scholarly journals Impact of homologous recombination on core genome phylogenies

2020 ◽  
Author(s):  
Caroline Marie Stott ◽  
Louis-Marie Bobay
Keyword(s):  
Homologous Recombination ◽  
Empirical Data ◽  
Gold Standard ◽  
Evolutionary History ◽  
Core Genome ◽  
Bacterial Strains ◽  
Recombination Rates ◽  
Selective Pressures ◽  
Large Sets ◽  
History Of

Abstract Background. Core genome phylogenies are widely used to build the evolutionary history of individual prokaryote species. By using hundreds or thousands of shared genes, these approaches are the gold standard to reconstruct the relationships of large sets of strains. However, there is growing evidence that bacterial strains exchange DNA through homologous recombination at rates that vary widely across prokaryote species, indicating that core genome phylogenies might not be able to reconstruct true phylogenies when recombination rate is high. Few attempts have been made to evaluate the robustness of core genome phylogenies to recombination, but some analyses suggest that reconstructed trees are not always accurate.Results. In this study, we tested the robustness of core genome phylogenies to various levels of recombination rates. By analyzing simulated and empirical data, we observed that core genome phylogenies are relatively robust to recombination rates; nevertheless, our results suggest that many reconstructed trees are not completely accurate even when bootstrap supports are high. We found that some core genome phylogenies are highly robust to recombination whereas others are strongly impacted by it, and we identified that the robustness of core genome phylogenies to recombination is highly linked to the levels of selective pressures acting on a species. Stronger selective pressures lead to less accurate tree reconstructions, presumably because selective pressures more strongly bias the routes of DNA transfers, thereby causing phylogenetic artifacts.Conclusions. Overall these results have important implications for the application of core genome phylogenies in prokaryotes.

scholarly journals Impact of homologous recombination on core genome phylogenies

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Caroline M. Stott ◽  
Louis-Marie Bobay
Keyword(s):  
Homologous Recombination ◽  
Empirical Data ◽  
Gold Standard ◽  
Evolutionary History ◽  
Core Genome ◽  
Bacterial Strains ◽  
Recombination Rates ◽  
Selective Pressures ◽  
Large Sets ◽  
History Of

Abstract Background Core genome phylogenies are widely used to build the evolutionary history of individual prokaryote species. By using hundreds or thousands of shared genes, these approaches are the gold standard to reconstruct the relationships of large sets of strains. However, there is growing evidence that bacterial strains exchange DNA through homologous recombination at rates that vary widely across prokaryote species, indicating that core genome phylogenies might not be able to reconstruct true phylogenies when recombination rate is high. Few attempts have been made to evaluate the robustness of core genome phylogenies to recombination, but some analyses suggest that reconstructed trees are not always accurate. Results In this study, we tested the robustness of core genome phylogenies to various levels of recombination rates. By analyzing simulated and empirical data, we observed that core genome phylogenies are relatively robust to recombination rates; nevertheless, our results suggest that many reconstructed trees are not completely accurate even when bootstrap supports are high. We found that some core genome phylogenies are highly robust to recombination whereas others are strongly impacted by it, and we identified that the robustness of core genome phylogenies to recombination is highly linked to the levels of selective pressures acting on a species. Stronger selective pressures lead to less accurate tree reconstructions, presumably because selective pressures more strongly bias the routes of DNA transfers, thereby causing phylogenetic artifacts. Conclusions Overall, these results have important implications for the application of core genome phylogenies in prokaryotes.

scholarly journals Impact of homologous recombination on core genome phylogenies

2020 ◽  
Author(s):  
Caroline Marie Stott ◽  
Louis-Marie Bobay
Keyword(s):  
Homologous Recombination ◽  
Empirical Data ◽  
Gold Standard ◽  
Evolutionary History ◽  
Core Genome ◽  
Bacterial Strains ◽  
Recombination Rates ◽  
Selective Pressures ◽  
Large Sets ◽  
History Of

