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Mei X, Wang X, Wu X, Liu G, Chen Y, Zhou S, Shang Y, Liu Z, Yang X, Sha W, Zhang H. Mitochondrial Genomic Evidence of Selective Constraints in Small-Bodied Terrestrial Cetartiodactyla. Animals (Basel) 2024; 14:1434. [PMID: 38791652 PMCID: PMC11117313 DOI: 10.3390/ani14101434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 05/06/2024] [Accepted: 05/09/2024] [Indexed: 05/26/2024] Open
Abstract
Body size may drive the molecular evolution of mitochondrial genes in response to changes in energy requirements across species of different sizes. In this study, we perform selection pressure analysis and phylogenetic independent contrasts (PIC) to investigate the association between molecular evolution of mitochondrial genome protein-coding genes (mtDNA PCGs) and body size in terrestrial Cetartiodactyla. Employing selection pressure analysis, we observe that the average non-synonymous/synonymous substitution rate ratio (ω) of mtDNA PCGs is significantly reduced in small-bodied species relative to their medium and large counterparts. PIC analysis further confirms that ω values are positively correlated with body size (R2 = 0.162, p = 0.0016). Our results suggest that mtDNA PCGs of small-bodied species experience much stronger purifying selection as they need to maintain a heightened metabolic rate. On the other hand, larger-bodied species may face less stringent selective pressures on their mtDNA PCGs, potentially due to reduced relative energy expenditure per unit mass. Furthermore, we identify several genes that undergo positive selection, possibly linked to species adaptation to specific environments. Therefore, despite purifying selection being the predominant force in the evolution of mtDNA PCGs, positive selection can also occur during the process of adaptive evolution.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Honghai Zhang
- School of Life Science, Qufu Normal University, Qufu 273165, China; (X.M.)
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2
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de Jong MJ, van Oosterhout C, Hoelzel AR, Janke A. Moderating the neutralist-selectionist debate: exactly which propositions are we debating, and which arguments are valid? Biol Rev Camb Philos Soc 2024; 99:23-55. [PMID: 37621151 DOI: 10.1111/brv.13010] [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: 03/15/2022] [Revised: 08/04/2023] [Accepted: 08/07/2023] [Indexed: 08/26/2023]
Abstract
Half a century after its foundation, the neutral theory of molecular evolution continues to attract controversy. The debate has been hampered by the coexistence of different interpretations of the core proposition of the neutral theory, the 'neutral mutation-random drift' hypothesis. In this review, we trace the origins of these ambiguities and suggest potential solutions. We highlight the difference between the original, the revised and the nearly neutral hypothesis, and re-emphasise that none of them equates to the null hypothesis of strict neutrality. We distinguish the neutral hypothesis of protein evolution, the main focus of the ongoing debate, from the neutral hypotheses of genomic and functional DNA evolution, which for many species are generally accepted. We advocate a further distinction between a narrow and an extended neutral hypothesis (of which the latter posits that random non-conservative amino acid substitutions can cause non-ecological phenotypic divergence), and we discuss the implications for evolutionary biology beyond the domain of molecular evolution. We furthermore point out that the debate has widened from its initial focus on point mutations, and also concerns the fitness effects of large-scale mutations, which can alter the dosage of genes and regulatory sequences. We evaluate the validity of neutralist and selectionist arguments and find that the tested predictions, apart from being sensitive to violation of underlying assumptions, are often derived from the null hypothesis of strict neutrality, or equally consistent with the opposing selectionist hypothesis, except when assuming molecular panselectionism. Our review aims to facilitate a constructive neutralist-selectionist debate, and thereby to contribute to answering a key question of evolutionary biology: what proportions of amino acid and nucleotide substitutions and polymorphisms are adaptive?
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Affiliation(s)
- Menno J de Jong
- Senckenberg Biodiversity and Climate Research Institute (SBiK-F), Georg-Voigt-Strasse 14-16, Frankfurt am Main, 60325, Germany
| | - Cock van Oosterhout
- Centre for Ecology, Evolution and Conservation, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - A Rus Hoelzel
- Department of Biosciences, Durham University, South Road, Durham, DH1 3LE, UK
| | - Axel Janke
- Senckenberg Biodiversity and Climate Research Institute (SBiK-F), Georg-Voigt-Strasse 14-16, Frankfurt am Main, 60325, Germany
- Institute for Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Strasse 9, Frankfurt am Main, 60438, Germany
- LOEWE-Centre for Translational Biodiversity Genomics (TBG), Senckenberg Nature Research Society, Georg-Voigt-Straße 14-16, Frankfurt am Main, 60325, Germany
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3
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Fleischmann Z, Cote-L'Heureux A, Franco M, Oreshkov S, Annis S, Khrapko M, Aidlen D, Popadin K, Woods DC, Tilly JL, Khrapko K. Reanalysis of mtDNA mutations of human primordial germ cells (PGCs) reveals NUMT contamination and suggests that selection in PGCs may be positive. Mitochondrion 2024; 74:101817. [PMID: 37914096 DOI: 10.1016/j.mito.2023.10.005] [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: 04/20/2023] [Revised: 10/19/2023] [Accepted: 10/28/2023] [Indexed: 11/03/2023]
Abstract
The resilience of the mitochondrial genome (mtDNA) to a high mutational pressure depends, in part, on negative purifying selection in the germline. A paradigm in the field has been that such selection, at least in part, takes place in primordial germ cells (PGCs). Specifically, Floros et al. (Nature Cell Biology 20: 144-51) reported an increase in the synonymity of mtDNA mutations (a sign of purifying selection) between early-stage and late-stage PGCs. We re-analyzed Floros' et al. data and determined that their mutational dataset was significantly contaminated with single nucleotide variants (SNVs) derived from a nuclear sequence of mtDNA origin (NUMT) located on chromosome 5. Contamination was caused by co-amplification of the NUMT sequence by cross-specific PCR primers. Importantly, when we removed NUMT-derived SNVs, the evidence of purifying selection was abolished. In addition to bulk PGCs, Floros et al. reported the analysis of single-cell late-stage PGCs, which were amplified with different sets of PCR primers that cannot amplify the NUMT sequence. Accordingly, there were no NUMT-derived SNVs among single PGC mutations. Interestingly, single PGC mutations show adecreaseof synonymity with increased intracellular mutant fraction. More specifically, nonsynonymous mutations show faster intracellular genetic drift towards higher mutant fraction than synonymous ones. This pattern is incompatible with predominantly negative selection. This suggests that germline selection of mtDNA mutations is a complex phenomenon and that the part of this process that takes place in PGCs may be predominantly positive. However counterintuitive, positive germline selection of detrimental mtDNA mutations has been reported previously andpotentially may be evolutionarily advantageous.
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Affiliation(s)
- Zoë Fleischmann
- Department of Biology, Northeastern University, Boston, MA, USA
| | | | - Melissa Franco
- Department of Biology, Northeastern University, Boston, MA, USA
| | - Sergey Oreshkov
- Center for Mitochondrial Functional Genomics, Institute of Living Systems, Immanuel Kant Baltic Federal University, 236040 Kaliningrad, Russia
| | - Sofia Annis
- Department of Biology, Northeastern University, Boston, MA, USA
| | - Mark Khrapko
- Department of Biology, Northeastern University, Boston, MA, USA
| | - Dylan Aidlen
- Department of Biology, Northeastern University, Boston, MA, USA
| | - Konstantin Popadin
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland; Center for Mitochondrial Functional Genomics, Institute of Living Systems, Immanuel Kant Baltic Federal University, 236040 Kaliningrad, Russia
| | - Dori C Woods
- Department of Biology, Northeastern University, Boston, MA, USA
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4
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Mikhailova AG, Mikhailova AA, Ushakova K, Tretiakov EO, Iliushchenko D, Shamansky V, Lobanova V, Kozenkov I, Efimenko B, Yurchenko AA, Kozenkova E, Zdobnov EM, Makeev V, Yurov V, Tanaka M, Gostimskaya I, Fleischmann Z, Annis S, Franco M, Wasko K, Denisov S, Kunz WS, Knorre D, Mazunin I, Nikolaev S, Fellay J, Reymond A, Khrapko K, Gunbin K, Popadin K. A mitochondria-specific mutational signature of aging: increased rate of A > G substitutions on the heavy strand. Nucleic Acids Res 2022; 50:10264-10277. [PMID: 36130228 PMCID: PMC9561281 DOI: 10.1093/nar/gkac779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 08/02/2022] [Accepted: 09/07/2022] [Indexed: 11/21/2022] Open
Abstract
The mutational spectrum of the mitochondrial DNA (mtDNA) does not resemble any of the known mutational signatures of the nuclear genome and variation in mtDNA mutational spectra between different organisms is still incomprehensible. Since mitochondria are responsible for aerobic respiration, it is expected that mtDNA mutational spectrum is affected by oxidative damage. Assuming that oxidative damage increases with age, we analyse mtDNA mutagenesis of different species in regards to their generation length. Analysing, (i) dozens of thousands of somatic mtDNA mutations in samples of different ages (ii) 70053 polymorphic synonymous mtDNA substitutions reconstructed in 424 mammalian species with different generation lengths and (iii) synonymous nucleotide content of 650 complete mitochondrial genomes of mammalian species we observed that the frequency of AH > GH substitutions (H: heavy strand notation) is twice bigger in species with high versus low generation length making their mtDNA more AH poor and GH rich. Considering that AH > GH substitutions are also sensitive to the time spent single-stranded (TSSS) during asynchronous mtDNA replication we demonstrated that AH > GH substitution rate is a function of both species-specific generation length and position-specific TSSS. We propose that AH > GH is a mitochondria-specific signature of oxidative damage associated with both aging and TSSS.
