scholarly journals Excessive Parallelism in Protein Evolution of Lake Baikal Amphipod Species Flock

2020 ◽  
Vol 12 (9) ◽  
pp. 1493-1503
Author(s):  
Valentina Burskaia ◽  
Sergey Naumenko ◽  
Mikhail Schelkunov ◽  
Daria Bedulina ◽  
Tatyana Neretina ◽  
...  
Keyword(s):  
Amino Acid ◽  
Lake Baikal ◽  
Related Species ◽  
Parallel Evolution ◽  
Amino Acid Level ◽  
Species Flock ◽  
Amphipod Species ◽  
Closely Related Species ◽  
Epistatic Interactions ◽  
Synonymous Sites

Abstract Repeated emergence of similar adaptations is often explained by parallel evolution of underlying genes. However, evidence of parallel evolution at amino acid level is limited. When the analyzed species are highly divergent, this can be due to epistatic interactions underlying the dynamic nature of the amino acid preferences: The same amino acid substitution may have different phenotypic effects on different genetic backgrounds. Distantly related species also often inhabit radically different environments, which makes the emergence of parallel adaptations less likely. Here, we hypothesize that parallel molecular adaptations are more prevalent between closely related species. We analyze the rate of parallel evolution in genome-size sets of orthologous genes in three groups of species with widely ranging levels of divergence: 46 species of the relatively recent lake Baikal amphipod radiation, a species flock of very closely related cichlids, and a set of significantly more divergent vertebrates. Strikingly, in genes of amphipods, the rate of parallel substitutions at nonsynonymous sites exceeded that at synonymous sites, suggesting rampant selection driving parallel adaptation. At sites of parallel substitutions, the intraspecies polymorphism is low, suggesting that parallelism has been driven by positive selection and is therefore adaptive. By contrast, in cichlids, the rate of nonsynonymous parallel evolution was similar to that at synonymous sites, whereas in vertebrates, this rate was lower than that at synonymous sites, indicating that in these groups of species, parallel substitutions are mainly fixed by drift.

scholarly journals Parallel evolution of metazoan mitochondrial proteins

2016 ◽  
Author(s):  
Galya V. Klink ◽  
Georgii A. Bazykin
Keyword(s):  
Amino Acid ◽  
Related Species ◽  
Parallel Evolution ◽  
Phylogenetic Reconstruction ◽  
Acid Sites ◽  
Mitochondrial Proteins ◽  
Phylogenetic Distance ◽  
Closely Related Species ◽  
Epistatic Interactions ◽  
The Mean

AbstractAmino acid propensities at amino acid sites change with time due to epistatic interactions or changing environment, affecting the probabilities of fixation of different amino acids. Such changes should lead to an increased rate of homoplasies (reversals, parallelisms, and convergences) at closely related species. Here, we reconstruct the phylogeny of twelve mitochondrial proteins from several thousand metazoan species, and measure the phylogenetic distances between branches at which either the same allele originated repeatedly due to homoplasies, or different alleles originated due to divergent substitutions. The mean phylogenetic distance between parallel substitutions is ∼20% lower than the mean phylogenetic distance between divergent substitutions, indicating that a variant fixed in a species is more likely to be deleterious in a more phylogenetically remote species, compared to a more closely related species. These findings are robust to artefacts of phylogenetic reconstruction or of pooling of sites from different conservation classes or functional groups, and imply that single-position fitness landscapes change at rates similar to rates of amino acid changes.

scholarly journals Nanopore amplicon sequencing reveals molecular convergence and local adaptation of opsin genes

2020 ◽  
Author(s):  
Katherine M. Eaton ◽  
Moisés A. Bernal ◽  
Nathan J.C. Backenstose ◽  
Trevor J. Krabbenhoft
Keyword(s):  
Local Adaptation ◽  
Environmental Gradients ◽  
Parallel Evolution ◽  
Amplicon Sequencing ◽  
Species Flock ◽  
Closely Related Species ◽  
Oxford Nanopore ◽  
Opsin Genes ◽  
Potential Case ◽  
Species Specific

