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Mussini G, Dunn FS. Decline and fall of the Ediacarans: late-Neoproterozoic extinctions and the rise of the modern biosphere. Biol Rev Camb Philos Soc 2024; 99:110-130. [PMID: 37667585 DOI: 10.1111/brv.13014] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 08/22/2023] [Accepted: 08/25/2023] [Indexed: 09/06/2023]
Abstract
The end-Neoproterozoic transition marked a gradual but permanent shift between distinct configurations of Earth's biosphere. This interval witnessed the demise of the enigmatic Ediacaran Biota, ushering in the structured trophic webs and disparate animal body plans of Phanerozoic ecosystems. However, little consensus exists on the reality, drivers, and macroevolutionary implications of end-Neoproterozoic extinctions. Here we evaluate potential drivers of late-Neoproterozoic turnover by addressing recent findings on Ediacaran geochronology, the persistence of classical Ediacaran macrobionts into the Cambrian, and the existence of Ediacaran crown-group eumetazoans. Despite renewed interest in the possibility of Phanerozoic-style 'mass extinctions' in the latest Neoproterozoic, our synthesis of the available evidence does not support extinction models based on episodic geochemical triggers, nor does it validate simple ecological interpretations centred on direct competitive displacement. Instead, we argue that the protracted and indirect effects of early bilaterian innovations, including escalations in sediment engineering, predation, and the largely understudied impacts of reef-building, may best account for the temporal structure and possible selectivity of late-Neoproterozoic extinctions. We integrate these processes into a generalised model of early eumetazoan-dominated ecologies, charting the disruption of spatial and temporal isotropy on the Ediacaran benthos as a consequence of diversifying macrofaunal interactions. Given the nature of resource distribution in Ediacaran ecologies, the continuities among Ediacaran and Cambrian faunas, and the convergent origins of ecologically disruptive innovations among bilaterians we suggest that the rise of Phanerozoic-type biotas may have been unstoppable.
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Affiliation(s)
- Giovanni Mussini
- Department of Earth Sciences, Downing Street, University of Cambridge, Cambridge, CB2 3EQ, UK
| | - Frances S Dunn
- Oxford University Museum of Natural History, Parks Road, University of Oxford, Oxford, OX1 3PW, UK
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2
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Wang R, Shen B, Lang X, Wen B, Mitchell RN, Ma H, Yin Z, Peng Y, Liu Y, Zhou C. A Great late Ediacaran ice age. Natl Sci Rev 2023; 10:nwad117. [PMID: 37389143 PMCID: PMC10306365 DOI: 10.1093/nsr/nwad117] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 04/23/2023] [Accepted: 04/24/2023] [Indexed: 07/01/2023] Open
Abstract
The emergence of the Ediacara biota soon after the Gaskiers glaciation ca. 580 million years ago (Ma) implies a possible glacial fuse for the evolution of animals. However, the timing of Ediacaran glaciation remains controversial because of poor age constraints on the ∼30 Ediacaran glacial deposits known worldwide. In addition, paleomagnetic constraints and a lack of convincing Snowball-like cap carbonates indicate that Ediacaran glaciations likely did not occur at low latitudes. Thus, reconciling the global occurrences without global glaciation remains a paradox. Here, we report that the large amplitude, globally synchronous ca. 571-562 Ma Shuram carbon isotope excursion occurs below the Ediacaran Hankalchough glacial deposit in Tarim, confirming a post-Shuram glaciation. Leveraging paleomagnetic evidence for a ∼90° reorientation of all continents due to true polar wander, and a non-Snowball condition that rules out low-latitude glaciations, we use paleogeographic reconstructions to further constrain glacial ages. Our results depict a 'Great Ediacaran Glaciation' occurring diachronously but continuously from ca. 580-560 Ma as different continents migrated through polar-temperate latitudes. The succession of radiation, turnover and extinction of the Ediacara biota strongly reflects glacial-deglacial dynamics.
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Affiliation(s)
- Ruimin Wang
- Key Laboratory of Orogenic Belts and Crustal Evolution, Ministry of Education and School of Earth and Space Sciences, Peking University, Beijing 100871, China
| | - Bing Shen
- Key Laboratory of Orogenic Belts and Crustal Evolution, Ministry of Education and School of Earth and Space Sciences, Peking University, Beijing 100871, China
| | - Xianguo Lang
- State Key Laboratory of Oil and Gas Reservoir Geology and Exploitation, and Institute of Sedimentary Geology, Chengdu University of Technology, Chengdu 610059, China
| | - Bin Wen
- State Key Laboratory of Geological Processes and Mineral Resources, School of Earth Sciences, China University of Geosciences, Wuhan 430074, China
| | - Ross N Mitchell
- State Key Laboratory of Lithospheric Evolution, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing 100029, China
- College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Haoran Ma
- School of Earth Sciences and Engineering, Nanjing University, Nanjing 210023, China
| | - Zongjun Yin
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, and Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Nanjing 210008, China
| | - Yongbo Peng
- School of Earth Sciences and Engineering, Nanjing University, Nanjing 210023, China
| | - Yonggang Liu
- School of Physics, Peking University, Beijing 100871, China
| | - Chuanming Zhou
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, and Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Nanjing 210008, China
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3
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Eden R, Manica A, Mitchell EG. Metacommunity analyses show an increase in ecological specialisation throughout the Ediacaran period. PLoS Biol 2022; 20:e3001289. [PMID: 35580078 PMCID: PMC9113585 DOI: 10.1371/journal.pbio.3001289] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 03/29/2022] [Indexed: 11/18/2022] Open
Abstract
The first animals appear during the late Ediacaran (572 to 541 Ma); an initial diversity increase was followed reduction in diversity, often interpreted as catastrophic mass extinction. We investigate Ediacaran ecosystem structure changes over this time period using the “Elements of Metacommunity Structure” framework to assess whether this diversity reduction in the Nama was likely caused by an external mass extinction, or internal metacommunity restructuring. The oldest metacommunity was characterised by taxa with wide environmental tolerances, and limited specialisation or intertaxa associations. Structuring increased in the second oldest metacommunity, with groups of taxa sharing synchronous responses to environmental gradients, aggregating into distinct communities. This pattern strengthened in the youngest metacommunity, with communities showing strong environmental segregation and depth structure. Thus, metacommunity structure increased in complexity, with increased specialisation and resulting in competitive exclusion, not a catastrophic environmental disaster, leading to diversity loss in the terminal Ediacaran. These results reveal that the complex eco-evolutionary dynamics associated with Cambrian diversification were established in the Ediacaran. This study shows that the eco-evolutionary dynamics of metazoan diversification known from the Cambrian Period started earlier in the Ediacaran Period with the Avalon assemblage and increased in complexity towards the Phanerozoic as new anatomical innovations appeared, culminating in the “Cambrian Explosion."