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Affiliation(s)
- Alina G Mikhailova
- Center for Mitochondrial Functional Genomics, Immanuel Kant Baltic Federal University, Kaliningrad, Russian Federation
- Vavilov Institute of General Genetics RAS, Moscow, Russia
| | - Alina A Mikhailova
- Center for Mitochondrial Functional Genomics, Immanuel Kant Baltic Federal University, Kaliningrad, Russian Federation
| | - Kristina Ushakova
- Center for Mitochondrial Functional Genomics, Immanuel Kant Baltic Federal University, Kaliningrad, Russian Federation
| | - Evgeny O Tretiakov
- Center for Mitochondrial Functional Genomics, Immanuel Kant Baltic Federal University, Kaliningrad, Russian Federation
- Department of Molecular Neurosciences, Center for Brain Research, Medical University of Vienna, Vienna, Austria
| | - Dmitrii Iliushchenko
- Center for Mitochondrial Functional Genomics, Immanuel Kant Baltic Federal University, Kaliningrad, Russian Federation
| | - Victor Shamansky
- Center for Mitochondrial Functional Genomics, Immanuel Kant Baltic Federal University, Kaliningrad, Russian Federation
| | - Valeria Lobanova
- Center for Mitochondrial Functional Genomics, Immanuel Kant Baltic Federal University, Kaliningrad, Russian Federation
| | - Ivan Kozenkov
- Center for Mitochondrial Functional Genomics, Immanuel Kant Baltic Federal University, Kaliningrad, Russian Federation
| | - Bogdan Efimenko
- Center for Mitochondrial Functional Genomics, Immanuel Kant Baltic Federal University, Kaliningrad, Russian Federation
| | - Andrey A Yurchenko
- INSERM U981, Gustave Roussy Cancer Campus, Université Paris Saclay, Villejuif, France
| | - Elena Kozenkova
- Institute of Physics, Mathematics and Information Technology, Immanuel Kant Baltic Federal University, Kaliningrad, Russian Federation
| | - Evgeny M Zdobnov
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Vsevolod Makeev
- Vavilov Institute of General Genetics RAS, Moscow, Russia
- Moscow Institute of Physics and Technology, Moscow, Russian Federation
| | - Valerian Yurov
- Institute of Physics, Mathematics and Information Technology, Immanuel Kant Baltic Federal University, Kaliningrad, Russian Federation
| | - Masashi Tanaka
- Department of Neurology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Irina Gostimskaya
- Manchester Institute of Biotechnology, The University of Manchester, Manchester, United Kingdom
| | - Zoe Fleischmann
- Department of Biology, Northeastern University, Boston, MA, USA
| | - Sofia Annis
- Department of Biology, Northeastern University, Boston, MA, USA
| | - Melissa Franco
- Department of Biology, Northeastern University, Boston, MA, USA
| | - Kevin Wasko
- Department of Biology, Northeastern University, Boston, MA, USA
| | - Stepan Denisov
- Center for Mitochondrial Functional Genomics, Immanuel Kant Baltic Federal University, Kaliningrad, Russian Federation
- School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
| | - Wolfram S Kunz
- Department of Epileptology and Institute of Experimental Epileptology and Cognition Research, University Bonn, Bonn, Germany
| | - Dmitry Knorre
- The A.N. Belozersky Institute Of Physico-Chemical Biology, Moscow State University, Moscow, Russian Federation
| | - Ilya Mazunin
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology (Skoltech), Skolkovo, Russian Federation
- Fomin Clinic, Moscow, Russian Federation
- Medical Genomics LLC, Moscow, Russian Federation
| | - Sergey Nikolaev
- INSERM U981, Gustave Roussy Cancer Campus, Université Paris Saclay, Villejuif, France
| | - Jacques Fellay
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Alexandre Reymond
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | | | - Konstantin Gunbin
- Center for Mitochondrial Functional Genomics, Immanuel Kant Baltic Federal University, Kaliningrad, Russian Federation
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russian Federation
| | - Konstantin Popadin
- Center for Mitochondrial Functional Genomics, Immanuel Kant Baltic Federal University, Kaliningrad, Russian Federation
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
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5
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Latrille T, Lartillot N. An Improved Codon Modeling Approach for Accurate Estimation of the Mutation Bias. Mol Biol Evol 2022; 39:6503505. [PMID: 35021218 PMCID: PMC8831783 DOI: 10.1093/molbev/msac005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Phylogenetic codon models are routinely used to characterize selective regimes in coding sequences. Their parametric design, however, is still a matter of debate, in particular concerning the question of how to account for differing nucleotide frequencies and substitution rates. This problem relates to the fact that nucleotide composition in protein-coding sequences is the result of the interactions between mutation and selection. In particular, because of the structure of the genetic code, the nucleotide composition differs between the three coding positions, with the third position showing a more extreme composition. Yet, phylogenetic codon models do not correctly capture this phenomenon and instead predict that the nucleotide composition should be the same for all three positions. Alternatively, some models allow for different nucleotide rates at the three positions, an approach conflating the effects of mutation and selection on nucleotide composition. In practice, it results in inaccurate estimation of the strength of selection. Conceptually, the problem comes from the fact that phylogenetic codon models do not correctly capture the fixation bias acting against the mutational pressure at the mutation–selection equilibrium. To address this problem and to more accurately identify mutation rates and selection strength, we present an improved codon modeling approach where the fixation rate is not seen as a scalar, but as a tensor. This approach gives an accurate representation of how mutation and selection oppose each other at equilibrium and yields a reliable estimate of the mutational process, while disentangling the mean fixation probabilities prevailing in different mutational directions.
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Affiliation(s)
- T Latrille
- CNRS, Laboratoire de Biométrie et Biologie Évolutive UMR, Université de Lyon, Université Lyon 1, 5558, Villeurbanne, F-69622, France.,École Normale Supérieure de Lyon, Université de Lyon, Université Lyon 1, Lyon, France
| | - N Lartillot
- CNRS, Laboratoire de Biométrie et Biologie Évolutive UMR, Université de Lyon, Université Lyon 1, 5558, Villeurbanne, F-69622, France
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6
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Luzuriaga-Neira AR, Alvarez-Ponce D. Rates of Protein Evolution across the Marsupial Phylogeny: Heterogeneity and Link to Life-History Traits. Genome Biol Evol 2022; 14:evab277. [PMID: 34894228 PMCID: PMC8759560 DOI: 10.1093/gbe/evab277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/06/2021] [Indexed: 11/15/2022] Open
Abstract
Despite the importance of effective population size (Ne) in evolutionary and conservation biology, it remains unclear what factors have an impact on this quantity. The Nearly Neutral Theory of Molecular Evolution predicts a faster accumulation of deleterious mutations (and thus a higher dN/dS ratio) in populations with small Ne; thus, measuring dN/dS ratios in different groups/species can provide insight into their Ne. Here, we used an exome data set of 1,550 loci from 45 species of marsupials representing 18 of the 22 extant families, to estimate dN/dS ratios across the different branches and families of the marsupial phylogeny. We found a considerable heterogeneity in dN/dS ratios among families and species, which suggests significant differences in their Ne. Furthermore, our multivariate analyses of several life-history traits showed that dN/dS ratios (and thus Ne) are affected by body weight, body length, and weaning age.
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7
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Abstract
The nearly neutral theory is a common framework to describe natural selection at the molecular level. This theory emphasizes the importance of slightly deleterious mutations by recognizing their ability to segregate and eventually get fixed due to genetic drift in spite of the presence of purifying selection. As genetic drift is stronger in smaller than in larger populations, a correlation between population size and molecular measures of natural selection is expected within the nearly neutral theory. However, this hypothesis was originally formulated under equilibrium conditions. As most natural populations are not in equilibrium, testing the relationship empirically may lead to confounded outcomes. Demographic nonequilibria, for instance following a change in population size, are common scenarios that are expected to push the selection–drift relationship off equilibrium. By explicitly modeling the effects of a change in population size on allele frequency trajectories in the Poisson random field framework, we obtain analytical solutions of the nonstationary allele frequency spectrum. This enables us to derive exact results of measures of natural selection and effective population size in a demographic nonequilibrium. The study of their time-dependent relationship reveals a substantial deviation from the equilibrium selection–drift balance after a change in population size. Moreover, we show that the deviation is sensitive to the combination of different measures. These results therefore constitute relevant tools for empirical studies to choose suitable measures for investigating the selection–drift relationship in natural populations. Additionally, our new modeling approach extends existing population genetics theory and can serve as foundation for methodological developments.
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Affiliation(s)
- Rebekka Müller
- Department of Mathematics, Uppsala University, 752 37 Uppsala, Sweden
| | - Ingemar Kaj
- Department of Mathematics, Uppsala University, 752 37 Uppsala, Sweden
| | - Carina F. Mugal
- Department of Ecology and Genetics, Uppsala University, 752 36 Uppsala, Sweden
- Corresponding author: E-mail:
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8
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Raj Kolora SR, Owens GL, Vazquez JM, Stubbs A, Chatla K, Jainese C, Seeto K, McCrea M, Sandel MW, Vianna JA, Maslenikov K, Bachtrog D, Orr JW, Love M, Sudmant PH. Origins and evolution of extreme life span in Pacific Ocean rockfishes. Science 2021; 374:842-847. [PMID: 34762458 PMCID: PMC8923369 DOI: 10.1126/science.abg5332] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Pacific Ocean rockfishes (genus Sebastes) exhibit extreme variation in life span, with some species being among the most long-lived extant vertebrates. We de novo assembled the genomes of 88 rockfish species and from these identified repeated signatures of positive selection in DNA repair pathways in long-lived taxa and 137 longevity-associated genes with direct effects on life span through insulin signaling and with pleiotropic effects through size and environmental adaptations. A genome-wide screen of structural variation reveals copy number expansions in the immune modulatory butyrophilin gene family in long-lived species. The evolution of different rockfish life histories is coupled to genetic diversity and reshapes the mutational spectrum driving segregating CpG→TpG variants in long-lived species. These analyses highlight the genetic innovations that underlie life history trait adaptations and, in turn, how they shape genomic diversity.
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Affiliation(s)
| | - Gregory L. Owens
- University of California Berkeley Department of Integrative Biology
- University of Victoria Department of Biology
| | | | - Alexander Stubbs
- University of California Berkeley Department of Integrative Biology
| | - Kamalakar Chatla
- University of California Berkeley Department of Integrative Biology
| | - Conner Jainese
- University of California Santa Barbara Marine Sciences Institute
| | - Katelin Seeto
- University of California Santa Barbara Marine Sciences Institute
| | - Merit McCrea
- University of California Santa Barbara Marine Sciences Institute
| | | | - Juliana A. Vianna
- Pontificia Universidad Católica de Chile, Departamento de Ecosistemas y Medio Ambiente
| | - Katherine Maslenikov
- University of Washington, School of Aquatic and Fishery Sciences and Burke Museum of Natural History and Culture
| | - Doris Bachtrog
- University of California Berkeley Department of Integrative Biology
| | - James W. Orr
- University of Washington, School of Aquatic and Fishery Sciences and Burke Museum of Natural History and Culture
| | - Milton Love
- University of California Santa Barbara Marine Sciences Institute
| | - Peter H. Sudmant
- University of California Berkeley Department of Integrative Biology
- University of California Berkeley Center for Computational Biology
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9
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Latrille T, Lartillot N. Quantifying the impact of changes in effective population size and expression level on the rate of coding sequence evolution. Theor Popul Biol 2021; 142:57-66. [PMID: 34563555 DOI: 10.1016/j.tpb.2021.09.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 09/08/2021] [Accepted: 09/11/2021] [Indexed: 02/07/2023]
Abstract
Molecular sequences are shaped by selection, where the strength of selection relative to drift is determined by effective population size (Ne). Populations with high Ne are expected to undergo stronger purifying selection, and consequently to show a lower substitution rate for selected mutations relative to the substitution rate for neutral mutations (ω). However, computational models based on biophysics of protein stability have suggested that ω can also be independent of Ne. Together, the response of ω to changes in Ne depends on the specific mapping from sequence to fitness. Importantly, an increase in protein expression level has been found empirically to result in decrease of ω, an observation predicted by theoretical models assuming selection for protein stability. Here, we derive a theoretical approximation for the response of ω to changes in Ne and expression level, under an explicit genotype-phenotype-fitness map. The method is generally valid for additive traits and log-concave fitness functions. We applied these results to protein undergoing selection for their conformational stability and corroborate out findings with simulations under more complex models. We predict a weak response of ω to changes in either Ne or expression level, which are interchangeable. Based on empirical data, we propose that fitness based on the conformational stability may not be a sufficient mechanism to explain the empirically observed variation in ω across species. Other aspects of protein biophysics might be explored, such as protein-protein interactions, which can lead to a stronger response of ω to changes in Ne.
