Relevant bibliographies by topics / Substitution rate variability

Academic literature on the topic 'Substitution rate variability'

Author: Grafiati
Published: 14 March 2023

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Journal articles on the topic "Substitution rate variability"

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Hicks, A. L., and S. Duffy. "Genus-Specific Substitution Rate Variability among Picornaviruses." Journal of Virology 85, no. 15 (May 25, 2011): 7942–47. http://dx.doi.org/10.1128/jvi.02535-10.

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Grigoras, Ioana, Tatiana Timchenko, Ana Grande-Pérez, Lina Katul, Heinrich-Josef Vetten, and Bruno Gronenborn. "High Variability and Rapid Evolution of a Nanovirus." Journal of Virology 84, no. 18 (June 30, 2010): 9105–17. http://dx.doi.org/10.1128/jvi.00607-10.

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ABSTRACT Nanoviruses are multipartite single-stranded DNA (ssDNA) plant viruses that cause important diseases of leguminous crops and banana. Little has been known about the variability and molecular evolution of these viruses. Here we report on the variability of faba bean necrotic stunt virus (FBNSV), a nanovirus from Ethiopia. We found mutation frequencies of 7.52 × 10−4 substitutions per nucleotide in a field population of the virus and 5.07 × 10−4 substitutions per nucleotide in a laboratory-maintained population derived thereof. Based on virus propagation for a period of more than 2 years, we determined a nucleotide substitution rate of 1.78 × 10−3 substitutions per nucleotide per year. This high molecular evolution rate places FBNSV, as a representative of the family Nanoviridae, among the fastest-evolving ssDNA viruses infecting plants or vertebrates.
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Alvarez-Valin, Fernando, José Francisco Tort, and Giorgio Bernardi. "Nonrandom Spatial Distribution of Synonymous Substitutions in the GP63 Gene From Leishmania." Genetics 155, no. 4 (August 1, 2000): 1683–92. http://dx.doi.org/10.1093/genetics/155.4.1683.

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AbstractIn this work we analyze the variability in substitution rates in the GP63 gene from Leishmania. By using a sliding window to estimate substitution rates along the gene, we found that the rate of synonymous substitutions along the GP63 gene is highly correlated with both the rate of amino acid substitution and codon bias. Furthermore, we show that comparisons involving genes that represent independent phylogenetic lines yield very similar divergence/conservation patterns, thus suggesting that deterministic forces (i.e., nonstochastic forces such as selection) generated these patterns. We present evidence indicating that the variability in substitution rates is unambiguously related to functionally relevant features. In particular, there is a clear relationship between rates and the tertiary structure of the encoded protein since all divergent segments are located on the surface of the molecule and facing one side (almost parallel to the cell membrane) on the exposed surface of the organism. Remarkably, the protein segments encoded by these variable regions encircle the active site in a funnel-like distribution. These results strongly suggest that the pattern of nucleotide divergence and, notably, of synonymous divergence is affected by functional constraints.
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Imran, Mohd. "Substitution Trends in the Mitochondrial Cytochrome B Protein Coding Gene and the Corresponding Changes in its Amino Acid Sequence in Catfish Species." International Journal of Research in Science and Technology 12, no. 03 (2022): 11–18. http://dx.doi.org/10.37648/ijrst.v12i03.003.

