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Errbii M, Gadau J, Becker K, Schrader L, Oettler J. Causes and consequences of a complex recombinational landscape in the ant Cardiocondyla obscurior. Genome Res 2024; 34:863-876. [PMID: 38839375 PMCID: PMC11293551 DOI: 10.1101/gr.278392.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 05/30/2024] [Indexed: 06/07/2024]
Abstract
Eusocial Hymenoptera have the highest recombination rates among all multicellular animals studied so far, but it is unclear why this is and how this affects the biology of individual species. A high-resolution linkage map for the ant Cardiocondyla obscurior corroborates genome-wide high recombination rates reported for ants (8.1 cM/Mb). However, recombination is locally suppressed in regions that are enriched with TEs, that have strong haplotype divergence, or that show signatures of epistatic selection in C. obscurior The results do not support the hypotheses that high recombination rates are linked to phenotypic plasticity or to modulating selection efficiency. Instead, genetic diversity and the frequency of structural variants correlate positively with local recombination rates, potentially compensating for the low levels of genetic variation expected in haplodiploid social Hymenoptera with low effective population size. Ultimately, the data show that recombination contributes to within-population polymorphism and to the divergence of the lineages within C. obscurior.
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Affiliation(s)
- Mohammed Errbii
- Institute for Evolution and Biodiversity, University of Münster, 48149 Münster, Germany
| | - Jürgen Gadau
- Institute for Evolution and Biodiversity, University of Münster, 48149 Münster, Germany
| | - Kerstin Becker
- Cologne Center for Genomics (CCG), Medical Faculty, University of Cologne, 50931 Cologne, Germany
| | - Lukas Schrader
- Institute for Evolution and Biodiversity, University of Münster, 48149 Münster, Germany;
| | - Jan Oettler
- Lehrstuhl für Zoologie/Evolutionsbiologie, University Regensburg, 93053 Regensburg, Germany
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2
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Raas MWD, Dutheil JY. The rate of adaptive molecular evolution in wild and domesticated Saccharomyces cerevisiae populations. Mol Ecol 2024; 33:e16980. [PMID: 37157166 DOI: 10.1111/mec.16980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 04/22/2023] [Accepted: 04/26/2023] [Indexed: 05/10/2023]
Abstract
Through its fermentative capacities, Saccharomyces cerevisiae was central in the development of civilisation during the Neolithic period, and the yeast remains of importance in industry and biotechnology, giving rise to bona fide domesticated populations. Here, we conduct a population genomic study of domesticated and wild populations of S. cerevisiae. Using coalescent analyses, we report that the effective population size of yeast populations decreased since the divergence with S. paradoxus. We fitted models of distributions of fitness effects to infer the rate of adaptive (ω a ) and non-adaptive (ω na ) non-synonymous substitutions in protein-coding genes. We report an overall limited contribution of positive selection to S. cerevisiae protein evolution, albeit with higher rates of adaptive evolution in wild compared to domesticated populations. Our analyses revealed the signature of background selection and possibly Hill-Robertson interference, as recombination was found to be negatively correlated withω na and positively correlated withω a . However, the effect of recombination onω a was found to be labile, as it is only apparent after removing the impact of codon usage bias on the synonymous site frequency spectrum and disappears if we control for the correlation withω na , suggesting that it could be an artefact of the decreasing population size. Furthermore, the rate of adaptive non-synonymous substitutions is significantly correlated with the residue solvent exposure, a relation that cannot be explained by the population's demography. Together, our results provide a detailed characterisation of adaptive mutations in protein-coding genes across S. cerevisiae populations.
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Affiliation(s)
- Maximilian W D Raas
- Research Group Molecular Systems Evolution, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Julien Y Dutheil
- Research Group Molecular Systems Evolution, Max Planck Institute for Evolutionary Biology, Plön, Germany
- Unité Mixte de Recherche 5554 Institut des Sciences de l'Evolution, CNRS, IRD, EPHE, Université de Montpellier, Montpellier, France
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3
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Schraiber JG, Edge MD, Pennell M. Unifying approaches from statistical genetics and phylogenetics for mapping phenotypes in structured populations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.10.579721. [PMID: 38496530 PMCID: PMC10942266 DOI: 10.1101/2024.02.10.579721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
In both statistical genetics and phylogenetics, a major goal is to identify correlations between genetic loci or other aspects of the phenotype or environment and a focal trait. In these two fields, there are sophisticated but disparate statistical traditions aimed at these tasks. The disconnect between their respective approaches is becoming untenable as questions in medicine, conservation biology, and evolutionary biology increasingly rely on integrating data from within and among species, and once-clear conceptual divisions are becoming increasingly blurred. To help bridge this divide, we derive a general model describing the covariance between the genetic contributions to the quantitative phenotypes of different individuals. Taking this approach shows that standard models in both statistical genetics (e.g., Genome-Wide Association Studies; GWAS) and phylogenetic comparative biology (e.g., phylogenetic regression) can be interpreted as special cases of this more general quantitative-genetic model. The fact that these models share the same core architecture means that we can build a unified understanding of the strengths and limitations of different methods for controlling for genetic structure when testing for associations. We develop intuition for why and when spurious correlations may occur using analytical theory and conduct population-genetic and phylogenetic simulations of quantitative traits. The structural similarity of problems in statistical genetics and phylogenetics enables us to take methodological advances from one field and apply them in the other. We demonstrate this by showing how a standard GWAS technique-including both the genetic relatedness matrix (GRM) as well as its leading eigenvectors, corresponding to the principal components of the genotype matrix, in a regression model-can mitigate spurious correlations in phylogenetic analyses. As a case study of this, we re-examine an analysis testing for co-evolution of expression levels between genes across a fungal phylogeny, and show that including covariance matrix eigenvectors as covariates decreases the false positive rate while simultaneously increasing the true positive rate. More generally, this work provides a foundation for more integrative approaches for understanding the genetic architecture of phenotypes and how evolutionary processes shape it.
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4
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Iverson ENK. Conservation Mitonuclear Replacement: Facilitated mitochondrial adaptation for a changing world. Evol Appl 2024; 17:e13642. [PMID: 38468713 PMCID: PMC10925831 DOI: 10.1111/eva.13642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 12/29/2023] [Accepted: 01/03/2024] [Indexed: 03/13/2024] Open
Abstract
Most species will not be able to migrate fast enough to cope with climate change, nor evolve quickly enough with current levels of genetic variation. Exacerbating the problem are anthropogenic influences on adaptive potential, including the prevention of gene flow through habitat fragmentation and the erosion of genetic diversity in small, bottlenecked populations. Facilitated adaptation, or assisted evolution, offers a way to augment adaptive genetic variation via artificial selection, induced hybridization, or genetic engineering. One key source of genetic variation, particularly for climatic adaptation, are the core metabolic genes encoded by the mitochondrial genome. These genes influence environmental tolerance to heat, drought, and hypoxia, but must interact intimately and co-evolve with a suite of important nuclear genes. These coadapted mitonuclear genes form some of the important reproductive barriers between species. Mitochondrial genomes can and do introgress between species in an adaptive manner, and they may co-introgress with nuclear genes important for maintaining mitonuclear compatibility. Managers should consider the relevance of mitonuclear genetic variability in conservation decision-making, including as a tool for facilitating adaptation. I propose a novel technique dubbed Conservation Mitonuclear Replacement (CmNR), which entails replacing the core metabolic machinery of a threatened species-the mitochondrial genome and key nuclear loci-with those from a closely related species or a divergent population, which may be better-adapted to climatic changes or carry a lower genetic load. The most feasible route to CmNR is to combine CRISPR-based nuclear genetic editing with mitochondrial replacement and assisted reproductive technologies. This method preserves much of an organism's phenotype and could allow populations to persist in the wild when no other suitable conservation options exist. The technique could be particularly important on mountaintops, where rising temperatures threaten an alarming number of species with almost certain extinction in the next century.
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Affiliation(s)
- Erik N. K. Iverson
- Department of Integrative BiologyThe University of Texas at AustinAustinTexasUSA
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5
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Lukaszewicz M, Salia OI, Hohenlohe PA, Buzbas EO. Approximate Bayesian computational methods to estimate the strength of divergent selection in population genomics models. JOURNAL OF COMPUTATIONAL MATHEMATICS AND DATA SCIENCE 2024; 10:100091. [PMID: 38616846 PMCID: PMC11014422 DOI: 10.1016/j.jcmds.2024.100091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Statistical estimation of parameters in large models of evolutionary processes is often too computationally inefficient to pursue using exact model likelihoods, even with single-nucleotide polymorphism (SNP) data, which offers a way to reduce the size of genetic data while retaining relevant information. Approximate Bayesian Computation (ABC) to perform statistical inference about parameters of large models takes the advantage of simulations to bypass direct evaluation of model likelihoods. We develop a mechanistic model to simulate forward-in-time divergent selection with variable migration rates, modes of reproduction (sexual, asexual), length and number of migration-selection cycles. We investigate the computational feasibility of ABC to perform statistical inference and study the quality of estimates on the position of loci under selection and the strength of selection. To expand the parameter space of positions under selection, we enhance the model by implementing an outlier scan on summarized observed data. We evaluate the usefulness of summary statistics well-known to capture the strength of selection, and assess their informativeness under divergent selection. We also evaluate the effect of genetic drift with respect to an idealized deterministic model with single-locus selection. We discuss the role of the recombination rate as a confounding factor in estimating the strength of divergent selection, and emphasize its importance in break down of linkage disequilibrium (LD). We answer the question for which part of the parameter space of the model we recover strong signal for estimating the selection, and determine whether population differentiation-based summary statistics or LD-based summary statistics perform well in estimating selection.
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Affiliation(s)
- Martyna Lukaszewicz
- Institute for Interdisciplinary Data Sciences (IIDS), University of Idaho, Moscow, ID, United States of America
- Department of Mathematics and Statistical Science, University of Idaho, Moscow, ID, United States of America
- Department of Biological Sciences, University of Idaho, Moscow, ID, United States of America
| | - Ousseini Issaka Salia
- Institute for Interdisciplinary Data Sciences (IIDS), University of Idaho, Moscow, ID, United States of America
- Institute for Modeling Collaboration and Innovation (IMCI), University of Idaho, Moscow, ID, United States of America
- Department of Mathematics and Statistical Science, University of Idaho, Moscow, ID, United States of America
- Department of Biological Sciences, University of Idaho, Moscow, ID, United States of America
- Department of Horticulture, Washington State University, Pullman, WA, United States of America
| | - Paul A. Hohenlohe
- Institute for Interdisciplinary Data Sciences (IIDS), University of Idaho, Moscow, ID, United States of America
- Institute for Modeling Collaboration and Innovation (IMCI), University of Idaho, Moscow, ID, United States of America
- Department of Mathematics and Statistical Science, University of Idaho, Moscow, ID, United States of America
- Department of Biological Sciences, University of Idaho, Moscow, ID, United States of America
| | - Erkan O. Buzbas
- Institute for Interdisciplinary Data Sciences (IIDS), University of Idaho, Moscow, ID, United States of America
- Institute for Modeling Collaboration and Innovation (IMCI), University of Idaho, Moscow, ID, United States of America
- Department of Mathematics and Statistical Science, University of Idaho, Moscow, ID, United States of America
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6
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Chase MA, Vilcot M, Mugal CF. The role of recombination dynamics in shaping signatures of direct and indirect selection across the Ficedula flycatcher genome †. Proc Biol Sci 2024; 291:20232382. [PMID: 38228173 DOI: 10.1098/rspb.2023.2382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 12/14/2023] [Indexed: 01/18/2024] Open
Abstract
Recombination is a central evolutionary process that reshuffles combinations of alleles along chromosomes, and consequently is expected to influence the efficacy of direct selection via Hill-Robertson interference. Additionally, the indirect effects of selection on neutral genetic diversity are expected to show a negative relationship with recombination rate, as background selection and genetic hitchhiking are stronger when recombination rate is low. However, owing to the limited availability of recombination rate estimates across divergent species, the impact of evolutionary changes in recombination rate on genomic signatures of selection remains largely unexplored. To address this question, we estimate recombination rate in two Ficedula flycatcher species, the taiga flycatcher (Ficedula albicilla) and collared flycatcher (Ficedula albicollis). We show that recombination rate is strongly correlated with signatures of indirect selection, and that evolutionary changes in recombination rate between species have observable impacts on this relationship. Conversely, signatures of direct selection on coding sequences show little to no relationship with recombination rate, even when restricted to genes where recombination rate is conserved between species. Thus, using measures of indirect and direct selection that bridge micro- and macro-evolutionary timescales, we demonstrate that the role of recombination rate and its dynamics varies for different signatures of selection.
