title: Measuring Accelerated Rates of Insertions and Deletions Independent of Rates of Nucleotide Substitution.
abstract: Evolutionary constraint for insertions and deletions (indels) is not necessarily equal to constraint for nucleotide substitutions for any given region of a genome. Knowing the variation in indel-specific evolutionary rates across the sequence will aid our understanding of evolutionary constraints on indels, and help us infer how indels have contributed to the evolution of the sequence. However, unlike for nucleotide substitutions, there has been no phylogenetic method that can statistically infer significantly different rates of indels across the sequence space independent of substitution rates. Here, we have developed a software that will find sites with accelerated evolutionary rates specific to indels, by introducing a scaling parameter that only applies to the indel rates and not to the nucleotide substitution rates. Using the software, we show that we can find regions of accelerated rates of indels in the protein alignments of primate genomes. We also confirm that the sites that have high rates of indels are different from the sites that have high rates of nucleotide substitutions within the protein sequences. By identifying regions with accelerated rates of indels independent of nucleotide substitutions, we will be able to better understand the impact of indel mutations on protein sequence evolution.
authors: School of Life Sciences, University of Nevada, Las Vegas, NV, 89154, USA.|Department of Computer Science, University of Nevada, Las Vegas, NV, 89154, USA.
authors: Omar
authors: O
authors: Navarro Leija
authors: School of Life Sciences, University of Nevada, Las Vegas, NV, 89154, USA.|Department of Computer Science, University of Nevada, Las Vegas, NV, 89154, USA.
authors: Sanju
authors: S
authors: Varghese
authors: School of Life Sciences, University of Nevada, Las Vegas, NV, 89154, USA. mira.han@unlv.edu.|Nevada Institute of Personalized Medicine, Las Vegas, NV, 89154, USA. mira.han@unlv.edu.
authors: Mira V
authors: http://orcid.org/0000-0002-0488-1170
authors: MV
authors: Han
mesh_terms: D000818:Animals; D003198:Computer Simulation; D019143:Evolution, Molecular; D006801:Humans; D054643:INDEL Mutation; D008957:Models, Genetic; D059645:Mutation Rate; D009711:Nucleotides / Q000235:genetics; D010802:Phylogeny; D011506:Proteins / Q000235:genetics; D017384:Sequence Deletion; D012984:Software; D013045:Species Specificity
chemical_list: D009711:Nucleotides; D011506:Proteins
keywords: Deletions; Evolutionary constraint; Insertions; Substitution rate