Genome-wide diversity and demographic dynamics of Cameroon goats and their divergence from east African, north African, and Asian conspecifics

Getinet Tarekegn*, Patrick Wouobeng, Kouam Simo Jaures, RA Mrode, Zewdu Edea, Bin Liu, Wenguang Zhang, Mwai Okeyo, Tadelle Dessie, Kassahun Tesfaye, Erling Strandberg, Britt Berglund, Collins Mutai, Sarah Osama, Asaminew Tassew Wolde, Josephine Birungi, Appolinaire Djikeng, Félix Meutchieye

*Corresponding author for this work

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Abstract

Indigenous goats make significant contributions to Cameroon’s national and local economy, but little effort has been devoted to identifying the populations. Here, we assessed the genetic diversity and demographic dynamics of Cameroon goat populations using mitochondrial DNA (two populations) and autosomal markers (four populations) generated with the Caprine 50K SNP chip. To infer genetic relationships at continental and global level, genotype data on six goat populations from Ethiopia and one population each from Egypt, Morocco, Iran, and China were included in the analysis. The mtDNA analysis revealed 83 haplotypes, all belonging to haplogroup A, in Cameroon goats. Four haplotypes were shared between goats found in Cameroon, Mozambique, Namibia, Zimbabwe, Kenya, and Ethiopia. Analysis of autosomal SNPs in Cameroon goats revealed the lowest HO (0.335±0.13) and HE (0.352±0.15) in the North-west Highland and Central Highland populations, respectively. Overall, the highest HO (0.401±0.12) and HE (0.422±0.12) were found for Barki and Iranian goats, respectively. Barki goats had the highest average MAF, while Central Highland Cameroon goats had the lowest. Overall, Cameroon goats demonstrated high FIS. AMOVA revealed that 13.29% of the variation was explained by genetic differences between the six population groups. Low average FST (0.01) suggests intermixing among Cameroon goats. All measures indicated that Cameroon goats are closer to Moroccan goats than to other goat populations. PCA and STRUCTURE analyses poorly differentiated the Cameroon goats, as did genetic distance, Neighbor-Net network, and neighbor-joining tree analyses. The haplotype analysis of mtDNA showed the initial dispersion of goats to Cameroon and central Africa from north-east Africa following the Nile Delta. Whereas, the approximate Bayesian computation indicated Cameroon goats were separated from Moroccan goats after 506 generations in later times (~1518 YA), as supported by the phylogenetic net-work and admixture outputs. Overall, indigenous goats in Cameroon show weak phylogenetic structure, suggesting either extensive intermixing.
Original languageEnglish
Article numbere0214843
JournalPLoS ONE
Volume14
Issue number4
Early online date19 Apr 2019
DOIs
Publication statusPrint publication - 19 Apr 2019

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Cameroon
Mitochondrial DNA
Goats
demographic statistics
Genes
goats
Demography
Genome
genome
Joining
Population
Haplotypes
Ethiopia
haplotypes
highlands
mitochondrial DNA
Single Nucleotide Polymorphism
Namibia
Mozambique
Central Africa

Keywords

  • Goats
  • Cameroon
  • Africa
  • Population genetics
  • Haplotypes
  • Mitochondrial DNA
  • Haplogroups
  • Ethiopia