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Affiliation(s)
- T Latrille
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Évolutive UMR 5558, F-69622 Villeurbanne, France; École Normale Supérieure de Lyon, Université de Lyon, Université Lyon 1, Lyon, France.
| | - N Lartillot
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Évolutive UMR 5558, F-69622 Villeurbanne, France
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10
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Jakovlić I, Zou H, Chen JH, Lei HP, Wang GT, Liu J, Zhang D. Slow crabs - fast genomes: Locomotory capacity predicts skew magnitude in crustacean mitogenomes. Mol Ecol 2021; 30:5488-5502. [PMID: 34418213 DOI: 10.1111/mec.16138] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 08/10/2021] [Accepted: 08/17/2021] [Indexed: 02/05/2023]
Abstract
Base composition skews (G-C/G+C) of mitochondrial genomes are believed to be primarily driven by mutational pressure, which is positively correlated with metabolic rate. In marine animals, metabolic rate is also positively correlated with locomotory capacity. Given the central role of mitochondria in energy metabolism, we hypothesised that selection for locomotory capacity should be positively correlated with the strength of purifying selection (dN/dS), and thus be negatively correlated with the skew magnitude. Therefore, these two models assume diametrically opposite associations between the metabolic rate and skew magnitude: positive correlation in the prevailing paradigm, and negative in our working hypothesis. We examined correlations between the skew magnitude, metabolic rate, locomotory capacity, and several other variables previously associated with mitochondrial evolution on 287 crustacean mitogenomes. Weakly locomotory taxa had higher skew magnitude and ω (dN/dS) values, but not the gene order rearrangement rate. Skew and ω magnitudes were correlated. Multilevel regression analyses indicated that three competing variables, body size, gene order rearrangement rate, and effective population size, had negligible impacts on the skew magnitude. In most crustacean lineages selection for locomotory capacity appears to be the primary factor determining the skew magnitude. Contrary to the prevailing paradigm, this implies that adaptive selection outweighs nonadaptive selection (mutation pressure) in crustaceans. However, we found indications that effective population size (nonadaptive factor) may outweigh the impact of locomotory capacity in sessile crustaceans (Thecostraca). In conclusion, skew magnitude is a product of the interplay between adaptive and nonadaptive factors, the balance of which varies among lineages.
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Affiliation(s)
- Ivan Jakovlić
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology, Lanzhou University, Lanzhou, China
| | - Hong Zou
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Jian-Hai Chen
- Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Hong-Peng Lei
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology, Lanzhou University, Lanzhou, China
| | - Gui-Tang Wang
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Jianquan Liu
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology, Lanzhou University, Lanzhou, China
| | - Dong Zhang
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology, Lanzhou University, Lanzhou, China
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11
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Brevet M, Lartillot N. Reconstructing the History of Variation in Effective Population Size along Phylogenies. Genome Biol Evol 2021; 13:6311658. [PMID: 34190972 PMCID: PMC8358220 DOI: 10.1093/gbe/evab150] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/21/2021] [Indexed: 12/19/2022] Open
Abstract
The nearly neutral theory predicts specific relations between effective population size (Ne) and patterns of divergence and polymorphism, which depend on the shape of the distribution of fitness effects (DFE) of new mutations. However, testing these relations is not straightforward, owing to the difficulty in estimating Ne. Here, we introduce an integrative framework allowing for an explicit reconstruction of the phylogenetic history of Ne, thus leading to a quantitative test of the nearly neutral theory and an estimation of the allometric scaling of the ratios of nonsynonymous over synonymous polymorphism (πN/πS) and divergence (dN/dS) with respect to Ne. As an illustration, we applied our method to primates, for which the nearly neutral predictions were mostly verified. Under a purely nearly neutral model with a constant DFE across species, we find that the variation in πN/πS and dN/dS as a function of Ne is too large to be compatible with current estimates of the DFE based on site frequency spectra. The reconstructed history of Ne shows a 10-fold variation across primates. The mutation rate per generation u, also reconstructed over the tree by the method, varies over a 3-fold range and is negatively correlated with Ne. As a result of these opposing trends for Ne and u, variation in πS is intermediate, primarily driven by Ne but substantially influenced by u. Altogether, our integrative framework provides a quantitative assessment of the role of Ne and u in modulating patterns of genetic variation, while giving a synthetic picture of their history over the clade.
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Affiliation(s)
- Mathieu Brevet
- Station d'Écologie Théorique et Expérimentale, UPR 2001, Moulis, France
| | - Nicolas Lartillot
- Laboratoire de Biométrie et Biologie Evolutive, UMR CNRS 5558, Université Lyon 1, Villeurbanne, France
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12
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Latrille T, Lanore V, Lartillot N. Inferring long-term effective population size with Mutation-Selection Models. Mol Biol Evol 2021; 38:4573-4587. [PMID: 34191010 PMCID: PMC8476147 DOI: 10.1093/molbev/msab160] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Mutation–selection phylogenetic codon models are grounded on population genetics first principles and represent a principled approach for investigating the intricate interplay between mutation, selection, and drift. In their current form, mutation–selection codon models are entirely characterized by the collection of site-specific amino-acid fitness profiles. However, thus far, they have relied on the assumption of a constant genetic drift, translating into a unique effective population size (Ne) across the phylogeny, clearly an unrealistic assumption. This assumption can be alleviated by introducing variation in Ne between lineages. In addition to Ne, the mutation rate (μ) is susceptible to vary between lineages, and both should covary with life-history traits (LHTs). This suggests that the model should more globally account for the joint evolutionary process followed by all of these lineage-specific variables (Ne, μ, and LHTs). In this direction, we introduce an extended mutation–selection model jointly reconstructing in a Bayesian Monte Carlo framework the fitness landscape across sites and long-term trends in Ne, μ, and LHTs along the phylogeny, from an alignment of DNA coding sequences and a matrix of observed LHTs in extant species. The model was tested against simulated data and applied to empirical data in mammals, isopods, and primates. The reconstructed history of Ne in these groups appears to correlate with LHTs or ecological variables in a way that suggests that the reconstruction is reasonable, at least in its global trends. On the other hand, the range of variation in Ne inferred across species is surprisingly narrow. This last point suggests that some of the assumptions of the model, in particular concerning the assumed absence of epistatic interactions between sites, are potentially problematic.
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Affiliation(s)
- T Latrille
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Évolutive UMR, 5558, F-69622, Villeurbanne, France.,École Normale Supérieure de Lyon, Université de Lyon, Université Lyon 1, Lyon, France,
| | - V Lanore
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Évolutive UMR, 5558, F-69622, Villeurbanne, France
| | - N Lartillot
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Évolutive UMR, 5558, F-69622, Villeurbanne, France
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13
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Herrera-Álvarez S, Karlsson E, Ryder OA, Lindblad-Toh K, Crawford AJ. How to Make a Rodent Giant: Genomic Basis and Tradeoffs of Gigantism in the Capybara, the World's Largest Rodent. Mol Biol Evol 2021; 38:1715-1730. [PMID: 33169792 PMCID: PMC8097284 DOI: 10.1093/molbev/msaa285] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Gigantism results when one lineage within a clade evolves extremely large body size relative to its small-bodied ancestors, a common phenomenon in animals. Theory predicts that the evolution of giants should be constrained by two tradeoffs. First, because body size is negatively correlated with population size, purifying selection is expected to be less efficient in species of large body size, leading to increased mutational load. Second, gigantism is achieved through generating a higher number of cells along with higher rates of cell proliferation, thus increasing the likelihood of cancer. To explore the genetic basis of gigantism in rodents and uncover genomic signatures of gigantism-related tradeoffs, we assembled a draft genome of the capybara (Hydrochoerus hydrochaeris), the world's largest living rodent. We found that the genome-wide ratio of nonsynonymous to synonymous mutations (ω) is elevated in the capybara relative to other rodents, likely caused by a generation-time effect and consistent with a nearly neutral model of molecular evolution. A genome-wide scan for adaptive protein evolution in the capybara highlighted several genes controlling postnatal bone growth regulation and musculoskeletal development, which are relevant to anatomical and developmental modifications for an increase in overall body size. Capybara-specific gene-family expansions included a putative novel anticancer adaptation that involves T-cell-mediated tumor suppression, offering a potential resolution to the increased cancer risk in this lineage. Our comparative genomic results uncovered the signature of an intragenomic conflict where the evolution of gigantism in the capybara involved selection on genes and pathways that are directly linked to cancer.
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Affiliation(s)
| | - Elinor Karlsson
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Oliver A Ryder
- San Diego Zoo Institute for Conservation Research, San Diego Zoo Global, Escondido, CA, USA
| | - Kerstin Lindblad-Toh
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Andrew J Crawford
- Department of Biological Sciences, Universidad de Los Andes, Bogotá, Colombia
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14
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Kakehashi R, Kurabayashi A. Patterns of Natural Selection on Mitochondrial Protein-Coding Genes in Lungless Salamanders: Relaxed Purifying Selection and Presence of Positively Selected Codon Sites in the Family Plethodontidae. Int J Genomics 2021; 2021:6671300. [PMID: 33928143 PMCID: PMC8053045 DOI: 10.1155/2021/6671300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 03/12/2021] [Accepted: 03/26/2021] [Indexed: 11/18/2022] Open
Abstract
There are two distinct lungless groups in caudate amphibians (salamanders and newts) (the family Plethodontidae and the genus Onychodactylus, from the family Hynobiidae). Lunglessness is considered to have evolved in response to environmental and/or ecological adaptation with respect to oxygen requirements. We performed selection analyses on lungless salamanders to elucidate the selective patterns of mitochondrial protein-coding genes associated with lunglessness. The branch model and RELAX analyses revealed the occurrence of relaxed selection (an increase of the dN/dS ratio = ω value) in most mitochondrial protein-coding genes of plethodontid salamander branches but not in those of Onychodactylus. Additional branch model and RELAX analyses indicated that direct-developing plethodontids showed the relaxed pattern for most mitochondrial genes, although metamorphosing plethodontids had fewer relaxed genes. Furthermore, aBSREL analysis detected positively selected codons in three plethodontid branches but not in Onychodactylus. One of these three branches corresponded to the most recent common ancestor, and the others corresponded with the most recent common ancestors of direct-developing branches within Hemidactyliinae. The positive selection of mitochondrial protein-coding genes in Plethodontidae is probably associated with the evolution of direct development.
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Affiliation(s)
- Ryosuke Kakehashi
- Faculty of Bio-Science, Nagahama Institute of Bio-Science and Technology, Shiga 526-0829, Japan
| | - Atsushi Kurabayashi
- Faculty of Bio-Science, Nagahama Institute of Bio-Science and Technology, Shiga 526-0829, Japan
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom 2520, South Africa
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15
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Rolland J, Schluter D, Romiguier J. Vulnerability to Fishing and Life History Traits Correlate with the Load of Deleterious Mutations in Teleosts. Mol Biol Evol 2021; 37:2192-2196. [PMID: 32163146 PMCID: PMC7403610 DOI: 10.1093/molbev/msaa067] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Understanding why some species accumulate more deleterious substitutions than others is an important question relevant in evolutionary biology and conservation sciences. Previous studies conducted in terrestrial taxa suggest that life history traits correlate with the efficiency of purifying selection and accumulation of deleterious mutations. Using a large genome data set of 76 species of teleostean fishes, we show that species with life history traits associated with vulnerability to fishing have an increased rate of deleterious mutation accumulation (measured via dN/dS, i.e., nonsynonymous over synonymous substitution rate). Our results, focusing on a large clade of aquatic species, generalize previous patterns found so far in few clades of terrestrial vertebrates. These results also show that vulnerable species to fishing inherently accumulate more deleterious substitutions than nonthreatened ones, which illustrates the potential links among population genetics, ecology, and fishing policies to prevent species extinction.