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Affiliation(s)
- Rebecca Eden
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Andrea Manica
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Emily G. Mitchell
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
- * E-mail:
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4
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Abramov O, Bebell KL, Mojzsis SJ. Emergent Bioanalogous Properties of Blockchain-based Distributed Systems. ORIGINS LIFE EVOL B 2021; 51:131-165. [PMID: 34363563 DOI: 10.1007/s11084-021-09608-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 03/27/2021] [Indexed: 11/24/2022]
Abstract
We apply a novel definition of biological systems to a series of reproducible observations on a blockchain-based distributed virtual machine (dVM). We find that such blockchain-based systems display a number of bioanalogous properties, such as response to the environment, growth and change, replication, and homeostasis, that fit some definitions of life. We further present a conceptual model for a simple self-sustaining, self-organizing, self-regulating distributed 'organism' as an operationally closed system that would fulfill all basic definitions and criteria for life, and describe developing technologies, particularly artificial neural network (ANN) based artificial intelligence (AI), that would enable it in the near future. Notably, such systems would have a number of specific advantages over biological life, such as the ability to pass acquired traits to offspring, significantly improved speed, accuracy, and redundancy of their genetic carrier, and potentially unlimited lifespans. Public blockchain-based dVMs provide an uncontained environment for the development of artificial general intelligence (AGI) with the capability to evolve by self-direction.
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Affiliation(s)
- Oleg Abramov
- Planetary Science Institute, 1700 E. Fort Lowell Rd., Suite 106, 85719-2395, Tucson, AZ, USA.
| | | | - Stephen J Mojzsis
- Origins Research Institute, Research Centre for Astronomy and Earth Sciences, 15-17 Konkoly Thege Miklós ut, Budapest, 1121, Hungary.,Department of Lithospheric Research, University Vienna, UZA 2, Althanstrasse 14, 1090, Vienna, Austria.,Department of Geological Sciences, University of Colorado at Boulder, 2200 Colorado Avenue UCB 399, 80309, Boulder, CO, USA
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5
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Dvornyk V, Mei Q. Evolution of kaiA, a key circadian gene of cyanobacteria. Sci Rep 2021; 11:9995. [PMID: 33976298 PMCID: PMC8113500 DOI: 10.1038/s41598-021-89345-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Accepted: 03/16/2021] [Indexed: 11/09/2022] Open
Abstract
The circadian system of cyanobacteria is built upon a central oscillator consisting of three genes, kaiA, kaiB, and kaiC. The KaiA protein plays a key role in phosphorylation/dephosphorylation cycles of KaiC, which occur over the 24-h period. We conducted a comprehensive evolutionary analysis of the kaiA genes across cyanobacteria. The results show that, in contrast to the previous reports, kaiA has an ancient origin and is as old as cyanobacteria. The kaiA homologs are present in nearly all analyzed cyanobacteria, except Gloeobacter, and have varying domain architecture. Some Prochlorococcales, which were previously reported to lack the kaiA gene, possess a drastically truncated homolog. The existence of the diverse kaiA homologs suggests significant variation of the circadian mechanism, which was described for the model cyanobacterium, Synechococcus elongatus PCC7942. The major structural modifications in the kaiA genes (duplications, acquisition and loss of domains) have apparently been induced by global environmental changes in the different geological periods.
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Affiliation(s)
- Volodymyr Dvornyk
- Department of Life Sciences, College of Science and General Studies, Alfaisal University, Riyadh, 11533, Kingdom of Saudi Arabia.
| | - Qiming Mei
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, People's Republic of China.,Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, People's Republic of China
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6
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On the waiting time until coordinated mutations get fixed in regulatory sequences. J Theor Biol 2021; 524:110657. [PMID: 33675769 DOI: 10.1016/j.jtbi.2021.110657] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 02/13/2021] [Accepted: 02/24/2021] [Indexed: 11/23/2022]
Abstract
In this paper we consider the time evolution of a population of size N with overlapping generations, in the vicinity of m genes. We assume that this population is subject to point mutations, genetic drift, and selection. More specifically, we analyze the statistical distribution of the waiting time Tm until the expression of these genes have changed for all individuals, when transcription factors recognize and attach to short DNA-sequences (binding sites) within regulatory sequences in the neighborhoods of the m genes. The evolutionary dynamics is described by a multitype Moran process, where each individual is assigned a m×L regulatory array that consists of regulatory sequences with L nucleotides for all m genes. We study how the waiting time distribution depends on the number of genes, the mutation rate, the length of the binding sites, the length of the regulatory sequences, and the way in which the targeted binding sites are coordinated for different genes in terms of selection coefficients. These selection coefficients depend on how many binding sites have appeared so far, and possibly on their order of appearance. We also allow for back mutations, whereby some acquired binding sites may be lost over time. It is further assumed that the mutation rate is small enough to warrant a fixed state population, so that all individuals have the same regulatory array, at any given time point, until the next successful mutation arrives in some individual and spreads to the rest of the population. We further incorporate stochastic tunneling, whereby successful mutations get mutated before their fixation. A crucial part of our approach is to divide the huge state space of regulatory arrays into a small number of components, assuming that the array component varies as a Markov process over time. This implies that Tm is the time until this Markov process hits an absorbing state, with a phase-type distribution. A number of interesting results can be derived from our general setup, for instance that the expected waiting time increases exponentially with m, for a selectively neutral model, when back-mutations are possible.
