1
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Anderson RP, Mughal S, Wedlake GO. Proterozoic microfossils continue to provide new insights into the rise of complex eukaryotic life. ROYAL SOCIETY OPEN SCIENCE 2024; 11:240154. [PMID: 39170929 PMCID: PMC11336685 DOI: 10.1098/rsos.240154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 07/11/2024] [Accepted: 07/12/2024] [Indexed: 08/23/2024]
Abstract
Eukaryotes have evolved to dominate the biosphere today, accounting for most documented living species and the vast majority of the Earth's biomass. Consequently, understanding how these biologically complex organisms initially diversified in the Proterozoic Eon over 539 million years ago is a foundational question in evolutionary biology. Over the last 70 years, palaeontologists have sought to document the rise of eukaryotes with fossil evidence. However, the delicate and microscopic nature of their sub-cellular features affords early eukaryotes diminished preservation potential. Chemical biomarker signatures of eukaryotes and the genetics of living eukaryotes have emerged as complementary tools for reconstructing eukaryote ancestry. In this review, we argue that exceptionally preserved Proterozoic microfossils are critical to interpreting these complementary tools, providing crucial calibrations to molecular clocks and testing hypotheses of palaeoecology. We highlight recent research on their preservation and biomolecular composition that offers new ways to enhance their utility.
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Affiliation(s)
- Ross P. Anderson
- Museum of Natural History, University of Oxford, OxfordOX1 3PW, UK
- All Souls College, University of Oxford, OxfordOX1 4AL, UK
| | - Sanaa Mughal
- Department of Earth and Atmospheric Sciences, University of Alberta, Edmonton, AlbertaT6G 2E3, Canada
| | - George O. Wedlake
- Department of Earth Sciences, University of Oxford, Oxford OX1 3AN, UK
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2
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Demoulin CF, Sforna MC, Lara YJ, Cornet Y, Somogyi A, Medjoubi K, Grolimund D, Sanchez DF, Tachoueres RT, Addad A, Fadel A, Compère P, Javaux EJ. Polysphaeroides filiformis, a proterozoic cyanobacterial microfossil and implications for cyanobacteria evolution. iScience 2024; 27:108865. [PMID: 38313056 PMCID: PMC10837632 DOI: 10.1016/j.isci.2024.108865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 11/29/2023] [Accepted: 01/08/2024] [Indexed: 02/06/2024] Open
Abstract
Deciphering the fossil record of cyanobacteria is crucial to understand their role in the chemical and biological evolution of the early Earth. They profoundly modified the redox conditions of early ecosystems more than 2.4 Ga ago, the age of the Great Oxidation Event (GOE), and provided the ancestor of the chloroplast by endosymbiosis, leading the diversification of photosynthetic eukaryotes. Here, we analyze the morphology, ultrastructure, chemical composition, and metals distribution of Polysphaeroides filiformis from the 1040-1006 Ma Mbuji-Mayi Supergroup (DR Congo). We evidence trilaminar and bilayered ultrastructures for the sheath and the cell wall, respectively, and the preservation of Ni-tetrapyrrole moieties derived from chlorophyll in intracellular inclusions. This approach allows an unambiguous interpretation of P. filiformis as a branched and multiseriate photosynthetic cyanobacterium belonging to the family of Stigonemataceae. It also provides a possible minimum age for the emergence of multiseriate true branching nitrogen-fixing and probably heterocytous cyanobacteria.
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Affiliation(s)
- Catherine F Demoulin
- Early Life Traces & Evolution-Astrobiology, UR Astrobiology, University of Liège, 4000 Liège, Belgium
| | - Marie Catherine Sforna
- Early Life Traces & Evolution-Astrobiology, UR Astrobiology, University of Liège, 4000 Liège, Belgium
- Centre de Biophysique Moléculaire, (UPR CNRS 4301), 45071 Orléans, France
| | - Yannick J Lara
- Early Life Traces & Evolution-Astrobiology, UR Astrobiology, University of Liège, 4000 Liège, Belgium
| | - Yohan Cornet
- Early Life Traces & Evolution-Astrobiology, UR Astrobiology, University of Liège, 4000 Liège, Belgium
| | | | | | - Daniel Grolimund
- Paul Scherrer Institut, Swiss Light Source, 5232 Villigen PSI, Switzerland
| | | | | | - Ahmed Addad
- Unité Matériaux et Transformations (UMR CNRS 8207), Université Lille 1 - Sciences et Technologies, 59650 Villeneuve d'Ascq, France
| | - Alexandre Fadel
- Unité Matériaux et Transformations (UMR CNRS 8207), Université Lille 1 - Sciences et Technologies, 59650 Villeneuve d'Ascq, France
| | - Philippe Compère
- Functional and Evolutive Morphology, UR FOCUS, and Center for Applied Research and Education in Microscopy (CAREM-ULiege), University of Liège, 4000 Liège, Belgium
| | - Emmanuelle J Javaux
- Early Life Traces & Evolution-Astrobiology, UR Astrobiology, University of Liège, 4000 Liège, Belgium
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3
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Jin Z, Wang X, Wang H, Ye Y, Zhang S. Organic carbon cycling and black shale deposition: an Earth System Science perspective. Natl Sci Rev 2023; 10:nwad243. [PMID: 37900193 PMCID: PMC10612131 DOI: 10.1093/nsr/nwad243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 08/15/2023] [Accepted: 08/27/2023] [Indexed: 10/31/2023] Open
Abstract
Earth has a prolonged history characterized by substantial cycling of matter and energy between multiple spheres. The production of organic carbon can be traced back to as early as ∼4.0 Ga, but the frequency and scale of organic-rich shales have varied markedly over geological time. In this paper, we discuss the organic carbon cycle and the development of black shale from the perspective of Earth System Science. We propose that black shale depositions are the results of interactions among lithospheric evolution, orbital forcing, weathering, photosynthesis and degradation. Black shales can record Earth's oxygenation process, provide petroleum and metallic mineral resources and reveal information about the driver, direction and magnitude of climate change. Future research on black shales should be expanded to encompass a more extensive and more multidimensional perspective.
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Affiliation(s)
- Zhijun Jin
- Institute of Energy, Peking University, Beijing100871, China
| | - Xiaomei Wang
- Key Laboratory of Petroleum Geochemistry, Central Laboratory of Geological Sciences, Research Institute of Petroleum Exploration and Development, China National Petroleum Corporation, Beijing100083, China
| | - Huajian Wang
- Key Laboratory of Petroleum Geochemistry, Central Laboratory of Geological Sciences, Research Institute of Petroleum Exploration and Development, China National Petroleum Corporation, Beijing100083, China
| | - Yuntao Ye
- Key Laboratory of Petroleum Geochemistry, Central Laboratory of Geological Sciences, Research Institute of Petroleum Exploration and Development, China National Petroleum Corporation, Beijing100083, China
- Key Laboratory of Orogenic Belts and Crustal Evolution, Ministry of Education, School of Earth and Space Sciences, Peking University, Beijing100871, China
| | - Shuichang Zhang
- Key Laboratory of Petroleum Geochemistry, Central Laboratory of Geological Sciences, Research Institute of Petroleum Exploration and Development, China National Petroleum Corporation, Beijing100083, China
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4
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Brocks JJ, Nettersheim BJ, Adam P, Schaeffer P, Jarrett AJM, Güneli N, Liyanage T, van Maldegem LM, Hallmann C, Hope JM. Lost world of complex life and the late rise of the eukaryotic crown. Nature 2023:10.1038/s41586-023-06170-w. [PMID: 37286610 DOI: 10.1038/s41586-023-06170-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 05/04/2023] [Indexed: 06/09/2023]
Abstract
Eukaryotic life appears to have flourished surprisingly late in the history of our planet. This view is based on the low diversity of diagnostic eukaryotic fossils in marine sediments of mid-Proterozoic age (around 1,600 to 800 million years ago) and an absence of steranes, the molecular fossils of eukaryotic membrane sterols1,2. This scarcity of eukaryotic remains is difficult to reconcile with molecular clocks that suggest that the last eukaryotic common ancestor (LECA) had already emerged between around 1,200 and more than 1,800 million years ago. LECA, in turn, must have been preceded by stem-group eukaryotic forms by several hundred million years3. Here we report the discovery of abundant protosteroids in sedimentary rocks of mid-Proterozoic age. These primordial compounds had previously remained unnoticed because their structures represent early intermediates of the modern sterol biosynthetic pathway, as predicted by Konrad Bloch4. The protosteroids reveal an ecologically prominent 'protosterol biota' that was widespread and abundant in aquatic environments from at least 1,640 to around 800 million years ago and that probably comprised ancient protosterol-producing bacteria and deep-branching stem-group eukaryotes. Modern eukaryotes started to appear in the Tonian period (1,000 to 720 million years ago), fuelled by the proliferation of red algae (rhodophytes) by around 800 million years ago. This 'Tonian transformation' emerges as one of the most profound ecological turning points in the Earth's history.
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Affiliation(s)
- Jochen J Brocks
- Research School of Earth Sciences, The Australian National University, Canberra, Australian Capital Territory, Australia.
| | - Benjamin J Nettersheim
- Research School of Earth Sciences, The Australian National University, Canberra, Australian Capital Territory, Australia.
