scholarly journals Homologous recombination substantially delays sequence but not gene content divergence of prokaryotic populations

2019 ◽  
Author(s):  
Jaime Iranzo ◽  
Yuri I. Wolf ◽  
Eugene V. Koonin ◽  
Itamar Sela
Keyword(s):  
Homologous Recombination ◽  
Genome Evolution ◽  
Phylogenetic Trees ◽  
Prokaryotic Genome ◽  
Sequence Divergence ◽  
Mechanistic Explanation ◽  
Gene Gain ◽  
Sequence Evolution ◽  
Gene Trees ◽  
Gain And Loss

AbstractEvolution of bacterial and archaeal genomes is a highly dynamic process that involves extensive gain and loss of genes. Therefore, phylogenetic trees of prokaryotes can be constructed both by the traditional sequence-based methods (gene trees) and by comparison of gene compositions (genome trees). Comparing the branch lengths in gene and genome trees with identical topologies for 34 clusters of closely related bacterial and archaeal genomes, we found that the terminal branches of gene trees were systematically compressed compared to those of genome trees. Thus, sequence evolution seems to be significantly delayed with respect to genome evolution by gene gain and loss. The extent of this delay widely differs among bacterial and archaeal lineages. We develop and explore mathematical models demonstrating that the delay of sequence divergence can be explained by sequence homogenization that is caused by homologous recombination. Once evolving genomes become isolated by barriers that impede homologous recombination, gene and genome evolution processes settle into parallel trajectories, and genomes diverge, resulting in speciation. This model of prokaryotic genome evolution gives a mechanistic explanation of our previous finding that archaeal genomes contain a class of genes that turn over rapidly, before significant sequence divergence occurs, and provides a framework for correcting phylogenetic trees, to make them consistent with the dynamics of gene turnover.

scholarly journals Gene gain and loss push prokaryotes beyond the homologous recombination barrier and accelerate genome sequence divergence

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Jaime Iranzo ◽  
Yuri I. Wolf ◽  
Eugene V. Koonin ◽  
Itamar Sela
Keyword(s):  
Homologous Recombination ◽  
Genome Evolution ◽  
Phylogenetic Trees ◽  
Sequence Divergence ◽  
Gene Gain ◽  
Sequence Evolution ◽  
Gene Trees ◽  
Branch Lengths ◽  
Gain And Loss ◽  
Recombination Gene

AbstractBacterial and archaeal evolution involve extensive gene gain and loss. Thus, phylogenetic trees of prokaryotes can be constructed both by traditional sequence-based methods (gene trees) and by comparison of gene compositions (genome trees). Comparing the branch lengths in gene and genome trees with identical topologies for 34 clusters of closely related bacterial and archaeal genomes, we show here that terminal branches of gene trees are systematically compressed compared to those of genome trees. Thus, sequence evolution is delayed compared to genome evolution by gene gain and loss. The extent of this delay differs widely among bacteria and archaea. Mathematical modeling shows that the divergence delay can result from sequence homogenization by homologous recombination. The model explains how homologous recombination maintains the cohesiveness of the core genome of a species while allowing extensive gene gain and loss within the accessory genome. Once evolving genomes become isolated by barriers impeding homologous recombination, gene and genome evolution processes settle into parallel trajectories, and genomes diverge, resulting in speciation.

scholarly journals Horizontal gene transfer: essentiality and evolvability in prokaryotes, and roles in evolutionary transitions

F1000Research ◽  
2016 ◽  
Vol 5 ◽  
pp. 1805 ◽  
Author(s):  
Eugene V. Koonin
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Phylogenetic Trees ◽  
Point Mutations ◽  
Theoretical Models ◽  
Microbial Evolution ◽  
Gene Gain ◽  
Gene Trees ◽  
Ratchet Effect ◽  
Evolutionary Transitions