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7
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Energetic requirements of the transition from solitary to group living. ECOLOGICAL COMPLEXITY 2020. [DOI: 10.1016/j.ecocom.2020.100874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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8
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Mitchell EG, Bobkov N, Bykova N, Dhungana A, Kolesnikov AV, Hogarth IRP, Liu AG, Mustill TMR, Sozonov N, Rogov VI, Xiao S, Grazhdankin DV. The influence of environmental setting on the community ecology of Ediacaran organisms. Interface Focus 2020; 10:20190109. [PMID: 32642052 DOI: 10.1098/rsfs.2019.0109] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/14/2020] [Indexed: 11/12/2022] Open
Abstract
The broad-scale environment plays a substantial role in shaping modern marine ecosystems, but the degree to which palaeocommunities were influenced by their environment is unclear. To investigate how broad-scale environment influenced the community ecology of early animal ecosystems, we employed spatial point process analyses (SPPA) to examine the community structure of seven late Ediacaran (558-550 Ma) bedding-plane assemblages drawn from a range of environmental settings and global localities. The studied palaeocommunities exhibit marked differences in the response of their component taxa to sub-metre-scale habitat heterogeneities on the seafloor. Shallow-marine (nearshore) palaeocommunities were heavily influenced by local habitat heterogeneities, in contrast to their deeper-water counterparts. The local patchiness within shallow-water communities may have been further accentuated by the presence of grazers and detritivores, whose behaviours potentially initiated a propagation of increasing habitat heterogeneity of benthic communities from shallow to deep-marine depositional environments. Higher species richness in shallow-water Ediacaran assemblages compared to deep-water counterparts across the studied time-interval could have been driven by this environmental patchiness, because habitat heterogeneities increase species richness in modern marine environments. Our results provide quantitative support for the 'Savannah' hypothesis for early animal diversification-whereby Ediacaran diversification was driven by patchiness in the local benthic environment.
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Affiliation(s)
- Emily G Mitchell
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| | - Nikolai Bobkov
- Trofimuk Institute of Petroleum Geology and Geophysics, 3, Ac. Koptyuga ave., Novosibirsk 630090, Russian Federation.,Novosibirsk State University, Novosibirsk, Novosibirsk Oblast 630090, Russian Federation
| | - Natalia Bykova
- Trofimuk Institute of Petroleum Geology and Geophysics, 3, Ac. Koptyuga ave., Novosibirsk 630090, Russian Federation.,Department of Geosciences, Virginia Tech, Blacksburg, VA 24061, USA
| | - Alavya Dhungana
- Department of Earth Sciences, Durham University, Lower Mountjoy, South Road, Durham DH1 3LE, UK
| | - Anton V Kolesnikov
- Trofimuk Institute of Petroleum Geology and Geophysics, 3, Ac. Koptyuga ave., Novosibirsk 630090, Russian Federation.,Geological Institute, Russian Academy of Sciences, Pygevsky 7, Moscow 119017, Russia.,Faculty of Geography, Moscow State Pedagogical University, Kibalchicha str. 16, Moscow 129626, Russia
| | - Ian R P Hogarth
- Department of Chemical Engineering, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, UK
| | - Alexander G Liu
- Department of Earth Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EQ, UK
| | - Tom M R Mustill
- Department of Earth Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EQ, UK
| | - Nikita Sozonov
- Trofimuk Institute of Petroleum Geology and Geophysics, 3, Ac. Koptyuga ave., Novosibirsk 630090, Russian Federation.,Novosibirsk State University, Novosibirsk, Novosibirsk Oblast 630090, Russian Federation
| | - Vladimir I Rogov
- Trofimuk Institute of Petroleum Geology and Geophysics, 3, Ac. Koptyuga ave., Novosibirsk 630090, Russian Federation
| | - Shuhai Xiao
- Department of Geosciences, Virginia Tech, Blacksburg, VA 24061, USA
| | - Dmitriy V Grazhdankin
- Trofimuk Institute of Petroleum Geology and Geophysics, 3, Ac. Koptyuga ave., Novosibirsk 630090, Russian Federation.,Novosibirsk State University, Novosibirsk, Novosibirsk Oblast 630090, Russian Federation
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9
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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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10
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Mitchell EG, Harris S, Kenchington CG, Vixseboxse P, Roberts L, Clark C, Dennis A, Liu AG, Wilby PR. The importance of neutral over niche processes in structuring Ediacaran early animal communities. Ecol Lett 2019; 22:2028-2038. [PMID: 31515929 PMCID: PMC6899650 DOI: 10.1111/ele.13383] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 08/01/2019] [Accepted: 08/11/2019] [Indexed: 01/22/2023]
Abstract
The relative influence of niche vs. neutral processes in ecosystem dynamics is an on-going debate, but the extent to which they structured the earliest animal communities is unknown. Some of the oldest known metazoan-dominated paleocommunities occur in Ediacaran age (~ 565 million years old) strata in Newfoundland, Canada and Charnwood Forest, UK. These comprise large and diverse populations of sessile organisms that are amenable to spatial point process analyses, enabling inference of the most likely underlying niche or neutral processes governing community structure. We mapped seven Ediacaran paleocommunities using LiDAR, photogrammetry and a laser line probe. We found that neutral processes dominate these paleocommunities, with niche processes exerting limited influence, in contrast with the niche-dominated dynamics of modern marine ecosystems. The dominance of neutral processes suggests that early metazoan diversification may not have been driven by systematic adaptations to the local environment, but instead may have resulted from stochastic demographic differences.
