Genetic Diversity in the 3′ Terminal 4.7-kb Region of Grapevine leafroll-associated virus 3

Grapevine leafroll-associated virus 3 (GLRaV-3; Ampelovirus, Closteroviridae), associated with grapevine leafroll disease, is an important pathogen found across all major grape-growing regions of the world. The genetic diversity of GLRaV-3 in Napa Valley, CA, was studied by sequencing 4.7 kb in the 3′ terminal region of 50 isolates obtained from Vitis vinifera ‘Merlot’. GLRaV-3 isolates were subdivided into four distinct phylogenetic clades. No evidence of positive selection was observed in the data set, although neutral selection (ratio of nonsynonymous to synonymous substitution rates = 1.1) was observed in one open reading frame (ORF 11, p4). Additionally, the four clades had variable degrees of overall nucleotide diversity. Moreover, no geographical structure among isolates was observed, and isolates belonging to different phylogenetic clades were found in distinct vineyards, with one exception. Considered with the evidence of purifying selection (i.e., against deleterious mutations), these data indicate that the population of GLRaV-3 in Napa Valley is not expanding and its effective population size is not increasing. Furthermore, research on the biological characterization of GLRaV-3 strains might provide valuable insights on the biology of this species that may have epidemiological relevance.

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The global impact of Wolbachia on mitochondrial diversity and evolution

10.1101/160226 ◽

2017 ◽

Cited By ~ 1

Author(s):

Marie Cariou ◽

Laurent Duret ◽

Sylvain Charlat

Keyword(s):

Genetic Diversity ◽

Population Size ◽

Effective Population Size ◽

Synonymous Substitution ◽

Selective Sweeps ◽

Effective Population ◽

Widespread Distribution ◽

Global Impact ◽

Synonymous Substitution Rates ◽

Extinction Events

AbstractThe spread of maternally inherited microorganisms, such as Wolbachia bacteria, can induce indirect selective sweeps on host mitochondria, to which they are linked within the cytoplasm. The resulting reduction in effective population size might lead to smaller mitochondrial diversity and reduced efficiency of natural selection. Although suggested by a few case studies, the global consequences of this process on mitochondrial diversity and evolution remains to be assessed. Here we address this question using a mapping of Wolbachia acquisition / extinction events on a large mitochondrial DNA tree, including over 1,000 species. We show that the presence of Wolbachia is associated with a twofold reduction in silent mitochondrial polymorphism, and a 13% increase in non-synonymous substitution rates. These findings validate the conjecture that the widespread distribution of Wolbachia infections throughout arthropods impacts the effective population size of mitochondria. These effects might in part explain the disconnection between genetic diversity and demographic population size in mitochondria, and also fuel red-queen-like cytonuclear coevolution through the fixation of deleterious mitochondrial alleles.

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Eusociality Shapes Convergent Patterns of Molecular Evolution across Mitochondrial Genomes of Snapping Shrimps

Molecular Biology and Evolution ◽

10.1093/molbev/msaa297 ◽

2020 ◽

Author(s):

Solomon T C Chak ◽

Juan Antonio Baeza ◽

Phillip Barden

Keyword(s):

Molecular Evolution ◽

Genome Evolution ◽

Purifying Selection ◽

Synonymous Substitution ◽

Mitochondrial Genomes ◽

Comparative Genomic ◽

Effective Population ◽

Protein Coding ◽

Marine Realm ◽

Snapping Shrimps

Abstract Eusociality is a highly conspicuous and ecologically impactful behavioral syndrome that has evolved independently across multiple animal lineages. So far, comparative genomic analyses of advanced sociality have been mostly limited to insects. Here, we study the only clade of animals known to exhibit eusociality in the marine realm—lineages of socially diverse snapping shrimps in the genus Synalpheus. To investigate the molecular impact of sociality, we assembled the mitochondrial genomes of eight Synalpheus species that represent three independent origins of eusociality and analyzed patterns of molecular evolution in protein-coding genes. Synonymous substitution rates are lower and potential signals of relaxed purifying selection are higher in eusocial relative to noneusocial taxa. Our results suggest that mitochondrial genome evolution was shaped by eusociality-linked traits—extended generation times and reduced effective population sizes that are hallmarks of advanced animal societies. This is the first direct evidence of eusociality impacting genome evolution in marine taxa. Our results also strongly support the idea that eusociality can shape genome evolution through profound changes in life history and demography.

