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Prabh N, Tautz D. Frequent lineage-specific substitution rate changes support an episodic model for protein evolution. G3-GENES GENOMES GENETICS 2021; 11:6372692. [PMID: 34542594 PMCID: PMC8664490 DOI: 10.1093/g3journal/jkab333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 09/13/2021] [Indexed: 12/04/2022]
Abstract
Since the inception of the molecular clock model for sequence evolution, the investigation of protein divergence has revolved around the question of a more or less constant change of amino acid sequences, with specific overall rates for each family. Although anomalies in clock-like divergence are well known, the assumption of a constant decay rate for a given protein family is usually taken as the null model for protein evolution. However, systematic tests of this null model at a genome-wide scale have lagged behind, despite the databases’ enormous growth. We focus here on divergence rate comparisons between very closely related lineages since this allows clear orthology assignments by synteny and reliable alignments, which are crucial for determining substitution rate changes. We generated a high-confidence dataset of syntenic orthologs from four ape species, including humans. We find that despite the appearance of an overall clock-like substitution pattern, several hundred protein families show lineage-specific acceleration and deceleration in divergence rates, or combinations of both in different lineages. Hence, our analysis uncovers a rather dynamic history of substitution rate changes, even between these closely related lineages, implying that one should expect that a large fraction of proteins will have had a history of episodic rate changes in deeper phylogenies. Furthermore, each of the lineages has a separate set of particularly fast diverging proteins. The genes with the highest percentage of branch-specific substitutions are ADCYAP1 in the human lineage (9.7%), CALU in chimpanzees (7.1%), SLC39A14 in the internal branch leading to humans and chimpanzees (4.1%), RNF128 in gorillas (9%), and S100Z in gibbons (15.2%). The mutational pattern in ADCYAP1 suggests a biased mutation process, possibly through asymmetric gene conversion effects. We conclude that a null model of constant change can be problematic for predicting the evolutionary trajectories of individual proteins.
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Affiliation(s)
- Neel Prabh
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, August-Thienemann-Str. 2, 24306 Plön, Germany
| | - Diethard Tautz
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, August-Thienemann-Str. 2, 24306 Plön, Germany
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Russell SL, Pepper-Tunick E, Svedberg J, Byrne A, Ruelas Castillo J, Vollmers C, Beinart RA, Corbett-Detig R. Horizontal transmission and recombination maintain forever young bacterial symbiont genomes. PLoS Genet 2020; 16:e1008935. [PMID: 32841233 PMCID: PMC7473567 DOI: 10.1371/journal.pgen.1008935] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Revised: 09/04/2020] [Accepted: 06/16/2020] [Indexed: 12/30/2022] Open
Abstract
Bacterial symbionts bring a wealth of functions to the associations they participate in, but by doing so, they endanger the genes and genomes underlying these abilities. When bacterial symbionts become obligately associated with their hosts, their genomes are thought to decay towards an organelle-like fate due to decreased homologous recombination and inefficient selection. However, numerous associations exist that counter these expectations, especially in marine environments, possibly due to ongoing horizontal gene flow. Despite extensive theoretical treatment, no empirical study thus far has connected these underlying population genetic processes with long-term evolutionary outcomes. By sampling marine chemosynthetic bacterial-bivalve endosymbioses that range from primarily vertical to strictly horizontal transmission, we tested this canonical theory. We found that transmission mode strongly predicts homologous recombination rates, and that exceedingly low recombination rates are associated with moderate genome degradation in the marine symbionts with nearly strict vertical transmission. Nonetheless, even the most degraded marine endosymbiont genomes are occasionally horizontally transmitted and are much larger than their terrestrial insect symbiont counterparts. Therefore, horizontal transmission and recombination enable efficient natural selection to maintain intermediate symbiont genome sizes and substantial functional genetic variation.
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Affiliation(s)
- Shelbi L. Russell
- Department of Molecular Cellular and Developmental Biology. University of California Santa Cruz, Santa Cruz, California, United States of America
- Department of Biomolecular Engineering. University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Evan Pepper-Tunick
- Department of Biomolecular Engineering. University of California Santa Cruz, Santa Cruz, California, United States of America
- Genomics Institute, University of California, Santa Cruz, California, United States of America
| | - Jesper Svedberg
- Department of Biomolecular Engineering. University of California Santa Cruz, Santa Cruz, California, United States of America
- Genomics Institute, University of California, Santa Cruz, California, United States of America
| | - Ashley Byrne
- Department of Molecular Cellular and Developmental Biology. University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Jennie Ruelas Castillo
- Department of Molecular Cellular and Developmental Biology. University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Christopher Vollmers
- Department of Biomolecular Engineering. University of California Santa Cruz, Santa Cruz, California, United States of America
- Genomics Institute, University of California, Santa Cruz, California, United States of America
| | - Roxanne A. Beinart
- Graduate School of Oceanography. University of Rhode Island, Narragansett, Rhode Island, United States of America
| | - Russell Corbett-Detig
- Department of Biomolecular Engineering. University of California Santa Cruz, Santa Cruz, California, United States of America
- Genomics Institute, University of California, Santa Cruz, California, United States of America
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Vos M, te Beek TAH, van Driel MA, Huynen MA, Eyre-Walker A, van Passel MWJ. ODoSE: a webserver for genome-wide calculation of adaptive divergence in prokaryotes. PLoS One 2013; 8:e62447. [PMID: 23671597 PMCID: PMC3646019 DOI: 10.1371/journal.pone.0062447] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Accepted: 03/21/2013] [Indexed: 11/30/2022] Open
Abstract
Quantifying patterns of adaptive divergence between taxa is a major goal in the comparative and evolutionary study of prokaryote genomes. When applied appropriately, the McDonald-Kreitman (MK) test is a powerful test of selection based on the relative frequency of non-synonymous and synonymous substitutions between species compared to non-synonymous and synonymous polymorphisms within species. The webserver ODoSE (Ortholog Direction of Selection Engine) allows the calculation of a novel extension of the MK test, the Direction of Selection (DoS) statistic, as well as the calculation of a weighted-average Neutrality Index (NI) statistic for the entire core genome, allowing for systematic analysis of the evolutionary forces shaping core genome divergence in prokaryotes. ODoSE is hosted in a Galaxy environment, which makes it easy to use and amenable to customization and is freely available at www.odose.nl.
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Affiliation(s)
- Michiel Vos
- European Centre for Environment and Human Health, The University of Exeter Medical School, University of Exeter, Truro, United Kingdom
- * E-mail: (MV); (MWJvP)
| | - Tim A. H. te Beek
- Netherlands Bioinformatics Centre, Nijmegen, The Netherlands
- Centre for Molecular and Biomolecular Informatics, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | | | - Martijn A. Huynen
- Centre for Molecular and Biomolecular Informatics, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Adam Eyre-Walker
- Centre for the Study of Evolution, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Mark W. J. van Passel
- Systems and Synthetic Biology, Wageningen University, Wageningen, The Netherlands
- * E-mail: (MV); (MWJvP)
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The Site-Wise Log-Likelihood Score is a Good Predictor of Genes under Positive Selection. J Mol Evol 2013; 76:280-94. [DOI: 10.1007/s00239-013-9557-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2012] [Accepted: 03/20/2013] [Indexed: 12/21/2022]
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Silby MW, Winstanley C, Godfrey SA, Levy SB, Jackson RW. Pseudomonasgenomes: diverse and adaptable. FEMS Microbiol Rev 2011; 35:652-80. [DOI: 10.1111/j.1574-6976.2011.00269.x] [Citation(s) in RCA: 578] [Impact Index Per Article: 44.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
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