scholarly journals Evolutionary Models Accounting for Layers of Selection in Protein-Coding Genes and their Impact on the Inference of Positive Selection

2011 ◽  
Vol 28 (12) ◽  
pp. 3297-3308 ◽  
Author(s):  
N. D. Rubinstein ◽  
A. Doron-Faigenboim ◽  
I. Mayrose ◽  
T. Pupko
Keyword(s):  
Positive Selection ◽  
Evolutionary Models ◽  
Protein Coding ◽  
Protein Coding Genes

scholarly journals Signals of positive selection in mitochondrial protein‐coding genes of woolly mammoth: Adaptation to extreme environments?

2019 ◽  
Vol 9 (12) ◽  
pp. 6821-6832 ◽  
Author(s):  
Jacob Njaramba Ngatia ◽  
Tian Ming Lan ◽  
Thi Dao Dinh ◽  
Le Zhang ◽  
Ahmed Khalid Ahmed ◽  
...  
Keyword(s):  
Positive Selection ◽  
Mitochondrial Protein ◽  
Extreme Environments ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Woolly Mammoth

scholarly journals Preliminary assessment of adaptive evolution of mitochondrial protein coding genes in darters (Percidae: Etheostomatinae)

F1000Research ◽  
2019 ◽  
Vol 8 ◽  
pp. 464 ◽  
Author(s):  
Leos G. Kral ◽  
Sara Watson
Keyword(s):  
Positive Selection ◽  
Adaptive Evolution ◽  
Gene Evolution ◽  
Mitochondrial Gene ◽  
Mitochondrial Protein ◽  
Preliminary Assessment ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Show Evidence ◽  
Selection Of

Background: Mitochondrial DNA of vertebrates contains genes for 13 proteins involved in oxidative phosphorylation. Some of these genes have been shown to undergo adaptive evolution in a variety of species. This study examines all mitochondrial protein coding genes in 11 darter species to determine if any of these genes show evidence of positive selection. Methods: The mitogenome from four darter was sequenced and annotated. Mitogenome sequences for another seven species were obtained from GenBank. Alignments of each of the protein coding genes were subject to codon-based identification of positive selection by Selecton, MEME and FEL. Results: Evidence of positive selection was obtained for six of the genes by at least one of the methods. CYTB was identified as having evolved under positive selection by all three methods at the same codon location. Conclusions: Given the evidence for positive selection of mitochondrial protein coding genes in darters, a more extensive analysis of mitochondrial gene evolution in all the extant darter species is warranted.

scholarly journals PSGfinder: fast identification of genes under divergent positive selection using the dynamic windows method

2017 ◽  
Author(s):  
Joël Tuberosa ◽  
Juan I. Montoya-Burgos
Keyword(s):  
Positive Selection ◽  
Research Laboratory ◽  
Orthologous Genes ◽  
Simple Method ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Link Type ◽  
Genome Wide ◽  
User Friendly ◽  
Multiple Comparison Correction

AbstractSummaryOrthologous genes evolving under divergent positive selection are those involved in divergent adaptive trajectories between related species. Current methods to identify such genes are complex and conservative or present some imperfections, limiting genome-wide searches. We present a simple method, Dynamic Windows, to detect regions of protein-coding genes evolving under divergent positive selection. This method is implemented in PSGfinder, a user-friendly and flexible software, allowing rapid genome-wide screenings of regions with a dN/dS >1. PSGfinder additionally includes an alignment cleaning procedure and an adapted multiple comparison correction to identify significant signals of positive selection.Availability and ImplementationPSGfinder is a software that implements the DWin method, is written in Python and is freely available with its documentation at: https://genev.unige.ch/research/laboratory/Juan-Montoya or at: https://github.com/joel-tuberosa/[email protected]; [email protected]

scholarly journals Pervasive positive selection on duplicated and nonduplicated vertebrate protein coding genes

2008 ◽  
Vol 18 (9) ◽  
pp. 1393-1402 ◽  
Author(s):  
R. A. Studer ◽  
S. Penel ◽  
L. Duret ◽  
M. Robinson-Rechavi
Keyword(s):  
Positive Selection ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Vertebrate Protein

scholarly journals Comparative Mitogenomes of Two Coreamachilis Species (Microcoryphia: Machilidae) along with Phylogenetic Analyses of Microcoryphia