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Affiliation(s)
- Madeline A Chase
- Department of Ecology and Genetics, Uppsala University, 75236 Uppsala, Sweden
- Swiss Ornithological Institute, 6204 Sempach, Switzerland
| | - Maurine Vilcot
- Department of Ecology and Genetics, Uppsala University, 75236 Uppsala, Sweden
- CEFE, University of Montpellier, CNRS, EPHE, IRD, 34293 Montpellier 5, France
| | - Carina F Mugal
- Department of Ecology and Genetics, Uppsala University, 75236 Uppsala, Sweden
- Laboratory of Biometry and Evolutionary Biology, University of Lyon 1, CNRS UMR 5558, 69622 Villeurbanne cedex, France
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7
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Hu G, Wang Y, Liu X, Strube ML, Wang B, Kovács ÁT. Species and condition shape the mutational spectrum in experimentally evolved biofilms. mSystems 2023; 8:e0054823. [PMID: 37768063 PMCID: PMC10654089 DOI: 10.1128/msystems.00548-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Accepted: 08/11/2023] [Indexed: 09/29/2023] Open
Abstract
IMPORTANCE Biofilm formation is a vital factor for the survival and adaptation of bacteria in diverse environmental niches. Experimental evolution combined with the advancement of whole-population genome sequencing provides us a powerful tool to understand the genomic dynamic of evolutionary adaptation to different environments, such as during biofilm development. Previous studies described the genetic and phenotypic changes of selected clones from experimentally evolved Bacillus thuringiensis and Bacillus subtilis that were adapted under abiotic and biotic biofilm conditions. However, the full understanding of the dynamic evolutionary landscapes was lacking. Furthermore, the differences and similarities of adaptive mechanisms in B. thuringiensis and B. subtilis were not identified. To overcome these limitations, we performed longitudinal whole-population genome sequencing to study the underlying genetic dynamics at high resolution. Our study provides the first comprehensive mutational landscape of two bacterial species' biofilms that is adapted to an abiotic and biotic surface.
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Affiliation(s)
- Guohai Hu
- China National GeneBank, BGI, Shenzhen, China
- BGI Research, Shenzhen, China
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Lyngby, Denmark
| | - Yue Wang
- China National GeneBank, BGI, Shenzhen, China
- BGI Research, Shenzhen, China
- BGI Research, Beijing, China
| | - Xin Liu
- China National GeneBank, BGI, Shenzhen, China
- BGI Research, Shenzhen, China
- BGI Research, Beijing, China
| | - Mikael Lenz Strube
- Bacterial Ecophysiology and Biotechnology Group, DTU Bioengineering, Technical University of Denmark, Lyngby, Denmark
| | - Bo Wang
- China National GeneBank, BGI, Shenzhen, China
- BGI Research, Shenzhen, China
- Shenzhen Key Laboratory of Environmental Microbial Genomics and Application, BGI Research, Shenzhen, China
| | - Ákos T. Kovács
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Lyngby, Denmark
- Institute of Biology, Leiden University, Leiden, The Netherlands
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8
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Wang X, Ingvarsson PK. Quantifying adaptive evolution and the effects of natural selection across the Norway spruce genome. Mol Ecol 2023; 32:5288-5304. [PMID: 37622583 DOI: 10.1111/mec.17106] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 08/07/2023] [Accepted: 08/09/2023] [Indexed: 08/26/2023]
Abstract
Detecting natural selection is one of the major goals of evolutionary genomics. Here, we sequenced the whole genome of 25 Picea abies individuals and quantified the amount of selection across the genome. Using an estimate of the distribution of fitness effects, we showed that both negative selection and the rate of positively selected substitutions are very limited in coding regions. We found a positive correlation between the rate of adaptive substitutions and recombination rate and a negative correlation between the rate of adaptive substitutions and gene density, suggesting a widespread influence from Hill-Robertson interference on the efficiency of protein adaptation in P. abies. Finally, the distinct population statistics between genomic regions under either positive or balancing selection with that under neutral regions indicated the impact of natural selection on the genomic architecture of Norway spruce. Further gene ontology enrichment analysis for genes located in regions identified as undergoing either positive or long-term balancing selection also highlighted the specific molecular functions and biological processes that appear to be targets of selection in Norway spruce.
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Affiliation(s)
- Xi Wang
- Umeå Plant Science Centre, Department of Ecology and Environmental Science, Umeå University, Umeå, Sweden
| | - Pär K Ingvarsson
- Linnean Centre for Plant Biology, Department of Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
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9
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Hwang HY, Wang J. Effect of recombination on genetic diversity of Caenorhabditis elegans. Sci Rep 2023; 13:16425. [PMID: 37777524 PMCID: PMC10542817 DOI: 10.1038/s41598-023-42600-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 09/12/2023] [Indexed: 10/02/2023] Open
Abstract
Greater molecular divergence and genetic diversity are present in regions of high recombination in many species. Studies describing the correlation between variant abundance and recombination rate have long focused on recombination in the context of linked selection models, whereby interference between linked sites under positive or negative selection reduces genetic diversity in regions of low recombination. Here, we show that indels, especially those of intermediate sizes, are enriched relative to single nucleotide polymorphisms in regions of high recombination in C. elegans. To explain this phenomenon, we reintroduce an alternative model that emphasizes the mutagenic effect of recombination. To extend the analysis, we examine the variants with a phylogenetic context and discuss how different models could be examined together. The number of variants generated by recombination in natural populations could be substantial including possibly the majority of some indel subtypes. Our work highlights the potential importance of a mutagenic effect of recombination, which could have a significant role in the shaping of natural genetic diversity.
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Affiliation(s)
- Ho-Yon Hwang
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Department of Neuroscience, School of Medicine, Johns Hopkins University, Baltimore, MD, 21205, USA.
| | - Jiou Wang
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Department of Neuroscience, School of Medicine, Johns Hopkins University, Baltimore, MD, 21205, USA.
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10
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Comai L. Unlikely heroes on the long and winding road to potato inbreeding. ABIOTECH 2023; 4:267-271. [PMID: 37970470 PMCID: PMC10638346 DOI: 10.1007/s42994-023-00109-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Accepted: 06/15/2023] [Indexed: 11/17/2023]
Abstract
Conversion of potato from a tetraploid, heterozygous, vegetatively propagated crop to a diploid F1 hybrid, propagated via botanical seed, would constitute a considerable advance for global agriculture, but faces multiple challenges. One such challenge is the difficulty in inbreeding potato, which involves purging deleterious alleles from its genome. This commentary discusses possible reasons for this difficulty and highlights a recent sequence-based effort to classify SNP variation, in potato germplasm, according to its deleterious potential. Tools and strategies connected to this database may facilitate development of F1 hybrids.
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Affiliation(s)
- Luca Comai
- Department of Plant Biology and Genome Center, University of California Davis, Davis, CA 95616 USA
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11
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Devi A, Speyer G, Lynch M. The divergence of mean phenotypes under persistent directional selection. Genetics 2023; 224:iyad091. [PMID: 37200616 PMCID: PMC10552002 DOI: 10.1093/genetics/iyad091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 02/26/2023] [Accepted: 05/04/2023] [Indexed: 05/20/2023] Open
Abstract
Numerous organismal traits, particularly at the cellular level, are likely to be under persistent directional selection across phylogenetic lineages. Unless all mutations affecting such traits have large enough effects to be efficiently selected in all species, gradients in mean phenotypes are expected to arise as a consequence of differences in the power of random genetic drift, which varies by approximately five orders of magnitude across the Tree of Life. Prior theoretical work examining the conditions under which such gradients can arise focused on the simple situation in which all genomic sites affecting the trait have identical and constant mutational effects. Here, we extend this theory to incorporate the more biologically realistic situation in which mutational effects on a trait differ among nucleotide sites. Pursuit of such modifications leads to the development of semi-analytic expressions for the ways in which selective interference arises via linkage effects in single-effects models, which then extend to more complex scenarios. The theory developed clarifies the conditions under which mutations of different selective effects mutually interfere with each others' fixation and shows how variance in effects among sites can substantially modify and extend the expected scaling relationships between mean phenotypes and effective population sizes.
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Affiliation(s)
- Archana Devi
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ 85287, USA
| | - Gil Speyer
- Knowledge Enterprise, Arizona State University, Tempe, AZ 85287, USA
| | - Michael Lynch
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ 85287, USA
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12
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Cutter AD. Speciation and development. Evol Dev 2023; 25:289-327. [PMID: 37545126 DOI: 10.1111/ede.12454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 06/13/2023] [Accepted: 07/20/2023] [Indexed: 08/08/2023]
Abstract
Understanding general principles about the origin of species remains one of the foundational challenges in evolutionary biology. The genomic divergence between groups of individuals can spawn hybrid inviability and hybrid sterility, which presents a tantalizing developmental problem. Divergent developmental programs may yield either conserved or divergent phenotypes relative to ancestral traits, both of which can be responsible for reproductive isolation during the speciation process. The genetic mechanisms of developmental evolution involve cis- and trans-acting gene regulatory change, protein-protein interactions, genetic network structures, dosage, and epigenetic regulation, all of which also have roots in population genetic and molecular evolutionary processes. Toward the goal of demystifying Darwin's "mystery of mysteries," this review integrates microevolutionary concepts of genetic change with principles of organismal development, establishing explicit links between population genetic process and developmental mechanisms in the production of macroevolutionary pattern. This integration aims to establish a more unified view of speciation that binds process and mechanism.
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Affiliation(s)
- Asher D Cutter
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
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13
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Lye Z, Choi JY, Purugganan MD. Deleterious mutations and the rare allele burden on rice gene expression. Mol Biol Evol 2022; 39:6693943. [PMID: 36073358 PMCID: PMC9512150 DOI: 10.1093/molbev/msac193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Deleterious genetic variation is maintained in populations at low frequencies. Under a model of stabilizing selection, rare (and presumably deleterious) genetic variants are associated with increase or decrease in gene expression from some intermediate optimum. We investigate this phenomenon in a population of largely Oryza sativa ssp. indica rice landraces under normal unstressed wet and stressful drought field conditions. We include single nucleotide polymorphisms, insertion/deletion mutations, and structural variants in our analysis and find a stronger association between rare variants and gene expression outliers under the stress condition. We also show an association of the strength of this rare variant effect with linkage, gene expression levels, network connectivity, local recombination rate, and fitness consequence scores, consistent with the stabilizing selection model of gene expression.
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Affiliation(s)
- Zoe Lye
- Center for Genomics and Systems Biology, New York University, New York, NY 10003
| | - Jae Young Choi
- Center for Genomics and Systems Biology, New York University, New York, NY 10003
| | - Michael D Purugganan
- Center for Genomics and Systems Biology, New York University, New York, NY 10003.,Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
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14
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Chen Y, Schreiber M, Bayer MM, Dawson IK, Hedley PE, Lei L, Akhunova A, Liu C, Smith KP, Fay JC, Muehlbauer GJ, Steffenson BJ, Morrell PL, Waugh R, Russell JR. The evolutionary patterns of barley pericentromeric chromosome regions, as shaped by linkage disequilibrium and domestication. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:1580-1594. [PMID: 35834607 PMCID: PMC9546296 DOI: 10.1111/tpj.15908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 06/30/2022] [Accepted: 07/13/2022] [Indexed: 05/17/2023]
Abstract
The distribution of recombination events along large cereal chromosomes is uneven and is generally restricted to gene-rich telomeric ends. To understand how the lack of recombination affects diversity in the large pericentromeric regions, we analysed deep exome capture data from a final panel of 815 Hordeum vulgare (barley) cultivars, landraces and wild barleys, sampled from across their eco-geographical ranges. We defined and compared variant data across the pericentromeric and non-pericentromeric regions, observing a clear partitioning of diversity both within and between chromosomes and germplasm groups. Dramatically reduced diversity was found in the pericentromeres of both cultivars and landraces when compared with wild barley. We observed a mixture of completely and partially differentiated single-nucleotide polymorphisms (SNPs) between domesticated and wild gene pools, suggesting that domesticated gene pools were derived from multiple wild ancestors. Patterns of genome-wide linkage disequilibrium, haplotype block size and number, and variant frequency within blocks showed clear contrasts among individual chromosomes and between cultivars and wild barleys. Although most cultivar chromosomes shared a single major pericentromeric haplotype, chromosome 7H clearly differentiated the two-row and six-row types associated with different geographical origins. Within the pericentromeric regions we identified 22 387 non-synonymous SNPs, 92 of which were fixed for alternative alleles in cultivar versus wild accessions. Surprisingly, only 29 SNPs found exclusively in the cultivars were predicted to be 'highly deleterious'. Overall, our data reveal an unconventional pericentromeric genetic landscape among distinct barley gene pools, with different evolutionary processes driving domestication and diversification.
