scholarly journals Rapid and parallel adaptive mutations in spike S1 drive clade success in SARS-CoV-2

2021 ◽  
Author(s):  
Kathryn E. Kistler ◽  
John Huddleston ◽  
Trevor Bedford
Keyword(s):  
Positive Selection ◽  
Time Scales ◽  
Adaptive Evolution ◽  
Sequence Data ◽  
Focal Point ◽  
Comprehensive Analysis ◽  
Evolutionary Time ◽  
Evolutionary Trajectory ◽  
Protein Coding ◽  
Adaptive Mutations

AbstractDespite the appearance of variant SARS-CoV-2 viruses with altered receptorbinding or antigenic phenotypes, traditional methods for detecting adaptive evolution from sequence data do not pick up strong signals of positive selection. Here, we present a new method for identifying adaptive evolution on short evolutionary time scales with densely-sampled populations. We apply this method to SARS-CoV-2 to perform a comprehensive analysis of adaptively-evolving regions of the genome. We find that spike S1 is a focal point of adaptive evolution, but also identify positively-selected mutations in other genes that are sculpting the evolutionary trajectory of SARS-CoV-2. Protein-coding mutations in S1 are temporally-clustered and, in 2021, the ratio of nonsynonymous to synonymous divergence in S1 is more than 4 times greater than in the equivalent influenza HA1 subunit.

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 Immune genes are hotspots of shared positive selection across birds and mammals

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Allison J Shultz ◽  
Timothy B Sackton
Keyword(s):  
Positive Selection ◽  
Selective Pressure ◽  
Transcriptome Data ◽  
Evolutionary Time ◽  
Protein Coding ◽  
Immune Genes ◽  
Pathogen Challenge ◽  
Significant Enrichment ◽  
Immune Pathways ◽  
Selection For

Consistent patterns of positive selection in functionally similar genes can suggest a common selective pressure across a group of species. We use alignments of orthologous protein-coding genes from 39 species of birds to estimate parameters related to positive selection for 11,000 genes conserved across birds. We show that functional pathways related to the immune system, recombination, lipid metabolism, and phototransduction are enriched for positively selected genes. By comparing our results with mammalian data, we find a significant enrichment for positively selected genes shared between taxa, and that these shared selected genes are enriched for viral immune pathways. Using pathogen-challenge transcriptome data, we show that genes up-regulated in response to pathogens are also enriched for positively selected genes. Together, our results suggest that pathogens, particularly viruses, consistently target the same genes across divergent clades, and that these genes are hotspots of host-pathogen conflict over deep evolutionary time.

scholarly journals The role of selection in the evolution of marine turtles mitogenomes

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Elisa Karen da Silva Ramos ◽  
Lucas Freitas ◽  
Mariana F. Nery
Keyword(s):  
Oxidative Phosphorylation ◽  
Positive Selection ◽  
Adaptive Evolution ◽  
Sea Turtles ◽  
Mitochondrial Protein ◽  
Strong Support ◽  
Sea Turtle ◽  
Protein Coding ◽  
Codon Positions

Abstract Sea turtles are the only extant chelonian representatives that inhabit the marine environment. One key to successful colonization of this habitat is the adaptation to different energetic demands. Such energetic requirement is intrinsically related to the mitochondrial ability to generate energy through oxidative phosphorylation (OXPHOS) process. Here, we estimated Testudines phylogenetic relationships from 90 complete chelonian mitochondrial genomes and tested the adaptive evolution of 13 mitochondrial protein-coding genes of sea turtles to determine how natural selection shaped mitochondrial genes of the Chelonioidea clade. Complete mitogenomes showed strong support and resolution, differing at the position of the Chelonioidea clade in comparison to the turtle phylogeny based on nuclear genomic data. Codon models retrieved a relatively increased dN/dS (ω) on three OXPHOS genes for sea turtle lineages. Also, we found evidence of positive selection on at least three codon positions, encoded by NADH dehydrogenase genes (ND4 and ND5). The accelerated evolutionary rates found for sea turtles on COX2, ND1 and CYTB and the molecular footprints of positive selection found on ND4 and ND5 genes may be related to mitochondrial molecular adaptation to stress likely resulted from a more active lifestyle in sea turtles. Our study provides insight into the adaptive evolution of the mtDNA genome in sea turtles and its implications for the molecular mechanism of oxidative phosphorylation.

scholarly journals Adaptive evolution of animal proteins over development: support for the Darwin selection opportunity hypothesis of Evo-Devo

