51
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Molecular Clocks without Rocks: New Solutions for Old Problems. Trends Genet 2020; 36:845-856. [PMID: 32709458 DOI: 10.1016/j.tig.2020.06.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Revised: 06/02/2020] [Accepted: 06/11/2020] [Indexed: 02/07/2023]
Abstract
Molecular data have been used to date species divergences ever since they were described as documents of evolutionary history in the 1960s. Yet, an inadequate fossil record and discordance between gene trees and species trees are persistently problematic. We examine how, by accommodating gene tree discordance and by scaling branch lengths to absolute time using mutation rate and generation time, multispecies coalescent (MSC) methods can potentially overcome these challenges. We find that time estimates can differ - in some cases, substantially - depending on whether MSC methods or traditional phylogenetic methods that apply concatenation are used, and whether the tree is calibrated with pedigree-based mutation rates or with fossils. We discuss the advantages and shortcomings of both approaches and provide practical guidance for data analysis when using these methods.
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52
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Yu L, Boström C, Franzenburg S, Bayer T, Dagan T, Reusch TBH. Somatic genetic drift and multilevel selection in a clonal seagrass. Nat Ecol Evol 2020; 4:952-962. [PMID: 32393866 DOI: 10.1038/s41559-020-1196-4] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Accepted: 04/02/2020] [Indexed: 11/09/2022]
Abstract
All multicellular organisms are genetic mosaics owing to somatic mutations. The accumulation of somatic genetic variation in clonal species undergoing asexual (or clonal) reproduction may lead to phenotypic heterogeneity among autonomous modules (termed ramets). However, the abundance and dynamics of somatic genetic variation under clonal reproduction remain poorly understood. Here we show that branching events in a seagrass (Zostera marina) clone or genet lead to population bottlenecks of tissue that result in the evolution of genetically differentiated ramets in a process of somatic genetic drift. By studying inter-ramet somatic genetic variation, we uncovered thousands of single nucleotide polymorphisms that segregated among ramets. Ultra-deep resequencing of single ramets revealed that the strength of purifying selection on mosaic genetic variation was greater within than among ramets. Our study provides evidence for multiple levels of selection during the evolution of seagrass genets. Somatic genetic drift during clonal propagation leads to the emergence of genetically unique modules that constitute an elementary level of selection and individuality in long-lived clonal species.
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Affiliation(s)
- Lei Yu
- GEOMAR Helmholtz-Centre for Ocean Research Kiel, Marine Evolutionary Ecology, Kiel, Germany
| | | | - Sören Franzenburg
- Institute for Clinical Molecular Biology, University of Kiel, Kiel, Germany
| | - Till Bayer
- GEOMAR Helmholtz-Centre for Ocean Research Kiel, Marine Evolutionary Ecology, Kiel, Germany
| | - Tal Dagan
- Institute of Microbiology, University of Kiel, Kiel, Germany
| | - Thorsten B H Reusch
- GEOMAR Helmholtz-Centre for Ocean Research Kiel, Marine Evolutionary Ecology, Kiel, Germany.
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53
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Abstract
Mutation accumulation in long-lived fairy-ring mushrooms is orders of magnitude lower than predicted based on per-cell division mutation rates in other organisms. A possible explanation is the maintenance of 'immortal' template-DNA in the active periphery of the fairy ring.
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Affiliation(s)
- Duur K Aanen
- Department of Plant Sciences, Laboratory of Genetics, Wageningen University, 6708 PB Wageningen, Netherlands.