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Molecular Evolution of the Vertebrate FK506 Binding Protein 25

International Journal of Genomics ◽

10.1155/2014/402603 ◽

2014 ◽

Vol 2014 ◽

pp. 1-9 ◽

Cited By ~ 1

Author(s):

Fei Liu ◽

Xiao-Long Wei ◽

Hao Li ◽

Ji-Fu Wei ◽

Yong-Qing Wang ◽

...

Keyword(s):

Binding Proteins ◽

Nuclear Dna ◽

Purifying Selection ◽

Synonymous Substitution ◽

Vertebrate Lineage ◽

Gene Splicing ◽

Fk506 Binding Protein ◽

Ppiase Domain ◽

Synonymous Substitution Rates ◽

Peptidyl Prolyl Isomerases

FK506 binding proteins (FKBPs) belong to immunophilins with peptidyl-prolyl isomerases (PPIases) activity. FKBP25 (also known as FKBP3) is one of the nuclear DNA-binding proteins in the FKBPs family, which plays an important role in regulating transcription and chromatin structure. The calculation of nonsynonymous and synonymous substitution rates suggested that FKBP25 undergoes purifying selection throughout the whole vertebrate evolution. Moreover, the result of site-specific tests showed that no sites were detected under positive selection. Only one PPIase domain was detected by searching FKBP25 sequences at Pfam and SMART domain databases. Mammalian FKBP25 possess exon-intron conservation, although conservation in the whole vertebrate lineage is incomplete. The result of this study suggests that the purifying selection triggers FKBP25 evolutionary history, which allows us to discover the complete role of the PPIase domain in the interaction between FKBP25 and nuclear proteins. Moreover, intron alterations during FKBP25 evolution that regulate gene splicing may be involved in the purifying selection.

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Trends in Prokaryotic Evolution Revealed by Comparison of Closely Related Bacterial and Archaeal Genomes

Journal of Bacteriology ◽

10.1128/jb.01237-08 ◽

2008 ◽

Vol 191 (1) ◽

pp. 65-73 ◽

Cited By ~ 97

Author(s):

Pavel S. Novichkov ◽

Yuri I. Wolf ◽

Inna Dubchak ◽

Eugene V. Koonin

Keyword(s):

Amino Acid ◽

Genome Rearrangement ◽

Selective Pressure ◽

Protein Sequences ◽

Purifying Selection ◽

Amino Acid Sequences ◽

Strong Positive Correlation ◽

Effective Population ◽

Data Set ◽

Positive Correlation

ABSTRACT In order to explore microevolutionary trends in bacteria and archaea, we constructed a data set of 41 alignable tight genome clusters (ATGCs). We show that the ratio of the medians of nonsynonymous to synonymous substitution rates (dN/dS) that is used as a measure of the purifying selection pressure on protein sequences is a stable characteristic of the ATGCs. In agreement with previous findings, parasitic bacteria, notwithstanding the sometimes dramatic genome shrinkage caused by gene loss, are typically subjected to relatively weak purifying selection, presumably owing to relatively small effective population sizes and frequent bottlenecks. However, no evidence of genome streamlining caused by strong selective pressure was found in any of the ATGCs. On the contrary, a significant positive correlation between the genome size, as well as gene size, and selective pressure was observed, although a variety of free-living prokaryotes with very close selective pressures span nearly the entire range of genome sizes. In addition, we examined the connections between the sequence evolution rate and other genomic features. Although gene order changes much faster than protein sequences during the evolution of prokaryotes, a strong positive correlation was observed between the “rearrangement distance” and the amino acid distance, suggesting that at least some of the events leading to genome rearrangement are subjected to the same type of selective constraints as the evolution of amino acid sequences.

