Evidence of purifying selection in exon 3 of interferon regulatory factor-5 (IRF-5) gene in Nigerian indigenous chickens

2020 ◽  
Vol 36 (2) ◽  
Author(s):  
S.O. Durosaro ◽  
M.O. Ozoje ◽  
A.O. Adebambo ◽  
O.M. Onagbesan
Keyword(s):  
Purifying Selection ◽  
Host Population ◽  
Synonymous Site ◽  
Selective Force ◽  
Synonymous Substitutions ◽  
Immune Genes ◽  
Indigenous Chickens ◽  
Pathogen Load ◽  
Selective Forces ◽  
The Mean

Immune genes are under acute selective pressure in order to resist pathogenic attacks. It is not really clear the type of selective force that acts on immune genes because of diverse pathogen load and host population density, so this experiment studied the selective force acting on exon 3 of IRF-5 gene in Nigerian indigenous chickens. DNA was extracted from 90 Nigerian indigenous chickens and exon 3 of IRF-5 gene was sequenced. The region was tested for deviation from neutrality using DnaSP. The Mean non-synonymous substitutions per non-synonymous site (dN) and mean synonymous substitutions per synonymous site (dS) were calculated to predict likely selective force/event acting on the region using HyPhy software implemented inside MEGA6 software. All the test of neutrality indices obtained for exon 3 of IRF-5 gene in Nigerian indigenous chickens were greater than 1 except Tajima’s D value of normal feather chickens (0.93) and Fu’s Fs value of naked neck chickens (0.71). The dN of 0.00 and negative dS were estimated for exon 3 of IRF-5 gene in all the three genotypes. This study therefore concluded that purifying selective forces are acting on exon 3 of IRF-5 gene in Nigerian indigenous chickens. Keywords: Chickens, co-evolution, immunity, pathogens, selection.

The Age of Nonsynonymous and Synonymous Mutations in Animal mtDNA and Implications for the Mildly Deleterious Theory

Genetics ◽  
1999 ◽  
Vol 153 (1) ◽  
pp. 497-506 ◽  
Author(s):  
Rasmus Nielsen ◽  
Daniel M Weinreich
Keyword(s):  
Dna Sequences ◽  
Purifying Selection ◽  
Data Sets ◽  
Deleterious Mutations ◽  
Synonymous Mutations ◽  
Weak Evidence ◽  
Mitochondrial Data ◽  
The Mean ◽  
Excess Number ◽  
Neutral Mutations

Abstract McDonald/Kreitman tests performed on animal mtDNA consistently reveal significant deviations from strict neutrality in the direction of an excess number of polymorphic nonsynonymous sites, which is consistent with purifying selection acting on nonsynonymous sites. We show that under models of recurrent neutral and deleterious mutations, the mean age of segregating neutral mutations is greater than the mean age of segregating selected mutations, even in the absence of recombination. We develop a test of the hypothesis that the mean age of segregating synonymous mutations equals the mean age of segregating nonsynonymous mutations in a sample of DNA sequences. The power of this age-of-mutation test and the power of the McDonald/Kreitman test are explored by computer simulations. We apply the new test to 25 previously published mitochondrial data sets and find weak evidence for selection against nonsynonymous mutations.

scholarly journals Genetic variation in West Nile virus from naturally infected mosquitoes and birds suggests quasispecies structure and strong purifying selection

2005 ◽  
Vol 86 (8) ◽  
pp. 2175-2183 ◽  
Author(s):  
Greta Jerzak ◽  
Kristen A. Bernard ◽  
Laura D. Kramer ◽  
Gregory D. Ebel
Keyword(s):  
Genetic Diversity ◽  
West Nile Virus ◽  
Consensus Sequence ◽  
Purifying Selection ◽  
Infected Mosquito ◽  
Structural Protein ◽  
Coding Region ◽  
West Nile ◽  
Transmission Cycle ◽  
The Mean