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54
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Ruan Y, Wang H, Chen B, Wen H, Wu CI. Mutations Beget More Mutations-Rapid Evolution of Mutation Rate in Response to the Risk of Runaway Accumulation. Mol Biol Evol 2020; 37:1007-1019. [PMID: 31778175 DOI: 10.1093/molbev/msz283] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The rapidity with which the mutation rate evolves could greatly impact evolutionary patterns. Nevertheless, most studies simply assume a constant rate in the time scale of interest (Kimura 1983; Drake 1991; Kumar 2005; Li 2007; Lynch 2010). In contrast, recent studies of somatic mutations suggest that the mutation rate may vary by several orders of magnitude within a lifetime (Kandoth et al. 2013; Lawrence et al. 2013). To resolve the discrepancy, we now propose a runaway model, applicable to both the germline and soma, whereby mutator mutations form a positive-feedback loop. In this loop, any mutator mutation would increase the rate of acquiring the next mutator, thus triggering a runaway escalation in mutation rate. The process can be initiated more readily if there are many weak mutators than a few strong ones. Interestingly, even a small increase in the mutation rate at birth could trigger the runaway process, resulting in unfit progeny. In slowly reproducing species, the need to minimize the risk of this uncontrolled accumulation would thus favor setting the mutation rate low. In comparison, species that starts and ends reproduction sooner do not face the risk and may set the baseline mutation rate higher. The mutation rate would evolve in response to the risk of runaway mutation, in particular, when the generation time changes. A rapidly evolving mutation rate may shed new lights on many evolutionary phenomena (Elango et al. 2006; Thomas et al. 2010, 2018; Langergraber et al. 2012; Besenbacher et al. 2019).
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Affiliation(s)
- Yongsen Ruan
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Haiyu Wang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Bingjie Chen
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Haijun Wen
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Chung-I Wu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China.,CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,Department of Ecology and Evolution, University of Chicago, Chicago, IL
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55
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Orr AJ, Padovan A, Kainer D, Külheim C, Bromham L, Bustos-Segura C, Foley W, Haff T, Hsieh JF, Morales-Suarez A, Cartwright RA, Lanfear R. A phylogenomic approach reveals a low somatic mutation rate in a long-lived plant. Proc Biol Sci 2020; 287:20192364. [PMID: 32156194 PMCID: PMC7126060 DOI: 10.1098/rspb.2019.2364] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Somatic mutations can have important effects on the life history, ecology, and evolution of plants, but the rate at which they accumulate is poorly understood and difficult to measure directly. Here, we develop a method to measure somatic mutations in individual plants and use it to estimate the somatic mutation rate in a large, long-lived, phenotypically mosaic Eucalyptus melliodora tree. Despite being 100 times larger than Arabidopsis, this tree has a per-generation mutation rate only ten times greater, which suggests that this species may have evolved mechanisms to reduce the mutation rate per unit of growth. This adds to a growing body of evidence that illuminates the correlated evolutionary shifts in mutation rate and life history in plants.
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Affiliation(s)
- Adam J Orr
- The Biodesign Institute and the School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Amanda Padovan
- Division of Ecology and Evolution, Research School of Biology, Australian National University, Canberra, Australia.,CSIRO Black Mountain Science and Innovation Park, Canberra, ACT 2601, Australia
| | - David Kainer
- Division of Ecology and Evolution, Research School of Biology, Australian National University, Canberra, Australia
| | - Carsten Külheim
- Division of Ecology and Evolution, Research School of Biology, Australian National University, Canberra, Australia.,School of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI 49931, USA
| | - Lindell Bromham
- Division of Ecology and Evolution, Research School of Biology, Australian National University, Canberra, Australia
| | - Carlos Bustos-Segura
- Division of Ecology and Evolution, Research School of Biology, Australian National University, Canberra, Australia
| | - William Foley