AbstractLocal adaptation can drive diversification of closely related species across environmental gradients and promote convergence of distantly related taxa that experience similar conditions. We examined a potential case of adaptation to novel visual environments in a species flock (Great Lakes salmonids, genus Coregonus) using a new amplicon genotyping protocol on the Oxford Nanopore Flongle. Five visual opsin genes were amplified for individuals of C. artedi, C. hoyi, C. kiyi, and C. zenithicus. Comparisons revealed species-specific differences in the coding sequence of rhodopsin (Tyr261Phe substitution), suggesting local adaptation by C. kiyi to the blue-shifted depths of Lake Superior. Parallel evolution and “toggling” at this amino acid residue has occurred several times across the fish tree of life, resulting in identical changes to the visual systems of distantly related taxa across replicated environmental gradients. Our results suggest that ecological differences and local adaptation to distinct visual environments are strong drivers of both evolutionary parallelism and diversification.

scholarly journals Host shifts result in parallel genetic changes when viruses evolve in closely related species

2017 ◽  
Author(s):  
Ben Longdon ◽  
Jonathan P Day ◽  
Joel M Alves ◽  
Sophia CL Smith ◽  
Thomas M Houslay ◽  
...  
Keyword(s):  
Host Species ◽  
Related Species ◽  
Rna Virus ◽  
Parallel Evolution ◽  
Emerging Infectious Diseases ◽  
New Host ◽  
Closely Related Species ◽  
Genetic Changes ◽  
Host Shifts ◽  
Novel Host

AbstractHost shifts, where a pathogen invades and establishes in a new host species, are a major source of emerging infectious diseases. They frequently occur between related host species and often rely on the pathogen evolving adaptations that increase their fitness in the novel host species. To investigate genetic changes in novel hosts, we experimentally evolved replicate lineages of an RNA virus (Drosophila C Virus) in 19 different species of Drosophilidae and deep sequenced the viral genomes. We found a strong pattern of parallel evolution, where viral lineages from the same host were genetically more similar to each other than to lineages from other host species. When we compared viruses that had evolved in different host species, we found that parallel genetic changes were more likely to occur if the two host species were closely related. This suggests that when a virus adapts to one host it might also become better adapted to closely related host species. This may explain in part why host shifts tend to occur between related species, and may mean that when a new pathogen appears in a given species, closely related species may become vulnerable to the new disease.

scholarly journals Molecular convergent and parallel evolution among four high-elevation anuran species from the Tibetan region

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Bin Lu ◽  
Hong Jin ◽  
Jinzhong Fu
Keyword(s):  
Amino Acid ◽  
Positive Selection ◽  
Convergent Evolution ◽  
Parallel Evolution ◽  
Amino Acid Level ◽  
High Elevation ◽  
Acid Sites ◽  
Anuran Species ◽  
Close Relatives ◽  
Relative Prevalence

Abstract Background To date, evidence for the relative prevalence or rarity of molecular convergent and parallel evolution is conflicting, and understanding of how these processes contribute to adaptation is limited. We compared four high-elevation anuran species (Bufo tibetanus, Nanorana parkeri, Rana kukunoris and Scutiger boulengeri) from the Tibetan region, and examined convergent and parallel amino acid substitutions between them and how they may have contributed to high-elevation adaptation. Results Genomic data of the four high-elevation species and eight of their low-elevation close relatives were gathered. A total of 1098 orthologs shared by all species were identified. We first conducted pairwise comparisons using Zhang and Kumar’s test. Then, the Rconv index was calculated and convergence/divergence correlation plotting was conducted. Furthermore, genes under positive selection and with elevated evolutionary rate were examined. We detected a large number of amino acid sites with convergent or parallel substitutions. Several pairs of high-elevation species, in particular, R. kukunoris vs N. parkeri and B. tibetanus vs S. boulengeri, had excessive amounts of convergent substitutions compared to neutral expectation. Nevertheless, these sites were mostly concentrated in a small number of genes (3–32), and no genome-wide convergence was detected. Furthermore, the majority of these convergent genes were neither under detectable positive selection nor had elevated evolutionary rates, although functional prediction analysis suggested some of the convergent genes could potentially contribute to high-elevation adaptation. Conclusions There is a substantial amount of convergent evolution at the amino-acid level among high-elevation amphibians, although these sites are concentrated in a few genes, not widespread across the genomes. This may attribute to the fact that all the target species are from the same environment. The relative prevalence of convergent substitutions among high-elevation amphibians provides an excellent opportunity for further study of molecular convergent evolution.

