scholarly journals Functional Bias and Demographic History Obscure Patterns of Selection among Single-Copy Genes in a Fungal Species Complex

2017 ◽  
Author(s):  
Santiago Sánchez-Ramírez ◽  
Jean-Marc Moncalvo
Keyword(s):  
Natural Selection ◽  
Positive Selection ◽  
Dna Sequences ◽  
Demographic History ◽  
Purifying Selection ◽  
Single Copy ◽  
Fungal Species ◽  
Ratio Test ◽  
Ontology Term ◽  
Slightly Deleterious Mutations

AbstractMany different evolutionary processes may be responsible for explaining natural variation within genomes, some of which include natural selection at the molecular level and changes in population size. Fungi are highly adaptable organisms, and their relatively small genomes and short generation times make them pliable for evolutionary genomic studies. However, adaptation in wild populations has been relatively less documented compared to experimental or clinical studies. Here, we analyzed DNA sequences from 502 putative single-copy orthologous genes in 63 samples that represent seven recently diverged North American Amanita (jacksonii-complex) lineages. For each gene and each species, we measured the genealogical sorting index (gsi) and infinite-site-based summary statistics, such as , and DTaj in coding and intron regions. MKT-based approaches and likelihood-ratio-test Kn/Ks models were used to measure natural selection in all coding sequences. Multi-locus (Extended) Bayesian Skyline Plots (eBSP) were used to model intraspecific demographic changes through time based on unlinked, putative neutral regions (introns). Most genes show evidence of long-term purifying selection, likely reflecting a functional bias implicit in single-copy genes. We find that two species have strongly negatively skewed Tajima’s D, while three other have a positive skew, corresponding well with patterns of demographic expansion and contraction. Standard MKT analyses resulted in a high incidence of near-zero α with a tendency towards negative values. In contrast, α estimates based on the distribution of fitness effects (DFE), which accounts for demographic effects and slightly deleterious mutations, suggest a higher proportion of sites fixed by positive selection. The difference was more notorious in species with expansion signatures or with historically low population sizes, evidencing the concealing effects of specific demographic histories. Finally, we attempt to mitigate Gene Ontology term overrepresentation, highlighting the potential adaptive or ecological roles of some genes under positive selection.

scholarly journals Natural selection and repeated patterns of molecular evolution following allopatric divergence

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Yibo Dong ◽  
Shichao Chen ◽  
Shifeng Cheng ◽  
Wenbin Zhou ◽  
Qing Ma ◽  
...  
Keyword(s):  
Positive Selection ◽  
Divergence Time ◽  
Purifying Selection ◽  
Single Copy ◽  
Orthologous Genes ◽  
Allopatric Species ◽  
Genome Wide ◽  
Allopatric Divergence ◽  
Selective Forces ◽  
Repeated Pattern

Although geographic isolation is a leading driver of speciation, the tempo and pattern of divergence at the genomic level remain unclear. We examine genome-wide divergence of putatively single-copy orthologous genes (POGs) in 20 allopatric species/variety pairs from diverse angiosperm clades, with 16 pairs reflecting the classic eastern Asia-eastern North America floristic disjunction. In each pair, >90% of POGs are under purifying selection, and <10% are under positive selection. A set of POGs are under strong positive selection, 14 of which are shared by 10–15 pairs, and one shared by all pairs; 15 POGs are annotated to biological processes responding to various stimuli. The relative abundance of POGs under different selective forces exhibits a repeated pattern among pairs despite an ~10 million-year difference in divergence time. Species divergence times are positively correlated with abundance of POGs under moderate purifying selection, but negatively correlated with abundance of POGs under strong purifying selection.

scholarly journals Effect of Recombination on the Accuracy of the Likelihood Method for Detecting Positive Selection at Amino Acid Sites

Genetics ◽  
2003 ◽  
Vol 164 (3) ◽  
pp. 1229-1236 ◽  
Author(s):  
Maria Anisimova ◽  
Rasmus Nielsen ◽  
Ziheng Yang
Keyword(s):  
Positive Selection ◽  
Dna Sequences ◽  
Empirical Bayes ◽  
Null Model ◽  
Likelihood Method ◽  
Ratio Test ◽  
Type I ◽  
Selective Pressures ◽  
Codon Substitution ◽  
History Of

