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HIV/AIDS
Published in Patricia G. Melloy, Viruses and Society, 2023
Having access to a viral genome isolated from a patient, as well as sequence data from earlier patient isolates and even related viral sequences, allows a scientist to conduct something known as “molecular clock” analysis. This analysis is based on the idea that mutations (changes in the DNA or RNA sequence) in any genome occur at relatively the same rate over time across species. The more time that passes, the more mutations. Eventually, a neutral mutation (not conferring an advantage or disadvantage to the organism) becomes “fixed in the population,” and the rate of these changes is known as the substitution rate (Ho 2008). Therefore, one can look at a gene sequence from one species and then from a related species and determine the time when they last had a common ancestor in the tree of life. If you see fewer sequence differences between two genomes, then they are more closely related than sequences where you see many differences (Ho 2008; Zimmer 2011). Many scientists conduct their analysis using a “relaxed clock model” where even if the mutations are not occurring at a regular rate in every organism, a correction can be made, such as through using an average substitution rate (Ho 2008).
Motoo Kimura (1924–1994)
Published in Krishna Dronamraju, A Century of Geneticists, 2018
The neutral theory of molecular evolution holds that at the molecular level, most evolutionary changes and most of the variation within and between species are not caused by natural selection but by genetic drift of mutant alleles that are neutral. A neutral mutation is one that does not affect an organism’s ability to survive and reproduce. The neutral theory allows for the possibility that most mutations are deleterious but holds that because these are rapidly purged by natural selection, they do not make significant contributions to variation within and between species at the molecular level. Mutations that are not deleterious are assumed to be mostly neutral rather than beneficial. In addition to assuming the primacy of neutral mutations, the theory also assumes that the fate of neutral mutations is determined by the sampling processes described by specific models of random genetic drift.
Mitochondrial DNAs and Phylogenetic Relationships
Published in S. K. Dutta, DNA Systematics, 2019
Comparison of the rate of evolution in nuclear and in mtDNA does not directly imply variation in the mutation rates of these two genomes. While the rate of gene substitution is directly related to the neutral mutation rate, the rate can also be influenced by evolutionary constraint upon the two genomes, implying greater constraint in gene substitution for the nuclear genome. Additionally, the rate of evolution is known to vary not only from protein to protein but also between different regions of nuclear DNA such as introns, exons, leader, and trailing sequences. Hence, the gross comparison of genomes may contain substantial heterogeneity in degree and relative level of evolutionary constraint. A particularly interesting and comparative analysis of evolutionary rates in mitochondrial and nuclear encoded proteins points to an elevation of the mitochondrial mutation rate by a factor of 3 over that of the nuclear genome.187 These authors examined the rate of evolution for synonymous substitutions in the URF1, cytochrome oxidase subunit 1 and cytochrome b mitochondrial genes with that in nuclear encoded amylase and immunoglobulin CK (IgCK). Where is defined as the species difference per synonymous nucleotide site, corrected for multiple site substitutions, the data obtained for rat and maize, with species divergence time () of 17 × 106 years (estimated from protein and DNA data) gave as about 0.2 for the protein coding nuclear genes and about 1.17 for the mitochondrial genes. The rate of evolution, estimated as K/2T, was found to be about 5.4 × 10−9 for nuclear genes and 35 × 10−9 for mitochondrial genes. The mitochondrial genome can be concluded to evolve about 6.5 times faster than the nuclear genome. The rate of evolution in nuclear pseudogenes is about twice as fast as it is for nuclear synonymous sites and probably approximates to an upper rate of DNA evolution.188 Hence, the rate of nucleotide substitution in the mitochondrial genome is about three times that in the nucleus and this is strong evidence for a threefold elevation of mutation rate in the mitochondrial genome.
Comparative genome analysis of Alkhumra hemorrhagic fever virus with Kyasanur forest disease and tick-borne encephalitis viruses by the in silico approach
Published in Pathogens and Global Health, 2018
Navaneethan Palanisamy, Dario Akaberi, Johan Lennerstrand, Åke Lundkvist
We studied non-synonymous (Ka) and synonymous (Ks) substitutions in the CDS of AHFV, KFDV and TBEV. Non-synonymous substitutions in the CDS leads to changes in the amino acid sequence, while synonymous substitution does not lead to any change in the amino acid sequence. This study yielded information about whether a virus acquired beneficial mutation (i.e. when Ka/Ks > 1) or neutral mutation (i.e. when Ka/Ks = 1) or negative mutation (i.e. when Ka/Ks < 1). Using 24 AHFV sequences, we found that all the proteins were undergoing negative selection. Similarly, using 6 KFDV sequences and 150 TBEV sequences separately, we found that all the proteins in these viruses were also undergoing purifying or negative selection. Tables 1A–1C shows Ka, Ks and Ka/Ks values for AHFV, KFDV and TBEV, respectively.
Genetic variation patterns of β-thalassemia in Western Andalusia (Spain) reveal a structure of specific mutations within the Iberian Peninsula
Published in Annals of Human Biology, 2021
Luis J. Sánchez-Martínez, Candela L. Hernández, Juan N. Rodríguez, Jean M. Dugoujon, Andrea Novelletto, Paloma Ropero, Luisa Pereira, Rosario Calderón
The sequencing of the gene revealed a total of five pathogenic mutations, listed in sequence order: IVS I-1 (G > A), IVS I-6 (T > C), IVS I-110 (G > A), CD39 (CAG > GAG), and IVS II-745 (C > G). In addition to these deleterious variations, neutral polymorphisms (CAP +20 C > T, CD 2 CAC > CAT [His > His], IVS II-16, IVS II-74 T > G, IVS II-81 C > T, IVS II-666 C > T) were also detected in both patients and control groups. Last, one of the patients harboured a neutral mutation on one chromosome at position 71,839 (A > C) that, to our knowledge, has not been previously described elsewhere.