A NEW METHOD OF INFERENCE OF ANCESTRAL NUCLEOTIDE AND AMINO-ACID-SEQUENCES

A statistical method was developed for reconstructing the nucleotide o r amino acid sequences of extinct ancestors, given the phylogeny and s equences of the extant species. A model of nucleotide or amino acid su bstitution was employed to analyze data of the present-day sequences, and maximum likelihood estimates of parameters such as branch lengths were used to compare the posterior probabilities of assignments of cha racter states (nucleotides or amino acids) to interior nodes of the tr ee; the assignment having the highest probability was the best reconst ruction at the site. The lysozyme c sequences of six mammals were anal yzed by using the likelihood and parsimony methods. The new likelihood -based method was found to be superior to the parsimony method. The pr obability that the amino acids for all interior nodes at a site recons tructed by the new method are correct was calculated to be 0.91, 0.86, and 0.73 for all, variable, and parsimony-informative sites, respecti vely, whereas the corresponding probabilities for the parsimony method were 0.84, 0.76, and 0.51, respectively. The probability that an amin o acid in an ancestral sequence is correctly reconstructed by the like lihood analysis ranged from 91.3 to 98.7% for the four ancestral seque nces.