Ethiopian indigenous goats offer insights into past and recent demographic dynamics and local adaptation in sub‐Saharan African goats
Abstract Knowledge on how adaptive evolution and human socio‐cultural and economic interests shaped livestock genomes particularly in sub‐Saharan Africa remains limited. Ethiopia is in a geographic region that has been critical in the history of African agriculture with ancient and diverse human eth...
Main Authors: | , , , , , , , , , , , |
---|---|
Format: | Article |
Language: | English |
Published: |
Wiley
2021-07-01
|
Series: | Evolutionary Applications |
Subjects: | |
Online Access: | https://doi.org/10.1111/eva.13118 |
id |
doaj-0b14d43200634700991a23d9942b28c0 |
---|---|
record_format |
Article |
spelling |
doaj-0b14d43200634700991a23d9942b28c02021-07-19T13:28:29ZengWileyEvolutionary Applications1752-45712021-07-011471716173110.1111/eva.13118Ethiopian indigenous goats offer insights into past and recent demographic dynamics and local adaptation in sub‐Saharan African goatsGetinet M. Tarekegn0Negar Khayatzadeh1Bin Liu2Sarah Osama3Aynalem Haile4Barbara Rischkowsky5Wenguang Zhang6Kassahun Tesfaye7Tadelle Dessie8Okeyo A. Mwai9Appolinaire Djikeng10Joram M. Mwacharo11Department of Animal Production and Technology School of Animal Sciences and Veterinary Medicine Bahir Dar University Bahir Dar EthiopiaDepartment of Sustainable Agricultural Systems Division of Livestock Sciences University of Natural Resources and Life Sciences Vienna AustriaInner Mongolia Agricultural University Hohhot ChinaThe University of Queensland Saint Lucia QLD AustraliaSmall Ruminant GenomicsInternational Centre for Agricultural Research in the Dry Areas (ICARDA) Addis Ababa EthiopiaSmall Ruminant GenomicsInternational Centre for Agricultural Research in the Dry Areas (ICARDA) Addis Ababa EthiopiaInner Mongolia Agricultural University Hohhot ChinaDepartment of Microbial, Cellular and Molecular Biology Addis Ababa University Addis Ababa EthiopiaInternational Livestock Research Institute (ILRI) Addis Ababa EthiopiaInternational Livestock Research Institute (ILRI) Nairobi KenyaAnimal and Veterinary Sciences Group, SRUC and Centre for Tropical Livestock Genetics and Health (CTLGH) The Roslin InstituteEaster Bush Midlothian UKSmall Ruminant GenomicsInternational Centre for Agricultural Research in the Dry Areas (ICARDA) Addis Ababa EthiopiaAbstract Knowledge on how adaptive evolution and human socio‐cultural and economic interests shaped livestock genomes particularly in sub‐Saharan Africa remains limited. Ethiopia is in a geographic region that has been critical in the history of African agriculture with ancient and diverse human ethnicity and bio‐climatic conditions. Using 52K genome‐wide data analysed in 646 individuals from 13 Ethiopian indigenous goat populations, we observed high levels of genetic variation. Although runs of homozygosity (ROH) were ubiquitous genome‐wide, there were clear differences in patterns of ROH length and abundance and in effective population sizes illustrating differences in genome homozygosity, evolutionary history, and management. Phylogenetic analysis incorporating patterns of genetic differentiation and gene flow with ancestry modelling highlighted past and recent intermixing and possible two deep ancient genetic ancestries that could have been brought by humans with the first introduction of goats in Africa. We observed four strong selection signatures that were specific to Arsi‐Bale and Nubian goats. These signatures overlapped genomic regions with genes associated with morphological, adaptation, reproduction and production traits due possibly to selection under environmental constraints and/or human preferences. The regions also overlapped uncharacterized genes, calling for a comprehensive annotation of the goat genome. Our results provide insights into mechanisms leading to genome variation and differentiation in sub‐Saharan Africa indigenous goats.https://doi.org/10.1111/eva.13118autozygositydiversityeffective population sizegenome dynamicsLD decayruns of homozygosity |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Getinet M. Tarekegn Negar Khayatzadeh Bin Liu Sarah Osama Aynalem Haile Barbara Rischkowsky Wenguang Zhang Kassahun Tesfaye Tadelle Dessie Okeyo A. Mwai Appolinaire Djikeng Joram M. Mwacharo |
spellingShingle |
Getinet M. Tarekegn Negar Khayatzadeh Bin Liu Sarah Osama Aynalem Haile Barbara Rischkowsky Wenguang Zhang Kassahun Tesfaye Tadelle Dessie Okeyo A. Mwai Appolinaire Djikeng Joram M. Mwacharo Ethiopian indigenous goats offer insights into past and recent demographic dynamics and local adaptation in sub‐Saharan African goats Evolutionary Applications autozygosity diversity effective population size genome dynamics LD decay runs of homozygosity |
