Reconstruction of Phylogenetic Trees and Evolution of Major Histocompatibility Complex Genes
There are many different methods of phylogenetic reconstruction for DNA sequence data, and their advantages and disadvantages are discussed by considering various factors such as the constancy of evolutionary rate, extent of sequence divergence, variation in evolutionary rate over the sequence, number of nucleotides examined, number of sequences used, etc. It is shown that the bootstrap method of testing the stability of the branching pattern of a tree is not really accurate in evaluating the probability level of the clustering of a group of sequences and that it sometimes leads to an erroneous conclusion particularly when it is applied to the maximum parsimony method. Nevertheless, it is a useful method for obtaining a rough idea of the stability of the branching pattern of a tree. Application of the neighbor-joining and maximum parsimony bootstrap methods to Gyllensten et al.’s sequence data for the DQB locus alleles from primates confirmed the trans-species polymorphism between humans and gorillas, but the trans-species polymorphism between humans and chimpanzees was ambiguous. However, sequence data for the DQA locus alleles confirmed the trans-species polymorphism among all of the humans, chimpanzees and gorillas.
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