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Affiliation(s)
- Emily G. Mitchell
- Department of Earth SciencesUniversity of CambridgeDowning StreetCambridgeCB2 3EQUK
| | - Simon Harris
- British Geological SurveyNicker HillKeyworth, NottinghamNG12 5GGUK
| | | | - Philip Vixseboxse
- School of Earth SciencesUniversity of BristolWills Memorial Building, Queens RoadBristolBS8 1RJUK
| | - Lucy Roberts
- Department of ZoologyUniversity of CambridgeDowning StreetCambridgeCB2 3EJUK
| | - Catherine Clark
- Department of Earth SciencesUniversity of CambridgeDowning StreetCambridgeCB2 3EQUK
| | - Alexandra Dennis
- Department of Earth SciencesUniversity of CambridgeDowning StreetCambridgeCB2 3EQUK
| | - Alexander G. Liu
- Department of Earth SciencesUniversity of CambridgeDowning StreetCambridgeCB2 3EQUK
| | - Philip R. Wilby
- British Geological SurveyNicker HillKeyworth, NottinghamNG12 5GGUK
- School of Geography, Geology & the EnvironmentUniversity of LeicesterUniversity RoadLeicesterLE1 7RHUK
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11
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Zhang F, Xiao S, Romaniello SJ, Hardisty D, Li C, Melezhik V, Pokrovsky B, Cheng M, Shi W, Lenton TM, Anbar AD. Global marine redox changes drove the rise and fall of the Ediacara biota. GEOBIOLOGY 2019; 17:594-610. [PMID: 31353777 PMCID: PMC6899691 DOI: 10.1111/gbi.12359] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 06/25/2019] [Accepted: 07/04/2019] [Indexed: 05/25/2023]
Abstract
The role of O2 in the evolution of early animals, as represented by some members of the Ediacara biota, has been heavily debated because current geochemical evidence paints a conflicting picture regarding global marine O2 levels during key intervals of the rise and fall of the Ediacara biota. Fossil evidence indicates that the diversification the Ediacara biota occurred during or shortly after the Ediacaran Shuram negative C-isotope Excursion (SE), which is often interpreted to reflect ocean oxygenation. However, there is conflicting evidence regarding ocean oxygen levels during the SE and the middle Ediacaran Period. To help resolve this debate, we examined U isotope variations (δ238 U) in three carbonate sections from South China, Siberia, and USA that record the SE. The δ238 U data from all three sections are in excellent agreement and reveal the largest positive shift in δ238 U ever reported in the geologic record (from ~ -0.74‰ to ~ -0.26‰). Quantitative modeling of these data suggests that the global ocean switched from a largely anoxic state (26%-100% of the seafloor overlain by anoxic waters) to near-modern levels of ocean oxygenation during the SE. This episode of ocean oxygenation is broadly coincident with the rise of the Ediacara biota. Following this initial radiation, the Ediacara biota persisted until the terminal Ediacaran period, when recently published U isotope data indicate a return to more widespread ocean anoxia. Taken together, it appears that global marine redox changes drove the rise and fall of the Ediacara biota.
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Affiliation(s)
- Feifei Zhang
- School of Earth Sciences and EngineeringNanjing UniversityNanjingChina
- Department of Geology and GeophysicsYale UniversityNew HavenCTUSA
- The Globe InstituteUniversity of CopenhagenCopenhagen KDenmark
- School of Earth and Space ExplorationArizona State UniversityTempeAZUSA
| | - Shuhai Xiao
- Department of GeosciencesVirginia TechBlacksburgVAUSA
| | | | - Dalton Hardisty
- Department of Earth and Environmental ScienceMichigan State UniversityEast LansingMIUSA
| | - Chao Li
- State Key Laboratory of Biogeology and Environmental GeologyChina University of GeosciencesWuhanChina
| | | | | | - Meng Cheng
- State Key Laboratory of Biogeology and Environmental GeologyChina University of GeosciencesWuhanChina
| | - Wei Shi
- State Key Laboratory of Biogeology and Environmental GeologyChina University of GeosciencesWuhanChina
| | | | - Ariel D. Anbar
- School of Earth and Space ExplorationArizona State UniversityTempeAZUSA
- School of Molecular ScienceArizona State UniversityTempeAZUSA
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12
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Early animal evolution and highly oxygenated seafloor niches hosted by microbial mats. Sci Rep 2019; 9:13628. [PMID: 31541156 PMCID: PMC6754419 DOI: 10.1038/s41598-019-49993-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 08/12/2019] [Indexed: 11/09/2022] Open
Abstract
The earliest unambiguous evidence for animals is represented by various trace fossils in the latest Ediacaran Period (550-541 Ma), suggesting that the earliest animals lived on or even penetrated into the seafloor. Yet, the O2 fugacity at the sediment-water interface (SWI) for the earliest animal proliferation is poorly defined. The preferential colonization of seafloor as a first step in animal evolution is also unusual. In order to understand the environmental background, we employed a new proxy, carbonate associated ferrous iron (Fecarb), to quantify the seafloor oxygenation. Fecarb of the latest Ediacaran Shibantan limestone in South China, which yields abundant animal traces, ranges from 2.27 to 85.43 ppm, corresponding to the seafloor O2 fugacity of 162 μmol/L to 297 μmol/L. These values are significantly higher than the oxygen saturation in seawater at the contemporary atmospheric pO2 levels. The highly oxygenated seafloor might be attributed to O2 production of the microbial mats. Despite the moderate atmospheric pO2 level, microbial mats possibly provided highly oxygenated niches for the evolution of benthic metazoans. Our model suggests that the O2 barrier could be locally overcome in the mat ground, questioning the long-held belief that atmospheric oxygenation was the key control of animal evolution.
