Signatures of Adaptation in Mitochondrial Genomes of Palearctic Subterranean Voles (Arvicolinae, Rodentia)

The current study evaluates the selection signals in the evolution of mitochondrial DNA of voles, subfamily Arvicolinae, during the colonization of subterranean environments. The comparative sequence analysis of mitochondrial protein-coding genes of eight subterranean vole species (Prometheomys schaposchnikowi, three species of the genus Ellobius: E. talpinus, E. fuscocapillus and E. lutescens, two species of the genus Terricola: T. subterraneus and T. daghestanicus, Lasiopodomys mandarinus and Hyperacrius fertilis) and their closest aboveground relatives using codon-substitution models was applied. The highest number of selection signatures was detected in genes ATP8 and CYTB. The relaxation of selection was observed in most mtDNA protein-coding genes. In mole voles (genus Ellobius) the signatures of adaptive evolution of mitochondrial genes related to subterranean niche were most pronounced. The number of selection signatures was found to be independent of the evolutionary age of the lineage but fits the degree of specialization to the subterranean niche. The common trends of selective pressures were observed among the evolutionary ancient and highly specialized subterranean rodent families and phylogenetically young lineages of voles. It suggests that the signatures of adaptations in individual mitochondrial protein-coding genes associated with the colonization of the subterranean niche may appear within a rather short evolutionary timespan.

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Mitochondrial DNA Medicine

Bioscience Reports ◽

10.1007/s10540-007-9032-5 ◽

2007 ◽

Vol 27 (1-3) ◽

pp. 5-9 ◽

Cited By ~ 24

Author(s):

Salvatore DiMauro

Keyword(s):

Mitochondrial Dna ◽

Protein Synthesis ◽

Mitochondrial Protein ◽

Point Mutations ◽

Specific Protein ◽

Mitochondrial Protein Synthesis ◽

Mitochondrial Genetics ◽

Protein Coding ◽

Protein Coding Genes ◽

Mitochondrial Medicine

The small, maternally inherited mitochondrial DNA (mtDNA) has turned out to be a hotbed of pathogenic mutations: 15 years into the era of ‘mitochondrial medicine’, over 150 pathogenic point mutations and countless rearrangements have been associated with a variety of multisystemic or tissue-specific human diseases. MtDNA-related disorders can be divided into two major groups: those due to mutations in genes affecting mitochondrial protein synthesis in toto and those due to mutations in specific protein-coding genes. Here we review the mitochondrial genetics and the clinical features of the mtDNA-related diseases.

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Phylogeny of water birds inferred from mitochondrial DNA sequences of nine protein coding genes

10.7287/peerj.preprints.272 ◽

2014 ◽

Author(s):

Tsendsesmee Lkhagvajav Treutlein ◽

Javier Gonzalez ◽

Michael Wink

Keyword(s):

Mitochondrial Dna ◽

Dna Sequences ◽

Mitochondrial Protein ◽

Sister Relationship ◽

Protein Coding ◽

Water Bird ◽

Protein Coding Genes ◽

Reconstruction Methods ◽

Mtdna Sequence ◽

Water Birds

Background: The phylogeny of birds which are adapted to aquatic environments is controversial because of convergent evolution. Methods: To understand water bird evolution in more detail, we sequenced the majority of mitochondrial protein coding genes (6699 nucleotides in length) of 14 water birds, and reconstructed their phylogeny in the context of other taxa across the whole class of birds for which complete mitochondrial DNA (mtDNA) sequences were available. Results: The water bird clade, as defined by Hackett et al. (2008) based on nuclear DNA (ncDNA) sequences, was also found in our study by Bayesian Inference (BI) and Maximum Likelihood (ML) analyses. In both reconstruction methods, genera belonging to the same family generally clustered together with moderate to high statistical support. Above the family level, we identified three monophyletic groups: one clade consisting of Procellariidae, Hydrobatidae and Diomedeidae, and a second clade consisting of Sulidae, Anhingidae and Phalacrocoracidae, and a third clade consisting of Ardeidae and Threskiornithidae. Discussion: Based on our mtDNA sequence data, we recovered a robust direct sister relationship between Ardeidae and Threskiornithidae for the first time for mtDNA. Our comprehensive phylogenetic reconstructions contribute to the knowledge of higher level relationships within the water birds and provide evolutionary hypotheses for further studies.

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Phylogeny of water birds inferred from mitochondrial DNA sequences of nine protein coding genes

10.7287/peerj.preprints.272v1 ◽

2014 ◽

Author(s):

Tsendsesmee Lkhagvajav Treutlein ◽

Javier Gonzalez ◽

Michael Wink

Keyword(s):

Mitochondrial Dna ◽

Dna Sequences ◽

Mitochondrial Protein ◽

Sister Relationship ◽

Protein Coding ◽

Water Bird ◽

Protein Coding Genes ◽

Reconstruction Methods ◽

Mtdna Sequence ◽

Water Birds

Background: The phylogeny of birds which are adapted to aquatic environments is controversial because of convergent evolution. Methods: To understand water bird evolution in more detail, we sequenced the majority of mitochondrial protein coding genes (6699 nucleotides in length) of 14 water birds, and reconstructed their phylogeny in the context of other taxa across the whole class of birds for which complete mitochondrial DNA (mtDNA) sequences were available. Results: The water bird clade, as defined by Hackett et al. (2008) based on nuclear DNA (ncDNA) sequences, was also found in our study by Bayesian Inference (BI) and Maximum Likelihood (ML) analyses. In both reconstruction methods, genera belonging to the same family generally clustered together with moderate to high statistical support. Above the family level, we identified three monophyletic groups: one clade consisting of Procellariidae, Hydrobatidae and Diomedeidae, and a second clade consisting of Sulidae, Anhingidae and Phalacrocoracidae, and a third clade consisting of Ardeidae and Threskiornithidae. Discussion: Based on our mtDNA sequence data, we recovered a robust direct sister relationship between Ardeidae and Threskiornithidae for the first time for mtDNA. Our comprehensive phylogenetic reconstructions contribute to the knowledge of higher level relationships within the water birds and provide evolutionary hypotheses for further studies.