AbstractMaximum-likelihood methods based on models of codon substitution accounting for heterogeneous selective pressures across sites have proved to be powerful in detecting positive selection in protein-coding DNA sequences. Those methods are phylogeny based and do not account for the effects of recombination. When recombination occurs, such as in population data, no unique tree topology can describe the evolutionary history of the whole sequence. This violation of assumptions raises serious concerns about the likelihood method for detecting positive selection. Here we use computer simulation to evaluate the reliability of the likelihood-ratio test (LRT) for positive selection in the presence of recombination. We examine three tests based on different models of variable selective pressures among sites. Sequences are simulated using a coalescent model with recombination and analyzed using codon-based likelihood models ignoring recombination. We find that the LRT is robust to low levels of recombination (with fewer than three recombination events in the history of a sample of 10 sequences). However, at higher levels of recombination, the type I error rate can be as high as 90%, especially when the null model in the LRT is unrealistic, and the test often mistakes recombination as evidence for positive selection. The test that compares the more realistic models M7 (β) against M8 (β and ω) is more robust to recombination, where the null model M7 allows the positive selection pressure to vary between 0 and 1 (and so does not account for positive selection), and the alternative model M8 allows an additional discrete class with ω= dN/dS that could be estimated to be &gt;1 (and thus accounts for positive selection). Identification of sites under positive selection by the empirical Bayes method appears to be less affected than the LRT by recombination.

scholarly journals Aspergillus fumigatus versus Genus Aspergillus: Conservation, adaptive evolution and specific virulence genes

2020 ◽  
Author(s):  
Shishir K Gupta ◽  
Mugdha Srivastava ◽  
Özge Osmanoglu ◽  
Zhuofei Xu ◽  
Axel A Brakhage ◽  
...  
Keyword(s):  
Positive Selection ◽  
Adaptive Evolution ◽  
Immune Evasion ◽  
Defense Mechanism ◽  
Gene Families ◽  
Single Copy ◽  
Fungal Species ◽  
Pathogenic Species ◽  
Important Species ◽  
Conserved Genes

AbstractAspergillus is an important fungal genus containing economically important species, as well as pathogenic species of animals and plants. Using eighteen fungal species of the genus Aspergillus, we conducted a comprehensive investigation of conserved genes and their evolution. This also allows to investigate the selection pressure driving the adaptive evolution in the pathogenic species A. fumigatus. Among single-copy orthologs (SCOs) for A. fumigatus and the closely related species A. fischeri, we identified 122 versus 50 positively selected genes (PSGs), respectively. Moreover, twenty conserved genes of unknown function were established to be clearly positively selected and thus important for adaption. A. fumigatus PSGs interacting with human host proteins show over-representation of adaptive, symbiosis-related, immunomodulatory, and virulence related pathways such as the TGF-β pathway, insulin receptor signaling, IL1 pathway and interfering with phagosomal of GTPase signaling. Additionally, among the virulence factor coding genes, secretory and membrane protein coding genes in multi-copy gene families, 212 genes underwent positive selection and also suggest increased adaptation such as fungal immune evasion mechanisms (aspf2), siderophore biosynthesis (sidD), fumarylalanine production (sidE), stress tolerance (atfA) and thermotolerance (sodA). These genes presumably contribute to host adaptation strategies. Genes for the biosynthesis of gliotoxin are shared among all the close relatives of A. fumigatus as ancient defense mechanism. Positive selection plays a crucial role in the adaptive evolution of A. fumigatus. The genome-wide profile of PSGs provides valuable targets for further research on the mechanisms of immune evasion, for antimycotic targeting and understanding fundamental processes of virulence.

scholarly journals Aspergillus fumigatus versus Genus Aspergillus: Conservation, Adaptive Evolution and Specific Virulence Genes

2021 ◽  
Vol 9 (10) ◽  
pp. 2014
Author(s):  
Shishir Gupta ◽  
Mugdha Srivastava ◽  
Özge Osmanoglu ◽  
Zhuofei Xu ◽  
Axel A. Brakhage ◽  
...  
Keyword(s):  
Positive Selection ◽  
Adaptive Evolution ◽  
Immune Evasion ◽  
Defense Mechanism ◽  
Gene Families ◽  
Single Copy ◽  
Fungal Species ◽  
Pathogenic Species ◽  
Important Species ◽  
Conserved Genes