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Population genomics of Mycobacterium tuberculosis in the Inuit

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1507071112 ◽

2015 ◽

Vol 112 (44) ◽

pp. 13609-13614 ◽

Cited By ~ 49

Author(s):

Robyn S. Lee ◽

Nicolas Radomski ◽

Jean-Francois Proulx ◽

Ines Levade ◽

B. Jesse Shapiro ◽

...

Keyword(s):

Genetic Diversity ◽

Mycobacterium Tuberculosis ◽

Population Genomics ◽

Purifying Selection ◽

Synonymous Substitution ◽

Nonsynonymous Snps ◽

Recent Common Ancestor ◽

Nucleotide Polymorphisms ◽

Most Recent Common Ancestor ◽

Bacterial Genetic

Nunavik, Québec suffers from epidemic tuberculosis (TB), with an incidence 50-fold higher than the Canadian average. Molecular studies in this region have documented limited bacterial genetic diversity among Mycobacterium tuberculosis isolates, consistent with a founder strain and/or ongoing spread. We have used whole-genome sequencing on 163 M. tuberculosis isolates from 11 geographically isolated villages to provide a high-resolution portrait of bacterial genetic diversity in this setting. All isolates were lineage 4 (Euro-American), with two sublineages present (major, n = 153; minor, n = 10). Among major sublineage isolates, there was a median of 46 pairwise single-nucleotide polymorphisms (SNPs), and the most recent common ancestor (MRCA) was in the early 20th century. Pairs of isolates within a village had significantly fewer SNPs than pairs from different villages (median: 6 vs. 47, P < 0.00005), indicating that most transmission occurs within villages. There was an excess of nonsynonymous SNPs after the diversification of M. tuberculosis within Nunavik: The ratio of nonsynonymous to synonymous substitution rates (dN/dS) was 0.534 before the MRCA but 0.777 subsequently (P = 0.010). Nonsynonymous SNPs were detected across all gene categories, arguing against positive selection and toward genetic drift with relaxation of purifying selection. Supporting the latter possibility, 28 genes were partially or completely deleted since the MRCA, including genes previously reported to be essential for M. tuberculosis growth. Our findings indicate that the epidemiologic success of M. tuberculosis in this region is more likely due to an environment conducive to TB transmission than a particularly well-adapted strain.

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Enhanced functional divergence of duplicate genes several million years after gene duplication in the Arabidopsis lineage

10.1101/047639 ◽

2016 ◽

Author(s):

Kousuke Hanada ◽

Ayumi Tezuka ◽

Masafumi Nozawa ◽

Yutaka Suzuki ◽

Sumio Sugano ◽

...

Keyword(s):