Intrahost genetic diversity was analysed in naturally infected mosquitoes and birds to determine whether West Nile virus (WNV) exists in nature as a quasispecies and to quantify selective pressures within and between hosts. WNV was sampled from ten infected birds and ten infected mosquito pools collected on Long Island, NY, USA, during the peak of the 2003 WNV transmission season. A 1938 nt fragment comprising the 3′ 1159 nt of the WNV envelope (E) coding region and the 5′ 779 nt of the non-structural protein 1 (NS1) coding region was amplified and cloned and 20 clones per specimen were sequenced. Results from this analysis demonstrate that WNV infections are derived from a genetically diverse population of genomes in nature. The mean nucleotide diversity was 0·016 % within individual specimens and the mean percentage of clones that differed from the consensus sequence was 19·5 %. WNV sequences in mosquitoes were significantly more genetically diverse than WNV in birds. No host-dependent bias for particular types of mutations was observed and estimates of genetic diversity did not differ significantly between E and NS1 coding sequences. Non-consensus clones obtained from two avian specimens had highly similar genetic signatures, providing preliminary evidence that WNV genetic diversity may be maintained throughout the enzootic transmission cycle, rather than arising independently during each infection. Evidence of purifying selection was obtained from both intra- and interhost WNV populations. Combined, these data support the observation that WNV populations may be structured as a quasispecies and document strong purifying natural selection in WNV populations.

scholarly journals Crossing fitness valleys via double substitutions within codons

BMC Biology ◽  
2019 ◽  
Vol 17 (1) ◽  
Author(s):  
Frida Belinky ◽  
Itamar Sela ◽  
Igor B. Rogozin ◽  
Eugene V. Koonin
Keyword(s):  
Amino Acid ◽  
Positive Selection ◽  
Fitness Landscape ◽  
Purifying Selection ◽  
Second Step ◽  
Nucleotide Substitutions ◽  
Protein Coding ◽  
Synonymous Substitutions ◽  
Ancestral States ◽  
Double Substitution

Abstract Background Single nucleotide substitutions in protein-coding genes can be divided into synonymous (S), with little fitness effect, and non-synonymous (N) ones that alter amino acids and thus generally have a greater effect. Most of the N substitutions are affected by purifying selection that eliminates them from evolving populations. However, additional mutations of nearby bases potentially could alleviate the deleterious effect of single substitutions, making them subject to positive selection. To elucidate the effects of selection on double substitutions in all codons, it is critical to differentiate selection from mutational biases. Results We addressed the evolutionary regimes of within-codon double substitutions in 37 groups of closely related prokaryotic genomes from diverse phyla by comparing the fractions of double substitutions within codons to those of the equivalent double S substitutions in adjacent codons. Under the assumption that substitutions occur one at a time, all within-codon double substitutions can be represented as “ancestral-intermediate-final” sequences (where “intermediate” refers to the first single substitution and “final” refers to the second substitution) and can be partitioned into four classes: (1) SS, S intermediate–S final; (2) SN, S intermediate–N final; (3) NS, N intermediate–S final; and (4) NN, N intermediate–N final. We found that the selective pressure on the second substitution markedly differs among these classes of double substitutions. Analogous to single S (synonymous) substitutions, SS double substitutions evolve neutrally, whereas analogous to single N (non-synonymous) substitutions, SN double substitutions are subject to purifying selection. In contrast, NS show positive selection on the second step because the original amino acid is recovered. The NN double substitutions are heterogeneous and can be subject to either purifying or positive selection, or evolve neutrally, depending on the amino acid similarity between the final or intermediate and the ancestral states. Conclusions The results of the present, comprehensive analysis of the evolutionary landscape of within-codon double substitutions reaffirm the largely conservative regime of protein evolution. However, the second step of a double substitution can be subject to positive selection when the first step is deleterious. Such positive selection can result in frequent crossing of valleys on the fitness landscape.

scholarly journals Molecular evolution in immune genes across the avian tree of life