- MARUM-Center for Marine Environmental Sciences and Faculty of Geosciences, University of Bremen, Bremen, Germany.
| | - Pierre Adam
- Université de Strasbourg, CNRS, Institut de Chimie de Strasbourg UMR 7177, Strasbourg, France
| | - Philippe Schaeffer
- Université de Strasbourg, CNRS, Institut de Chimie de Strasbourg UMR 7177, Strasbourg, France
| | - Amber J M Jarrett
- Research School of Earth Sciences, The Australian National University, Canberra, Australian Capital Territory, Australia
- Northern Territory Geological Survey, Darwin, Northern Territory, Australia
| | - Nur Güneli
- Research School of Earth Sciences, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Tharika Liyanage
- Research School of Earth Sciences, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Lennart M van Maldegem
- Research School of Earth Sciences, The Australian National University, Canberra, Australian Capital Territory, Australia
| | | | - Janet M Hope
- Research School of Earth Sciences, The Australian National University, Canberra, Australian Capital Territory, Australia
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5
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Moore KR, Daye M, Gong J, Williford K, Konhauser K, Bosak T. A review of microbial-environmental interactions recorded in Proterozoic carbonate-hosted chert. GEOBIOLOGY 2023; 21:3-27. [PMID: 36268586 PMCID: PMC10092529 DOI: 10.1111/gbi.12527] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 09/14/2022] [Accepted: 09/19/2022] [Indexed: 06/16/2023]
Abstract
The record of life during the Proterozoic is preserved by several different lithologies, but two in particular are linked both spatially and temporally: chert and carbonate. These lithologies capture a snapshot of dominantly peritidal environments during the Proterozoic. Early diagenetic chert preserves some of the most exceptional Proterozoic biosignatures in the form of microbial body fossils and mat textures. This fossiliferous and kerogenous chert formed in shallow marine environments, where chert nodules, layers, and lenses are often surrounded by and encased within carbonate deposits that themselves often contain kerogen and evidence of former microbial mats. Here, we review the record of biosignatures preserved in peritidal Proterozoic chert and chert-hosting carbonate and discuss this record in the context of experimental and environmental studies that have begun to shed light on the roles that microbes and organic compounds may have played in the formation of these deposits. Insights gained from these studies suggest temporal trends in microbial-environmental interactions and place new constraints on past environmental conditions, such as the concentration of silica in Proterozoic seawater, interactions among organic compounds and cations in seawater, and the influence of microbial physiology and biochemistry on selective preservation by silicification.
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Affiliation(s)
- Kelsey R. Moore
- Division of Geological and Planetary SciencesCalifornia Institute of TechnologyPasadenaCaliforniaUSA
| | - Mirna Daye
- Department of Earth, Atmospheric and Planetary SciencesMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
| | - Jian Gong
- Department of Earth, Atmospheric and Planetary SciencesMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
| | | | - Kurt Konhauser
- Department of Earth and Atmospheric SciencesUniversity of AlbertaEdmontonAlbertaCanada
| | - Tanja Bosak
- Department of Earth, Atmospheric and Planetary SciencesMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
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6
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da Silva VS, Machado CR. Sex in protists: A new perspective on the reproduction mechanisms of trypanosomatids. Genet Mol Biol 2022; 45:e20220065. [PMID: 36218381 PMCID: PMC9552303 DOI: 10.1590/1678-4685-gmb-2022-0065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 08/07/2022] [Indexed: 11/04/2022] Open
Abstract
The Protist kingdom individuals are the most ancestral representatives of eukaryotes. They have inhabited Earth since ancient times and are currently found in the most diverse environments presenting a great heterogeneity of life forms. The unicellular and multicellular algae, photosynthetic and heterotrophic organisms, as well as free-living and pathogenic protozoa represents the protist group. The evolution of sex is directly associated with the origin of eukaryotes being protists the earliest protagonists of sexual reproduction on earth. In eukaryotes, the recombination through genetic exchange is a ubiquitous mechanism that can be stimulated by DNA damage. Scientific evidences support the hypothesis that reactive oxygen species (ROS) induced DNA damage can promote sexual recombination in eukaryotes which might have been a decisive factor for the origin of sex. The fact that some recombination enzymes also participate in meiotic sex in modern eukaryotes reinforces the idea that sexual reproduction emerged as consequence of specific mechanisms to cope with mutations and alterations in genetic material. In this review we will discuss about origin of sex and different strategies of evolve sexual reproduction in some protists such that cause human diseases like malaria, toxoplasmosis, sleeping sickness, Chagas disease, and leishmaniasis.
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Affiliation(s)
- Verônica Santana da Silva
- Universidade Federal de Minas Gerais, Departamento de Genética,
Ecologia e Evolução, Belo Horizonte, MG, Brazil
| | - Carlos Renato Machado
- Universidade Federal de Minas Gerais, Departamento de Bioquímica e
Imunologia, Belo Horizonte, MG, Brazil
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7
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Kim PS, Shin NR, Lee JB, Kim MS, Whon TW, Hyun DW, Yun JH, Jung MJ, Kim JY, Bae JW. Host habitat is the major determinant of the gut microbiome of fish. MICROBIOME 2021; 9:166. [PMID: 34332628 PMCID: PMC8325807 DOI: 10.1186/s40168-021-01113-x] [Citation(s) in RCA: 78] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 06/14/2021] [Indexed: 05/09/2023]
Abstract
BACKGROUND Our understanding of the gut microbiota of animals is largely based on studies of mammals. To better understand the evolutionary basis of symbiotic relationships between animal hosts and indigenous microbes, it is necessary to investigate the gut microbiota of non-mammalian vertebrate species. In particular, fish have the highest species diversity among groups of vertebrates, with approximately 33,000 species. In this study, we comprehensively characterized gut bacterial communities in fish. RESULTS We analyzed 227 individual fish representing 14 orders, 42 families, 79 genera, and 85 species. The fish gut microbiota was dominated by Proteobacteria (51.7%) and Firmicutes (13.5%), different from the dominant taxa reported in terrestrial vertebrates (Firmicutes and Bacteroidetes). The gut microbial community in fish was more strongly shaped by host habitat than by host taxonomy or trophic level. Using a machine learning approach trained on the microbial community composition or predicted functional profiles, we found that the host habitat exhibited the highest classification accuracy. Principal coordinate analysis revealed that the gut bacterial community of fish differs significantly from those of other vertebrate classes (reptiles, birds, and mammals). CONCLUSIONS Collectively, these data provide a reference for future studies of the gut microbiome of aquatic animals as well as insights into the relationship between fish and their gut bacteria, including the key role of host habitat and the distinct compositions in comparison with those of mammals, reptiles, and birds. Video Abstract.
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Affiliation(s)
- Pil Soo Kim
- Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Dongdaemun-gu, Seoul, 02447 Republic of Korea
| | - Na-Ri Shin
- Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Dongdaemun-gu, Seoul, 02447 Republic of Korea
- Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup, Jeollabuk-do 56212 Republic of Korea
| | - Jae-Bong Lee
- Distant-water Fisheries Resources Division, National Institute of Fisheries Science, Gijang-eup, Busan, 46083 Republic of Korea
| | - Min-Soo Kim
- Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Dongdaemun-gu, Seoul, 02447 Republic of Korea
| | - Tae Woong Whon
- Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Dongdaemun-gu, Seoul, 02447 Republic of Korea
| | - Dong-Wook Hyun
- Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Dongdaemun-gu, Seoul, 02447 Republic of Korea
| | - Ji-Hyun Yun
- Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Dongdaemun-gu, Seoul, 02447 Republic of Korea
| | - Mi-Ja Jung
- Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Dongdaemun-gu, Seoul, 02447 Republic of Korea
| | - Joon Yong Kim
- Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Dongdaemun-gu, Seoul, 02447 Republic of Korea
| | - Jin-Woo Bae
- Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Dongdaemun-gu, Seoul, 02447 Republic of Korea
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8
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Precambrian and early Cambrian palaeobiology of India: Quo Vadis. PROCEEDINGS OF THE INDIAN NATIONAL SCIENCE ACADEMY 2021. [DOI: 10.1007/s43538-021-00029-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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9
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Abstract
Diagnosis and treatment of disease demand a sound understanding of the underlying mechanisms, determining any Achilles' heel that can be targeted in effective therapies. Throughout history, this endeavour to decipher the origin and mechanism of transformation of a normal cell into cancer has led to various theories-from cancer as a curse to an understanding at the level of single-cell heterogeneity, meaning even among a single sub-type of cancer there are myriad molecular challenges to overcome. With increasing insight into cancer genetics and biology, the disease has become ever more complex to understand. The complexity of cancer as a disease was distilled into key traits by Hanahan and Weinberg in their seminal 'Hallmarks of Cancer' reviews. This lucid conceptualization of complex cancer biology is widely accepted and has helped advance cancer therapeutics by targeting the various hallmarks but, with the advancement in technologies, there is greater granularity in how we view cancer as a disease, and the additional understanding over the past decade requires us to revisit the hallmarks of cancer. Based on extensive study of the cancer research literature, we propose four novel hallmarks of cancer, namely, the ability of cells to regress from a specific specialized functional state, epigenetic changes that can affect gene expression, the role of microorganisms and neuronal signalling, to be included in the hallmark conceptualization along with evidence of various means to exploit them therapeutically.