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Affiliation(s)
- Yun‐Yu Chen
- The James Hutton Institute, InvergowrieDundeeDD2 5DAUK
- Fios GenomicsBioQuarter, 13 Little France RdEdinburghEH16 4UXUK
| | - Miriam Schreiber
- The James Hutton Institute, InvergowrieDundeeDD2 5DAUK
- Division of Plant Sciences, School of Life SciencesUniversity of DundeeDow StreetDundeeDD1 5EHUK
| | | | - Ian K. Dawson
- The James Hutton Institute, InvergowrieDundeeDD2 5DAUK
- Scotland's Rural College, Kings BuildingsWest Mains RdEdinburghEH9 3JGUK
| | | | - Li Lei
- Department of Agronomy & Plant GeneticsUniversity of Minnesota411 Borlaug Hall, 1991 Buford CircleSt PaulMN55108USA
| | - Alina Akhunova
- Department of Agronomy & Plant GeneticsUniversity of Minnesota411 Borlaug Hall, 1991 Buford CircleSt PaulMN55108USA
- Department of Plant PathologyKansas State UniversityThrockmorton HallManhattanKS66506USA
| | - Chaochih Liu
- Department of Agronomy & Plant GeneticsUniversity of Minnesota411 Borlaug Hall, 1991 Buford CircleSt PaulMN55108USA
| | - Kevin P. Smith
- Department of Agronomy & Plant GeneticsUniversity of Minnesota411 Borlaug Hall, 1991 Buford CircleSt PaulMN55108USA
| | - Justin C. Fay
- Department of BiologyUniversity of Rochester319 HutchisonRochesterNY14627USA
| | - Gary J. Muehlbauer
- Department of Agronomy & Plant GeneticsUniversity of Minnesota411 Borlaug Hall, 1991 Buford CircleSt PaulMN55108USA
| | - Brian J. Steffenson
- Department of Plant PathologyUniversity of Minnesota495 Borlaug Hall, 1991 Buford CircleSt PaulMN55108USA
| | - Peter L. Morrell
- Department of Agronomy & Plant GeneticsUniversity of Minnesota411 Borlaug Hall, 1991 Buford CircleSt PaulMN55108USA
| | - Robbie Waugh
- The James Hutton Institute, InvergowrieDundeeDD2 5DAUK
- Division of Plant Sciences, School of Life SciencesUniversity of DundeeDow StreetDundeeDD1 5EHUK
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15
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LaMont C, Otwinowski J, Vanshylla K, Gruell H, Klein F, Nourmohammad A. Design of an optimal combination therapy with broadly neutralizing antibodies to suppress HIV-1. eLife 2022; 11:76004. [PMID: 35852143 PMCID: PMC9467514 DOI: 10.7554/elife.76004] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 07/04/2022] [Indexed: 11/13/2022] Open
Abstract
Infusion of broadly neutralizing antibodies (bNAbs) has shown promise as an alternative to anti-retroviral therapy against HIV. A key challenge is to suppress viral escape, which is more effectively achieved with a combination of bNAbs. Here, we propose a computational approach to predict the efficacy of a bNAb therapy based on the population genetics of HIV escape, which we parametrize using high-throughput HIV sequence data from bNAb-naive patients. By quantifying the mutational target size and the fitness cost of HIV-1 escape from bNAbs, we predict the distribution of rebound times in three clinical trials. We show that a cocktail of three bNAbs is necessary to effectively suppress viral escape, and predict the optimal composition of such bNAb cocktail. Our results offer a rational therapy design for HIV, and show how genetic data can be used to predict treatment outcomes and design new approaches to pathogenic control.
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Affiliation(s)
- Colin LaMont
- Max Planck Institute for Dynamics and Self-Organization
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16
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Toncheva D, Marinova M, Borovska P, Serbezov D. Spatio-temporal dynamics of pathogenic variants associated with monogenic disorders reconstructed with ancient DNA. PLoS One 2022; 17:e0269628. [PMID: 35749392 PMCID: PMC9231702 DOI: 10.1371/journal.pone.0269628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 05/24/2022] [Indexed: 11/18/2022] Open
Abstract
Genetic disease burden in ancient communities has barely been evaluated despite an ever expanding body of ancient genomes becoming available. In this study, we inspect 2729 publicly available ancient genomes (100 BP—52000 BP) for the presence of pathogenic variants in 32643 disease-associated loci. We base our subsequent analyses on 19 variants in seven genes—PAH, EDAR, F11, HBB, LRRK2, SLC12A6 and MAOA, associated with monogenic diseases and with well-established pathogenic impact in contemporary populations. We determine 230 homozygote genotypes of these variants in the screened 2729 ancient DNA samples. Eleven of these are in the PAH gene (126 ancient samples in total), a gene associated with the condition phenylketonuria in modern populations. The variants examined seem to show varying dynamics over the last 10000 years, some exhibiting a single upsurge in frequency and subsequently disappearing, while others maintain high frequency levels (compared to contemporary population frequencies) over long time periods. The geographic distribution and age of the ancient DNA samples with established pathogenic variants suggests multiple independent origin of these variants. Comparison of estimates of the geographic prevalence of these variants from ancient and contemporary data show discontinuity in their prevalence and supports their recurrent emergence. The oldest samples in which a variant is established might give an indication of their age and place origin, and an EDAR gene pathogenic variant was established in a sample estimated to be 33210–32480 calBCE. Knowledge about the historical prevalence of variants causing monogenic disorders provides insight on their emergence, dynamics and spread.
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Affiliation(s)
- Draga Toncheva
- Department of Medical Genetics, Medical Faculty, Medical University-Sofia, Sofia, Bulgaria
- Bulgarian Academy of Sciences, Sofia, Bulgaria
- * E-mail:
| | - Maria Marinova
- Department of Computer systems and Technologies, Faculty of Electronics and Automation, Technical University–Sofia, Branch Plovdiv, Bulgaria
| | - Plamenka Borovska
- Department of Informatics, Faculty of Applied Mathematics and Informatics, Technical University of Sofia, Sofia, Bulgaria
| | - Dimitar Serbezov
- Department of Medical Genetics, Medical Faculty, Medical University-Sofia, Sofia, Bulgaria
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17
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Harwood MP, Alves I, Edgington H, Agbessi M, Bruat V, Soave D, Lamaze FC, Favé MJ, Awadalla P. Recombination affects allele-specific expression of deleterious variants in human populations. SCIENCE ADVANCES 2022; 8:eabl3819. [PMID: 35559670 PMCID: PMC9106294 DOI: 10.1126/sciadv.abl3819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 03/29/2022] [Indexed: 06/15/2023]
Abstract
How the genetic composition of a population changes through stochastic processes, such as genetic drift, in combination with deterministic processes, such as selection, is critical to understanding how phenotypes vary in space and time. Here, we show how evolutionary forces affecting selection, including recombination and effective population size, drive genomic patterns of allele-specific expression (ASE). Integrating tissue-specific genotypic and transcriptomic data from 1500 individuals from two different cohorts, we demonstrate that ASE is less often observed in regions of low recombination, and loci in high or normal recombination regions are more efficient at using ASE to underexpress harmful mutations. By tracking genetic ancestry, we discriminate between ASE variability due to past demographic effects, including subsequent bottlenecks, versus local environment. We observe that ASE is not randomly distributed along the genome and that population parameters influencing the efficacy of natural selection alter ASE levels genome wide.
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Affiliation(s)
- Michelle P. Harwood
- Ontario Institute for Cancer Research, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Isabel Alves
- Université de Nantes, CHU Nantes, CNRS, INSERM, L’Institut du thorax, F-44000 Nantes, France
| | | | | | - Vanessa Bruat
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - David Soave
- Ontario Institute for Cancer Research, Toronto, ON, Canada
- Department of Mathematics, Wilfrid Laurier University, Waterloo, ON, Canada
| | - Fabien C. Lamaze
- Ontario Institute for Cancer Research, Toronto, ON, Canada
- Institut universitaire de cardiologie et de pneumologie de Québec, Université Laval, Québec, QC, Canada
| | | | - Philip Awadalla
- Ontario Institute for Cancer Research, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
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18
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Stolyarova AV, Neretina TV, Zvyagina EA, Fedotova AV, Kondrashov A, Bazykin GA. Complex fitness landscape shapes variation in a hyperpolymorphic species. eLife 2022; 11:76073. [PMID: 35532122 PMCID: PMC9187340 DOI: 10.7554/elife.76073] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 05/09/2022] [Indexed: 11/13/2022] Open
Abstract
It is natural to assume that patterns of genetic variation in hyperpolymorphic species can reveal large-scale properties of the fitness landscape that are hard to detect by studying species with ordinary levels of genetic variation. Here, we study such patterns in a fungus Schizophyllum commune, the most polymorphic species known. Throughout the genome, short-range linkage disequilibrium (LD) caused by attraction of minor alleles is higher between pairs of nonsynonymous than of synonymous variants. This effect is especially pronounced for pairs of sites that are located within the same gene, especially if a large fraction of the gene is covered by haploblocks, genome segments where the gene pool consists of two highly divergent haplotypes, which is a signature of balancing selection. Haploblocks are usually shorter than 1000 nucleotides, and collectively cover about 10% of the S. commune genome. LD tends to be substantially higher for pairs of nonsynonymous variants encoding amino acids that interact within the protein. There is a substantial correlation between LDs at the same pairs of nonsynonymous mutations in the USA and the Russian populations. These patterns indicate that selection in S. commune involves positive epistasis due to compensatory interactions between nonsynonymous alleles. When less polymorphic species are studied, analogous patterns can be detected only through interspecific comparisons. Changes to DNA known as mutations may alter how the proteins and other components of a cell work, and thus play an important role in allowing living things to evolve new traits and abilities over many generations. Whether a mutation is beneficial or harmful may differ depending on the genetic background of the individual – that is, depending on other mutations present in other positions within the same gene – due to a phenomenon called epistasis. Epistasis is known to affect how various species accumulate differences in their DNA compared to each other over time. For example, a mutation that is rare in humans and known to cause disease may be widespread in other primates because its negative effect is canceled out by another mutation that is standard for these species but absent in humans. However, it remains unclear whether epistasis plays a significant part in shaping genetic differences between individuals of the same species. A type of fungus known as Schizophyllum commune lives on rotting wood and is found across the world. It is one of the most genetically diverse species currently known, so there is a higher chance of pairs of compensatory mutations occurring and persisting for a long time in S. commune than in most other species, providing a unique opportunity to study epistasis. Here, Stolyarova et al. studied two distinct populations of S. commune, one from the USA and one from Russia. The team found that – unlike in humans, flies and other less genetically diverse species – epistasis maintains combinations of mutations in S. commune that individually would be harmful to the fungus but together compensate for each other. For example, pairs of mutations affecting specific molecules known as amino acids – the building blocks of proteins – that physically interact with each other tended to be found together in the same individuals. One potential downside of having pairs of compensatory mutations in the genome is that when the organism reproduces, the process of making sex cells may split up these pairs so that harmful mutations are inherited without their partner mutations. Thus, epistasis may have helped shape the way S. commune and other genetically diverse species have evolved.
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Affiliation(s)
| | - Tatiana V Neretina
- Biological Faculty, Lomonosov Moscow State University, Moscow, Russian Federation
| | - Elena A Zvyagina
- Biological Faculty, Lomonosov Moscow State University, Moscow, Russian Federation
| | - Anna V Fedotova
- Skolkovo Institute of Science and Technology, Moscow, Russian Federation
| | - Alexey Kondrashov
- Department of Ecology and Evolutionary Biology, University of Michigan-Ann Arbor, Ann Arbor, United States
| | - Georgii A Bazykin
- Institute for Information Transmission Problems (Kharkevich Institute), Russian Academy of Sciences, Moscow, Russian Federation
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19
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Abstract
Abstract
Few doubt that effective population size (Ne) is one of the most important parameters in evolutionary biology, but how many can say they really understand the concept? Ne is the evolutionary analogue of the number of individuals (or adults) in the population, N. Whereas ecological consequences of population size depend on N, evolutionary consequences (rates of loss of genetic diversity and increase in inbreeding; relative effectiveness of selection) depend on Ne. Formal definitions typically relate effective size to a key population genetic parameter, such as loss of heterozygosity or variance in allele frequency. However, for practical application to real populations, it is more useful to define Ne in terms of three demographic parameters: number of potential parents (adult N), and mean and variance in offspring number. Defined this way, Ne determines the rate of random genetic drift across the entire genome in the offspring generation. Other evolutionary forces (mutation, migration, selection)—together with factors such as variation in recombination rate—can also affect genetic variation, and this leads to heterogeneity across the genome in observed rates of genetic change. For some, it has been convenient to interpret this heterogeneity in terms of heterogeneity in Ne, but unfortunately this has muddled the concepts of genetic drift and effective population size. A commonly-repeated misconception is that Ne is the number of parents that actually contribute genes to the next generation (NP). In reality, NP can be smaller or larger than Ne, and the NP/Ne ratio depends on the sex ratio, the mean and variance in offspring number, and whether inbreeding or variance Ne is of interest.
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Affiliation(s)
- Robin S Waples
- Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, WA, 98112 USA
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20
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Cosme LV, Lima JBP, Powell JR, Martins AJ. Genome-wide Association Study Reveals New Loci Associated With Pyrethroid Resistance in Aedes aegypti. Front Genet 2022; 13:867231. [PMID: 35480313 PMCID: PMC9035894 DOI: 10.3389/fgene.2022.867231] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 03/21/2022] [Indexed: 11/21/2022] Open
Abstract
Genome-wide association studies (GWAS) use genetic polymorphism across the genomes of individuals with distinct characteristics to identify genotype-phenotype associations. In mosquitoes, complex traits such as vector competence and insecticide resistance could benefit from GWAS. We used the Aedes aegypti 50k SNP chip to genotype populations with different levels of pyrethroid resistance from Northern Brazil. Pyrethroids are widely used worldwide to control mosquitoes and agricultural pests, and their intensive use led to the selection of resistance phenotypes in many insects including mosquitoes. For Ae. aegypti, resistance phenotypes are mainly associated with several mutations in the voltage-gated sodium channel, known as knockdown resistance (kdr). We phenotyped those populations with the WHO insecticide bioassay using deltamethrin impregnated papers, genotyped the kdr alleles using qPCR, and determined allele frequencies across the genome using the SNP chip. We identified single-nucleotide polymorphisms (SNPs) directly associated with resistance and one epistatic SNP pair. We also observed that the novel SNPs correlated with the known kdr genotypes, although on different chromosomes or not in close physical proximity to the voltage gated sodium channel gene. In addition, pairwise comparison of resistance and susceptible mosquitoes from each population revealed differentiated genomic regions not associated with pyrethroid resistance. These new bi-allelic markers can be used to genotype other populations along with kdr alleles to understand their worldwide distribution. The functional roles of the genes near the newly discovered SNPs require new studies to determine if they act synergistically with kdr alleles or reduce the fitness cost of maintaining resistant alleles.
