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Filatov DA, Kirkpatrick M. How does evolution work in superabundant microbes? Trends Microbiol 2024; 32:836-846. [PMID: 38360431 DOI: 10.1016/j.tim.2024.01.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 01/24/2024] [Accepted: 01/26/2024] [Indexed: 02/17/2024]
Abstract
Marine phytoplankton play crucial roles in the Earth's ecological, chemical, and geological processes. They are responsible for about half of global primary production and drive the ocean biological carbon pump. Understanding how plankton species may adapt to the Earth's rapidly changing environments is evidently an urgent priority. This problem requires evolutionary genetic approaches as evolution occurs at the level of allele frequency change within populations driven by genetic drift and natural selection (microevolution). Plankters such as the coccolithophore Gephyrocapsa huxleyi and the cyanobacterium Prochlorococcus 'marinus' are among Earth's most abundant organisms. In this opinion paper we discuss how evolution in astronomically large populations of superabundant microbes (SAMs) may act fundamentally differently than it does in the populations of more modest size found in well-studied organisms. This offers exciting opportunities to study evolution in the conditions that have yet to be explored and also leads to unique challenges. Exploring these opportunities and challenges is the goal of this article.
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Affiliation(s)
- Dmitry A Filatov
- Department of Biology, University of Oxford, Oxford, OX1 3RB, UK.
| | - Mark Kirkpatrick
- Department of Integrative Biology, University of Texas, Austin, TX 78712, USA
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2
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Galtier N. Half a Century of Controversy: The Neutralist/Selectionist Debate in Molecular Evolution. Genome Biol Evol 2024; 16:evae003. [PMID: 38311843 PMCID: PMC10839204 DOI: 10.1093/gbe/evae003] [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] [Accepted: 01/01/2024] [Indexed: 02/06/2024] Open
Abstract
The neutral and nearly neutral theories, introduced more than 50 yr ago, have raised and still raise passionate discussion regarding the forces governing molecular evolution and their relative importance. The debate, initially focused on the amount of within-species polymorphism and constancy of the substitution rate, has spread, matured, and now underlies a wide range of topics and questions. The neutralist/selectionist controversy has structured the field and influences the way molecular evolutionary scientists conceive their research.
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Affiliation(s)
- Nicolas Galtier
- ISEM, CNRS, IRD, Université de Montpellier, Montpellier, France
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3
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Filatov DA. How does speciation in marine plankton work? Trends Microbiol 2023; 31:989-991. [PMID: 37500364 DOI: 10.1016/j.tim.2023.07.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 07/06/2023] [Accepted: 07/11/2023] [Indexed: 07/29/2023]
Abstract
Marine plankton species are ecologically important, yet, it remains unclear how they originate in the ocean, where few barriers are apparent to cause the most common type of speciation - divergence in isolation. Here I discuss the use of modern evolutionary genetic approaches to shed light on longstanding questions regarding their evolution.
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4
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Bendif EM, Probert I, Archontikis OA, Young JR, Beaufort L, Rickaby RE, Filatov D. Rapid diversification underlying the global dominance of a cosmopolitan phytoplankton. THE ISME JOURNAL 2023; 17:630-640. [PMID: 36747097 PMCID: PMC10030636 DOI: 10.1038/s41396-023-01365-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 01/10/2023] [Accepted: 01/11/2023] [Indexed: 02/08/2023]
Abstract
Marine phytoplankton play important roles in the global ecosystem, with a limited number of cosmopolitan keystone species driving their biomass. Recent studies have revealed that many of these phytoplankton are complexes composed of sibling species, but little is known about the evolutionary processes underlying their formation. Gephyrocapsa huxleyi, a widely distributed and abundant unicellular marine planktonic algae, produces calcified scales (coccoliths), thereby significantly affects global biogeochemical cycles via sequestration of inorganic carbon. This species is composed of morphotypes defined by differing degrees of coccolith calcification, the evolutionary ecology of which remains unclear. Here, we report an integrated morphological, ecological and genomic survey across globally distributed G. huxleyi strains to reconstruct evolutionary relationships between morphotypes in relation to their habitats. While G. huxleyi has been considered a single cosmopolitan species, our analyses demonstrate that it has evolved to comprise at least three distinct species, which led us to formally revise the taxonomy of the G. huxleyi complex. Moreover, the first speciation event occurred before the onset of the last interglacial period (~140 ka), while the second followed during this interglacial. Then, further rapid diversifications occurred during the most recent ice-sheet expansion of the last glacial period and established morphotypes as dominant populations across environmental clines. These results suggest that glacial-cycle dynamics contributed to the isolation of ocean basins and the segregations of oceans fronts as extrinsic drivers of micro-evolutionary radiations in extant marine phytoplankton.
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Affiliation(s)
- El Mahdi Bendif
- Department of Earth Sciences, University of Oxford, Oxford, UK.
- Department of Plant Sciences, University of Oxford, Oxford, UK.