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Affiliation(s)
- Sasi S. Senga
- Centre for Tumour Biology, Barts Cancer Institute, Queen
Mary University of London, London EC1M
6BQ, UK
| | - Richard P. Grose
- Centre for Tumour Biology, Barts Cancer Institute, Queen
Mary University of London, London EC1M
6BQ, UK
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10
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Huang Q, Sham RC, Deng Y, Mao Y, Wang C, Zhang T, Leung KMY. Diversity of gut microbiomes in marine fishes is shaped by host-related factors. Mol Ecol 2020; 29:5019-5034. [PMID: 33084100 PMCID: PMC7756402 DOI: 10.1111/mec.15699] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 10/09/2020] [Accepted: 10/13/2020] [Indexed: 12/25/2022]
Abstract
Microorganisms in the gastrointestinal tract of animals play vital roles in food digestion, homeostasis and immune response regulation. Globally, there are 33,700 fish species, representing almost half of all vertebrate diversity and a wide range of physiologies, ecologies and life histories. To investigate gut microbiomes with high coverage, we performed 16S rRNA gene amplicon sequencing with 115 samples of 20 common marine fish species. The fish gut microbiome is a remarkably simple community with low microbial diversity (a maximum of 300 amplicon sequence variants only) and has up to 70% of unknown species in some fish species. The gut microbial community structure was significantly shaped by the combined influence of host-associated factors, including the fish taxon (p < .001, R2 = 0.16, ω2 = 0.04), feeding habit (p < .001, R2 = 0.06, ω2 = 0.02) and trophic level (p < .01, R2 = 0.04, ω2 = 0.01), although the influence was subtle with a small effect size. The core gut microbiomes of different feeding habits were also previously discovered in animal-associated and corresponding habitat samples. Certain energy metabolism pathways were enriched in herbivore/omnivore and zooplanktivore/zoobenthivore fishes, whereas lipid metabolism and glycan metabolism were enriched in zoobenthivore/piscivore fishes. Moreover, substantial taxonomic variability was found between the gut microbiomes of fish and animals, indicated by their low degree of shared microbiota. The data and observations reported herein pave the way for further investigations on the co-evolution of fish gut microbiomes and their hosts, the physiological functions of gut microorganisms and the development of probiotics for improving the nutrition and health of aquaculture fish species.
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Affiliation(s)
- Qi Huang
- School of Biological SciencesThe University of Hong KongHong KongChina
- Department of Civil EngineeringEnvironmental Microbiome Engineering and Biotechnology LabThe University of Hong KongHong KongChina
| | - Ronia C. Sham
- School of Biological SciencesThe University of Hong KongHong KongChina
| | - Yu Deng
- Department of Civil EngineeringEnvironmental Microbiome Engineering and Biotechnology LabThe University of Hong KongHong KongChina
| | - Yanping Mao
- Department of Civil EngineeringEnvironmental Microbiome Engineering and Biotechnology LabThe University of Hong KongHong KongChina
- College of Chemistry and Environmental EngineeringShenzhen UniversityShenzhenChina
| | - Chunxiao Wang
- Department of Civil EngineeringEnvironmental Microbiome Engineering and Biotechnology LabThe University of Hong KongHong KongChina
| | - Tong Zhang
- Department of Civil EngineeringEnvironmental Microbiome Engineering and Biotechnology LabThe University of Hong KongHong KongChina
| | - Kenneth M. Y. Leung
- School of Biological SciencesThe University of Hong KongHong KongChina
- State Key Laboratory of Marine Pollution and Department of ChemistryCity University of Hong KongHong KongChina
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11
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van Maldegem LM, Nettersheim BJ, Leider A, Brocks JJ, Adam P, Schaeffer P, Hallmann C. Geological alteration of Precambrian steroids mimics early animal signatures. Nat Ecol Evol 2020; 5:169-173. [PMID: 33230255 DOI: 10.1038/s41559-020-01336-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 09/23/2020] [Indexed: 11/09/2022]
Abstract
The absence of unambiguous animal body fossils in rocks older than the late Ediacaran has rendered fossil lipids the most promising tracers of early organismic complexity. Yet much debate surrounds the various potential biological sources of putative metazoan steroids found in Precambrian rocks. Here we show that 26-methylated steranes-hydrocarbon structures currently attributed to the earliest animals-can form via geological alteration of common algal sterols, which carries important implications for palaeo-ecological interpretations and inhibits the use of such unconventional 'sponge' steranes for reconstructing early animal evolution.
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Affiliation(s)
- Lennart M van Maldegem
- Max Planck Institute for Biogeochemistry, Jena, Germany. .,MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany. .,The Australian National University, Canberra, Australian Capital Territory, Australia.
| | - Benjamin J Nettersheim
- Max Planck Institute for Biogeochemistry, Jena, Germany. .,MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany.
| | - Arne Leider
- Max Planck Institute for Biogeochemistry, Jena, Germany.,MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Jochen J Brocks
- The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Pierre Adam
- University of Strasbourg, CNRS-UMR 7177, Strasbourg, France
| | | | - Christian Hallmann
- Max Planck Institute for Biogeochemistry, Jena, Germany. .,MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany.
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12
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Abstract
Phagocytosis, or 'cell eating', is a eukaryote-specific process where particulate matter is engulfed via invaginations of the plasma membrane. The origin of phagocytosis has been central to discussions on eukaryogenesis for decades-, where it is argued as being either a prerequisite for, or consequence of, the acquisition of the ancestral mitochondrion. Recently, genomic and cytological evidence has increasingly supported the view that the pre-mitochondrial host cell-a bona fide archaeon branching within the 'Asgard' archaea-was incapable of phagocytosis and used alternative mechanisms to incorporate the alphaproteobacterial ancestor of mitochondria. Indeed, the diversity and variability of proteins associated with phagosomes across the eukaryotic tree suggest that phagocytosis, as seen in a variety of extant eukaryotes, may have evolved independently several times within the eukaryotic crown-group. Since phagocytosis is critical to the functioning of modern marine food webs (without it, there would be no microbial loop or animal life), multiple late origins of phagocytosis could help explain why many of the ecological and evolutionary innovations of the Neoproterozoic Era (e.g. the advent of eukaryotic biomineralization, the 'Rise of Algae' and the origin of animals) happened when they did.
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Affiliation(s)
- Daniel B. Mills
- Department of Geological Sciences, Stanford University, Stanford, CA 94305, USA
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13
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Nan FR, Feng J, Lv JP, Liu Q, Liu XD, Gao F, Xie SL. Comparison of the transcriptomes of different life history stages of the freshwater Rhodophyte Thorea hispida. Genomics 2020; 112:3978-3990. [PMID: 32650096 DOI: 10.1016/j.ygeno.2020.07.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 03/04/2020] [Accepted: 07/02/2020] [Indexed: 10/23/2022]
Abstract
Thorea hispida exclusively inhabits freshwater environments and is characterized by a triphasic life history. In this study, the organelle genomes and transcriptomes of different life history stages of T. hispida were examined using next generation sequencing. The chloroplast and mitochondrial genomes of the chantransia stage were 175,747 and 25,411 bp in length, respectively. The chantransia stage was highly similar to the gametophyte stage based on comparisons of organelle genomes and phylogenetic reconstruction. Transcriptomic comparisons of two stages found that ribosome-related genes were the most up-regulated in the gametophyte stage of T. hispida. Seven meiosis-specific genes, including SPO11 initiator of meiotic double-stranded breaks(spo11), meiotic nuclear divisions 1(mnd1), RAD51 recombinase(rad51), mutS homolog 4(msh4), mutS homolog 5(msh5), REC8 meiotic recombination protein(rec8), and DNA helicase Mer3(mer3), were differentially regulated between the two life history stages. The organelle genomes and transcriptomes from T. hispida provided in this study will be valuable for future studies of freshwater red algae.
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Affiliation(s)
- Fang-Ru Nan
- School of Life Science, Shanxi University, Taiyuan, China
| | - Jia Feng
- School of Life Science, Shanxi University, Taiyuan, China
| | - Jun-Ping Lv
- School of Life Science, Shanxi University, Taiyuan, China
| | - Qi Liu
- School of Life Science, Shanxi University, Taiyuan, China
| | - Xu-Dong Liu
- School of Life Science, Shanxi University, Taiyuan, China
| | - Fan Gao
- School of Life Science, Shanxi University, Taiyuan, China
| | - Shu-Lian Xie
- School of Life Science, Shanxi University, Taiyuan, China.
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14
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Demoulin CF, Lara YJ, Cornet L, François C, Baurain D, Wilmotte A, Javaux EJ. Cyanobacteria evolution: Insight from the fossil record. Free Radic Biol Med 2019; 140:206-223. [PMID: 31078731 PMCID: PMC6880289 DOI: 10.1016/j.freeradbiomed.2019.05.007] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 03/13/2019] [Accepted: 05/05/2019] [Indexed: 11/07/2022]
Abstract
Cyanobacteria played an important role in the evolution of Early Earth and the biosphere. They are responsible for the oxygenation of the atmosphere and oceans since the Great Oxidation Event around 2.4 Ga, debatably earlier. They are also major primary producers in past and present oceans, and the ancestors of the chloroplast. Nevertheless, the identification of cyanobacteria in the early fossil record remains ambiguous because the morphological criteria commonly used are not always reliable for microfossil interpretation. Recently, new biosignatures specific to cyanobacteria were proposed. Here, we review the classic and new cyanobacterial biosignatures. We also assess the reliability of the previously described cyanobacteria fossil record and the challenges of molecular approaches on modern cyanobacteria. Finally, we suggest possible new calibration points for molecular clocks, and strategies to improve our understanding of the timing and pattern of the evolution of cyanobacteria and oxygenic photosynthesis.