Cite this

Tarekegn, Getinet ; Wouobeng, Patrick ; Simo Jaures, Kouam ; Mrode, RA ; Edea, Zewdu ; Liu, Bin ; Zhang, Wenguang ; Okeyo, Mwai ; Dessie, Tadelle ; Tesfaye, Kassahun ; Strandberg, Erling ; Berglund, Britt ; Mutai, Collins ; Osama, Sarah ; Tassew Wolde, Asaminew ; Birungi, Josephine ; Djikeng, Appolinaire ; Meutchieye, Félix. / Genome-wide diversity and demographic dynamics of Cameroon goats and their divergence from east African, north African, and Asian conspecifics. In: PLoS ONE. 2019 ; Vol. 14, No. 4.
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abstract = "Indigenous goats make significant contributions to Cameroon’s national and local economy, but little effort has been devoted to identifying the populations. Here, we assessed the genetic diversity and demographic dynamics of Cameroon goat populations using mitochondrial DNA (two populations) and autosomal markers (four populations) generated with the Caprine 50K SNP chip. To infer genetic relationships at continental and global level, genotype data on six goat populations from Ethiopia and one population each from Egypt, Morocco, Iran, and China were included in the analysis. The mtDNA analysis revealed 83 haplotypes, all belonging to haplogroup A, in Cameroon goats. Four haplotypes were shared between goats found in Cameroon, Mozambique, Namibia, Zimbabwe, Kenya, and Ethiopia. Analysis of autosomal SNPs in Cameroon goats revealed the lowest HO (0.335±0.13) and HE (0.352±0.15) in the North-west Highland and Central Highland populations, respectively. Overall, the highest HO (0.401±0.12) and HE (0.422±0.12) were found for Barki and Iranian goats, respectively. Barki goats had the highest average MAF, while Central Highland Cameroon goats had the lowest. Overall, Cameroon goats demonstrated high FIS. AMOVA revealed that 13.29{\%} of the variation was explained by genetic differences between the six population groups. Low average FST (0.01) suggests intermixing among Cameroon goats. All measures indicated that Cameroon goats are closer to Moroccan goats than to other goat populations. PCA and STRUCTURE analyses poorly differentiated the Cameroon goats, as did genetic distance, Neighbor-Net network, and neighbor-joining tree analyses. The haplotype analysis of mtDNA showed the initial dispersion of goats to Cameroon and central Africa from north-east Africa following the Nile Delta. Whereas, the approximate Bayesian computation indicated Cameroon goats were separated from Moroccan goats after 506 generations in later times (~1518 YA), as supported by the phylogenetic net-work and admixture outputs. Overall, indigenous goats in Cameroon show weak phylogenetic structure, suggesting either extensive intermixing.",
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author = "Getinet Tarekegn and Patrick Wouobeng and {Simo Jaures}, Kouam and RA Mrode and Zewdu Edea and Bin Liu and Wenguang Zhang and Mwai Okeyo and Tadelle Dessie and Kassahun Tesfaye and Erling Strandberg and Britt Berglund and Collins Mutai and Sarah Osama and {Tassew Wolde}, Asaminew and Josephine Birungi and Appolinaire Djikeng and F{\'e}lix Meutchieye",
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Tarekegn, G, Wouobeng, P, Simo Jaures, K, Mrode, RA, Edea, Z, Liu, B, Zhang, W, Okeyo, M, Dessie, T, Tesfaye, K, Strandberg, E, Berglund, B, Mutai, C, Osama, S, Tassew Wolde, A, Birungi, J, Djikeng, A & Meutchieye, F 2019, 'Genome-wide diversity and demographic dynamics of Cameroon goats and their divergence from east African, north African, and Asian conspecifics', PLoS ONE, vol. 14, no. 4, e0214843. https://doi.org/10.1371/journal.pone.0214843

Genome-wide diversity and demographic dynamics of Cameroon goats and their divergence from east African, north African, and Asian conspecifics. / Tarekegn, Getinet; Wouobeng, Patrick; Simo Jaures, Kouam ; Mrode, RA; Edea, Zewdu; Liu, Bin ; Zhang, Wenguang ; Okeyo, Mwai; Dessie, Tadelle; Tesfaye, Kassahun ; Strandberg, Erling ; Berglund, Britt; Mutai, Collins; Osama, Sarah; Tassew Wolde, Asaminew ; Birungi, Josephine ; Djikeng, Appolinaire ; Meutchieye, Félix.

In: PLoS ONE, Vol. 14, No. 4, e0214843, 19.04.2019.

Research output: Contribution to journalArticle

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T1 - Genome-wide diversity and demographic dynamics of Cameroon goats and their divergence from east African, north African, and Asian conspecifics

