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Lindsey CR, Knoll AH, Herron MD, Rosenzweig F. Fossil-calibrated molecular clock data enable reconstruction of steps leading to differentiated multicellularity and anisogamy in the Volvocine algae. BMC Biol 2024; 22:79. [PMID: 38600528 PMCID: PMC11007952 DOI: 10.1186/s12915-024-01878-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 04/03/2024] [Indexed: 04/12/2024] Open
Abstract
BACKGROUND Throughout its nearly four-billion-year history, life has undergone evolutionary transitions in which simpler subunits have become integrated to form a more complex whole. Many of these transitions opened the door to innovations that resulted in increased biodiversity and/or organismal efficiency. The evolution of multicellularity from unicellular forms represents one such transition, one that paved the way for cellular differentiation, including differentiation of male and female gametes. A useful model for studying the evolution of multicellularity and cellular differentiation is the volvocine algae, a clade of freshwater green algae whose members range from unicellular to colonial, from undifferentiated to completely differentiated, and whose gamete types can be isogamous, anisogamous, or oogamous. To better understand how multicellularity, differentiation, and gametes evolved in this group, we used comparative genomics and fossil data to establish a geologically calibrated roadmap of when these innovations occurred. RESULTS Our ancestral-state reconstructions, show that multicellularity arose independently twice in the volvocine algae. Our chronograms indicate multicellularity evolved during the Carboniferous-Triassic periods in Goniaceae + Volvocaceae, and possibly as early as the Cretaceous in Tetrabaenaceae. Using divergence time estimates we inferred when, and in what order, specific developmental changes occurred that led to differentiated multicellularity and oogamy. We find that in the volvocine algae the temporal sequence of developmental changes leading to differentiated multicellularity is much as proposed by David Kirk, and that multicellularity is correlated with the acquisition of anisogamy and oogamy. Lastly, morphological, molecular, and divergence time data suggest the possibility of cryptic species in Tetrabaenaceae. CONCLUSIONS Large molecular datasets and robust phylogenetic methods are bringing the evolutionary history of the volvocine algae more sharply into focus. Mounting evidence suggests that extant species in this group are the result of two independent origins of multicellularity and multiple independent origins of cell differentiation. Also, the origin of the Tetrabaenaceae-Goniaceae-Volvocaceae clade may be much older than previously thought. Finally, the possibility of cryptic species in the Tetrabaenaceae provides an exciting opportunity to study the recent divergence of lineages adapted to live in very different thermal environments.
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Affiliation(s)
- Charles Ross Lindsey
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Andrew H Knoll
- Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford St., Cambridge, MA, 02138, USA
| | - Matthew D Herron
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Frank Rosenzweig
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA.
- Parker H. Petit Institute for Bioengineering and Biosciences, Atlanta, GA, 30332, USA.
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2
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Bowles AMC, Williamson CJ, Williams TA, Donoghue PCJ. Cryogenian Origins of Multicellularity in Archaeplastida. Genome Biol Evol 2024; 16:evae026. [PMID: 38333966 PMCID: PMC10883732 DOI: 10.1093/gbe/evae026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 01/30/2024] [Accepted: 02/03/2024] [Indexed: 02/10/2024] Open
Abstract
Earth was impacted by global glaciations during the Cryogenian (720 to 635 million years ago; Ma), events invoked to explain both the origins of multicellularity in Archaeplastida and radiation of the first land plants. However, the temporal relationship between these environmental and biological events is poorly established, due to a paucity of molecular and fossil data, precluding resolution of the phylogeny and timescale of archaeplastid evolution. We infer a time-calibrated phylogeny of early archaeplastid evolution based on a revised molecular dataset and reappraisal of the fossil record. Phylogenetic topology testing resolves deep archaeplastid relationships, identifying two clades of Viridiplantae and placing Bryopsidales as sister to the Chlorophyceae. Our molecular clock analysis infers an origin of Archaeplastida in the late-Paleoproterozoic to early-Mesoproterozoic (1712 to 1387 Ma). Ancestral state reconstruction of cytomorphological traits on this time-calibrated tree reveals many of the independent origins of multicellularity span the Cryogenian, consistent with the Cryogenian multicellularity hypothesis. Multicellular rhodophytes emerged 902 to 655 Ma while crown-Anydrophyta (Zygnematophyceae and Embryophyta) originated 796 to 671 Ma, broadly compatible with the Cryogenian plant terrestrialization hypothesis. Our analyses resolve the timetree of Archaeplastida with age estimates for ancestral multicellular archaeplastids coinciding with the Cryogenian, compatible with hypotheses that propose a role of Snowball Earth in plant evolution.
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Affiliation(s)
- Alexander M C Bowles
- School of Geographical Sciences, University of Bristol, Bristol BS8 1SS, UK
- Bristol Palaeobiology Group, School of Biological Sciences and School of Earth Sciences, Life Sciences Building, University of Bristol, Bristol BS8 1TQ, UK
| | | | - Tom A Williams
- Bristol Palaeobiology Group, School of Biological Sciences and School of Earth Sciences, Life Sciences Building, University of Bristol, Bristol BS8 1TQ, UK
| | - Philip C J Donoghue
- Bristol Palaeobiology Group, School of Biological Sciences and School of Earth Sciences, Life Sciences Building, University of Bristol, Bristol BS8 1TQ, UK
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3
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Yang Z, Ma X, Wang Q, Tian X, Sun J, Zhang Z, Xiao S, De Clerck O, Leliaert F, Zhong B. Phylotranscriptomics unveil a Paleoproterozoic-Mesoproterozoic origin and deep relationships of the Viridiplantae. Nat Commun 2023; 14:5542. [PMID: 37696791 PMCID: PMC10495350 DOI: 10.1038/s41467-023-41137-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 08/23/2023] [Indexed: 09/13/2023] Open
Abstract
The Viridiplantae comprise two main clades, the Chlorophyta (including a diverse array of marine and freshwater green algae) and the Streptophyta (consisting of the freshwater charophytes and the land plants). Lineages sister to core Chlorophyta, informally refer to as prasinophytes, form a grade of mainly planktonic green algae. Recently, one of these lineages, Prasinodermophyta, which is previously grouped with prasinophytes, has been identified as the sister lineage to both Chlorophyta and Streptophyta. Resolving the deep relationships among green plants is crucial for understanding the historical impact of green algal diversity on marine ecology and geochemistry, but has been proven difficult given the ancient timing of the diversification events. Through extensive taxon and gene sampling, we conduct large-scale phylogenomic analyses to resolve deep relationships and reveal the Prasinodermophyta as the lineage sister to Chlorophyta, raising questions about the necessity of classifying the Prasinodermophyta as a distinct phylum. We unveil that incomplete lineage sorting is the main cause of discordance regarding the placement of Prasinodermophyta. Molecular dating analyses suggest that crown-group green plants and crown-group Prasinodermophyta date back to the Paleoproterozoic-Mesoproterozoic. Our study establishes a plausible link between oxygen levels in the Paleoproterozoic-Mesoproterozoic and the origin of Viridiplantae.
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Affiliation(s)
- Zhiping Yang
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Xiaoya Ma
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Qiuping Wang
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Xiaolin Tian
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Jingyan Sun
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Zhenhua Zhang
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Shuhai Xiao
- Department of Geosciences and Global Change Center, Virginia Tech, Blacksburg, VA, USA
| | - Olivier De Clerck
- Phycology Research Group and Center for Molecular Phylogenetics and Evolution, Ghent University, Ghent, Belgium
| | | | - Bojian Zhong
- College of Life Sciences, Nanjing Normal University, Nanjing, China.
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4
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Yao H, Li T, Ma Z, Wang X, Xu L, Zhang Y, Cai Y, Tang Z. Codon usage pattern of the ancestor of green plants revealed through Rhodophyta. BMC Genomics 2023; 24:538. [PMID: 37697255 PMCID: PMC10496412 DOI: 10.1186/s12864-023-09586-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Accepted: 08/14/2023] [Indexed: 09/13/2023] Open
Abstract
Rhodophyta are among the closest known relatives of green plants. Studying the codons of their genomes can help us understand the codon usage pattern and characteristics of the ancestor of green plants. By studying the codon usage pattern of all available red algae, it was found that although there are some differences among species, high-bias genes in most red algae prefer codons ending with GC. Correlation analysis, Nc-GC3s plots, parity rule 2 plots, neutrality plot analysis, differential protein region analysis and comparison of the nucleotide content of introns and flanking sequences showed that the bias phenomenon is likely to be influenced by local mutation pressure and natural selection, the latter of which is the dominant factor in terms of translation accuracy and efficiency. It is worth noting that selection on translation accuracy could even be detected in the low-bias genes of individual species. In addition, we identified 15 common optimal codons in seven red algae except for G. sulphuraria for the first time, most of which were found to be complementary and bound to the tRNA genes with the highest copy number. Interestingly, tRNA modification was found for the highly degenerate amino acids of all multicellular red algae and individual unicellular red algae, which indicates that highly biased genes tend to use modified tRNA in translation. Our research not only lays a foundation for exploring the characteristics of codon usage of the red algae as green plant ancestors, but will also facilitate the design and performance of transgenic work in some economic red algae in the future.