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Affiliation(s)
- Jonathan Rolland
- Department of Zoology, University of British Columbia, Vancouver, BC, Canada.,Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada.,Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - Dolph Schluter
- Department of Zoology, University of British Columbia, Vancouver, BC, Canada.,Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Jonathan Romiguier
- CNRS, UMR 5554 Institut des Sciences de l'Evolution, Université de Montpellier, Montpellier, France
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16
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Mortz M, Levivier A, Lartillot N, Dufresne F, Blier PU. Long-Lived Species of Bivalves Exhibit Low MT-DNA Substitution Rates. Front Mol Biosci 2021; 8:626042. [PMID: 33791336 PMCID: PMC8005583 DOI: 10.3389/fmolb.2021.626042] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 01/28/2021] [Indexed: 01/21/2023] Open
Abstract
Bivalves represent valuable taxonomic group for aging studies given their wide variation in longevity (from 1–2 to >500 years). It is well known that aging is associated to the maintenance of Reactive Oxygen Species homeostasis and that mitochondria phenotype and genotype dysfunctions accumulation is a hallmark of these processes. Previous studies have shown that mitochondrial DNA mutation rates are linked to lifespan in vertebrate species, but no study has explored this in invertebrates. To this end, we performed a Bayesian Phylogenetic Covariance model of evolution analysis using 12 mitochondrial protein-coding genes of 76 bivalve species. Three life history traits (maximum longevity, generation time and mean temperature tolerance) were tested against 1) synonymous substitution rates (dS), 2) conservative amino acid replacement rates (Kc) and 3) ratios of radical over conservative amino acid replacement rates (Kr/Kc). Our results confirm the already known correlation between longevity and generation time and show, for the first time in an invertebrate class, a significant negative correlation between dS and longevity. This correlation was not as strong when generation time and mean temperature tolerance variations were also considered in our model (marginal correlation), suggesting a confounding effect of these traits on the relationship between longevity and mtDNA substitution rate. By confirming the negative correlation between dS and longevity previously documented in birds and mammals, our results provide support for a general pattern in substitution rates.
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Affiliation(s)
- Mathieu Mortz
- Institut Des Sciences De La Mer De Rimouski, Université Du Québec à Rimouski, Rimouski, QC, Canada
| | - Aurore Levivier
- Institut Des Sciences De La Mer De Rimouski, Université Du Québec à Rimouski, Rimouski, QC, Canada
| | - Nicolas Lartillot
- Laboratoire De Biométrie et Biologie Evolutive, UMR CNRS, Université Lyon 1, Villeurbanne, France
| | - France Dufresne
- Laboratoire D'écologie Moléculaire, Département De Biologie, Université Du Québec à Rimouski, Rimouski, QC, Canada.,Laboratoire De Physiologie Intégrative Et Evolutive, Département De Biologie, Université Du Québec à Rimouski, Rimouski, QC, Canada
| | - Pierre U Blier
- Laboratoire De Physiologie Intégrative Et Evolutive, Département De Biologie, Université Du Québec à Rimouski, Rimouski, QC, Canada
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17
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Neverov AD, Popova AV, Fedonin GG, Cheremukhin EA, Klink GV, Bazykin GA. Episodic evolution of coadapted sets of amino acid sites in mitochondrial proteins. PLoS Genet 2021; 17:e1008711. [PMID: 33493156 PMCID: PMC7861529 DOI: 10.1371/journal.pgen.1008711] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 02/04/2021] [Accepted: 12/07/2020] [Indexed: 11/19/2022] Open
Abstract
The rate of evolution differs between protein sites and changes with time. However, the link between these two phenomena remains poorly understood. Here, we design a phylogenetic approach for distinguishing pairs of amino acid sites that evolve concordantly, i.e., such that substitutions at one site trigger subsequent substitutions at the other; and also pairs of sites that evolve discordantly, so that substitutions at one site impede subsequent substitutions at the other. We distinguish groups of amino acid sites that undergo coordinated evolution and evolve discordantly from other such groups. In mitochondrion-encoded proteins of metazoans and fungi, we show that concordantly evolving sites are clustered in protein structures. By analysing the phylogenetic patterns of substitutions at concordantly and discordantly evolving site pairs, we find that concordant evolution has two distinct causes: epistatic interactions between amino acid substitutions and episodes of selection independently affecting substitutions at different sites. The rate of substitutions at concordantly evolving groups of protein sites changes in the course of evolution, indicating episodes of selection limited to some of the lineages. The phylogenetic positions of these changes are consistent between proteins, suggesting common selective forces underlying them. The mode and rate of evolution of a protein site depends on the effect of its mutations on protein fitness. The fitness effect of a mutation itself can change in the course of evolution for at least two reasons. First, it can be modulated by substitutions occurring at other sites, a phenomenon called epistasis. Second, changes in selection can be non-epistatic, affecting sites independently of one another. Here, we analyse substitutions accumulated by the evolving lineages of the five proteins encoded by the mitochondrial genomes of thousands of species of metazoans and fungi. We show that substitutions at different amino acid sites occur in a coordinated fashion, and this coordination is caused both by epistasis and by episodes of selection affecting groups of sites. We partition each protein into several groups of concordantly evolving sites such that evolution of sites from different groups is discordant, and show that the proteins encoded by the mitochondrial genome consist of coevolving structural blocks. Some of these blocks have a clear functional specialization, e.g. are associated with interfaces between proteins composing respiratory complexes. Together, our results reveal a previously unrecognized complexity in the causes of variation in evolutionary rates between protein sites.
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Affiliation(s)
- Alexey D. Neverov
- Department of Molecular Diagnostics, Central Research Institute for Epidemiology, Moscow, Russia
- * E-mail:
| | - Anfisa V. Popova
- Department of Molecular Diagnostics, Central Research Institute for Epidemiology, Moscow, Russia
| | - Gennady G. Fedonin
- Department of Molecular Diagnostics, Central Research Institute for Epidemiology, Moscow, Russia
- Institute for Information Transmission Problems (Kharkevich Institute), Russian Academy of Sciences, Moscow, Russia
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow region, Russia
| | | | - Galya V. Klink
- Institute for Information Transmission Problems (Kharkevich Institute), Russian Academy of Sciences, Moscow, Russia
| | - Georgii A. Bazykin
- Institute for Information Transmission Problems (Kharkevich Institute), Russian Academy of Sciences, Moscow, Russia
- Skolkovo Institute of Science and Technology, Skolkovo, Russia
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18
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Xu W, Zhao Y, Chen S, Xie J, Zhang D. Evolution and Functional Divergence of the Fructokinase Gene Family in Populus. FRONTIERS IN PLANT SCIENCE 2020; 11:484. [PMID: 32499793 PMCID: PMC7243158 DOI: 10.3389/fpls.2020.00484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Accepted: 03/31/2020] [Indexed: 05/06/2023]
Abstract
New kinase has emerged throughout evolution, but how new kinase evolve while maintaining their functions and acquiring new functions remains unclear. Fructokinase (FRK), the gateway kinase to fructose metabolism, plays essential roles in plant development, and stress tolerance. Here, we explored the evolution of FRK gene family in 20 plant species (from green algae to angiosperms) and their functional roles in Populus. We identified 125 putative FRK genes in the 20 plant species with an average of 6 members per species. Phylogenetic analysis separated these 125 genes into 8 clades including 3 conserved clades and 5 specific clades, the 5 of which only exist in green algae or angiosperms. Evolutionary analysis revealed that FRK genes in ancient land plants have the largest number of functional domains with the longest amino acid sequences, and the length of FRK genes became shorter during the transition to vascular plants. This was accompanied by loss, acquisition, and diversification of functional domains. In Populus, segmental duplication appears to be the main mechanism for the expansion of FRK genes. Specially, most FRK genes duplicated in salicoids are regulated by Populus-specific microRNAs. Furthermore, compared with common FRKs, Populus-specific FRKs have showed higher expression specificity and are associated with fewer growth and wood property traits, which suggests that these FRKs may have undergone functional divergence. Our study explores the specific roles of FRKs in the Populus genome and provides new insights for functional investigation of this gene family.
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Affiliation(s)
- Weijie Xu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Forestry University, Ministry of Education, Beijing, China
| | - Yiyang Zhao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Forestry University, Ministry of Education, Beijing, China
| | - Sisi Chen
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Forestry University, Ministry of Education, Beijing, China
| | - Jianbo Xie
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Forestry University, Ministry of Education, Beijing, China
| | - Deqiang Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Forestry University, Ministry of Education, Beijing, China
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19
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Kudryavtseva OA, Safina KR, Vakhrusheva OA, Logacheva MD, Penin AA, Neretina TV, Moskalenko VN, Glagoleva ES, Bazykin GA, Kondrashov AS. Genetics of Adaptation of the Ascomycetous Fungus Podospora anserina to Submerged Cultivation. Genome Biol Evol 2019; 11:2807-2817. [PMID: 31529025 PMCID: PMC6786475 DOI: 10.1093/gbe/evz194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/03/2019] [Indexed: 12/02/2022] Open
Abstract
Podospora anserina is a model ascomycetous fungus which shows pronounced phenotypic senescence when grown on solid medium but possesses unlimited lifespan under submerged cultivation. In order to study the genetic aspects of adaptation of P. anserina to submerged cultivation, we initiated a long-term evolution experiment. In the course of the first 4 years of the experiment, 125 single-nucleotide substitutions and 23 short indels were fixed in eight independently evolving populations. Six proteins that affect fungal growth and development evolved in more than one population; in particular, in the G-protein alpha subunit FadA, new alleles fixed in seven out of eight experimental populations, and these fixations affected just four amino acid sites, which is an unprecedented level of parallelism in experimental evolution. Parallel evolution at the level of genes and pathways, an excess of nonsense and missense substitutions, and an elevated conservation of proteins and their sites where the changes occurred suggest that many of the observed fixations were adaptive and driven by positive selection.
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Affiliation(s)
- Olga A Kudryavtseva
- Department of Mycology and Phycology, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Ksenia R Safina
- Skolkovo Institute of Science and Technology, Moscow, Russia
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
| | - Olga A Vakhrusheva
- Skolkovo Institute of Science and Technology, Moscow, Russia
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
| | - Maria D Logacheva
- Skolkovo Institute of Science and Technology, Moscow, Russia
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Aleksey A Penin
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Tatiana V Neretina
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
- White Sea Biological Station, Lomonosov Moscow State University, Republic of Karelia, Russia
| | | | - Elena S Glagoleva
- Department of Plant Physiology, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Georgii A Bazykin
- Skolkovo Institute of Science and Technology, Moscow, Russia
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
| | - Alexey S Kondrashov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor
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20
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Weber CC, Whelan S. Physicochemical Amino Acid Properties Better Describe Substitution Rates in Large Populations. Mol Biol Evol 2019; 36:679-690. [PMID: 30668757 DOI: 10.1093/molbev/msz003] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Substitutions between chemically distant amino acids are known to occur less frequently than those between more similar amino acids. This knowledge, however, is not reflected in most codon substitution models, which treat all nonsynonymous changes as if they were equivalent in terms of impact on the protein. A variety of methods for integrating chemical distances into models have been proposed, with a common approach being to divide substitutions into radical or conservative categories. Nevertheless, it remains unclear whether the resulting models describe sequence evolution better than their simpler counterparts. We propose a parametric codon model that distinguishes between radical and conservative substitutions, allowing us to assess if radical substitutions are preferentially removed by selection. Applying our new model to a range of phylogenomic data, we find differentiating between radical and conservative substitutions provides significantly better fit for large populations, but see no equivalent improvement for smaller populations. Comparing codon and amino acid models using these same data shows that alignments from large populations tend to select phylogenetic models containing information about amino acid exchangeabilities, whereas the structure of the genetic code is more important for smaller populations. Our results suggest selection against radical substitutions is, on average, more pronounced in large populations than smaller ones. The reduced observable effect of selection in smaller populations may be due to stronger genetic drift making it more challenging to detect preferences. Our results imply an important connection between the life history of a phylogenetic group and the model that best describes its evolution.
