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Mitogenomes from Egyptian Cattle Breeds: New Clues on the Origin of Haplogroup Q and the Early Spread of Bos taurus from the Near East.

Olivieri A, Gandini F, Achilli A, Fichera A, Rizzi E, Bonfiglio S, Battaglia V, Brandini S, De Gaetano A, El-Beltagi A, Lancioni H, Agha S, Semino O, Ferretti L, Torroni A - PLoS ONE (2015)

Bottom Line: However, despite the proven effectiveness of whole mitochondrial genome data in providing valuable information concerning the origin of taurine cattle, until now no population surveys have been carried out at the level of mitogenomes in local breeds from the Near East or surrounding areas.Phylogenetic and Bayesian analyses were subsequently performed.Phylogenetic analyses of the 31 mitogenomes confirmed the prevalence of haplogroup T1, similar to most African cattle breeds, but showed also high frequencies for haplogroups T2, T3 and Q1, and an extremely high haplotype diversity, while Bayesian skyline plots pointed to a main episode of population growth ~12.5 ky ago.

View Article: PubMed Central - PubMed

Affiliation: Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, Italy.

ABSTRACT

Background: Genetic studies support the scenario that Bos taurus domestication occurred in the Near East during the Neolithic transition about 10 thousand years (ky) ago, with the likely exception of a minor secondary event in Italy. However, despite the proven effectiveness of whole mitochondrial genome data in providing valuable information concerning the origin of taurine cattle, until now no population surveys have been carried out at the level of mitogenomes in local breeds from the Near East or surrounding areas. Egypt is in close geographic and cultural proximity to the Near East, in particular the Nile Delta region, and was one of the first neighboring areas to adopt the Neolithic package. Thus, a survey of mitogenome variation of autochthonous taurine breeds from the Nile Delta region might provide new insights on the early spread of cattle rearing outside the Near East.

Methodology: Using Illumina high-throughput sequencing we characterized the mitogenomes from two cattle breeds, Menofi (N = 17) and Domiaty (N = 14), from the Nile Delta region. Phylogenetic and Bayesian analyses were subsequently performed.

Conclusions: Phylogenetic analyses of the 31 mitogenomes confirmed the prevalence of haplogroup T1, similar to most African cattle breeds, but showed also high frequencies for haplogroups T2, T3 and Q1, and an extremely high haplotype diversity, while Bayesian skyline plots pointed to a main episode of population growth ~12.5 ky ago. Comparisons of Nile Delta mitogenomes with those from other geographic areas revealed that (i) most Egyptian mtDNAs are probably direct local derivatives from the founder domestic herds which first arrived from the Near East and the extent of gene flow from and towards the Nile Delta region was limited after the initial founding event(s); (ii) haplogroup Q1 was among these founders, thus proving that it underwent domestication in the Near East together with the founders of the T clades.

No MeSH data available.


Related in: MedlinePlus

Worldwide phylogeny of taurine haplogroups T2 and Q.This most parsimonious tree encompasses the Egyptian mitogenomes belonging to haplogroups T2 (N = 6) and Q1 (N = 2) and all previously published worldwide mitogenomes from the same haplogroups (T2, N = 17 and Q, N = 16). Branches display mutations with numbers according to the BRS; they are transitions unless a base is explicitly indicated for transversions (to A, G, C, or T) or a suffix for indels (+, d) and heteroplasmy (h). Recurrent mutations within the phylogeny are underlined and back mutations are marked with the suffix @. Coalescence times are maximum likelihood (ML) estimates.
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pone.0141170.g002: Worldwide phylogeny of taurine haplogroups T2 and Q.This most parsimonious tree encompasses the Egyptian mitogenomes belonging to haplogroups T2 (N = 6) and Q1 (N = 2) and all previously published worldwide mitogenomes from the same haplogroups (T2, N = 17 and Q, N = 16). Branches display mutations with numbers according to the BRS; they are transitions unless a base is explicitly indicated for transversions (to A, G, C, or T) or a suffix for indels (+, d) and heteroplasmy (h). Recurrent mutations within the phylogeny are underlined and back mutations are marked with the suffix @. Coalescence times are maximum likelihood (ML) estimates.

Mentions: In order to further assess the phylogenetic relationships of the Egyptian cattle mitogenomes, in particular the possible links with those from other geographic areas, we compared their sequence variation with all available mitogenomes (from the same haplogroup) from public databases. The phylogenetic relationships of T2 and Q mitogenomes are illustrated in Fig 2, while those of the T3 mitogenomes are shown in S1 Fig This comparison is illustrated with detailed figures only for haplogroups Q, T2 and T3 because the phylogeny of T1 has been reassessed recently [27, 28].