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Jiang CQ, Wang GY, Xiong J, Yang WT, Sun ZY, Feng JM, Warren A, Miao W. Insights into the origin and evolution of Peritrichia (Oligohymenophorea, Ciliophora) based on analyses of morphology and phylogenomics. Mol Phylogenet Evol 2019; 132:25-35. [DOI: 10.1016/j.ympev.2018.11.018] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Revised: 10/29/2018] [Accepted: 11/24/2018] [Indexed: 11/30/2022]
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Affiliation(s)
- Frances S Dunn
- School of Earth Sciences, University of Bristol, Bristol, UK.
| | - Alexander G Liu
- Department of Earth Sciences, University of Cambridge, Cambridge, UK
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Gilpin W, Feldman MW. Cryptic selection forces and dynamic heritability in generalized phenotypic evolution. Theor Popul Biol 2018; 125:20-29. [PMID: 30528351 DOI: 10.1016/j.tpb.2018.11.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 11/10/2018] [Accepted: 11/14/2018] [Indexed: 11/26/2022]
Abstract
Individuals with different phenotypes can have widely-varying responses to natural selection, yet many classical approaches to evolutionary dynamics emphasize only how a population's average phenotype increases in fitness over time. However, recent experimental results have produced examples of populations that have multiple fitness peaks, or that experience frequency-dependence that affects the direction and strength of selection on certain individuals. Here, we extend classical fitness gradient formulations of natural selection in order to describe the dynamics of a phenotype distribution in terms of its moments-such as the mean, variance, and skewness. The number of governing equations in our model can be adjusted in order to capture different degrees of detail about the population. We compare our simplified model to direct Wright-Fisher simulations of evolution in several canonical fitness landscapes, and we find that our model provides a low-dimensional description of complex dynamics not typically explained by classical theory, such as cryptic selection forces due to selection on trait ranges, time-variation of the heritability, and nonlinear responses to stabilizing or disruptive selection due to asymmetric trait distributions. In addition to providing a framework for extending general understanding of common qualitative concepts in phenotypic evolution - such as fitness gradients, selection pressures, and heritability - our approach has practical importance for studying evolution in contexts in which genetic analysis is infeasible.
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Affiliation(s)
- William Gilpin
- Department of Applied Physics, Stanford University, Stanford, CA, United States.
| | - Marcus W Feldman
- Department of Biology, Stanford University, Stanford, CA, United States
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Zhang F, Xiao S, Kendall B, Romaniello SJ, Cui H, Meyer M, Gilleaudeau GJ, Kaufman AJ, Anbar AD. Extensive marine anoxia during the terminal Ediacaran Period. SCIENCE ADVANCES 2018; 4:eaan8983. [PMID: 29938217 PMCID: PMC6010336 DOI: 10.1126/sciadv.aan8983] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2017] [Accepted: 05/07/2018] [Indexed: 05/29/2023]
Abstract
The terminal Ediacaran Period witnessed the decline of the Ediacara biota (which may have included many stem-group animals). To test whether oceanic anoxia might have played a role in this evolutionary event, we measured U isotope compositions (δ238U) in sedimentary carbonates from the Dengying Formation of South China to obtain new constraints on the extent of global redox change during the terminal Ediacaran. We found the most negative carbonate δ238U values yet reported (-0.95 per mil), which were reproduced in two widely spaced coeval sections spanning the terminal Ediacaran Period (551 to 541 million years ago). Mass balance modeling indicates an episode of extensive oceanic anoxia, during which anoxia covered >21% of the seafloor and most U entering the oceans was removed into sediments below anoxic waters. The results suggest that an expansion of oceanic anoxia and temporal-spatial redox heterogeneity, independent of other environmental and ecological factors, may have contributed to the decline of the Ediacara biota and may have also stimulated animal motility.
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Affiliation(s)
- Feifei Zhang
- School of Earth and Space Exploration, Arizona State University, Tempe, AZ 85287, USA
| | - Shuhai Xiao
- Department of Geosciences, Virginia Tech, Blacksburg, VA 24061, USA
| | - Brian Kendall
- Department of Earth and Environmental Sciences, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Stephen J. Romaniello
- School of Earth and Space Exploration, Arizona State University, Tempe, AZ 85287, USA
| | - Huan Cui
- Department of Geoscience and NASA Astrobiology Institute, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Mike Meyer
- Carnegie Institution for Science, Washington, DC 20005, USA
| | | | - Alan J. Kaufman
- Geology Department and Earth System Science Interdisciplinary Center, University of Maryland, College Park, MD 20742, USA
| | - Ariel D. Anbar
- School of Earth and Space Exploration, Arizona State University, Tempe, AZ 85287, USA
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA
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Cavalier-Smith T. Origin of animal multicellularity: precursors, causes, consequences-the choanoflagellate/sponge transition, neurogenesis and the Cambrian explosion. Philos Trans R Soc Lond B Biol Sci 2017; 372:rstb.2015.0476. [PMID: 27994119 PMCID: PMC5182410 DOI: 10.1098/rstb.2015.0476] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/05/2016] [Indexed: 02/07/2023] Open
Abstract
Evolving multicellularity is easy, especially in phototrophs and osmotrophs whose multicells feed like unicells. Evolving animals was much harder and unique; probably only one pathway via benthic ‘zoophytes’ with pelagic ciliated larvae allowed trophic continuity from phagocytic protozoa to gut-endowed animals. Choanoflagellate protozoa produced sponges. Converting sponge flask cells mediating larval settling to synaptically controlled nematocysts arguably made Cnidaria. I replace Haeckel's gastraea theory by a sponge/coelenterate/bilaterian pathway: Placozoa, hydrozoan diploblasty and ctenophores were secondary; stem anthozoan developmental mutations arguably independently generated coelomate bilateria and ctenophores. I emphasize animal origin's conceptual aspects (selective, developmental) related to feeding modes, cell structure, phylogeny of related protozoa, sequence evidence, ecology and palaeontology. Epithelia and connective tissue could evolve only by compensating for dramatically lower feeding efficiency that differentiation into non-choanocytes entails. Consequentially, larger bodies enabled filtering more water for bacterial food and harbouring photosynthetic bacteria, together adding more food than cell differentiation sacrificed. A hypothetical presponge of sessile triploblastic sheets (connective tissue sandwiched between two choanocyte epithelia) evolved oogamy through selection for larger dispersive ciliated larvae to accelerate benthic trophic competence and overgrowing protozoan competitors. Extinct Vendozoa might be elaborations of this organismal grade with choanocyte-bearing epithelia, before poriferan water channels and cnidarian gut/nematocysts/synapses evolved. This article is part of the themed issue ‘Evo-devo in the genomics era, and the origins of morphological diversity’.