Gene Duplication ◽

Functional Divergence ◽

Purifying Selection ◽

Orthologous Gene ◽

Synonymous Substitution ◽

Duplicate Genes ◽

Duplicated Genes ◽

Highly Qualified ◽

Duplication Events ◽

Synonymous Substitution Rates

AbstractLineage-specifically duplicated genes likely contribute to the phenotypic divergence in closely related species. However, neither the frequency of duplication events nor the degree of selective pressures immediately after gene duplication is clear in the speciation process. Plants have substantially higher gene duplication rates than most other eukaryotes. Here, using Illumina short reads from Arabidopsis halleri, which has highly qualified plant genomes in close species (Brassica rapa, A. thaliana and A. lyrata), we succeeded in generating orthologous gene groups among B. rapa, A. thaliana, A. lyrata and A. halleri. The frequency of duplication events in the Arabidopsis lineage was approximately 10 times higher than the frequency inferred by comparative genomics of Arabidopsis, poplar, rice and moss. Of the currently retained genes in A. halleri, 11–24% had undergone gene duplication in the Arabidopsis lineage. To examine the degree of selective pressure for duplicated genes, we calculated the ratios of nonsynonymous to synonymous substitution rates (KA/KS) in the A. halleri-lyrata and A. halleri lineages. Using a maximum-likelihood framework, we examined positive (KA/KS > 1) and purifying selection (KA/KS < 1) at a significant level (P < 0.01). Duplicate genes tended to have a higher proportion of positive selection compared with non-duplicated genes. More interestingly, we found that functional divergence of duplicated genes was accelerated several million years after gene duplication at a higher proportion than immediately after gene duplication.

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Vulnerability to Fishing and Life History Traits Correlate with the Load of Deleterious Mutations in Teleosts

Molecular Biology and Evolution ◽

10.1093/molbev/msaa067 ◽

2020 ◽

Vol 37 (8) ◽

pp. 2192-2196 ◽

Cited By ~ 2

Author(s):

Jonathan Rolland ◽

Dolph Schluter ◽

Jonathan Romiguier

Keyword(s):

Life History ◽

Evolutionary Biology ◽

Life History Traits ◽

Deleterious Mutation ◽

Purifying Selection ◽

Synonymous Substitution ◽

Deleterious Mutations ◽

Data Set ◽

Terrestrial Vertebrates ◽

Genome Data

Abstract Understanding why some species accumulate more deleterious substitutions than others is an important question relevant in evolutionary biology and conservation sciences. Previous studies conducted in terrestrial taxa suggest that life history traits correlate with the efficiency of purifying selection and accumulation of deleterious mutations. Using a large genome data set of 76 species of teleostean fishes, we show that species with life history traits associated with vulnerability to fishing have an increased rate of deleterious mutation accumulation (measured via dN/dS, i.e., nonsynonymous over synonymous substitution rate). Our results, focusing on a large clade of aquatic species, generalize previous patterns found so far in few clades of terrestrial vertebrates. These results also show that vulnerable species to fishing inherently accumulate more deleterious substitutions than nonthreatened ones, which illustrates the potential links among population genetics, ecology, and fishing policies to prevent species extinction.

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Genetic characterization of the endangered and endemic anchialine squat lobster Munidopsis polymorpha from Lanzarote (Canary Islands): management implications

ICES Journal of Marine Science ◽

10.1093/icesjms/fss062 ◽

2012 ◽

Vol 69 (6) ◽

pp. 1030-1037 ◽

Cited By ~ 3

Author(s):

Patricia Cabezas ◽

Fernando Alda ◽

Enrique Macpherson ◽

Annie Machordom

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Population Size ◽

Effective Population Size ◽

Canary Islands ◽

Genetic Characterization ◽

Effective Population ◽

Management Implications ◽

Squat Lobster

Abstract Cabezas, P., Alda, F., Macpherson, E., and Machordom, A. 2012. Genetic characterization of the endangered and endemic anchialine squat lobster Munidopsis polymorpha from Lanzarote (Canary Islands): management implications. – ICES Journal of Marine Science, 69: 1030–1037. Anchialine species show restricted geographic ranges, high habitat specificity, and small population sizes. These factors make them particularly vulnerable to human activities, yet little is known about their ecology and evolutionary history. Munidopsis polymorpha is a decapod endemic to an anchialine cave system of the Corona lava tube in Lanzarote (Canary Islands). The present study, the first genetic survey conducted on this largely unknown species, was designed to characterize its genetic diversity, population structure and recent demographic history, using sequence data for the cytochrome oxidase I gene and eight microsatellites. A single haplotype was identified in the mitochondrial dataset. Nuclear genetic diversity was also low (average = 4.375 ± 1.685). No significant genetic structure was detected between sampling sites and years, either by analysis of molecular variance (FST = 0.006, p = 0.110) or Bayesian clustering analysis (K = 1), indicating this species should be treated as a single management unit. Neither did we find evidence for a recent bottleneck event, and estimates of effective population size were extremely low (∼50). The lack of population structure, low genetic diversity and extremely low effective population size reinforce the high degree of isolation and endemicity of this species, and, consequently, the need to implement appropriate management actions.

