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Phylogeography and domestication of Indian river buffalo.

Kumar S, Nagarajan M, Sandhu JS, Kumar N, Behl V - BMC Evol. Biol. (2007)

Bottom Line: In addition, we found several singleton haplotypes.The multidimensional display of breed pairwise FST values showed significant breed differentiation.Present day river buffalo is the result of complex domestication processes involving more than one maternal lineage and a significant maternal gene flow from the wild populations after the initial domestication events.

View Article: PubMed Central - HTML - PubMed

Affiliation: Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad-500007, India. satishk@ccmb.res.in

ABSTRACT

Background: The water buffalo- Bubalus bubalis holds tremendous potential in livestock sector in many Asian countries, particularly India. The origin, domestication and genetic structure of the Indian river buffalo are poorly understood. Therefore, to understand the relationship among the maternal lineages of Indian river buffalo breeds and their domestication process, we analysed mitochondrial D-loop region of 217 animals representing eight breeds from eight different locations in India along with published sequences of Mediterranean buffalo.

Results: The maximum parsimony tree showed one major clade with six internal branches. Reduced median network revealed expansion from more than one set of haplotypes indicating complex domestication events for this species. In addition, we found several singleton haplotypes. Using rho statistics, we obtained a time estimate of 6300 years BP for the expansion of one set of hapltoypes of the Indian domestic buffalo. A few breed specific branches in the network indicated an ancient time depth of differentiation of some of the maternal lineages of river buffalo breeds. The multidimensional display of breed pairwise FST values showed significant breed differentiation.

Conclusion: Present day river buffalo is the result of complex domestication processes involving more than one maternal lineage and a significant maternal gene flow from the wild populations after the initial domestication events. Our data are consistent with the available archaeological information in supporting the proposition that the river buffalo was likely to be domesticated in the Western region of the Indian subcontinent, specifically the present day breeding tracts of the Mehsana, Surati and Pandharpuri breeds.

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Reduced median network of Indian and Mediterranean river buffalo. The reduced median network was constructed using NETWORK 4.1.1.2 program with 921 bp sequences of mtDNA D-loop region of the Indian and Mediterranean river buffalo. The size of the circle is proportional to the number of animals represented. The length of the line represents the number of mutational steps.
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Figure 4: Reduced median network of Indian and Mediterranean river buffalo. The reduced median network was constructed using NETWORK 4.1.1.2 program with 921 bp sequences of mtDNA D-loop region of the Indian and Mediterranean river buffalo. The size of the circle is proportional to the number of animals represented. The length of the line represents the number of mutational steps.

Mentions: Reduced median network based upon a 921 bp sequence (Fig. 4) revealed the lack of a single star-like appearance of the network connecting all the present day river buffalo haplotypes. This was contrary to the typical signatures of expansion of a few seeding haplotypes after domestication, and the subsequent derivation of the present day haplotypes through mutational steps. Nevertheless, within a complex network of a plethora of singletons, there were two regions, one at each end of the network, suggesting expansion from the founding haplotypes. At one end, there were four haplotypes, interconnected through one mutational step, three of which acted as radiating nodes for a large number of haplotypes. At the other end of the network, there was an isolated node (R1) connecting twenty-five animals within one mutational step. To test the significance of this grouping, we performed AMOVA analysis by classifying 217 Indian animals into two groups, viz.; 1) twenty-five animals with one mutation step away from the node R1, and b) all the remaining Indian buffalo as a separate group. This classification explained 55.75% of the total molecular variation present in the Indian animals data. To determine whether this duality was encompassing various geographical regions, we constructed reduced median networks based on the hypervariable region I (375 bp) for each breeds (data not shown). The Mehsana network was extremely complex. In all the remaining breeds, excepting the Nagpuri from Central India, there was a general tendency towards this dichotomy. It may be noted that all animals shown on internal branches of the river buffalo clade in parsimony tree were also located distantly in the network away from the expanding haplotypes. Interestingly, majority of the individuals of the Mehsana and Surati breeds sampled from Western India, were distributed all over the network as singletons. Further, we found a few breed-specific maternal branches in the network.