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Abstract
This chapter reviews major types of statistical resampling approaches used in paleontology. They are an increasingly popular alternative to the classic parametric approach because they can approximate behaviors of parameters that are not understood theoretically. The primary goal of most resampling methods is an empirical approximation of a sampling distribution of a statistic of interest, whether simple (mean or standard error) or more complicated (median, kurtosis, or eigenvalue). This chapter focuses on the conceptual and practical aspects of resampling methods that a user is likely to face when designing them, rather than the relevant mathematical derivations and intricate details of the statistical theory. The chapter reviews the concept of sampling distributions, outlines a generalized methodology for designing resampling methods, summarizes major types of resampling strategies, highlights some commonly used resampling protocols, and addresses various practical decisions involved in designing algorithm details. A particular emphasis has been placed here on bootstrapping, a resampling strategy used extensively in quantitative paleontological analyses, but other resampling techniques are also reviewed in detail. In addition,ad hocand literature-based case examples are provided to illustrate virtues, limitations, and potential pitfalls of resampling methods.
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A Dome-Headed Stem Archosaur Exemplifies Convergence among Dinosaurs and Their Distant Relatives. Curr Biol 2016; 26:2674-2680. [DOI: 10.1016/j.cub.2016.07.066] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Revised: 07/23/2016] [Accepted: 07/26/2016] [Indexed: 11/22/2022]
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Arrouy MJ, Warren LV, Quaglio F, Poiré DG, Simões MG, Rosa MB, Peral LEG. Ediacaran discs from South America: probable soft-bodied macrofossils unlock the paleogeography of the Clymene Ocean. Sci Rep 2016; 6:30590. [PMID: 27460966 PMCID: PMC4962044 DOI: 10.1038/srep30590] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 07/05/2016] [Indexed: 12/04/2022] Open
Abstract
The origin, affinity and paleoecology of macrofossils of soft-bodied organisms of the terminal Ediacaran Period have been highly debated. Previous discoveries in South America are restricted to small shelly metazoans of the Nama Assemblage. Here we report for the first time the occurrence of discoidal structures from the Upper Ediacaran Cerro Negro Formation, La Providencia Group, Argentina. Specimens are preserved in tabular sandstones with microbially-induced sedimentary structures. Flute marks and linear scours at the base of the sandstone layers indicate deposition under high energy, episodic flows. Stratigraphic, sedimentologic, petrographic and taphonomic analyses indicate that the origin of these structures is not related to abiotic process. Preservational and morphological features, as invagination and the presence of radial grooves, indicate that they resemble typical morphs of the Aspidella plexus. The large number of small-sized individuals and the wide range of size classes with skewed distribution suggest that they lived in high-density communities. The presence of Aspidella in the Cerro Negro Formation would represent the first reliable record of Ediacaran soft-bodied organisms in South America. It also supports the paleogeographic scenario of the Clymene Ocean, in which a shallow sea covered part of the southwest Gondwana at the end of the Ediacaran.
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Affiliation(s)
- María Julia Arrouy
- Centro de Investigaciones Geológicas - CONICET - FCNyM (UNLP), Diagonal 113 N°275, La Plata, Argentina
| | - Lucas V Warren
- Departamento de Geologia Aplicada, Instituto de Geociências e Ciências Exatas, Universidade Estadual Paulista, Avenida 24A, 1515, Rio Claro 13506-900, Brazil
| | - Fernanda Quaglio
- Departamento de Geologia Aplicada, Instituto de Geociências e Ciências Exatas, Universidade Estadual Paulista, Avenida 24A, 1515, Rio Claro 13506-900, Brazil.,Curso de Geologia, Instituto de Geografia, Universidade Federal de Uberlândia, Rodovia LMG 746, Km 1, Monte Carmelo 38500-000, Brazil
| | - Daniel G Poiré
- Centro de Investigaciones Geológicas - CONICET - FCNyM (UNLP), Diagonal 113 N°275, La Plata, Argentina
| | - Marcello Guimarães Simões
- Departamento de Zoologia, Instituto de Biociências, Universidade Estadual Paulista, Distrito de Rubião Júnior, Botucatu 18618-000, Brazil
| | - Milena Boselli Rosa
- Departamento de Geologia Aplicada, Instituto de Geociências e Ciências Exatas, Universidade Estadual Paulista, Avenida 24A, 1515, Rio Claro 13506-900, Brazil
| | - Lucía E Gómez Peral
- Centro de Investigaciones Geológicas - CONICET - FCNyM (UNLP), Diagonal 113 N°275, La Plata, Argentina
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Reconstructing the reproductive mode of an Ediacaran macro-organism. Nature 2015; 524:343-6. [PMID: 26237408 DOI: 10.1038/nature14646] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 06/08/2015] [Indexed: 11/08/2022]
Abstract
Enigmatic macrofossils of late Ediacaran age (580-541 million years ago) provide the oldest known record of diverse complex organisms on Earth, lying between the microbially dominated ecosystems of the Proterozoic and the Cambrian emergence of the modern biosphere. Among the oldest and most enigmatic of these macrofossils are the Rangeomorpha, a group characterized by modular, self-similar branching and a sessile benthic habit. Localized occurrences of large in situ fossilized rangeomorph populations allow fundamental aspects of their biology to be resolved using spatial point process techniques. Here we use such techniques to identify recurrent clustering patterns in the rangeomorph Fractofusus, revealing a complex life history of multigenerational, stolon-like asexual reproduction, interspersed with dispersal by waterborne propagules. Ecologically, such a habit would have allowed both for the rapid colonization of a localized area and for transport to new, previously uncolonized areas. The capacity of Fractofusus to derive adult morphology by two distinct reproductive modes documents the sophistication of its underlying developmental biology.
