scholarly journals HD-AGPs as Speciation Genes: Positive Selection on a Proline-Rich Domain in Non-Hybridizing Species of Petunia, Solanum, and Nicotiana

Plants ◽  
2019 ◽  
Vol 8 (7) ◽  
pp. 211 ◽  
Author(s):  
Tara D. Callaway ◽  
Anu Singh-Cundy
Keyword(s):  
Positive Selection ◽  
Seed Set ◽  
Sequence Divergence ◽  
Ecological Factors ◽  
Purifying Selection ◽  
Rich Region ◽  
Rich Domain ◽  
Species Pairs ◽  
Specific Proteins ◽  
Petunia Integrifolia

Transmitting tissue-specific proteins (TTS proteins) are abundant in the extracellular matrix of Nicotiana pistils, and vital for optimal pollen tube growth and seed set. We have identified orthologs from several species in the Solanaceae, including Petunia axillaris axillaris and Petunia integrifolia. We refer to TTS proteins and their orthologs as histidine domain-arabinogalactan proteins (HD-APGs). HD-AGPs have distinctive domains, including a small histidine-rich region and a C-terminal PAC domain. Pairwise comparisons between HD-AGPs of 15 species belonging to Petunia, Nicotiana, and Solanum show that the his-domain and PAC domain are under purifying selection. In contrast, a proline-rich domain (HV2) is conserved among cross-hybridizing species, but variant in species-pairs that are reproductively isolated by post-pollination pre-fertilization reproductive barriers. In particular, variation in a tetrapeptide motif (XKPP) is systematically correlated with the presence of an interspecific reproductive barrier. Ka/Ks ratios are not informative at the infrageneric level, but the ratios reveal a clear signature of positive selection on two hypervariable domains (HV1 and HV2) when HD-AGPs from five solanaceous genera are compared. We propose that sequence divergence in the hypervariable domains of HD-AGPs reinforces sympatric speciation in incipient species that may have first diverged as a consequence of pollinator preferences or other ecological factors.

scholarly journals Evolution of subgenomic RNA shapes dengue virus adaptation and epidemiological fitness

2018 ◽  
Author(s):  
Esteban Finol ◽  
Eng Eong Ooi
Keyword(s):  
Dengue Virus ◽  
Positive Selection ◽  
Protein Interactions ◽  
Untranslated Region ◽  
Sequence Divergence ◽  
Purifying Selection ◽  
Viral Fitness ◽  
List Type ◽  
Nucleotide Substitutions ◽  
Genetic Changes

AbstractGenetic changes in the dengue virus (DENV) genome affects viral fitness both clinically and epidemiologically. Even in the 3’ untranslated region (3’UTR), mutations could impact the formation of subgenomic flaviviral RNA (sfRNA) and the specificity of sfRNA in inhibiting host proteins necessary for successful viral replication. Indeed, we have recently shown that mutations in the 3’UTR of DENV2 affected its ability to inhibit TRIM25 E3 ligase activity to reduce interferon (IFN) expression, which potentially contributed to the emergence of a new viral clade during the 1994 dengue epidemic in Puerto Rico. However, whether differences in 3’UTRs shaped DENV evolution on a larger scale remains incompletely understood. Herein, we combined RNA phylogeny with phylogenetics to gain insights on sfRNA evolution. We found that sfRNA structures are under purifying selection and highly conserved despite sequence divergence. Interestingly, only the second flaviviral Nuclease-resistant RNA (fNR2) structure of DENV-2 has undergone strong positive selection. Epidemiological reports also suggest that nucleotide substitutions in fNR2 may drive DENV-2 epidemiological fitness, possibly through sfRNA-protein interactions. Collectively, our findings indicate that 3’UTRs are important determinants of DENV fitness in human-mosquito cycles.HighlightsDengue viruses (DENV) preserve RNA elements in their 3’ untranslated region (UTR).Site-specific quantification of natural selection revealed positive selection on DENV2 sfRNA.Flaviviral nuclease-resistant RNA (fNR) structures in DENV 3’UTRs contribute to DENV speciation.A highly evolving fNR structure appears to increase DENV-2 epidemiological fitness.

scholarly journals Reduced purifying selection prevails over positive selection in human copy number variant evolution

2008 ◽  
Vol 18 (11) ◽  
pp. 1711-1723 ◽  
Author(s):  
D.-Q. Nguyen ◽  
C. Webber ◽  
J. Hehir-Kwa ◽  
R. Pfundt ◽  
J. Veltman ◽  
...  
Keyword(s):  
Positive Selection ◽  
Copy Number ◽  
Purifying Selection ◽  
Copy Number Variant

Adaptive evolution of interferon induced protein with tetratricopeptide repeats 5(IFIT5) in birds