Abstract Background. Core genome phylogenies are widely used to build the evolutionary history of individual prokaryote species. By using hundreds or thousands of shared genes, these approaches are the gold standard to reconstruct the relationships of large sets of strains. However, there is growing evidence that bacterial strains exchange DNA through homologous recombination at rates that vary widely across prokaryote species, indicating that core genome phylogenies might not be able to reconstruct true phylogenies when recombination rate is high. Few attempts have been made to evaluate the robustness of core genome phylogenies to recombination, but some analyses suggest that reconstructed trees are not always accurate.Results. In this study, we tested the robustness of core genome phylogenies to various levels of recombination rates. By analyzing simulated and empirical data, we observed that core genome phylogenies are relatively robust to recombination rates; nevertheless, our results suggest that many reconstructed trees are not completely accurate even when bootstrap supports are high. We found that some core genome phylogenies are highly robust to recombination whereas others are strongly impacted by it, and we identified that the robustness of core genome phylogenies to recombination is highly linked to the levels of selective pressures acting on a species. Stronger selective pressures lead to less accurate tree reconstructions, presumably because selective pressures more strongly bias the routes of DNA transfers, thereby causing phylogenetic artifacts. Conclusions. Overall, these results have important implications for the application of core genome phylogenies in prokaryotes.

scholarly journals Belowground Carbohydrate Reserves of Mature Southern Pines Reflect Seedling Strategy to Evolutionary History of Disturbance

Forests ◽  
2018 ◽  
Vol 9 (10) ◽  
pp. 653 ◽  
Author(s):  
Joshua Mims ◽  
Joseph O’Brien ◽  
Doug Aubrey
Keyword(s):  
Evolutionary History ◽  
Temporal Dynamics ◽  
Pinus Palustris ◽  
Life History Stage ◽  
Southern Pine ◽  
Mature Trees ◽  
Carbohydrate Reserves ◽  
Selective Pressures ◽  
Southern Pines ◽  
History Of

Carbohydrate reserves provide advantages for mature trees experiencing frequent disturbances; however, it is unclear if selective pressures operate on this characteristic at the seedling or mature life history stage. We hypothesized that natural selection has favored carbohydrate reserves in species that have an evolutionary history of frequent disturbance and tested this using three southern pine species that have evolved across a continuum of fire frequencies. Longleaf pine (Pinus palustris) roots exhibited higher maximum starch concentrations than slash (P. elliottii) and loblolly (P. taeda), which were similar. Longleaf also relied on starch reserves in roots more than slash or loblolly, depleting 64, 41, and 23 mg g−1 of starch, respectively, between seasonal maximum and minimum, which represented 52%, 45%, and 26% of reserves, respectively. Starch reserves in stems did not differ among species or exhibit temporal dynamics. Our results suggest that an evolutionary history of disturbance partly explains patterns of carbohydrate reserves observed in southern pines. However, similarities between slash and loblolly indicate that carbohydrate reserves do not strictly follow the continuum of disturbance frequencies among southern pine, but rather reflect the different seedling strategies exhibited by longleaf compared to those shared by slash and loblolly. We propose that the increased carbohydrate reserves in mature longleaf may simply be a relic of selective pressures imposed at the juvenile stage that are maintained through development, thus allowing mature trees to be more resilient and to recover from chronic disturbances such as frequent fire.

scholarly journals Tribalism Is Human Nature

2019 ◽  
Vol 28 (6) ◽  
pp. 587-592 ◽  
Author(s):  
Cory J. Clark ◽  
Brittany S. Liu ◽  
Bo M. Winegard ◽  
Peter H. Ditto
Keyword(s):  
Evolutionary History ◽  
Cognitive Biases ◽  
Meta Analysis ◽  
Human Cognition ◽  
Partisan Bias ◽  
Selective Pressures ◽  
Group Loyalty ◽  
History Of ◽  
The Common ◽  
Political Spectrum