2019 ◽  
Vol 5 ◽  
Author(s):  
Diana C. Outlaw ◽  
V. Woody Walstrom ◽  
Haley N. Bodden ◽  
Chuan-yu Hsu ◽  
Mark Arick ◽  
...  
Keyword(s):  
Purifying Selection ◽  
Tree Of Life ◽  
Innate Immune ◽  
Phylogenetic Study ◽  
Significant Differential Expression ◽  
Immune Genes ◽  
Treatment Groups ◽  
Show Evidence ◽  
Differential Gene ◽  
Innate Immune Genes

Abstract All organisms encounter pathogens, and birds are especially susceptible to infection by malaria parasites and other haemosporidians. It is important to understand how immune genes, primarily innate immune genes which are the first line of host defense, have evolved across birds, a highly diverse group of tetrapods. Here, we find that innate immune genes are highly conserved across the avian tree of life and that although most show evidence of positive or diversifying selection within specific lineages or clades, the number of sites is often proportionally low in this broader context of putative constraint. Rather, evidence shows a much higher level of negative or purifying selection in these innate immune genes – rather than adaptive immune genes – which is consistent with birds' long coevolutionary history with pathogens and the need to maintain a rapid response to infection. We further explored avian responses to haemosporidians by comparing differential gene expression in wild birds (1) uninfected with haemosporidians, (2) infected with Plasmodium and (3) infected with Haemoproteus (Parahaemoproteus). We found patterns of significant differential expression with some genes unique to infection with each genus and a few shared between ‘treatment’ groups, but none that overlapped with the genes included in the phylogenetic study.

Fish population size, and not density, as the determining factor of parasite infection: a case study

Parasitology ◽  
2004 ◽  
Vol 128 (3) ◽  
pp. 305-313 ◽  
Author(s):  
A. M. BAGGE ◽  
R. POULIN ◽  
E. T. VALTONEN
Keyword(s):  
Species Richness ◽  
Population Density ◽  
Population Size ◽  
Fish Population ◽  
Host Population ◽  
Fish Length ◽  
Total Fish ◽  
Infection Parameters ◽  
The Mean

The diversity and abundance of parasites vary widely among populations of the same host species. These infection parameters are, to some extent, determined by characteristics of the host population or of its habitat. Recent studies have supported predictions derived from epidemiological models regarding the influence of host population density: parasite abundance and parasite species richness are expected to increase with increasing host population density, at least for directly transmitted parasites. Here, we test this prediction using a natural system in which populations of the crucian carp, Carassius carassius (L.), occur alone, with no other fish species, in a series of 9 isolated ponds in Finland. The ectoparasite communities in these fish populations consist of only 4 species of monogeneans (Dactylogyrus formosus, D. wegeneri, D. intermedius and Gyrodactylus carassii); the total and relative abundance of these 4 species varies among ponds, with one or two of the species missing from certain ponds. Across ponds, only one factor, total fish population size, explained a significant portion of the variance in both the mean number of monogenean species per fish and the mean total abundance of monogenean individual per fish. In contrast, fish population density did not influence either monogenean abundance or species richness, and neither did any of the other variables investigated (mean fish length per pond, number of fish examined per pond, distance to the nearest lake, and several water quality measures). In our system, proximity among fish individuals (i.e. host population density) may not be relevant to the proliferation of monogeneans; instead, the overall availability of host individuals in the host population appeared to be the main constraint limiting parasite population growth.

The Phakopsora pachyrhizi-Kennedia rubicunda host-pathogen association and its relation to leaf rust of Glycine spp

1989 ◽  
Vol 40 (2) ◽  
pp. 265 ◽  
Author(s):  
JJ Burdon ◽  
JM Lenne
Keyword(s):  
Leaf Rust ◽  
Host Population ◽  
Phakopsora Pachyrhizi ◽  
Commercial Cultivar ◽  
Host Pathogen ◽  
The Mean ◽  
Relationship Of ◽  
The Relationship ◽  
Considerable Range