- Division of Ecology and Evolution, Research School of Biology, Australian National University, Canberra, Australia
| | - Tonya Haff
- Division of Ecology and Evolution, Research School of Biology, Australian National University, Canberra, Australia
| | - Ji-Fan Hsieh
- Division of Ecology and Evolution, Research School of Biology, Australian National University, Canberra, Australia
| | | | - Reed A Cartwright
- The Biodesign Institute and the School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Robert Lanfear
- Division of Ecology and Evolution, Research School of Biology, Australian National University, Canberra, Australia.,Department of Biological Sciences, Macquarie University, Sydney, Australia
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56
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Tsujimoto M, Araki KS, Honjo MN, Yasugi M, Nagano AJ, Akama S, Hatakeyama M, Shimizu-Inatsugi R, Sese J, Shimizu KK, Kudoh H. Genet assignment and population structure analysis in a clonal forest-floor herb, Cardamine leucantha, using RAD-seq. AOB PLANTS 2020; 12:plz080. [PMID: 32002176 PMCID: PMC6983914 DOI: 10.1093/aobpla/plz080] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 12/18/2019] [Indexed: 06/10/2023]
Abstract
To study the genetic structure of clonal plant populations, genotyping and genet detection using genetic markers are necessary to assign ramets to corresponding genets. Assignment is difficult as it involves setting a robust threshold of genetic distance for genet distinction as neighbouring genets in a plant population are often genetically related. Here, we used restriction site-associated DNA sequencing (RAD-seq) for a rhizomatous clonal herb, Cardamine leucantha [Brassicaceae] to accurately determine genet structure in a natural population. We determined a draft genome sequence of this species for the first time, which resulted in 66 617 scaffolds with N50 = 6086 bp and an estimated genome size of approximately 253 Mbp. Using genetic distances based on the RAD-seq analysis, we successfully distinguished ramets that belonged to distinct genets even from a half-sib family. We applied these methods to 372 samples of C. leucantha collected at 1-m interval grids within a 20 × 20 m plot in a natural population in Hokkaido, Japan. From these samples, we identified 61 genets with high inequality in terms of genet size and patchy distribution. Spatial autocorrelation analyses indicated significant aggregation within 7 and 4 m at ramet and genet levels, respectively. An analysis of parallel DNA microsatellite loci (simple sequence repeats) suggested that RAD-seq can provide data that allows robust genet assignment. It remains unclear whether the large genets identified here became dominant stochastically or deterministically. Precise identification of genets will assist further study and characterization of dominant genets.
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Affiliation(s)
| | - Kiwako S Araki
- Center for Ecological Research, Kyoto University, Hirano Otsu, Japan
- Faculty of Life Sciences, Ritsumeikan University, Nojihigashi, Kusatsu, Japan
| | - Mie N Honjo
- Center for Ecological Research, Kyoto University, Hirano Otsu, Japan
| | - Masaki Yasugi
- Center for Ecological Research, Kyoto University, Hirano Otsu, Japan
- Faculty of Engineering, Utsunomiya University, Yoto, Utsunomiya, Japan
| | - Atsushi J Nagano
- Center for Ecological Research, Kyoto University, Hirano Otsu, Japan
- Faculty of Agriculture, Ryukoku University, Yokatani, Seta Ohe-cho, Otsu, Japan
| | - Satoru Akama
- National Institute of Advanced Industrial Science and Technology (AIST), Aomi, Koto-ku, Tokyo, Japan
| | - Masaomi Hatakeyama
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse, Zurich, Switzerland
- Functional Genomics Center Zurich, Winterthurerstrasse, Zurich, Switzerland
| | - Rie Shimizu-Inatsugi
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse, Zurich, Switzerland
| | - Jun Sese
- National Institute of Advanced Industrial Science and Technology (AIST), Aomi, Koto-ku, Tokyo, Japan
- Humanome Lab., Inc. 2-4-10-2F, Tsukiji, Chuo-ku, Tokyo, Japan
| | - Kentaro K Shimizu
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse, Zurich, Switzerland
- Kihara Institute for Biological Research, Yokohama City University, Maioka, Totsuka-ku, Yokohama, Japan
| | - Hiroshi Kudoh
- Center for Ecological Research, Kyoto University, Hirano Otsu, Japan
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57
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Affiliation(s)
- Matthias Galipaud
- Department of evolutionary biology and environmental studies University of Zurich Zurich Switzerland
| | - Hanna Kokko
- Department of evolutionary biology and environmental studies University of Zurich Zurich Switzerland