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Affiliation(s)
- Claudia C Weber
- Center for Computational Genetics and Genomics, Department of Biology, Temple University, Philadelphia, PA.,European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Simon Whelan
- Evolutionary Biology Center, Uppsala University, Uppsala, Sweden
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21
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Castellano D, James J, Eyre-Walker A. Nearly Neutral Evolution across the Drosophila melanogaster Genome. Mol Biol Evol 2019; 35:2685-2694. [PMID: 30418639 DOI: 10.1093/molbev/msy164] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Under the nearly neutral theory of molecular evolution, the proportion of effectively neutral mutations is expected to depend upon the effective population size (Ne). Here, we investigate whether this is the case across the genome of Drosophila melanogaster using polymorphism data from North American and African lines. We show that the ratio of the number of nonsynonymous and synonymous polymorphisms is negatively correlated to the number of synonymous polymorphisms, even when the nonindependence is accounted for. The relationship is such that the proportion of effectively neutral nonsynonymous mutations increases by ∼45% as Ne is halved. However, we also show that this relationship is steeper than expected from an independent estimate of the distribution of fitness effects from the site frequency spectrum. We investigate a number of potential explanations for this and show, using simulation, that this is consistent with a model of genetic hitchhiking: Genetic hitchhiking depresses diversity at neutral and weakly selected sites, but has little effect on the diversity of strongly selected sites.
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Affiliation(s)
- David Castellano
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - Jennifer James
- School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Adam Eyre-Walker
- School of Life Sciences, University of Sussex, Brighton, United Kingdom
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22
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Stupnikova AN, Vasilyeva JV, Neretina TV, Kondrashov AS. Artificial Selection for Reduced Fitness in Panmictic Populations of Drosophila melanogaster. RUSS J GENET+ 2019. [DOI: 10.1134/s1022795419040148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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23
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Bernardo PH, Sánchez-Ramírez S, Sánchez-Pacheco SJ, Álvarez-Castañeda ST, Aguilera-Miller EF, Mendez-de la Cruz FR, Murphy RW. Extreme mito-nuclear discordance in a peninsular lizard: the role of drift, selection, and climate. Heredity (Edinb) 2019; 123:359-370. [PMID: 30833746 PMCID: PMC6781153 DOI: 10.1038/s41437-019-0204-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 02/13/2019] [Accepted: 02/18/2019] [Indexed: 12/22/2022] Open
Abstract
Nuclear and mitochondrial genomes coexist within cells but are subject to different tempos and modes of evolution. Evolutionary forces such as drift, mutation, selection, and migration are expected to play fundamental roles in the origin and maintenance of diverged populations; however, divergence may lag between genomes subject to different modes of inheritance and functional specialization. Herein, we explore whole mitochondrial genome data and thousands of nuclear single nucleotide polymorphisms to evidence extreme mito-nuclear discordance in the small black-tailed brush lizard, Urosaurus nigricaudus, of the Peninsula of Baja California, Mexico and southern California, USA, and discuss potential drivers. Results show three deeply divergent mitochondrial lineages dating back to the later Miocene (ca. 5.5 Ma) and Pliocene (ca. 2.8 Ma) that likely followed geographic isolation due to trans-peninsular seaways. This contrasts with very low levels of genetic differentiation in nuclear loci (FST < 0.028) between mtDNA lineages. Analyses of protein-coding genes reveal substantial fixed variation between mitochondrial lineages, of which a significant portion comes from non-synonymous mutations. A mixture of drift and selection is likely responsible for the rise of these mtDNA groups, albeit with little evidence of marked differences in climatic niche space between them. Finally, future investigations can look further into the role that mito-nuclear incompatibilities and mating systems play in explaining contrasting nuclear gene flow.
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Affiliation(s)
- Pedro Henrique Bernardo
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, ON, M5S 3B2, Canada. .,Department of Natural History, Royal Ontario Museum, Toronto, ON, Canada.
| | - Santiago Sánchez-Ramírez
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, ON, M5S 3B2, Canada.,Department of Natural History, Royal Ontario Museum, Toronto, ON, Canada
| | - Santiago J Sánchez-Pacheco
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, ON, M5S 3B2, Canada.,Department of Natural History, Royal Ontario Museum, Toronto, ON, Canada
| | | | | | | | - Robert W Murphy
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, ON, M5S 3B2, Canada.,Department of Natural History, Royal Ontario Museum, Toronto, ON, Canada
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24
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Bolívar P, Guéguen L, Duret L, Ellegren H, Mugal CF. GC-biased gene conversion conceals the prediction of the nearly neutral theory in avian genomes. Genome Biol 2019; 20:5. [PMID: 30616647 PMCID: PMC6322265 DOI: 10.1186/s13059-018-1613-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 12/17/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The nearly neutral theory of molecular evolution predicts that the efficacy of natural selection increases with the effective population size. This prediction has been verified by independent observations in diverse taxa, which show that life-history traits are strongly correlated with measures of the efficacy of selection, such as the dN/dS ratio. Surprisingly, avian taxa are an exception to this theory because correlations between life-history traits and dN/dS are apparently absent. Here we explore the role of GC-biased gene conversion on estimates of substitution rates as a potential driver of these unexpected observations. RESULTS We analyze the relationship between dN/dS estimated from alignments of 47 avian genomes and several proxies for effective population size. To distinguish the impact of GC-biased gene conversion from selection, we use an approach that accounts for non-stationary base composition and estimate dN/dS separately for changes affected or unaffected by GC-biased gene conversion. This analysis shows that the impact of GC-biased gene conversion on substitution rates can explain the lack of correlations between life-history traits and dN/dS. Strong correlations between life-history traits and dN/dS are recovered after accounting for GC-biased gene conversion. The correlations are robust to variation in base composition and genomic location. CONCLUSIONS Our study shows that gene sequence evolution across a wide range of avian lineages meets the prediction of the nearly neutral theory, the efficacy of selection increases with effective population size. Moreover, our study illustrates that accounting for GC-biased gene conversion is important to correctly estimate the strength of selection.
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Affiliation(s)
- Paulina Bolívar
- Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden
| | - Laurent Guéguen
- Laboratoire de Biologie et Biométrie Évolutive CNRS UMR 5558, Université Claude Bernard Lyon 1, Lyon, France
| | - Laurent Duret
- Laboratoire de Biologie et Biométrie Évolutive CNRS UMR 5558, Université Claude Bernard Lyon 1, Lyon, France
| | - Hans Ellegren
- Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden
| | - Carina F. Mugal
- Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden
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25
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Lyons DM, Lauring AS. Evidence for the Selective Basis of Transition-to-Transversion Substitution Bias in Two RNA Viruses. Mol Biol Evol 2018; 34:3205-3215. [PMID: 29029187 PMCID: PMC5850290 DOI: 10.1093/molbev/msx251] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The substitution rates of transitions are higher than expected by chance relative to those of transversions. Many have argued that selection disfavors transversions, as nonsynonymous transversions are less likely to conserve biochemical properties of the original amino acid. Only recently has it become feasible to directly test this selective hypothesis by comparing the fitness effects of a large number of transition and transversion mutations. For example, a recent study of six viruses and one beta-lactamase gene did not find evidence supporting the selective hypothesis. Here, we analyze the relative fitness effects of transition and transversion mutations from our recently published genome-wide study of mutational fitness effects in influenza virus. In contrast to prior work, we find that transversions are significantly more detrimental than transitions. Using what we believe to be an improved statistical framework, we also identify a similar trend in two HIV data sets. We further demonstrate a fitness difference in transition and transversion mutations using four deep mutational scanning data sets of influenza virus and HIV, which provided adequate statistical power. We find that three of the most commonly cited radical/conservative amino acid categories are predictive of fitness, supporting their utility in studies of positive selection and codon usage bias. We conclude that selection is a major contributor to the transition:transversion substitution bias in viruses and that this effect is only partially explained by the greater likelihood of transversion mutations to cause radical as opposed to conservative amino acid changes.
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Affiliation(s)
- Daniel M Lyons
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI
| | - Adam S Lauring
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI.,Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI.,Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, MI
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26
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Kondrashov AS. Through Sex, Nature Is Telling Us Something Important. Trends Genet 2018; 34:352-361. [DOI: 10.1016/j.tig.2018.01.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 01/02/2018] [Accepted: 01/05/2018] [Indexed: 11/28/2022]
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27
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Sharbrough J, Luse M, Boore JL, Logsdon JM, Neiman M. Radical amino acid mutations persist longer in the absence of sex. Evolution 2018. [PMID: 29520921 DOI: 10.1111/evo.13465] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Harmful mutations are ubiquitous and inevitable, and the rate at which these mutations are removed from populations is a critical determinant of evolutionary fate. Closely related sexual and asexual taxa provide a particularly powerful setting to study deleterious mutation elimination because sexual reproduction should facilitate mutational clearance by reducing selective interference between sites and by allowing the production of offspring with different mutational complements than their parents. Here, we compared the rate of removal of conservative (i.e., similar biochemical properties) and radical (i.e., distinct biochemical properties) nonsynonymous mutations from mitochondrial genomes of sexual versus asexual Potamopyrgus antipodarum, a New Zealand freshwater snail characterized by coexisting and ecologically similar sexual and asexual lineages. Our analyses revealed that radical nonsynonymous mutations are cleared at higher rates than conservative changes and that sexual lineages eliminate radical changes more rapidly than asexual counterparts. These results are consistent with reduced efficacy of purifying selection in asexual lineages allowing harmful mutations to remain polymorphic longer than in sexual lineages. Together, these data illuminate some of the population-level processes contributing to mitochondrial mutation accumulation and suggest that mutation accumulation could influence the outcome of competition between sexual and asexual lineages.
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Affiliation(s)
- Joel Sharbrough
- Department of Biology, University of Iowa, Iowa City, Iowa 52242.,Department of Biology, Colorado State University, Fort Collins, Colorado 80523
| | - Meagan Luse
- Department of Biology, University of Iowa, Iowa City, Iowa 52242
| | - Jeffrey L Boore
- Department of Integrative Biology, University of California, Berkeley, Berkeley, California 94720.,Providence St. Joseph Health and Institute for Systems Biology, Seattle, Washington 98109
| | - John M Logsdon
- Department of Biology, University of Iowa, Iowa City, Iowa 52242
| | - Maurine Neiman
- Department of Biology, University of Iowa, Iowa City, Iowa 52242
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28
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Allio R, Donega S, Galtier N, Nabholz B. Large Variation in the Ratio of Mitochondrial to Nuclear Mutation Rate across Animals: Implications for Genetic Diversity and the Use of Mitochondrial DNA as a Molecular Marker. Mol Biol Evol 2018; 34:2762-2772. [PMID: 28981721 DOI: 10.1093/molbev/msx197] [Citation(s) in RCA: 171] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
It is commonly assumed that mitochondrial DNA (mtDNA) evolves at a faster rate than nuclear DNA (nuDNA) in animals. This has contributed to the popularity of mtDNA as a molecular marker in evolutionary studies. Analyzing 121 multilocus data sets and four phylogenomic data sets encompassing 4,676 species of animals, we demonstrate that the ratio of mitochondrial over nuclear mutation rate is highly variable among animal taxa. In nonvertebrates, such as insects and arachnids, the ratio of mtDNA over nuDNA mutation rate varies between 2 and 6, whereas it is above 20, on average, in vertebrates such as scaled reptiles and birds. Interestingly, this variation is sufficient to explain the previous report of a similar level of mitochondrial polymorphism, on average, between vertebrates and nonvertebrates, which was originally interpreted as reflecting the effect of pervasive positive selection. Our analysis rather indicates that the among-phyla homogeneity in within-species mtDNA diversity is due to a negative correlation between mtDNA per-generation mutation rate and effective population size, irrespective of the action of natural selection. Finally, we explore the variation in the absolute per-year mutation rate of both mtDNA and nuDNA using a reduced data set for which fossil calibration is available, and discuss the potential determinants of mutation rate variation across genomes and taxa. This study has important implications regarding DNA-based identification methods in predicting that mtDNA barcoding should be less reliable in nonvertebrates than in vertebrates.