The wide spread of gene exchange and loss in the prokaryotic world has prompted the concept of ‘lateral genomics’ to the point of an outright denial of the relevance of phylogenetic trees for evolution. However, the pronounced coherence congruence of the topologies of numerous gene trees, particularly those for (nearly) universal genes, translates into the notion of a statistical tree of life (STOL), which reflects a central trend of vertical evolution. The STOL can be employed as a framework for reconstruction of the evolutionary processes in the prokaryotic world. Quantitatively, however, horizontal gene transfer (HGT) dominates microbial evolution, with the rate of gene gain and loss being comparable to the rate of point mutations and much greater than the duplication rate. Theoretical models of evolution suggest that HGT is essential for the survival of microbial populations that otherwise deteriorate due to the Muller’s ratchet effect. Apparently, at least some bacteria and archaea evolved dedicated vehicles for gene transfer that evolved from selfish elements such as plasmids and viruses. Recent phylogenomic analyses suggest that episodes of massive HGT were pivotal for the emergence of major groups of organisms such as multiple archaeal phyla as well as eukaryotes. Similar analyses appear to indicate that, in addition to donating hundreds of genes to the emerging eukaryotic lineage, mitochondrial endosymbiosis severely curtailed HGT. These results shed new light on the routes of evolutionary transitions, but caution is due given the inherent uncertainty of deep phylogenies.

Phylogenetic identification of Pneumocystis murina sp. nov., a new species in laboratory mice

Microbiology ◽  
2004 ◽  
Vol 150 (5) ◽  
pp. 1153-1165 ◽  
Author(s):  
Scott P. Keely ◽  
Jared M. Fischer ◽  
Melanie T. Cushion ◽  
James R. Stringer
Keyword(s):  
Phylogenetic Trees ◽  
Statistical Tests ◽  
Pneumocystis Carinii ◽  
Sequence Divergence ◽  
18S Rrna Gene ◽  
Genetic Distances ◽  
Rrna Gene ◽  
Gene Trees ◽  
Laboratory Mice ◽  
Multiple Species

Pneumocystis is a fungal genus that contains multiple species. One member of the genus that has not been formally analysed for its phylogenetic relationships and possible species status is the Pneumocystis found in laboratory mice, Pneumocystis murina sp. nov. (type strain ATCC PRA-111T=CBS 114898T), formerly known as Pneumocystis carinii f. sp. muris. To advance research in this area, approximately 3000 bp of additional DNA sequence were obtained from the locus encoding rRNAs. This sequence and others were used to determine genetic distances between P. murina and other members of the genus. These distances indicated that P. murina DNA is most similar to that of the species of Pneumocystis found in laboratory rats. Nevertheless, P. murina is at least as diverged from these other Pneumocystis species as species in other fungal genera are from each other. The 18S rRNA gene sequence divergence exhibited by P. murina could not be ascribed to accelerated evolution of this gene as similar levels of divergence were observed at seven other loci. When five genes were used to construct phylogenetic trees for five Pneumocystis taxa, including P. murina, all the trees had the same topology, indicating that genes do not flow among these taxa. The gene trees were all strongly supported by statistical tests. When sequences from the rRNA-encoding locus were used to estimate the time of divergence of P. murina, the results indicated that P. murina is as old as the mouse. Taken together, these data support previous recognition of multiple species in the genus and indicate that P. murina is a phylogenetic species as well.

scholarly journals Heterozygosity, Heteromorphy, and Phylogenetic Trees in Asexual Eukaryotes

Genetics ◽  
1996 ◽  
Vol 144 (1) ◽  
pp. 427-437 ◽  
Author(s):  
C William Birky
Keyword(s):  
Phylogenetic Trees ◽  
Elementary Theory ◽  
Chromosomal Rearrangements ◽  
Sequence Divergence ◽  
Crossing Over ◽  
Sequence Evolution ◽  
Protein Coding ◽  
Mitotic Gene Conversion ◽  
Eukaryotic Organisms

Abstract Little attention has been paid to the consequences of long-term asexual reproduction for sequence evolution in diploid or polyploid eukaryotic organisms. Some elementary theory shows that the amount of neutral sequence divergence between two alleles of a protein-coding gene in an asexual individual will be greater than that in a sexual species by a factor of 2tu, where t is the number of generations since sexual reproduction was lost and u is the mutation rate per generation in the asexual lineage. Phylogenetic trees based on only one allele from each of two or more species will show incorrect divergence times and, more often than not, incorrect topologies. This allele sequence divergence can be stopped temporarily by mitotic gene conversion, mitotic crossing-over, or ploidy reduction. If these convergence events are rare, ancient asexual lineages can be recognized by their high allele sequence divergence. At intermediate frequencies of convergence events, it will be impossible to reconstruct the correct phylogeny of an asexual clade from the sequences of protein coding genes. Convergence may be limited by allele sequence divergence and heterozygous chromosomal rearrangements which reduce the homology needed for recombination and result in aneuploidy after crossing-over or ploidy cycles.