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Affiliation(s)
- Luciano V. Cosme
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, United States
- *Correspondence: Luciano V. Cosme,
| | - José Bento Pereira Lima
- Laboratório de Fisiologia e Controle de Artrópodes Vetores, Instituto Oswaldo Cruz/ FIOCRUZ, Rio de Janeiro, Brazil
| | - Jeffrey R. Powell
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, United States
| | - Ademir Jesus Martins
- Laboratório de Fisiologia e Controle de Artrópodes Vetores, Instituto Oswaldo Cruz/ FIOCRUZ, Rio de Janeiro, Brazil
- Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular, INCT-EM, UFRJ, Rio de Janeiro, Brazil
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21
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Fields PD, McTaggart S, Reisser CMO, Haag C, Palmer WH, Little TJ, Ebert D, Obbard DJ. Population-genomic analysis identifies a low rate of global adaptive fixation in the proteins of the cyclical parthenogen Daphnia magna. Mol Biol Evol 2022; 39:6542319. [PMID: 35244177 PMCID: PMC8963301 DOI: 10.1093/molbev/msac048] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Daphnia are well-established ecological and evolutionary models, and the interaction between D. magna and its microparasites is widely considered a paragon of the host-parasite coevolutionary process. Like other well-studied arthropods such as Drosophila melanogaster and Anopheles gambiae, D. magna is a small, widespread, and abundant species that is therefore expected to display a large long-term population size and high rates of adaptive protein evolution. However, unlike these other species, D. magna is cyclically asexual and lives in a highly structured environment (ponds and lakes) with moderate levels of dispersal, both of which are predicted to impact upon long-term effective population size and adaptive protein evolution. To investigate patterns of adaptive protein fixation, we produced the complete coding genomes of 36 D. magna clones sampled from across the European range (Western Palaearctic), along with draft sequences for the close relatives D. similis and D. lumholtzi, used as outgroups. We analyzed genome-wide patterns of adaptive fixation, with a particular focus on genes that have an a priori expectation of high rates, such as those likely to mediate immune responses, RNA interference against viruses and transposable elements, and those with a strongly male-biased expression pattern. We find that, as expected, D. magna displays high levels of diversity and that this is highly structured among populations. However, compared with Drosophila, we find that D. magna proteins appear to have a high proportion of weakly deleterious variants and do not show evidence of pervasive adaptive fixation across its entire range. This is true of the genome as a whole, and also of putative ‘arms race’ genes that often show elevated levels of adaptive substitution in other species. In addition to the likely impact of extensive, and previously documented, local adaptation, we speculate that these findings may reflect reduced efficacy of selection associated with cyclical asexual reproduction.
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Affiliation(s)
- Peter D Fields
- University of Basel, Department of Environmental Sciences, Zoology, Vesalgasse 1, Basel, CH-4051, Switzerland
| | - Seanna McTaggart
- Institute of Evolutionary Biology; School of Biological Sciences University of Edinburgh, Edinburgh, EH9 3JT, United Kingdom
| | - Céline M O Reisser
- Centre d'Ecologie Fonctionnelle et Evolutive CEFE UMR 5175, Univ Montpellier, CNRS, EPHE, IRD, Univ Paul Valéry Montpellier 3, campus CNRS, 1919, route de Mende, 34293 Montpellier Cedex 5, France.,MARBEC, Univ Montpellier, CNRS, IFREMER, IRD, Montpellier, France
| | - Christoph Haag
- Centre d'Ecologie Fonctionnelle et Evolutive CEFE UMR 5175, Univ Montpellier, CNRS, EPHE, IRD, Univ Paul Valéry Montpellier 3, campus CNRS, 1919, route de Mende, 34293 Montpellier Cedex 5, France
| | - William H Palmer
- Institute of Evolutionary Biology; School of Biological Sciences University of Edinburgh, Edinburgh, EH9 3JT, United Kingdom
| | - Tom J Little
- Institute of Evolutionary Biology; School of Biological Sciences University of Edinburgh, Edinburgh, EH9 3JT, United Kingdom
| | - Dieter Ebert
- University of Basel, Department of Environmental Sciences, Zoology, Vesalgasse 1, Basel, CH-4051, Switzerland
| | - Darren J Obbard
- Institute of Evolutionary Biology; School of Biological Sciences University of Edinburgh, Edinburgh, EH9 3JT, United Kingdom
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22
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White NJ, Beckerman AP, Snook RR, Brockhurst MA, Butlin RK, Eyres I. Experimental evolution of local adaptation under unidimensional and multidimensional selection. Curr Biol 2022; 32:1310-1318.e4. [DOI: 10.1016/j.cub.2022.01.048] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Revised: 11/25/2021] [Accepted: 01/18/2022] [Indexed: 01/17/2023]
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23
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Pei Y, Forstmeier W, Ruiz-Ruano FJ, Mueller JC, Cabrero J, Camacho JPM, Alché JD, Franke A, Hoeppner M, Börno S, Gessara I, Hertel M, Teltscher K, Knief U, Suh A, Kempenaers B. Occasional paternal inheritance of the germline-restricted chromosome in songbirds. Proc Natl Acad Sci U S A 2022; 119:e2103960119. [PMID: 35058355 PMCID: PMC8794876 DOI: 10.1073/pnas.2103960119] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 11/06/2021] [Indexed: 11/29/2022] Open
Abstract
Songbirds have one special accessory chromosome, the so-called germline-restricted chromosome (GRC), which is only present in germline cells and absent from all somatic tissues. Earlier work on the zebra finch (Taeniopygia guttata castanotis) showed that the GRC is inherited only through the female line-like the mitochondria-and is eliminated from the sperm during spermatogenesis. Here, we show that the GRC has the potential to be paternally inherited. Confocal microscopy using GRC-specific fluorescent in situ hybridization probes indicated that a considerable fraction of sperm heads (1 to 19%) in zebra finch ejaculates still contained the GRC. In line with these cytogenetic data, sequencing of ejaculates revealed that individual males from two families differed strongly and consistently in the number of GRCs in their ejaculates. Examining a captive-bred male hybrid of the two zebra finch subspecies (T. g. guttata and T. g. castanotis) revealed that the mitochondria originated from a castanotis mother, whereas the GRC came from a guttata father. Moreover, analyzing GRC haplotypes across nine castanotis matrilines, estimated to have diverged for up to 250,000 y, showed surprisingly little variability among GRCs. This suggests that a single GRC haplotype has spread relatively recently across all examined matrilines. A few diagnostic GRC mutations that arose since this inferred spreading suggest that the GRC has continued to jump across matriline boundaries. Our findings raise the possibility that certain GRC haplotypes could selfishly spread through the population via occasional paternal transmission, thereby outcompeting other GRC haplotypes that were limited to strict maternal inheritance, even if this was partly detrimental to organismal fitness.
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Affiliation(s)
- Yifan Pei
- Department of Behavioral Ecology and Evolutionary Genetics, Max Planck Institute for Ornithology 82319 Seewiesen, Germany;
| | - Wolfgang Forstmeier
- Department of Behavioral Ecology and Evolutionary Genetics, Max Planck Institute for Ornithology 82319 Seewiesen, Germany;
| | - Francisco J Ruiz-Ruano
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TU, United Kingdom;
- Department of Organismal Biology, Evolutionary Biology Centre, Science for Life Laboratory, Uppsala University SE-752 36 Uppsala, Sweden
| | - Jakob C Mueller
- Department of Behavioral Ecology and Evolutionary Genetics, Max Planck Institute for Ornithology 82319 Seewiesen, Germany
| | - Josefa Cabrero
- Department of Genetics, University of Granada E-18071 Granada, Spain
| | | | - Juan D Alché
- Department of Biochemistry, Cell and Molecular Biology of Plants, Estación Experimental del Zaidín, Spanish National Research Council E-18008 Granada, Spain
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-Universität zu Kiel 24118 Kiel, Germany
| | - Marc Hoeppner
- Institute of Clinical Molecular Biology, Christian-Albrechts-Universität zu Kiel 24118 Kiel, Germany
| | - Stefan Börno
- Sequencing Core Facility, Max Planck Institute for Molecular Genetics 14195 Berlin, Germany
| | - Ivana Gessara
- Department of Behavioral Neurobiology, Max Planck Institute for Ornithology 82319 Seewiesen, Germany
| | - Moritz Hertel
- Department of Behavioral Neurobiology, Max Planck Institute for Ornithology 82319 Seewiesen, Germany
| | - Kim Teltscher
- Department of Behavioral Ecology and Evolutionary Genetics, Max Planck Institute for Ornithology 82319 Seewiesen, Germany
| | - Ulrich Knief
- Division of Evolutionary Biology, Faculty of Biology, Ludwig Maximilian University of Munich D-82152 Planegg-Martinsried, Germany
| | - Alexander Suh
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TU, United Kingdom;
- Department of Organismal Biology, Evolutionary Biology Centre, Science for Life Laboratory, Uppsala University SE-752 36 Uppsala, Sweden
| | - Bart Kempenaers
- Department of Behavioral Ecology and Evolutionary Genetics, Max Planck Institute for Ornithology 82319 Seewiesen, Germany
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24
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Gay L, Dhinaut J, Jullien M, Vitalis R, Navascués M, Ranwez V, Ronfort J. Evolution of flowering time in a selfing annual plant: Roles of adaptation and genetic drift. Ecol Evol 2022; 12:e8555. [PMID: 35127051 PMCID: PMC8794724 DOI: 10.1002/ece3.8555] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 12/10/2021] [Indexed: 11/10/2022] Open
Abstract
Resurrection studies are a useful tool to measure how phenotypic traits have changed in populations through time. If these trait modifications correlate with the environmental changes that occurred during the time period, it suggests that the phenotypic changes could be a response to selection. Selfing, through its reduction of effective size, could challenge the ability of a population to adapt to environmental changes. Here, we used a resurrection study to test for adaptation in a selfing population of Medicago truncatula, by comparing the genetic composition and flowering times across 22 generations. We found evidence for evolution toward earlier flowering times by about two days and a peculiar genetic structure, typical of highly selfing populations, where some multilocus genotypes (MLGs) are persistent through time. We used the change in frequency of the MLGs through time as a multilocus fitness measure and built a selection gradient that suggests evolution toward earlier flowering times. Yet, a simulation model revealed that the observed change in flowering time could be explained by drift alone, provided the effective size of the population is small enough (<150). These analyses suffer from the difficulty to estimate the effective size in a highly selfing population, where effective recombination is severely reduced.
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Affiliation(s)
- Laurène Gay
- CIRADINRAEInstitut AgroUMR AGAP InstitutUniv MontpellierMontpellierFrance
| | - Julien Dhinaut
- CIRADINRAEInstitut AgroUMR AGAP InstitutUniv MontpellierMontpellierFrance
- Present address:
Evolutionary Biology and Ecology of AlgaeUPMCUniversity of Paris VI, UC, UACH, UMI 3614CNRSSorbonne UniversitésRoscoffFrance
| | - Margaux Jullien
- CIRADINRAEInstitut AgroUMR AGAP InstitutUniv MontpellierMontpellierFrance
- Present address:
INRAUniv. Paris‐SudCNRSAgroParisTechGQE – Le MoulonUniversité Paris‐SaclayGif‐sur‐YvetteFrance
| | - Renaud Vitalis
- CIRADINRAEInstitut AgroIRDCBGPUniv MontpellierMontpellierFrance
| | | | - Vincent Ranwez
- CIRADINRAEInstitut AgroUMR AGAP InstitutUniv MontpellierMontpellierFrance
| | - Joëlle Ronfort
- CIRADINRAEInstitut AgroUMR AGAP InstitutUniv MontpellierMontpellierFrance
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25
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Harris KB, Flynn KM, Cooper VS. Polygenic Adaptation and Clonal Interference Enable Sustained Diversity in Experimental Pseudomonas aeruginosa Populations. Mol Biol Evol 2021; 38:5359-5375. [PMID: 34410431 PMCID: PMC8662654 DOI: 10.1093/molbev/msab248] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
How biodiversity arises and can be maintained in asexual microbial populations growing on a single resource remains unclear. Many models presume that beneficial genotypes will outgrow others and purge variation via selective sweeps. Environmental structure like that found in biofilms, which are associated with persistence during infection and other stressful conditions, may oppose this process and preserve variation. We tested this hypothesis by evolving Pseudomonas aeruginosa populations in biofilm-promoting arginine media for 3 months, using both a bead model of the biofilm life cycle and planktonic serial transfer. Surprisingly, adaptation and diversification were mostly uninterrupted by fixation events that eliminate diversity, with hundreds of mutations maintained at intermediate frequencies. The exceptions included genotypes with mutator alleles that also accelerated genetic diversification. Despite the rarity of hard sweeps, a remarkable 40 genes acquired parallel mutations in both treatments and often among competing genotypes within a population. These incomplete soft sweeps include several transporters (including pitA, pntB, nosD, and pchF) suggesting adaptation to the growth media that becomes highly alkaline during growth. Further, genes involved in signal transduction (including gacS, aer2, bdlA, and PA14_71750) reflect likely adaptations to biofilm-inducing conditions. Contrary to evolution experiments that select mutations in a few genes, these results suggest that some environments may expose a larger fraction of the genome and select for many adaptations at once. Thus, even growth on a sole carbon source can lead to persistent genetic and phenotypic variation despite strong selection that would normally purge diversity.