- Institut des sciences de la mer de Rimouski (ISMER), Université du Québec à Rimouski, Rimouski, Canada.
| | - Ian Probert
- Sorbonne Université - CNRS, Roscoff Culture Collection, FR2424 Station Biologique de Roscoff, Roscoff, France
| | - Odysseas A Archontikis
- Department of Earth Sciences, University of Oxford, Oxford, UK
- Department of Earth Sciences, The Natural History Museum, London, UK
| | - Jeremy R Young
- Department of Earth Sciences, University College London, London, UK
| | - Luc Beaufort
- Aix Marseille Université, CNRS, IRD, INRAE, CEREGE, Aix-en-Provence, France
| | | | - Dmitry Filatov
- Department of Plant Sciences, University of Oxford, Oxford, UK
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5
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Le Gac M, Mary L, Metegnier G, Quéré J, Siano R, Rodríguez F, Destombe C, Sourisseau M. Strong population genomic structure of the toxic dinoflagellate Alexandrium minutum inferred from meta-transcriptome samples. Environ Microbiol 2022; 24:5966-5983. [PMID: 36302091 DOI: 10.1111/1462-2920.16257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 10/20/2022] [Indexed: 01/12/2023]
Abstract
Despite theoretical expectations, marine microeukaryote population are often highly structured and the mechanisms behind such patterns remain to be elucidated. These organisms display huge census population sizes, yet genotyping usually requires clonal strains originating from single cells, hindering proper population sampling. Estimating allelic frequency directly from population wide samples, without any isolation step, offers an interesting alternative. Here, we validate the use of meta-transcriptome environmental samples to determine the population genetic structure of the dinoflagellate Alexandrium minutum. Strain and meta-transcriptome based results both indicated a strong genetic structure for A. minutum in Western Europe, to the level expected between cryptic species. The presence of numerous private alleles, and even fixed polymorphism, would indicate ancient divergence and absence of gene flow between populations. Single nucleotide polymorphisms (SNPs) displaying strong allele frequency differences were distributed throughout the genome, which might indicate pervasive selection from standing genetic variation (soft selective sweeps). However, a few genomic regions displayed extremely low diversity that could result from the fixation of adaptive de novo mutations (hard selective sweeps) within the populations.
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Affiliation(s)
| | - Lou Mary
- Ifremer, Dyneco, Plouzané, France
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6
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Kao T, Wang T, Ku C. Rampant nuclear-mitochondrial-plastid phylogenomic discordance in globally distributed calcifying microalgae. THE NEW PHYTOLOGIST 2022; 235:1394-1408. [PMID: 35556250 PMCID: PMC9539906 DOI: 10.1111/nph.18219] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 05/04/2022] [Indexed: 06/15/2023]
Abstract
Incongruent phylogenies have been widely observed between nuclear and plastid or mitochondrial genomes in terrestrial plants and animals. However, few studies have examined these patterns in microalgae or the discordance between the two organelles. Here we investigated the nuclear-mitochondrial-plastid phylogenomic incongruence in Emiliania-Gephyrocapsa, a group of cosmopolitan calcifying phytoplankton with enormous populations and recent speciations. We assembled mitochondrial and plastid genomes of 27 strains from across global oceans and temperature regimes, and analyzed the phylogenomic histories of the three compartments using concatenation and coalescence methods. Six major clades with varying morphology and distribution are well recognized in the nuclear phylogeny, but such relationships are absent in the mitochondrial and plastid phylogenies, which also differ substantially from each other. The rampant phylogenomic discordance is due to a combination of organellar capture (introgression), organellar genome recombination, and incomplete lineage sorting of ancient polymorphic organellar genomes. Hybridization can lead to replacements of whole organellar genomes without introgression of nuclear genes and the two organelles are not inherited as a single cytoplasmic unit. This study illustrates the convoluted evolution and inheritance of organellar genomes in isogamous haplodiplontic microalgae and provides a window into the phylogenomic complexity of marine unicellular eukaryotes.
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Affiliation(s)
- Tzu‐Tong Kao
- Institute of Plant and Microbial BiologyAcademia SinicaTaipei11529Taiwan
| | - Tzu‐Haw Wang
- Institute of Plant and Microbial BiologyAcademia SinicaTaipei11529Taiwan
| | - Chuan Ku
- Institute of Plant and Microbial BiologyAcademia SinicaTaipei11529Taiwan
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7
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Abstract
We discuss the genetic, demographic, and selective forces that are likely to be at play in restricting observed levels of DNA sequence variation in natural populations to a much smaller range of values than would be expected from the distribution of census population sizes alone-Lewontin's Paradox. While several processes that have previously been strongly emphasized must be involved, including the effects of direct selection and genetic hitchhiking, it seems unlikely that they are sufficient to explain this observation without contributions from other factors. We highlight a potentially important role for the less-appreciated contribution of population size change; specifically, the likelihood that many species and populations may be quite far from reaching the relatively high equilibrium diversity values that would be expected given their current census sizes.
