Goodman M
J Mol Evol. 1981;17(2):114-20. doi: 10.1007/BF01732683.
Kimura mistook ambiguous maximum parsimony codons for wrong codons. The maximum parsimony method performed well as judged by the two classes of serine codons (which can not be connected by silent mutations) on comparing the parsimony codons for serines in human, rabbit, and mouse alpha hemoglobin chains to actual codons determined by nucleotide sequencing. In genealogical reconstructions involving 247 eucaryotic globins, the maximum parsimony distances separating the contemporary sequences show that Kimura's Poisson and Dayhoff's PAM estimates of rate of globin evolution miss most of the superimposed replacements and are therefore seriously in error. Nor is Kimura's constant rate assumption and his belief in a single origin of myoglobin supported. Lamprey myoglobin appears to be most like lamprey hemoglobin, while gnathostome myoglobin seems closest to gnathostome hemoglobin. It was found that the three types of gnathostome globins (Mb, alpha Hb, beta Hb) evolved between the shark-boney vertebrate and bird-mammal ancestors at a much faster rate than from the latter ancestor to the present. The data indicate that rates were exceedingly fast during the origin of these globin chains because a high proportion of substitutions were adaptive. It was concluded that wherever strong stabilizing selection acts on a protein, somewhere in the past positive Darwinian selection must have spread the amino acid substitutions now being preserved.
木村资生将模糊的最大简约密码子误认为错误密码子。在将人类、兔子和小鼠α-血红蛋白链中丝氨酸的简约密码子与通过核苷酸测序确定的实际密码子进行比较时，根据两类丝氨酸密码子（它们不能通过沉默突变相连）判断，最大简约法表现良好。在涉及247种真核生物珠蛋白的系统发育重建中，当代序列之间的最大简约距离表明，木村资生对珠蛋白进化速率的泊松估计以及戴霍夫的PAM估计遗漏了大部分叠加的替换，因此存在严重错误。木村资生的恒定速率假设以及他关于肌红蛋白单一起源的观点也未得到支持。七鳃鳗肌红蛋白似乎最像七鳃鳗血红蛋白，而有颌类动物的肌红蛋白似乎最接近有颌类动物的血红蛋白。研究发现，有颌类动物的三种珠蛋白（Mb、α-Hb、β-Hb）在鲨鱼-硬骨脊椎动物和鸟类-哺乳动物祖先之间的进化速度比从后者祖先到现在要快得多。数据表明，在这些珠蛋白链起源期间，进化速率非常快，因为很大比例的替换是适应性的。研究得出结论，无论在何处，只要强大的稳定选择作用于一种蛋白质，那么在过去的某个时候，正向达尔文选择必定已经传播了现在被保留的氨基酸替换。