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Affiliation(s)
- Katrina B Harris
- Department of Microbiology and Molecular Genetics, and Center for Evolutionary Biology and Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Kenneth M Flynn
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, USA
| | - Vaughn S Cooper
- Department of Microbiology and Molecular Genetics, and Center for Evolutionary Biology and Medicine, University of Pittsburgh, Pittsburgh, PA, USA
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Horvath R, Josephs EB, Pesquet E, Stinchcombe JR, Wright SI, Scofield D, Slotte T. Selection on Accessible Chromatin Regions in Capsella grandiflora. Mol Biol Evol 2021; 38:5563-5575. [PMID: 34498072 PMCID: PMC8662636 DOI: 10.1093/molbev/msab270] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Accurate estimates of genome-wide rates and fitness effects of new mutations are essential for an improved understanding of molecular evolutionary processes. Although eukaryotic genomes generally contain a large noncoding fraction, functional noncoding regions and fitness effects of mutations in such regions are still incompletely characterized. A promising approach to characterize functional noncoding regions relies on identifying accessible chromatin regions (ACRs) tightly associated with regulatory DNA. Here, we applied this approach to identify and estimate selection on ACRs in Capsella grandiflora, a crucifer species ideal for population genomic quantification of selection due to its favorable population demography. We describe a population-wide ACR distribution based on ATAC-seq data for leaf samples of 16 individuals from a natural population. We use population genomic methods to estimate fitness effects and proportions of positively selected fixations (α) in ACRs and find that intergenic ACRs harbor a considerable fraction of weakly deleterious new mutations, as well as a significantly higher proportion of strongly deleterious mutations than comparable inaccessible intergenic regions. ACRs are enriched for expression quantitative trait loci (eQTL) and depleted of transposable element insertions, as expected if intergenic ACRs are under selection because they harbor regulatory regions. By integrating empirical identification of intergenic ACRs with analyses of eQTL and population genomic analyses of selection, we demonstrate that intergenic regulatory regions are an important source of nearly neutral mutations. These results improve our understanding of selection on noncoding regions and the role of nearly neutral mutations for evolutionary processes in outcrossing Brassicaceae species.
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Affiliation(s)
- Robert Horvath
- Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Emily B Josephs
- Department of Plant Biology, Michigan State University, Lansing, MI, USA
| | - Edouard Pesquet
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - John R Stinchcombe
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Stephen I Wright
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Douglas Scofield
- Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| | - Tanja Slotte
- Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
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Xu K. Mutation accumulation in inbreeding populations under evolution of the selfing rate. J Evol Biol 2021; 35:23-39. [PMID: 34860448 DOI: 10.1111/jeb.13968] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 11/17/2021] [Accepted: 11/23/2021] [Indexed: 11/28/2022]
Abstract
It is theoretically established that self-fertilization can facilitate mutation accumulation, thus increasing extinction risk. However, in previous studies, selfing rates are often set as fixed parameters, but in natural systems, evolution of selfing rates and deleterious mutations may mutually affect each other. I carried out simulations to investigate the dynamics of selfing rates and mutation accumulation, by allowing deleterious mutations to coevolve with alleles that modify the selfing rate (selfing modifiers). I found that selfing rates will often fluctuate over time, due to successive invasion of alleles that increase selfing and outcrossing. Since mutation fixation is mainly caused by Muller's ratchet, its rate is sensitive to the change of the selfing rate mutations will accumulate in a punctuated pattern. The dynamics are influenced by several factors, such as recombination and the selfing rate effects of selfing modifier loci. Also, such temporal variation produces variation of selfing rates and mutation accumulation rates between multiple conspecific populations, which can increase the average fitness across populations. As factors, such as the genomic mutation rate of deleterious mutations, can simultaneously influence the selfing rate and mutation fixation, effects of these factors on mutation accumulation rates can be complicated and non-monotonic.
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Affiliation(s)
- Kuangyi Xu
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina, USA
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Turbek SP, Semenov GA, Enbody ED, Campagna L, Taylor SA. Variable Signatures of Selection Despite Conserved Recombination Landscapes Early in Speciation. J Hered 2021; 112:485-496. [PMID: 34499149 DOI: 10.1093/jhered/esab054] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 09/08/2021] [Indexed: 11/14/2022] Open
Abstract
Recently diverged taxa often exhibit heterogeneous landscapes of genomic differentiation, characterized by regions of elevated differentiation on an otherwise homogeneous background. While divergence peaks are generally interpreted as regions responsible for reproductive isolation, they can also arise due to background selection, selective sweeps unrelated to speciation, and variation in recombination and mutation rates. To investigate the association between patterns of recombination and landscapes of genomic differentiation during the early stages of speciation, we generated fine-scale recombination maps for six southern capuchino seedeaters (Sporophila) and two subspecies of White Wagtail (Motacilla alba), two recent avian radiations in which divergent selection on pigmentation genes has likely generated peaks of differentiation. We compared these recombination maps to those of Collared (Ficedula albicollis) and Pied Flycatchers (Ficedula hypoleuca), non-sister taxa characterized by moderate genomic divergence and a heterogenous landscape of genomic differentiation shaped in part by background selection. Although recombination landscapes were conserved within all three systems, we documented a weaker negative correlation between recombination rate and genomic differentiation in the recent radiations. All divergence peaks between capuchinos, wagtails, and flycatchers were located in regions with lower-than-average recombination rates, and most divergence peaks in capuchinos and flycatchers fell in regions of exceptionally reduced recombination. Thus, co-adapted allelic combinations in these regions may have been protected early in divergence, facilitating rapid diversification. Despite largely conserved recombination landscapes, divergence peaks are specific to each focal comparison in capuchinos, suggesting that regions of elevated differentiation have not been generated by variation in recombination rate alone.
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Affiliation(s)
- Sheela P Turbek
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - Georgy A Semenov
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - Erik D Enbody
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Leonardo Campagna
- Fuller Evolutionary Biology Program, Cornell Lab of Ornithology, Ithaca, NY, USA.,Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - Scott A Taylor
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
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29
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Garcia JA, Lohmueller KE. Negative linkage disequilibrium between amino acid changing variants reveals interference among deleterious mutations in the human genome. PLoS Genet 2021; 17:e1009676. [PMID: 34319975 PMCID: PMC8351996 DOI: 10.1371/journal.pgen.1009676] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 08/09/2021] [Accepted: 06/22/2021] [Indexed: 11/18/2022] Open
Abstract
Evolutionary forces like Hill-Robertson interference and negative epistasis can lead to deleterious mutations being found on distinct haplotypes. However, the extent to which these forces depend on the selection and dominance coefficients of deleterious mutations and shape genome-wide patterns of linkage disequilibrium (LD) in natural populations with complex demographic histories has not been tested. In this study, we first used forward-in-time simulations to predict how negative selection impacts LD. Under models where deleterious mutations have additive effects on fitness, deleterious variants less than 10 kb apart tend to be carried on different haplotypes relative to pairs of synonymous SNPs. In contrast, for recessive mutations, there is no consistent ordering of how selection coefficients affect LD decay, due to the complex interplay of different evolutionary effects. We then examined empirical data of modern humans from the 1000 Genomes Project. LD between derived alleles at nonsynonymous SNPs is lower compared to pairs of derived synonymous variants, suggesting that nonsynonymous derived alleles tend to occur on different haplotypes more than synonymous variants. This result holds when controlling for potential confounding factors by matching SNPs for frequency in the sample (allele count), physical distance, magnitude of background selection, and genetic distance between pairs of variants. Lastly, we introduce a new statistic HR(j) which allows us to detect interference using unphased genotypes. Application of this approach to high-coverage human genome sequences confirms our finding that nonsynonymous derived alleles tend to be located on different haplotypes more often than are synonymous derived alleles. Our findings suggest that interference may play a pervasive role in shaping patterns of LD between deleterious variants in the human genome, and consequently influences genome-wide patterns of LD.
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Affiliation(s)
- Jesse A. Garcia
- Interdepartmental Program in Bioinformatics, University of California, Los Angeles, California, United States of America
| | - Kirk E. Lohmueller
- Interdepartmental Program in Bioinformatics, University of California, Los Angeles, California, United States of America
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California, United States of America
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, California, United States of America
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O'Connor CH, Sikkink KL, Nelson TC, Fierst JL, Cresko WA, Phillips PC. Complex pleiotropic genetic architecture of evolved heat stress and oxidative stress resistance in the nematode Caenorhabditis remanei. G3 (BETHESDA, MD.) 2021; 11:jkab045. [PMID: 33605401 PMCID: PMC8049431 DOI: 10.1093/g3journal/jkab045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 02/01/2021] [Indexed: 12/04/2022]
Abstract
The adaptation of complex organisms to changing environments has been a central question in evolutionary quantitative genetics since its inception. The structure of the genotype-phenotype maps is critical because pleiotropic effects can generate widespread correlated responses to selection and potentially restrict the extent of evolutionary change. In this study, we use experimental evolution to dissect the genetic architecture of natural variation for acute heat stress and oxidative stress response in the nematode Caenorhabiditis remanei. Previous work in the classic model nematode Caenorhabiditis elegans has found that abiotic stress response is controlled by a handful of genes of major effect and that mutations in any one of these genes can have widespread pleiotropic effects on multiple stress response traits. Here, we find that acute heat stress response and acute oxidative response in C. remanei are polygenic, complex traits, with hundreds of genomic regions responding to selection. In contrast to expectation from mutation studies, we find that evolved acute heat stress and acute oxidative stress response for the most part display independent genetic bases. This lack of correlation is reflected at the levels of phenotype, gene expression, and in the genomic response to selection. Thus, while these findings support the general view that rapid adaptation can be generated by changes at hundreds to thousands of sites in the genome, the architecture of segregating variation is likely to be determined by the pleiotropic structure of the underlying genetic networks.
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Affiliation(s)
- Christine H O'Connor
- Institute for Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
| | - Kristin L Sikkink
- Institute for Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
| | - Thomas C Nelson
- Institute for Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
| | - Janna L Fierst
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL 35487, USA
| | - William A Cresko
- Institute for Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
| | - Patrick C Phillips
- Institute for Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
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31
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Chak STC, Baeza JA, Barden P. Eusociality Shapes Convergent Patterns of Molecular Evolution across Mitochondrial Genomes of Snapping Shrimps. Mol Biol Evol 2021; 38:1372-1383. [PMID: 33211078 PMCID: PMC8480187 DOI: 10.1093/molbev/msaa297] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
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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Affiliation(s)
- Solomon T C Chak
- Department of Biological Sciences, New Jersey Institute of Technology, Newark, NJ
- Department of Biological Sciences, SUNY College at Old Westbury, Old Westbury, NY
| | - Juan Antonio Baeza
- Department of Biological Sciences, Clemson University, Clemson, SC
- Smithsonian Institution, Smithsonian Marine Station at Fort Pierce, Fort Pierce, FL
- Departamento de Biología Marina, Facultad de Ciencias del Mar, Universidad Católica del Norte, Coquimbo, Chile
| | - Phillip Barden
- Department of Biological Sciences, New Jersey Institute of Technology, Newark, NJ
- Division of Invertebrate Zoology, American Museum of Natural History, New York, NY
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32
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Lucek K, Willi Y. Drivers of linkage disequilibrium across a species' geographic range. PLoS Genet 2021; 17:e1009477. [PMID: 33770075 PMCID: PMC8026057 DOI: 10.1371/journal.pgen.1009477] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 04/07/2021] [Accepted: 03/09/2021] [Indexed: 11/25/2022] Open
Abstract
While linkage disequilibrium (LD) is an important parameter in genetics and evolutionary biology, the drivers of LD remain elusive. Using whole-genome sequences from across a species’ range, we assessed the impact of demographic history and mating system on LD. Both range expansion and a shift from outcrossing to selfing in North American Arabidopsis lyrata were associated with increased average genome-wide LD. Our results indicate that range expansion increases short-distance LD at the farthest range edges by about the same amount as a shift to selfing. However, the extent over which LD in genic regions unfolds was shorter for range expansion compared to selfing. Linkage among putatively neutral variants and between neutral and deleterious variants increased to a similar degree with range expansion, providing support that genome-wide LD was positively associated with mutational load. As a consequence, LD combined with mutational load may decelerate range expansions and set range limits. Finally, a small number of genes were identified as LD outliers, suggesting that they experience selection by either of the two demographic processes. These included genes involved in flowering and photoperiod for range expansion, and the self-incompatibility locus for mating system. Nearby genomic variants are often co-inherited because of limited recombination. The extent of non-random association of alleles at different loci is called linkage disequilibrium (LD) and is commonly used in genomic analyses, for example to detect regions under selection or to determine effective population size. Here we reversed testing and addressed how demographic history may affect LD within a species. Using genomic data from more than a thousand individuals of North American Arabidopsis lyrata from across the entire species’ range, we quantified the effect of postglacial range expansion and a shift in mating system from outcrossing to selfing on LD. We show that both factors lead to increased LD, and that the maximal effect of range expansion is comparable with a shift in mating system to selfing. Heightened LD involves deleterious mutations, and therefore, LD can also serve as an indicator of mutation accumulation. Furthermore, we provide evidence that some genes experienced stronger increases in LD possibly due to selection associated with the two demographic changes. Our results provide a novel and broad view on the evolutionary factors shaping LD that may also apply to the very many species that underwent postglacial range expansion.