Aspergillus is an important fungal genus containing economically important species, as well as pathogenic species of animals and plants. Using eighteen fungal species of the genus Aspergillus, we conducted a comprehensive investigation of conserved genes and their evolution. This also allows us to investigate the selection pressure driving the adaptive evolution in the pathogenic species A. fumigatus. Among single-copy orthologs (SCOs) for A. fumigatus and the closely related species A. fischeri, we identified 122 versus 50 positively selected genes (PSGs), respectively. Moreover, twenty conserved genes of unknown function were established to be positively selected and thus important for adaption. A. fumigatus PSGs interacting with human host proteins show over-representation of adaptive, symbiosis-related, immunomodulatory and virulence-related pathways, such as the TGF-β pathway, insulin receptor signaling, IL1 pathway and interfering with phagosomal GTPase signaling. Additionally, among the virulence factor coding genes, secretory and membrane protein-coding genes in multi-copy gene families, 212 genes underwent positive selection and also suggest increased adaptation, such as fungal immune evasion mechanisms (aspf2), siderophore biosynthesis (sidD), fumarylalanine production (sidE), stress tolerance (atfA) and thermotolerance (sodA). These genes presumably contribute to host adaptation strategies. Genes for the biosynthesis of gliotoxin are shared among all the close relatives of A. fumigatus as an ancient defense mechanism. Positive selection plays a crucial role in the adaptive evolution of A. fumigatus. The genome-wide profile of PSGs provides valuable targets for further research on the mechanisms of immune evasion, antimycotic targeting and understanding fundamental virulence processes.

scholarly journals Influence of pathway topology and functional class on the molecular evolution of human metabolic genes

2018 ◽  
Author(s):  
Ludovica Montanucci ◽  
Hafid Laayouni ◽  
Begoña Dobón ◽  
Kevin L. Keys ◽  
Jaume Bertranpetit ◽  
...  
Keyword(s):  
Natural Selection ◽  
Dna Sequences ◽  
Metabolic Pathways ◽  
Purifying Selection ◽  
Enzymatic Reactions ◽  
Adaptive Selection ◽  
Selective Pressures ◽  
Genome Data ◽  
Metabolic Genes ◽  
Topological Characteristics

AbstractMetabolic networks comprise thousands of enzymatic reactions functioning in a controlled manner and have been shaped by natural selection. Thanks to the genome data, the footprints of adaptive (positive) selection are detectable, and the strength of purifying selection can be measured. This has made possible to know where, in the metabolic network, adaptive selection has acted and where purifying selection is more or less strong and efficient. We have carried out a comprehensive molecular evolutionary study of all the genes involved in the human metabolism. We investigated the type and strength of the selective pressures that acted on the enzyme-coding genes belonging to metabolic pathways during the divergence of primates and rodents. Then, we related those selective pressures to the functional and topological characteristics of the pathways. We have used DNA sequences of all enzymes (956) of the metabolic pathways comprised in the HumanCyc database, using genome data for humans and five other mammalian species.We have found that the evolution of metabolic genes is primarily constrained by the layer of the metabolism in which the genes participate: while genes encoding enzymes of the inner core of metabolism are much conserved, those encoding enzymes participating in the outer layer, mediating the interaction with the environment, are evolutionarily less constrained and more plastic, having experienced faster functional evolution. Genes that have been targeted by adaptive selection are endowed by higher out-degree centralities than non-adaptive genes, while genes with high in-degree centralities are under stronger purifying selection. When the position along the pathway is considered, a funnel-like distribution of the strength of the purifying selection is found. Genes at bottom positions are highly preserved by purifying selection, whereas genes at top positions, catalyzing the first steps, are open to evolutionary changes.These results show how functional and topological characteristics of metabolic pathways contribute to shape the patterns of evolutionary pressures driven by natural selection and how pathway network structure matters in the evolutionary process that shapes the evolution of the system.

scholarly journals Molecular evolution of DNMT1 in vertebrates: duplications in marsupials followed by positive selection

2018 ◽  
Author(s):  
David Alvarez-Ponce ◽  
María Torres-Sánchez ◽  
Felix Feyertag ◽  
Asmita Kulkarni ◽  
Taylen Nappi
Keyword(s):  
Dna Methylation ◽  
Molecular Evolution ◽  
Positive Selection ◽  
Phylogenetic Analyses ◽  
Purifying Selection ◽  
Single Copy ◽  
Tammar Wallaby ◽  
Dna Methyltransferases ◽  
Tasmanian Devil ◽  
Genes Encoding