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Affiliation(s)
- Catherine F Demoulin
- Early Life Traces & Evolution - Astrobiology, UR ASTROBIOLOGY, Geology Department, University of Liège, Liège, Belgium.
| | - Yannick J Lara
- Early Life Traces & Evolution - Astrobiology, UR ASTROBIOLOGY, Geology Department, University of Liège, Liège, Belgium
| | - Luc Cornet
- Early Life Traces & Evolution - Astrobiology, UR ASTROBIOLOGY, Geology Department, University of Liège, Liège, Belgium; Eukaryotic Phylogenomics, InBioS-PhytoSYSTEMS, University of Liège, Liège, Belgium
| | - Camille François
- Early Life Traces & Evolution - Astrobiology, UR ASTROBIOLOGY, Geology Department, University of Liège, Liège, Belgium
| | - Denis Baurain
- Eukaryotic Phylogenomics, InBioS-PhytoSYSTEMS, University of Liège, Liège, Belgium
| | - Annick Wilmotte
- BCCM/ULC Cyanobacteria Collection, InBioS-CIP, Centre for Protein Engineering, University of Liège, Liège, Belgium
| | - Emmanuelle J Javaux
- Early Life Traces & Evolution - Astrobiology, UR ASTROBIOLOGY, Geology Department, University of Liège, Liège, Belgium
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15
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Braakman R. Evolution of cellular metabolism and the rise of a globally productive biosphere. Free Radic Biol Med 2019; 140:172-187. [PMID: 31082508 DOI: 10.1016/j.freeradbiomed.2019.05.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 02/28/2019] [Accepted: 05/02/2019] [Indexed: 01/14/2023]
Abstract
Metabolic processes in cells and chemical processes in the environment are fundamentally intertwined and have evolved in concert for most of Earth's existence. Here I argue that intrinsic properties of cellular metabolism imposed central constraints on the historical trajectories of biopsheric productivity and atmospheric oxygenation. Photosynthesis depends on iron, but iron is highly insoluble under the aerobic conditions produced by oxygenic photosynthesis. These counteracting constraints led to two major stages of Earth oxygenation. After a cyanobacteria-driven biospheric expansion near the Archean-Proterozoic boundary, productivity remained largely restricted to continental boundaries and shallow aquatic environments where weathering inputs made iron more accessible. The anoxic deep open ocean was rich in free iron during the Proterozoic, but this iron was largely inaccessible, partly because an otherwise nutrient-poor ocean was limiting to photosynthesis, but also because a photosynthetic expansion would have quenched its own iron supply. Near the Proterozoic-Phanerozoic boundary, bioenergetics innovations allowed eukaryotic photosynthesis to overcome these interconnected negative feedbacks and begin expanding into the deep open oceans and onto the continents, where nutrients are inherently harder to come by. Key insights into what drove the ecological rise of eukaryotic photosynthesis emerge from analyses of marine Synechococcus and Prochlorococcus, abundant marine picocyanobacteria whose ancestors colonized the oceans in the Neoproterozoic. The reconstructed evolution of this group reveals a sequence of innovations that ultimately produced a form of photosynthesis in Prochlorococcus that is more like that of green plant cells than other cyanobacteria. Innovations increased the energy flux of cells, thereby enhancing their ability to acquire sparse nutrients, and as by-product also increased the production of organic carbon waste. Some of these organic waste products had the ability to chelate iron and make it bioavailable, thereby indirectly pushing the oceans through a transition from an anoxic state rich in free iron to an oxygenated state with organic carbon-bound iron. Resulting conditions (and parallel processes on the continents) in turn led to a series of positive feedbacks that increased the availability of other nutrients, thereby promoting the rise of a globally productive biosphere. In addition to the occurrence of major biospheric expansions, the several hundred million-year periods around the Archean-Proterozoic and Proterozoic-Phanerozoic boundaries share a number of other parallels. Both epochs have also been linked to major carbon cycle perturbations and global glaciations, as well as changes in the nature of plate tectonics and increases in continental exposure and weathering. This suggests the dynamics of life and Earth are intimately intertwined across many levels and that general principles governed transitions in these coupled dynamics at both times in Earth history.
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Affiliation(s)
- Rogier Braakman
- Department of Civil & Environmental Engineering, Massachusetts Institute of Technology, USA; Department of Earth, Atmospheric & Planetary Sciences, Massachusetts Institute of Technology, USA.
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16
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Barlow EV, Van Kranendonk MJ. Snapshot of an early Paleoproterozoic ecosystem: Two diverse microfossil communities from the Turee Creek Group, Western Australia. GEOBIOLOGY 2018; 16:449-475. [PMID: 30091832 DOI: 10.1111/gbi.12304] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2017] [Revised: 05/22/2018] [Accepted: 06/04/2018] [Indexed: 06/08/2023]
Abstract
Eighteen microfossil morphotypes from two distinct facies of black chert from a deep-water setting of the c. 2.4 Ga Turee Creek Group, Western Australia, are reported here. A primarily in situ, deep-water benthic community preserved in nodular black chert occurs as a tangled network of a variety of long filamentous microfossils, unicells of one size distribution and fine filamentous rosettes, together with relatively large spherical aggregates of cells interpreted as in-fallen, likely planktonic, forms. Bedded black cherts, in contrast, preserve microfossils primarily within, but also between, rounded clasts of organic material that are coated by thin, convoluted carbonaceous films interpreted as preserved extracellular polymeric substance (EPS). Microfossils preserved within the clasts include a wide range of unicells, both much smaller and larger than those in the nodular black chert, along with relatively short, often degraded filaments, four types of star-shaped rosettes and umbrella-like rosettes. Large, complexly branching filamentous microfossils are found between the clasts. The grainstone clasts in the bedded black chert are interpreted as transported from shallower water, and the contained microfossils thus likely represent a phototrophic community. Combined, the two black chert facies provide a snapshot of a microbial ecosystem spanning shallow to deeper-water environments, and an insight into the diversity of life present during the rise in atmospheric oxygen. The preserved microfossils include two new, distinct morphologies previously unknown from the geological record, as well as a number of microfossils from the bedded black chert that are morphologically similar to-but 400-500 Ma older than-type specimens from the c. 1.88 Ga Gunflint Iron Formation. Thus, the Turee Creek Group microfossil assemblage creates a substantial reference point in the sparse fossil record of the earliest Paleoproterozoic and demonstrates that microbial life diversified quite rapidly after the end of the Archean.
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Affiliation(s)
- Erica Victoria Barlow
- Australian Centre for Astrobiology, School of Biological, Earth and Environmental Sciences, University of New South Wales, Kensington, New South Wales, Australia
- Australian Research Council Centre of Excellence for Core to Crust Fluid Systems (CCFS), Macquarie University, Sydney, New South Wales, Australia
| | - Martin Julian Van Kranendonk
- Australian Centre for Astrobiology, School of Biological, Earth and Environmental Sciences, University of New South Wales, Kensington, New South Wales, Australia
- Australian Research Council Centre of Excellence for Core to Crust Fluid Systems (CCFS), Macquarie University, Sydney, New South Wales, Australia
- Big Questions Institute, University of New South Wales, Kensington, New South Wales, Australia
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17
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Integrated genomic and fossil evidence illuminates life's early evolution and eukaryote origin. Nat Ecol Evol 2018; 2:1556-1562. [PMID: 30127539 PMCID: PMC6152910 DOI: 10.1038/s41559-018-0644-x] [Citation(s) in RCA: 182] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2018] [Accepted: 07/13/2018] [Indexed: 11/08/2022]
Abstract
Establishing a unified timescale for the early evolution of Earth and life is challenging and mired in controversy because of the paucity of fossil evidence, the difficulty of interpreting it and dispute over the deepest branching relationships in the tree of life. Surprisingly, it remains perhaps the only episode in the history of life where literal interpretations of the fossil record hold sway, revised with every new discovery and reinterpretation. We derive a timescale of life, combining a reappraisal of the fossil material with new molecular clock analyses. We find the last universal common ancestor of cellular life to have predated the end of late heavy bombardment (>3.9 billion years ago (Ga)). The crown clades of the two primary divisions of life, Eubacteria and Archaebacteria, emerged much later (<3.4 Ga), relegating the oldest fossil evidence for life to their stem lineages. The Great Oxidation Event significantly predates the origin of modern Cyanobacteria, indicating that oxygenic photosynthesis evolved within the cyanobacterial stem lineage. Modern eukaryotes do not constitute a primary lineage of life and emerged late in Earth's history (<1.84 Ga), falsifying the hypothesis that the Great Oxidation Event facilitated their radiation. The symbiotic origin of mitochondria at 2.053-1.21 Ga reflects a late origin of the total-group Alphaproteobacteria to which the free living ancestor of mitochondria belonged.
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18
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The first plastid genome of a filamentous taxon 'Bangia' sp. OUCPT-01 in the Bangiales. Sci Rep 2018; 8:10688. [PMID: 30013114 PMCID: PMC6048033 DOI: 10.1038/s41598-018-29083-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 07/02/2018] [Indexed: 11/22/2022] Open
Abstract
Red algae are important primary photosynthetic organisms. The Bangiales comprise a morphologically diverse order of red algae. Until now, complete plastid genomes of the Bangiales were only mapped for foliose species. To date, no filamentous plastomes have been published. The aim of this study was to determine and analyze the complete plastid genome of the filamentous marine species ‘Bangia’ sp. OUCPT-01. It is a circular molecule, 196,913 bps in length with a guanine-cytosine (GC) content of 33.5%. It has a quadripartite structure with two single copy regions separated by two direct non-identical repeats. It has 205 protein-coding genes, 37 tRNAs, and 6 rRNAs. Therefore, it has a high coding capacity and is highly similar to other Bangiales species in terms of content and structure. In particular, it reveals that the genera in the Bangiales have highly conserved gene content and plastome synteny. This plastome and existing data provide insights into the phylogenetic relationships among the Bangiales genera of the Rhodophyta. According to its plastid- and mitochondrial genomes, ‘Bangia 2′ is a sister group to Porphyra. However, the position of Wildemania schizophylla in the Bangiales is still controversial. Our results show that the Bangiales divergence time was ~225 million years ago.
