Molecular Evolution of rbcL in Orthotrichales (Bryophyta): Site Variation, Adaptive Evolution, and Coevolutionary Patterns of Amino Acid Replacements

2021 ◽  
Author(s):  
Moisès Bernabeu ◽  
Josep A. Rosselló
Keyword(s):  
Amino Acid ◽  
Molecular Evolution ◽  
Adaptive Evolution ◽  
Site Variation

scholarly journals Searching for signatures of positive selection in cytochrome b gene associated with subterranean lifestyle in fast-evolving arvicolines (Arvicolinae, Cricetidae, Rodentia)

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Olga V. Bondareva ◽  
Nadezhda A. Potapova ◽  
Kirill A. Konovalov ◽  
Tatyana V. Petrova ◽  
Natalia I. Abramson
Keyword(s):  
Amino Acid ◽  
Oxidative Phosphorylation ◽  
Adaptive Evolution ◽  
Complex Structure ◽  
Subterranean Rodents ◽  
Amino Acid Sequence Variation ◽  
Tertiary Protein Structure ◽  
Metabolic Performance ◽  
The Impact ◽  
Subterranean Species

Abstract Background Mitochondrial genes encode proteins involved in oxidative phosphorylation. Variations in lifestyle and ecological niche can be directly reflected in metabolic performance. Subterranean rodents represent a good model for testing hypotheses on adaptive evolution driven by important ecological shifts. Voles and lemmings of the subfamily Arvicolinae (Rodentia: Cricetidae) provide a good example for studies of adaptive radiation. This is the youngest group within the order Rodentia showing the fastest rates of diversification, including the transition to the subterranean lifestyle in several phylogenetically independent lineages. Results We evaluated the signatures of selection in the mitochondrial cytochrome b (cytB) gene in 62 Arvicolinae species characterized by either subterranean or surface-dwelling lifestyle by assessing amino acid sequence variation, exploring the functional consequences of the observed variation in the tertiary protein structure, and estimating selection pressure. Our analysis revealed that: (1) three of the convergent amino acid substitutions were found among phylogenetically distant subterranean species and (2) these substitutions may have an influence on the protein complex structure, (3) cytB showed an increased ω and evidence of relaxed selection in subterranean lineages, relative to non-subterranean, and (4) eight protein domains possess increased nonsynonymous substitutions ratio in subterranean species. Conclusions Our study provides insights into the adaptive evolution of the cytochrome b gene in the Arvicolinae subfamily and its potential implications in the molecular mechanism of adaptation. We present a framework for future characterizations of the impact of specific mutations on the function, physiology, and interactions of the mtDNA-encoded proteins involved in oxidative phosphorylation.

scholarly journals A Comparative Genomic Survey Provides Novel Insights into Molecular Evolution of l-Aromatic Amino Acid Decarboxylase in Vertebrates

Molecules ◽  
2018 ◽  
Vol 23 (4) ◽  
pp. 917 ◽  
Author(s):  
Yanping Li ◽  
Yunyun Lv ◽  
Chao Bian ◽  
Xinxin You ◽  
Li Deng ◽  
...  
Keyword(s):  
Amino Acid ◽  
Molecular Evolution ◽  
Aromatic Amino Acid ◽  
Comparative Genomic ◽  
Acid Decarboxylase ◽  
Amino Acid Decarboxylase ◽  
Aromatic Amino Acid Decarboxylase

scholarly journals Inferring the frequency spectrum of derived variants to quantify adaptive molecular evolution in protein-coding genes of Drosophila melanogaster

2016 ◽  
Author(s):  
Peter D. Keightley ◽  
Jose Campos ◽  
Tom Booker ◽  
Brian Charlesworth
Keyword(s):  
Amino Acid ◽  
Molecular Evolution ◽  
Frequency Spectrum ◽  
Population Genomics ◽  
Selective Constraint ◽  
Accurate Estimation ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Adaptive Molecular Evolution ◽  
Amino Acid Mutations