Humans evolved in the context of intense intergroup competition, and groups comprised of loyal members more often succeeded than groups comprised of nonloyal members. Therefore, selective pressures have sculpted human minds to be tribal, and group loyalty and concomitant cognitive biases likely exist in all groups. Modern politics is one of the most salient forms of modern coalitional conflict and elicits substantial cognitive biases. The common evolutionary history of liberals and conservatives gives little reason to expect protribe biases to be higher on one side of the political spectrum than the other. This evolutionarily plausible null hypothesis has been supported by recent research. In a recent meta-analysis, liberals and conservatives showed similar levels of partisan bias, and several protribe cognitive tendencies often ascribed to conservatives (e.g., intolerance toward dissimilar other people) were found in similar degrees in liberals. We conclude that tribal bias is a natural and nearly ineradicable feature of human cognition and that no group—not even one’s own—is immune.

scholarly journals Evolutionary history of phycoerythrin pigmentation in the water bloom-forming cyanobacteriumMicrocystis aeruginosa

2018 ◽  
Author(s):  
Yuuhiko Tanabe ◽  
Haruyo Yamaguchi
Keyword(s):  
Evolutionary History ◽  
Core Genome ◽  
Genomic Organization ◽  
Phylogenetic Analyses ◽  
Green Light ◽  
Water Bloom ◽  
Phylogenetic Groups ◽  
Genome Phylogeny ◽  
History Of ◽  
Genomic Basis

AbstractMicrocystis aeruginosais a bloom-forming cyanobacterium found in eutrophic fresh-and brackish water bodies worldwide. As typical for cyanobacteria, mostM. aeruginosastrains are blue-green in color owing to the concomitance of two photosynthetic pigments, phycocyanin (PC) and chlorophylla. Although less common,M. aeruginosastrains that are brownish in color owing to the presence of another pigment phycoerythrin (PE) have been documented. However, the genomic basis, phylogeny, and evolutionary origin of PE pigmentation inM. aeruginosahave only been poorly characterized until date. In the present study, we sequenced and characterized the genomes of five PE-containingM. aeruginosastrains. Putative PE synthesis and regulation genes (thecpecluster) were identified in all five sequenced genomes as well as in three previously publishedM. aeruginosagenomes. Of note, Absorption spectra indicated that the PE content, but not PC content, was markedly altered in response to availability of red/green light in all PE-containing strains. This was consistent with the presence ofccaS/ccaR, a hallmark of type II chromatic adapter, in thecpecluster. Phylogenetic analyses of core genome genes indicated that PE-containing genotypes were located in three different phylogenetic groups. In contrast, the genomic organization of thecpecluster was mostly conserved regardless of genomic background. Additionally, the phylogenies of PE genes were found to be congruent, consistent with the core genome phylogeny. A comparison of core genome and PE genes showed a similar level of genetic divergence between two PE-containing groups. These results suggest that genes responsible for PE pigmentation were introduced intoM. aeruginosaearly during evolution and were repeatedly lost thereafter possibly due to ecological adaptation. Additional horizontal gene transfer (HGT) later during evolution also contributed to the present phylogenetic distribution of PE inM. aeruginosa.

β-Defensin evolution: selection complexity and clues for residues of functional importance

2006 ◽  
Vol 34 (2) ◽  
pp. 257-262 ◽  
Author(s):  
C.A.M. Semple ◽  
K. Taylor ◽  
H. Eastwood ◽  
P.E. Barran ◽  
J.R. Dorin
Keyword(s):  
Positive Selection ◽  
Evolutionary History ◽  
Mammalian Genome ◽  
Functional Importance ◽  
Selective Pressures ◽  
History Of ◽  
Orthologous Loci ◽  
Window Approach ◽  
First Time ◽  
Evolutionary Lineages

We have examined the evolution of the genes at the major human β-defensin locus and the orthologous loci in a range of other primates and mammals. For the first time, these data allow us to examine selective episodes in the more recent evolutionary history of this locus as well as in the ancient past. We have used a combination of maximum-likelihood-based tests and a maximum-parsimony-based sliding window approach to give a detailed view of the varying modes of selection operating at this locus. We provide evidence for strong positive selection soon after the duplication of these genes within an ancestral mammalian genome. During the divergence of primates, however, variable selective pressures have acted on β-defensin genes in different evolutionary lineages, with episodes of both negative and, more rarely, positive selection. Positive selection appears to have been more common in the rodent lineage, accompanying the birth of novel rodent-specific β-defensin gene clades. Sites in the second exon have been subject to positive selection and, by implication, are important in functional diversity. A small number of sites in the mature human peptides were found to have undergone repeated episodes of selection in different primate lineages. Particular sites were consistently implicated by multiple methods at positions throughout the mature peptides. These sites are clustered at positions that are predicted to be important for the function of β-defensins.