Insects ◽  
2021 ◽  
Vol 12 (9) ◽  
pp. 795
Author(s):  
Jia-Yin Guan ◽  
Shi-Qi Shen ◽  
Zi-Yi Zhang ◽  
Xiao-Dong Xu ◽  
Kenneth B. Storey ◽  
...  
Keyword(s):  
16S Rrna ◽  
Positive Selection ◽  
Adaptive Evolution ◽  
Reproductive Strategies ◽  
Phylogenetic Analyses ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Sister Clade

The order Microcoryphia, commonly known as bristletails, is considered as the most primitive one among living insects. Within this order, two species, Coreamachilis coreanus and C. songi (Machilidae: Machilinae), display the following contrasting reproductive strategies: parthenogenesis occurs in C. coreanus, whereas sexual reproduction is found in C. songi. In the present study, the complete mitogenomes of C. coreanus and C. songi were sequenced to compare their mitogenome structure, analyze relationships within the Microcoryphia, and assess adaptive evolution. The length of the mitogenomes of C. coreanus and C. songi were 15,578 bp and 15,570 bp, respectively, and the gene orders were those of typical insects. A long hairpin structure was found between the ND1 and 16S rRNA genes of both species that seem to be characteristic of Machilinae and Petrobiinae species. Phylogenetic assessment of Coreamachilis was conducted using BI and ML analyses with concatenated nucleotide sequences of the 13 protein-coding genes. The results showed that the monophyly of Machilidae, Machilinae, and Petrobiinae was not supported. The genus Coreamachilis (C. coreanus and C. songi) was a sister clade to Allopsontus helanensis, and then the clade of ((C. coreanus + C. songi) + A. helanensis) was a sister clade to A. baii, which suggests that the monophyly of Allopsontus was not supported. Positive selection analysis of the 13 protein-coding genes failed to reveal any positive selection in C. coreanus or C. songi. The long hairpin structures found in Machilinae and Petrobiinae were highly consistent with the phylogenetic results and could potentially be used as an additional molecular characteristic to further discuss relationships within the Microcoryphia.

scholarly journals Preliminary assessment of adaptive evolution of mitochondrial protein coding genes in darters (Percidae: Etheostomatinae)

F1000Research ◽  
2019 ◽  
Vol 8 ◽  
pp. 464
Author(s):  
Leos G. Kral ◽  
Sara Watson
Keyword(s):  
Positive Selection ◽  
Adaptive Evolution ◽  
Gene Evolution ◽  
Mitochondrial Gene ◽  
Mitochondrial Protein ◽  
Preliminary Assessment ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Show Evidence ◽  
Selection Of

Background: Mitochondrial DNA of vertebrates contains genes for 13 proteins involved in oxidative phosphorylation. Some of these genes have been shown to undergo adaptive evolution in a variety of species. This study examines all mitochondrial protein coding genes in 11 darter species to determine if any of these genes show evidence of positive selection. Methods: The mitogenome from four darter was sequenced and annotated. Mitogenome sequences for another seven species were obtained from GenBank. Alignments of each of the protein coding genes were subject to codon-based identification of positive selection by Selecton, MEME and FEL. Results: Evidence of positive selection was obtained for six of the genes by at least one of the methods. CYTB was identified as having evolved under positive selection by all three methods at the same codon location. Conclusions: Given the evidence for positive selection of mitochondrial protein coding genes in darters, a more extensive analysis of mitochondrial gene evolution in all the extant darter species is warranted.

scholarly journals Tissue-specific evolution of protein coding genes in human and mouse

2014 ◽  
Author(s):  
Nadezda Kryuchkova-Mostacci ◽  
Marc Robinson-Rechavi
Keyword(s):  
Gene Expression ◽  
Positive Selection ◽  
Evolutionary Rate ◽  
Purifying Selection ◽  
Expression Level ◽  
Neutral Evolution ◽  
Protein Coding ◽  
Tissue Specific ◽  
Protein Coding Genes ◽  
Mouse Tissues

Protein-coding genes evolve at different rates, and the influence of different parameters, from gene size to expression level, has been extensively studied. While in yeast gene expression level is the major causal factor of gene evolutionary rate, the situation is more complex in animals. Here we investigate these relations further, especially taking in account gene expression in different organs as well as indirect correlations between parameters. We used RNA-seq data from two large datasets, covering 22 mouse tissues and 27 human tissues. Over all tissues, evolutionary rate only correlates weakly with levels and breadth of expression. The strongest explanatory factors of strong purifying selection are GC content, expression in many developmental stages, and expression in brain tissues. While the main component of evolutionary rate is purifying selection, we also find tissue-specific patterns for sites under neutral evolution and for positive selection. We observe fast evolution of genes expressed in testis, but also in other tissues, notably liver, which are explained by weak purifying selection rather than by positive selection.

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