scholarly journals Orthopoxvirus K3 orthologs show virus- and host-specific inhibition of the antiviral protein kinase PKR

2020 ◽  
Author(s):  
Chorong Park ◽  
Chen Peng ◽  
M. Julhasur Rahman ◽  
Sherry L. Haller ◽  
Loubna Tazi ◽  
...  
Keyword(s):  
Amino Acid ◽  
Protein Kinase ◽  
Vaccinia Virus ◽  
Related Species ◽  
Translation Initiation Factor ◽  
Virus Species ◽  
Specific Inhibition ◽  
Antiviral Protein ◽  
Closely Related Species ◽  
Species Specific

AbstractThe antiviral protein kinase R (PKR) is an important host restriction factor, which poxviruses must overcome to productively infect host cells. To inhibit PKR, many poxviruses encode a pseudosubstrate mimic of the alpha subunit of eukaryotic translation initiation factor 2 (eIF2), designated K3 in vaccinia virus. Although the interaction between PKR and eIF2α is highly conserved, some K3 orthologs were previously shown to inhibit PKR in a species-specific manner. To better define this host range function, we compared the sensitivity of PKR from 17 mammals to inhibition by K3 orthologs from closely related orthopoxviruses. The K3 orthologs showed species-specific inhibition of PKR and exhibited three distinct inhibition profiles. In some cases, PKR from closely related species showed dramatic differences in their sensitivity to K3 orthologs. Vaccinia virus expressing the camelpox virus K3 ortholog replicated more than three orders of magnitude better in human and sheep cells than a virus expressing vaccinia virus K3, but both viruses replicated comparably well in cow cells. Strikingly, in site-directed mutagenesis experiments between the variola virus and camelpox virus K3 orthologs, we found that different amino acid combinations were necessary to mediate improved or diminished inhibition of PKR derived from different host species. Because there is likely a limited number of possible variations in PKR that affect K3-interactions but still maintain PKR/eIF2α interactions, by chance PKR from some potential new hosts may be susceptible to K3-mediated inhibition from a virus it has never previously encountered. We conclude that neither the sensitivity of host proteins to virus inhibition nor the effectiveness of viral immune antagonists can be inferred from their phylogenetic relatedness but must be experimentally determined.Authors summaryMost virus families are composed of large numbers of virus species. However, in general, only a few prototypic viruses are experimentally studied in-depth, and it is often assumed that the obtained results are representative of other viruses in the same family. In order to test this assumption, we compared the sensitivity of the antiviral protein kinase PKR from various mammals to inhibition by multiple orthologs of K3, a PKR inhibitor expressed by several closely related orthopoxviruses. We found strong differences in PKR inhibition by the K3 orthologs, demonstrating that sensitivity to a specific inhibitor was not indicative of broad sensitivity to orthologs of these inhibitors from closely related viruses. We also show that PKR from even closely related species displayed markedly different sensitivities to these poxvirus inhibitors. Furthermore, we identified amino acid residues in these K3 orthologs that are critical for enhanced or decreased PKR inhibition and found that distinct amino acid combinations affected PKRs from various species differently. Our study shows that even closely related inhibitors of an antiviral protein can vary dramatically in their inhibitory potential, and cautions that results from host-virus interaction studies of a prototypic virus genus member cannot necessarily be extrapolated to other viruses in the same genus without experimental verification.

scholarly journals Revalidation of the stygobiotic species Haber zavreli (Hrabĕ, 1942) (Clitellata, Naididae, Tubificinae) with discussion on the closely related species Haber speciosus (Hrabĕ, 1931) and Haber monfalconensis (Hrabĕ, 1966)

2021 ◽  
Vol 39 ◽  
pp. 143-156
Author(s):  
Elzbieta Dumnicka ◽  
Agata Z. Wojtal
Keyword(s):  
Lake Baikal ◽  
Related Species ◽  
Setal Formula ◽  
Closely Related Species ◽  
Aquatic Fauna ◽  
The Usa