2020 ◽  
Author(s):  
Bei Zhang ◽  
Chuansheng Zhang ◽  
Jie Meng ◽  
Yifan Ren ◽  
Jing Gong ◽  
...  
Keyword(s):  
Positive Selection ◽  
Gene Family ◽  
Purifying Selection ◽  
Functional Domain ◽  
Immune Mechanism ◽  
Tetratricopeptide Repeats ◽  
Host Interaction ◽  
Domestic Bird ◽  
Episodic Selection ◽  
Joint Influence

Abstract Background : Previous studies have revealed that wild birds are reservoirs and mobile vectors of viruses, many of which cause illness and mortality in domestic bird and humans. In birds, the invasion of viruses will quickly trigger the innate immune mechanism induced by interferon (IFN). As IFN-stimulated genes (ISGs), the IFIT gene family plays an important role in innate immunity. However, only IFIT5 of the IFIT gene family exists in birds, and the direction and strength of selection acting on IFIT5 are largely unknown. Results : Here, we studied the selection on IFIT5 based on the coding sequence (CDS) data of 20 birds. We identified 12 persistent positive selection sites (PSS), other sites suffered purifying selection and neutral selection; probably due to functional constraints. We also found humans have only 3PSS (189,197and 295), likely due to having more IFIT gene family member that can cooperate to resist virus invasion. The 12 PSS located in the closed clamp structure of the IFIT5 protein, except for position 45. In particular, 3 PSS (335, 342 and 367) were located in the TPR domain, which implied their important roles in virus recognition. We only found 2 episodic PSS (30,332) in Passeriformes, indicating episodic selection pressure in Passeriformes lineage. The positive selection of IFIT5 might provide a theoretical basis for the pathogen-host interaction in birds. Conclusions : We found that the diversity of IFIT5 domains in birds, and that the PSS of IFIT5 is the joint influence of functional domain conservation and the pressure of virus evolution.We speculated that persistent PSS may affect the antiviral function of IFIT5, especially in the region of closed clamp structure. These results lay a theoretical foundation for the further study of the antiviral immune mechanism of IFIT5 in birds.

scholarly journals Genetic Variability and Taxonomic Status of the Nihoa and Laysan Millerbirds

The Condor ◽  
2007 ◽  
Vol 109 (4) ◽  
pp. 954-962
Author(s):  
Robert C. Fleischer ◽  
Beth Slikas ◽  
Jon Beadell ◽  
Colm Atkins ◽  
Carl E. McINTOSH ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Microsatellite Loci ◽  
Sequence Divergence ◽  
Taxonomic Status ◽  
Small Population ◽  
Base Pairs ◽  
Stochastic Effects ◽  
Mtdna Sequence ◽  
Species Pairs ◽  
Two Populations

Abstract The Millerbird (Acrocephalus familiaris) is an endemic Northwestern Hawaiian Islands reed warbler that existed until about 1923 on Laysan Island (A. f. familiaris) and currently occurs in a small population on Nihoa Island (A. f. kingi). The two populations are described as separate subspecies or species on the basis of size and plumage differences. We assessed genetic variation in blood samples from 15 individuals in the modern Nihoa population using approximately 3000 base pairs (bp) of mitochondrial DNA (mtDNA) sequence and 14 microsatellite loci. We also obtained up to 1028 bp of mtDNA sequence from the fragmented DNA of museum specimens of three birds collected on Nihoa in 1923 and five birds collected on Laysan in 1902 and 1911 (ancient samples). Genetic variation in both marker types was extremely low in the modern Nihoa population (nucleotide diversity [π]  =  0.00005 for mtDNA sequences; observed heterozygosity was 7.2% for the microsatellite loci). In contrast, we found three mtDNA haplotypes among the five Laysan individuals (π  =  0.0023), indicating substantially greater genetic variation. The Nihoa and Laysan taxa differed by 1.7% uncorrected mtDNA sequence divergence, a magnitude that would support designation at the subspecies, and perhaps species, level relative to other closely related Acrocephalus species pairs. However, in light of strong ecological similarity between the two taxa, and a need to have additional populations to prevent extinction from stochastic effects and catastrophes, we believe these genetic differences should not deter a potential translocation of individuals from Nihoa to Laysan.

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 Computational Inference of Selection Underlying the Evolution of the Novel Coronavirus, Severe Acute Respiratory Syndrome Coronavirus 2

2020 ◽  
Vol 94 (12) ◽  
Author(s):  
Rachele Cagliani ◽  
Diego Forni ◽  
Mario Clerici ◽  
Manuela Sironi
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
Positive Selection ◽  
Common Ancestor ◽  
Purifying Selection ◽  
Population Variation ◽  
Binding Motif ◽  
The Novel ◽  
Species Barrier ◽  
The Common ◽  
Novel Coronavirus