Many approaches for inferring adaptive molecular evolution analyze the unfolded site frequency spectrum (SFS), a vector of counts of sites with different numbers of copies of derived alleles in a sample of alleles from a population. Accurate inference of the high copy number elements of the SFS is difficult, however, because of misassignment of alleles as derived versus ancestral. This is a known problem with parsimony using outgroup species. Here, we show that the problem is particularly serious if there is variation in the substitution rate among sites brought about by variation in selective constraint levels. We present a new method for inferring the SFS using one or two outgroups, which attempts to overcome the problem of misassignment. We show that two outgroups are required for accurate estimation of the SFS if there is substantial variation in selective constraints, which is expected to be the case for nonsynonymous sites of protein-coding genes. We apply the method to estimate unfolded SFSs for synonymous and nonsynonymous sites from Phase 2 of the Drosophila Population Genomics Project. We use the unfolded spectra to estimate the frequency and strength of advantageous and deleterious mutations, and estimate that ~50% of amino acid substitutions are positively selected, but that less than 0.5% of new amino acid mutations are beneficial, with a scaled selection strength of Nes ≈ 12.

Rates of Albumin Evolution in Parrots (Aves, Psittaciformes)

1992 ◽  
Vol 40 (3) ◽  
pp. 313 ◽  
Author(s):  
PR Baverstock ◽  
L Christidis ◽  
M Krieg ◽  
J Birrell
Keyword(s):  
Amino Acid ◽  
Molecular Evolution ◽  
Amino Acid Sequence ◽  
Sequence Divergence ◽  
Modern Distribution ◽  
Rate Of Molecular Evolution ◽  
Microcomplement Fixation ◽  
Amino Acid Sequence Divergence ◽  
Lines Of Evidence

A number of lines of evidence suggest that the rate of molecular evolution in birds is slower than in other vertebrates. This hypothesis was tested by measuring the extent of amino-acid sequence divergence in albumin among species of parrots by means of microcomplement fixation. This group was chosen because its modern distribution is strongly suggestive of a Gondwanan origin. The results show that the intercontinental albumin distances are well below those expected for a Gondwanan group. These data are in accord with the hypothesis that birds have a slower rate of molecular evolution, although other explanations are possible.

scholarly journals Neutral theory of molecular evolution and adaptive evolution. 3.

1985 ◽  
Vol 23 (10) ◽  
pp. 682-688
Author(s):  
TERUMI MUKAI
Keyword(s):  
Molecular Evolution ◽  
Adaptive Evolution ◽  
Neutral Theory

scholarly journals Molecular Evolution of the H-NS Protein: Interaction with Hha-Like Proteins Is Restricted to Enterobacteriaceae

2006 ◽  
Vol 189 (1) ◽  
pp. 265-268 ◽  
Author(s):  
Cristina Madrid ◽  
Jesús García ◽  
Miquel Pons ◽  
Antonio Juárez
Keyword(s):  
Amino Acid ◽  
Molecular Evolution ◽  
Amino Acid Sequence ◽  
Protein Interaction ◽  
Terminal Domain ◽  
Key Residues

ABSTRACT We show here that chromosomal hha-like genes are restricted to the Enterobacteriaceae. The H-NS N-terminal domain of members of this family includes an unaltered seven-amino-acid sequence located between helixes 1 and 2, termed the Hha signature, that contains key residues for H-NS-Hha interaction.

Molecular evolution of ion channels: Amino acid sequences and 3D structures

2016 ◽  
Vol 52 (1) ◽  
pp. 28-36
Author(s):  
V. S. Korkosh ◽  
B. S. Zhorov ◽  
D. B. Tikhonov
Keyword(s):  
Amino Acid ◽  
Molecular Evolution ◽  
Ion Channels ◽  
Amino Acid Sequences ◽  
3D Structures
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