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Affiliation(s)
- Kay Lucek
- Department of Environmental Sciences, University of Basel, Basel, Switzerland
- * E-mail:
| | - Yvonne Willi
- Department of Environmental Sciences, University of Basel, Basel, Switzerland
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33
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Whigham PA, Spencer HG. Graph-structured populations and the Hill-Robertson effect. ROYAL SOCIETY OPEN SCIENCE 2021; 8:201831. [PMID: 33959343 PMCID: PMC8074956 DOI: 10.1098/rsos.201831] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 02/23/2021] [Indexed: 05/27/2023]
Abstract
The Hill-Robertson effect describes how, in a finite panmictic diploid population, selection at one diallelic locus reduces the fixation probability of a selectively favoured allele at a second, linked diallelic locus. Here we investigate the influence of population structure on the Hill-Robertson effect in a population of size N. We model population structure as a network by assuming that individuals occupy nodes on a graph connected by edges that link members who can reproduce with each other. Three regular networks (fully connected, ring and torus), two forms of scale-free network and a star are examined. We find that (i) the effect of population structure on the probability of fixation of the favourable allele is invariant for regular structures, but on some scale-free networks and a star, this probability is greatly reduced; (ii) compared to a panmictic population, the mean time to fixation of the favoured allele is much greater on a ring, torus and linear scale-free network, but much less on power-2 scale-free and star networks; (iii) the likelihood with which each of the four possible haplotypes eventually fix is similar across regular networks, but scale-free populations and the star are consistently less likely and much faster to fix the optimal haplotype; (iv) increasing recombination increases the likelihood of fixing the favoured haplotype across all structures, whereas the time to fixation of that haplotype usually increased, and (v) star-like structures were overwhelmingly likely to fix the least fit haplotype and did so significantly more rapidly than other populations. Last, we find that small (N < 64) panmictic populations do not exhibit the scaling property expected from Hill & Robertson (1966 Genet. Res. 8, 269-294. (doi:10.1017/S0016672300010156)).
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Affiliation(s)
- Peter A. Whigham
- Department of Information Science, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Hamish G. Spencer
- Department of Zoology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
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Multiple mechanisms drive genomic adaptation to extreme O 2 levels in Drosophila melanogaster. Nat Commun 2021; 12:997. [PMID: 33579965 PMCID: PMC7881140 DOI: 10.1038/s41467-021-21281-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 01/06/2021] [Indexed: 12/18/2022] Open
Abstract
To detect the genomic mechanisms underlying evolutionary dynamics of adaptation in sexually reproducing organisms, we analyze multigenerational whole genome sequences of Drosophila melanogaster adapting to extreme O2 conditions over an experiment conducted for nearly two decades. We develop methods to analyze time-series genomics data and predict adaptive mechanisms. Here, we report a remarkable level of synchronicity in both hard and soft selective sweeps in replicate populations as well as the arrival of favorable de novo mutations that constitute a few asynchronized sweeps. We additionally make direct experimental observations of rare recombination events that combine multiple alleles on to a single, better-adapted haplotype. Based on the analyses of the genes in genomic intervals, we provide a deeper insight into the mechanisms of genome adaptation that allow complex organisms to survive harsh environments. The genomic details of adaptation to extreme environments remain challenging to characterize. Using new methods to analyze flies experimentally evolved to survive extreme O2 conditions, the authors find a surprising level of synchronicity in selective sweeps, de novo mutations and adaptive recombination events.
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Wendt FR, Pathak GA, Overstreet C, Tylee DS, Gelernter J, Atkinson EG, Polimanti R. Characterizing the effect of background selection on the polygenicity of brain-related traits. Genomics 2021; 113:111-119. [PMID: 33278486 PMCID: PMC7855394 DOI: 10.1016/j.ygeno.2020.11.032] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 11/20/2020] [Accepted: 11/30/2020] [Indexed: 01/10/2023]
Abstract
BACKGROUND Genome-wide association studies (GWAS) have demonstrated that psychopathology phenotypes are affected by many risk alleles with small effect (polygenicity). It is unclear how ubiquitously evolutionary pressures influence the genetic architecture of these traits. METHODS We partitioned SNP heritability to assess the contribution of background (BGS) and positive selection, Neanderthal local ancestry, functional significance, and genotype networks in 75 brain-related traits (8411 ≤ N ≤ 1,131,181, mean N = 205,289). We applied binary annotations by dichotomizing each measure based on top 2%, 1%, and 0.5% of all scores genome-wide. Effect size distribution features were calculated using GENESIS. We tested the relationship between effect size distribution descriptive statistics and natural selection. In a subset of traits, we explore the inclusion of diagnostic heterogeneity (e.g., number of diagnostic combinations and total symptoms) in the tested relationship. RESULTS SNP-heritability was enriched (false discovery rate q < 0.05) for loci with elevated BGS (7 phenotypes) and in genic (34 phenotypes) and loss-of-function (LoF)-intolerant regions (67 phenotypes). These effects were strongest in GWAS of schizophrenia (1.90-fold BGS, 1.16-fold genic, and 1.92-fold LoF), educational attainment (1.86-fold BGS, 1.12-fold genic, and 1.79-fold LoF), and cognitive performance (2.29-fold BGS, 1.12-fold genic, and 1.79-fold LoF). BGS (top 2%) significantly predicted effect size variance for trait-associated loci (σ2 parameter) in 75 brain-related traits (β = 4.39 × 10-5, p = 1.43 × 10-5, model r2 = 0.548). Considering the number of DSM-5 diagnostic combinations per psychiatric disorder improved model fit (σ2 ~ BTop2% × Genic × diagnostic combinations; model r2 = 0.661). CONCLUSIONS Brain-related phenotypes with larger variance in risk locus effect sizes are associated with loci under BGS. We show exploratory results suggesting that diagnostic complexity may also contribute to the increased polygenicity of psychiatric disorders.
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Affiliation(s)
- Frank R Wendt
- Department of Psychiatry, Yale School of Medicine and VA CT Healthcare System, West Haven, CT 06516, USA
| | - Gita A Pathak
- Department of Psychiatry, Yale School of Medicine and VA CT Healthcare System, West Haven, CT 06516, USA
| | - Cassie Overstreet
- National Center for Posttraumatic Stress Disorder, Clinical Neurosciences Division, VA CT Healthcare System and Department of Psychiatry, Yale University School of Medicine, USA
| | - Daniel S Tylee
- Department of Psychiatry, Yale School of Medicine and VA CT Healthcare System, West Haven, CT 06516, USA
| | - Joel Gelernter
- Department of Psychiatry, Yale School of Medicine and VA CT Healthcare System, West Haven, CT 06516, USA; Departments of Genetics and Neuroscience, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Elizabeth G Atkinson
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Renato Polimanti
- Department of Psychiatry, Yale School of Medicine and VA CT Healthcare System, West Haven, CT 06516, USA.
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Gimenez S, Abdelgaffar H, Goff GL, Hilliou F, Blanco CA, Hänniger S, Bretaudeau A, Legeai F, Nègre N, Jurat-Fuentes JL, d'Alençon E, Nam K. Adaptation by copy number variation increases insecticide resistance in the fall armyworm. Commun Biol 2020; 3:664. [PMID: 33184418 PMCID: PMC7661717 DOI: 10.1038/s42003-020-01382-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 10/14/2020] [Indexed: 12/19/2022] Open
Abstract
Understanding the genetic basis of insecticide resistance is a key topic in agricultural ecology. The adaptive evolution of multi-copy detoxification genes has been interpreted as a cause of insecticide resistance, yet the same pattern can also be generated by the adaptation to host-plant defense toxins. In this study, we tested in the fall armyworm, Spodoptera frugiperda (Lepidoptera: Noctuidae), if adaptation by copy number variation caused insecticide resistance in two geographically distinct populations with different levels of resistance and the two host-plant strains. We observed a significant allelic differentiation of genomic copy number variations between the two geographic populations, but not between host-plant strains. A locus with positively selected copy number variation included a CYP gene cluster. Toxicological tests supported a central role for CYP enzymes in deltamethrin resistance. Our results indicate that copy number variation of detoxification genes might be responsible for insecticide resistance in fall armyworm and that evolutionary forces causing insecticide resistance could be independent of host-plant adaptation.
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Affiliation(s)
- Sylvie Gimenez
- DGIMI, Univ of Montpellier, INRA, Place Eugène Bataillon, 34095, Montpellier, France
| | - Heba Abdelgaffar
- Department of Entomology and Plant Pathology, University of Tennessee, 370 Plant Biotechnology Building, 2505 E J. Chapman Dr, Knoxville, TN, 37996, USA
| | - Gaelle Le Goff
- Université Côte d'Azur, INRAE, CNRS, ISA, 400 Route des Chappes, 06903, Sophia Antipolis, France
| | - Frédérique Hilliou
- Université Côte d'Azur, INRAE, CNRS, ISA, 400 Route des Chappes, 06903, Sophia Antipolis, France
| | - Carlos A Blanco
- United States Department of Agriculture, Animal and Plant Health Inspection Service, 4700 River Rd, Riverdale, 20737, MD, USA
| | - Sabine Hänniger
- Max Planck Institute for Chemical Ecology, Hans-Knoell-Straße 8, 07745, Jena, Germany
| | - Anthony Bretaudeau
- IGEPP, INRAE, Institut Agro, Univ Rennes, Campus de Beaulieu, 263 Avenue Général Leclerc, 35042, Rennes, France
- GenOuest Core Facility, Univ Rennes, Inria, CNRS, IRISA, Campus de Beaulieu, 263 Avenue Général Leclerc, 35042, Rennes, France
| | - Fabrice Legeai
- IGEPP, INRAE, Institut Agro, Univ Rennes, Campus de Beaulieu, 263 Avenue Général Leclerc, 35042, Rennes, France
- GenOuest Core Facility, Univ Rennes, Inria, CNRS, IRISA, Campus de Beaulieu, 263 Avenue Général Leclerc, 35042, Rennes, France
| | - Nicolas Nègre
- DGIMI, Univ of Montpellier, INRA, Place Eugène Bataillon, 34095, Montpellier, France
| | - Juan Luis Jurat-Fuentes
- Department of Entomology and Plant Pathology, University of Tennessee, 370 Plant Biotechnology Building, 2505 E J. Chapman Dr, Knoxville, TN, 37996, USA
| | - Emmanuelle d'Alençon
- DGIMI, Univ of Montpellier, INRA, Place Eugène Bataillon, 34095, Montpellier, France
| | - Kiwoong Nam
- DGIMI, Univ of Montpellier, INRA, Place Eugène Bataillon, 34095, Montpellier, France.
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Ruane LG, Mangum SM, Horner KM, Moeller DA. The opportunity for outcrossing varies across the geographic range of the primarily selfing Clarkia xantiana ssp. parviflora. AMERICAN JOURNAL OF BOTANY 2020; 107:1198-1207. [PMID: 32700343 DOI: 10.1002/ajb2.1510] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 02/22/2020] [Indexed: 06/11/2023]
Abstract
PREMISE The timing of self-fertilization has potentially important consequences for the trajectory of mating system evolution, the opportunity for outcrossing, and the maintenance of genetic variation in populations. For primarily selfing taxa, it remains poorly understood as to how floral variation influences the opportunity for outcrossing and whether those attributes vary among populations across geographic ranges. METHODS We examined variation in floral traits (herkogamy, protandry, flower size, stigma stage at anthesis, timing of stigma receptivity) in seven populations of Clarkia xantiana ssp. parviflora, a primarily selfing taxon, spanning from the western to eastern margins of its distribution. We also performed experimental emasculations and pollinations (followed by stigma severing) to quantify the extent of opportunities for outcrossing across flower development. RESULTS There was marked among-population variation in all floral traits, particularly between far eastern and western populations. Emasculation experiments showed that the eastern populations had minimal autonomous selfing, but western populations had high rates of selfing within 24 h after anthesis. Population variation in autofertility was significantly predicted by floral trait variation, especially protandry and petal size. CONCLUSIONS Greater protandry both extended the time over which outcrossing could potentially occur and reduced the probability of autonomous selfing, suggesting that there may be a tradeoff that results in fitness loss when pollinator visits are not common. The east-west pattern of differentiation in some floral traits parallels that of postglacial range expansion, suggesting that selection on the mating system may have been strong in the process of range expansion.