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1.1-billion-year-old porphyrins establish a marine ecosystem dominated by bacterial primary producers. Proc Natl Acad Sci U S A 2018; 115:E6978-E6986. [PMID: 29987033 DOI: 10.1073/pnas.1803866115] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The average cell size of marine phytoplankton is critical for the flow of energy and nutrients from the base of the food web to higher trophic levels. Thus, the evolutionary succession of primary producers through Earth's history is important for our understanding of the radiation of modern protists ∼800 million years ago and the emergence of eumetazoan animals ∼200 million years later. Currently, it is difficult to establish connections between primary production and the proliferation of large and complex organisms because the mid-Proterozoic (∼1,800-800 million years ago) rock record is nearly devoid of recognizable phytoplankton fossils. We report the discovery of intact porphyrins, the molecular fossils of chlorophylls, from 1,100-million-year-old marine black shales of the Taoudeni Basin (Mauritania), 600 million years older than previous findings. The porphyrin nitrogen isotopes (δ15Npor = 5.6-10.2‰) are heavier than in younger sedimentary sequences, and the isotopic offset between sedimentary bulk nitrogen and porphyrins (εpor = -5.1 to -0.5‰) points to cyanobacteria as dominant primary producers. Based on fossil carotenoids, anoxygenic green (Chlorobiacea) and purple sulfur bacteria (Chromatiaceae) also contributed to photosynthate. The low εpor values, in combination with a lack of diagnostic eukaryotic steranes in the time interval of 1,600-1,000 million years ago, demonstrate that algae played an insignificant role in mid-Proterozoic oceans. The paucity of algae and the small cell size of bacterial phytoplankton may have curtailed the flow of energy to higher trophic levels, potentially contributing to a diminished evolutionary pace toward complex eukaryotic ecosystems and large and active organisms.
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20
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The transition from a cyanobacterial to algal world and the emergence of animals. Emerg Top Life Sci 2018; 2:181-190. [PMID: 32412625 DOI: 10.1042/etls20180039] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 05/24/2018] [Accepted: 05/25/2018] [Indexed: 12/21/2022]
Abstract
The Neoproterozoic, 1000-541 million years (Myr) ago, saw the transition from a largely bacterial world to the emergence of multicellular grazers, suspension feeders and predators. This article explores the hypothesis that the first appearance of large, multicellular heterotrophs was fueled by an elevated supply of nutrients and carbon from the bottom of the food chain to higher trophic levels. A refined record of molecular fossils of algal sterols reveals that the transition from dominantly bacterial to eukaryotic primary production in open marine habitat occurred between 659 and 645 Myr ago, in the hot interlude between two Snowball Earth glaciations. This bacterial-eukaryotic transition reveals three characteristics: it was rapid on geological timescales, it followed an extreme environmental catastrophe and it was permanent - hallmarks of an ecological hysteresis that shifted Earth's oceans between two self-stabilizing steady states. More than 50 million years of Snowball glaciations and their hot aftermath may have purged old-world bacterial phytoplankton, providing empty but nutrient-rich ecospace for recolonization by larger algae and transforming the base of the food web. Elevated average and maximum particle sizes at the base of the food chain may have provided more efficient energy and nutrient transfer to higher trophic levels, fueling an arms race toward larger grazers, predators and prey, and the development of increasingly complex feeding and defense strategies.
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21
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Kacar B, Hanson‐Smith V, Adam ZR, Boekelheide N. Constraining the timing of the Great Oxidation Event within the Rubisco phylogenetic tree. GEOBIOLOGY 2017; 15:628-640. [PMID: 28670785 PMCID: PMC5575542 DOI: 10.1111/gbi.12243] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 05/09/2017] [Indexed: 05/04/2023]
Abstract
Ribulose 1,5-bisphosphate (RuBP) carboxylase/oxygenase (RuBisCO, or Rubisco) catalyzes a key reaction by which inorganic carbon is converted into organic carbon in the metabolism of many aerobic and anaerobic organisms. Across the broader Rubisco protein family, homologs exhibit diverse biochemical characteristics and metabolic functions, but the evolutionary origins of this diversity are unclear. Evidence of the timing of Rubisco family emergence and diversification of its different forms has been obscured by a meager paleontological record of early Earth biota, their subcellular physiology and metabolic components. Here, we use computational models to reconstruct a Rubisco family phylogenetic tree, ancestral amino acid sequences at branching points on the tree, and protein structures for several key ancestors. Analysis of historic substitutions with respect to their structural locations shows that there were distinct periods of amino acid substitution enrichment above background levels near and within its oxygen-sensitive active site and subunit interfaces over the divergence between Form III (associated with anoxia) and Form I (associated with oxia) groups in its evolutionary history. One possible interpretation is that these periods of substitutional enrichment are coincident with oxidative stress exerted by the rise of oxygenic photosynthesis in the Precambrian era. Our interpretation implies that the periods of Rubisco substitutional enrichment inferred near the transition from anaerobic Form III to aerobic Form I ancestral sequences predate the acquisition of Rubisco by fully derived cyanobacterial (i.e., dual photosystem-bearing, oxygen-evolving) clades. The partitioning of extant lineages at high clade levels within our Rubisco phylogeny indicates that horizontal transfer of Rubisco is a relatively infrequent event. Therefore, it is possible that the mutational enrichment periods between the Form III and Form I common ancestral sequences correspond to the adaptation of key oxygen-sensitive components of Rubisco prior to, or coincident with, the Great Oxidation Event.
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Affiliation(s)
- B. Kacar
- Department of Organismic and Evolutionary BiologyHarvard UniversityCambridgeMAUSA
| | - V. Hanson‐Smith
- Department of Microbiology and ImmunologyUniversity of California San FranciscoSan FranciscoCAUSA
| | - Z. R. Adam
- Department of Earth and Planetary SciencesHarvard UniversityCambridgeMAUSA
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22
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Abstract
The Cambrian explosion can be thought of as the culmination of a diversification of eukaryotes that had begun several hundred million years before. Eukaryotes - one of the three domains of life — originated by late Archean time, and probably underwent a long period of stem group evolution during the Paleoproterozoic Era. A suite of taxonomically resolved body fossils and biomarkers, together with estimates of acritarch and compression fossil diversity, suggest that while divergences among major eukaryotic clades or 'super-groups' may have occurred as early as latest Paleoproterozoic through Mesoproterozoic time, the main phase of eukaryotic diversification took place several hundred million years later, during the middle Neoproterozoic Era. Hypotheses for Neoproterozoic diversification must therefore explain why eukaryotic diversification is delayed several hundred million years after the origin of the eukaryotic crown group, and why diversification appears to have occurred independently within several eukaryotic super-groups at the same time. Evolutionary explanations for eukaryotic diversification (the evolution of sex; the acquisition of plastids) fail to account for these patterns, but ecological explanations (the advent of microbial predators) and environmental explanations (changes in ocean chemistry) are both consistent with them. Both ecology and environment may have played a role in triggering or at least fueling Neoproterozoic eukaryotic diversification.
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23
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Shih PM, Hemp J, Ward LM, Matzke NJ, Fischer WW. Crown group Oxyphotobacteria postdate the rise of oxygen. GEOBIOLOGY 2017; 15:19-29. [PMID: 27392323 DOI: 10.1111/gbi.12200] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 05/30/2016] [Indexed: 05/24/2023]
Abstract
The rise of oxygen ca. 2.3 billion years ago (Ga) is the most distinct environmental transition in Earth history. This event was enabled by the evolution of oxygenic photosynthesis in the ancestors of Cyanobacteria. However, long-standing questions concern the evolutionary timing of this metabolism, with conflicting answers spanning more than one billion years. Recently, knowledge of the Cyanobacteria phylum has expanded with the discovery of non-photosynthetic members, including a closely related sister group termed Melainabacteria, with the known oxygenic phototrophs restricted to a clade recently designated Oxyphotobacteria. By integrating genomic data from the Melainabacteria, cross-calibrated Bayesian relaxed molecular clock analyses show that crown group Oxyphotobacteria evolved ca. 2.0 billion years ago (Ga), well after the rise of atmospheric dioxygen. We further estimate the divergence between Oxyphotobacteria and Melainabacteria ca. 2.5-2.6 Ga, which-if oxygenic photosynthesis is an evolutionary synapomorphy of the Oxyphotobacteria-marks an upper limit for the origin of oxygenic photosynthesis. Together, these results are consistent with the hypothesis that oxygenic photosynthesis evolved relatively close in time to the rise of oxygen.
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Affiliation(s)
- P M Shih
- Joint BioEnergy Institute, Emeryville, CA, USA
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - J Hemp
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA
| | - L M Ward
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA
| | - N J Matzke
- National Institute for Mathematical and Biological Synthesis, University of Tennessee, Knoxville, TN, USA
| | - W W Fischer
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA
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24
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Shih PM, Occhialini A, Cameron JC, Andralojc PJ, Parry MAJ, Kerfeld CA. Biochemical characterization of predicted Precambrian RuBisCO. Nat Commun 2016; 7:10382. [PMID: 26790750 PMCID: PMC4735906 DOI: 10.1038/ncomms10382] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 12/04/2015] [Indexed: 01/02/2023] Open
Abstract
The antiquity and global abundance of the enzyme, RuBisCO, attests to the crucial and longstanding role it has played in the biogeochemical cycles of Earth over billions of years. The counterproductive oxygenase activity of RuBisCO has persisted over billions of years of evolution, despite its competition with the carboxylase activity necessary for carbon fixation, yet hypotheses regarding the selective pressures governing RuBisCO evolution have been limited to speculation. Here we report the resurrection and biochemical characterization of ancestral RuBisCOs, dating back to over one billion years ago (Gyr ago). Our findings provide an ancient point of reference revealing divergent evolutionary paths taken by eukaryotic homologues towards improved specificity for CO2, versus the evolutionary emphasis on increased rates of carboxylation observed in bacterial homologues. Consistent with these distinctions, in vivo analysis reveals the propensity of ancestral RuBisCO to be encapsulated into modern-day carboxysomes, bacterial organelles central to the cyanobacterial CO2 concentrating mechanism.