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Affiliation(s)
- Brian Charlesworth
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Jeffrey D Jensen
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
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8
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Evolution of Phytoplankton as Estimated from Genetic Diversity. JOURNAL OF MARINE SCIENCE AND ENGINEERING 2022. [DOI: 10.3390/jmse10040456] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Phytoplankton are photosynthetic, single-celled organisms producing almost half of all oxygen on Earth and play a central role as prey for higher organisms, making them irreplaceable in the marine food web. As Global Change proceeds, imposing rapidly intensifying selection pressures, phytoplankton are forced to undergo evolution, local extinction, or redistribution, with potentially cascading effects throughout the marine ecosystem. Recent results from the field of population genetics display high levels of standing genetic diversity in natural phytoplankton populations, providing ample ‘evolutionary options’ and implying high adaptive potential to changing conditions. This potential for adaptive evolution is realized in several studies of experimental evolution, even though most of these studies investigate the evolution of only single strains. This, however, shows that phytoplankton not only evolve from standing genetic diversity, but also rely on de novo mutations. Recent global sampling campaigns show that the immense intraspecific diversity of phytoplankton in the marine ecosystem has been significantly underestimated, meaning we are only studying a minor portion of the relevant variability in the context of Global Change and evolution. An increased understanding of genomic diversity is primarily hampered by the low number of ecologically representative reference genomes of eukaryotic phytoplankton and the functional annotation of these. However, emerging technologies relying on metagenome and transcriptome data may offer a more realistic understanding of phytoplankton diversity.
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9
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Abstract
Non-random usage of synonymous codons, known as “codon bias”, has been described in many organisms, from bacteria to Drosophila, but little is known about it in phytoplankton. This phenomenon is thought to be driven by selection for translational efficiency. As the efficacy of selection is proportional to the effective population size, species with large population sizes, such as phytoplankton, are expected to have strong codon bias. To test this, we measured codon bias in 215 strains from Haptophyta, Chlorophyta, Ochrophyta (except diatoms that were studied previously), Dinophyta, Cryptophyta, Ciliophora, unicellular Rhodophyta and Chlorarachniophyta. Codon bias is modest in most groups, despite the astronomically large population sizes of marine phytoplankton. The strength of the codon bias, measured with the effective number of codons, is the strongest in Haptophyta and the weakest in Chlorarachniophyta. The optimal codons are GC-ending in most cases, but several shifts to AT-ending codons were observed (mainly in Ochrophyta and Ciliophora). As it takes a long time to reach a new equilibrium after such shifts, species having AT-ending codons show a lower frequency of optimal codons compared to other species. Genetic diversity, calculated for species with more than three strains sequenced, is modest, indicating that the effective population sizes are many orders of magnitude lower than the astronomically large census population sizes, which helps to explain the modest codon bias in marine phytoplankton. This study represents the first comparative analysis of codon bias across multiple major phytoplankton groups.
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10
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Cyclic evolution of phytoplankton forced by changes in tropical seasonality. Nature 2021; 601:79-84. [PMID: 34853471 DOI: 10.1038/s41586-021-04195-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 10/29/2021] [Indexed: 11/09/2022]
Abstract
Although the role of Earth's orbital variations in driving global climate cycles has long been recognized, their effect on evolution is hitherto unknown. The fossil remains of coccolithophores, a key calcifying phytoplankton group, enable a detailed assessment of the effect of cyclic orbital-scale climate changes on evolution because of their abundance in marine sediments and the preservation of their morphological adaptation to the changing environment1,2. Evolutionary genetic analyses have linked broad changes in Pleistocene fossil coccolith morphology to species radiation events3. Here, using high-resolution coccolith data, we show that during the last 2.8 million years the morphological evolution of coccolithophores was forced by Earth's orbital eccentricity with rhythms of around 100,000 years and 405,000 years-a distinct spectral signature to that of coeval global climate cycles4. Simulations with an Earth System Model5 coupled with an ocean biogeochemical model6 show a strong eccentricity modulation of the seasonal cycle, which we suggest directly affects the diversity of ecological niches that occur over the annual cycle in the tropical ocean. Reduced seasonality in surface ocean conditions favours species with mid-size coccoliths, increasing coccolith carbonate export and burial; whereas enhanced seasonality favours a larger range of coccolith sizes and reduced carbonate export. We posit that eccentricity pacing of phytoplankton evolution contributed to the strong 405,000-year cyclicity that is seen in global carbon cycle records.