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Affiliation(s)
- Lauren G Ruane
- Department of Organismal and Environmental Biology, Christopher Newport University, 1 Avenue of the Arts, Newport News, Virginia, 23606, United States
| | - Samantha M Mangum
- Department of Organismal and Environmental Biology, Christopher Newport University, 1 Avenue of the Arts, Newport News, Virginia, 23606, United States
| | - Kaitlyn M Horner
- Department of Organismal and Environmental Biology, Christopher Newport University, 1 Avenue of the Arts, Newport News, Virginia, 23606, United States
| | - David A Moeller
- Department of Plant and Microbial Biology, University of Minnesota, 1479 Gortner Avenue, St. Paul, Minnesota, 55108, United States
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38
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Jordan KW, He F, de Soto MF, Akhunova A, Akhunov E. Differential chromatin accessibility landscape reveals structural and functional features of the allopolyploid wheat chromosomes. Genome Biol 2020; 21:176. [PMID: 32684157 PMCID: PMC7368981 DOI: 10.1186/s13059-020-02093-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 07/06/2020] [Indexed: 12/19/2022] Open
Abstract
Background Our understanding of how the complexity of the wheat genome influences the distribution of chromatin states along the homoeologous chromosomes is limited. Using a differential nuclease sensitivity assay, we investigate the chromatin states of the coding and repetitive regions of the allopolyploid wheat genome. Results Although open chromatin is found to be significantly enriched around genes, the majority of MNase-sensitive regions are located within transposable elements (TEs). Chromatin of the smaller D genome is more accessible than that of the larger A and B genomes. Chromatin states of different TEs vary among families and are influenced by the TEs’ chromosomal position and proximity to genes. While the chromatin accessibility of genes is influenced by proximity to TEs, and not by their position on the chromosomes, we observe a negative chromatin accessibility gradient along the telomere-centromere axis in the intergenic regions, positively correlated with the distance between genes. Both gene expression levels and homoeologous gene expression bias are correlated with chromatin accessibility in promoter regions. The differential nuclease sensitivity assay accurately predicts previously detected centromere locations. SNPs located within more accessible chromatin explain a higher proportion of genetic variance for a number of agronomic traits than SNPs located within more closed chromatin. Conclusions Chromatin states in the wheat genome are shaped by the interplay of repetitive and gene-encoding regions that are predictive of the functional and structural organization of chromosomes, providing a powerful framework for detecting genomic features involved in gene regulation and prioritizing genomic variation to explain phenotypes.
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Affiliation(s)
- Katherine W Jordan
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA.,USDA-ARS, Hard Winter Wheat Genetics Research Unit, Manhattan, KS, USA
| | - Fei He
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
| | - Monica Fernandez de Soto
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA.,Integrated Genomics Facility, Kansas State University, Manhattan, KS, USA.,Genomic Sciences Laboratory, North Carolina State University, Raleigh, NC, USA
| | - Alina Akhunova
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA.,Integrated Genomics Facility, Kansas State University, Manhattan, KS, USA
| | - Eduard Akhunov
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA.
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Population genomics of Vibrionaceae isolated from an endangered oasis reveals local adaptation after an environmental perturbation. BMC Genomics 2020; 21:418. [PMID: 32571204 PMCID: PMC7306931 DOI: 10.1186/s12864-020-06829-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 06/15/2020] [Indexed: 12/17/2022] Open
Abstract
Background In bacteria, pan-genomes are the result of an evolutionary “tug of war” between selection and horizontal gene transfer (HGT). High rates of HGT increase the genetic pool and the effective population size (Ne), resulting in open pan-genomes. In contrast, selective pressures can lead to local adaptation by purging the variation introduced by HGT and mutation, resulting in closed pan-genomes and clonal lineages. In this study, we explored both hypotheses, elucidating the pan-genome of Vibrionaceae isolates after a perturbation event in the endangered oasis of Cuatro Ciénegas Basin (CCB), Mexico, and looking for signals of adaptation to the environments in their genomes. Results We obtained 42 genomes of Vibrionaceae distributed in six lineages, two of them did not showed any close reference strain in databases. Five of the lineages showed closed pan-genomes and were associated to either water or sediment environment; their high Ne estimates suggest that these lineages are not from a recent origin. The only clade with an open pan-genome was found in both environments and was formed by ten genetic groups with low Ne, suggesting a recent origin. The recombination and mutation estimators (r/m) ranged from 0.005 to 2.725, which are similar to oceanic Vibrionaceae estimations. However, we identified 367 gene families with signals of positive selection, most of them found in the core genome; suggesting that despite recombination, natural selection moves the Vibrionaceae CCB lineages to local adaptation, purging the genomes and keeping closed pan-genome patterns. Moreover, we identify 598 SNPs associated with an unstructured environment; some of the genes associated with these SNPs were related to sodium transport. Conclusions Different lines of evidence suggest that the sampled Vibrionaceae, are part of the rare biosphere usually living under famine conditions. Two of these lineages were reported for the first time. Most Vibrionaceae lineages of CCB are adapted to their micro-habitats rather than to the sampled environments. This pattern of adaptation is concordant with the association of closed pan-genomes and local adaptation.
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40
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Reay WR, Cairns MJ. Pairwise common variant meta-analyses of schizophrenia with other psychiatric disorders reveals shared and distinct gene and gene-set associations. Transl Psychiatry 2020; 10:134. [PMID: 32398653 PMCID: PMC7217970 DOI: 10.1038/s41398-020-0817-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 04/20/2020] [Accepted: 04/23/2020] [Indexed: 01/09/2023] Open
Abstract
The complex aetiology of schizophrenia is postulated to share components with other psychiatric disorders. We investigated pleiotropy amongst the common variant genomics of schizophrenia and seven other psychiatric disorders using a multimarker association test. Transcriptomic imputation was then leveraged to investigate the functional significance of variation mapped to these genes, prioritising several interesting functional candidates. Gene-based analysis of common variation revealed 67 schizophrenia-associated genes shared with other psychiatric phenotypes, including bipolar disorder, major depressive disorder, ADHD and autism-spectrum disorder. In addition, we uncovered 78 genes significantly enriched with common variant associations for schizophrenia that were not linked to any of these seven disorders (P > 0.05). Multivariable gene-set association suggested that common variation enrichment within biologically constrained genes observed for schizophrenia also occurs across several psychiatric phenotypes. Pairwise meta-analysis of schizophrenia and each psychiatric phenotype was implemented and identified 330 significantly associated genes (PMeta < 2.7 × 10-6) that were only nominally associated with each disorder individually (P < 0.05). These analyses consolidate the overlap between the genomic architecture of schizophrenia and other psychiatric disorders, uncovering several candidate pleiotropic genes which warrant further investigation.
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Affiliation(s)
- William R Reay
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, Callaghan, NSW, Australia
- Centre for Brain and Mental Health Research, Hunter Medical Research Institute, Newcastle, NSW, Australia
| | - Murray J Cairns
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, Callaghan, NSW, Australia.
- Centre for Brain and Mental Health Research, Hunter Medical Research Institute, Newcastle, NSW, Australia.
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41
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Wang J, Street NR, Park EJ, Liu J, Ingvarsson PK. Evidence for widespread selection in shaping the genomic landscape during speciation of Populus. Mol Ecol 2020; 29:1120-1136. [PMID: 32068935 DOI: 10.1111/mec.15388] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 02/13/2020] [Accepted: 02/14/2020] [Indexed: 12/13/2022]
Abstract
Increasing our understanding of how evolutionary processes drive the genomic landscape of variation is fundamental to a better understanding of the genomic consequences of speciation. However, genome-wide patterns of within- and between- species variation have not been fully investigated in most forest tree species despite their global ecological and economic importance. Here, we use whole-genome resequencing data from four Populus species spanning the speciation continuum to reconstruct their demographic histories and investigate patterns of diversity and divergence within and between species. Using Populus trichocarpa as an outgroup species, we further infer the genealogical relationships and estimate the extent of ancient introgression among the three aspen species (Populus tremula, Populus davidiana and Populus tremuloides) throughout the genome. Our results show substantial variation in these patterns along the genomes with this variation being strongly predicted by local recombination rates and the density of functional elements. This implies that the interaction between recurrent selection and intrinsic genomic features has dramatically sculpted the genomic landscape over long periods of time. In addition, our findings provide evidence that, apart from background selection, recent positive selection and long-term balancing selection have also been crucial components in shaping patterns of genome-wide variation during the speciation process.
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Affiliation(s)
- Jing Wang
- Key Laboratory for Bio-Resources and Eco-Environment, College of Life Science, Sichuan University, Chengdu, China
| | - Nathaniel R Street
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå, Sweden
| | - Eung-Jun Park
- Department of Bioresources, National Institute of Forest Science, Suwon, Korea
| | - Jianquan Liu
- Key Laboratory for Bio-Resources and Eco-Environment, College of Life Science, Sichuan University, Chengdu, China
| | - Pär K Ingvarsson
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Uppsala, Sweden
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42
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Yan Z, Martin SH, Gotzek D, Arsenault SV, Duchen P, Helleu Q, Riba-Grognuz O, Hunt BG, Salamin N, Shoemaker D, Ross KG, Keller L. Evolution of a supergene that regulates a trans-species social polymorphism. Nat Ecol Evol 2020; 4:240-249. [PMID: 31959939 DOI: 10.1038/s41559-019-1081-1] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 12/04/2019] [Indexed: 11/09/2022]
Abstract
Supergenes are clusters of linked genetic loci that jointly affect the expression of complex phenotypes, such as social organization. Little is known about the origin and evolution of these intriguing genomic elements. Here we analyse whole-genome sequences of males from native populations of six fire ant species and show that variation in social organization is under the control of a novel supergene haplotype (termed Sb), which evolved by sequential incorporation of three inversions spanning half of a 'social chromosome'. Two of the inversions interrupt protein-coding genes, resulting in the increased expression of one gene and modest truncation in the primary protein structure of another. All six socially polymorphic species studied harbour the same three inversions, with the single origin of the supergene in their common ancestor inferred by phylogenomic analyses to have occurred half a million years ago. The persistence of Sb along with the ancestral SB haplotype through multiple speciation events provides a striking example of a functionally important trans-species social polymorphism presumably maintained by balancing selection. We found that while recombination between the Sb and SB haplotypes is severely restricted in all species, a low level of gene flux between the haplotypes has occurred following the appearance of the inversions, potentially mitigating the evolutionary degeneration expected at genomic regions that cannot freely recombine. These results provide a detailed picture of the structural genomic innovations involved in the formation of a supergene controlling a complex social phenotype.
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Affiliation(s)
- Zheng Yan
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Simon H Martin
- Institute of Evolutionary Biology, the University of Edinburgh, Edinburgh, UK
| | - Dietrich Gotzek
- Department of Entomology and Laboratories of Analytical Biology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | | | - Pablo Duchen
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - Quentin Helleu
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Oksana Riba-Grognuz
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Brendan G Hunt
- Department of Entomology, University of Georgia, Athens, GA, USA
| | - Nicolas Salamin
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - DeWayne Shoemaker
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, USA
| | - Kenneth G Ross
- Department of Entomology, University of Georgia, Athens, GA, USA.
| | - Laurent Keller
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.
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Repetti SI, Jackson CJ, Judd LM, Wick RR, Holt KE, Verbruggen H. The inflated mitochondrial genomes of siphonous green algae reflect processes driving expansion of noncoding DNA and proliferation of introns. PeerJ 2020; 8:e8273. [PMID: 31915577 PMCID: PMC6944098 DOI: 10.7717/peerj.8273] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 11/22/2019] [Indexed: 02/06/2023] Open
Abstract
Within the siphonous green algal order Bryopsidales, the size and gene arrangement of chloroplast genomes has been examined extensively, while mitochondrial genomes have been mostly overlooked. The recently published mitochondrial genome of Caulerpa lentillifera is large with expanded noncoding DNA, but it remains unclear if this is characteristic of the entire order. Our study aims to evaluate the evolutionary forces shaping organelle genome dynamics in the Bryopsidales based on the C. lentillifera and Ostreobium quekettii mitochondrial genomes. In this study, the mitochondrial genome of O. quekettii was characterised using a combination of long and short read sequencing, and bioinformatic tools for annotation and sequence analyses. We compared the mitochondrial and chloroplast genomes of O. quekettii and C. lentillifera to examine hypotheses related to genome evolution. The O. quekettii mitochondrial genome is the largest green algal mitochondrial genome sequenced (241,739 bp), considerably larger than its chloroplast genome. As with the mtDNA of C. lentillifera, most of this excess size is from the expansion of intergenic DNA and proliferation of introns. Inflated mitochondrial genomes in the Bryopsidales suggest effective population size, recombination and/or mutation rate, influenced by nuclear-encoded proteins, differ between the genomes of mitochondria and chloroplasts, reducing the strength of selection to influence evolution of their mitochondrial genomes.
