Differential Selection Pressure Among Duplicated Genes In Teleosts
Date
2018-08
Authors
Nuckels, Richard J.
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Abstract
Gene and genomic duplications provide organisms with new genetic material subject to selection. Using myo5, rab11, and rab27 gene families as models, I examined the evolutionary rate differences among duplicated genes and whether selective forces (e.g. purifying selection or positive selection) could be identified in one or both duplicated gene clades. I used phylogenetic and syntenic analyses along with ancestral chromosomal mapping to identify each duplicate. I then analyzed the duplicates using tests for evolutionary selection at the molecular level. Using a branch site-random effects likelihood test, I found evolutionary rate values (ω) to fall into two or three rate classes along at least one branch for one duplicated gene clade for each of the gene trees created. One rate value (ω1) for a percentage of codon sites was close to zero, representing purifying selection. A second rate value (ω2) for a percentage of the codons was much greater than one (ω2 >>>1), signifying positive selection. Two rate classes were observed in the teleost myo5bb branch for the motor domain, two other rate classes were observed for the cargo binding domain for the teleost myo5bb branch, and two rate classes were present in teleost myo5ba for the cargo binding domain. Also, in teleosts, I found two rate classes for the rab11a branch, rab11a1 branch, and rab27bb. Using sequences from 7-10 organisms that diverged from a common ancestor 140-440 million years ago, I found ω values between 0.01 and 0.24 for the whole coding sequence for duplicated genes ranging in size from 200-220 codons. For longer coding sequences (1915 codons), ω ranged from 0.26 to 0.41. Sequences with rates (ω values) that are near or below 0.1 represent more highly conserved sequences. Conversely, sequences with more variation at the nucleotide and amino acid level represent less well conserved sequences, and the possibility for new functioning proteins or domains increases. I examined the percentage of invariant codons present in each of the gene clades and found the percentage of codons that were invariant to range from 6% for the highly variable neck region of myo5 to more than 30% for some highly conserved duplicated rab11 and rab27 genes and some highly conserved regions for some myo5 duplicates. I identified a highly conserved ω for codons for amino acids that have previously been linked with the functionality of the Myo5 and Rab proteins. These data lead me to infer that the duplicated genes remain functional and suggest they have some modified, acquired functionality that remains to be identified.
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Keywords
genetics, genomics, molecular evolution
Citation
Nuckels, R. J. (2018). Differential selection pressure among duplicated genes In teleosts (Unpublished dissertation). Texas State University, San Marcos, Texas.