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Affiliation(s)
- Huipeng Yao
- College of Life Science, Sichuan Agriculture University, Ya'an, 625014, Sichuan, People's Republic of China.
| | - Tingting Li
- College of Life Science, Sichuan Agriculture University, Ya'an, 625014, Sichuan, People's Republic of China
| | - Zheng Ma
- College of Life Science, Sichuan Agriculture University, Ya'an, 625014, Sichuan, People's Republic of China
| | - Xiyuan Wang
- College of Life Science, Sichuan Agriculture University, Ya'an, 625014, Sichuan, People's Republic of China
| | - Lixiao Xu
- College of Life Science, Sichuan Agriculture University, Ya'an, 625014, Sichuan, People's Republic of China
| | - Yuxin Zhang
- College of Life Science, Sichuan Agriculture University, Ya'an, 625014, Sichuan, People's Republic of China
| | - Yi Cai
- College of Life Science, Sichuan Agriculture University, Ya'an, 625014, Sichuan, People's Republic of China
| | - Zizhong Tang
- College of Life Science, Sichuan Agriculture University, Ya'an, 625014, Sichuan, People's Republic of China
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5
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Bowles AMC, Williamson CJ, Williams TA, Lenton TM, Donoghue PCJ. The origin and early evolution of plants. TRENDS IN PLANT SCIENCE 2023; 28:312-329. [PMID: 36328872 DOI: 10.1016/j.tplants.2022.09.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 09/23/2022] [Accepted: 09/30/2022] [Indexed: 06/16/2023]
Abstract
Plant (archaeplastid) evolution has transformed the biosphere, but we are only now beginning to learn how this took place through comparative genomics, phylogenetics, and the fossil record. This has illuminated the phylogeny of Archaeplastida, Viridiplantae, and Streptophyta, and has resolved the evolution of key characters, genes, and genomes - revealing that many key innovations evolved long before the clades with which they have been casually associated. Molecular clock analyses estimate that Streptophyta and Viridiplantae emerged in the late Mesoproterozoic to late Neoproterozoic, whereas Archaeplastida emerged in the late-mid Palaeoproterozoic. Together, these insights inform on the coevolution of plants and the Earth system that transformed ecology and global biogeochemical cycles, increased weathering, and precipitated snowball Earth events, during which they would have been key to oxygen production and net primary productivity (NPP).
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Affiliation(s)
- Alexander M C Bowles
- School of Geographical Sciences, University of Bristol, University Road, Bristol BS8 1SS, UK; Bristol Palaeobiology Group, School of Biological Sciences and School of Earth Sciences, Life Sciences Building, University of Bristol, Bristol BS8 1TQ, UK.
| | | | - Tom A Williams
- Bristol Palaeobiology Group, School of Biological Sciences and School of Earth Sciences, Life Sciences Building, University of Bristol, Bristol BS8 1TQ, UK
| | - Timothy M Lenton
- Global Systems Institute, University of Exeter, Laver Building, North Park Road, Exeter EX4 4QE, UK
| | - Philip C J Donoghue
- Bristol Palaeobiology Group, School of Biological Sciences and School of Earth Sciences, Life Sciences Building, University of Bristol, Bristol BS8 1TQ, UK.
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6
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Yin Z, Sun W, Liu P, Chen J, Bottjer DJ, Li J, Zhu M. Diverse and complex developmental mechanisms of early Ediacaran embryo-like fossils from the Weng'an Biota, southwest China. Philos Trans R Soc Lond B Biol Sci 2022; 377:20210032. [PMID: 35125006 PMCID: PMC8819369 DOI: 10.1098/rstb.2021.0032] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The origin and early evolution of animal development remain among the many deep, unresolved problems in evolutionary biology. As a compelling case for the existence of pre-Cambrian animals, the Ediacaran embryo-like fossils (EELFs) from the Weng'an Biota (approx. 609 Myr old, Doushantuo Formation, South China) have great potential to cast light on the origin and early evolution of animal development. However, their biological implications can be fully realized only when their phylogenetic positions are correctly established, and unfortunately, this is the key problem under debate. As a significant feature of developmental biology, the cell division pattern (CDP) characterized by the dynamic spatial arrangement of cells and associated developmental mechanisms is critical to reassess these hypotheses and evaluate the diversity of the EELFs; however, their phylogenetic implications have not been fully realized. Additionally, the scarcity of fossil specimens representing late developmental stages with cell differentiation accounts for much of this debate too. Here, we reconstructed a large number of EELFs using submicron resolution X-ray tomographic microscopy and focused on the CDPs and associated developmental mechanisms as well as features of cell differentiation. Four types of CDPs and specimens with cell differentiation were identified. Contrary to the prevailing view, our results together with recent studies suggest that the diversity and complexity of developmental mechanisms documented by the EELFs are much higher than is often claimed. The diverse CDPs and associated development features including palintomic cleavage, maternal nutrition, asymmetric cell divisions, symmetry breaking, establishment of polarity or axis, spatial cell migration and differentiation constrain some, if not all, EELFs as total-group metazoans. This article is part of the theme issue ‘The impact of Chinese palaeontology on evolutionary research’.
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Affiliation(s)
- Zongjun Yin
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing 210008, People's Republic of China.,Centre for Excellence in Life and Palaeoenvironment, Chinese Academy of Sciences, Nanjing 210008, People's Republic of China.,Nanjing College, University of Chinese Academy of Sciences, Nanjing 211135, People's Republic of China.,College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Weichen Sun
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing 210008, People's Republic of China.,University of Science and Technology of China, Hefei 230026, People's Republic of China
| | - Pengju Liu
- Institute of Geology, Chinese Academy of Geological Sciences, Beijing 100037, People's Republic of China
| | - Junyuan Chen
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing 210008, People's Republic of China
| | - David J Bottjer
- Department of Earth Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Jinhua Li
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Innovation Academy for Earth Science, Chinese Academy of Sciences, Beijing 100029, People's Republic of China
| | - Maoyan Zhu
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing 210008, People's Republic of China.,Centre for Excellence in Life and Palaeoenvironment, Chinese Academy of Sciences, Nanjing 210008, People's Republic of China.,Nanjing College, University of Chinese Academy of Sciences, Nanjing 211135, People's Republic of China.,College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
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7
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Schopf JW. Precambrian Paleobiology: Precedents, Progress, and Prospects. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.707072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
In 1859, C. R. Darwin highlighted the “inexplicable” absence of evidence of life prior to the beginning of the Cambrian. Given this lack of evidence and the natural rather than theological unfolding of life’s development Darwin espoused, over the following 50 years his newly minted theory was disputed. At the turn of the 19th century, beginning with the discoveries of C. D. Walcott, glimmerings of the previously “unknown and unknowable” early fossil record came to light – but Walcott’s Precambrian finds were also discounted. It was not until the breakthrough advances of the 1950’s and the identification of modern stromatolites (1956), Precambrian phytoplankton in shales (1950’s), stromatolitic microbes in cherts (1953), and terminal-Precambrian soft-bodied animal fossils (1950’s) that the field was placed on firm footing. Over the following half-century, the development and application of new analytical techniques coupled with the groundbreaking contributions of the Precambrian Paleobiology Research Group spurred the field to its international and distinctly interdisciplinary status. Significant progress has been made worldwide. Among these advances, the known fossil record has been extended sevenfold (from ∼0.5 to ∼3.5 Ga); the fossil record has been shown consistent with rRNA phylogenies (adding credence to both); and the timing and evolutionary significance of an increase of environmental oxygen (∼2.3 Ga), of eukaryotic organisms (∼2.0 Ga), and of evolution-speeding and biota-diversifying eukaryotic sexual reproduction (∼1.2 Ga) have been identified. Nevertheless, much remains to be learned. Such major unsolved problems include the absence of definitive evidence of the widely assumed life-generating “primordial soup”; the timing of the origin of oxygenic photosynthesis; the veracity of postulated changes in global photic-zone temperature from 3.5 Ga to the present; the bases of the advent of eukaryotic sexuality-requiring gametogenesis and syngamy; and the timing of origin and affinities of the small soft-bodied precursors of the Ediacaran Fauna.
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8
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Abstract
The Ediacaran period (635–541 Ma) was a time of major environmental change, accompanied by a transition from a microbial world to the animal world we know today. Multicellular, macroscopic organisms preserved as casts and molds in Ediacaran siliciclastic rocks are preserved worldwide and provide snapshots of early organismal, including animal, evolution. Remarkable evolutionary advances are also witnessed by diverse cellular and subcellular phosphatized microfossils described from the Doushantuo Formation in China, the only source showing a diversified assemblage of microfossils. Here, we greatly extend the known distribution of this Doushantuo-type biota in reporting an Ediacaran Lagerstätte from Laurentia (Portfjeld Formation, North Greenland), with phosphatized animal-like eggs, embryos, acritarchs, and cyanobacteria, the age of which is constrained by the Shuram–Wonoka anomaly (c. 570–560 Ma). The discovery of these Ediacaran phosphatized microfossils from outside East Asia extends the distribution of the remarkable biota to a second palaeocontinent in the other hemisphere of the Ediacaran world, considerably expanding our understanding of the temporal and environmental distribution of organisms immediately prior to the Cambrian explosion. The Doushantuo biota of China is incredibly important for understanding the evolution of complex animals. Willman et al. report on evidence of Doushantuo-like biota from the Ediacaran of North Greenland, indicating that these important organisms were distributed across multiple palaeocontinents.
