Computational protocol: Evolutionary History of Hunter-Gatherer Marriage Practices

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Protocol publication

[…] Mitochondrial sequences were manually aligned with the revised Cambridge Reference Sequence . Aligned sequences were then used to construct phylogenies using a general time-reversible model with gamma-distributed rate variation (GTR+Γ+I) and a strict molecular clock in BEAST version 1.6.1 . BEAST does not require an out-group to be specified but instead samples the root position along with the rest of the nodes in the tree. Posterior distributions of parameters were estimated by Markov chain Monte Carlo (MCMC) sampling. Samples were drawn every 10,000 MCMC generations from a total of 20,000,000 generations. The initial half of runs was disregarded to allow for ample burn-in. Tracer software was used to verify convergence to a stationary distribution and sufficient sampling. This method yielded 1,000 hunter-gatherer phylogenies used for the reconstruction of marriage traits. [...] Marriage data (arranged versus courtship, presence versus absence of brideservice or brideprice, and low versus high levels of polygyny) were reconstructed by mapping variation onto mtDNA phylogenies. Three separate reconstruction methods were used in Mesquite software : 1) Bayesian stochastic character mapping , 2) maximum likelihood, and 3) maximum parsimony. All three methods account for phylogenetic uncertainty by running reconstructions over the posterior sample of 1,000 MCMC trees. The advantage of the Bayesian and maximum likelihood techniques is that they explicitly model the rate of loss and gain of particular traits . In contrast, maximum parsimony simply minimizes the total number of losses and gains. Ancestral reconstruction using maximum parsimony is driven by the states of the earliest branch to diverge (in this case, African hunter-gatherers). […]

Pipeline specifications

Software tools BEAST, Mesquite
Application Phylogenetics
Organisms Homo sapiens, Ilex paraguariensis