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Affiliation(s)
- Sonja I Repetti
- School of BioSciences, University of Melbourne, Melbourne, VIC, Australia
| | | | - Louise M Judd
- Department of Infectious Diseases, Monash University, Melbourne, VIC, Australia
| | - Ryan R Wick
- Department of Infectious Diseases, Monash University, Melbourne, VIC, Australia
| | - Kathryn E Holt
- Department of Infectious Diseases, Monash University, Melbourne, VIC, Australia
| | - Heroen Verbruggen
- School of BioSciences, University of Melbourne, Melbourne, VIC, Australia
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44
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Tourrette E, Bernardo R, Falque M, Martin OC. Assessing by Modeling the Consequences of Increased Recombination in Recurrent Selection of Oryza sativa and Brassica rapa. G3 (BETHESDA, MD.) 2019; 9:4169-4181. [PMID: 31628152 PMCID: PMC6893184 DOI: 10.1534/g3.119.400545] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 10/15/2019] [Indexed: 02/08/2023]
Abstract
Meiotic recombination generates genetic diversity but in most species the number of crossovers per meiosis is limited. Previous modeling studies showed that increasing recombination can enhance response to selection. However, such studies did not assume a specific method of modifying recombination. Our objective was to test whether two methods used to increase recombination in plants could increase genetic gain in a population undergoing recurrent selection such as in genomic selection programs. The first method, in Oryza sativa, used a mutant of anti-crossover genes, increasing global recombination without affecting the recombination landscape shape. The second one used the ploidy level of a cross between Brassica rapa and Brassica napus, increasing recombination especially in pericentromeric regions. Our modeling framework used these recombination landscapes and sampled quantitative trait loci positions from the actual gene distributions. We simulated selection programs with initially a cross between two inbred lines, for two species. Increased recombination enhanced the response to selection. The amount of enhancement in the cumulative gain largely depended on the species and the number of quantitative trait loci (2, 10, 20, 50, 200 or 1000 per chromosome). Genetic gains were increased up to 30% after 20 generations. Furthermore, increasing recombination in cold regions was the most effective: the gain was larger by 25% with the first method and 34% with the second one in B. rapa, and 12% compared to 16% in O. sativa In summary, increased recombination enhances the genetic gain in long-term selection programs, with visible effects after four to five generations.
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Affiliation(s)
- Elise Tourrette
- GQE - Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France and
| | - Rex Bernardo
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul
| | - Matthieu Falque
- GQE - Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France and
| | - Olivier C Martin
- GQE - Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France and
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45
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Hasan AR, Duggal JK, Ness RW. Consequences of recombination for the evolution of the mating type locus in Chlamydomonas reinhardtii. THE NEW PHYTOLOGIST 2019; 224:1339-1348. [PMID: 31222749 DOI: 10.1111/nph.16003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 06/10/2019] [Indexed: 06/09/2023]
Abstract
Recombination suppression in sex chromosomes and mating type loci can lead to degeneration as a result of reduced selection efficacy and Muller's ratchet effects. However, genetic exchange in the form of noncrossover gene conversions may still take place within crossover-suppressed regions. Recent work has found evidence that gene conversion may explain the low degrees of allelic differentiation in the dimorphic mating-type locus (MT) of the isogamous alga Chlamydomonas reinhardtii. However, no one has tested whether gene conversion is sufficient to avoid the degeneration of functional sequence within MT. Here, we calculate degree of linkage disequilibrium (LD) across MT as a proxy for recombination rate and investigate its relationship to patterns of population genetic variation and the efficacy of selection in the region. We find that degree of LD predicts selection efficacy across MT, and that purifying selection is stronger in shared genes than in MT-limited genes to the point of being equivalent to that of autosomal genes. We argue that while crossover suppression is needed in the mating-type loci of many isogamous systems, these loci are less likely to experience selection to differentiate further. Thus, recombination can act in these regions and prevent degeneration caused by Hill-Robertson effects.
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Affiliation(s)
- Ahmed R Hasan
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, M5S 3G5, Canada
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, L5L 1C6, Canada
| | - Jaspreet K Duggal
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, L5L 1C6, Canada
| | - Rob W Ness
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, M5S 3G5, Canada
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, L5L 1C6, Canada
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Mark S, Weiss J, Sharma E, Liu T, Wang W, Claycomb JM, Cutter AD. Genome structure predicts modular transcriptome responses to genetic and environmental conditions. Mol Ecol 2019; 28:3681-3697. [PMID: 31325381 DOI: 10.1111/mec.15185] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 07/05/2019] [Accepted: 07/10/2019] [Indexed: 12/13/2022]
Abstract
Understanding the plasticity, robustness and modularity of transcriptome expression to genetic and environmental conditions is crucial to deciphering how organisms adapt in nature. To test how genome architecture influences transcriptome profiles, we quantified expression responses for distinct temperature-adapted genotypes of the nematode Caenorhabditis briggsae when exposed to chronic temperature stresses throughout development. We found that 56% of the 8,795 differentially expressed genes show genotype-specific changes in expression in response to temperature (genotype-by-environment interactions, GxE). Most genotype-specific responses occur under heat stress, indicating that cold vs. heat stress responses involve distinct genomic architectures. The 22 co-expression modules that we identified differ in their enrichment of genes with genetic vs. environmental vs. interaction effects, as well as their genomic spatial distributions, functional attributes and rates of molecular evolution at the sequence level. Genes in modules enriched for simple effects of either genotype or temperature alone tend to evolve especially rapidly, consistent with disproportionate influence of adaptation or weaker constraint on these subsets of loci. Chromosome-scale heterogeneity in nucleotide polymorphism, however, rather than the scale of individual genes predominates as the source of genetic differences among expression profiles, and natural selection regimes are largely decoupled between coding sequences and noncoding flanking sequences that contain cis-regulatory elements. These results illustrate how the form of transcriptome modularity and genome structure contribute to predictable profiles of evolutionary change.
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Affiliation(s)
- Stephanie Mark
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Joerg Weiss
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Eesha Sharma
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Ting Liu
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Wei Wang
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Julie M Claycomb
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Asher D Cutter
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
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Mignerot L, Avia K, Luthringer R, Lipinska AP, Peters AF, Cock JM, Coelho SM. A key role for sex chromosomes in the regulation of parthenogenesis in the brown alga Ectocarpus. PLoS Genet 2019; 15:e1008211. [PMID: 31194744 PMCID: PMC6592573 DOI: 10.1371/journal.pgen.1008211] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 06/25/2019] [Accepted: 05/24/2019] [Indexed: 02/06/2023] Open
Abstract
Although evolutionary transitions from sexual to asexual reproduction are frequent in eukaryotes, the genetic bases of these shifts remain largely elusive. Here, we used classic quantitative trait analysis, combined with genomic and transcriptomic information to dissect the genetic basis of asexual, parthenogenetic reproduction in the brown alga Ectocarpus. We found that parthenogenesis is controlled by the sex locus, together with two additional autosomal loci, highlighting the key role of the sex chromosome as a major regulator of asexual reproduction. We identify several negative effects of parthenogenesis on male fitness, and different fitness effects of parthenogenetic capacity depending on the life cycle generation. Although allele frequencies in natural populations are currently unknown, we discuss the possibility that parthenogenesis may be under both sex-specific selection and generation/ploidally-antagonistic selection, and/or that the action of fluctuating selection on this trait may contribute to the maintenance of polymorphisms in populations. Importantly, our data provide the first empirical illustration, to our knowledge, of a trade-off between the haploid and diploid stages of the life cycle, where distinct parthenogenesis alleles have opposing effects on sexual and asexual reproduction and may help maintain genetic variation. These types of fitness trade-offs have profound evolutionary implications in natural populations and may structure life history evolution in organisms with haploid-diploid life cycles.
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Affiliation(s)
- Laure Mignerot
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Roscoff, France
| | - Komlan Avia
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Roscoff, France
| | - Remy Luthringer
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Roscoff, France
| | - Agnieszka P. Lipinska
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Roscoff, France
| | | | - J. Mark Cock
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Roscoff, France
| | - Susana M. Coelho
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Roscoff, France
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Whitlock AOB, Azevedo RBR, Burch CL. Population structure promotes the evolution of costly sex in artificial gene networks. Evolution 2019; 73:1089-1100. [PMID: 30997680 DOI: 10.1111/evo.13733] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 03/25/2019] [Indexed: 11/30/2022]
Abstract
We build on previous observations that Hill-Robertson interference generates an advantage of sex that, in structured populations, can be large enough to explain the evolutionary maintenance of costly sex. We employed a gene network model that explicitly incorporates interactions between genes. Mutations in the gene networks have variable effects that depend on the genetic background in which they appear. Consequently, our simulations include two costs of sex-recombination and migration loads-that were missing from previous studies of the evolution of costly sex. Our results suggest a critical role for population structure that lies in its ability to align the long- and short-term advantages of sex. We show that the addition of population structure favored the evolution of sex by disproportionately decreasing the equilibrium mean fitness of asexual populations, primarily by increasing the strength of Muller's Ratchet. Population structure also increased the ability of the short-term advantage of sex to counter the primary limit to the evolution of sex in the gene network model-recombination load. On the other hand, highly structured populations experienced migration load in the form of Dobzhansky-Muller incompatibilities, decreasing the effective rate of migration between demes and, consequently, accelerating the accumulation of drift load in the sexual populations.
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Affiliation(s)
- Alexander O B Whitlock
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, North Carolina
| | - Ricardo B R Azevedo
- Department of Biology and Biochemistry, University of Houston, Houston, Texas
| | - Christina L Burch
- Biology Department, University of North Carolina, Chapel Hill, North Carolina
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Cocker JM, Wright J, Li J, Swarbreck D, Dyer S, Caccamo M, Gilmartin PM. Primula vulgaris (primrose) genome assembly, annotation and gene expression, with comparative genomics on the heterostyly supergene. Sci Rep 2018; 8:17942. [PMID: 30560928 PMCID: PMC6299000 DOI: 10.1038/s41598-018-36304-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 11/14/2018] [Indexed: 11/24/2022] Open
Abstract
Primula vulgaris (primrose) exhibits heterostyly: plants produce self-incompatible pin- or thrum-form flowers, with anthers and stigma at reciprocal heights. Darwin concluded that this arrangement promotes insect-mediated cross-pollination; later studies revealed control by a cluster of genes, or supergene, known as the S (Style length) locus. The P. vulgaris S locus is absent from pin plants and hemizygous in thrum plants (thrum-specific); mutation of S locus genes produces self-fertile homostyle flowers with anthers and stigma at equal heights. Here, we present a 411 Mb P. vulgaris genome assembly of a homozygous inbred long homostyle, representing ~87% of the genome. We annotate over 24,000 P. vulgaris genes, and reveal more genes up-regulated in thrum than pin flowers. We show reduced genomic read coverage across the S locus in other Primula species, including P. veris, where we define the conserved structure and expression of the S locus genes in thrum. Further analysis reveals the S locus has elevated repeat content (64%) compared to the wider genome (37%). Our studies suggest conservation of S locus genetic architecture in Primula, and provide a platform for identification and evolutionary analysis of the S locus and downstream targets that regulate heterostyly in diverse heterostylous species.
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Affiliation(s)
- Jonathan M Cocker
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, United Kingdom.,Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, United Kingdom
| | - Jonathan Wright
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, United Kingdom
| | - Jinhong Li
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, United Kingdom.,Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, United Kingdom
| | - David Swarbreck
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, United Kingdom
| | - Sarah Dyer
- National Institute for Agricultural Botany, Huntingdon Road, Cambridge, CB3 0LE, United Kingdom
| | - Mario Caccamo
- National Institute for Agricultural Botany, Huntingdon Road, Cambridge, CB3 0LE, United Kingdom
| | - Philip M Gilmartin
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, United Kingdom. .,Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, United Kingdom.
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50
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Zhou L, Xiao Q, Bi J, Wang Z, Li Y. RabGTD: a comprehensive database of rabbit genome and transcriptome. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2018; 2018:5053987. [PMID: 30010730 PMCID: PMC6047408 DOI: 10.1093/database/bay075] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 06/22/2018] [Indexed: 12/28/2022]
Abstract
The rabbit is a very important species for both biomedical research and agriculture animal breeding. They are not only the most-used experimental animals for the production of antibodies, but also widely used for studying a variety of human diseases. Here we developed RabGTD, the first comprehensive rabbit database containing both genome and transcriptome data generated by next-generation sequencing. Genomic variations coming from 79 samples were identified and annotated, including 33 samples of wild rabbits and 46 samples of domestic rabbits with diverse populations. Gene expression profiles of 86 tissue samples were complied, including those from the most commonly used models for hyperlipidemia and atherosclerosis. RabGTD is a web-based and open-access resource, which also provides convenient functions and friendly interfaces of searching, browsing and downloading for users to explore the big data. Database URL: http://www.picb.ac.cn/RabGTD/
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Affiliation(s)
- Lu Zhou
- Key Lab of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Rd., Xuhui District, Shanghai 200031, China.,University of Chinese Academy of Sciences, 52 Sanlihe Rd., Xicheng District, Beijing 100049, China
| | - Qingyu Xiao
- Key Lab of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Rd., Xuhui District, Shanghai 200031, China.,University of Chinese Academy of Sciences, 52 Sanlihe Rd., Xicheng District, Beijing 100049, China
| | - Jie Bi
- Key Lab of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Rd., Xuhui District, Shanghai 200031, China.,University of Chinese Academy of Sciences, 52 Sanlihe Rd., Xicheng District, Beijing 100049, China
| | - Zhen Wang
- Key Lab of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Rd., Xuhui District, Shanghai 200031, China
| | - Yixue Li
- Key Lab of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Rd., Xuhui District, Shanghai 200031, China.,Shanghai Center for Bioinformation Technology, Shanghai Industrial Technology Institute, 1278 Keyuan Rd., Pudong District, Shanghai 201203, China.,Collaborative Innovation Center for Genetics and Development, Fudan University, 2005 Songhu Rd., Yangpu District, Shanghai 200433, China
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