2017 ◽  
Author(s):  
Jialin Liu ◽  
Marc Robinson-Rechavi
Keyword(s):  
Positive Selection ◽  
Adaptive Evolution ◽  
Morphological Diversity ◽  
Evolutionary Divergence ◽  
Late Development ◽  
Developmental Constraints ◽  
Protein Coding ◽  
Development Support ◽  
Evo Devo ◽  
Cumulative Evidence

AbstractA driving hypothesis of Evo-Devo is that animal morphological diversity is shaped both by adaptation and by developmental constraints. Here we have tested Darwin’s “selection opportunity” hypothesis, according to which high evolutionary divergence in late development is due to strong positive selection. We contrasted it to a “developmental constraint” hypothesis, according to which late development is under relaxed negative selection. Indeed, the highest divergence between species, both at the morphological and molecular levels, is observed late in embryogenesis and post-embryonically. To distinguish between adaptation and relaxation hypotheses, we investigated the evidence of positive selection on protein-coding genes in relation to their expression over development, in fly Drosohila melanogaster, zebrafish Danio rerio, and mouse Mus musculus. First, we found that genes specifically expressed in late development have stronger signals of positive selection. Second, over the full transcriptome, genes with evidence for positive selection trend to be expressed in late development. Finally, genes involved in pathways with cumulative evidence of positive selection have higher expression in late development. Overall, there is a consistent signal that positive selection mainly affects genes and pathways expressed in late embryonic development and in adult. Our results imply that the evolution of embryogenesis is mostly conservative, with most adaptive evolution affecting some stages of post-embryonic gene expression, and thus post-embryonic phenotypes. This is consistent with the diversity of environmental challenges to which juveniles and adults are exposed.

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 The molecular chaperone DnaK accelerates protein evolution

2016 ◽  
Author(s):  
Jose Aguilar-Rodriguez ◽  
Beatriz Sabater-Munoz ◽  
Victor Berlanga ◽  
David Alvarez-Ponce ◽  
Andreas Wagner ◽  
...  
Keyword(s):  
Time Scales ◽  
Protein Evolution ◽  
Sequence Data ◽  
Evolutionary Rates ◽  
Evolutionary Time ◽  
Nucleotide Substitutions ◽  
Chaperone Dnak ◽  
Nucleotide Insertions ◽  
Shock Proteins ◽  
And Function

Molecular chaperones, also known as heat-shock proteins, refold misfolded proteins and help other proteins reach their native conformation. Thanks to these abilities, some chaperones, such as the Hsp90 protein or the chaperonin GroEL, can buffer the deleterious phenotypic effects of mutations that alter protein structure and function. Hsp70 chaperones use a chaperoning mechanism different from Hsp90 and GroEL, and it is not known whether they can also buffer mutations. Here, we show that they can. To this end, we performed a mutation accumulation experiment inEscherichia coli, followed by whole-genome resequencing. Our sequence data shows that overexpression of the Hsp70 chaperone DnaK increases the tolerance of its clients for nonsynonymous nucleotide substitutions and nucleotide insertions and deletions. We also show that this elevated mutational buffering on short evolutionary time scales translates into differences in evolutionary rates on intermediate and long evolutionary time scales. To this end, we compared the evolutionary rates of DnaK clients and nonclients using the genomes ofE. coli,Salmonella typhimurium, and 83 other gamma-proteobacterial species. We find that clients that interact strongly with DnaK evolve faster than weakly interacting clients. Our results imply that all three major chaperone classes can buffer mutations and affect protein evolution. They illustrate how an individual protein like a chaperone can have a disproportionate effect on proteome evolution.

scholarly journals Immune genes are hotspots of shared positive selection across birds and mammals

2018 ◽  
Author(s):  
Allison J. Shultz ◽  
Timothy B. Sackton
Keyword(s):  
Positive Selection ◽  
Selective Pressure ◽  
Transcriptome Data ◽  
Evolutionary Time ◽  
Protein Coding ◽  
Immune Genes ◽  
Pathogen Challenge ◽  
Significant Enrichment ◽  
Immune Pathways ◽  
Selection For

Consistent patterns of positive selection in functionally similar genes can suggest a common selective pressure across a group of species. We use alignments of orthologous protein-coding genes from 39 species of birds to estimate parameters related to positive selection for 11,000 genes conserved across birds. We show that functional pathways related to the immune system, recombination, lipid metabolism, and phototransduction are enriched for positively selected genes. By comparing our results with mammalian data, we find a significant enrichment for positively selected genes shared between taxa, and that these shared selected genes are enriched for viral immune pathways. Using pathogen-challenge transcriptome data, we show that genes up-regulated in response to pathogens are also enriched for positively selected genes. Together, our results suggest that pathogens, particularly viruses, consistently target the same genes across divergent clades, and that these genes are hotspots of host-pathogen conflict over deep evolutionary time.

