This project employs the Maximum Likelihood (ML) approach to reconstruct the ancestral states of bird plumage colors, with a special focus on the belly colors of male birds due to their diversity and significance. Markov chain Monte Carlo simulations are used to assess the accuracy of the ML model in inferring the correct states, examining the influence of factors such as phylogenetic tree size, number of states, transition rates, node positions, and the root state’s prior probability. The study finds orange to be the most likely color for the most ancient ancestor in the bird phylogenetic tree. However, the accuracy of these predictions is greatly influenced by the evolutionary rates, becoming less reliable for nodes further from the tips, especially for the root node. The research suggests that lower evolutionary rates, larger trees, and fewer states enhance the accuracy of the ML models.