Mitogenomes from Egyptian Cattle Breeds: New Clues on the Origin of Haplogroup Q and the Early Spread of Bos taurus from the Near East.

Olivieri A, Gandini F, Achilli A, Fichera A, Rizzi E, Bonfiglio S, Battaglia V, Brandini S, De Gaetano A, El-Beltagi A, Lancioni H, Agha S, Semino O, Ferretti L, Torroni A - PLoS ONE (2015)

Worldwide phylogeny of taurine haplogroups T2 and Q.This most parsimonious tree encompasses the Egyptian mitogenomes belonging to haplogroups T2 (N = 6) and Q1 (N = 2) and all previously published worldwide mitogenomes from the same haplogroups (T2, N = 17 and Q, N = 16). Branches display mutations with numbers according to the BRS; they are transitions unless a base is explicitly indicated for transversions (to A, G, C, or T) or a suffix for indels (+, d) and heteroplasmy (h). Recurrent mutations within the phylogeny are underlined and back mutations are marked with the suffix @. Coalescence times are maximum likelihood (ML) estimates.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4626031&req=5

pone.0141170.g002: Worldwide phylogeny of taurine haplogroups T2 and Q.This most parsimonious tree encompasses the Egyptian mitogenomes belonging to haplogroups T2 (N = 6) and Q1 (N = 2) and all previously published worldwide mitogenomes from the same haplogroups (T2, N = 17 and Q, N = 16). Branches display mutations with numbers according to the BRS; they are transitions unless a base is explicitly indicated for transversions (to A, G, C, or T) or a suffix for indels (+, d) and heteroplasmy (h). Recurrent mutations within the phylogeny are underlined and back mutations are marked with the suffix @. Coalescence times are maximum likelihood (ML) estimates.
Mentions: In order to further assess the phylogenetic relationships of the Egyptian cattle mitogenomes, in particular the possible links with those from other geographic areas, we compared their sequence variation with all available mitogenomes (from the same haplogroup) from public databases. The phylogenetic relationships of T2 and Q mitogenomes are illustrated in Fig 2, while those of the T3 mitogenomes are shown in S1 Fig This comparison is illustrated with detailed figures only for haplogroups Q, T2 and T3 because the phylogeny of T1 has been reassessed recently [27, 28].

Bottom Line: However, despite the proven effectiveness of whole mitochondrial genome data in providing valuable information concerning the origin of taurine cattle, until now no population surveys have been carried out at the level of mitogenomes in local breeds from the Near East or surrounding areas.Phylogenetic and Bayesian analyses were subsequently performed.Phylogenetic analyses of the 31 mitogenomes confirmed the prevalence of haplogroup T1, similar to most African cattle breeds, but showed also high frequencies for haplogroups T2, T3 and Q1, and an extremely high haplotype diversity, while Bayesian skyline plots pointed to a main episode of population growth ~12.5 ky ago.

View Article: PubMed Central - PubMed

Affiliation: Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, Italy.

ABSTRACT

Background: Genetic studies support the scenario that Bos taurus domestication occurred in the Near East during the Neolithic transition about 10 thousand years (ky) ago, with the likely exception of a minor secondary event in Italy. However, despite the proven effectiveness of whole mitochondrial genome data in providing valuable information concerning the origin of taurine cattle, until now no population surveys have been carried out at the level of mitogenomes in local breeds from the Near East or surrounding areas. Egypt is in close geographic and cultural proximity to the Near East, in particular the Nile Delta region, and was one of the first neighboring areas to adopt the Neolithic package. Thus, a survey of mitogenome variation of autochthonous taurine breeds from the Nile Delta region might provide new insights on the early spread of cattle rearing outside the Near East.

Methodology: Using Illumina high-throughput sequencing we characterized the mitogenomes from two cattle breeds, Menofi (N = 17) and Domiaty (N = 14), from the Nile Delta region. Phylogenetic and Bayesian analyses were subsequently performed.

Conclusions: Phylogenetic analyses of the 31 mitogenomes confirmed the prevalence of haplogroup T1, similar to most African cattle breeds, but showed also high frequencies for haplogroups T2, T3 and Q1, and an extremely high haplotype diversity, while Bayesian skyline plots pointed to a main episode of population growth ~12.5 ky ago. Comparisons of Nile Delta mitogenomes with those from other geographic areas revealed that (i) most Egyptian mtDNAs are probably direct local derivatives from the founder domestic herds which first arrived from the Near East and the extent of gene flow from and towards the Nile Delta region was limited after the initial founding event(s); (ii) haplogroup Q1 was among these founders, thus proving that it underwent domestication in the Near East together with the founders of the T clades.

No MeSH data available.


Related in: MedlinePlus