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Polyphyletic Origins of Schizothoracinae Fishes (Cyprinidae) in Respect to Their Mitochondrial Protein-Coding Genes

10.35248/2375-446x.19.7.207 ◽

2019 ◽

Vol 07 (02) ◽

Author(s):

Saira Bibi ◽

Muhammad Fiaz Khan ◽

Aqsa Rehman ◽

Faisal Nouroz

Keyword(s):

Mitochondrial Protein ◽

Protein Coding ◽

Protein Coding Genes

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Patterns of Nucleotide Substitution in Mitochondrial Protein Coding Genes of Vertebrates

Genetics ◽

10.1093/genetics/143.1.537 ◽

1996 ◽

Vol 143 (1) ◽

pp. 537-548 ◽

Cited By ~ 4

Author(s):

Sudhir Kumar

Keyword(s):

Nucleotide Substitution ◽

Mitochondrial Protein ◽

Likelihood Estimation ◽

Nucleotide Composition ◽

Substitution Rates ◽

Protein Coding ◽

Protein Coding Genes ◽

Conserved Genes ◽

Maximum Likelihood Methods ◽

Position Data

Abstract Maximum likelihood methods were used to study the differences in substitution rates among the four nucleotides and among different nucleotide sites in mitochondrial protein-coding genes of vertebrates. In the lst+2nd codon position data, the frequency of nucleotide G is negatively correlated with evolutionary rates of genes, substitution rates vary substantially among sites, and the transition / transversion rate bias (R) is two to five times larger than that expected at random. Generally, largest transition biases and greatest differences in substitution rates among sites are found in the highly conserved genes. The 3rd positions in placental mammal genes exhibit strong nucleotide composition biases and the transitional rates exceed transversional rates by one to two orders of magnitude. Tamura-Nei and Hasegawa-Kishino-Yano models with gamma distributed variable rates among sites (gamma parameter, α) adequately describe the nucleotide substitution process in 1st+2nd position data. In these data, ignoring differences in substitution rates among sites leads to largest biases while estimating substitution rates. Kimura's two-parameter model with variable-rates among sites performs satisfactorily in likelihood estimation of R, α, and overall amount of evolution for lst+2nd position data. It can also be used to estimate pairwise distances with appropriate values of α for a majority of genes.

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Comparative genomic analysis of mitochondrial protein-coding genes in Veneroida clams: Analysis of superfamily-specific genomic and evolutionary features

Marine Genomics ◽

10.1016/j.margen.2015.08.004 ◽

2015 ◽

Vol 24 ◽

pp. 329-334 ◽

Cited By ~ 2

Author(s):

Jae Yeon Hwang ◽

Chang-kyu Lee ◽

Heebal Kim ◽

Bo-Hye Nam ◽

Cheul Min An ◽

...

Keyword(s):

Mitochondrial Protein ◽

Genomic Analysis ◽

Comparative Genomic Analysis ◽

Comparative Genomic ◽

Protein Coding ◽

Protein Coding Genes ◽

Evolutionary Features

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Analysis of codon usage pattern of mitochondrial protein-coding genes in different hookworms

Molecular and Biochemical Parasitology ◽

10.1016/j.molbiopara.2017.11.005 ◽

2018 ◽

Vol 219 ◽

pp. 24-32 ◽

Cited By ~ 6

Author(s):

Bornali Deb ◽

Arif Uddin ◽

Gulshana Akthar Mazumder ◽

Supriyo Chakraborty

Keyword(s):

Codon Usage ◽

Mitochondrial Protein ◽

Codon Usage Pattern ◽

Usage Pattern ◽

Protein Coding ◽

Protein Coding Genes

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A Bayesian Mutation–Selection Framework for Detecting Site-Specific Adaptive Evolution in Protein-Coding Genes

Molecular Biology and Evolution ◽

10.1093/molbev/msaa265 ◽

2020 ◽

Author(s):

Nicolas Rodrigue ◽

Thibault Latrille ◽

Nicolas Lartillot

Keyword(s):

Adaptive Evolution ◽

Real Data ◽

Data Sets ◽

Protein Coding ◽

Site Specific ◽

Protein Coding Genes ◽

Codon Substitution ◽

Selection Framework ◽

Dna Alignment ◽

The Impact

Abstract In recent years, codon substitution models based on the mutation–selection principle have been extended for the purpose of detecting signatures of adaptive evolution in protein-coding genes. However, the approaches used to date have either focused on detecting global signals of adaptive regimes—across the entire gene—or on contexts where experimentally derived, site-specific amino acid fitness profiles are available. Here, we present a Bayesian site-heterogeneous mutation–selection framework for site-specific detection of adaptive substitution regimes given a protein-coding DNA alignment. We offer implementations, briefly present simulation results, and apply the approach on a few real data sets. Our analyses suggest that the new approach shows greater sensitivity than traditional methods. However, more study is required to assess the impact of potential model violations on the method, and gain a greater empirical sense its behavior on a broader range of real data sets. We propose an outline of such a research program.

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