author_facet |
Getinet M. Tarekegn Negar Khayatzadeh Bin Liu Sarah Osama Aynalem Haile Barbara Rischkowsky Wenguang Zhang Kassahun Tesfaye Tadelle Dessie Okeyo A. Mwai Appolinaire Djikeng Joram M. Mwacharo |
author_sort |
Getinet M. Tarekegn |
title |
Ethiopian indigenous goats offer insights into past and recent demographic dynamics and local adaptation in sub‐Saharan African goats |
title_short |
Ethiopian indigenous goats offer insights into past and recent demographic dynamics and local adaptation in sub‐Saharan African goats |
title_full |
Ethiopian indigenous goats offer insights into past and recent demographic dynamics and local adaptation in sub‐Saharan African goats |
title_fullStr |
Ethiopian indigenous goats offer insights into past and recent demographic dynamics and local adaptation in sub‐Saharan African goats |
title_full_unstemmed |
Ethiopian indigenous goats offer insights into past and recent demographic dynamics and local adaptation in sub‐Saharan African goats |
title_sort |
ethiopian indigenous goats offer insights into past and recent demographic dynamics and local adaptation in sub‐saharan african goats |
publisher |
Wiley |
series |
Evolutionary Applications |
issn |
1752-4571 |
publishDate |
2021-07-01 |
description |
Abstract Knowledge on how adaptive evolution and human socio‐cultural and economic interests shaped livestock genomes particularly in sub‐Saharan Africa remains limited. Ethiopia is in a geographic region that has been critical in the history of African agriculture with ancient and diverse human ethnicity and bio‐climatic conditions. Using 52K genome‐wide data analysed in 646 individuals from 13 Ethiopian indigenous goat populations, we observed high levels of genetic variation. Although runs of homozygosity (ROH) were ubiquitous genome‐wide, there were clear differences in patterns of ROH length and abundance and in effective population sizes illustrating differences in genome homozygosity, evolutionary history, and management. Phylogenetic analysis incorporating patterns of genetic differentiation and gene flow with ancestry modelling highlighted past and recent intermixing and possible two deep ancient genetic ancestries that could have been brought by humans with the first introduction of goats in Africa. We observed four strong selection signatures that were specific to Arsi‐Bale and Nubian goats. These signatures overlapped genomic regions with genes associated with morphological, adaptation, reproduction and production traits due possibly to selection under environmental constraints and/or human preferences. The regions also overlapped uncharacterized genes, calling for a comprehensive annotation of the goat genome. Our results provide insights into mechanisms leading to genome variation and differentiation in sub‐Saharan Africa indigenous goats. |
topic |
autozygosity diversity effective population size genome dynamics LD decay runs of homozygosity |
url |
https://doi.org/10.1111/eva.13118 |
work_keys_str_mv |
AT getinetmtarekegn ethiopianindigenousgoatsofferinsightsintopastandrecentdemographicdynamicsandlocaladaptationinsubsaharanafricangoats AT negarkhayatzadeh ethiopianindigenousgoatsofferinsightsintopastandrecentdemographicdynamicsandlocaladaptationinsubsaharanafricangoats AT binliu ethiopianindigenousgoatsofferinsightsintopastandrecentdemographicdynamicsandlocaladaptationinsubsaharanafricangoats AT sarahosama ethiopianindigenousgoatsofferinsightsintopastandrecentdemographicdynamicsandlocaladaptationinsubsaharanafricangoats AT aynalemhaile ethiopianindigenousgoatsofferinsightsintopastandrecentdemographicdynamicsandlocaladaptationinsubsaharanafricangoats AT barbararischkowsky ethiopianindigenousgoatsofferinsightsintopastandrecentdemographicdynamicsandlocaladaptationinsubsaharanafricangoats AT wenguangzhang ethiopianindigenousgoatsofferinsightsintopastandrecentdemographicdynamicsandlocaladaptationinsubsaharanafricangoats AT kassahuntesfaye ethiopianindigenousgoatsofferinsightsintopastandrecentdemographicdynamicsandlocaladaptationinsubsaharanafricangoats AT tadelledessie ethiopianindigenousgoatsofferinsightsintopastandrecentdemographicdynamicsandlocaladaptationinsubsaharanafricangoats AT okeyoamwai ethiopianindigenousgoatsofferinsightsintopastandrecentdemographicdynamicsandlocaladaptationinsubsaharanafricangoats AT appolinairedjikeng ethiopianindigenousgoatsofferinsightsintopastandrecentdemographicdynamicsandlocaladaptationinsubsaharanafricangoats AT jorammmwacharo ethiopianindigenousgoatsofferinsightsintopastandrecentdemographicdynamicsandlocaladaptationinsubsaharanafricangoats |
_version_ |
1721294834272043008 |