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Peña V, Vieira C, Braga JC, Aguirre J, Rösler A, Baele G, De Clerck O, Le Gall L. Radiation of the coralline red algae (Corallinophycidae, Rhodophyta) crown group as inferred from a multilocus time-calibrated phylogeny. Mol Phylogenet Evol 2020; 150:106845. [DOI: 10.1016/j.ympev.2020.106845] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 04/21/2020] [Accepted: 04/21/2020] [Indexed: 01/20/2023]
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10
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Del Cortona A, Jackson CJ, Bucchini F, Van Bel M, D'hondt S, Škaloud P, Delwiche CF, Knoll AH, Raven JA, Verbruggen H, Vandepoele K, De Clerck O, Leliaert F. Neoproterozoic origin and multiple transitions to macroscopic growth in green seaweeds. Proc Natl Acad Sci U S A 2020; 117:2551-2559. [PMID: 31911467 PMCID: PMC7007542 DOI: 10.1073/pnas.1910060117] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The Neoproterozoic Era records the transition from a largely bacterial to a predominantly eukaryotic phototrophic world, creating the foundation for the complex benthic ecosystems that have sustained Metazoa from the Ediacaran Period onward. This study focuses on the evolutionary origins of green seaweeds, which play an important ecological role in the benthos of modern sunlit oceans and likely played a crucial part in the evolution of early animals by structuring benthic habitats and providing novel niches. By applying a phylogenomic approach, we resolve deep relationships of the core Chlorophyta (Ulvophyceae or green seaweeds, and freshwater or terrestrial Chlorophyceae and Trebouxiophyceae) and unveil a rapid radiation of Chlorophyceae and the principal lineages of the Ulvophyceae late in the Neoproterozoic Era. Our time-calibrated tree points to an origin and early diversification of green seaweeds in the late Tonian and Cryogenian periods, an interval marked by two global glaciations with strong consequent changes in the amount of available marine benthic habitat. We hypothesize that unicellular and simple multicellular ancestors of green seaweeds survived these extreme climate events in isolated refugia, and diversified in benthic environments that became increasingly available as ice retreated. An increased supply of nutrients and biotic interactions, such as grazing pressure, likely triggered the independent evolution of macroscopic growth via different strategies, including true multicellularity, and multiple types of giant-celled forms.
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Affiliation(s)
- Andrea Del Cortona
- Department of Biology, Phycology Research Group, Ghent University, 9000 Ghent, Belgium;
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Zwijnaarde, Belgium
- Vlaams Instituut voor Biotechnologie Center for Plant Systems Biology, 9052 Zwijnaarde, Belgium
- Bioinformatics Institute Ghent, Ghent University, 9052 Zwijnaarde, Belgium
| | | | - François Bucchini
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Zwijnaarde, Belgium
- Vlaams Instituut voor Biotechnologie Center for Plant Systems Biology, 9052 Zwijnaarde, Belgium
| | - Michiel Van Bel
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Zwijnaarde, Belgium
- Vlaams Instituut voor Biotechnologie Center for Plant Systems Biology, 9052 Zwijnaarde, Belgium
| | - Sofie D'hondt
- Department of Biology, Phycology Research Group, Ghent University, 9000 Ghent, Belgium
| | - Pavel Škaloud
- Department of Botany, Faculty of Science, Charles University, CZ-12800 Prague 2, Czech Republic
| | - Charles F Delwiche
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742
| | - Andrew H Knoll
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138
| | - John A Raven
- Division of Plant Sciences, University of Dundee at the James Hutton Institute, Dundee DD2 5DA, United Kingdom
- School of Biological Sciences, University of Western Australia, WA 6009, Australia
- Climate Change Cluster, University of Technology, Ultimo, NSW 2006, Australia
| | - Heroen Verbruggen
- School of Biosciences, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Klaas Vandepoele
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Zwijnaarde, Belgium;
- Vlaams Instituut voor Biotechnologie Center for Plant Systems Biology, 9052 Zwijnaarde, Belgium
- Bioinformatics Institute Ghent, Ghent University, 9052 Zwijnaarde, Belgium
| | - Olivier De Clerck
- Department of Biology, Phycology Research Group, Ghent University, 9000 Ghent, Belgium;
| | - Frederik Leliaert
- Department of Biology, Phycology Research Group, Ghent University, 9000 Ghent, Belgium;
- Meise Botanic Garden, 1860 Meise, Belgium
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11
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Green Biological Synthesis of Nanoparticles and Their Biomedical Applications. NANOTECHNOLOGY IN THE LIFE SCIENCES 2020. [DOI: 10.1007/978-3-030-44176-0_10] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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12
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Yin Z, Vargas K, Cunningham J, Bengtson S, Zhu M, Marone F, Donoghue P. The Early Ediacaran Caveasphaera Foreshadows the Evolutionary Origin of Animal-like Embryology. Curr Biol 2019; 29:4307-4314.e2. [DOI: 10.1016/j.cub.2019.10.057] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 08/21/2019] [Accepted: 10/29/2019] [Indexed: 01/01/2023]
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13
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Shen J, Zerkle AL, Stueeken E, Claire MW. Nitrates as a Potential N Supply for Microbial Ecosystems in a Hyperarid Mars Analog System. Life (Basel) 2019; 9:life9040079. [PMID: 31635024 PMCID: PMC6958444 DOI: 10.3390/life9040079] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 10/08/2019] [Accepted: 10/17/2019] [Indexed: 11/16/2022] Open
Abstract
Nitrate is common in Mars sediments owing to long-term atmospheric photolysis, oxidation, and potentially, impact shock heating. The Atacama Desert in Chile, which is the driest region on Earth and rich in nitrate deposits, is used as a Mars analog in this study to explore the potential effects of high nitrate levels on growth of extremophilic ecosystems. Seven study sites sampled across an aridity gradient in the Atacama Desert were categorized into 3 clusters—hyperarid, middle, and arid sites—as defined by essential soil physical and chemical properties. Intriguingly, the distribution of nitrate concentrations in the shallow subsurface suggests that the buildup of nitrate is not solely controlled by precipitation. Correlations of nitrate with SiO2/Al2O3 and grain sizes suggest that sedimentation rates may also be important in controlling nitrate distribution. At arid sites receiving more than 10 mm/yr precipitation, rainfall shows a stronger impact on biomass than nitrate does. However, high nitrate to organic carbon ratios are generally beneficial to N assimilation, as evidenced both by soil geochemistry and enriched culturing experiments. This study suggests that even in the absence of precipitation, nitrate levels on a more recent, hyperarid Mars could be sufficiently high to benefit potentially extant Martian microorganisms.
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Affiliation(s)
- Jianxun Shen
- School of Earth and Environmental Sciences and Centre for Exoplanet Science, University of St Andrews, St Andrews KY16 9AL, Scotland, UK.
| | - Aubrey L Zerkle
- School of Earth and Environmental Sciences and Centre for Exoplanet Science, University of St Andrews, St Andrews KY16 9AL, Scotland, UK.
| | - Eva Stueeken
- School of Earth and Environmental Sciences and Centre for Exoplanet Science, University of St Andrews, St Andrews KY16 9AL, Scotland, UK.
| | - Mark W Claire
- School of Earth and Environmental Sciences and Centre for Exoplanet Science, University of St Andrews, St Andrews KY16 9AL, Scotland, UK.
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Organically-preserved multicellular eukaryote from the early Ediacaran Nyborg Formation, Arctic Norway. Sci Rep 2019; 9:14659. [PMID: 31601898 PMCID: PMC6787099 DOI: 10.1038/s41598-019-50650-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 09/12/2019] [Indexed: 02/04/2023] Open
Abstract
Eukaryotic multicellularity originated in the Mesoproterozoic Era and evolved multiple times since, yet early multicellular fossils are scarce until the terminal Neoproterozoic and often restricted to cases of exceptional preservation. Here we describe unusual organically-preserved fossils from mudrocks, that provide support for the presence of organisms with differentiated cells (potentially an epithelial layer) in the late Neoproterozoic. Cyathinema digermulense gen. et sp. nov. from the Nyborg Formation, Vestertana Group, Digermulen Peninsula in Arctic Norway, is a new carbonaceous organ-taxon which consists of stacked tubes with cup-shaped ends. It represents parts of a larger organism (multicellular eukaryote or a colony), likely with greater preservation potential than its other elements. Arrangement of open-ended tubes invites comparison with cells of an epithelial layer present in a variety of eukaryotic clades. This tissue may have benefitted the organism in: avoiding overgrowth, limiting fouling, reproduction, or water filtration. C. digermulense shares characteristics with extant and fossil groups including red algae and their fossils, demosponge larvae and putative sponge fossils, colonial protists, and nematophytes. Regardless of its precise affinity, C. digermulense was a complex and likely benthic marine eukaryote exhibiting cellular differentiation, and a rare occurrence of early multicellularity outside of Konservat-Lagerstätten.