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11
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Filatov DA, Bendif EM, Archontikis OA, Hagino K, Rickaby REM. The mode of speciation during a recent radiation in open-ocean phytoplankton. Curr Biol 2021; 31:5439-5449.e5. [PMID: 34687611 DOI: 10.1016/j.cub.2021.09.073] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 08/03/2021] [Accepted: 09/24/2021] [Indexed: 12/30/2022]
Abstract
Despite the enormous ecological importance of marine phytoplankton, surprisingly little is known about how new phytoplankton species originate and evolve in the open ocean, in the absence of apparent geographic barriers that typically act as isolation mechanisms in speciation. To investigate the mechanism of open-ocean speciation, we combined fossil and climatic records from the late Quaternary with genome-wide evolutionary genetic analyses of speciation in the ubiquitous and abundant pelagic coccolithophore genus Gephyrocapsa (including G. huxleyi, formerly known as Emiliania huxleyi). Based on the analysis of 43 sequenced genomes, we report that the best-fitting scenario for all speciation events analyzed included an extended period of complete isolation followed by recent (Holocene) secondary contact, supporting the role of geographic or oceanographic barriers in population divergence and speciation. Consistent with this, fossil data reveal considerable diachroneity of species first occurrence. The timing of all speciation events coincided with glacial phases of glacial-interglacial cycles, suggesting that stronger isolation between the ocean basins and increased segregation of ecological niches during glaciations are important drivers of speciation in marine phytoplankton. The similarity across multiple speciation events implies the generality of this inferred speciation scenario for marine phytoplankton.
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Affiliation(s)
- Dmitry A Filatov
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK.
| | - El Mahdi Bendif
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK; Department of Earth Sciences, University of Oxford, South Parks Road, Oxford OX1 3AN, UK
| | - Odysseas A Archontikis
- Department of Earth Sciences, University of Oxford, South Parks Road, Oxford OX1 3AN, UK
| | - Kyoko Hagino
- Centre for Advanced Marine Core Research, Kochi University, Nankoku, Kochi 783-8502, Japan
| | - Rosalind E M Rickaby
- Department of Earth Sciences, University of Oxford, South Parks Road, Oxford OX1 3AN, UK
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12
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Hasan AR, Ness RW. Recombination Rate Variation and Infrequent Sex Influence Genetic Diversity in Chlamydomonas reinhardtii. Genome Biol Evol 2021; 12:370-380. [PMID: 32181819 PMCID: PMC7186780 DOI: 10.1093/gbe/evaa057] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/13/2020] [Indexed: 12/12/2022] Open
Abstract
Recombination confers a major evolutionary advantage by breaking up linkage disequilibrium between harmful and beneficial mutations, thereby facilitating selection. However, in species that are only periodically sexual, such as many microbial eukaryotes, the realized rate of recombination is also affected by the frequency of sex, meaning that infrequent sex can increase the effects of selection at linked sites despite high recombination rates. Despite this, the rate of sex of most facultatively sexual species is unknown. Here, we use genomewide patterns of linkage disequilibrium to infer fine-scale recombination rate variation in the genome of the facultatively sexual green alga Chlamydomonas reinhardtii. We observe recombination rate variation of up to two orders of magnitude and find evidence of recombination hotspots across the genome. Recombination rate is highest flanking genes, consistent with trends observed in other nonmammalian organisms, though intergenic recombination rates vary by intergenic tract length. We also find a positive relationship between nucleotide diversity and physical recombination rate, suggesting a widespread influence of selection at linked sites in the genome. Finally, we use estimates of the effective rate of recombination to calculate the rate of sex that occurs in natural populations, estimating a sexual cycle roughly every 840 generations. We argue that the relatively infrequent rate of sex and large effective population size creates a population genetic environment that increases the influence of selection on linked sites across the genome.
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Affiliation(s)
- Ahmed R Hasan
- Department of Cell and Systems Biology, University of Toronto, Ontario, Canada.,Department of Biology, University of Toronto Mississauga, Ontario, Canada
| | - Rob W Ness
- Department of Cell and Systems Biology, University of Toronto, Ontario, Canada.,Department of Biology, University of Toronto Mississauga, Ontario, Canada
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13
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Krasovec M, Rickaby REM, Filatov DA. Evolution of Mutation Rate in Astronomically Large Phytoplankton Populations. Genome Biol Evol 2021; 12:1051-1059. [PMID: 32645145 PMCID: PMC7486954 DOI: 10.1093/gbe/evaa131] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/02/2020] [Indexed: 02/06/2023] Open
Abstract
Genetic diversity is expected to be proportional to population size, yet, there is a well-known, but unexplained lack of genetic diversity in large populations-the "Lewontin's paradox." Larger populations are expected to evolve lower mutation rates, which may help to explain this paradox. Here, we test this conjecture by measuring the spontaneous mutation rate in a ubiquitous unicellular marine phytoplankton species Emiliania huxleyi (Haptophyta) that has modest genetic diversity despite an astronomically large population size. Genome sequencing of E. huxleyi mutation accumulation lines revealed 455 mutations, with an unusual GC-biased mutation spectrum. This yielded an estimate of the per site mutation rate µ = 5.55×10-10 (CI 95%: 5.05×10-10 - 6.09×10-10), which corresponds to an effective population size Ne ∼ 2.7×106. Such a modest Ne is surprising for a ubiquitous and abundant species that accounts for up to 10% of global primary productivity in the oceans. Our results indicate that even exceptionally large populations do not evolve mutation rates lower than ∼10-10 per nucleotide per cell division. Consequently, the extreme disparity between modest genetic diversity and astronomically large population size in the plankton species cannot be explained by an unusually low mutation rate.
