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Assessing the accuracy of ancestral protein reconstruction methods.

ABSTRACT: The phylogenetic inference of ancestral protein sequences is a powerful technique for the study of molecular evolution, but any conclusions drawn from such studies are only as good as the accuracy of the reconstruction method. Every inference method leads to errors in the ancestral protein sequence, resulting in potentially misleading estimates of the ancestral protein's properties. To assess the accuracy of ancestral protein reconstruction methods, we performed computational population evolution simulations featuring near-neutral evolution under purifying selection, speciation, and divergence using an off-lattice protein model where fitness depends on the ability to be stable in a specified target structure. We were thus able to compare the thermodynamic properties of the true ancestral sequences with the properties of "ancestral sequences" inferred by maximum parsimony, maximum likelihood, and Bayesian methods. Surprisingly, we found that methods such as maximum parsimony and maximum likelihood that reconstruct a "best guess" amino acid at each position overestimate thermostability, while a Bayesian method that sometimes chooses less-probable residues from the posterior probability distribution does not. Maximum likelihood and maximum parsimony apparently tend to eliminate variants at a position that are slightly detrimental to structural stability simply because such detrimental variants are less frequent. Other properties of ancestral proteins might be similarly overestimated. This suggests that ancestral reconstruction studies require greater care to come to credible conclusions regarding functional evolution. Inferred functional patterns that mimic reconstruction bias should be reevaluated.

SUBMITTER: Williams PD

PROVIDER: S-EPMC1480538 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:BackgroundAs one of the most widely used parsimony methods for ancestral reconstruction, the Fitch method minimizes the total number of hypothetical substitutions along all branches of a tree to explain the evolution of a character. Due to the extensive usage of this method, it has become a scientific endeavor in recent years to study the reconstruction accuracies of the Fitch method. However, most studies are restricted to 2-state evolutionary models and a study for higher-state models is needed since DNA sequences take the format of 4-state series and protein sequences even have 20 states.ResultsIn this paper, the ambiguous and unambiguous reconstruction accuracy of the Fitch method are studied for N-state evolutionary models. Given an arbitrary phylogenetic tree, a recurrence system is first presented to calculate iteratively the two accuracies. As complete binary tree and comb-shaped tree are the two extremal evolutionary tree topologies according to balance, we focus on the reconstruction accuracies on these two topologies and analyze their asymptotic properties. Then, 1000 Yule trees with 1024 leaves are generated and analyzed to simulate real evolutionary scenarios. It is known that more taxa not necessarily increase the reconstruction accuracies under 2-state models. The result under N-state models is also tested.ConclusionsIn a large tree with many leaves, the reconstruction accuracies of using all taxa are sometimes less than those of using a leaf subset under N-state models. For complete binary trees, there always exists an equilibrium interval [a, b] of conservation probability, in which the limiting ambiguous reconstruction accuracy equals to the probability of randomly picking a state. The value b decreases with the increase of the number of states, and it seems to converge. When the conservation probability is greater than b, the reconstruction accuracies of the Fitch method increase rapidly. The reconstruction accuracies on 1000 simulated Yule trees also exhibit similar behaviors. For comb-shaped trees, the limiting reconstruction accuracies of using all taxa are always less than or equal to those of using the nearest root-to-leaf path when the conservation probability is not less than 1/N. As a result, more taxa are suggested for ancestral reconstruction when the tree topology is balanced and the sequences are highly similar, and a few taxa close to the root are recommended otherwise.

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Assessing the accuracy of ancestral protein reconstruction methods.

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