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15
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Cardona T, Sánchez‐Baracaldo P, Rutherford AW, Larkum AW. Early Archean origin of Photosystem II. GEOBIOLOGY 2019; 17:127-150. [PMID: 30411862 PMCID: PMC6492235 DOI: 10.1111/gbi.12322] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 10/03/2018] [Accepted: 10/11/2018] [Indexed: 05/09/2023]
Abstract
Photosystem II is a photochemical reaction center that catalyzes the light-driven oxidation of water to molecular oxygen. Water oxidation is the distinctive photochemical reaction that permitted the evolution of oxygenic photosynthesis and the eventual rise of eukaryotes. At what point during the history of life an ancestral photosystem evolved the capacity to oxidize water still remains unknown. Here, we study the evolution of the core reaction center proteins of Photosystem II using sequence and structural comparisons in combination with Bayesian relaxed molecular clocks. Our results indicate that a homodimeric photosystem with sufficient oxidizing power to split water had already appeared in the early Archean about a billion years before the most recent common ancestor of all described Cyanobacteria capable of oxygenic photosynthesis, and well before the diversification of some of the known groups of anoxygenic photosynthetic bacteria. Based on a structural and functional rationale, we hypothesize that this early Archean photosystem was capable of water oxidation to oxygen and had already evolved protection mechanisms against the formation of reactive oxygen species. This would place primordial forms of oxygenic photosynthesis at a very early stage in the evolutionary history of life.
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Affiliation(s)
- Tanai Cardona
- Department of Life SciencesImperial College LondonLondonUK
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16
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Teichert S, Woelkerling W, Munnecke A. Coralline red algae from the Silurian of Gotland indicate that the order Corallinales (Corallinophycidae, Rhodophyta) is much older than previously thought. Angew Chem Int Ed Engl 2019. [DOI: 10.1111/ange.12418-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Sebastian Teichert
- Fachgruppe Paläoumwelt GeoZentrum Nordbayern Friedrich‐Alexander‐Universität Erlangen‐Nürnberg (FAU) Erlangen Germany
| | - William Woelkerling
- Department of Ecology, Environment & Evolution La Trobe University Kingsbury Drive Bundoora Victoria 3086 Australia
| | - Axel Munnecke
- Fachgruppe Paläoumwelt GeoZentrum Nordbayern Friedrich‐Alexander‐Universität Erlangen‐Nürnberg (FAU) Erlangen Germany
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17
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Teichert S, Woelkerling W, Munnecke A. Coralline red algae from the Silurian of Gotland indicate that the order Corallinales (Corallinophycidae, Rhodophyta) is much older than previously thought. J Microsc 2019. [DOI: 10.1111/j.12418-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Sebastian Teichert
- Fachgruppe Paläoumwelt GeoZentrum Nordbayern Friedrich‐Alexander‐Universität Erlangen‐Nürnberg (FAU) Erlangen Germany
| | - William Woelkerling
- Department of Ecology, Environment & Evolution La Trobe University Kingsbury Drive Bundoora Victoria 3086 Australia
| | - Axel Munnecke
- Fachgruppe Paläoumwelt GeoZentrum Nordbayern Friedrich‐Alexander‐Universität Erlangen‐Nürnberg (FAU) Erlangen Germany
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18
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Teichert S, Woelkerling W, Munnecke A. Coralline red algae from the Silurian of Gotland indicate that the order Corallinales (Corallinophycidae, Rhodophyta) is much older than previously thought. Angew Chem Int Ed Engl 2019. [DOI: 10.1111/ange.12418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sebastian Teichert
- Fachgruppe Paläoumwelt GeoZentrum Nordbayern Friedrich‐Alexander‐Universität Erlangen‐Nürnberg (FAU) Erlangen Germany
| | - William Woelkerling
- Department of Ecology, Environment & Evolution La Trobe University Kingsbury Drive Bundoora Victoria 3086 Australia
| | - Axel Munnecke
- Fachgruppe Paläoumwelt GeoZentrum Nordbayern Friedrich‐Alexander‐Universität Erlangen‐Nürnberg (FAU) Erlangen Germany
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19
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Lee JM, Song HJ, Park SI, Lee YM, Jeong SY, Cho TO, Kim JH, Choi HG, Choi CG, Nelson WA, Fredericq S, Bhattacharya D, Yoon HS. Mitochondrial and Plastid Genomes from Coralline Red Algae Provide Insights into the Incongruent Evolutionary Histories of Organelles. Genome Biol Evol 2018; 10:2961-2972. [PMID: 30364957 PMCID: PMC6279150 DOI: 10.1093/gbe/evy222] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/27/2018] [Indexed: 11/14/2022] Open
Abstract
Mitochondria and plastids are generally uniparentally inherited and have a conserved gene content over hundreds of millions of years, which makes them potentially useful phylogenetic markers. Organelle single gene-based trees have long been the basis for elucidating interspecies relationships that inform taxonomy. More recently, high-throughput genome sequencing has enabled the construction of massive organelle genome databases from diverse eukaryotes, and these have been used to infer species relationships in deep evolutionary time. Here, we test the idea that despite their expected utility, conflicting phylogenetic signal may exist in mitochondrial and plastid genomes from the anciently diverged coralline red algae (Rhodophyta). We generated complete organelle genome data from five coralline red algae (Lithothamnion sp., Neogoniolithon spectabile, Renouxia sp., Rhodogorgon sp., and Synarthrophyton chejuensis) for comparative analysis with existing organelle genome data from two other species (Calliarthron tuberculosum and Sporolithon durum). We find strong evidence for incongruent phylogenetic signal from both organelle genomes that may be explained by incomplete lineage sorting that has maintained anciently derived gene copies or other molecular evolutionary processes such as hybridization or gene flow during the evolutionary history of coralline red algae.
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Affiliation(s)
- Jun Mo Lee
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Korea
| | - Hae Jung Song
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Korea
| | - Seung In Park
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Korea
| | - Yu Min Lee
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Korea
| | - So Young Jeong
- Department of Marine Life Science, Chosun University, Gwangju, Korea
| | - Tae Oh Cho
- Department of Marine Life Science, Chosun University, Gwangju, Korea
| | - Ji Hee Kim
- Division of Life Sciences, Korea Polar Research Institute, KOPRI, Incheon, Korea
| | - Han-Gu Choi
- Division of Life Sciences, Korea Polar Research Institute, KOPRI, Incheon, Korea
| | - Chang Geun Choi
- Department of Ecological Engineering, Pukyong National University, Busan, Korea
| | - Wendy A Nelson
- National Institute for Water and Atmospheric Research, Wellington, New Zealand.,School of Biological Sciences, University of Auckland, New Zealand
| | - Suzanne Fredericq
- Biology Department, University of Louisiana at Lafayette, Lafayette, Louisiana
| | | | - Hwan Su Yoon
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Korea
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20
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Animal origins and the Tonian Earth system. Emerg Top Life Sci 2018; 2:289-298. [PMID: 32412615 DOI: 10.1042/etls20170160] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 05/23/2018] [Accepted: 05/25/2018] [Indexed: 01/30/2023]
Abstract
The Neoproterozoic Era (1000-541 million years ago, Ma) was characterized by dramatic environmental and evolutionary change, including at least two episodes of extensive, low-latitude glaciation, potential changes in the redox structure of the global ocean, and the origin and diversification of animal life. How these different events related to one another remains an active area of research, particularly how these environmental changes influenced, and were influenced by, the earliest evolution of animals. Animal multicellularity is estimated to have evolved in the Tonian Period (1000-720 Ma) and represents one of at least six independent acquisitions of complex multicellularity, characterized by cellular differentiation, three-dimensional body plans, and active nutrient transport. Compared with the other instances of complex multicellularity, animals represent the only clade to have evolved from wall-less, phagotrophic flagellates, which likely placed unique cytological and trophic constraints on the evolution of animal multicellularity. Here, we compare recent molecular clock estimates with compilations of the chromium isotope, micropaleontological, and organic biomarker records, suggesting that, as of now, the origin of animals was not obviously correlated to any environmental-ecological change in the Tonian Period. This lack of correlation is consistent with the idea that the evolution of animal multicellularity was primarily dictated by internal, developmental constraints and occurred independently of the known environmental-ecological changes that characterized the Neoproterozoic Era.
