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 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 Episodic evolution of coadapted sets of amino acid sites in mitochondrial proteins

PLoS Genetics ◽  
2021 ◽  
Vol 17 (1) ◽  
pp. e1008711
Author(s):  
Alexey D. Neverov ◽  
Anfisa V. Popova ◽  
Gennady G. Fedonin ◽  
Evgeny A. Cheremukhin ◽  
Galya V. Klink ◽  
...  
Keyword(s):  
Amino Acid ◽  
Protein Structures ◽  
Acid Sites ◽  
The Other ◽  
Mitochondrial Proteins ◽  
Amino Acid Substitutions ◽  
Epistatic Interactions ◽  
Rate Of Evolution ◽  
Episodic Evolution ◽  
Selective Forces

The rate of evolution differs between protein sites and changes with time. However, the link between these two phenomena remains poorly understood. Here, we design a phylogenetic approach for distinguishing pairs of amino acid sites that evolve concordantly, i.e., such that substitutions at one site trigger subsequent substitutions at the other; and also pairs of sites that evolve discordantly, so that substitutions at one site impede subsequent substitutions at the other. We distinguish groups of amino acid sites that undergo coordinated evolution and evolve discordantly from other such groups. In mitochondrion-encoded proteins of metazoans and fungi, we show that concordantly evolving sites are clustered in protein structures. By analysing the phylogenetic patterns of substitutions at concordantly and discordantly evolving site pairs, we find that concordant evolution has two distinct causes: epistatic interactions between amino acid substitutions and episodes of selection independently affecting substitutions at different sites. The rate of substitutions at concordantly evolving groups of protein sites changes in the course of evolution, indicating episodes of selection limited to some of the lineages. The phylogenetic positions of these changes are consistent between proteins, suggesting common selective forces underlying them.

scholarly journals Evolutionary Spread and Recombination of Porcine Endogenous Retroviruses in the Suiformes

2005 ◽  
Vol 79 (1) ◽  
pp. 649-654 ◽  
Author(s):  
Marcus Niebert ◽  
Ralf R. Tönjes
Keyword(s):  
Long Terminal Repeat ◽  
Related Species ◽  
Sus Scrofa ◽  
Endogenous Retroviruses ◽  
Phylogenetic Distance ◽  
African Origin ◽  
Closely Related Species ◽  
Separate Event ◽  
Porcine Endogenous Retroviruses ◽  
The Common

ABSTRACT Different Suiformes with increasing phylogenetic distance to the common pig (Sus scrofa) were assayed for the presence of porcine endogenous retroviruses (PERV) in general (pol gene), while the distribution of long terminal repeat (LTR) types (with or without repeats in U3) and env genes (classes A, B, and C) were determined in detail. PERV was not detectable in the most distantly related species, while classes PERV-A and PERV-B are present in Suiformes originating in the Pliocene epoch, and class PERV-C was detectable only in S. scrofa and in closely related species originating in the Holocene epoch. This distribution pattern of PERV classes is in line with our previous study on the age of PERV (45) and suggests an African origin of about 7.5 million years ago (MYA) and a gradual spread of PERV through the Suiformes. It seems likely that PERV-C originated more recently (1.5 to 3.5 MYA) by recombination with a homologue of unknown descent, while the origin of the repeatless LTR was a separate event approximately 3.5 MYA.

scholarly journals A coarse-graining, ultrametric approach to resolve the phylogeny of prokaryotic strains with frequent homologous recombination

2020 ◽  
Author(s):  
Tin Yau Pang
Keyword(s):  
Amino Acid ◽  
Homologous Recombination ◽  
Empirical Distribution ◽  
Local Density ◽  
Phylogenetic Reconstruction ◽  
Sequence Divergence ◽  
Coarse Graining ◽  
Amino Acid Sequences ◽  
Phylogenetic Distance ◽  
Frequent Event

Abstract Background A frequent event in the evolution of prokaryotic genomes is homologous recombination, where a foreign DNA stretch replaces a genomic region similar in sequence. Recombination can affect the relative position of two genomes in a phylogenetic reconstruction in two different ways: (i) one genome can recombine with a DNA stretch that is similar to the other genome, thereby reducing their pairwise sequence divergence; (ii) one genome can recombine with a DNA stretch from an outgroup genome, increasing the pairwise divergence. While several recombination-aware phylogenetic algorithms exist, many of these cannot account for both types of recombination; some algorithms can, but do so inefficiently. Moreover, many of them reconstruct the ancestral recombination graph (ARG) to help infer the genome tree, and require that a substantial portion of each genome has not been affected by recombination, a sometimes unrealistic assumption. Results Here, we propose a coarse-graining approach for phylogenetic reconstruction (CGP), which is recombination-aware but forgoes ARG reconstruction. It accounts for the tendency of a higher effective recombination rate between genomes with a lower phylogenetic distance. It is applicable even if all genomic regions have experienced substantial amounts of recombination, and can be used on both nucleotide and amino acid sequences. CGP considers the local density of substitutions along pairwise genome alignments, fitting a model to the empirical distribution of substitution density to infer the pairwise coalescent time. Given all pairwise coalescent times, CGP reconstructs an ultrametric tree representing vertical inheritance. Based on simulations, we show that the proposed approach can reconstruct ultrametric trees with accurate topology, branch lengths, and root positioning. Applied to a set of E. coli strains, the reconstructed trees are most consistent with gene distributions when inferred from amino acid sequences, a data type that cannot be utilized by many alternative approaches. Conclusions The CGP algorithm is more accurate than alternative recombination-aware methods for ultrametric phylogenetic reconstructions.