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Ecological constraints on the origin of neurones. J Math Biol 2015; 71:1299-324. [DOI: 10.1007/s00285-015-0862-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Revised: 01/14/2015] [Indexed: 12/20/2022]
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Rachamim T, Morgenstern D, Aharonovich D, Brekhman V, Lotan T, Sher D. The Dynamically Evolving Nematocyst Content of an Anthozoan, a Scyphozoan, and a Hydrozoan. Mol Biol Evol 2014; 32:740-53. [DOI: 10.1093/molbev/msu335] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
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Monk T, Paulin MG. Predation and the origin of neurones. BRAIN, BEHAVIOR AND EVOLUTION 2014; 84:246-61. [PMID: 25472692 DOI: 10.1159/000368177] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Accepted: 04/24/2014] [Indexed: 11/19/2022]
Abstract
The core design of spiking neurones is remarkably similar throughout the animal kingdom. Their basic function as fast-signalling thresholding cells might have been established very early in their evolutionary history. Identifying the selection pressures that drove animals to evolve spiking neurones could help us interpret their design and function today. We review fossil, ecological and molecular evidence to investigate when and why animals evolved spiking neurones. Fossils suggest that animals evolved nervous systems soon after the advent of animal-on-animal predation, 550 million years ago (MYa). Between 550 and 525 MYa, we see the first fossil appearances of many animal innovations, including eyes. Animal behavioural complexity increased during this period as well, as evidenced by their traces, suggesting that nervous systems were an innovation of that time. Fossils further suggest that, before 550 MYa, animals were either filter feeders or microbial mat grazers. Extant sponges and Trichoplax perform these tasks using energetically cheaper alternatives than spiking neurones. Genetic evidence testifies that nervous systems evolved before the protostome-deuterostome split. It is less clear whether nervous systems evolved before the cnidarian-bilaterian split, so cnidarians and bilaterians might have evolved their nervous systems independently. The fossil record indicates that the advent of predation could fit into the window of time between those two splits, though molecular clock studies dispute this claim. Collectively, these lines of evidence indicate that animals evolved spiking neurones soon after they started eating each other. The first sensory neurones could have been threshold detectors that spiked in response to other animals in their proximity, alerting them to perform precisely timed actions, such as striking or fleeing.
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Affiliation(s)
- Travis Monk
- Department of Zoology, University of Otago, Dunedin, New Zealand
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KELLNER ALEXANDERW. First evidence of the Ediacaran fauna in Northeastern Brazil, an albino dolphin, and trophic groups of a bird community in Alagoas. AN ACAD BRAS CIENC 2014; 86:1013-4. [DOI: 10.1590/0001-3765201486.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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Fractal branching organizations of Ediacaran rangeomorph fronds reveal a lost Proterozoic body plan. Proc Natl Acad Sci U S A 2014; 111:13122-6. [PMID: 25114255 DOI: 10.1073/pnas.1408542111] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The branching morphology of Ediacaran rangeomorph fronds has no exact counterpart in other complex macroorganisms. As such, these fossils pose major questions as to growth patterns, functional morphology, modes of feeding, and adaptive optimality. Here, using parametric Lindenmayer systems, a formal model of rangeomorph morphologies reveals a fractal body plan characterized by self-similar, axial, apical, alternate branching. Consequent morphological reconstruction for 11 taxa demonstrates an adaptive radiation based on 3D space-filling strategies. The fractal body plan of rangeomorphs is shown to maximize surface area, consistent with diffusive nutrient uptake from the water column (osmotrophy). The enigmas of rangeomorph morphology, evolution, and extinction are resolved by the realization that they were adaptively optimized for unique ecological and geochemical conditions in the late Proterozoic. Changes in ocean conditions associated with the Cambrian explosion sealed their fate.
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Evolution of PAS domains and PAS-containing genes in eukaryotes. Chromosoma 2014; 123:385-405. [PMID: 24699836 DOI: 10.1007/s00412-014-0457-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Revised: 02/21/2014] [Accepted: 03/11/2014] [Indexed: 01/18/2023]
Abstract
The PAS domains are signal modules, which are widely distributed in proteins across all kingdoms of life. They are common in photoreceptors and transcriptional regulators of eukaryotic circadian clocks q(bHLH-PAS proteins and PER in animals; PHY and ZTL in plants; and WC-1, 2, and VVD in fungi) and possess mainly protein-protein interaction and light-sensing functions. We conducted several evolutionary analyses of the PAS superfamily. Although the whole superfamily evolved primarily under strong purifying selection (average ω ranges from 0.0030 to 0.1164), some lineages apparently experienced strong episodic positive selection at some periods of the evolution. Although the PAS domains from different proteins vary in sequence and length, but they maintain a fairly conserved 3D structure, which is determined by only eight residues. The WC-1 and WC- 2, bHLH-PAS, and P er genes probably originated in the Neoproterozoic Era (1000-542 Mya), plant P hy and ZTL evolved in the Paleozoic (541-252 Mya), which might be a result of adaptation to the major climate and global light regime changes having occurred in those eras.