scholarly journals Polygenic adaptation and convergent evolution across both growth and cardiac genetic pathways in African and Asian rainforest hunter-gatherers

2018 ◽  
Author(s):  
Christina M. Bergey ◽  
Marie Lopez ◽  
Genelle F. Harrison ◽  
Etienne Patin ◽  
Jacob Cohen ◽  
...  
Keyword(s):  
Positive Selection ◽  
Cardiac Development ◽  
Sequence Data ◽  
Human Populations ◽  
High Coverage ◽  
Hunter Gatherers ◽  
Protein Coding ◽  
Genetic Changes ◽  
Evolutionary Pattern ◽  
Northern Latitudes

AbstractDifferent human populations facing similar environmental challenges have sometimes evolved convergent biological adaptations, for example hypoxia resistance at high altitudes and depigmented skin in northern latitudes on separate continents. The pygmy phenotype (small adult body size), a characteristic of hunter-gatherer populations inhabiting both African and Asian tropical rainforests, is often highlighted as another case of convergent adaptation in humans. However, the degree to which phenotypic convergence in this polygenic trait is due to convergent vs. population-specific genetic changes is unknown. To address this question, we analyzed high-coverage sequence data from the protein-coding portion of the genomes (exomes) of two pairs of populations, Batwa rainforest hunter-gatherers and neighboring Bakiga agriculturalists from Uganda, and Andamanese rainforest hunter-gatherers (Jarawa and Onge) and Brahmin agriculturalists from India. We observed signatures of convergent positive selection between the Batwa and Andamanese rainforest hunter-gatherers across the set of genes with annotated ‘growth factor binding’ functions (p < 0.001). Unexpectedly, for the rainforest groups we also observed convergent and population-specific signatures of positive selection in pathways related to cardiac development (e.g. ‘cardiac muscle tissue development’; p = 0.001). We hypothesize that the growth hormone sub-responsiveness likely underlying the pygmy phenotype may have led to compensatory changes in cardiac pathways, in which this hormone also plays an essential role. Importantly, in the agriculturalist populations we did not observe similar patterns of positive selection on sets of genes associated with either growth or cardiac development, indicating that our results most likely reflect a history of convergent adaptation to the similar ecology of rainforest hunter-gatherers rather than a more common or general evolutionary pattern for human populations.

Manifestations of the bias of an unreliable narrator in novel by V. Domontovich “Doctor Serafikus”

2018 ◽  
pp. 132-138
Author(s):  
М. І. Підодвірна
Keyword(s):  
Narrative Analysis ◽  
Focal Point ◽  
Comprehensive Analysis ◽  
The Novel ◽  
Personal Interest ◽  
Cognitive Approach ◽  
Personal Story ◽  
Unreliable Narrator ◽  
German Researcher ◽  
Different Levels

The results and achievements of the main schools and directions of naratology indicate the need to reread both well-known and recondite texts in order to spell out the meanings. We believe that the narrative analysis of prose by Victor Domontovich (the Ukrainian intellectual writer) is interesting and relevant. The article attempts to characterize the manifestations of the bias of an unreliable narato in the novel “Doctor Seraficus” based on the A. Nyuninga’s cognitive approach. A modern German researcher provides a set of tools that can supplemented for a multidimensional consideration of all ambiguities and contradictions in the text. An intelligent game that unfolds in the text manifests itself at different levels. V. Domontovych conducts the biggest game, the game with meaning through the pending authority of unreliable presenter. The text of the novel consists of abstract reflections, notes, dreams, illusions, fantasies, dreams and retrospective journeys. The main law of the text is the game. Irony and contradictions in the narrator’s words encourage the reader to feel dissonance, uncertainty. Therefore, in a narrative analysis, attention is focused on the speaker and who sees (the focal point). It was investigated that the artist Corvin is the narrator of the novel “Doctor Serafikus”, he tries to give as much as possible objectively the personal story. The motives for the unreliability narration based on the personal interest and bias of the character are determined. We identified the main symptoms of the unreliability of the narrator in the work, and the different levels at which the corresponding narrative is expressed, are highlighted. It is established that an unreliable narrative forces distancing itself from a narrator and takes everything that has been said with caution and detachment. Detailed narrative analysis of the work sheds light on the meanings, which for some reason masked, and allows you to establish artistic functions of an unreliable narrator. We believe that understanding this phenomenon makes it possible to make a comprehensive analysis of artistic text.

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