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The study describes the divergence trends in the partial segment cytochrome b gene (cyt. b) in six catfish species on the basis of the nucleotide substitutions and their location in the triplet codons of the resulting amino acid sequence. The nucleotide sequences of all six species were found A+T rich with average nucleotide frequencies as A: 28.6%; T: 29.3%; G: 13.6%; C: 28.5%, showing an antiguanine bias which was found strongest in R. rita. The transition substitution rate was found highest at 3rd codon position in all the species. The evolutionary divergence follows the trend as highest at 3rd codon position followed by 1st codon position and the least on 2 nd codon position among all species. When amino acid sequences of cytochrome b were aligned, only 12 sites were found with a total 29 amino acid substitutions. which is a resultant of the substitution trend of three codon positions. Majority of the amino acid substitutions were found synonymous and conservative. Three different variability trends are observed in the cyt. b gene which run simultaneously on three different codon positions of triplet codons. Nucleotide substitutions at three codon positions follows the order 3 rd (87) >1st (32) >2nd (03) the frequency of amino acid substitution follows the order 1 st (11) >3rd (04) >2 nd (02); and the frequency of non-conservative amino acid changes found as 2 nd (1:2) >1st (5:11) >3rd (1:4). The study has provided an in-depth understanding of the relative variability and substitution trends in the mitochondrial cytochrome b gene in catfish species at both DNA and protein level.
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Martínez-Arias, Rosa, Francesc Calafell, Eva Mateu, David Comas, Aida Andrés, and Jaume Bertranpetit. "Sequence Variability of a Human Pseudogene." Genome Research 11, no. 6 (May 8, 2001): 1071–85. http://dx.doi.org/10.1101/gr.167701.

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We have obtained haplotypes from the autosomal glucocerebrosidase pseudogene (psGBA) for 100 human chromosomes from worldwide populations, as well as for four chimpanzee and four gorilla chromosomes. In humans, in a 5420-nucleotide stretch analyzed, variation comprises 17 substitutions, a 3-bp deletion, and a length polymorphism at a polyadenine tract. The substitution rate on the pseudogene (1.23 ± 0.22 × 10−9 per nucleotide and year) is within the range of previous estimates considering phylogenetic estimations. Recombination within the pseudogene was recognized, although the low variability of this locus prevented an accurate measure of recombination rates. At least 13% of the psGBAsequence could be attributed to gene conversion from the contiguousGBA gene, whereas the reciprocal event has been shown to lead to Gaucher disease. Human psGBA sequences showed a recent coalescence time (∼200,000 yr ago), and the most ancestral haplotype was found only in Africans; both observations are compatible with the replacement hypothesis of human origins. In a deeper timeframe, phylogenetic analysis showed that the duplication event that created psGBA could be dated at ∼27 million years ago, in agreement with previous estimates.
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Grishin, N. V. "From Complete Genomes to Measures of Substitution Rate Variability Within and Between Proteins." Genome Research 10, no. 7 (July 1, 2000): 991–1000. http://dx.doi.org/10.1101/gr.10.7.991.

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Yeh, So-Wei, Tsun-Tsao Huang, Jen-Wei Liu, Sung-Huan Yu, Chien-Hua Shih, Jenn-Kang Hwang, and Julian Echave. "Local Packing Density Is the Main Structural Determinant of the Rate of Protein Sequence Evolution at Site Level." BioMed Research International 2014 (2014): 1–10. http://dx.doi.org/10.1155/2014/572409.

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Functional and biophysical constraints result in site-dependent patterns of protein sequence variability. It is commonly assumed that the key structural determinant of site-specific rates of evolution is the Relative Solvent Accessibility (RSA). However, a recent study found that amino acid substitution rates correlate better with two Local Packing Density (LPD) measures, the Weighted Contact Number (WCN) and the Contact Number (CN), than with RSA. This work aims at a more thorough assessment. To this end, in addition to substitution rates, we considered four other sequence variability scores, four measures of solvent accessibility (SA), and other CN measures. We compared all properties for each protein of a structurally and functionally diverse representative dataset of monomeric enzymes. We show that the best sequence variability measures take into account phylogenetic tree topology. More importantly, we show that both LPD measures (WCN and CN) correlate better than all of the SA measures, regardless of the sequence variability score used. Moreover, the independent contribution of the best LPD measure is approximately four times larger than that of the best SA measure. This study strongly supports the conclusion that a site’s packing density rather than its solvent accessibility is the main structural determinant of its rate of evolution.
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Mannino, Frank, Sadie Wisotsky, Sergei L. Kosakovsky Pond, and Spencer V. Muse. "Equiprobable discrete models of site-specific substitution rates underestimate the extent of rate variability." PLOS ONE 15, no. 3 (March 2, 2020): e0229493. http://dx.doi.org/10.1371/journal.pone.0229493.

