Christopher Smith
UM #30858384
Dr. Jianzhi Zhang
1. The field of study is molecular evolutionary genetics.
2. An hypothesis tested was whether the rate of nonsynonymous nucleotide substitution was significantly higher than that of synonymous substitution for the ECP gene in primates.
3. This hypothesis is important to test because if proven it gives evidence that Darwinian selection did take place at the molecular level in the evolution of the ECP gene from the EDN gene.
4. Two methods were used. Method one was a test of positive selection by comparing the number of synonymous and nonsynonymous nucleotide substitutions per site for each evolutionary branch in the primate family for the ECP and EDN genes. Method two was a test of positive selection by using synonymous and nonsynonymous substations per sequence for each evolutionary branch in the primate family for ECP and EDN genes.
5. The researchers were trying to prove that the ECP gene had evolved from the EDN gene through gene duplication and subsequent Darwinian (positive) selection rather than through random mutations over time. But changes in the genes after the possible duplication mask the effect of the selection, so the rates of both synonymous and nonsynonymous substitutions in the ECP and EDN gene were estimated through methods one and two.
6. The two results possible were that ECP did or did not evolve due to positive selection from EDN. Also, the genes could have been found to be unrelated. If the ECP gene was found to not have evolved from EDN through positive selection, then the explanation would have been that though gene duplication did occur 31 million years ago, no advantageous nonsynonymous substitutions occurred afterwards. Therefore, the mutations would have occurred randomly and would not be linked to any known pathways in the evolution of primates. If ECP was found to have evolved from EDN, then advantageous mutations of the EDN duplicate would have lead it to anti-pathogen toxicity capabilities. A specific time period would have been singled out as having abnormally high rates of nonsynonymous substitution in the EDN duplicate gene and in amino acid chains. The result of ECP and EDN genes not being related would have been nonsensical.
7.
This figure shows the number of arginine changes in the ECP and EDN genes of early evolving primates. A specific time period has been singled out when gene duplication took place (31 MYA), and then over the next 6 years the evolution of the ECP gene occurred. The figure sites specific changes in the number of arginine amino acids in the protein product of the EDN and ECP changes. While the number was consistent throughout time in the EDN gene, an abnormal number of substitutions of arginine took place leading up to the divergence between OW monkeys and hominoids. The figure furthers the hypothesis that there was positive selection in the evolution of ECP. Advantageous mutations occurred before the divergence in the EDN duplicate and were fixated through selection until the ECP gene developed its own important function. Note that EDN remained an important gene and is still present in OW monkeys and hominoids.
8. How do you tell the difference between synonymous and nonsynonymous substitutions in genes?