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Nagy LG, Kovács GM, Krizsán K. Complex multicellularity in fungi: evolutionary convergence, single origin, or both? Biol Rev Camb Philos Soc 2018; 93:1778-1794. [DOI: 10.1111/brv.12418] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 03/23/2018] [Accepted: 03/28/2018] [Indexed: 12/22/2022]
Affiliation(s)
- László G. Nagy
- Synthetic and Systems Biology Unit; Institute of Biochemistry, BRC-HAS, 62 Temesvári krt; 6726 Szeged Hungary
| | - Gábor M. Kovács
- Department of Plant Anatomy; Institute of Biology, Eötvös Loránd University, Pázmány Péter sétány 1/C; H-1117 Budapest Hungary
- Plant Protection Institute, Centre for Agricultural Research; Hungarian Academy of Sciences (MTA-ATK); PO Box 102, H-1525 Budapest Hungary
| | - Krisztina Krizsán
- Synthetic and Systems Biology Unit; Institute of Biochemistry, BRC-HAS, 62 Temesvári krt; 6726 Szeged Hungary
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22
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Early Archean origin of heterodimeric Photosystem I. Heliyon 2018; 4:e00548. [PMID: 29560463 PMCID: PMC5857716 DOI: 10.1016/j.heliyon.2018.e00548] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 02/02/2018] [Accepted: 02/14/2018] [Indexed: 11/26/2022] Open
Abstract
When and how oxygenic photosynthesis originated remains controversial. Wide uncertainties exist for the earliest detection of biogenic oxygen in the geochemical record or the origin of water oxidation in ancestral lineages of the phylum Cyanobacteria. A unique trait of oxygenic photosynthesis is that the process uses a Type I reaction centre with a heterodimeric core, also known as Photosystem I, made of two distinct but homologous subunits, PsaA and PsaB. In contrast, all other known Type I reaction centres in anoxygenic phototrophs have a homodimeric core. A compelling hypothesis for the evolution of a heterodimeric Type I reaction centre is that the gene duplication that allowed the divergence of PsaA and PsaB was an adaptation to incorporate photoprotective mechanisms against the formation of reactive oxygen species, therefore occurring after the origin of water oxidation to oxygen. Here I show, using sequence comparisons and Bayesian relaxed molecular clocks that this gene duplication event may have occurred in the early Archean more than 3.4 billion years ago, long before the most recent common ancestor of crown group Cyanobacteria and the Great Oxidation Event. If the origin of water oxidation predated this gene duplication event, then that would place primordial forms of oxygenic photosynthesis at a very early stage in the evolutionary history of life.
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23
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Sánchez-Baracaldo P, Raven JA, Pisani D, Knoll AH. Early photosynthetic eukaryotes inhabited low-salinity habitats. Proc Natl Acad Sci U S A 2017; 114:E7737-E7745. [PMID: 28808007 PMCID: PMC5603991 DOI: 10.1073/pnas.1620089114] [Citation(s) in RCA: 148] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The early evolutionary history of the chloroplast lineage remains an open question. It is widely accepted that the endosymbiosis that established the chloroplast lineage in eukaryotes can be traced back to a single event, in which a cyanobacterium was incorporated into a protistan host. It is still unclear, however, which Cyanobacteria are most closely related to the chloroplast, when the plastid lineage first evolved, and in what habitats this endosymbiotic event occurred. We present phylogenomic and molecular clock analyses, including data from cyanobacterial and chloroplast genomes using a Bayesian approach, with the aim of estimating the age for the primary endosymbiotic event, the ages of crown groups for photosynthetic eukaryotes, and the independent incorporation of a cyanobacterial endosymbiont by Paulinella Our analyses include both broad taxon sampling (119 taxa) and 18 fossil calibrations across all Cyanobacteria and photosynthetic eukaryotes. Phylogenomic analyses support the hypothesis that the chloroplast lineage diverged from its closet relative Gloeomargarita, a basal cyanobacterial lineage, ∼2.1 billion y ago (Bya). Our analyses suggest that the Archaeplastida, consisting of glaucophytes, red algae, green algae, and land plants, share a common ancestor that lived ∼1.9 Bya. Whereas crown group Rhodophyta evolved in the Mesoproterozoic Era (1,600-1,000 Mya), crown groups Chlorophyta and Streptophyta began to radiate early in the Neoproterozoic (1,000-542 Mya). Stochastic mapping analyses indicate that the first endosymbiotic event occurred in low-salinity environments. Both red and green algae colonized marine environments early in their histories, with prasinophyte green phytoplankton diversifying 850-650 Mya.
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Affiliation(s)
| | - John A Raven
- Division of Plant Science, University of Dundee at the James Hutton Institute, Dundee DD2 5DA, United Kingdom
- Plant Functional Biology and Climate Change Cluster, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Davide Pisani
- School of Biological Sciences, University of Bristol, Bristol BS8 1TH, United Kingdom
- School of Earth Sciences, University of Bristol, Bristol BS8 1TH, United Kingdom
| | - Andrew H Knoll
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138
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24
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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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25
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LoDuca ST, Bykova N, Wu M, Xiao S, Zhao Y. Seaweed morphology and ecology during the great animal diversification events of the early Paleozoic: A tale of two floras. GEOBIOLOGY 2017; 15:588-616. [PMID: 28603844 DOI: 10.1111/gbi.12244] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 05/16/2017] [Indexed: 06/07/2023]
Abstract
Non-calcified marine macroalgae ("seaweeds") play a variety of key roles in the modern Earth system, and it is likely that they were also important players in the geological past, particularly during critical transitions such as the Cambrian Explosion (CE) and the Great Ordovician Biodiversification Event (GOBE). To investigate the morphology and ecology of seaweeds spanning the time frame from the CE through the GOBE, a carefully vetted database was constructed that includes taxonomic and morphometric information for non-calcified macroalgae from 69 fossil deposits. Analysis of the database shows a pattern of seaweed history that can be explained in terms of two floras: the Cambrian Flora and the Ordovician Flora. The Cambrian Flora was dominated by rather simple morphogroups, whereas the Ordovician Flora, which replaced the Cambrian Flora in the Ordovician and extended through the Silurian, mainly comprised comparatively complex morphogroups. In addition to morphogroup representation, the two floras show marked differences in taxonomic composition, morphospace occupation, functional-form group representation, and life habit, thereby pointing to significant morphological and ecological changes for seaweeds roughly concomitant with the GOBE and the transition from the Cambrian to Paleozoic Evolutionary Faunas. Macroalgal changes of a similar nature and magnitude, however, are not evident in concert with the CE, as the Cambrian Flora consists largely of forms established during the Ediacaran. The cause of such a lag in macroalgal morphological diversification remains unclear, but an intriguing possibility is that it signals a previously unknown difference between the CE and GOBE with regard to the introduction of novel grazing pressures. The consequences of the establishment of the Ordovician Flora for shallow marine ecosystems and Earth system dynamics remain to be explored in detail but could have been multifaceted and potentially include impacts on the global carbon cycle.
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Affiliation(s)
- S T LoDuca
- Department of Geography and Geology, Eastern Michigan University, Ypsilanti, MI, USA
| | - N Bykova
- Department of Geosciences, Virginia Tech, Blacksburg, VA, USA
- Trofimuk Institute of Petroleum Geology and Geophysics, Siberian Branch Russian Academy of Sciences, Novosibirsk, Russia
| | - M Wu
- Department of Economics and Management, Guiyang University, Guiyang, Guizhou, China
| | - S Xiao
- Department of Geosciences, Virginia Tech, Blacksburg, VA, USA
| | - Y Zhao
- College of Resource and Environment Engineering, Guizhou University, Guiyang, Guizhou, China
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Cunningham JA, Vargas K, Marone F, Bengtson S, Donoghue PCJ. A multicellular organism with embedded cell clusters from the Ediacaran Weng'an biota (Doushantuo Formation, South China). Evol Dev 2017; 18:308-316. [PMID: 27870211 PMCID: PMC6849543 DOI: 10.1111/ede.12210] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Three‐dimensional analyses of the early Ediacaran microfossils from the Weng'an biota (Doushantuo Formation) have focused predominantly on multicellular forms that have been interpreted as embryos, and yet they have defied phylogenetic interpretation principally because of absence of evidence from other stages in their life cycle. It is therefore unfortunate that the affinities of the various other Doushantuo microfossils have been neglected. A new conical fossil that is preserved at a cellular level is described here. The fossil contains distinct cell clusters that are characterized and analysed in three dimensions. These clusters are often exposed at the specimen surface, and the fossil preserves many hemispherical craters that are interpreted as positions where clusters have left the organism. The cell clusters may be either reproductive propagules or infesting organisms. Similar clusters are found in a variety of Doushantuo organisms including putative animal embryos and algae.