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Affiliation(s)
- Remi Allio
- ISEM, Univ. Montpellier, CNRS, IRD, EPHE, Montpellier, France
| | - Stefano Donega
- ISEM, Univ. Montpellier, CNRS, IRD, EPHE, Montpellier, France
| | - Nicolas Galtier
- ISEM, Univ. Montpellier, CNRS, IRD, EPHE, Montpellier, France
| | - Benoit Nabholz
- ISEM, Univ. Montpellier, CNRS, IRD, EPHE, Montpellier, France
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29
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Bezmenova AV, Bazykin GA, Kondrashov AS. Prevalence of loss-of-function alleles does not correlate with lifetime fecundity and other life-history traits in metazoans. Biol Direct 2018; 13:4. [PMID: 29499764 PMCID: PMC5834895 DOI: 10.1186/s13062-018-0206-9] [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] [Received: 10/31/2017] [Accepted: 02/26/2018] [Indexed: 11/10/2022] Open
Abstract
Background Natural selection is possible only because all species produce more offsprings than what is needed to maintain the population. Still, the lifetime number of offspring varies widely across species. One may expect natural selection to be stronger in high-fecundity species. Alternatively, natural selection could be stronger in species where a female invests more into an individual offspring. This issue needed to be addressed empirically. Results We analyzed the prevalence of loss-of-function alleles in 35 metazoan species and have found that the strength of negative selection does not correlate with lifetime fecundity or other life-history traits. Conclusions Higher random mortality in high-fecundity species may negate the effect of increased opportunity for selection. Perhaps, invariance of the strength of negative selection across a wide variety of species emerges because natural selection optimized the life history in each of them, leading to the strongest possible competition. Reviewers This article was reviewed by Nicolas Galtier and I. King Jordan. Electronic supplementary material The online version of this article (10.1186/s13062-018-0206-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Aleksandra V Bezmenova
- Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Moscow, 143026, Russia. .,Laboratory of Evolutionary Genomics, A.N. Belozersky Institute of Physico-Chemical Biology of Lomonosov Moscow State Universit, Moscow, 119992, Russia.
| | - Georgii A Bazykin
- Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Moscow, 143026, Russia.,Sector for Molecular Evolution, Kharkevich Institute of Information Transmission Problems of the Russian Academy of Sciences, Moscow, 127051, Russia
| | - Alexey S Kondrashov
- Laboratory of Evolutionary Genomics, A.N. Belozersky Institute of Physico-Chemical Biology of Lomonosov Moscow State Universit, Moscow, 119992, Russia.,Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, 48109, USA
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30
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Chen J, Ni P, Li X, Han J, Jakovlić I, Zhang C, Zhao S. Population size may shape the accumulation of functional mutations following domestication. BMC Evol Biol 2018; 18:4. [PMID: 29351740 PMCID: PMC5775542 DOI: 10.1186/s12862-018-1120-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 01/09/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Population genetics theory predicts an important role of differences in the effective population size (N e ) among species on shaping the accumulation of functional mutations by regulating the selection efficiency. However, this correlation has never been tested in domesticated animals. RESULTS Here, we synthesized 62 whole genome data in eight domesticated species (cat, dog, pig, goat, sheep, chicken, cattle and horse) and compared domesticates with their wild (or ancient) relatives. Genes with significantly different selection pressures (revealed by nonsynonymous/synonymous substitution rate ratios, Ka/Ks or ω) between domesticated (Dω) and wild animals (Wω) were determined by likelihood-ratio tests. Species-level effective population sizes (N e ) were evaluated by the pairwise sequentially Markovian coalescent (PSMC) model, and Dω/Wω were calculated for each species to evaluate the changes in accumulation of functional mutations after domestication relative to pre-domestication period. Correlation analysis revealed that the most recent (~ 10.000 years ago) N e (s) are positively correlated with Dω/Wω. This result is consistent with the corollary of the nearly neutral theory, that higher N e could boost the efficiency of positive selection, which might facilitate the overall accumulation of functional mutations. In addition, we also evaluated the accumulation of radical and conservative mutations during the domestication transition as: Dradical/Wradical and Dconservative/Wconservative, respectively. Surprisingly, only Dradical/Wradical ratio exhibited a positive correlation with N e (p < 0.05), suggesting that domestication process might magnify the accumulation of radical mutations in species with larger N e . CONCLUSIONS Our results confirm the classical population genetics theory prediction and highlight the important role of species' N e in shaping the patterns of accumulation of functional mutations, especially radical mutations, in domesticated animals. The results aid our understanding of the mechanisms underlying the accumulation of functional mutations after domestication, which is critical for understanding the phenotypic diversification associated with this process.
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Affiliation(s)
- Jianhai Chen
- Key Lab of Agricultural Animal Genetics and Breeding, Ministry of Education, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
- The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
| | - Pan Ni
- Key Lab of Agricultural Animal Genetics and Breeding, Ministry of Education, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
- The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
| | - Xinyun Li
- Key Lab of Agricultural Animal Genetics and Breeding, Ministry of Education, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
- The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
| | - Jianlin Han
- International Livestock Research Institute (ILRI), Nairobi, 00100 Kenya
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193 People’s Republic of China
| | - Ivan Jakovlić
- Bio-Transduction Lab, Wuhan Institute of Biotechnology, Wuhan, 430075 People’s Republic of China
| | - Chengjun Zhang
- Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201 People’s Republic of China
| | - Shuhong Zhao
- Key Lab of Agricultural Animal Genetics and Breeding, Ministry of Education, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
- The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
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31
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Popadin K, Peischl S, Garieri M, Sailani MR, Letourneau A, Santoni F, Lukowski SW, Bazykin GA, Nikolaev S, Meyer D, Excoffier L, Reymond A, Antonarakis SE. Slightly deleterious genomic variants and transcriptome perturbations in Down syndrome embryonic selection. Genome Res 2017; 28:1-10. [PMID: 29237728 PMCID: PMC5749173 DOI: 10.1101/gr.228411.117] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2017] [Accepted: 11/20/2017] [Indexed: 12/13/2022]
Abstract
The majority of aneuploid fetuses are spontaneously miscarried. Nevertheless, some aneuploid individuals survive despite the strong genetic insult. Here, we investigate if the survival probability of aneuploid fetuses is affected by the genome-wide burden of slightly deleterious variants. We analyzed two cohorts of live-born Down syndrome individuals (388 genotyped samples and 16 fibroblast transcriptomes) and observed a deficit of slightly deleterious variants on Chromosome 21 and decreased transcriptome-wide variation in the expression level of highly constrained genes. We interpret these results as signatures of embryonic selection, and propose a genetic handicap model whereby an individual bearing an extremely severe deleterious variant (such as aneuploidy) could escape embryonic lethality if the genome-wide burden of slightly deleterious variants is sufficiently low. This approach can be used to study the composition and effect of the numerous slightly deleterious variants in humans and model organisms.
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Affiliation(s)
- Konstantin Popadin
- Department of Genetic Medicine and Development, University of Geneva Medical School, 1211 Geneva, Switzerland.,Center for Integrative Genomics, University of Lausanne, CH-1015 Lausanne, Switzerland.,Immanuel Kant Baltic Federal University, Kaliningrad, 236041, Russia.,Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Stephan Peischl
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.,Interfaculty Bioinformatics Unit, University of Bern, 3012 Bern, Switzerland
| | - Marco Garieri
- Department of Genetic Medicine and Development, University of Geneva Medical School, 1211 Geneva, Switzerland
| | - M Reza Sailani
- Stanford School of Medicine, Stanford University, Stanford, California 94305, USA
| | - Audrey Letourneau
- Department of Genetic Medicine and Development, University of Geneva Medical School, 1211 Geneva, Switzerland
| | - Federico Santoni
- Department of Genetic Medicine and Development, University of Geneva Medical School, 1211 Geneva, Switzerland
| | - Samuel W Lukowski
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia
| | - Georgii A Bazykin
- Institute for Information Transmission Problems (Kharkevich Institute) of the Russian Academy of Sciences, Moscow, 127051, Russia.,Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Skolkovo, 143026, Russia
| | - Sergey Nikolaev
- Department of Genetic Medicine and Development, University of Geneva Medical School, 1211 Geneva, Switzerland
| | - Diogo Meyer
- Department of Genetics and Evolutionary Biology, University of Sao Paulo, 05508-090, Sao Paulo, Brazil
| | - Laurent Excoffier
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.,Institute for Ecology and Evolution, University of Bern, CH-3012 Bern, Switzerland
| | - Alexandre Reymond
- Center for Integrative Genomics, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Stylianos E Antonarakis
- Department of Genetic Medicine and Development, University of Geneva Medical School, 1211 Geneva, Switzerland
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32
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Botero-Castro F, Figuet E, Tilak MK, Nabholz B, Galtier N. Avian Genomes Revisited: Hidden Genes Uncovered and the Rates versus Traits Paradox in Birds. Mol Biol Evol 2017; 34:3123-3131. [DOI: 10.1093/molbev/msx236] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
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33
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Ren Y, Zhu Y, Wang Q, Xiang H, Wang B. Transcriptome of Pterospermum kingtungense provides implications on the mechanism underlying its rapid vegetative growth and limestone adaption. Sci Rep 2017; 7:3198. [PMID: 28600559 PMCID: PMC5466617 DOI: 10.1038/s41598-017-03433-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Accepted: 05/11/2017] [Indexed: 01/07/2023] Open
Abstract
Pterospermum kingtungense C.Y.Wu ex Hsue is a typical tree species living in the relatively adverse limestone habitat. Due to its excellent wood quality and big size, it is an important timber resource which caused its endangered. We firstly provide the data resources by reporting an annotated transcriptome assembly. 203 million unique Illumina RNA-seq reads were produced with totally 50,333 transcripts, among which 48,778 transcripts were annotated. By a global comparison of homology between P. kingtungense and cacao, we identified 9,507 single copy orthologues and 990 P. kingtungense specific genes. GO enrichment analyses indicate that P. kingtungense specific genes are enriched in defense response, implying potential adaptation to limestone environment. As to cell compartment, the genes are enriched in thylakoid component. Consistently, KEGG enrichment indicates that genes are enriched in photosynthesis. In addition, we identified two genes under positive selection in P. kingtungense species. These results suggest that P. kingtungense have strong photosynthetic capacity, which related to vegetation growth. Our work provides the genomic resources of a limestone specific tree with economic importance to local society and suggests possible mechanism on its characteristics on the limestone adaption and excellent wood properties, which will be important for its conservation and sustainable utilization.
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Affiliation(s)
- Yandong Ren
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China. 32 East Jiaochang Road, Kunming, Yunnan Province, 650223, China
- Yunnan Forestry Technological College. No.1 JinDian, Kunming, Yunnan Province, 650224, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yanan Zhu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China. 32 East Jiaochang Road, Kunming, Yunnan Province, 650223, China
- Kunming University of Science and Technology, No.727, South Jingming Road, Chenggong District, Kunming, Yunnan Province, 650500, China
| | - Qi Wang
- Yunnan Forestry Technological College. No.1 JinDian, Kunming, Yunnan Province, 650224, China
| | - Hui Xiang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China. 32 East Jiaochang Road, Kunming, Yunnan Province, 650223, China.
- Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology & School of Life Sciences, South China Normal University, Guangzhou, 510631, China.
| | - Boyi Wang
- Yunnan Forestry Technological College. No.1 JinDian, Kunming, Yunnan Province, 650224, China.
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34
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Vasemägi A, Sulku J, Bruneaux M, Thalmann O, Mäkinen H, Ozerov M. Prediction of harmful variants on mitochondrial genes: Test of habitat-dependent and demographic effects in a euryhaline fish. Ecol Evol 2017; 7:3826-3835. [PMID: 28616179 PMCID: PMC5468147 DOI: 10.1002/ece3.2989] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Revised: 03/10/2017] [Accepted: 03/21/2017] [Indexed: 11/27/2022] Open
Abstract
Both effective population size and life history may influence the efficacy of purifying selection, but it remains unclear if the environment affects the accumulation of weakly deleterious nonsynonymous polymorphisms. We hypothesize that the reduced energetic cost of osmoregulation in brackish water habitat may cause relaxation of selective constraints at mitochondrial oxidative phosphorylation (OXPHOS) genes. To test this hypothesis, we analyzed 57 complete mitochondrial genomes of Pungitius pungitius collected from brackish and freshwater habitats. Based on inter‐ and intraspecific comparisons, we estimated that 84% and 68% of the nonsynonymous polymorphisms in the freshwater and brackish water populations, respectively, are weakly or moderately deleterious. Using in silico prediction tools (MutPred, SNAP2), we subsequently identified nonsynonymous polymorphisms with potentially harmful effect. Both prediction methods indicated that the functional effects of the fixed nonsynonymous substitutions between nine‐ and three‐spined stickleback were weaker than for polymorphisms within species, indicating that harmful nonsynonymous polymorphisms within populations rarely become fixed between species. No significant differences in mean estimated functional effects were identified between freshwater and brackish water nine‐spined stickleback to support the hypothesis that reduced osmoregulatory energy demand in the brackish water environment reduces the strength of purifying selection at OXPHOS genes. Instead, elevated frequency of nonsynonymous polymorphisms in the freshwater environment (Pn/Ps = 0.549 vs. 0.283; Fisher's exact test p = .032) suggested that purifying selection is less efficient in small freshwater populations. This study shows the utility of in silico functional prediction tools in population genetic and evolutionary research in a nonmammalian vertebrate and demonstrates that mitochondrial energy production genes represent a promising system to characterize the demographic, life history and potential habitat‐dependent effects of segregating amino acid variants.
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Affiliation(s)
- Anti Vasemägi
- Department of Biology University of Turku Turku Finland.,Department of Aquaculture Estonian University of Life Sciences Tartu Estonia
| | - Janne Sulku
- Department of Biology University of Turku Turku Finland
| | - Matthieu Bruneaux
- Department of Biology University of Turku Turku Finland.,Department of Biological and Environmental Science Centre of Excellence in Biological Interactions University of Jyväskylä Jyväskylä Finland
| | - Olaf Thalmann
- Department of Biology University of Turku Turku Finland.,Department of Pediatric Gastroenterology and Metabolic Diseases Poznan University of Medical Sciences Poznan Poland
| | - Hannu Mäkinen
- Department of Biology University of Turku Turku Finland
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35
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Chen J, Glémin S, Lascoux M. Genetic Diversity and the Efficacy of Purifying Selection across Plant and Animal Species. Mol Biol Evol 2017; 34:1417-1428. [DOI: 10.1093/molbev/msx088] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
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36
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Hua X, Bromham L. Darwinism for the Genomic Age: Connecting Mutation to Diversification. Front Genet 2017; 8:12. [PMID: 28224003 PMCID: PMC5293951 DOI: 10.3389/fgene.2017.00012] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 01/19/2017] [Indexed: 12/30/2022] Open
Abstract
A growing body of evidence suggests that rates of diversification of biological lineages are correlated with differences in genome-wide mutation rate. Given that most research into differential patterns of diversification rate have focused on species traits or ecological parameters, a connection to the biochemical processes of genome change is an unexpected observation. While the empirical evidence for a significant association between mutation rate and diversification rate is mounting, there has been less effort in explaining the factors that mediate this connection between genetic change and species richness. Here we draw together empirical studies and theoretical concepts that may help to build links in the explanatory chain that connects mutation to diversification. First we consider the way that mutation rates vary between species. We then explore how differences in mutation rates have flow-through effects to the rate at which populations acquire substitutions, which in turn influences the speed at which populations become reproductively isolated from each other due to the acquisition of genomic incompatibilities. Since diversification rate is commonly measured from phylogenetic analyses, we propose a conceptual approach for relating events of reproductive isolation to bifurcations on molecular phylogenies. As we examine each of these relationships, we consider theoretical models that might shine a light on the observed association between rate of molecular evolution and diversification rate, and critically evaluate the empirical evidence for these links, focusing on phylogenetic comparative studies. Finally, we ask whether we are getting closer to a real understanding of the way that the processes of molecular evolution connect to the observable patterns of diversification.
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Affiliation(s)
- Xia Hua
- Centre for Macroevolution and Macroecology, Research School of Biology, Australian National University, Canberra ACT, Australia
| | - Lindell Bromham
- Centre for Macroevolution and Macroecology, Research School of Biology, Australian National University, Canberra ACT, Australia
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37
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DNA sequence diversity and the efficiency of natural selection in animal mitochondrial DNA. Heredity (Edinb) 2016; 118:88-95. [PMID: 27827387 DOI: 10.1038/hdy.2016.108] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Revised: 09/07/2016] [Accepted: 09/19/2016] [Indexed: 12/21/2022] Open
Abstract
Selection is expected to be more efficient in species that are more diverse because both the efficiency of natural selection and DNA sequence diversity are expected to depend upon the effective population size. We explore this relationship across a data set of 751 mammal species for which we have mitochondrial polymorphism data. We introduce a method by which we can examine the relationship between our measure of the efficiency of natural selection, the nonsynonymous relative to the synonymous nucleotide site diversity (πN/πS), and synonymous nucleotide diversity (πS), avoiding the statistical non-independence between the two quantities. We show that these two variables are strongly negatively and linearly correlated on a log scale. The slope is such that as πS doubles, πN/πS is reduced by 34%. We show that the slope of this relationship differs between the two phylogenetic groups for which we have the most data, rodents and bats, and that it also differs between species with high and low body mass, and between those with high and low mass-specific metabolic rate.
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Mohlhenrich ER, Mueller RL. Genetic drift and mutational hazard in the evolution of salamander genomic gigantism. Evolution 2016; 70:2865-2878. [DOI: 10.1111/evo.13084] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2015] [Revised: 09/27/2016] [Accepted: 09/27/2016] [Indexed: 12/25/2022]
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Lavrov DV, Pett W. Animal Mitochondrial DNA as We Do Not Know It: mt-Genome Organization and Evolution in Nonbilaterian Lineages. Genome Biol Evol 2016; 8:2896-2913. [PMID: 27557826 PMCID: PMC5633667 DOI: 10.1093/gbe/evw195] [Citation(s) in RCA: 130] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/06/2016] [Indexed: 12/11/2022] Open
Abstract
Animal mitochondrial DNA (mtDNA) is commonly described as a small, circular molecule that is conserved in size, gene content, and organization. Data collected in the last decade have challenged this view by revealing considerable diversity in animal mitochondrial genome organization. Much of this diversity has been found in nonbilaterian animals (phyla Cnidaria, Ctenophora, Placozoa, and Porifera), which, from a phylogenetic perspective, form the main branches of the animal tree along with Bilateria. Within these groups, mt-genomes are characterized by varying numbers of both linear and circular chromosomes, extra genes (e.g. atp9, polB, tatC), large variation in the number of encoded mitochondrial transfer RNAs (tRNAs) (0-25), at least seven different genetic codes, presence/absence of introns, tRNA and mRNA editing, fragmented ribosomal RNA genes, translational frameshifting, highly variable substitution rates, and a large range of genome sizes. This newly discovered diversity allows a better understanding of the evolutionary plasticity and conservation of animal mtDNA and provides insights into the molecular and evolutionary mechanisms shaping mitochondrial genomes.
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Affiliation(s)
- Dennis V Lavrov
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University
| | - Walker Pett
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University Laboratoire de Biométrie et Biologie Évolutive, Université Lyon 1, Villeurbanne, France
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Macrosystematics of Didymodon sensu lato (Pottiaceae, Bryophyta) using an analytic key and information theory. UKRAINIAN BOTANICAL JOURNAL 2016. [DOI: 10.15407/ukrbotj73.04.319] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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41
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Figuet E, Nabholz B, Bonneau M, Mas Carrio E, Nadachowska-Brzyska K, Ellegren H, Galtier N. Life History Traits, Protein Evolution, and the Nearly Neutral Theory in Amniotes. Mol Biol Evol 2016; 33:1517-27. [DOI: 10.1093/molbev/msw033] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
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42
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James JE, Piganeau G, Eyre‐Walker A. The rate of adaptive evolution in animal mitochondria. Mol Ecol 2016; 25:67-78. [PMID: 26578312 PMCID: PMC4737298 DOI: 10.1111/mec.13475] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Accepted: 11/10/2015] [Indexed: 11/28/2022]
Abstract
We have investigated whether there is adaptive evolution in mitochondrial DNA, using an extensive data set containing over 500 animal species from a wide range of taxonomic groups. We apply a variety of McDonald-Kreitman style methods to the data. We find that the evolution of mitochondrial DNA is dominated by slightly deleterious mutations, a finding which is supported by a number of previous studies. However, when we control for the presence of deleterious mutations using a new method, we find that mitochondria undergo a significant amount of adaptive evolution, with an estimated 26% (95% confidence intervals: 5.7-45%) of nonsynonymous substitutions fixed by adaptive evolution. We further find some weak evidence that the rate of adaptive evolution is correlated to synonymous diversity. We interpret this as evidence that at least some adaptive evolution is limited by the supply of mutations.
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Affiliation(s)
| | - Gwenael Piganeau
- UPMC Univ Paris 06UMR 7232Observatoire OceanologiqueAvenue de FontauléBP 44, 66651 Banyuls‐sur‐MerFrance
- CNRSUMR 7232Observatoire OceanologiqueAvenue de FontauléBP 44, 66651 Banyuls‐sur‐MerFrance
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43
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Weber CC, Nabholz B, Romiguier J, Ellegren H. Kr/Kc but not dN/dS correlates positively with body mass in birds, raising implications for inferring lineage-specific selection. Genome Biol 2015; 15:542. [PMID: 25607475 PMCID: PMC4264323 DOI: 10.1186/s13059-014-0542-8] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Accepted: 11/13/2014] [Indexed: 02/02/2023] Open
Abstract
Background The ratio of the rates of non-synonymous and synonymous substitution (dN/dS) is commonly used to estimate selection in coding sequences. It is often suggested that, all else being equal, dN/dS should be lower in populations with large effective size (Ne) due to increased efficacy of purifying selection. As Ne is difficult to measure directly, life history traits such as body mass, which is typically negatively associated with population size, have commonly been used as proxies in empirical tests of this hypothesis. However, evidence of whether the expected positive correlation between body mass and dN/dS is consistently observed is conflicting. Results Employing whole genome sequence data from 48 avian species, we assess the relationship between rates of molecular evolution and life history in birds. We find a negative correlation between dN/dS and body mass, contrary to nearly neutral expectation. This raises the question whether the correlation might be a method artefact. We therefore in turn consider non-stationary base composition, divergence time and saturation as possible explanations, but find no clear patterns. However, in striking contrast to dN/dS, the ratio of radical to conservative amino acid substitutions (Kr/Kc) correlates positively with body mass. Conclusions Our results in principle accord with the notion that non-synonymous substitutions causing radical amino acid changes are more efficiently removed by selection in large populations, consistent with nearly neutral theory. These findings have implications for the use of dN/dS and suggest that caution is warranted when drawing conclusions about lineage-specific modes of protein evolution using this metric. Electronic supplementary material The online version of this article (doi:10.1186/s13059-014-0542-8) contains supplementary material, which is available to authorized users.