scholarly journals Robust methods for detecting convergent shifts in evolutionary rates

2018 ◽  
Author(s):  
Raghavendran Partha ◽  
Amanda Kowalczyk ◽  
Nathan Clark ◽  
Maria Chikina
Keyword(s):  
Evolutionary Biology ◽  
Phylogenetic Trees ◽  
Sequence Divergence ◽  
Evolutionary Rates ◽  
Sequence Evolution ◽  
Protein Coding ◽  
Robust Detection ◽  
Genetic Elements ◽  
Rates Of Evolution ◽  
Improved Performance

AbstractIdentifying genomic elements underlying phenotypic adaptations is an important problem in evolutionary biology. Comparative analyses learning from convergent evolution of traits are gaining momentum in accurately detecting such elements. We previously developed a method for predicting phenotypic associations of genetic elements by contrasting patterns of sequence evolution in species showing a phenotype with those that do not. Using this method, we successfully demonstrated convergent evolutionary rate shifts in genetic elements associated with two phenotypic adaptations, namely the independent subterranean and marine transitions of terrestrial mammalian lineages. Our method calculates gene-specific rates of evolution on branches of phylogenetic trees using linear regression. These rates represent the extent of sequence divergence on a branch after removing the expected divergence on the branch due to background factors. The rates calculated using this regression analysis exhibit an important statistical limitation, namely heteroscedasticity. We observe that the rates on branches that are longer on average show higher variance, and describe how this problem adversely affects the confidence with which we can make inferences about rate shifts. Using a combination of data transformation and weighted regression, we have developed an updated method that corrects this heteroscedasticity in the rates. We additionally illustrate the improved performance offered by the updated method at robust detection of convergent rate shifts in phylogenetic trees of protein-coding genes across mammals, as well as using simulated tree datasets. Overall, we present an important extension to our evolutionary-rates-based method that performs more robustly and consistently at detecting convergent shifts in evolutionary rates.

scholarly journals Robust Method for Detecting Convergent Shifts in Evolutionary Rates

2019 ◽  
Vol 36 (8) ◽  
pp. 1817-1830 ◽  
Author(s):  
Raghavendran Partha ◽  
Amanda Kowalczyk ◽  
Nathan L Clark ◽  
Maria Chikina
Keyword(s):  
Evolutionary Biology ◽  
Phylogenetic Trees ◽  
Sequence Divergence ◽  
Original Method ◽  
Evolutionary Rates ◽  
Sequence Evolution ◽  
Protein Coding ◽  
Robust Detection ◽  
Genetic Elements ◽  
Improved Performance

AbstractIdentifying genomic elements underlying phenotypic adaptations is an important problem in evolutionary biology. Comparative analyses learning from convergent evolution of traits are gaining momentum in accurately detecting such elements. We previously developed a method for predicting phenotypic associations of genetic elements by contrasting patterns of sequence evolution in species showing a phenotype with those that do not. Using this method, we successfully demonstrated convergent evolutionary rate shifts in genetic elements associated with two phenotypic adaptations, namely the independent subterranean and marine transitions of terrestrial mammalian lineages. Our original method calculates gene-specific rates of evolution on branches of phylogenetic trees using linear regression. These rates represent the extent of sequence divergence on a branch after removing the expected divergence on the branch due to background factors. The rates calculated using this regression analysis exhibit an important statistical limitation, namely heteroscedasticity. We observe that the rates on branches that are longer on average show higher variance, and describe how this problem adversely affects the confidence with which we can make inferences about rate shifts. Using a combination of data transformation and weighted regression, we have developed an updated method that corrects this heteroscedasticity in the rates. We additionally illustrate the improved performance offered by the updated method at robust detection of convergent rate shifts in phylogenetic trees of protein-coding genes across mammals, as well as using simulated tree data sets. Overall, we present an important extension to our evolutionary-rates-based method that performs more robustly and consistently at detecting convergent shifts in evolutionary rates.