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Pesole, Graziano, and Cecilia Saccone. "A Novel Method for Estimating Substitution Rate Variation Among Sites in a Large Dataset of Homologous DNA Sequences." Genetics 157, no. 2 (February 1, 2001): 859–65. http://dx.doi.org/10.1093/genetics/157.2.859.

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Abstract We present here a novel method to estimate the site-specific relative variability in large sets of homologous sequences. It is based on the simple idea that the more closely related are the compared sequences, the higher the probability of observing nucleotide changes at rapidly evolving sites. A simulation study has been carried out to support the reliability of the method, which has been applied also to analyzing the site variability of all available human sequences corresponding to the two hypervariable regions of the mitochondrial D-loop.
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Ryynänen, Heikki J., and Craig R. Primmer. "Varying signals of the effects of natural selection during teleost growth hormone gene evolution." Genome 49, no. 1 (January 1, 2006): 42–53. http://dx.doi.org/10.1139/g05-079.

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The growth hormone (GH) gene of teleost fish exhibits a higher degree of variability compared with other vertebrate groups. However, the different selective constraints at the sequence level are not well understood. In this study, maximum-likelihood (ML) models of codon substitutions were used to investigate Darwinian adaptive evolution of the GH gene in teleost fishes. Complete GH gene sequences of 54 fish species were classified into 4 orders, and the variable nature of GH was examined by determining the dN and dS rate variation and the rates of molecular evolution for each teleost order. The results indicate that although the overall evolution rate for teleost GH is high ((1.15 ± 0.01) × 10–9 substitutions/(aa site·y)) compared with the "slow phases" in mammals ((0.21 to 0.28 ± 0.05) × 10–9), the vital structure of this gene has been retained. While the majority of the amino acid changes appear to be due to relaxation of purifying selection, some positively selected sites were detected in regions with no specifically identified role in protein function. The positively selected regions observed in salmoniformes lineage suggests a possible role for positive selection driving functional divergence in paralogous forms of the GH gene after whole-genome duplication in this lineage.Key words: teleost fish, growth hormone, positive selection, synonymous substitution, non-synonymous substitution, molecular evolution.
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Book chapters on the topic "Substitution rate variability"

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Landau, Alejandra, Franco Lencina, María Elizabeth Petterson, María Gabriela Pacheco, Susana Costoya, Vanina Brizuela, and Alberto Prina. "The barley chloroplast mutator (cpm) mutant, an extraordinary source of plastome variability." In Mutation breeding, genetic diversity and crop adaptation to climate change, 271–79. Wallingford: CABI, 2021. http://dx.doi.org/10.1079/9781789249095.0027.

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Abstract The plastome is usually considered a highly conserved genome. Compared with the nuclear genome, it is small and has different genetic rules. Through different molecular methods (TILLING, candidate gene sequencing, amplicon massive sequencing and plastome re-sequencing) applied to barley chloroplast mutator (cpm) seedlings, we detected more than 60 polymorphisms affecting a wide variety of plastid genes and several intergenic regions. The genes affected belonged mostly to the plastid genetic machinery and the photosynthetic apparatus, but there were also genes like matK, whose functions are so far not clearly established. Among the isolated mutants, we found the first infA gene mutant in higher plants, two mutants in ycf3 locus and the first psbA gene mutant in barley. The latter is used in breeding barley cultivars where PSII is tolerant to toxic herbicides. Most of the molecular changes were substitutions, and small indels located in microsatellites. However, particular combinations of polymorphisms observed in the rpl23 gene and pseudogene suggest that, besides an increased rate of mutations, an augmented rate of illegitimate recombination also occurred. Although a few substitutions were observed in the mitochondria of cpm plants, we have not yet determined the implications of the cpm for mitochondrial stability. The spectrum of plastome polymorphisms highly suggests that the cpm gene is involved in plastid DNA repair, more precisely taking part in the mismatch repair system. All results show that the cpm mutant is an extraordinary source of plastome variability for plant research and/or plant breeding. This mutant also provides an interesting experimental system in which to investigate the mechanisms responsible for maintaining plastid stability.
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Conference papers on the topic "Substitution rate variability"

