay Kabede
, Maria Lozano-Jaramillo
, Tadelle Dessie
, Jacqueline Smith
, Olivier Hanotte
, Almas Gheyas

Research output: Contribution to journal › Article › peer-review

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 ecotypeField Code Changed
Field Code Changed
Field Code Changed
Ecological genomics of livestock ecotypes 2
This is a provisional file, not the final typeset article 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 x environment (GxE) interactions.

Original language	English
Article number	866587
Pages (from-to)	1-21
Number of pages	21
Journal	Frontiers in Ecology and Evolution
Volume	10
Early online date	4 Aug 2022
DOIs	https://doi.org/10.3389/fevo.2022.866587
Publication status	Published - 4 Aug 2022

Keywords / Materials (for Non-textual outputs)

environmental adaptation
Ecological Niche Modelling
Ethiopian village chicken
Redundancy Analysis
selection signature analysis

Access to Document

10.3389/fevo.2022.866587Licence: Creative Commons: Attribution (CC-BY)

fevo-10-866587 (1)Final published version, 3.86 MBLicence: Creative Commons: Attribution (CC-BY)

CTLGH: A global shared data biological sample resource to support productivity improvement for tropical livestock
Freeman, P. (Principal Investigator), Bronsvoort, M. (Co-investigator), Clark, E. (Co-investigator), Connelley, T. (Co-investigator), Hassan, M. (Co-investigator), McGrew, M. (Co-investigator), Morrison, L. (Co-investigator), Prendergast, J. (Co-investigator), Robert, C. (Co-investigator), Smith, J. (Co-investigator), Sparks, N. (Co-investigator), Watson, M. (Co-investigator) & Whitelaw, B. (Co-investigator)
Non-EU-based charities
1/10/15 → 31/03/22
Project: Research

Cite this

@article{c2b213347ebb4d30a9c71c338e8ee52d,

title = "Ecological niche modelling for delineating livestock ecotypes and exploring environmental genomic adaptation: the example of Ethiopian village chicken",

abstract = "In evolutionary ecology, an {\textquoteleft}ecotype{\textquoteright} 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 ecotypeField Code Changed Field Code Changed Field Code Changed Ecological genomics of livestock ecotypes 2 This is a provisional file, not the final typeset article 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 \textasciitilde{}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 x environment (GxE) interactions.",

keywords = "environmental adaptation, Ecological Niche Modelling, Ethiopian village chicken, Redundancy Analysis, selection signature analysis",

author = "Trujillo, \{Adriana Vallejo\} and Adebabay Kabede and Maria Lozano-Jaramillo and Tadelle Dessie and Jacqueline Smith and Olivier Hanotte and Almas Gheyas",

note = "Funding Information: This research was funded in part by the Bill \& Melinda Gates Foundation (BMGF) and with UK aid from the UK Foreign, Commonwealth and Development Office (Grant Agreement OPP1127286). The study constituted part of AV-T{\textquoteright}s Ph.D. research that was funded by Vice-Chancellor Scholarship for Research Excellence International at University of Nottingham and Administrative Department of Science, Technology and Innovation (Colciencias) – Colombian Government (Call 2015 N°728). This study was carried out under the auspices of the Centre for Tropical Livestock Genetics and Health (CTLGH), established jointly by The University of Edinburgh, SRUC (Scotland{\textquoteright}s Rural College), and the International Livestock Research Institute. The findings and conclusions contained within were those of the authors and do not necessarily reflect positions or policies of the BMGF nor the United Kingdom Government. This research was conducted as part of the Consultative Group on International Agricultural Research (CGIAR) Research Program on Livestock and was supported by contributors to the CGIAR Trust Fund. Funding Information: This research was funded in part by the Bill \& Melinda Gates Foundation (BMGF) and with UK aid from the UK Foreign, Commonwealth and Development Office (Grant Agreement OPP1127286). The study constituted part of AV-T{\textquoteright}s Ph.D. research that was funded by Vice-Chancellor Scholarship for Research Excellence International at University of Nottingham and Administrative Department of Science, Technology and Innovation (Colciencias) – Colombian Government (Call 2015 N°728). This study was carried out under the auspices of the Centre for Tropical Livestock Genetics and Health (CTLGH), established jointly by The University of Edinburgh, SRUC (Scotland{\textquoteright}s Rural College), and the International Livestock Research Institute. The findings and conclusions contained within were those of the authors and do not necessarily reflect positions or policies of the BMGF nor the United Kingdom Government. This research was conducted as part of the Consultative Group on International Agricultural Research (CGIAR) Research Program on Livestock and was supported by contributors to the CGIAR Trust Fund. Publisher Copyright: Copyright {\textcopyright} 2022 Vallejo-Trujillo, Kebede, Lozano-Jaramillo, Dessie, Smith, Hanotte and Gheyas.",