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Affiliation(s)
- Marc Krasovec
- Department of Plant Sciences, University of Oxford, United Kingdom
| | | | - Dmitry A Filatov
- Department of Plant Sciences, University of Oxford, United Kingdom
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14
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Wang X, Bernhardsson C, Ingvarsson PK. Demography and Natural Selection Have Shaped Genetic Variation in the Widely Distributed Conifer Norway Spruce (Picea abies). Genome Biol Evol 2020; 12:3803-3817. [PMID: 31958121 PMCID: PMC7046165 DOI: 10.1093/gbe/evaa005] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/14/2020] [Indexed: 12/13/2022] Open
Abstract
Under the neutral theory, species with larger effective population size are expected to harbor higher genetic diversity. However, across a wide variety of organisms, the range of genetic diversity is orders of magnitude more narrow than the range of effective population size. This observation has become known as Lewontin’s paradox and although aspects of this phenomenon have been extensively studied, the underlying causes for the paradox remain unclear. Norway spruce (Picea abies) is a widely distributed conifer species across the northern hemisphere, and it consequently plays a major role in European forestry. Here, we use whole-genome resequencing data from 35 individuals to perform population genomic analyses in P. abies in an effort to understand what drives genome-wide patterns of variation in this species. Despite having a very wide geographic distribution and an corresponding enormous current population size, our analyses find that genetic diversity of P. abies is low across a number of populations (π = 0.0049 in Central-Europe, π = 0.0063 in Sweden-Norway, π = 0.0063 in Finland). To assess the reasons for the low levels of genetic diversity, we infer the demographic history of the species and find that it is characterized by several reoccurring bottlenecks with concomitant decreases in effective population size can, at least partly, provide an explanation for low polymorphism we observe in P. abies. Further analyses suggest that recurrent natural selection, both purifying and positive selection, can also contribute to the loss of genetic diversity in Norway spruce by reducing genetic diversity at linked sites. Finally, the overall low mutation rates seen in conifers can also help explain the low genetic diversity maintained in Norway spruce.
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Affiliation(s)
- Xi Wang
- Umeå Plant Science Centre, Department of Ecology and Environmental Science, Umeå University, Sweden.,Linnean Centre for Plant Biology, Department of Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Carolina Bernhardsson
- Umeå Plant Science Centre, Department of Ecology and Environmental Science, Umeå University, Sweden.,Linnean Centre for Plant Biology, Department of Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden.,Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Pär K Ingvarsson
- Linnean Centre for Plant Biology, Department of Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
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15
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Ababaikeri B, Abduriyim S, Tohetahong Y, Mamat T, Ahmat A, Halik M. Whole-genome sequencing of Tarim red deer ( Cervus elaphus yarkandensis) reveals demographic history and adaptations to an arid-desert environment. Front Zool 2020; 17:31. [PMID: 33072165 PMCID: PMC7565370 DOI: 10.1186/s12983-020-00379-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 10/02/2020] [Indexed: 01/08/2023] Open
Abstract
Background The initiation of desert conditions in the Tarim Basin in China since the late Miocene has led to the significant genetic structuring of local organisms. Tarim Red Deer (Cervus elaphus yarkandensis, TRD) have adapted to the harsh environmental conditions in this basin, including high solar radiation and temperature, aridity, and poor nutritional conditions. However, the underlying genetic basis of this adaptation is poorly understood. Results We sequenced the whole genomes of 13 TRD individuals, conducted comparative genomic analyses, and estimated demographic fluctuation. The ∂a∂i model estimated that the TRD and Tule elk (Cervus canadensis nannodes) populations diverged approximately 0.98 Mya. Analyses revealed a substantial influence of the Earth’s climate on the effective population size of TRD, associated with glacial advances and retreat, and human activities likely underlie a recent serious decline in population. A marked bottleneck may have profoundly affected the genetic diversity of TRD populations. We detected a set of candidate genes, pathways, and GO categories related to oxidative stress, water reabsorption, immune regulation, energy metabolism, eye protection, heat stress, respiratory system adaptation, prevention of high blood pressure, and DNA damage and repair that may directly or indirectly be involved in the adaptation of TRD to an arid-desert environment. Conclusions Our analyses highlight the role of historical global climates in the population dynamics of TRD. In light of ongoing global warming and the increasing incidence of droughts, our study offers insights into the genomic adaptations of animals, especially TRD, to extreme arid-desert environments and provides a valuable resource for future research on conservation design and biological adaptations to environmental change.