The relationship of isolates of Phakopsora pachyrhizi found on the coastal legume Kennedia rubicunda to isolates found on Glycine spp. was determined by assessing the virulence of ten Kennedia-derived isolates on a wild line of Glycine canescens and on a commercial cultivar of G. max. These two lines are both known to be susceptible to all Glycine-derived isolates of the pathogen. Three patterns of pathogenicity were detected among the Kennedia-derived isolates with isolates being either avirulent or virulent on both host lines; or being avirulent on G. canescens and virulent on G. max.The pathogenicity of five of these Kennedia isolates of P. pachyrhizi was also tested on ten populations of K. rubicunda. The mean levels of resistance and virulence of the host populations and pathogen isolates respectively showed a considerable range. Significant interactions were detected between particular host population-pathogen isolate combinations. These results were compared with those obtained with two representative isolates of P. pachyrhizi collected on Glycine hosts.

scholarly journals Diseases of indigenous chickens in Bokaa village, Kgatleng district, Botswana

2006 ◽  
Vol 77 (3) ◽  
Author(s):  
E.Z. Mushi ◽  
M.G. Binta ◽  
R.G. Chabo ◽  
K. Itebeng
Keyword(s):  
Parasite Burden ◽  
Poultry Feed ◽  
Flock Size ◽  
Ascaridia Galli ◽  
Management Level ◽  
Indigenous Chickens ◽  
Body Weights ◽  
Bursal Disease ◽  
Commercial Poultry ◽  
The Mean

his study examined flock size and management, level of internal and external parasite burden and seroprevalence of antibodies to poultry pathogens in indigenous chickens in Bokaa village, Kgatleng district, Botswana. The mean flock size was 22.6±6.85 with a range of 11-34. The mean body weights of cocks and hens were 2.28±0.56 kg and 1.70 ±0.38 kg, respectively. Housing and commercial poultry feed were not provided. Ascaridia galli, Heterakis gallinarum and Syngamus trachea were found in some birds. Although the chickens were not vaccinated against any poultry diseases, serum antibodies to Newcastle disease, infectious bursal disease and infectious bronchitis were detected.

scholarly journals Calibration of Multiple Poliovirus Molecular Clocks Covering an Extended Evolutionary Range

2008 ◽  
Vol 82 (9) ◽  
pp. 4429-4440 ◽  
Author(s):  
Jaume Jorba ◽  
Ray Campagnoli ◽  
Lina De ◽  
Olen Kew
Keyword(s):  
Rapid Evolution ◽  
Purifying Selection ◽  
Molecular Clocks ◽  
Capsid Region ◽  
Synonymous Substitutions ◽  
Wild Poliovirus ◽  
Nonsynonymous Substitutions ◽  
Antigenic Sites ◽  
Codon Positions

ABSTRACT We have calibrated five different molecular clocks for circulating poliovirus based upon the rates of fixation of total substitutions (K t ), synonymous substitutions (K s ), synonymous transitions (A s ), synonymous transversions (B s ), and nonsynonymous substitutions (K a ) into the P1/capsid region (2,643 nucleotides). Rates were determined over a 10-year period by analysis of sequences of 31 wild poliovirus type 1 isolates representing a well-defined phylogeny derived from a common imported ancestor. Similar rates were obtained by linear regression, the maximum likelihood/single-rate dated-tip method, and Bayesian inference. The very rapid K t [(1.03 ± 0.10) × 10−2 substitutions/site/year] and K s [(1.00 ± 0.08) × 10−2] clocks were driven primarily by the A s clock [(0.96 ± 0.09) × 10−2], the B s clock was ∼10-fold slower [(0.10 ± 0.03) × 10−2], and the more stochastic K a clock was ∼30-fold slower [(0.03 ± 0.01) × 10−2]. Nonsynonymous substitutions at all P1/capsid sites, including the neutralizing antigenic sites, appeared to be constrained by purifying selection. Simulation of the evolution of third-codon positions suggested that saturation of synonymous transitions would be evident at 10 years and complete at ∼65 years of independent transmission. Saturation of synonymous transversions was predicted to be minimal at 20 years and incomplete at 100 years. The rapid evolution of the K t , K s , and A s clocks can be used to estimate the dates of divergence of closely related viruses, whereas the slower B s and K a clocks may be used to explore deeper evolutionary relationships within and across poliovirus genotypes.