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Affiliation(s)
- John A Cunningham
- Department of Palaeobiology and Nordic Center for Earth Evolution, Swedish Museum of Natural History, Stockholm 10405, Sweden.,School of Earth Sciences, University of Bristol, Life Sciences Building, 24 Tyndall Avenue, Bristol BS8 1TQ, England
| | - Kelly Vargas
- School of Earth Sciences, University of Bristol, Life Sciences Building, 24 Tyndall Avenue, Bristol BS8 1TQ, England
| | - Federica Marone
- Swiss Light Source, Paul Scherrer Institute, Villigen 5232, Switzerland
| | - Stefan Bengtson
- Department of Palaeobiology and Nordic Center for Earth Evolution, Swedish Museum of Natural History, Stockholm 10405, Sweden
| | - Philip C J Donoghue
- School of Earth Sciences, University of Bristol, Life Sciences Building, 24 Tyndall Avenue, Bristol BS8 1TQ, England
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27
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Three-dimensional preservation of cellular and subcellular structures suggests 1.6 billion-year-old crown-group red algae. PLoS Biol 2017; 15:e2000735. [PMID: 28291791 PMCID: PMC5349422 DOI: 10.1371/journal.pbio.2000735] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 02/07/2017] [Indexed: 01/10/2023] Open
Abstract
The ~1.6 Ga Tirohan Dolomite of the Lower Vindhyan in central India contains phosphatized stromatolitic microbialites. We report from there uniquely well-preserved fossils interpreted as probable crown-group rhodophytes (red algae). The filamentous form Rafatazmia chitrakootensis n. gen, n. sp. has uniserial rows of large cells and grows through diffusely distributed septation. Each cell has a centrally suspended, conspicuous rhomboidal disk interpreted as a pyrenoid. The septa between the cells have central structures that may represent pit connections and pit plugs. Another filamentous form, Denaricion mendax n. gen., n. sp., has coin-like cells reminiscent of those in large sulfur-oxidizing bacteria but much more recalcitrant than the liquid-vacuole-filled cells of the latter. There are also resemblances with oscillatoriacean cyanobacteria, although cell volumes in the latter are much smaller. The wider affinities of Denaricion are uncertain. Ramathallus lobatus n. gen., n. sp. is a lobate sessile alga with pseudoparenchymatous thallus, “cell fountains,” and apical growth, suggesting florideophycean affinity. If these inferences are correct, Rafatazmia and Ramathallus represent crown-group multicellular rhodophytes, antedating the oldest previously accepted red alga in the fossil record by about 400 million years. The last common ancestor of modern eukaryotes is generally believed to have lived during the Mesoproterozoic era, about 1.6 to 1 billion years ago, or possibly somewhat earlier. We studied exquisitely preserved fossil communities from ~1.6 billion-year-old sedimentary rocks in central India representing a shallow-water marine environment characterized by photosynthetic biomats. We discovered amidst extensive cyanobacterial mats a biota of filamentous and lobate organisms that share significant features with modern eukaryotic algae, more specifically red algae. The rocks mainly consist of calcium and magnesium carbonates, but the microbial mats and the fossils are preserved in calcium phosphate, letting us view the cellular and subcellular structures in three dimensions with the use of synchrotron-radiation X-ray tomographic microscopy. The most conspicuous internal objects in the cells of the filamentous forms are rhomboidal platelets that we interpret to be part of the photosynthetic machinery of red algae. The lobate forms grew as radiating globular or finger-like protrusions from a common centre. These fossils predate the previously earliest accepted red algae by about 400 million years, suggesting that eukaryotes may have a longer history than commonly assumed.
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28
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Cunningham JA, Vargas K, Pengju L, Belivanova V, Marone F, Martínez-Pérez C, Guizar-Sicairos M, Holler M, Bengtson S, Donoghue PCJ. Critical appraisal of tubular putative eumetazoans from the Ediacaran Weng'an Doushantuo biota. Proc Biol Sci 2016; 282:20151169. [PMID: 26180072 PMCID: PMC4528530 DOI: 10.1098/rspb.2015.1169] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Molecular clock analyses estimate that crown-group animals began diversifying hundreds of millions of years before the start of the Cambrian period. However, the fossil record has not yielded unequivocal evidence for animals during this interval. Some of the most promising candidates for Precambrian animals occur in the Weng'an biota of South China, including a suite of tubular fossils assigned to Sinocyclocyclicus, Ramitubus, Crassitubus and Quadratitubus, that have been interpreted as soft-bodied eumetazoans comparable to tabulate corals. Here, we present new insights into the anatomy, original composition and phylogenetic affinities of these taxa based on data from synchrotron radiation X-ray tomographic microscopy, ptychographic nanotomography, scanning electron microscopy and electron probe microanalysis. The patterns of deformation observed suggest that the cross walls of Sinocyclocyclicus and Quadratitubus were more rigid than those of Ramitubus and Crassitubus. Ramitubus and Crassitubus specimens preserve enigmatic cellular clusters at terminal positions in the tubes. Specimens of Sinocyclocyclicus and Ramitubus have biological features that might be cellular tissue or subcellular structures filling the spaces between the cross walls. These observations are incompatible with a cnidarian interpretation, in which the spaces between cross walls are abandoned parts of the former living positions of the polyp. The affinity of the Weng'an tubular fossils may lie within the algae.
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Affiliation(s)
- John A Cunningham
- School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK Department of Palaeobiology and Nordic Center for Earth Evolution, Swedish Museum of Natural History, Stockholm 10405, Sweden
| | - Kelly Vargas
- School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Liu Pengju
- Institute of Geology, Chinese Academy of Geological Sciences, 26 Baiwanzhuang Road, Beijing 100037, People's Republic of China
| | - Veneta Belivanova
- Department of Palaeobiology and Nordic Center for Earth Evolution, Swedish Museum of Natural History, Stockholm 10405, Sweden
| | - Federica Marone
- Swiss Light Source, Paul Scherrer Institute, Villigen 5232, Switzerland
| | - Carlos Martínez-Pérez
- School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK Department of Geology, University of Valencia, C/Dr. Moliner 50, Burjassot, Valencia 46100, Spain
| | | | - Mirko Holler
- Swiss Light Source, Paul Scherrer Institute, Villigen 5232, Switzerland
| | - Stefan Bengtson
- Department of Palaeobiology and Nordic Center for Earth Evolution, Swedish Museum of Natural History, Stockholm 10405, Sweden
| | - Philip C J Donoghue
- School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
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Divergence time estimates and the evolution of major lineages in the florideophyte red algae. Sci Rep 2016; 6:21361. [PMID: 26892537 PMCID: PMC4759575 DOI: 10.1038/srep21361] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 01/19/2016] [Indexed: 11/08/2022] Open
Abstract
The Florideophyceae is the most abundant and taxonomically diverse class of red algae (Rhodophyta). However, many aspects of the systematics and divergence times of the group remain unresolved. Using a seven-gene concatenated dataset (nuclear EF2, LSU and SSU rRNAs, mitochondrial cox1, and plastid rbcL, psaA and psbA genes), we generated a robust phylogeny of red algae to provide an evolutionary timeline for florideophyte diversification. Our relaxed molecular clock analysis suggests that the Florideophyceae diverged approximately 943 (817-1,049) million years ago (Ma). The major divergences in this class involved the emergence of Hildenbrandiophycidae [ca. 781 (681-879) Ma], Nemaliophycidae [ca. 661 (597-736) Ma], Corallinophycidae [ca. 579 (543-617) Ma], and the split of Ahnfeltiophycidae and Rhodymeniophycidae [ca. 508 (442-580) Ma]. Within these clades, extant diversity reflects largely Phanerozoic diversification. Divergences within Florideophyceae were accompanied by evolutionary changes in the carposporophyte stage, leading to a successful strategy for maximizing spore production from each fertilization event. Our research provides robust estimates for the divergence times of major lineages within the Florideophyceae. This timeline was used to interpret the emergence of key morphological innovations that characterize these multicellular red algae.
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Yang EC, Kim KM, Kim SY, Lee J, Boo GH, Lee JH, Nelson WA, Yi G, Schmidt WE, Fredericq S, Boo SM, Bhattacharya D, Yoon HS. Highly Conserved Mitochondrial Genomes among Multicellular Red Algae of the Florideophyceae. Genome Biol Evol 2015; 7:2394-406. [PMID: 26245677 PMCID: PMC4558864 DOI: 10.1093/gbe/evv147] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/28/2015] [Indexed: 11/12/2022] Open
Abstract
Two red algal classes, the Florideophyceae (approximately 7,100 spp.) and Bangiophyceae (approximately 193 spp.), comprise 98% of red algal diversity in marine and freshwater habitats. These two classes form well-supported monophyletic groups in most phylogenetic analyses. Nonetheless, the interordinal relationships remain largely unresolved, in particular in the largest subclass Rhodymeniophycidae that includes 70% of all species. To elucidate red algal phylogenetic relationships and study organelle evolution, we determined the sequence of 11 mitochondrial genomes (mtDNA) from 5 florideophycean subclasses. These mtDNAs were combined with existing data, resulting in a database of 25 florideophytes and 12 bangiophytes (including cyanidiophycean species). A concatenated alignment of mt proteins was used to resolve ordinal relationships in the Rhodymeniophycidae. Red algal mtDNA genome comparisons showed 47 instances of gene rearrangement including 12 that distinguish Bangiophyceae from Hildenbrandiophycidae, and 5 that distinguish Hildenbrandiophycidae from Nemaliophycidae. These organelle data support a rapid radiation and surprisingly high conservation of mtDNA gene syntheny among the morphologically divergent multicellular lineages of Rhodymeniophycidae. In contrast, we find extensive mitochondrial gene rearrangements when comparing Bangiophyceae and Florideophyceae and multiple examples of gene loss among the different red algal lineages.