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Affiliation(s)
- Buweihailiqiemu Ababaikeri
- College of Life Sciences and Technology, Xinjiang University, Urumqi, 830046 Xinjiang China.,College of Xinjiang Uyghur Medicine, Hoten, 848000 Xinjiang China
| | - Shamshidin Abduriyim
- College of Life Science, Shihezi University, Shihezi, 832003 Xinjiang China.,Department of Ecology, Hubei Key Laboratory of Cell Homeostasis, College of Life Science, Wuhan University, Wuhan, 430072 Hubei China
| | - Yilamujiang Tohetahong
- College of Life Sciences and Technology, Xinjiang University, Urumqi, 830046 Xinjiang China
| | - Tayerjan Mamat
- College of Life Sciences and Technology, Xinjiang University, Urumqi, 830046 Xinjiang China
| | - Adil Ahmat
- College of Life Sciences and Technology, Xinjiang University, Urumqi, 830046 Xinjiang China
| | - Mahmut Halik
- College of Life Sciences and Technology, Xinjiang University, Urumqi, 830046 Xinjiang China
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16
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Galtier N, Rousselle M. How Much Does Ne Vary Among Species? Genetics 2020; 216:559-572. [PMID: 32839240 PMCID: PMC7536855 DOI: 10.1534/genetics.120.303622] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 08/20/2020] [Indexed: 11/18/2022] Open
Abstract
Genetic drift is an important evolutionary force of strength inversely proportional to Ne , the effective population size. The impact of drift on genome diversity and evolution is known to vary among species, but quantifying this effect is a difficult task. Here we assess the magnitude of variation in drift power among species of animals via its effect on the mutation load - which implies also inferring the distribution of fitness effects of deleterious mutations. To this aim, we analyze the nonsynonymous (amino-acid changing) and synonymous (amino-acid conservative) allele frequency spectra in a large sample of metazoan species, with a focus on the primates vs. fruit flies contrast. We show that a Gamma model of the distribution of fitness effects is not suitable due to strong differences in estimated shape parameters among taxa, while adding a class of lethal mutations essentially solves the problem. Using the Gamma + lethal model and assuming that the mean deleterious effects of nonsynonymous mutations is shared among species, we estimate that the power of drift varies by a factor of at least 500 between large-Ne and small-Ne species of animals, i.e., an order of magnitude more than the among-species variation in genetic diversity. Our results are relevant to Lewontin's paradox while further questioning the meaning of the Ne parameter in population genomics.
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Affiliation(s)
- Nicolas Galtier
- Institute of Evolution Sciences of Montpellier (ISEM), CNRS, University of Montpellier, IRD, EPHE, 34095 Montpellier, France
| | - Marjolaine Rousselle
- Institute of Evolution Sciences of Montpellier (ISEM), CNRS, University of Montpellier, IRD, EPHE, 34095 Montpellier, France
- Bioinformatics Research Centre, Aarhus University, DK Aarhus, Denmark
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17
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Rastogi A, Vieira FRJ, Deton-Cabanillas AF, Veluchamy A, Cantrel C, Wang G, Vanormelingen P, Bowler C, Piganeau G, Hu H, Tirichine L. A genomics approach reveals the global genetic polymorphism, structure, and functional diversity of ten accessions of the marine model diatom Phaeodactylum tricornutum. THE ISME JOURNAL 2020; 14:347-363. [PMID: 31624346 PMCID: PMC6976637 DOI: 10.1038/s41396-019-0528-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 08/24/2019] [Accepted: 09/11/2019] [Indexed: 12/31/2022]
Abstract
Diatoms emerged in the Mesozoic period and presently constitute one of the main primary producers in the world's ocean and are of a major economic importance. In the current study, using whole genome sequencing of ten accessions of the model diatom Phaeodactylum tricornutum, sampled at broad geospatial and temporal scales, we draw a comprehensive landscape of the genomic diversity within the species. We describe strong genetic subdivisions of the accessions into four genetic clades (A-D) with constituent populations of each clade possessing a conserved genetic and functional makeup, likely a consequence of the limited dispersal of P. tricornutum in the open ocean. We further suggest dominance of asexual reproduction across all the populations, as implied by high linkage disequilibrium. Finally, we show limited yet compelling signatures of genetic and functional convergence inducing changes in the selection pressure on many genes and metabolic pathways. We propose these findings to have significant implications for understanding the genetic structure of diatom populations in nature and provide a framework to assess the genomic underpinnings of their ecological success and impact on aquatic ecosystems where they play a major role. Our work provides valuable resources for functional genomics and for exploiting the biotechnological potential of this model diatom species.