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Genomic descriptors of biodiversity – A review

Die Bodenkultur Journal of Land Management Food and Environment ◽

10.2478/boku-2018-0007 ◽

2018 ◽

Vol 69 (2) ◽

pp. 73-83 ◽

Cited By ~ 2

Author(s):

Gábor Mészáros

Keyword(s):

Genetic Diversity ◽

Nucleotide Polymorphisms ◽

Negative Consequences ◽

Effective Population ◽

Single Nucleotide ◽

Diversity Assessment ◽

Wide Range ◽

Core Concepts

Summary The characterization of livestock genetic diversity has experienced extensive changes with the availability of dense nucleotide markers. Among the various forms of markers, the single nucleotide polymorphisms (SNP) have arguably the largest influence. A wide range of indicators for the assessment of genetic diversity was developed, or the existing methods were improved, enabling us to make informed decisions on the management of livestock populations. This review discusses the selected aspects of diversity assessment, with special attention to the SNP based methods. One of the core concepts in genomics of diversity is the linkage disequilibrium (LD), as it was shaped by demographic events during the development of breeds and species. These events, either natural or artificial, left detectable signals within the livestock genomes. Further changes were induced by human activity when mating related animals, leading to fixing or improving the desired traits in the breed, but reducing their genetic variability. The assessment of relatedness is also pivotal to construct meaningful mating plans and to avoid the negative consequences of inbreeding depression that might be detrimental especially in small, endangered populations. Both LD and relatedness are of interest on their own, as well as in their follow-up applications deriving overall measures of effective population size.

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A comparison of one-rate and two-rate inference frameworks for site-specific dN/dS estimation

10.1101/032805 ◽

2015 ◽

Author(s):

Stephanie J. Spielman ◽

Suyang Wan ◽

Claus O. Wilke

Keyword(s):

Model Misspecification ◽

Purifying Selection ◽

Synonymous Substitution ◽

Selective Constraint ◽

Model Specification ◽

Inference Model ◽

Specific Context ◽

Point Estimates ◽

Synonymous Substitution Rates ◽

Excessive Noise

AbstractTwo broad paradigms exist for inferring dN/dS, the ratio of nonsynonymous to synonymous substitution rates, from coding sequences: i) a one-rate approach, where dN/dS is represented with a single parameter, or ii) a two-rate approach, where dN and dS are estimated separately. The performances of these two approaches have been well-studied in the specific context of proper model specification, i.e. when the inference model matches the simulation model. By contrast, the relative performances of one-rate vs. two-rate parameterizations when applied to data generated according to a different mechanism remains unclear. Here, we compare the relative merits of one-rate and two-rate approaches in the specific context of model misspecification by simulating alignments with mutation-selection models rather than with dN/dS-based models. We find that one-rate frameworks generally infer more accurate dN/dS point estimates, even when dS varies among sites. In other words, modeling dS variation may substantially reduce accuracy of dN/dS point estimates. These results appear to depend on the selective constraint operating at a given site. In particular, for sites under strong purifying selection (dN/dS<~0.3), one-rate and two-rate models show comparable performances. However, one-rate models significantly outperform two-rate models for sites under moderate-to-weak purifying selection. We attribute this distinction to the fact that, for these more quickly evolving sites, a given substitution is more likely to be nonsynonymous than synonymous. The data will therefore be relatively enriched for nonsynonymous changes, and modeling dS contributes excessive noise to dN/dS estimates. We additionally find that high levels of divergence among sequences, rather than the number of sequences in the alignment, are more critical for obtaining precise point estimates.

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