Poxvirus genome evolution by gene gain and loss

2005 ◽  
Vol 35 (1) ◽  
pp. 186-195 ◽  
Author(s):  
Austin L. Hughes ◽  
Robert Friedman
Keyword(s):  
Genome Evolution ◽  
Gene Gain ◽  
Poxvirus Genome ◽  
Gain And Loss

Analysis of gene gain and loss in the evolution of predatory bacteria

Gene ◽  
2017 ◽  
Vol 598 ◽  
pp. 63-70 ◽  
Author(s):  
Nan Li ◽  
Kai Wang ◽  
Henry N Williams ◽  
Jun Sun ◽  
Changling Ding ◽  
...  
Keyword(s):  
Gene Gain ◽  
Predatory Bacteria ◽  
Gain And Loss

scholarly journals Evolutionary Analysis of Plastid Genomes of Seven Lonicera L. Species: Implications for Sequence Divergence and Phylogenetic Relationships

2018 ◽  
Vol 19 (12) ◽  
pp. 4039 ◽  
Author(s):  
Mi-Li Liu ◽  
Wei-Bing Fan ◽  
Ning Wang ◽  
Peng-Bin Dong ◽  
Ting-Ting Zhang ◽  
...  
Keyword(s):  
Molecular Genetic ◽  
Phylogenetic Reconstruction ◽  
Sequence Divergence ◽  
Genomic Analysis ◽  
Repeat Sequence ◽  
Biological Research ◽  
Comparative Genomic ◽  
Sequence Evolution ◽  
Evolutionary Analysis ◽  
Plastid Genomes

Plant plastomes play crucial roles in species evolution and phylogenetic reconstruction studies due to being maternally inherited and due to the moderate evolutionary rate of genomes. However, patterns of sequence divergence and molecular evolution of the plastid genomes in the horticulturally- and economically-important Lonicera L. species are poorly understood. In this study, we collected the complete plastomes of seven Lonicera species and determined the various repeat sequence variations and protein sequence evolution by comparative genomic analysis. A total of 498 repeats were identified in plastid genomes, which included tandem (130), dispersed (277), and palindromic (91) types of repeat variations. Simple sequence repeat (SSR) elements analysis indicated the enriched SSRs in seven genomes to be mononucleotides, followed by tetra-nucleotides, dinucleotides, tri-nucleotides, hex-nucleotides, and penta-nucleotides. We identified 18 divergence hotspot regions (rps15, rps16, rps18, rpl23, psaJ, infA, ycf1, trnN-GUU-ndhF, rpoC2-rpoC1, rbcL-psaI, trnI-CAU-ycf2, psbZ-trnG-UCC, trnK-UUU-rps16, infA-rps8, rpl14-rpl16, trnV-GAC-rrn16, trnL-UAA intron, and rps12-clpP) that could be used as the potential molecular genetic markers for the further study of population genetics and phylogenetic evolution of Lonicera species. We found that a large number of repeat sequences were distributed in the divergence hotspots of plastid genomes. Interestingly, 16 genes were determined under positive selection, which included four genes for the subunits of ribosome proteins (rps7, rpl2, rpl16, and rpl22), three genes for the subunits of photosystem proteins (psaJ, psbC, and ycf4), three NADH oxidoreductase genes (ndhB, ndhH, and ndhK), two subunits of ATP genes (atpA and atpB), and four other genes (infA, rbcL, ycf1, and ycf2). Phylogenetic analysis based on the whole plastome demonstrated that the seven Lonicera species form a highly-supported monophyletic clade. The availability of these plastid genomes provides important genetic information for further species identification and biological research on Lonicera.

scholarly journals Patterns and Implications of Gene Gain and Loss in the Evolution of Prochlorococcus

PLoS Genetics ◽  
2005 ◽  
Vol preprint (2007) ◽  
pp. e231
Author(s):  
Gregory C Kettler ◽  
Adam C. Martiny ◽  
Katherine Huang ◽  
Jeremy Zucker ◽  
Maureen Coleman ◽  
...  
Keyword(s):  
Gene Gain ◽  
Gain And Loss
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