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Affiliation(s)
- Achal Rastogi
- Institut de biologie de l'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, PSL Université Paris, 75005, Paris, France
- Corteva Agriscience™, The V Ascendas, Atria Block, 12th Floor, Madhapur, Hyderabad, 500081, India
| | - Fabio Rocha Jimenez Vieira
- Institut de biologie de l'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, PSL Université Paris, 75005, Paris, France
| | - Anne-Flore Deton-Cabanillas
- Institut de biologie de l'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, PSL Université Paris, 75005, Paris, France
| | - Alaguraj Veluchamy
- Institut de biologie de l'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, PSL Université Paris, 75005, Paris, France
- Biological and Environmental Sciences and Engineering Division, Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Catherine Cantrel
- Institut de biologie de l'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, PSL Université Paris, 75005, Paris, France
| | - Gaohong Wang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, 430072, Wuhan, China
| | - Pieter Vanormelingen
- Department of Biology, Research Group Protistology and Aquatic Ecology, Ghent University, Krijgslaan 281/S8 9000, Gent, Belgium
| | - Chris Bowler
- Institut de biologie de l'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, PSL Université Paris, 75005, Paris, France
| | - Gwenael Piganeau
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, F-66650, Banyuls/Mer, France
| | - Hanhua Hu
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, 430072, Wuhan, China.
| | - Leila Tirichine
- Institut de biologie de l'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, PSL Université Paris, 75005, Paris, France.
- Université de Nantes, CNRS, UFIP, UMR 6286, F-44000, Nantes, France.
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18
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Krasovec M, Filatov DA. Evolution of Codon Usage Bias in Diatoms. Genes (Basel) 2019; 10:genes10110894. [PMID: 31698749 PMCID: PMC6896221 DOI: 10.3390/genes10110894] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 10/29/2019] [Accepted: 11/02/2019] [Indexed: 12/22/2022] Open
Abstract
Codon usage bias (CUB)-preferential use of one of the synonymous codons, has been described in a wide range of organisms from bacteria to mammals, but it has not yet been studied in marine phytoplankton. CUB is thought to be caused by weak selection for translational accuracy and efficiency. Weak selection can overpower genetic drift only in species with large effective population sizes, such as Drosophila that has relatively strong CUB, while organisms with smaller population sizes (e.g., mammals) have weak CUB. Marine plankton species tend to have extremely large populations, suggesting that CUB should be very strong. Here we test this prediction and describe the patterns of codon usage in a wide range of diatom species belonging to 35 genera from 4 classes. We report that most of the diatom species studied have surprisingly modest CUB (mean Effective Number of Codons, ENC = 56), with some exceptions showing stronger codon bias (ENC = 44). Modest codon bias in most studied diatom species may reflect extreme disparity between astronomically large census and modest effective population size (Ne), with fluctuations in population size and linked selection limiting long-term Ne and rendering selection for optimal codons less efficient. For example, genetic diversity (pi ~0.02 at silent sites) in Skeletonema marinoi corresponds to Ne of about 10 million individuals, which is likely many orders of magnitude lower than its census size. Still, Ne ~107 should be large enough to make selection for optimal codons efficient. Thus, we propose that an alternative process-frequent changes of preferred codons, may be a more plausible reason for low CUB despite highly efficient selection for preferred codons in diatom populations. The shifts in the set of optimal codons should result in the changes of the direction of selection for codon usage, so the actual codon usage never catches up with the moving target of the optimal set of codons and the species never develop strong CUB. Indeed, we detected strong shifts in preferential codon usage within some diatom genera, with switches between preferentially GC-rich and AT-rich 3rd codon positions (GC3). For example, GC3 ranges from 0.6 to 1 in most Chaetoceros species, while for Chaetoceros dichaeta GC3 = 0.1. Both variation in selection intensity and mutation spectrum may drive such shifts in codon usage and limit the observed CUB. Our study represents the first genome-wide analysis of CUB in diatoms and the first such analysis for a major phytoplankton group.
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19
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Repeated species radiations in the recent evolution of the key marine phytoplankton lineage Gephyrocapsa. Nat Commun 2019; 10:4234. [PMID: 31530807 PMCID: PMC6748936 DOI: 10.1038/s41467-019-12169-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 08/22/2019] [Indexed: 11/10/2022] Open
Abstract
Phytoplankton account for nearly half of global primary productivity and strongly affect the global carbon cycle, yet little is known about the forces that drive the evolution of these keystone microscopic organisms. Here we combine morphometric data from the fossil record of the ubiquitous coccolithophore genus Gephyrocapsa with genomic analyses of extant species to assess the genetic processes underlying Pleistocene palaeontological patterns. We demonstrate that all modern diversity in Gephyrocapsa (including Emiliania huxleyi) originated in a rapid species radiation during the last 0.6 Ma, coincident with the latest of the three pulses of Gephyrocapsa diversification and extinction documented in the fossil record. Our evolutionary genetic analyses indicate that new species in this genus have formed in sympatry or parapatry, with occasional hybridisation between species. This sheds light on the mode of speciation during evolutionary radiation of marine phytoplankton and provides a model of how new plankton species form. The phytoplankton Gephyrocapsa have gone through repeated macroevolutionary shifts in size. Here, Bendif et al. combine fossil and genomic data to show the latest shift was coincident with a species radiation and suggest that previous shifts have also resulted from cycles of radiation and extinction.
