Exam #2 1. Mutation accumulation lines are created by bottlenecking an organism into one or two individuals for many generations. This is done to reduce natural selection as much as possible by ensuring that all but the most deleterious mutations have accumulated in basically a neutral fashion. The authors used these mutations accumulation lines instead of the wild-type C.elegans in order to minimize the possibility of natural selection mutations occurring. Therefore, making it possible for them to observe and analyze other mutations that occur spontaneously. 2. Subfunctionalization is when both copies of the duplicate gene are preserved, but can the job of the original gene can sometimes be split between the two genes. Whereas in neofunctionalization the duplicate gene is transformed into a new gene. Genetic mutations that may have led to functional differences could have been nonsynonymous substitutions or a frame shift that could have happened because of insertion or deletion. These both could lead to some change in the amino acid sequence that would result in a change in the genes function. Subfunctionalization can be distinguished from neofunctionalization by comparing the two genes after duplication. In subfunctionalization the two genes will have two separate functions that have derived from an ancestral gene. Whereas in neofunctionalization, the ancestral gene still exists with no changes to it while there is a new gene function created from the duplicated gene. 3. A paleopolyploid is in an organism that has undergone polyploidization several millions of years ago. In order for organism to be reduced to “paleopolyploid” status, the organism has to under a process known as diploidization. Paleopolyploids are also known as diploids. 4. The example of nefunctionalization that I found was a paper called: Evidence that strong positive selection drives neofunctionalization in the tandemly duplicated polyhomeotic genes in Drosophila. In this the authors are looking at the two polyhomeotic loci genes, ph-d(distal) and ph-p(proximal)are a result of a duplication event and are still in the beginning of their functional divergence. The CG3835 regions of both of the genes were compared in D. melanogaster, D. yakuba, and the D. simulans lines for comparison to each other. This was done to determine how the mutations of the polyhomeotic genes were behaving. They found that even though the ph-d and ph-p are still nearly identical now, the functional divergence is compelled by strong positive selection. It was also determined that they are regulated very differently and this may contribute to their early stage of their divergence. 5. The reason that some DNA sequences are deleted rapidly upon polyploidization is to eliminate genomic incompatibility of the parental genome. These sequences are thought to be too divergent and incapable of existing in the single organism harmoniously. Therefore, eliminating the incompatibility increases the chance of the organism having high fertility and reduces the size of the resultant genome compared to its expected size. 6. Four possible genetic processes that can result in new gene creation are exon shuffling, gene duplication, retroposition, and gene fusion. Exon shuffling is when two or more exons from different genes are brought together or an exon is