Computational protocol: Mitochondrial DNA Variability of Domestic River Buffalo (Bubalus bubalis) Populations: Genetic Evidence for Domestication of River Buffalo in Indian Subcontinent

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Protocol publication

[…] We have analyzed 414 river buffalo mtDNA control region sequences representing India, Pakistan, Iran, and Egypt () to unravel the domestication history of the river buffalo. These 414 sequences were retrieved from the Gene Bank (supplementary table S1, Supplementary Material online). The complete mtDNA control region sequence was available for 291 river buffalo sampled from India, Iran, and Egypt, whereas only 505-bp mtDNA control region sequence was available for the Pakistani buffalo. Therefore, all the sequences were truncated into 492 bp size, which accommodated the hypervariable region I of the control region. The sequences were edited and aligned using AUTOASSEMBLER (Perkin Elmer) and ClustalX () programs. The population genetic parameters, haplotype diversity, FST values, mismatch distribution, Fu’s Fs statistics, and AMOVA were estimated using ARLEQUIN (). The MDS plot was drawn for the pairwise FST values using package PSYCH in R statistical package (www.r-project.org). Phylogenetic trees were constructed based on 151 unique haplotypes of the river buffalo and a Bos taurus sequence (NC_006853) was used as an outgroup. Bayesian phylogenetic tree was constructed by MrBayes () using the general time reversible model with invariant site plus eight gamma categories. The Markov chain Monte Carlo (MCMC) chains were run for 10 × 106 cycles. A total of 20,000 trees were sampled, and a 50% majority rule consensus tree was generated with burnin = 5,000. The tree construction was repeated three times. The MP tree was generated using the software MEGA (). The close-neighbor-interchange algorithm was employed with 1,000 bootstrapping values. The reduced median network was drawn for the 414 control region sequences using NETWORK program (). The BSP method implemented in BEAST () was used to infer the demographic history of river and swamp buffalo. We used a data set of 414 (492 bp) and 403 (506 bp) mtDNA control region sequences of river and swamp buffalo, respectively (supplementary table S1, Supplementary Material online) for BSP. The MCMC was run for 5 × 107 iterations with a burn-in of 5 × 106 under the Hasegawa–Kishino–Yano model with the substitution rate of 32% per nucleotide Myr−1 (). The genealogies and model parameters were sampled every 5,000 iterations. All the operators were kept at default settings. The MCMC runs were repeated to refine skyline parameters and the convergence of the chains to the stationary distribution was confirmed by effective sample size (>100) for all parameters using TRACER (). […]

Pipeline specifications

Software tools Clustal W, Arlequin, MrBayes, MEGA, BEAST
Applications Phylogenetics, Population genetic analysis
Organisms Bubalus bubalis, Bos taurus