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58
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Maintenance of High Genome Integrity over Vegetative Growth in the Fairy-Ring Mushroom Marasmius oreades. Curr Biol 2019; 29:2758-2765.e6. [PMID: 31402298 DOI: 10.1016/j.cub.2019.07.025] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 05/25/2019] [Accepted: 07/09/2019] [Indexed: 01/06/2023]
Abstract
Most mutations in coding regions of the genome are deleterious, causing selection to favor mechanisms that minimize the mutational load over time [1-5]. DNA replication during cell division is a major source of new mutations. It is therefore important to limit the number of cell divisions between generations, particularly for large and long-lived organisms [6-9]. The germline cells of animals and the slowly dividing cells in plant meristems are adaptations to control the number of mutations that accumulate over generations [9-11]. Fungi lack a separated germline while harboring species with very large and long-lived individuals that appear to maintain highly stable genomes within their mycelia [8, 12, 13]. Here, we studied genomic mutation accumulation in the fairy-ring mushroom Marasmius oreades. We generated a chromosome-level genome assembly using a combination of cutting-edge DNA sequencing technologies and re-sequenced 40 samples originating from six individuals of this fungus. The low number of mutations recovered in the sequencing data suggests the presence of an unknown mechanism that works to maintain extraordinary genome integrity over vegetative growth in M. oreades. The highly structured growth pattern of M. oreades allowed us to estimate the number of cell divisions leading up to each sample [14, 15], and from this data, we infer an incredibly low per mitosis mutation rate (3.8 × 10-12 mutations per site and cell division) as one of several possible explanations for the low number of identified mutations.
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59
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Durante MK, Baums IB, Williams DE, Vohsen S, Kemp DW. What drives phenotypic divergence among coral clonemates of Acropora palmata? Mol Ecol 2019; 28:3208-3224. [PMID: 31282031 PMCID: PMC6852117 DOI: 10.1111/mec.15140] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 05/10/2019] [Accepted: 05/13/2019] [Indexed: 12/16/2022]
Abstract
Evolutionary rescue of populations depends on their ability to produce phenotypic variation that is heritable and adaptive. DNA mutations are the best understood mechanisms to create phenotypic variation, but other, less well-studied mechanisms exist. Marine benthic foundation species provide opportunities to study these mechanisms because many are dominated by isogenic stands produced through asexual reproduction. For example, Caribbean acroporid corals are long lived and reproduce asexually via breakage of branches. Fragmentation is often the dominant mode of local population maintenance. Thus, large genets with many ramets (colonies) are common. Here, we observed phenotypic variation in stress responses within genets following the coral bleaching events in 2014 and 2015 caused by high water temperatures. This was not due to genetic variation in their symbiotic dinoflagellates (Symbiodinium "fitti") because each genet of this coral species typically harbours a single strain of S. "fitti". Characterization of the microbiome via 16S tag sequencing correlated the abundance of only two microbiome members (Tepidiphilus, Endozoicomonas) with a bleaching response. Epigenetic changes were significantly correlated with the host's genetic background, the location of the sampled polyps within the colonies (e.g., branch vs. base of colony), and differences in the colonies' condition during the bleaching event. We conclude that long-term microenvironmental differences led to changes in the way the ramets methylated their genomes, contributing to the differential bleaching response. However, most of the variation in differential bleaching response among clonemates of Acropora palmata remains unexplained. This research provides novel data and hypotheses to help understand intragenet variability in stress phenotypes of sessile marine species.
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Affiliation(s)
| | | | - Dana E. Williams
- National Oceanic and Atmospheric AdministrationSoutheast Fisheries Science CenterMiamiFLUSA
| | - Sam Vohsen
- The Pennsylvania State UniversityUniversity ParkPAUSA
| | - Dustin W. Kemp
- The Pennsylvania State UniversityUniversity ParkPAUSA
- Present address:
University of Alabama at BirminghamBirminghamALUSA
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