AU - Tarekegn, Getinet

AU - Wouobeng, Patrick

AU - Simo Jaures, Kouam

AU - Mrode, RA

AU - Edea, Zewdu

AU - Liu, Bin

AU - Zhang, Wenguang

AU - Okeyo, Mwai

AU - Dessie, Tadelle

AU - Tesfaye, Kassahun

AU - Strandberg, Erling

AU - Berglund, Britt

AU - Mutai, Collins

AU - Osama, Sarah

AU - Tassew Wolde, Asaminew

AU - Birungi, Josephine

AU - Djikeng, Appolinaire

AU - Meutchieye, Félix

PY - 2019/4/19

Y1 - 2019/4/19

N2 - Indigenous goats make significant contributions to Cameroon’s national and local economy, but little effort has been devoted to identifying the populations. Here, we assessed the genetic diversity and demographic dynamics of Cameroon goat populations using mitochondrial DNA (two populations) and autosomal markers (four populations) generated with the Caprine 50K SNP chip. To infer genetic relationships at continental and global level, genotype data on six goat populations from Ethiopia and one population each from Egypt, Morocco, Iran, and China were included in the analysis. The mtDNA analysis revealed 83 haplotypes, all belonging to haplogroup A, in Cameroon goats. Four haplotypes were shared between goats found in Cameroon, Mozambique, Namibia, Zimbabwe, Kenya, and Ethiopia. Analysis of autosomal SNPs in Cameroon goats revealed the lowest HO (0.335±0.13) and HE (0.352±0.15) in the North-west Highland and Central Highland populations, respectively. Overall, the highest HO (0.401±0.12) and HE (0.422±0.12) were found for Barki and Iranian goats, respectively. Barki goats had the highest average MAF, while Central Highland Cameroon goats had the lowest. Overall, Cameroon goats demonstrated high FIS. AMOVA revealed that 13.29% of the variation was explained by genetic differences between the six population groups. Low average FST (0.01) suggests intermixing among Cameroon goats. All measures indicated that Cameroon goats are closer to Moroccan goats than to other goat populations. PCA and STRUCTURE analyses poorly differentiated the Cameroon goats, as did genetic distance, Neighbor-Net network, and neighbor-joining tree analyses. The haplotype analysis of mtDNA showed the initial dispersion of goats to Cameroon and central Africa from north-east Africa following the Nile Delta. Whereas, the approximate Bayesian computation indicated Cameroon goats were separated from Moroccan goats after 506 generations in later times (~1518 YA), as supported by the phylogenetic net-work and admixture outputs. Overall, indigenous goats in Cameroon show weak phylogenetic structure, suggesting either extensive intermixing.

AB - Indigenous goats make significant contributions to Cameroon’s national and local economy, but little effort has been devoted to identifying the populations. Here, we assessed the genetic diversity and demographic dynamics of Cameroon goat populations using mitochondrial DNA (two populations) and autosomal markers (four populations) generated with the Caprine 50K SNP chip. To infer genetic relationships at continental and global level, genotype data on six goat populations from Ethiopia and one population each from Egypt, Morocco, Iran, and China were included in the analysis. The mtDNA analysis revealed 83 haplotypes, all belonging to haplogroup A, in Cameroon goats. Four haplotypes were shared between goats found in Cameroon, Mozambique, Namibia, Zimbabwe, Kenya, and Ethiopia. Analysis of autosomal SNPs in Cameroon goats revealed the lowest HO (0.335±0.13) and HE (0.352±0.15) in the North-west Highland and Central Highland populations, respectively. Overall, the highest HO (0.401±0.12) and HE (0.422±0.12) were found for Barki and Iranian goats, respectively. Barki goats had the highest average MAF, while Central Highland Cameroon goats had the lowest. Overall, Cameroon goats demonstrated high FIS. AMOVA revealed that 13.29% of the variation was explained by genetic differences between the six population groups. Low average FST (0.01) suggests intermixing among Cameroon goats. All measures indicated that Cameroon goats are closer to Moroccan goats than to other goat populations. PCA and STRUCTURE analyses poorly differentiated the Cameroon goats, as did genetic distance, Neighbor-Net network, and neighbor-joining tree analyses. The haplotype analysis of mtDNA showed the initial dispersion of goats to Cameroon and central Africa from north-east Africa following the Nile Delta. Whereas, the approximate Bayesian computation indicated Cameroon goats were separated from Moroccan goats after 506 generations in later times (~1518 YA), as supported by the phylogenetic net-work and admixture outputs. Overall, indigenous goats in Cameroon show weak phylogenetic structure, suggesting either extensive intermixing.

KW - Goats

KW - Cameroon

KW - Africa

KW - Population genetics

KW - Haplotypes

KW - Mitochondrial DNA

KW - Haplogroups

KW - Ethiopia

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JO - PLoS ONE

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SN - 1932-6203

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