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Affiliation(s)
- Eun Chan Yang
- Marine Ecosystem Research Division, Korea Institute of Ocean Science & Technology, Ansan, Korea Department of Marine Biology, Korea University of Science and Technology, Daejeon, Korea
| | - Kyeong Mi Kim
- Bioresource Systematics Department, National Marine Biodiversity Institute of Korea, Seocheon, Chungnam, Korea
| | - Su Yeon Kim
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Korea
| | - JunMo Lee
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Korea
| | - Ga Hun Boo
- Department of Biology, Chungnam National University, Daejeon, Korea
| | - Jung-Hyun Lee
- Marine Biotechnology Research Division, Korea Institute of Ocean Science & Technology, Ansan, Korea
| | - Wendy A Nelson
- National Institute for Water and Atmospheric Research, Wellington, New Zealand School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Gangman Yi
- Department of Computer Science and Engineering, Gangneung-Wonju National University, Wonju, Korea
| | | | | | - Sung Min Boo
- Department of Biology, Chungnam National University, Daejeon, Korea
| | - Debashish Bhattacharya
- Department of Ecology, Evolution and Natural Resources and Department of Marine and Coastal Sciences, Rutgers University
| | - Hwan Su Yoon
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Korea
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Nelson WA, Sutherland JE, Farr TJ, Hart DR, Neill KF, Kim HJ, Yoon HS. Multi-gene phylogenetic analyses of New Zealand coralline algae: Corallinapetra Novaezelandiae gen. et sp. nov. and recognition of the Hapalidiales ord. nov. JOURNAL OF PHYCOLOGY 2015; 51:454-468. [PMID: 26986662 DOI: 10.1111/jpy.12288] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2014] [Accepted: 12/11/2014] [Indexed: 06/05/2023]
Abstract
Coralline red algae from the New Zealand region were investigated in a study focused on documenting regional diversity. We present a multi-gene analysis using sequence data obtained for four genes (nSSU, psaA, psbA, rbcL) from 68 samples. The study revealed cryptic diversity at both genus and species levels, confirming and providing further evidence of problems with current taxonomic concepts in the Corallinophycidae. In addition, a new genus Corallinapetra novaezelandiae gen. et sp. nov. is erected for material from northern New Zealand. Corallinapetra is excluded from all currently recognized families and orders within the Corallinophycidae and thus represents a previously unrecognized lineage within this subclass. We discuss rank in the Corallinophycidae and propose the order Hapalidiales.
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Affiliation(s)
- Wendy A Nelson
- National Institute of Water and Atmospheric Research, Private Bag 14-901, Wellington, 6241, New Zealand
- School of Biological Sciences, University of Auckland, Private Bag 92-019, Auckland, 1142, New Zealand
| | - Judith E Sutherland
- School of Biological Sciences, University of Auckland, Private Bag 92-019, Auckland, 1142, New Zealand
| | - Tracy J Farr
- Royal Society of New Zealand, PO Box 598, Wellington, 6140, New Zealand
| | - Darren R Hart
- Department of Biochemistry, University of Otago, PO Box 56, Dunedin, 9054, New Zealand
| | - Kate F Neill
- National Institute of Water and Atmospheric Research, Private Bag 14-901, Wellington, 6241, New Zealand
| | - Hee Jeong Kim
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 440-746, Korea
| | - Hwan Su Yoon
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 440-746, Korea
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Sponge grade body fossil with cellular resolution dating 60 Myr before the Cambrian. Proc Natl Acad Sci U S A 2015; 112:E1453-60. [PMID: 25775601 DOI: 10.1073/pnas.1414577112] [Citation(s) in RCA: 148] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
An extraordinarily well preserved, 600-million-year (Myr)-old, three-dimensionally phosphatized fossil displaying multiple independent characters of modern adult sponges has been analyzed by SEM and synchrotron X-ray tomography. The fossilized animal (Eocyathispongia qiania gen. et sp. nov.) is slightly more than 1.2 mm wide and 1.1 mm tall, is composed of hundreds of thousands of cells, and has a gross structure consisting of three adjacent hollow tubes sharing a common base. The main tube is crowned with a large open funnel, and the others end in osculum-like openings to the exterior. The external surface is densely covered with flat tile-like cells closely resembling sponge pinacocytes, and this layer is punctuated with smaller pores. A dense patch of external structures that display the form of a lawn of sponge papillae has also survived. Within the main funnel, an area where features of the inner surface are preserved displays a regular pattern of uniform pits. Many of them are surrounded individually by distinct collars, mounted in a supporting reticulum. The possibility cannot be excluded that these pits are the remains of a field of choanocytes. The character set evinced by this specimen, ranging from general anatomy to cell type, uniquely indicates that this specimen is a fossil of probable poriferan affinity. So far, we have only this single specimen, and although its organized and complex cellular structure precludes any reasonable interpretation that its origin is abiogenic, confirmation that it is indeed a fossilized sponge will clearly require discovery of additional specimens.
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Cock JM, Collén J. Independent Emergence of Complex Multicellularity in the Brown and Red Algae. EVOLUTIONARY TRANSITIONS TO MULTICELLULAR LIFE 2015. [DOI: 10.1007/978-94-017-9642-2_16] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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Xiao S, Muscente AD, Chen L, Zhou C, Schiffbauer JD, Wood AD, Polys NF, Yuan X. The Weng'an biota and the Ediacaran radiation of multicellular eukaryotes. Natl Sci Rev 2014. [DOI: 10.1093/nsr/nwu061] [Citation(s) in RCA: 97] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
The rise of multicellularity represents a major evolutionary transition and it occurred independently in multiple eukaryote clades. Although simple multicellular organisms may have evolved in the Mesoproterozoic Era or even earlier, complex multicellular eukaryotes began to diversify only in the Ediacaran Period, just before the Cambrian explosion. Thus, the Ediacaran fossil record can provide key paleontological evidence about the early radiation of multicellular eukaryotes that ultimately culminated in the Cambrian explosion. The Ediacaran Weng'an biota in South China hosts exceptionally preserved eukaryote fossils, including various acanthomorphic acritarchs, pseudoparenchymatous thalli, tubular microfossils, and spheroidal fossils such as Megasphaera, Helicoforamina, Spiralicellula, and Caveasphaera. Many of these fossils have been interpreted as multicellular eukaryotes, although alternative interpretations have also been proposed. In this review, we critically examine these various interpretations, focusing particularly on Megasphaera, which has been variously interpreted as a sulfur-oxidizing bacterium, a unicellular protist, a mesomycetozoean-like holozoan, a volvocine green alga, a stem-group animal, or a crown-group animal. We conclude that Megasphaera is a multicellular eukaryote with evidence for cell-to-cell adhesion, a flexible membrane unconstrained by a rigid cell wall, spatial cellular differentiation, germ–soma separation, and programmed cell death. These features are inconsistent with the bacterium, unicellular protist, and mesomycetozoean-like holozoan interpretations. Thus, the surviving hypotheses, particularly the stem-group animal and algal interpretations, should be further tested with additional evidence. The Weng'an biota also hosts cellularly differentiated pseudoparenchymatous thalli with specialized reproductive structures indicative of an affinity with florideophyte red algae. The other Weng'an fossils reviewed here may also be multicellular eukaryotes, although direct cellular evidence is lacking in some and phylogenetic affinities are poorly constrained in others. The Weng'an biota offers many research opportunities to resolve the life histories and phylogenetic diversity of early multicellular eukaryotes and to illuminate the evolutionary prelude to the Cambrian explosion.
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Affiliation(s)
- Shuhai Xiao
- Department of Geosciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - A. D. Muscente
- Department of Geosciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Lei Chen
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Paleontology, Chinese Academy of Sciences, Nanjing 210008, China
- College of Earth Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chuanming Zhou
- Key Laboratory of Economic Stratigraphy and Palaeogeography, Nanjing Institute of Geology and Paleontology, Chinese Academy of Sciences, Nanjing 210008, China
| | - James D. Schiffbauer
- Department of Geological Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Andrew D. Wood
- Advanced Research Computing, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Nicholas F. Polys
- Advanced Research Computing, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Xunlai Yuan
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Paleontology, Chinese Academy of Sciences, Nanjing 210008, China
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Chen L, Xiao S, Pang K, Zhou C, Yuan X. Cell differentiation and germ–soma separation in Ediacaran animal embryo-like fossils. Nature 2014; 516:238-41. [DOI: 10.1038/nature13766] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Accepted: 08/07/2014] [Indexed: 11/09/2022]
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Blank CE. Origin and early evolution of photosynthetic eukaryotes in freshwater environments: reinterpreting proterozoic paleobiology and biogeochemical processes in light of trait evolution. JOURNAL OF PHYCOLOGY 2013; 49:1040-55. [PMID: 27007625 DOI: 10.1111/jpy.12111] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2012] [Accepted: 08/04/2013] [Indexed: 05/19/2023]
Abstract
Phylogenetic analyses were performed on concatenated data sets of 31 genes and 11,789 unambiguously alignable characters from 37 cyanobacterial and 35 chloroplast genomes. The plastid lineage emerged somewhat early in the cyanobacterial tree, at a time when Cyanobacteria were likely unicellular and restricted to freshwater ecosystems. Using relaxed molecular clocks and 22 age constraints spanning cyanobacterial and eukaryote nodes, the common ancestor to the photosynthetic eukaryotes was predicted to have also inhabited freshwater environments around the time that oxygen appeared in the atmosphere (2.0-2.3 Ga). Early diversifications within each of the three major plastid clades were also inferred to have occurred in freshwater environments, through the late Paleoproterozoic and into the middle Mesoproterozoic. The colonization of marine environments by photosynthetic eukaryotes may not have occurred until after the middle Mesoproterozoic (1.2-1.5 Ga). The evolutionary hypotheses proposed here predict that early photosynthetic eukaryotes may have never experienced the widespread anoxia or euxinia suggested to have characterized marine environments in the Paleoproterozoic to early Mesoproterozoic. It also proposes that earliest acritarchs (1.5-1.7 Ga) may have been produced by freshwater taxa. This study highlights how the early evolution of habitat preference in photosynthetic eukaryotes, along with Cyanobacteria, could have contributed to changing biogeochemical conditions on the early Earth.