scholarly journals Evolutionary History of hrgA, Which Replaces the Restriction Gene hpyIIIR in the hpyIII Locus of Helicobacter pylori

2003 ◽  
Vol 185 (1) ◽  
pp. 295-301 ◽  
Author(s):  
T. Ando ◽  
R. A. Aras ◽  
K. Kusugami ◽  
M. J. Blaser ◽  
T. M. Wassenaar
Keyword(s):  
Helicobacter Pylori ◽  
Sequence Analysis ◽  
Homologous Recombination ◽  
Restriction Endonuclease ◽  
Evolutionary History ◽  
Chromosomal Dna ◽  
History Of ◽  
Flanking Sequences ◽  
H Pylori

ABSTRACT A recently identified Helicobacter pylori gene, hrgA, was previously reported to be present in 70 (33%) of 208 strains examined (T. Ando, T. M. Wassenaar, R. M. Peek, R. A. Aras, A. I. Tschumi, L.-J. Van Doorn, K. Kusugami, and M. J. Blaser, Cancer Res. 62:2385-2389, 2002). Sequence analysis of nine such strains indicated that in each strain hrgA replaced hpyIIIR, which encodes a restriction endonuclease and which, together with the gene for its cognate methyltransferase, constitutes the hpyIII locus. As a consequence of either the hrgA insertion or independent mutations, hpyIIIM function was lost in 11 (5%) of the 208 strains examined, rendering chromosomal DNA sensitive to MboI digestion. The evolutionary history of the locus containing either hpyIII or hrgA was reconstructed. By homologous recombination involving flanking sequences, hrgA and hpyIIIR can replace one another in the hpyIII locus, and there is simultaneous replacement of several flanking genes. These findings, combined with the hpyIM/iceA2 locus discovered previously, suggest that the two most strongly conserved methylase genes of H. pylori, hpyIIIM and hpyIM, are both preceded by alternative genes that compete for presence at their loci.

scholarly journals Independent accretion of TIM22 complex subunits in the animal and fungal lineages

F1000Research ◽  
2020 ◽  
Vol 9 ◽  
pp. 1060
Author(s):  
Sergio A. Muñoz-Gómez ◽  
Shannon N. Snyder ◽  
Samantha J. Montoya ◽  
Jeremy G. Wideman
Keyword(s):  
Evolutionary History ◽  
Protein Import ◽  
Protein Complexes ◽  
Mitochondrial Protein ◽  
Mitochondrial Protein Import ◽  
Mutation Pressure ◽  
Selective Pressures ◽  
Fungal Evolution ◽  
Structural Divergence ◽  
History Of

Background: The mitochondrial protein import complexes arose early in eukaryogenesis. Most of the components of the protein import pathways predate the last eukaryotic common ancestor. For example, the carrier-insertase TIM22 complex comprises the widely conserved Tim22 channel core. However, the auxiliary components of fungal and animal TIM22 complexes are exceptions to this ancient conservation. Methods: Using comparative genomics and phylogenetic approaches, we identified precisely when each TIM22 accretion occurred. Results: In animals, we demonstrate that Tim29 and Tim10b arose early in the holozoan lineage. Tim29 predates the metazoan lineage being present in the animal sister lineages, choanoflagellate and filastereans, whereas the erroneously named Tim10b arose from a duplication of Tim9 at the base of metazoans. In fungi, we show that Tim54 has representatives present in every holomycotan lineage including microsporidians and fonticulids, whereas Tim18 and Tim12 appeared much later in fungal evolution. Specifically, Tim18 and Tim12 arose from duplications of Sdh3 and Tim10, respectively, early in the Saccharomycotina. Surprisingly, we show that Tim54 is distantly related to AGK suggesting that AGK and Tim54 are extremely divergent orthologues and the origin of AGK/Tim54 interaction with Tim22 predates the divergence of animals and fungi. Conclusions: We argue that the evolutionary history of the TIM22 complex is best understood as the neutral structural divergence of an otherwise strongly functionally conserved protein complex. This view suggests that many of the differences in structure/subunit composition of multi-protein complexes are non-adaptive. Instead, most of the phylogenetic variation of functionally conserved molecular machines, which have been under stable selective pressures for vast phylogenetic spans, such as the TIM22 complex, is most likely the outcome of the interplay of random genetic drift and mutation pressure.