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Polishchuk LV, Popadin KY, Baranova MA, Kondrashov AS. A genetic component of extinction risk in mammals. OIKOS 2015. [DOI: 10.1111/oik.01734] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Leonard V. Polishchuk
- Dept of General Ecology; Biological Faculty, M.V. Lomonosov Moscow State Univ.; RU-119992 Moscow Russia
| | - Konstantin Y. Popadin
- Dept of Genetic Medicine and Development; Univ. of Geneva Medical School; 1 rue Michel-Servet CH-1211 Geneva Switzerland
- Inst. of Genetics and Genomics in Geneva (iGE3); CH-1211 Geneva Switzerland
- Inst. for Information Transmission Problems (Kharkevich Inst.), Russian Academy of Sciences; RU-127994 Moscow Russia
| | - Maria A. Baranova
- Faculty of Bioengineering and Bioinformatics, M.V. Lomonosov Moscow State Univ.; RU-119992 Moscow Russia
| | - Aleksey S. Kondrashov
- Faculty of Bioengineering and Bioinformatics, M.V. Lomonosov Moscow State Univ.; RU-119992 Moscow Russia
- Life Sciences Inst. and Dept of Ecology and Evolutionary Biology; Univ. of Michigan; Ann Arbor MI 48109 USA
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Strohm JHT, Gwiazdowski RA, Hanner R. Fast fish face fewer mitochondrial mutations: Patterns of dN/dS across fish mitogenomes. Gene 2015; 572:27-34. [PMID: 26149654 DOI: 10.1016/j.gene.2015.06.074] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Revised: 06/17/2015] [Accepted: 06/27/2015] [Indexed: 01/26/2023]
Abstract
Mitochondrial DNA is routinely used to answer a variety of biological questions; and there is growing evidence suggesting that its accumulation of mutations is influenced by life history, effective population size and cellular energy requirements. This study examines the influence of phylogenetic patterns of metabolic activity on the evolution of mitochondrial DNA in fishes, given energy requirements associated with high performance versus sedentary life histories. It was determined that all 13 protein coding genes of the mitogenome experience a relaxation of purifying selection in sedentary fishes. This phenomenon was not detected in nuclear housekeeping genes, suggesting that it can be explained by the energy requirements of these groups, and possibly their effective population sizes. This study also examined the subunit binding sites of two subunits of cytochrome c oxidase (COXI and COXIII), and did not detect any differences in selection between these groups of fishes. These cytochrome c oxidase subunits interact with subunits that are encoded by the nuclear genome and it has been suggested that a unique form of coevolution occurs between these genomes in order to maintain function, and may have implications for speciation. Although this was not a main focus of this study, our preliminary results suggest that substitutions in subunit binding site regions are rare. The results from this study add to the growing literature on the complex relationship between mitochondrial DNA and the evolution of life histories across the tree of life.
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Affiliation(s)
- Jeff H T Strohm
- Centre for Biodiversity Genomics, Department of Integrative Biology, University of Guelph, Ontario, Canada.
| | - Rodger A Gwiazdowski
- Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Robert Hanner
- Centre for Biodiversity Genomics, Department of Integrative Biology, University of Guelph, Ontario, Canada
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46
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Pellissier L. Stability and the competition-dispersal trade-off as drivers of speciation and biodiversity gradients. Front Ecol Evol 2015. [DOI: 10.3389/fevo.2015.00052] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
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Castellana S, Rónai J, Mazza T. MitImpact: an exhaustive collection of pre-computed pathogenicity predictions of human mitochondrial non-synonymous variants. Hum Mutat 2014; 36:E2413-22. [PMID: 25516408 DOI: 10.1002/humu.22720] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Mitochondrial DNA carries a tiny, but fundamental portion of the eukaryotic genetic code. As its nuclear counterpart, it is susceptible to point mutations. Their level of pathogenicity has been assessed for the newly discovered mutations only, leaving some degree of uncertainty on the potential impact of the unknown mutations. Here we present Mitochondrial mutation Impact (MitImpact), a queryable lightweight web interface to a reasoned collection of structurally and evolutionary annotated pathogenicity predictions, obtained by assembling pre-computed with on-the-fly-computed sets of pathogenicity estimations, for all the possible mitochondrial missense variants. It presents itself as a resource for fast and reliable evaluation of gene-specific susceptibility of unknown and verified amino acid changes. MitImpact is freely available at http://bioinformatics.css-mendel.it/ (tools section). ©2014 Wiley Periodicals, Inc.
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Affiliation(s)
- Stefano Castellana
- IRCCS Casa Sollievo della Sofferenza, Istituto Mendel, Bioinformatics Unit. Viale Regina Margherita, 261. 00198, Roma, Italy
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48
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Usmanova DR, Ferretti L, Povolotskaya IS, Vlasov PK, Kondrashov FA. A model of substitution trajectories in sequence space and long-term protein evolution. Mol Biol Evol 2014; 32:542-54. [PMID: 25415964 DOI: 10.1093/molbev/msu318] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The nature of factors governing the tempo and mode of protein evolution is a fundamental issue in evolutionary biology. Specifically, whether or not interactions between different sites, or epistasis, are important in directing the course of evolution became one of the central questions. Several recent reports have scrutinized patterns of long-term protein evolution claiming them to be compatible only with an epistatic fitness landscape. However, these claims have not yet been substantiated with a formal model of protein evolution. Here, we formulate a simple covarion-like model of protein evolution focusing on the rate at which the fitness impact of amino acids at a site changes with time. We then apply the model to the data on convergent and divergent protein evolution to test whether or not the incorporation of epistatic interactions is necessary to explain the data. We find that convergent evolution cannot be explained without the incorporation of epistasis and the rate at which an amino acid state switches from being acceptable at a site to being deleterious is faster than the rate of amino acid substitution. Specifically, for proteins that have persisted in modern prokaryotic organisms since the last universal common ancestor for one amino acid substitution approximately ten amino acid states switch from being accessible to being deleterious, or vice versa. Thus, molecular evolution can only be perceived in the context of rapid turnover of which amino acids are available for evolution.
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Affiliation(s)
- Dinara R Usmanova
- Moscow Institute of Physics and Technology, Institutskiy Pereulok 9, g.Dolgoprudny, Russia Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Barcelona, Spain Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Luca Ferretti
- Systématique, Adaptation et Evolution (UMR 7138), UPMC University Paris 06, CNRS, MNHN, IRD, Paris, France CIRB, Collège de France, Paris, France
| | - Inna S Povolotskaya
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Barcelona, Spain Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Peter K Vlasov
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Barcelona, Spain Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Fyodor A Kondrashov
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Barcelona, Spain Universitat Pompeu Fabra (UPF), Barcelona, Spain Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
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Shirai K, Inomata N, Mizoiri S, Aibara M, Terai Y, Okada N, Tachida H. High prevalence of non-synonymous substitutions in mtDNA of cichlid fishes from Lake Victoria. Gene 2014; 552:239-45. [PMID: 25241383 DOI: 10.1016/j.gene.2014.09.039] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2014] [Revised: 08/28/2014] [Accepted: 09/17/2014] [Indexed: 10/24/2022]
Abstract
When a population size is reduced, genetic drift may fix slightly deleterious mutations, and an increase in nonsynonymous substitution is expected. It has been suggested that past aridity has seriously affected and decreased the populations of cichlid fishes in Lake Victoria, while geographical studies have shown that the water levels in Lake Tanganyika and Lake Malawi have remained fairly constant. The comparably stable environments in the latter two lakes might have kept the populations of cichlid fishes large enough to remove slightly deleterious mutations. The difference in the stability of cichlid fish population sizes between Lake Victoria and the Lakes Tanganyika and Malawi is expected to have caused differences in the nonsynonymous/synonymous ratio, ω (=dN/dS), of the evolutionary rate. Here, we estimated ω and compared it between the cichlids of the three lakes for 13 mitochondrial protein-coding genes using maximum likelihood methods. We found that the lineages of the cichlids in Lake Victoria had a significantly higher ω for several mitochondrial loci. Moreover, positive selection was indicated for several codons in the mtDNA of the Lake Victoria cichlid lineage. Our results indicate that both adaptive and slightly deleterious molecular evolution has taken place in the Lake Victoria cichlids' mtDNA genes, whose nonsynonymous sites are generally conserved.
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Affiliation(s)
- Kazumasa Shirai
- Graduate School of Systems Life Sciences, Kyushu University, Fukuoka, Japan
| | - Nobuyuki Inomata
- International College of Arts and Sciences, Fukuoka Women's University, Fukuoka, Japan
| | | | - Mitsuto Aibara
- Foundation for Advancement of International Science, Tsukuba, Japan
| | - Yohey Terai
- The Graduate University for Advanced Studies, Kanagawa, Japan
| | - Norihiro Okada
- Foundation for Advancement of International Science, Tsukuba, Japan; Department of Life Sciences, National Cheng Kung University, Tainan 701, Taiwan
| | - Hidenori Tachida
- Department of Biology, Faculty of Sciences, Kyushu University, Fukuoka, Japan.
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50
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Merker S, Thomas S, Völker E, Perwitasari-Farajallah D, Feldmeyer B, Streit B, Pfenninger M. Control region length dynamics potentially drives amino acid evolution in tarsier mitochondrial genomes. J Mol Evol 2014; 79:40-51. [PMID: 25008552 DOI: 10.1007/s00239-014-9631-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Accepted: 06/19/2014] [Indexed: 11/25/2022]
Abstract
Patterns and processes of molecular evolution critically influence inferences in phylogeny and phylogeography. Within primates, a shift in evolutionary rates has been identified as the rationale for contrasting findings from mitochondrial and nuclear DNA studies as to the position of Tarsius. While the latter now seems settled, we sequenced complete mitochondrial genomes of three Sulawesi tarsiers (Tarsius dentatus, T. lariang, and T. wallacei) and analyzed substitution rates among tarsiers and other primates to infer driving processes of molecular evolution. We found substantial length polymorphism of the D-loop within tarsier individuals, but little variation of predominant lengths among them, regardless of species. Length variation was due to repetitive elements in the CSB domain-minisatellite motifs of 35 bp length and microsatellite motifs of 6 bp length. Amino acid evolutionary rates were second highest among major primate taxa relative to nucleotide substitution rates. We observed many radical possibly function-altering amino acid changes that were rarely driven by positive selection and thus potentially slightly deleterious or neutral. We hypothesize that the observed pattern of an increased amino acid evolutionary rate in tarsier mitochondrial genomes may be caused by hitchhiking of slightly deleterious mutations with favored D-loop length variants selected for maximizing replication success within the cell or the mitochondrion.
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Affiliation(s)
- Stefan Merker
- Department of Zoology, State Museum of Natural History Stuttgart, Rosenstein 1, 70191, Stuttgart, Germany,
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