When each segment was analyzed individually, 31 supported the "Homo"-"Pan" clade, 10 supported the "Homo"-"Gorilla" clade, and 12 supported the "Pan"-"Gorilla" clade. Using the molecular clock the authors estimated that gorillas split up first 6.2-8.4 MYA and chimpanzees and humans split up 1.6-2.2 million years later (internodal time span) 4.6-6.2 MYA. The internodal time span is useful to estimate the ancestral effective population size of the common ancestor of humans and chimpanzees. A parsimonious analysis revealed that 24 loci supported the "Homo"-"Pan" clade, 7 supported the "Homo"-"Gorilla" clade, 2 supported the "Pan"-"Gorilla" clade and 20 gave no resolution. Additionally they took 35 protein coding loci from databases. Of these 12 supported the "Homo"-"Pan" clade, 3 the "Homo"-"Gorilla" clade, 4 the "Pan"-"Gorilla" clade and 16 gave no resolution. Therefore, only ~70% of the 52 loci that gave a resolution (33 intergenic, 19 protein coding) support the 'correct' species tree. From the fraction of loci which did not support the species tree and the internodal time span they estimated previously, the effective population of the common ancestor of humans and chimpanzees was estimated to be ~52 000 to 96 000. This value is not as high as that from the first study (Takahata), but still much higher than present day effective population size of humans. A third study (Yang, 2002) used the same dataset that Chen and Li used but estimated the ancestral effective population of 'only' ~12,000 to 21,000, using a different statistical method. The alignable sequences within genomes of humans and chimpanzees differ by about 35 million single-nucleotide substitutions. Additionally about 3% of the complete genomes differ by deletions, insertions and duplications. Since mutation rate is relatively constant, roughly one half of these changes occurred in the human lineage. Only a very tiny fraction of those fixed differences gave rise to the different phenotypes of humans and chimpanzees and finding those is a great challenge. The vast majority of the differences are neutral and do not affect the phenotype. Molecular evolution may act in different ways, through protein evolution, gene loss, differential gene regulation and RNA evolution.