ABSTRACT The novel coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that recently emerged in China is thought to have a bat origin, as its closest known relative (BatCoV RaTG13) was described previously in horseshoe bats. We analyzed the selective events that accompanied the divergence of SARS-CoV-2 from BatCoV RaTG13. To this end, we applied a population genetics-phylogenetics approach, which leverages within-population variation and divergence from an outgroup. Results indicated that most sites in the viral open reading frames (ORFs) evolved under conditions of strong to moderate purifying selection. The most highly constrained sequences corresponded to some nonstructural proteins (nsps) and to the M protein. Conversely, nsp1 and accessory ORFs, particularly ORF8, had a nonnegligible proportion of codons evolving under conditions of very weak purifying selection or close to selective neutrality. Overall, limited evidence of positive selection was detected. The 6 bona fide positively selected sites were located in the N protein, in ORF8, and in nsp1. A signal of positive selection was also detected in the receptor-binding motif (RBM) of the spike protein but most likely resulted from a recombination event that involved the BatCoV RaTG13 sequence. In line with previous data, we suggest that the common ancestor of SARS-CoV-2 and BatCoV RaTG13 encoded/encodes an RBM similar to that observed in SARS-CoV-2 itself and in some pangolin viruses. It is presently unknown whether the common ancestor still exists and, if so, which animals it infects. Our data, however, indicate that divergence of SARS-CoV-2 from BatCoV RaTG13 was accompanied by limited episodes of positive selection, suggesting that the common ancestor of the two viruses was poised for human infection. IMPORTANCE Coronaviruses are dangerous zoonotic pathogens; in the last 2 decades, three coronaviruses have crossed the species barrier and caused human epidemics. One of these is the recently emerged SARS-CoV-2. We investigated how, since its divergence from a closely related bat virus, natural selection shaped the genome of SARS-CoV-2. We found that distinct coding regions in the SARS-CoV-2 genome evolved under conditions of different degrees of constraint and are consequently more or less prone to tolerate amino acid substitutions. In practical terms, the level of constraint provides indications about which proteins/protein regions are better suited as possible targets for the development of antivirals or vaccines. We also detected limited signals of positive selection in three viral ORFs. However, we warn that, in the absence of knowledge about the chain of events that determined the human spillover, these signals should not be necessarily interpreted as evidence of an adaptation to our species.

scholarly journals Positive selection causes purifying selection (reply)

Nature ◽  
1982 ◽  
Vol 295 (5850) ◽  
pp. 630-630
Author(s):  
WEN-HSIUNG Li ◽  
TAKASHI GOJOBORI ◽  
MASATOSHI NEI
Keyword(s):  
Positive Selection ◽  
Purifying Selection

scholarly journals Positive selection causes purifying selection

Nature ◽  
1982 ◽  
Vol 295 (5850) ◽  
pp. 630-630 ◽  
Author(s):  
MORRIS GOODMAN
Keyword(s):  
Positive Selection ◽  
Purifying Selection

scholarly journals Loss of Cysteine Rich domain was critical for evolution of heterodimerization in Toll proteins

2021 ◽  
Author(s):  
Poonam Ranga ◽  
Suresh Kumar Sawanth ◽  
Nirotpal Mrinal
Keyword(s):  
Positive Selection ◽  
Functional Diversity ◽  
Critical Event ◽  
Major Step ◽  
Protein Dimerization ◽  
Rich Domain ◽  
Disulphide Bonds ◽  
Mammalian Tlrs ◽  
Molecular Patterns ◽  
Cysteine Rich Domain

AbstractToll proteins play roles in immunity/development which have largely remained conserved. However, there are differences in Toll biology as mammalian TLRs recognise pathogen associated molecular patterns (PAMPs) but not their invertebrate homologues. The reason for the same is not known. One critical molecular difference is absence of Cysteine Rich Domain (CRD) in vertebrate Tolls and their presence in invertebrates. Interestingly, in Drosophila, all Toll proteins have CRD except Toll9. This provided us the appropriate model to investigate significance of loss of CRD in Toll evolution. CRDs nudge protein dimerization by forming disulphide bonds hence we asked if they did same in Drosophila Toll-proteins. We tested if, Toll-1(which forms homodimer) can heterodimerize with Toll-9. We found that wildtype Toll-1 didn’t interact with Toll9 however; when CRD of Toll1 was deleted/mutated it formed heterodimer with Toll9. This indicates that presence of CRD limits Toll proteins to form homodimer and thus its loss was a critical event which pushed Toll proteins towards heterodimerization. We further show that Drosophila Toll9 can directly bind dsRNA, a PAMP. Interestingly, dsRNA affinity for toll-9 monomer was twice as that for the dimer, which can be attributed to CRD loss. Thus, we show that loss of CRD was a major step in Toll evolution as it resulted in functional diversity and was a first step towards heterodimer formation. Therefore, we propose that CRD loss was under positive selection and also that heterodimerization of Toll-proteins is an evolved property.One line summaryLoss of Cysteine Rich Domain in Drosophila Toll9 and recognition of dsRNA.

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