year = "2022",

month = aug,

day = "4",

doi = "10.3389/fevo.2022.866587",

language = "English",

volume = "10",

pages = "1--21",

journal = " Frontiers in Ecology and Evolution",

issn = "2296-701X",

publisher = "Frontiers Media SA",

}

Ecological niche modelling for delineating livestock ecotypes and exploring environmental genomic adaptation: the example of Ethiopian village chicken. / Trujillo, Adriana Vallejo; Kabede, Adebabay ; Lozano-Jaramillo, Maria et al.
In: Frontiers in Ecology and Evolution, Vol. 10, 866587, 04.08.2022, p. 1-21.

Research output: Contribution to journal › Article › peer-review

TY - JOUR

T1 - Ecological niche modelling for delineating livestock ecotypes and exploring environmental genomic adaptation: the example of Ethiopian village chicken

AU - Trujillo, Adriana Vallejo

AU - Kabede, Adebabay

AU - Lozano-Jaramillo, Maria

AU - Dessie, Tadelle

AU - Smith, Jacqueline

AU - Hanotte, Olivier

AU - Gheyas, Almas

N1 - Funding Information: This research was funded in part by the Bill & Melinda Gates Foundation (BMGF) and with UK aid from the UK Foreign, Commonwealth and Development Office (Grant Agreement OPP1127286). The study constituted part of AV-T’s Ph.D. research that was funded by Vice-Chancellor Scholarship for Research Excellence International at University of Nottingham and Administrative Department of Science, Technology and Innovation (Colciencias) – Colombian Government (Call 2015 N°728). This study was carried out under the auspices of the Centre for Tropical Livestock Genetics and Health (CTLGH), established jointly by The University of Edinburgh, SRUC (Scotland’s Rural College), and the International Livestock Research Institute. The findings and conclusions contained within were those of the authors and do not necessarily reflect positions or policies of the BMGF nor the United Kingdom Government. This research was conducted as part of the Consultative Group on International Agricultural Research (CGIAR) Research Program on Livestock and was supported by contributors to the CGIAR Trust Fund. Funding Information: This research was funded in part by the Bill & Melinda Gates Foundation (BMGF) and with UK aid from the UK Foreign, Commonwealth and Development Office (Grant Agreement OPP1127286). The study constituted part of AV-T’s Ph.D. research that was funded by Vice-Chancellor Scholarship for Research Excellence International at University of Nottingham and Administrative Department of Science, Technology and Innovation (Colciencias) – Colombian Government (Call 2015 N°728). This study was carried out under the auspices of the Centre for Tropical Livestock Genetics and Health (CTLGH), established jointly by The University of Edinburgh, SRUC (Scotland’s Rural College), and the International Livestock Research Institute. The findings and conclusions contained within were those of the authors and do not necessarily reflect positions or policies of the BMGF nor the United Kingdom Government. This research was conducted as part of the Consultative Group on International Agricultural Research (CGIAR) Research Program on Livestock and was supported by contributors to the CGIAR Trust Fund. Publisher Copyright: Copyright © 2022 Vallejo-Trujillo, Kebede, Lozano-Jaramillo, Dessie, Smith, Hanotte and Gheyas.

PY - 2022/8/4

Y1 - 2022/8/4

N2 - 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 ecotypeField Code Changed Field Code Changed Field Code Changed Ecological genomics of livestock ecotypes 2 This is a provisional file, not the final typeset article 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 x environment (GxE) interactions.

AB - 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 ecotypeField Code Changed Field Code Changed Field Code Changed Ecological genomics of livestock ecotypes 2 This is a provisional file, not the final typeset article 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 x environment (GxE) interactions.

KW - environmental adaptation

KW - Ecological Niche Modelling

KW - Ethiopian village chicken

KW - Redundancy Analysis

KW - selection signature analysis

U2 - 10.3389/fevo.2022.866587

DO - 10.3389/fevo.2022.866587

M3 - Article

SN - 2296-701X

VL - 10

SP - 1

EP - 21

JO - Frontiers in Ecology and Evolution

JF - Frontiers in Ecology and Evolution

M1 - 866587

ER -

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

Abstract

Keywords / Materials (for Non-textual outputs)

Access to Document

Fingerprint

Projects

CTLGH: A global shared data biological sample resource to support productivity improvement for tropical livestock

Cite this