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20
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Craig RJ, Böndel KB, Arakawa K, Nakada T, Ito T, Bell G, Colegrave N, Keightley PD, Ness RW. Patterns of population structure and complex haplotype sharing among field isolates of the green algaChlamydomonas reinhardtii. Mol Ecol 2019; 28:3977-3993. [DOI: 10.1111/mec.15193] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 07/05/2019] [Accepted: 07/17/2019] [Indexed: 12/22/2022]
Affiliation(s)
- Rory J. Craig
- Institute of Evolutionary Biology School of Biological Sciences University of Edinburgh Edinburgh UK
- Department of Biology University of Toronto Mississauga Mississauga ON Canada
| | - Katharina B. Böndel
- Institute of Evolutionary Biology School of Biological Sciences University of Edinburgh Edinburgh UK
- Institute of Plant Breeding, Seed Science and Population Genetics University of Hohenheim Stuttgart Germany
| | - Kazuharu Arakawa
- Institute for Advanced Biosciences Keio University Tsuruoka Japan
- Systems Biology Program Graduate School of Media and Governance Keio University Fujisawa Japan
| | - Takashi Nakada
- Institute for Advanced Biosciences Keio University Tsuruoka Japan
- Systems Biology Program Graduate School of Media and Governance Keio University Fujisawa Japan
- Faculty of Environment and Information Sciences Yokohama National University Yokohama Japan
| | - Takuro Ito
- Institute for Advanced Biosciences Keio University Tsuruoka Japan
- Systems Biology Program Graduate School of Media and Governance Keio University Fujisawa Japan
| | - Graham Bell
- Department of Biology McGill University Montreal QC Canada
| | - Nick Colegrave
- Institute of Evolutionary Biology School of Biological Sciences University of Edinburgh Edinburgh UK
| | - Peter D. Keightley
- Institute of Evolutionary Biology School of Biological Sciences University of Edinburgh Edinburgh UK
| | - Rob W. Ness
- Department of Biology University of Toronto Mississauga Mississauga ON Canada
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21
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Xu S, Stapley J, Gablenz S, Boyer J, Appenroth KJ, Sree KS, Gershenzon J, Widmer A, Huber M. Low genetic variation is associated with low mutation rate in the giant duckweed. Nat Commun 2019; 10:1243. [PMID: 30886148 PMCID: PMC6423293 DOI: 10.1038/s41467-019-09235-5] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 02/27/2019] [Indexed: 12/30/2022] Open
Abstract
Mutation rate and effective population size (Ne) jointly determine intraspecific genetic diversity, but the role of mutation rate is often ignored. Here we investigate genetic diversity, spontaneous mutation rate and Ne in the giant duckweed (Spirodela polyrhiza). Despite its large census population size, whole-genome sequencing of 68 globally sampled individuals reveals extremely low intraspecific genetic diversity. Assessed under natural conditions, the genome-wide spontaneous mutation rate is at least seven times lower than estimates made for other multicellular eukaryotes, whereas Ne is large. These results demonstrate that low genetic diversity can be associated with large-Ne species, where selection can reduce mutation rates to very low levels. This study also highlights that accurate estimates of mutation rate can help to explain seemingly unexpected patterns of genome-wide variation.
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Affiliation(s)
- Shuqing Xu
- Institute for Evolution and Biodiversity, University of Münster, Hüfferstrasse 1, 48149, Münster, Germany.
| | - Jessica Stapley
- Center for Adaptation to a Changing Environment, ETH Zurich, Universitätstrasse 16, 8092, Zürich, Switzerland
| | - Saskia Gablenz
- Department of Biochemistry, Max Planck Institute for Chemical Ecology, Hans-Knöll-Strasse 8, 07745, Jena, Germany
| | - Justin Boyer
- Department of Biochemistry, Max Planck Institute for Chemical Ecology, Hans-Knöll-Strasse 8, 07745, Jena, Germany
| | - Klaus J Appenroth
- Matthias-Schleiden-Institute, Plant Physiology, Friedrich Schiller University of Jena, Dornburgerstraße 159, 07743, Jena, Germany
| | - K Sowjanya Sree
- Department of Environmental Science, Central University of Kerala, Periye, 671316, India
| | - Jonathan Gershenzon
- Department of Biochemistry, Max Planck Institute for Chemical Ecology, Hans-Knöll-Strasse 8, 07745, Jena, Germany
| | - Alex Widmer
- Institute of Integrative Biology, ETH Zurich, Universitätstrasse 16, 8092, Zürich, Switzerland
| | - Meret Huber
- Department of Biochemistry, Max Planck Institute for Chemical Ecology, Hans-Knöll-Strasse 8, 07745, Jena, Germany.
- Institute of Plant Biology and Biotechnology, University of Münster, Schlossplatz 7, 48143, Münster, Germany.
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