Phylogeography and domestication of Indian river buffalo.

Kumar S, Nagarajan M, Sandhu JS, Kumar N, Behl V - BMC Evol. Biol. (2007)

Reduced median network of Indian and Mediterranean river buffalo. The reduced median network was constructed using NETWORK 4.1.1.2 program with 921 bp sequences of mtDNA D-loop region of the Indian and Mediterranean river buffalo. The size of the circle is proportional to the number of animals represented. The length of the line represents the number of mutational steps.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2140268&req=5

Figure 4: Reduced median network of Indian and Mediterranean river buffalo. The reduced median network was constructed using NETWORK 4.1.1.2 program with 921 bp sequences of mtDNA D-loop region of the Indian and Mediterranean river buffalo. The size of the circle is proportional to the number of animals represented. The length of the line represents the number of mutational steps.
Mentions: Reduced median network based upon a 921 bp sequence (Fig. 4) revealed the lack of a single star-like appearance of the network connecting all the present day river buffalo haplotypes. This was contrary to the typical signatures of expansion of a few seeding haplotypes after domestication, and the subsequent derivation of the present day haplotypes through mutational steps. Nevertheless, within a complex network of a plethora of singletons, there were two regions, one at each end of the network, suggesting expansion from the founding haplotypes. At one end, there were four haplotypes, interconnected through one mutational step, three of which acted as radiating nodes for a large number of haplotypes. At the other end of the network, there was an isolated node (R1) connecting twenty-five animals within one mutational step. To test the significance of this grouping, we performed AMOVA analysis by classifying 217 Indian animals into two groups, viz.; 1) twenty-five animals with one mutation step away from the node R1, and b) all the remaining Indian buffalo as a separate group. This classification explained 55.75% of the total molecular variation present in the Indian animals data. To determine whether this duality was encompassing various geographical regions, we constructed reduced median networks based on the hypervariable region I (375 bp) for each breeds (data not shown). The Mehsana network was extremely complex. In all the remaining breeds, excepting the Nagpuri from Central India, there was a general tendency towards this dichotomy. It may be noted that all animals shown on internal branches of the river buffalo clade in parsimony tree were also located distantly in the network away from the expanding haplotypes. Interestingly, majority of the individuals of the Mehsana and Surati breeds sampled from Western India, were distributed all over the network as singletons. Further, we found a few breed-specific maternal branches in the network.

Bottom Line: In addition, we found several singleton haplotypes.The multidimensional display of breed pairwise FST values showed significant breed differentiation.Present day river buffalo is the result of complex domestication processes involving more than one maternal lineage and a significant maternal gene flow from the wild populations after the initial domestication events.

View Article: PubMed Central - HTML - PubMed

Affiliation: Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad-500007, India. satishk@ccmb.res.in

ABSTRACT

Background: The water buffalo- Bubalus bubalis holds tremendous potential in livestock sector in many Asian countries, particularly India. The origin, domestication and genetic structure of the Indian river buffalo are poorly understood. Therefore, to understand the relationship among the maternal lineages of Indian river buffalo breeds and their domestication process, we analysed mitochondrial D-loop region of 217 animals representing eight breeds from eight different locations in India along with published sequences of Mediterranean buffalo.

Results: The maximum parsimony tree showed one major clade with six internal branches. Reduced median network revealed expansion from more than one set of haplotypes indicating complex domestication events for this species. In addition, we found several singleton haplotypes. Using rho statistics, we obtained a time estimate of 6300 years BP for the expansion of one set of hapltoypes of the Indian domestic buffalo. A few breed specific branches in the network indicated an ancient time depth of differentiation of some of the maternal lineages of river buffalo breeds. The multidimensional display of breed pairwise FST values showed significant breed differentiation.

Conclusion: Present day river buffalo is the result of complex domestication processes involving more than one maternal lineage and a significant maternal gene flow from the wild populations after the initial domestication events. Our data are consistent with the available archaeological information in supporting the proposition that the river buffalo was likely to be domesticated in the Western region of the Indian subcontinent, specifically the present day breeding tracts of the Mehsana, Surati and Pandharpuri breeds.

Show MeSH