AbstractDNA methylation is mediated by a conserved family of DNA methyltransferases (Dnmts). The human genome encodes five Dnmts: Dnmt1, Dnmt2, Dnmt3a, Dnmt3b and Dnmt3L. Despite their high degree of conservation among different species, genes encoding Dnmts have been duplicated and/or lost in multiple lineages throughout evolution, indicating that the DNA methylation machinery has some potential to undergo evolutionary change. However, little is known about the extent to which this machinery, or the methylome, varies among vertebrates. Here, we study the molecular evolution of Dnmt1, the enzyme responsible for maintenance of DNA methylation patterns after replication, in 79 vertebrate species. Our analyses show that all studied species exhibit a single copy of DNMT1, with the exception of tilapia and marsupials (tammar wallaby, koala, Tasmanian devil and opossum), each of which exhibits two apparently functional DNMT1 copies. Our phylogenetic analyses indicate that DNMT1 duplicated before the divergence of marsupials (i.e., at least ~75 million years ago), thus giving rise to two DNMT1 copies in marsupials (copy 1 and copy 2). In the opossum lineage, copy 2 was lost, and copy 1 recently duplicated again, generating three DNMT1 copies: two putatively functional genes (copy 1a and 1b) and one pseudogene (copy 1ψ). Both marsupial copies (DNMT1 copies 1 and 2) are under purifying selection, and copy 2 exhibits elevated rates of evolution and signatures of positive selection, suggesting a scenario of neofunctionalization. This gene duplication might have resulted in modifications in marsupial methylomes and their dynamics.

scholarly journals Positive natural selection in primate genes of the type I interferon response

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Elena N. Judd ◽  
Alison R. Gilchrist ◽  
Nicholas R. Meyerson ◽  
Sara L. Sawyer
Keyword(s):  
Natural Selection ◽  
Positive Selection ◽  
Type I Interferon ◽  
Interferon Response ◽  
Type I ◽  
Sequence Alignments ◽  
Multiple Sequence ◽  
Multiple Sequence Alignments ◽  
Interferon Stimulated Genes ◽  
Interferon Induction

Abstract Background The Type I interferon response is an important first-line defense against viruses. In turn, viruses antagonize (i.e., degrade, mis-localize, etc.) many proteins in interferon pathways. Thus, hosts and viruses are locked in an evolutionary arms race for dominance of the Type I interferon pathway. As a result, many genes in interferon pathways have experienced positive natural selection in favor of new allelic forms that can better recognize viruses or escape viral antagonists. Here, we performed a holistic analysis of selective pressures acting on genes in the Type I interferon family. We initially hypothesized that the genes responsible for inducing the production of interferon would be antagonized more heavily by viruses than genes that are turned on as a result of interferon. Our logic was that viruses would have greater effect if they worked upstream of the production of interferon molecules because, once interferon is produced, hundreds of interferon-stimulated proteins would activate and the virus would need to counteract them one-by-one. Results We curated multiple sequence alignments of primate orthologs for 131 genes active in interferon production and signaling (herein, “induction” genes), 100 interferon-stimulated genes, and 100 randomly chosen genes. We analyzed each multiple sequence alignment for the signatures of recurrent positive selection. Counter to our hypothesis, we found the interferon-stimulated genes, and not interferon induction genes, are evolving significantly more rapidly than a random set of genes. Interferon induction genes evolve in a way that is indistinguishable from a matched set of random genes (22% and 18% of genes bear signatures of positive selection, respectively). In contrast, interferon-stimulated genes evolve differently, with 33% of genes evolving under positive selection and containing a significantly higher fraction of codons that have experienced selection for recurrent replacement of the encoded amino acid. Conclusion Viruses may antagonize individual products of the interferon response more often than trying to neutralize the system altogether.