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Affiliation(s)
- Patrick M. Shih
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720-3102, USA
| | - Alessandro Occhialini
- Department of Plant Biology and Crop Science, Rothamsted Research, Harpenden, Herts AL5 2JQ, UK
| | - Jeffrey C. Cameron
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720-3102, USA
| | - P John Andralojc
- Department of Plant Biology and Crop Science, Rothamsted Research, Harpenden, Herts AL5 2JQ, UK
| | - Martin A. J. Parry
- Department of Plant Biology and Crop Science, Rothamsted Research, Harpenden, Herts AL5 2JQ, UK
- Lancaster Environment Centre, Lancaster University, Bailrigg, Lancaster LA1, 4YQ, UK
| | - Cheryl A. Kerfeld
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720-3102, USA
- Department of Biochemistry and Molecular Biology, DOE Plant Research Laboratories, Michigan State University, East Lansing, Michigan 488242, USA
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
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25
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McFadden GI. Origin and evolution of plastids and photosynthesis in eukaryotes. Cold Spring Harb Perspect Biol 2014; 6:a016105. [PMID: 24691960 DOI: 10.1101/cshperspect.a016105] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Recent progress in understanding the origins of plastids from endosymbiotic cyanobacteria is reviewed. Establishing when during geological time the endosymbiosis occurred remains elusive, but progress has been made in defining the cyanobacterial lineage most closely related to plastids, and some mechanistic insight into the possible existence of cryptic endosymbioses perhaps involving Chlamydia-like infections of the host have also been presented. The phylogenetic affinities of the host remain obscure. The existence of a second lineage of primary plastids in euglyphid amoebae has now been confirmed, but the quasipermanent acquisition of plastids by animals has been shown to be more ephemeral than initially suspected. A new understanding of how plastids have been integrated into their hosts by transfer of photosynthate, by endosymbiotic gene transfer and repatriation of gene products back to the endosymbiont, and by regulation of endosymbiont division is presented in context.
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26
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Koumandou VL, Wickstead B, Ginger ML, van der Giezen M, Dacks JB, Field MC. Molecular paleontology and complexity in the last eukaryotic common ancestor. Crit Rev Biochem Mol Biol 2014; 48:373-96. [PMID: 23895660 PMCID: PMC3791482 DOI: 10.3109/10409238.2013.821444] [Citation(s) in RCA: 133] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Eukaryogenesis, the origin of the eukaryotic cell, represents one of the fundamental evolutionary transitions in the history of life on earth. This event, which is estimated to have occurred over one billion years ago, remains rather poorly understood. While some well-validated examples of fossil microbial eukaryotes for this time frame have been described, these can provide only basic morphology and the molecular machinery present in these organisms has remained unknown. Complete and partial genomic information has begun to fill this gap, and is being used to trace proteins and cellular traits to their roots and to provide unprecedented levels of resolution of structures, metabolic pathways and capabilities of organisms at these earliest points within the eukaryotic lineage. This is essentially allowing a molecular paleontology. What has emerged from these studies is spectacular cellular complexity prior to expansion of the eukaryotic lineages. Multiple reconstructed cellular systems indicate a very sophisticated biology, which by implication arose following the initial eukaryogenesis event but prior to eukaryotic radiation and provides a challenge in terms of explaining how these early eukaryotes arose and in understanding how they lived. Here, we provide brief overviews of several cellular systems and the major emerging conclusions, together with predictions for subsequent directions in evolution leading to extant taxa. We also consider what these reconstructions suggest about the life styles and capabilities of these earliest eukaryotes and the period of evolution between the radiation of eukaryotes and the eukaryogenesis event itself.
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Affiliation(s)
- V Lila Koumandou
- Biomedical Research Foundation, Academy of Athens, Soranou Efesiou 4, Athens 115 27, Greece
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27
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Raven JA, Edwards D. Photosynthesis in Early Land Plants: Adapting to the Terrestrial Environment. ADVANCES IN PHOTOSYNTHESIS AND RESPIRATION 2014. [DOI: 10.1007/978-94-007-6988-5_3] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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28
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Bhattacharya D, Price DC, Chan CX, Qiu H, Rose N, Ball S, Weber APM, Arias MC, Henrissat B, Coutinho PM, Krishnan A, Zäuner S, Morath S, Hilliou F, Egizi A, Perrineau MM, Yoon HS. Genome of the red alga Porphyridium purpureum. Nat Commun 2013; 4:1941. [PMID: 23770768 PMCID: PMC3709513 DOI: 10.1038/ncomms2931] [Citation(s) in RCA: 145] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2012] [Accepted: 04/26/2013] [Indexed: 11/09/2022] Open
Abstract
The limited knowledge we have about red algal genomes comes from the highly specialized extremophiles, Cyanidiophyceae. Here, we describe the first genome sequence from a mesophilic, unicellular red alga, Porphyridium purpureum. The 8,355 predicted genes in P. purpureum, hundreds of which are likely to be implicated in a history of horizontal gene transfer, reside in a genome of 19.7 Mbp with 235 spliceosomal introns. Analysis of light-harvesting complex proteins reveals a nuclear-encoded phycobiliprotein in the alga. We uncover a complex set of carbohydrate-active enzymes, identify the genes required for the methylerythritol phosphate pathway of isoprenoid biosynthesis, and find evidence of sexual reproduction. Analysis of the compact, function-rich genome of P. purpureum suggests that ancestral lineages of red algae acted as mediators of horizontal gene transfer between prokaryotes and photosynthetic eukaryotes, thereby significantly enriching genomes across the tree of photosynthetic life.
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Affiliation(s)
- Debashish Bhattacharya
- Department of Ecology, Evolution and Natural Resources and Institute of Marine and Coastal Science, Rutgers University, New Brunswick, New Jersey 08901, USA.
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Herron MD, Rashidi A, Shelton DE, Driscoll WW. Cellular differentiation and individuality in the 'minor' multicellular taxa. Biol Rev Camb Philos Soc 2013; 88:844-61. [PMID: 23448295 PMCID: PMC4103886 DOI: 10.1111/brv.12031] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2012] [Revised: 01/30/2013] [Accepted: 02/05/2013] [Indexed: 01/07/2023]
Abstract
Biology needs a concept of individuality in order to distinguish organisms from parts of organisms and from groups of organisms, to count individuals and compare traits across taxa, and to distinguish growth from reproduction. Most of the proposed criteria for individuality were designed for 'unitary' or 'paradigm' organisms: contiguous, functionally and physiologically integrated, obligately sexually reproducing multicellular organisms with a germ line sequestered early in development. However, the vast majority of the diversity of life on Earth does not conform to all of these criteria. We consider the issue of individuality in the 'minor' multicellular taxa, which collectively span a large portion of the eukaryotic tree of life, reviewing their general features and focusing on a model species for each group. When the criteria designed for unitary organisms are applied to other groups, they often give conflicting answers or no answer at all to the question of whether or not a given unit is an individual. Complex life cycles, intimate bacterial symbioses, aggregative development, and strange genetic features complicate the picture. The great age of some of the groups considered shows that 'intermediate' forms, those with some but not all of the traits traditionally associated with individuality, cannot reasonably be considered ephemeral or assumed transitional. We discuss a handful of recent attempts to reconcile the many proposed criteria for individuality and to provide criteria that can be applied across all the domains of life. Finally, we argue that individuality should be defined without reference to any particular taxon and that understanding the emergence of new kinds of individuals requires recognizing individuality as a matter of degree.
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Affiliation(s)
- Matthew D. Herron
- Department of Ecology and Evolutionary Biology, University of Arizona, 1041 Lowell St, Tucson, AZ 85721, USA
| | | | - Deborah E. Shelton
- Department of Ecology and Evolutionary Biology, University of Arizona, 1041 Lowell St, Tucson, AZ 85721, USA
| | - William W. Driscoll
- Department of Ecology and Evolutionary Biology, University of Arizona, 1041 Lowell St, Tucson, AZ 85721, USA
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Yuan X, Chen Z, Xiao S, Wan B, Guan C, Wang W, Zhou C, Hua H. The Lantian biota: A new window onto the origin and early evolution of multicellular organisms. ACTA ACUST UNITED AC 2012. [DOI: 10.1007/s11434-012-5483-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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31
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Abstract
Comparisons of ribosomal RNAs and various protein coding genes have contributed to a new view of eukaryote phylogeny. Analyses of paralogous protein coding genes suggest that archaebacteria and eukaryotes are sistergroups. Sequence diversity of small subunit rRNAs in protists by far exceeds that of any multicellular or prokaryote taxon. Remarkably, a group of taxa that lack mitochondria first branches off in the small subunit rRNA tree. The later radiations are formed by a series of clades that were once thought to be more ancestral. Furthermore, tracing of the evolutionary origin of secondary endobiontic events is now possible with sequence comparisons.
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Affiliation(s)
- M Schlegel
- Martin Schlegel is at the Universität Tübingen, Zoologisches Institut, Abteilung Zellbiologie, Auf der Morgenstelle 28, D-72076 Tübingen, Germany
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Huynen MA, Duarte I, Szklarczyk R. Loss, replacement and gain of proteins at the origin of the mitochondria. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2012; 1827:224-31. [PMID: 22902511 DOI: 10.1016/j.bbabio.2012.08.001] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2012] [Revised: 07/19/2012] [Accepted: 08/05/2012] [Indexed: 01/28/2023]
Abstract
We review what has been inferred about the changes at the level of the proteome that accompanied the evolution of the mitochondrion from an alphaproteobacterium. We regard these changes from an alphaproteobacterial perspective: which proteins were lost during mitochondrial evolution? And, of the proteins that were lost, which ones have been replaced by other, non-orthologous proteins with a similar function? Combining literature-supported replacements with quantitative analyses of mitochondrial proteomics data we infer that most of the loss and replacements that separate current day mitochondria in mammals from alphaproteobacteria took place before the radiation of the eukaryotes. Recent analyses show that also the acquisition of new proteins to the large protein complexes of the oxidative phosphorylation and the mitochondrial ribosome occurred mainly before the divergence of the eukaryotes. These results indicate a significant number of pivotal evolutionary events between the acquisition of the endosymbiont and the radiation of the eukaryotes and therewith support an early acquisition of mitochondria in eukaryotic evolution. Technically, advancements in the reconstruction of the evolutionary trajectories of loss, replacement and gain of mitochondrial proteins depend on using profile-based homology detection methods for sequence analysis. We highlight the mitochondrial Holliday junction resolvase endonuclease, for which such methods have detected new "family members" and in which function differentiation is accompanied by the loss of catalytic residues for the original enzymatic function and the gain of a protein domain for the new function. This article is part of a Special Issue entitled: The evolutionary aspects of bioenergetic systems.