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Affiliation(s)
- Carrine E Blank
- Department of Geosciences, University of Montana, 32 Campus Drive #1296, Missoula, Montana, 59812-1296, USA
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Xiao S. Neoproterozoic Glaciations and the Fossil Record. THE EXTREME PROTEROZOIC: GEOLOGY, GEOCHEMISTRY, AND CLIMATE 2013. [DOI: 10.1029/146gm16] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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Written in Stone: The Fossil Record of Early Eukaryotes. SOCIAL AND ECOLOGICAL INTERACTIONS IN THE GALAPAGOS ISLANDS 2013. [DOI: 10.1007/978-1-4614-6732-8_8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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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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40
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Xiao S, Knoll AH, Schiffbauer JD, Zhou C, Yuan X. Comment on “Fossilized Nuclei and Germination Structures Identify Ediacaran ‘Animal Embryos’ as Encysting Protists”. Science 2012; 335:1169; author reply 1169. [DOI: 10.1126/science.1218814] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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41
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Raven JA, Giordano M, Beardall J, Maberly SC. Algal evolution in relation to atmospheric CO2: carboxylases, carbon-concentrating mechanisms and carbon oxidation cycles. Philos Trans R Soc Lond B Biol Sci 2012; 367:493-507. [PMID: 22232762 PMCID: PMC3248706 DOI: 10.1098/rstb.2011.0212] [Citation(s) in RCA: 146] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Oxygenic photosynthesis evolved at least 2.4 Ga; all oxygenic organisms use the ribulose bisphosphate carboxylase-oxygenase (Rubisco)-photosynthetic carbon reduction cycle (PCRC) rather than one of the five other known pathways of autotrophic CO(2) assimilation. The high CO(2) and (initially) O(2)-free conditions permitted the use of a Rubisco with a high maximum specific reaction rate. As CO(2) decreased and O(2) increased, Rubisco oxygenase activity increased and 2-phosphoglycolate was produced, with the evolution of pathways recycling this inhibitory product to sugar phosphates. Changed atmospheric composition also selected for Rubiscos with higher CO(2) affinity and CO(2)/O(2) selectivity correlated with decreased CO(2)-saturated catalytic capacity and/or for CO(2)-concentrating mechanisms (CCMs). These changes increase the energy, nitrogen, phosphorus, iron, zinc and manganese cost of producing and operating Rubisco-PCRC, while biosphere oxygenation decreased the availability of nitrogen, phosphorus and iron. The majority of algae today have CCMs; the timing of their origins is unclear. If CCMs evolved in a low-CO(2) episode followed by one or more lengthy high-CO(2) episodes, CCM retention could involve a combination of environmental factors known to favour CCM retention in extant organisms that also occur in a warmer high-CO(2) ocean. More investigations, including studies of genetic adaptation, are needed.
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Affiliation(s)
- John A Raven
- Division of Plant Sciences, The James Hutton Institute, University of Dundee at TJHI, Invergowrie, Dundee DD2 5DA, UK.
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Estimating the timing of early eukaryotic diversification with multigene molecular clocks. Proc Natl Acad Sci U S A 2011; 108:13624-9. [PMID: 21810989 DOI: 10.1073/pnas.1110633108] [Citation(s) in RCA: 492] [Impact Index Per Article: 37.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Although macroscopic plants, animals, and fungi are the most familiar eukaryotes, the bulk of eukaryotic diversity is microbial. Elucidating the timing of diversification among the more than 70 lineages is key to understanding the evolution of eukaryotes. Here, we use taxon-rich multigene data combined with diverse fossils and a relaxed molecular clock framework to estimate the timing of the last common ancestor of extant eukaryotes and the divergence of major clades. Overall, these analyses suggest that the last common ancestor lived between 1866 and 1679 Ma, consistent with the earliest microfossils interpreted with confidence as eukaryotic. During this interval, the Earth's surface differed markedly from today; for example, the oceans were incompletely ventilated, with ferruginous and, after about 1800 Ma, sulfidic water masses commonly lying beneath moderately oxygenated surface waters. Our time estimates also indicate that the major clades of eukaryotes diverged before 1000 Ma, with most or all probably diverging before 1200 Ma. Fossils, however, suggest that diversity within major extant clades expanded later, beginning about 800 Ma, when the oceans began their transition to a more modern chemical state. In combination, paleontological and molecular approaches indicate that long stems preceded diversification in the major eukaryotic lineages.
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Boo SM, Kim HS, Shin W, Boo GH, Cho SM, Jo BY, Kim JH, Kim JH, Yang EC, Siver PA, Wolfe AP, Bhattacharya D, Andersen RA, Yoon HS. Complex phylogeographic patterns in the freshwater alga Synura provide new insights into ubiquity vs. endemism in microbial eukaryotes. Mol Ecol 2010; 19:4328-38. [PMID: 25241409 DOI: 10.1111/j.1365-294x.2010.04813.x] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The global distribution, abundance, and diversity of microscopic freshwater algae demonstrate an ability to overcome significant barriers such as dry land and oceans by exploiting a range of biotic and abiotic colonization vectors. If these vectors are considered unlimited and colonization occurs in proportion to population size, then globally ubiquitous distributions are predicted to arise. This model contrasts with observations that many freshwater microalgal taxa possess true biogeographies. Here, using a concatenated multigene data set, we study the phylogeography of the freshwater heterokont alga Synura petersenii sensu lato. Our results suggest that this Synura morphotaxon contains both cosmopolitan and regionally endemic cryptic species, co-occurring in some cases, and masked by a common ultrastructural morphology. Phylogenies based on both proteins (seven protein-coding plastid and mitochondrial genes) and DNA (nine genes including ITS and 18S rDNA) reveal pronounced biogeographic delineations within phylotypes of this cryptic species complex while retaining one clade that is globally distributed. Relaxed molecular clock calculations, constrained by fossil records, suggest that the genus Synura is considerably older than currently proposed. The availability of tectonically relevant geological time (10⁷-10⁸ years) has enabled the development of the observed, complex biogeographic patterns. Our comprehensive analysis of freshwater algal biogeography suggests that neither ubiquity nor endemism wholly explains global patterns of microbial eukaryote distribution and that processes of dispersal remain poorly understood.
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Evolutionary History and Taxonomy of Red Algae. CELLULAR ORIGIN, LIFE IN EXTREME HABITATS AND ASTROBIOLOGY 2010. [DOI: 10.1007/978-90-481-3795-4_2] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Azúa-Bustos A, González-Silva C, Mancilla RA, Salas L, Palma RE, Wynne JJ, McKay CP, Vicuña R. Ancient photosynthetic eukaryote biofilms in an Atacama Desert coastal cave. MICROBIAL ECOLOGY 2009; 58:485-496. [PMID: 19259626 DOI: 10.1007/s00248-009-9500-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2008] [Accepted: 02/06/2009] [Indexed: 05/27/2023]
Abstract
Caves offer a stable and protected environment from harsh and changing outside prevailing conditions. Hence, they represent an interesting habitat for studying life in extreme environments. Here, we report the presence of a member of the ancient eukaryote red algae Cyanidium group in a coastal cave of the hyperarid Atacama Desert. This microorganism was found to form a seemingly monospecific biofilm growing under extremely low photon flux levels. Our work suggests that this species, Cyanidium sp. Atacama, is a new member of a recently proposed novel monophyletic lineage of mesophilic "cave" Cyanidium sp., distinct from the remaining three other lineages which are all thermo-acidophilic. The cave described in this work may represent an evolutionary island for life in the midst of the Atacama Desert.
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Affiliation(s)
- A Azúa-Bustos
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Alameda 340, Santiago, Chile.
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Amunts A, Nelson N. Plant Photosystem I Design in the Light of Evolution. Structure 2009; 17:637-50. [DOI: 10.1016/j.str.2009.03.006] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2008] [Revised: 03/23/2009] [Accepted: 03/25/2009] [Indexed: 11/26/2022]
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Halverson GP, Hurtgen MT, Porter SM, Collins AS. Chapter 10 Neoproterozoic-Cambrian Biogeochemical Evolution. NEOPROTEROZOIC-CAMBRIAN TECTONICS, GLOBAL CHANGE AND EVOLUTION: A FOCUS ON SOUTH WESTERN GONDWANA 2009. [DOI: 10.1016/s0166-2635(09)01625-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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48
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Discovery of Lignin in Seaweed Reveals Convergent Evolution of Cell-Wall Architecture. Curr Biol 2009; 19:169-75. [DOI: 10.1016/j.cub.2008.12.031] [Citation(s) in RCA: 305] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2008] [Revised: 12/08/2008] [Accepted: 12/10/2008] [Indexed: 11/22/2022]
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49
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Jiang G, Zhang S, Shi X, Wang X. Chemocline instability and isotope variations of the Ediacaran Doushantuo basin in South China. ACTA ACUST UNITED AC 2008. [DOI: 10.1007/s11430-008-0116-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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50
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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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