scholarly journals Search for the Mechanism of Genetic Variation in the pro Gene of Human Immunodeficiency Virus

1999 ◽  
Vol 73 (10) ◽  
pp. 8167-8178 ◽  
Author(s):  
I. M. Rouzine ◽  
J. M. Coffin
Keyword(s):  
Human Immunodeficiency Virus ◽  
Purifying Selection ◽  
Host Population ◽  
Hiv Protease ◽  
Protease Gene ◽  
Transmission Chain ◽  
Variable Site ◽  
Immunodeficiency Virus ◽  
Synonymous Sites ◽  
The Moment

ABSTRACT To study the mechanism of evolution of the human immunodeficiency virus (HIV) protease gene (pro), we analyzed a database of 213 pro sequences isolated from 11 HIV type 1-infected patients who had not been treated with protease inhibitors. Variation in pro is restricted to rare variable bases which are highly diverse and differ in location among individuals; an average variable base appears in about 16% of individuals. The average intrapatient distance per individual variable site, 27%, is similar for synonymous and nonsynonymous sites, although synonymous sites are twice as abundant. The latter observation excludes selection for diversity as an important, permanently acting factor in the evolution of pro and leaves purifying selection as the only kind of selection. Based on this, we developed a model of evolution, both within individuals and along the transmission chain, which explains variable sites as slightly deleterious mutants slowly reverting to the better-fit variant during individual infection. In the case of a single-source transmission, genetic bottlenecks at the moment of transmission effectively suppress selection, allowing mutants to accumulate along the transmission chain to high levels. However, even very rare coinfections from independent sources are, as we show, able to counteract the bottleneck effect. Therefore, there are two possible explanations for the high mutant frequency. First, the frequency of coinfection in the natural host population may be quite low. Alternatively, a strong variation of the best-adapted sequence between individuals could be caused by a combination of an immune response present in early infection and coselection.

scholarly journals Genomic analysis reveals major determinants of cis-regulatory variation in Capsella grandiflora

2015 ◽  
Author(s):  
Kim A. Steige ◽  
Benjamin Laenen ◽  
Johan Reimegård ◽  
Douglas Scofield ◽  
Tanja Slotte
Keyword(s):  
Evolutionary Biology ◽  
Genomic Analysis ◽  
Purifying Selection ◽  
Gene Body ◽  
Gene Body Methylation ◽  
Specific Expression ◽  
Regulatory Variation ◽  
Wide Range ◽  
Allele Specific ◽  
Selective Forces

Understanding the causes of cis-regulatory variation is a long-standing aim in evolutionary biology. Although cis-regulatory variation has long been considered important for adaptation, we still have a limited understanding of the selective importance and genomic determinants of standing cis-regulatory variation. To address these questions, we studied the prevalence, genomic determinants and selective forces shaping cis-regulatory variation in the outcrossing plant Capsella grandiflora. We first identified a set of 1,010 genes with common cis-regulatory variation using analyses of allele-specific expression (ASE). Population genomic analyses of whole-genome sequences from 32 individuals showed that genes with common cis-regulatory variation are 1) under weaker purifying selection and 2) undergo less frequent positive selection than other genes. We further identified genomic determinants of cis-regulatory variation. Gene-body methylation (gbM) was a major factor constraining cis-regulatory variation, whereas presence of nearby TEs and tissue specificity of expression increased the odds of ASE. Our results suggest that most common cis-regulatory variation in C. grandiflora is under weak purifying selection, and that gene-specific functional constraints are more important for the maintenance of cis-regulatory variation than genome-scale variation in the intensity of selection. Our results agree with previous findings that suggest TE silencing affects nearby gene expression, and provide novel evidence for a link between gbM and cis-regulatory constraint, possibly reflecting greater dosage-sensitivity of body-methylated genes. Given the extensive conservation of gene-body methylation in flowering plants, this suggests that gene-body methylation could be an important predictor of cis-regulatory variation in a wide range of plant species.

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