Computational protocol: The “Out of Africa Tribe” (II)

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Protocol publication

[…] The trees were generated using MrBayes (http://mrbayes.sourceforge.net), which is the most widely used (bayesian) approach for phylogenies. Then I used the program Simmap 1.5 (www.simmap.com/) which allowed to perform the filtering. SIMMAP 1.5 will also estimate whether two characters are correlated (or associated) using mutational maps. Most ethnographic data was obtained from the The Cambridge Encyclopedia of Hunters and Gatherers (Cambridge University Press, 1999) and by examining the ethnographic collections at the University of British Columbia’s Anthropology Museum, National Anthropology Museum and the Ainu Village of Poroto Kotan. Photographs were also taken at those sites.Each correlation analysis was configured to have an observed sample size > 2,000 and a predictive sample size > 1,000 and was performed as in Huelsenbeck et al. (2003). D (D = ∑i = 1n∑j = 1m∣∣dij∣∣∣) is the overall association between character i and j. d is a measure of the association between the individual states of each character. a is the observed (o) or expected (e) association between character state i and j (n is the number of states for character 1 and m is the number of states for character 2. The association between one state and another is the frequency of occurrence of states on the phylogeny and was given a p-value for correlated evolution significance. It is important to note that some cultural traits may be more prone to change than others,, and for this reason stochastic character mapping is an ideal choice, because this method allows one to measure the probability that a trait changes in a unit of time and, therefore, it also can estimate how “stable” vs. “prone to change” a character is. The null hypothesis is that characters evolve independently of each other and that associations are the result of chance rather than correlated evolution. Since the phenotypes are Boolean data and the number of phenotypes was not too high (< 10) I drew random trees from the genetic data and then filter them using the phenotypes. Ancestral State Reconstruction was also performed using MrBayes and SIMMAP 1.5 using a Bayesian approach. The tree(s) and model parameters were derived from an external program (MrBayes). […]

Pipeline specifications

Software tools MrBayes, SIMMAP
Application Phylogenetics
Organisms Homo sapiens