scholarly journals Recombination patterns in coronaviruses

2021 ◽  
Author(s):  
Nicola F. Müller ◽  
Kathryn E. Kistler ◽  
Trevor Bedford
Keyword(s):  
Evolutionary History ◽  
Sequence Data ◽  
Template Switching ◽  
Recombination Rates ◽  
Genetic Sequence ◽  
Recombinant Viruses ◽  
Switching Model ◽  
Shared History ◽  
Phylogenetic Methods ◽  
History Of

AbstractAs shown during the SARS-CoV-2 pandemic, phylogenetic and phylodynamic methods are essential tools to study the spread and evolution of pathogens. One of the central assumptions of these methods is that the shared history of pathogens isolated from different hosts can be described by a branching phylogenetic tree. Recombination breaks this assumption. This makes it problematic to apply phylogenetic methods to study recombining pathogens, including, for example, coronaviruses. Here, we introduce a Markov chain Monte Carlo approach that allows inference of recombination networks from genetic sequence data under a template switching model of recombination. Using this method, we first show that recombination is extremely common in the evolutionary history of SARS-like coronaviruses. We then show how recombination rates across the genome of the human seasonal coronaviruses 229E, OC43 and NL63 vary with rates of adaptation. This suggests that recombination could be beneficial to fitness of human seasonal coronaviruses. Additionally, this work sets the stage for Bayesian phylogenetic tracking of the spread and evolution of SARS-CoV-2 in the future, even as recombinant viruses become prevalent.

scholarly journals Evolutionary History of the phl Gene Cluster in the Plant-Associated Bacterium Pseudomonas fluorescens

2009 ◽  
Vol 75 (7) ◽  
pp. 2122-2131 ◽  
Author(s):  
Jennifer A. Moynihan ◽  
John P. Morrissey ◽  
Eric R. Coppoolse ◽  
Willem J. Stiekema ◽  
Fergal O'Gara ◽  
...  
Keyword(s):  
Pseudomonas Fluorescens ◽  
Evolutionary History ◽  
Biological Control Agent ◽  
Control Agent ◽  
Systemic Resistance ◽  
Plant Association ◽  
Selective Pressures ◽  
Functional Implications ◽  
History Of

ABSTRACT Pseudomonas fluorescens is of agricultural and economic importance as a biological control agent largely because of its plant association and production of secondary metabolites, in particular 2,4-diacetylphloroglucinol (2,4-DAPG). This polyketide, which is encoded by the eight-gene phl cluster, has antimicrobial effects on phytopathogens, promotes amino acid exudation from plant roots, and induces systemic resistance in plants. Despite its importance, 2,4-DAPG production is limited to a subset of P. fluorescens strains. Determination of the evolution of the phl cluster and understanding the selective pressures promoting its retention or loss in lineages of P. fluorescens will help in the development of P. fluorescens as a viable and effective inoculant for application in agriculture. In this study, genomic and sequence-based approaches were integrated to reconstruct the phylogeny of P. fluorescens and the phl cluster. It was determined that 2,4-DAPG production is an ancestral trait in the species P. fluorescens but that most lineages have lost this capacity through evolution. Furthermore, intragenomic recombination has relocated the phl cluster within the P. fluorescens genome at least three times, but the integrity of the cluster has always been maintained. The possible evolutionary and functional implications for retention of the phl cluster and 2,4-DAPG production in some lineages of P. fluorescens are discussed.

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