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Affiliation(s)
- Martijn A Huynen
- Centre for Molecular and Biomolecular Informatics, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, P.O. Box 9101, 6400 HB Nijmegen, The Netherlands.
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33
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Evolving Phytoplankton Stoichiometry Fueled Diversification of the Marine Biosphere. GEOSCIENCES 2012. [DOI: 10.3390/geosciences2020130] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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34
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Giezen M, Lenton TM. The Rise of Oxygen and Complex Life. J Eukaryot Microbiol 2012; 59:111-3. [DOI: 10.1111/j.1550-7408.2011.00605.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2011] [Accepted: 12/04/2011] [Indexed: 11/29/2022]
Affiliation(s)
- Mark Giezen
- Centre for Eukaryotic Evolutionary Microbiology, Biosciences; College of Life & Environmental Sciences; University of Exeter; UK
| | - Timothy M. Lenton
- Geography; College of Life & Environmental Sciences; University of Exeter; UK
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35
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Blouin NA, Lane CE. Red algal parasites: models for a life history evolution that leaves photosynthesis behind again and again. Bioessays 2012; 34:226-35. [PMID: 22247039 DOI: 10.1002/bies.201100139] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Many of the most virulent and problematic eukaryotic pathogens have evolved from photosynthetic ancestors, such as apicomplexans, which are responsible for a wide range of diseases including malaria and toxoplasmosis. The primary barrier to understanding the early stages of evolution of these parasites has been the difficulty in finding parasites with closely related free-living lineages with which to make comparisons. Parasites found throughout the florideophyte red algal lineage, however, provide a unique and powerful model to investigate the genetic origins of a parasitic lifestyle. This is because they share a recent common ancestor with an extant free-living red algal species and parasitism has independently arisen over 100 times within this group. Here, we synthesize the relevant hypotheses with respect to how these parasites have proliferated. We also place red algal research in the context of recent developments in understanding the genome evolution of other eukaryotic photosynthesizers turned parasites.
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Affiliation(s)
- Nicolas A Blouin
- Department of Biological Sciences, University of Rhode Island, Kingston, RI, USA.
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36
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Low Molecular Weight Carbohydrates in Red Algae – an Ecophysiological and Biochemical Perspective. CELLULAR ORIGIN, LIFE IN EXTREME HABITATS AND ASTROBIOLOGY 2010. [DOI: 10.1007/978-90-481-3795-4_24] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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38
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Sharma M, Shukla Y. The evolution and distribution of life in the Precambrian eon-global perspective and the Indian record. J Biosci 2009; 34:765-76. [PMID: 20009270 DOI: 10.1007/s12038-009-0065-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The discovery of Precambrian microfossils in 1954 opened a new vista of investigations in the field of evolution of life. Although the Precambrian encompasses 87% of the earth's history, the pace of organismal evolution was quite slow. The life forms as categorised today in the three principal domains viz. the Bacteria, the Archaea and the Eucarya evolved during this period. In this paper, we review the advancements made in the Precambrian palaeontology and its contribution in understanding the evolution of life forms on earth. These studies have enriched the data base on the Precambrian life. Most of the direct evidence includes fossil prokaryotes, protists, advanced algal fossils, acritarchs, and the indirect evidence is represented by the stromatolites, trace fossils and geochemical fossils signatures. The Precambrian fossils are preserved in the form of compressions, impressions, and permineralized and biomineralized remains.
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Affiliation(s)
- M Sharma
- Birbal Sahni Institute of Palaeobotany, 53 University Road, Lucknow 226 007, India.
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39
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Raven JA. The early evolution of land plants: Aquatic ancestors and atmospheric interactions. ACTA ACUST UNITED AC 2009. [DOI: 10.1080/03746609508684827] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Ley RE, Lozupone CA, Hamady M, Knight R, Gordon JI. Worlds within worlds: evolution of the vertebrate gut microbiota. Nat Rev Microbiol 2008; 6:776-88. [PMID: 18794915 PMCID: PMC2664199 DOI: 10.1038/nrmicro1978] [Citation(s) in RCA: 1064] [Impact Index Per Article: 66.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In this Analysis we use published 16S ribosomal RNA gene sequences to compare the bacterial assemblages that are associated with humans and other mammals, metazoa and free-living microbial communities that span a range of environments. The composition of the vertebrate gut microbiota is influenced by diet, host morphology and phylogeny, and in this respect the human gut bacterial community is typical of an omnivorous primate. However, the vertebrate gut microbiota is different from free-living communities that are not associated with animal body habitats. We propose that the recently initiated international Human Microbiome Project should strive to include a broad representation of humans, as well as other mammalian and environmental samples, as comparative analyses of microbiotas and their microbiomes are a powerful way to explore the evolutionary history of the biosphere.
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Affiliation(s)
- Ruth E Ley
- Center for Genome Sciences, Washington University School of Medicine, St Louis, Missouri 63108, USA
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41
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Javaux EJ. The Early Eukaryotic Fossil Record. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2008; 607:1-19. [DOI: 10.1007/978-0-387-74021-8_1] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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42
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The riddle of “life,” a biologist’s critical view. Naturwissenschaften 2008; 96:1-23. [DOI: 10.1007/s00114-008-0422-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2007] [Revised: 06/17/2008] [Accepted: 06/24/2008] [Indexed: 10/21/2022]
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43
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An expanded inventory of conserved meiotic genes provides evidence for sex in Trichomonas vaginalis. PLoS One 2007; 3:e2879. [PMID: 18663385 PMCID: PMC2488364 DOI: 10.1371/journal.pone.0002879] [Citation(s) in RCA: 192] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2008] [Accepted: 06/08/2008] [Indexed: 12/23/2022] Open
Abstract
Meiosis is a defining feature of eukaryotes but its phylogenetic distribution has not been broadly determined, especially among eukaryotic microorganisms (i.e. protists)-which represent the majority of eukaryotic 'supergroups'. We surveyed genomes of animals, fungi, plants and protists for meiotic genes, focusing on the evolutionarily divergent parasitic protist Trichomonas vaginalis. We identified homologs of 29 components of the meiotic recombination machinery, as well as the synaptonemal and meiotic sister chromatid cohesion complexes. T. vaginalis has orthologs of 27 of 29 meiotic genes, including eight of nine genes that encode meiosis-specific proteins in model organisms. Although meiosis has not been observed in T. vaginalis, our findings suggest it is either currently sexual or a recent asexual, consistent with observed, albeit unusual, sexual cycles in their distant parabasalid relatives, the hypermastigotes. T. vaginalis may use meiotic gene homologs to mediate homologous recombination and genetic exchange. Overall, this expanded inventory of meiotic genes forms a useful "meiosis detection toolkit". Our analyses indicate that these meiotic genes arose, or were already present, early in eukaryotic evolution; thus, the eukaryotic cenancestor contained most or all components of this set and was likely capable of performing meiotic recombination using near-universal meiotic machinery.
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Cavalier-Smith T. Cell evolution and Earth history: stasis and revolution. Philos Trans R Soc Lond B Biol Sci 2006; 361:969-1006. [PMID: 16754610 PMCID: PMC1578732 DOI: 10.1098/rstb.2006.1842] [Citation(s) in RCA: 147] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
This synthesis has three main parts. The first discusses the overall tree of life and nature of the last common ancestor (cenancestor). I emphasize key steps in cellular evolution important for ordering and timing the major evolutionary innovations in the history of the biosphere, explaining especially the origins of the eukaryote cell and of bacterial flagella and cell envelope novelties. Second, I map the tree onto the fossil record and discuss dates of key events and their biogeochemical impact. Finally, I present a broad synthesis, discussing evidence for a three-phase history of life. The first phase began perhaps ca 3.5 Gyr ago, when the origin of cells and anoxic photosynthesis generated the arguably most primitive prokaryote phylum, Chlorobacteria (= Chloroflexi), the first negibacteria with cells bounded by two acyl ester phospholipid membranes. After this 'chlorobacterial age' of benthic anaerobic evolution protected from UV radiation by mineral grains, two momentous quantum evolutionary episodes of cellular innovation and microbial radiation dramatically transformed the Earth's surface: the glycobacterial revolution initiated an oxygenic 'age of cyanobacteria' and, as the ozone layer grew, the rise of plankton; immensely later, probably as recently as ca 0.9 Gyr ago, the neomuran revolution ushered in the 'age of eukaryotes', Archaebacteria (arguably the youngest bacterial phylum), and morphological complexity. Diversification of glycobacteria ca 2.8 Gyr ago, predominantly inhabiting stratified benthic mats, I suggest caused serial depletion of 13C by ribulose 1,5-bis-phosphate caboxylase/oxygenase (Rubisco) to yield ultralight late Archaean organic carbon formerly attributed to methanogenesis plus methanotrophy. The late origin of archaebacterial methanogenesis ca 720 Myr ago perhaps triggered snowball Earth episodes by slight global warming increasing weathering and reducing CO2 levels, to yield runaway cooling; the origin of anaerobic methane oxidation ca 570 Myr ago reduced methane flux at source, stabilizing Phanerozoic climates. I argue that the major cellular innovations exhibit a pattern of quantum evolution followed by very rapid radiation and then substantial stasis, as described by Simpson. They yielded organisms that are a mosaic of extremely conservative and radically novel features, as characterized by De Beer's phrase 'mosaic evolution'. Evolution is not evenly paced and there are no real molecular clocks.