Mapping by Sequencing the Pneumocystis Genome Using the Ordering DNA Sequences V3 Tool

Genetics ◽  
2003 ◽  
Vol 163 (4) ◽  
pp. 1299-1313
Author(s):  
Zheng Xu ◽  
Britton Lance ◽  
Claudia Vargas ◽  
Budak Arpinar ◽  
Suchendra Bhandarkar ◽  
...  
Keyword(s):  
Physical Mapping ◽  
Dna Sequences ◽  
Pneumocystis Carinii ◽  
Single Copy ◽  
Fungal Genome ◽  
Mapping Data ◽  
Genome Database ◽  
Rdna Genes ◽  
Genome Map ◽  
Mapping By Sequencing

Abstract A bioinformatics tool called ODS3 has been created for mapping by sequencing. The tool allows the creation of integrated genomic maps from genetic, physical mapping, and sequencing data and permits an integrated genome map to be stored, retrieved, viewed, and queried in a stand-alone capacity, in a client/server relationship with the Fungal Genome Database (FGDB), and as a web-browsing tool for the FGDB. In that ODS3 is programmed in Java, the tool promotes platform independence and supports export of integrated genome-mapping data in the extensible markup language (XML) for data interchange with other genome information systems. The tool ODS3 is used to create an initial integrated genome map of the AIDS-related fungal pathogen, Pneumocystis carinii. Contig dynamics would indicate that this physical map is ∼50% complete with ∼200 contigs. A total of 10 putative multigene families were found. Two of these putative families were previously characterized in P. carinii, namely the major surface glycoproteins (MSGs) and HSP70 proteins; three of these putative families (not previously characterized in P. carinii) were found to be similar to families encoding the HSP60 in Schizosaccharomyces pombe, the heat-shock Ψ protein in S. pombe, and the RNA synthetase family (i.e., MES1) in Saccharomyces cerevisiae. Physical mapping data are consistent with the 16S, 5.8S, and 26S rDNA genes being single copy in P. carinii. No other fungus outside this genus is known to have the rDNA genes in single copy.

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 Inter- and Intra-Continental Genetic Variation in the Generalist Conifer Wood Saprobic Fungus Phlebiopsis gigantea

Forests ◽  
2021 ◽  
Vol 12 (6) ◽  
pp. 751
Author(s):  
Francesco Dovana ◽  
Paolo Gonthier ◽  
Matteo Garbelotto
Keyword(s):  
North America ◽  
Genetic Differentiation ◽  
Dna Sequences ◽  
North American ◽  
Fungal Species ◽  
Coniferous Forests ◽  
Native Forest ◽  
Western North America ◽  
Phlebiopsis Gigantea ◽  
Conifer Wood

Phlebiopsis gigantea (Fr.) Jülich is a well-known generalist conifer wood saprobe and a biocontrol fungus used in several world countries to prevent stump infection by tree pathogenic Heterobasidion fungal species. Previous studies have reported the presence of regional and continental genetic differentiation in host-specific fungi, but the presence of such differentiation for generalist wood saprobes such as P. gigantea has not been often studied or demonstrated. Additionally, little information exists on the distribution of this fungus in western North America. The main purposes of this study were: (I) to assess the presence of P. gigantea in California, (II) to explore the genetic variability of P. gigantea at the intra and inter-continental levels and (III) to analyze the phylogeographic relationships between American and European populations. Seven loci (nrITS, ML5–ML6, ATP6, RPB1, RPB2, GPD and TEF1-α) from 26 isolates of P. gigantea from coniferous forests in diverse geographic distribution and from different hosts were analyzed in this study together with 45 GenBank sequences. One hundred seventy-four new sequences were generated using either universal or specific primers designed in this study. The mitochondrial ML5–ML6 DNA and ATP6 regions were highly conserved and did not show differences between any of the isolates. Conversely, DNA sequences from the ITS, RPB1, RPB2, GPD and TEF1-α loci were variable among samples. Maximum likelihood analysis of GPD and TEF1-α strongly supported the presences of two different subgroups within the species but without congruence or geographic partition, suggesting the presence of retained ancestral polymorphisms. RPB1 and RPB2 sequences separated European isolates from American ones, while the GPD locus separated western North American samples from eastern North American ones. This study reports the presence of P. gigantea in California for the first time using DNA-based confirmation and identifies two older genetically distinct subspecific groups, as well as three genetically differentiated lineages within the species: one from Europe, one from eastern North America and one from California, with the latter presumably including individuals from the rest of western North America. The genetic differentiation identified here among P. gigantea individuals from coniferous forests from different world regions indicates that European isolates of this fungus should not be used in North America (or vice versa), and, likewise, commercially available eastern North American P. gigantea isolates should not be used in western North America forests. The reported lack of host specificity of P. gigantea was documented by the field survey and further reinforces the need to only use local isolates of this biocontrol fungus, given that genetically distinct exotic genotypes of a broad generalist microbe may easily spread and permanently alter the microbial biodiversity of native forest ecosystems.

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