Additions to Taiwan fungal flora 2: Ophiosphaerella taiwanica sp. nov.

Phytotaxa ◽  
2019 ◽  
Vol 413 (1) ◽  
pp. 39-48 ◽  
Author(s):  
HIRAN A. ARIYAWANSA ◽  
E. B. GARETH JONES
Keyword(s):  
Dna Sequences ◽  
Related Species ◽  
Phylogenetic Reconstruction ◽  
New Taxon ◽  
The Novel ◽  
Fungal Flora ◽  
Closely Related Species ◽  
Natural Classification

The genus Ophiosphaerella contains 14 formerly illustrated species and is characterized by papillated ascomata bearing fissitunicate cylindrical asci frequently narrower near the base, with a short furcate pedicel and filamentous, pale brown, multi-septate ascospores without swollen cells or separating into part spores. We describe an Ophiosphaerella taxon that is new to science isolated from Yushania niitakayamensis in Cilai Mountain, Taiwan. We conducted polyphasic methods using single and multi-locus (ITS, LSU, SSU, and tef1-α) phylogenetic reconstruction united with morphology to evaluate the natural classification of the novel taxon. The results show that our Ophiosphaerella isolates are different from closely related species O. aquaticus and O. agrostidis based on distinct size differences of the ascomata, asci, ascospores, host and DNA sequences data, thus should be recognised here as a new taxon Ophiosphaerella taiwanica sp. nov.

scholarly journals Divergence and introgression among the virilis group of Drosophila

2022 ◽  
Author(s):  
Leeban Yusuf ◽  
Venera Tyukmaeva ◽  
Anneli Hoikkala ◽  
Michael G Ritchie
Keyword(s):  
Gene Flow ◽  
Related Species ◽  
De Novo ◽  
Phylogenetic Reconstruction ◽  
Sequence Divergence ◽  
Sexual Isolation ◽  
Whole Genome Sequencing Data ◽  
Sequencing Data ◽  
Closely Related Species ◽  
Virilis Group

Speciation with gene flow is now widely regarded as common. However, the frequency of introgression between recently diverged species and the evolutionary consequences of gene flow are still poorly understood. The virilis group of Drosophila contains around a dozen species that are geographically widespread and show varying levels of pre-zygotic and post-zygotic isolation. Here, we utilize de novo genome assemblies and whole-genome sequencing data to resolve phylogenetic relationships and describe patterns of introgression and divergence across the group. We suggest that the virilis group consists of three, rather than the traditional two, subgroups. We found evidence of pervasive phylogenetic discordance caused by ancient introgression events between distant lineages within the group, and much more recent gene flow between closely-related species. When assessing patterns of genome-wide divergence in species pairs across the group, we found no consistent genomic evidence of a disproportionate role for the X chromosome. Some genes undergoing rapid sequence divergence across the group were involved in chemical communication and may be related to the evolution of sexual isolation. We suggest that gene flow between closely-related species has potentially had an impact on lineage-specific adaptation and the evolution of reproductive barriers. Our results show how ancient and recent introgression confuse phylogenetic reconstruction, and suggest that shared variation can facilitate adaptation and speciation.

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 Additive and epistatic effects influence spectral tuning in molluscan retinochrome opsin

2021 ◽  
Author(s):  
G Dalton Smedley ◽  
Kyle E McElroy ◽  
Jeanne M Serb
Keyword(s):  
Amino Acid ◽  
Blue Shift ◽  
Binding Pocket ◽  
Acid Sites ◽  
Site Directed Mutagenesis ◽  
Spectral Tuning ◽  
Closely Related Species ◽  
Absorbance Peak ◽  
The Relationship

The relationship between genotype and phenotype is nontrivial due to often complex molecular pathways that make it difficult to unambiguously relate phenotypes to specific genotypes. Photopigments, an opsin apoprotein bound to a light-absorbing chromophore, present an opportunity to directly relate the amino acid sequence to an absorbance peak phenotype (λmax). We examined this relationship by conducting a series of site-directed mutagenesis experiments of retinochrome, a non-visual opsin, from two closely related species: the common bay scallop, Argopecten irradians, and the king scallop, Pecten maximus. Using protein folding models, we identified three amino acid sites of likely functional importance and expressed mutated retinochrome proteins in vitro. Our results show that the mutation of amino acids lining the opsin binding pocket are responsible for fine spectral tuning, or small changes in the λmax of these light sensitive proteins. Most mutations caused a blue shift regardless of the retinochrome background, with shifts ranging from a 12 nm blue shift to a 5 nm red shift from the wild-type λmax. These mutations do not show an additive effect, but rather suggests the presence of epistatic interactions. This work highlights the importance of binding pocket shape in the evolution of spectral tuning and builds on our ability to relate genotypic changes to phenotypes in an emerging model for opsin functional analysis.

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.

Sign in / Sign up

Export Citation Format

Share Document