During studies of aquatic fauna in wells situated near Kraków (South Poland), many specimens of clitellates were found. The detailed description of the setal formula and genital organs of the collected individuals made it possible to distinguish Haber zavreli (Hrabĕ, 1942) from the related species: H. speciosus (Hrabĕ, 1931) including synonymized H. simsi and its forms known from the USA (H. speciosus simsi and H. speciosus fluminialis) and H. monfalconensis (Hrabĕ, 1966). In addition, remarks concerning the morphologically similar Haber vetus (Semernoy, 1982) described from Lake Baikal and the stygobiotic species H. turquinae (Juget & Lafont, 1979) are included.

scholarly journals Nucleotide Variation at the Gpdh Locus in the Genus Drosophila

Genetics ◽  
1996 ◽  
Vol 143 (1) ◽  
pp. 375-384
Author(s):  
R Spencer Wells
Keyword(s):  
Amino Acid ◽  
Acid Level ◽  
Amino Acid Level ◽  
Evolutionary Constraint ◽  
Nucleotide Variation ◽  
Neutral Model ◽  
Nucleotide Polymorphism ◽  
Amino Acid Divergence ◽  
Synonymous Sites ◽  
Obscura Group

Abstract The Gpdh locus was sequenced in a broad range of Drosophila species. In contrast to the extreme evolutionary constraint seen at the amino acid level, the synonymous sites evolve at rates comparable to those of other genes. Gpdh nucleotide sequences were used to infer a phylogenetic tree, and the relationships among the species of the obscura group were examined in detail. A survey of nucleotide polymorphism within D. pseudoobscura revealed no amino acid variation in this species. Applying a modified McDonald-Kreitman test, the amino acid divergence between species in the obscura group does not appear to be excessive, implying that drift is adequate to explain the patterns of amino acid change at this locus. In addition, the level of polymorphism at the Gpdh locus in D. pseudoobscura is comparable to that found at other loci, as determined by a Hudson-Kreitman-Aguadé test. Thus, the pattern of nucleotide variation within and between species at the Gpdh locus is consistent with a neutral model.

scholarly journals Transcriptome-based phylogeny of endemic Lake Baikal amphipod species flock: fast speciation accompanied by frequent episodes of positive selection

2017 ◽  
Vol 26 (2) ◽  
pp. 536-553 ◽  
Author(s):  
Sergey A. Naumenko ◽  
Maria D. Logacheva ◽  
Nina V. Popova ◽  
Anna V. Klepikova ◽  
Aleksey A. Penin ◽  
...  
Keyword(s):  
Positive Selection ◽  
Lake Baikal ◽  
Species Flock ◽  
Amphipod Species ◽  
Frequent Episodes

scholarly journals Simultaneous Positive and Purifying Selection on Overlapping Reading Frames of the tat andvpr Genes of Simian Immunodeficiency Virus

2001 ◽  
Vol 75 (17) ◽  
pp. 7966-7972 ◽  
Author(s):  
Austin L. Hughes ◽  
Kristi Westover ◽  
Jack da Silva ◽  
David H. O'Connor ◽  
David I. Watkins
Keyword(s):  
Amino Acid ◽  
Simian Immunodeficiency Virus ◽  
Cytotoxic T Cells ◽  
Parallel Evolution ◽  
Amino Acid Level ◽  
Purifying Selection ◽  
Nucleotide Substitutions ◽  
Reading Frame ◽  
Immunodeficiency Virus ◽  
Reading Frames

ABSTRACT Tat-specific cytotoxic T cells have previously been shown to exert positive Darwinian selection favoring amino acid replacements of an epitope of simian immunodeficiency virus (SIV). The region of thetat gene encoding this epitope falls within a region of overlap between the tat and vpr reading frames, and nonsynonymous nucleotide substitutions in thetat reading frame were found to occur disproportionately in such a way as to cause synonymous changes in the vprreading frame. Comparison of published complete SIV genomes showed Tat to be the least conserved at the amino acid level of nine proteins encoded by the virus, while Vpr was one of the most conserved. Numerous parallel amino acid changes occurred within the Tat epitope independently in different monkeys, and purifying selection on thevpr reading frame, by limiting acceptable nonsynonymous substitutions in the tat reading frame, evidently has enhanced the probability of parallel evolution.

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