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Maddulapalli, K., and S. Azarm. "Product Design Selection With Variability in Preferences for an Implicit Value Function." In ASME 2004 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference. ASMEDC, 2004. http://dx.doi.org/10.1115/detc2004-57339.

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Many existing selection methods require that the Decision Maker (DM) state his/her preferences precisely. However, the DM may not have enough information about the needs of end users thus causing variability in the preferences. To address this problem, we present a method for selection that accounts for variability in the DM’s preferences. Our method is interactive and iterative and assumes only that the preferences of the DM reflect an implicit value function that is quasi-concave and non-decreasing with respect to attributes. Due to the variability, the DM states his/her preferences with a range for Marginal Rate of Substitution (MRS) between attributes at a series of trial designs. The method uses the range of MRS preferences to eliminate “dominated designs” and find a set of “non-eliminated designs”. We present a heuristic to reduce the set of non-eliminated designs and obtain a set of “potentially optimal designs”. The significance of potentially optimal designs is that only one of these designs will be the most preferred for any subset of the range of MRS preferences. We present a payload design selection example to demonstrate and verify that our method indeed finds the set of potentially optimal designs.
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Dulkarnaev, Marat Rafailevich, Yuri Alexeyevich Kotenev, Shamil Khanifovich Sultanov, Alexander Viacheslavovich Chibisov, Daria Yurievna Chudinova, Alexander Yurievich Katashov, Evgeny Alexandrovich Malyavko, Anton Vitalievich Buyanov, Ekaterina Evgenievna Semyonova, and Oksana Alexandrovna Gorbokonenko. "Geological and Field Feasibility Study of Field Development Management Using Marker-Based Production Profiling Surveillance in Horizontal Wells: The Case Study of the Yuzhno-Vyintoiskoye Field." In SPE Russian Petroleum Technology Conference. SPE, 2021. http://dx.doi.org/10.2118/206509-ms.

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In pursuit of efficient oil and gas field development, including hard-to-recover reserves, the key objective is to develop and provide the rationale for oil recovery improvement recommendations. This paper presents the results of the use of the workflow process for optimized field development at two field clusters of the Yuzhno-Vyintoiskoye field using geological and reservoir modelling and dynamic marker-based flow production surveillance in producing horizontal wells. The target reservoir of the Yuzhno-Vyntoiskoye deposit is represented by a series of wedge-shaped Neocomian sandstones. Sand bodies typically have a complex geological structure, lateral continuity and a complex distribution of reservoir rocks. Reservoir beds are characterised by low thickness and permeability. The pay zone of the section is a highly heterogeneous formation, which is manifested through vertical variability of the lithological type of reservoir rocks, lithological substitutions, and the high clay content of reservoirs. The target reservoir of the Yuzhno-Vyintoiskoye field is marked by an extensive water-oil zone with highly variable water saturation. According to paleogeographic data, the reservoir was formed in shallow marine settings. Sand deposits are represented by regressive cyclites that are typical for the progressing coastal shallow water (Dulkarnaev et al., 2020). Currently, the reservoir is in production increase cycle. That is why an integrated approach is used in this work to provide a further rationale and creation of the starting points of the reservoir pressure maintenance system impact at new drilling fields to improve oil recovery and secure sustainable oil production and the reserve development rate under high uncertainty.
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