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Filatov DA, Kirkpatrick M. How does evolution work in superabundant microbes? Trends Microbiol 2024:S0966-842X(24)00024-6. [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] [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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Dillon EM, Dunne EM, Womack TM, Kouvari M, Larina E, Claytor JR, Ivkić A, Juhn M, Carmona PSM, Robson SV, Saha A, Villafaña JA, Zill ME. Challenges and directions in analytical paleobiology. PALEOBIOLOGY 2023; 49:377-393. [PMID: 37809321 PMCID: PMC7615171 DOI: 10.1017/pab.2023.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Over the last 50 years, access to new data and analytical tools has expanded the study of analytical paleobiology, contributing to innovative analyses of biodiversity dynamics over Earth's history. Despite-or even spurred by-this growing availability of resources, analytical paleobiology faces deep-rooted obstacles that stem from the need for more equitable access to data and best practices to guide analyses of the fossil record. Recent progress has been accelerated by a collective push toward more collaborative, interdisciplinary, and open science, especially by early-career researchers. Here, we survey four challenges facing analytical paleobiology from an early-career perspective: (1) accounting for biases when interpreting the fossil record; (2) integrating fossil and modern biodiversity data; (3) building data science skills; and (4) increasing data accessibility and equity. We discuss recent efforts to address each challenge, highlight persisting barriers, and identify tools that have advanced analytical work. Given the inherent linkages between these challenges, we encourage discourse across disciplines to find common solutions. We also affirm the need for systemic changes that reevaluate how we conduct and share paleobiological research.
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Affiliation(s)
- Erin M. Dillon
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, California 93106, U.S.A.; Smithsonian Tropical Research Institute, Balboa, Republic of Panama
| | - Emma M. Dunne
- GeoZentrum Nordbayern, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany; School of Geography, Earth and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Tom M. Womack
- School of Geography, Environment and Earth Sciences, Victoria University of Wellington, P.O. Box 600, Wellington, New Zealand
| | - Miranta Kouvari
- Department of Earth Sciences, University College London, Gower Street, London WC1E 6BT, United Kingdom; Life Sciences Department, Natural History Museum, Cromwell Road, London SW7 5BD, United Kingdom
| | - Ekaterina Larina
- Jackson School of Geosciences, University of Texas, Austin, Texas 78712, U.S.A
| | - Jordan Ray Claytor
- Department of Biology, University of Washington, Seattle, Washington 98195, U.S.A; Burke Museum of Natural History and Culture, Seattle, Washington 98195, U.S.A
| | - Angelina Ivkić
- Department of Palaeontology, University of Vienna, Josef-Holaubek-Platz 2,1090 Vienna, Austria
| | - Mark Juhn
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, California 90095, U.S.A
| | - Pablo S. Milla Carmona
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Ciencias Geológicas, Buenos Aires C1428EGA, Argentina; Instituto de Estudios Andinos “Don Pablo Groeber” (IDEAN, UBA-CONICET), Buenos Aires C1428EGA, Argentina
| | - Selina Viktor Robson
- Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Anwesha Saha
- Institute of Palaeobiology, Polish Academy of Sciences, ul. Twarda 51/55, 00-818 Warsaw, Poland; Laboratory of Paleogenetics and Conservation Genetics, Centre of New Technologies (CeNT), University of Warsaw, S. Banacha 2c, 02-097 Warsaw, Poland
| | - Jaime A. Villafaña
- Department of Palaeontology, University of Vienna, Josef-Holaubek-Platz 2, 1090 Vienna, Austria; Centro de Investigación en Recursos Naturales y Sustentabilidad, Universidad Bernardo O ‘Higgins, Santiago 8370993, Chile
| | - Michelle E. Zill
- Department of Earth and Planetary Sciences, University of California Riverside, Riverside, California 92521, U.S.A
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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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Evolutionary Rates in the Haptophyta: Exploring Molecular and Phenotypic Diversity. JOURNAL OF MARINE SCIENCE AND ENGINEERING 2022. [DOI: 10.3390/jmse10060798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
Haptophytes are photosynthetic protists found in both freshwater and marine environments with an origin possibly dating back to the Neoproterozoic era. The most recent molecular phylogeny reveals several haptophyte “mystery clades” that await morphological verification, but it is otherwise highly consistent with morphology-based phylogenies, including that of the coccolithophores (calcifying haptophytes). The fossil coccolith record offers unique insights into extinct lineages, including the adaptive radiations that produced extant descendant species. By combining molecular data of extant coccolithophores and phenotype-based studies of their ancestral lineages, it has become possible to probe the modes and rates of speciation in more detail, although this approach is still limited to only few taxa because of the lack of whole-genome datasets. The evolution of calcification likely involved several steps, but its origin can be traced back to an early association with organic scales typical for all haptophytes. Other key haptophyte traits, including the haplo-diplontic life cycle, are herein mapped upon the coccolithophorid phylogeny to help navigate a discussion of their ecological benefits and trade-offs in a rapidly changing ocean.
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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: 1] [Impact Index Per Article: 0.5] [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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