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45
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Knoll AH, Javaux EJ, Hewitt D, Cohen P. Eukaryotic organisms in Proterozoic oceans. Philos Trans R Soc Lond B Biol Sci 2006; 361:1023-38. [PMID: 16754612 PMCID: PMC1578724 DOI: 10.1098/rstb.2006.1843] [Citation(s) in RCA: 177] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The geological record of protists begins well before the Ediacaran and Cambrian diversification of animals, but the antiquity of that history, its reliability as a chronicle of evolution and the causal inferences that can be drawn from it remain subjects of debate. Well-preserved protists are known from a relatively small number of Proterozoic formations, but taphonomic considerations suggest that they capture at least broad aspects of early eukaryotic evolution. A modest diversity of problematic, possibly stem group protists occurs in ca 1800-1300 Myr old rocks. 1300-720 Myr fossils document the divergence of major eukaryotic clades, but only with the Ediacaran-Cambrian radiation of animals did diversity increase within most clades with fossilizable members. While taxonomic placement of many Proterozoic eukaryotes may be arguable, the presence of characters used for that placement is not. Focus on character evolution permits inferences about the innovations in cell biology and development that underpin the taxonomic and morphological diversification of eukaryotic organisms.
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Affiliation(s)
- A H Knoll
- Harvard University, Department of Organismic and Evolutionary Biology, Cambridge, MA 02139, USA.
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46
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Roger AJ, Hug LA. The origin and diversification of eukaryotes: problems with molecular phylogenetics and molecular clock estimation. Philos Trans R Soc Lond B Biol Sci 2006; 361:1039-54. [PMID: 16754613 PMCID: PMC1578731 DOI: 10.1098/rstb.2006.1845] [Citation(s) in RCA: 138] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Determining the relationships among and divergence times for the major eukaryotic lineages remains one of the most important and controversial outstanding problems in evolutionary biology. The sequencing and phylogenetic analyses of ribosomal RNA (rRNA) genes led to the first nearly comprehensive phylogenies of eukaryotes in the late 1980s, and supported a view where cellular complexity was acquired during the divergence of extant unicellular eukaryote lineages. More recently, however, refinements in analytical methods coupled with the availability of many additional genes for phylogenetic analysis showed that much of the deep structure of early rRNA trees was artefactual. Recent phylogenetic analyses of a multiple genes and the discovery of important molecular and ultrastructural phylogenetic characters have resolved eukaryotic diversity into six major hypothetical groups. Yet relationships among these groups remain poorly understood because of saturation of sequence changes on the billion-year time-scale, possible rapid radiations of major lineages, phylogenetic artefacts and endosymbiotic or lateral gene transfer among eukaryotes. Estimating the divergence dates between the major eukaryote lineages using molecular analyses is even more difficult than phylogenetic estimation. Error in such analyses comes from a myriad of sources including: (i) calibration fossil dates, (ii) the assumed phylogenetic tree, (iii) the nucleotide or amino acid substitution model, (iv) substitution number (branch length) estimates, (v) the model of how rates of evolution change over the tree, (vi) error inherent in the time estimates for a given model and (vii) how multiple gene data are treated. By reanalysing datasets from recently published molecular clock studies, we show that when errors from these various sources are properly accounted for, the confidence intervals on inferred dates can be very large. Furthermore, estimated dates of divergence vary hugely depending on the methods used and their assumptions. Accurate dating of divergence times among the major eukaryote lineages will require a robust tree of eukaryotes, a much richer Proterozoic fossil record of microbial eukaryotes assignable to extant groups for calibration, more sophisticated relaxed molecular clock methods and many more genes sampled from the full diversity of microbial eukaryotes.
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Affiliation(s)
- Andrew J Roger
- Canadian Institute for Advanced Research, Department of Biochemistry and Molecular Biology, Dalhousie University, Program in Evolutionary Biology Halifax, Nova Scotia, B3H 1X5 Canada.
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Saunders GW, Hommersand MH. Assessing red algal supraordinal diversity and taxonomy in the context of contemporary systematic data. AMERICAN JOURNAL OF BOTANY 2004; 91:1494-507. [PMID: 21652305 DOI: 10.3732/ajb.91.10.1494] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The wondrously diverse eukaryotes that constitute the red algae have been the focus of numerous recent molecular surveys and remain a rich source of undescribed and little known species for the traditional taxonomist. Molecular studies place the red algae in the kingdom Plantae; however, supraordinal classification has been largely confined to debate on subclass vs. class level status for the two recognized subgroups, one of which is widely acknowledged as paraphyletic. This narrow focus has generally masked the extent to which red algal classification needs modification. We provide a comprehensive review of the literature pertaining to the antiquity, diversity, and systematics of the red algae and propose a contemporary classification based on recent and traditional evidence.
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Affiliation(s)
- Gary W Saunders
- Centre for Environmental & Molecular Algal Research, Department of Biology, University of New Brunswick, Fredericton, New Brunswick, Canada, E3B 6E1
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48
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Broom JES, Farr TJ, Nelson WA. Phylogeny of the Bangia flora of New Zealand suggests a southern origin for Porphyra and Bangia (Bangiales, Rhodophyta). Mol Phylogenet Evol 2004; 31:1197-207. [PMID: 15120409 DOI: 10.1016/j.ympev.2003.10.015] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2003] [Revised: 10/12/2003] [Indexed: 10/26/2022]
Abstract
Analysis of nuclear small subunit ribosomal RNA gene (18S rDNA) sequence data from 123 samples of the red algal genus Bangia from mainland New Zealand has revealed diversity exceeding that reported for the genus from any other region in the world. Our study resolves two New Zealand Bangia taxa basal to the order Bangiales, and five clades of Bangia, four of which include New Zealand members. The basal taxa are separated from each other by 139 bp and differ from all other Bangia taxa in the New Zealand region by 103-163 bp over approximately 1750 bp 18S rDNA sequence data. Our results reveal a Bangia flora of previously unsuspected richness, and show that the simple morphology of these organisms obscures significant levels of genetic diversity. The presence of high diversity and retention of basal taxa in New Zealand Bangia raises the prospect that the southern hemisphere, and particularly eastern Gondwana, is not only a centre of diversity, but a centre of origin for the modern Bangiales.
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Affiliation(s)
- J E S Broom
- Department of Biochemistry, University of Otago, P.O. Box 56, Dunedin, New Zealand.
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49
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Xiao S, Knoll AH, Yuan X, Pueschel CM. Phosphatized multicellular algae in the Neoproterozoic Doushantuo Formation, China, and the early evolution of florideophyte red algae. AMERICAN JOURNAL OF BOTANY 2004; 91:214-27. [PMID: 21653378 DOI: 10.3732/ajb.91.2.214] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Phosphatic sediments of the Late Neoproterozoic (ca. 600 million years old [Myr]) Doushantuo Formation at Weng'an, South China, contain fossils of multicellular algae preserved in anatomical detail. As revealed by light microscopy and scanning electron microscopy, these fossils include both simple pseudoparenchymatous thalli with apical growth but no cortex-medulla differentiation and more complex thalli characterized by cortex-medulla differentiation and structures interpretable as carposporophytes, suggesting a multiphasic life cycle. Simple pseudoparenchymatous thalli, represented by Wengania, Gremiphyca, and Thallophycoides, are interpreted as stem group florideophytes. In contrast, complex pseudoparenchymatous thalli, such as Thallophyca and Paramecia, compare more closely to fossil and living corallinaleans than to other florideophyte orders, although they also differ in some important aspects (e.g., lack of biocalcification). These more complex thalli are interpreted as early stem group corallinaleans that diverged before Paleozoic stem groups such as Arenigiphyllum, Petrophyton, Graticula, and Archaeolithophyllum. This phylogenetic interpretation implies that (1) the phylogenetic divergence between the Florideophyceae and its sister group, the Bangiales, must have taken place before Doushantuo time-an inference supported by the occurrence of bangialean fossils in Mesoproterozoic rocks; (2) the initial diversification of the florideophytes occurred no later than the Doushantuo time; and (3) the corallinalean clade had a "soft" (uncalcified) evolutionary history in the Neoproterozoic before evolving biocalcification in the Paleozoic and undergoing crown group diversification in the Mesozoic.
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Affiliation(s)
- Shuhai Xiao
- Department of Geological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061 USA
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50
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Javaux EJ, Knoll AH, Walter M. Recognizing and interpreting the fossils of early eukaryotes. ORIGINS LIFE EVOL B 2003; 33:75-94. [PMID: 12967274 DOI: 10.1023/a:1023992712071] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Using molecular sequence data, biologists can generate hypotheses of protistan phylogeny and divergence times. Fossils, however, provide our only direct constraints on the timing and environmental context of early eukaryotic diversification. For this reason, recognition of eukaryotic fossils in Proterozoic rocks is key to the integration of geological and comparative biological perspectives on protistan evolution. Microfossils preserved in shales of the ca. 1500 Ma Roper Group, northern Australia, display characters that ally them to the Eucarya, but, at present, attribution to any particular protistan clade is uncertain. Continuing research on wall ultrastructure and microchemistry promises new insights into the nature and systematic relationships of early eukaryotic fossils.
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Affiliation(s)
- Emmanuelle J Javaux
- Organismic and Evolutionary Biology Department, Botanical Museum, Harvard University, Cambridge, MA, USA
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