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Hughes M, Gerber S, Wills MA. Clades reach highest morphological disparity early in their evolution. Proc Natl Acad Sci U S A 2013; 110:13875-9. [PMID: 23884651 PMCID: PMC3752257 DOI: 10.1073/pnas.1302642110] [Citation(s) in RCA: 126] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
There are few putative macroevolutionary trends or rules that withstand scrutiny. Here, we test and verify the purported tendency for animal clades to reach their maximum morphological variety relatively early in their evolutionary histories (early high disparity). We present a meta-analysis of 98 metazoan clades radiating throughout the Phanerozoic. The disparity profiles of groups through time are summarized in terms of their center of gravity (CG), with values above and below 0.50 indicating top- and bottom-heaviness, respectively. Clades that terminate at one of the "big five" mass extinction events tend to have truncated trajectories, with a significantly top-heavy CG distribution overall. The remaining 63 clades show the opposite tendency, with a significantly bottom-heavy mean CG (relatively early high disparity). Resampling tests are used to identify groups with a CG significantly above or below 0.50; clades not terminating at a mass extinction are three times more likely to be significantly bottom-heavy than top-heavy. Overall, there is no clear temporal trend in disparity profile shapes from the Cambrian to the Recent, and early high disparity is the predominant pattern throughout the Phanerozoic. Our results do not allow us to distinguish between ecological and developmental explanations for this phenomenon. To the extent that ecology has a role, however, the paucity of bottom-heavy clades radiating in the immediate wake of mass extinctions suggests that early high disparity more probably results from the evolution of key apomorphies at the base of clades rather than from physical drivers or catastrophic ecospace clearing.
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Affiliation(s)
- Martin Hughes
- Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, United Kingdom
| | - Sylvain Gerber
- Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, United Kingdom
| | - Matthew Albion Wills
- Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, United Kingdom
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Jeltsch A. Oxygen, epigenetic signaling, and the evolution of early life. Trends Biochem Sci 2013; 38:172-6. [PMID: 23454078 DOI: 10.1016/j.tibs.2013.02.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Revised: 01/22/2013] [Accepted: 02/03/2013] [Indexed: 12/16/2022]
Abstract
After approximately 3 billion years of unicellular life on Earth, multicellular animals appeared some 600 million years ago, followed by the rapid emergence of most animal phyla during the Cambrian radiation. This evolutionary jump was paralleled by an increase in atmospheric oxygen, which I propose allowed the generation of epigenetic signaling systems that are essential for cellular differentiation in animals. Epigenetic signaling is based on the reversible deposition of chemically stable marks in DNA and histone proteins, with methylation of cytosine and lysine residues, respectively, playing a central role. Recent evidence indicates that the removal of such methyl groups critically depends on oxygenases. Hence, reversible epigenetic systems could only appear after accumulation of oxygen in the atmosphere.
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Affiliation(s)
- Albert Jeltsch
- Institute of Biochemistry, Stuttgart University, Pfaffenwaldring 55, D-70569 Stuttgart, Germany.
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Erwin DH, Laflamme M, Tweedt SM, Sperling EA, Pisani D, Peterson KJ. The Cambrian conundrum: early divergence and later ecological success in the early history of animals. Science 2012; 334:1091-7. [PMID: 22116879 DOI: 10.1126/science.1206375] [Citation(s) in RCA: 490] [Impact Index Per Article: 40.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Diverse bilaterian clades emerged apparently within a few million years during the early Cambrian, and various environmental, developmental, and ecological causes have been proposed to explain this abrupt appearance. A compilation of the patterns of fossil and molecular diversification, comparative developmental data, and information on ecological feeding strategies indicate that the major animal clades diverged many tens of millions of years before their first appearance in the fossil record, demonstrating a macroevolutionary lag between the establishment of their developmental toolkits during the Cryogenian [(850 to 635 million years ago (Ma)], and the later ecological success of metazoans during the Ediacaran (635 to 541 Ma) and Cambrian (541 to 488 Ma) periods. We argue that this diversification involved new forms of developmental regulation, as well as innovations in networks of ecological interaction within the context of permissive environmental circumstances.
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Affiliation(s)
- Douglas H Erwin
- Department of Paleobiology, National Museum of Natural History, Washington, DC 20013-7012, USA.
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Müller M, Mentel M, van Hellemond JJ, Henze K, Woehle C, Gould SB, Yu RY, van der Giezen M, Tielens AGM, Martin WF. Biochemistry and evolution of anaerobic energy metabolism in eukaryotes. Microbiol Mol Biol Rev 2012; 76:444-95. [PMID: 22688819 PMCID: PMC3372258 DOI: 10.1128/mmbr.05024-11] [Citation(s) in RCA: 505] [Impact Index Per Article: 42.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Major insights into the phylogenetic distribution, biochemistry, and evolutionary significance of organelles involved in ATP synthesis (energy metabolism) in eukaryotes that thrive in anaerobic environments for all or part of their life cycles have accrued in recent years. All known eukaryotic groups possess an organelle of mitochondrial origin, mapping the origin of mitochondria to the eukaryotic common ancestor, and genome sequence data are rapidly accumulating for eukaryotes that possess anaerobic mitochondria, hydrogenosomes, or mitosomes. Here we review the available biochemical data on the enzymes and pathways that eukaryotes use in anaerobic energy metabolism and summarize the metabolic end products that they generate in their anaerobic habitats, focusing on the biochemical roles that their mitochondria play in anaerobic ATP synthesis. We present metabolic maps of compartmentalized energy metabolism for 16 well-studied species. There are currently no enzymes of core anaerobic energy metabolism that are specific to any of the six eukaryotic supergroup lineages; genes present in one supergroup are also found in at least one other supergroup. The gene distribution across lineages thus reflects the presence of anaerobic energy metabolism in the eukaryote common ancestor and differential loss during the specialization of some lineages to oxic niches, just as oxphos capabilities have been differentially lost in specialization to anoxic niches and the parasitic life-style. Some facultative anaerobes have retained both aerobic and anaerobic pathways. Diversified eukaryotic lineages have retained the same enzymes of anaerobic ATP synthesis, in line with geochemical data indicating low environmental oxygen levels while eukaryotes arose and diversified.
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Affiliation(s)
| | - Marek Mentel
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia
| | - Jaap J. van Hellemond
- Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Katrin Henze
- Institute of Molecular Evolution, University of Düsseldorf, Düsseldorf, Germany
| | - Christian Woehle
- Institute of Molecular Evolution, University of Düsseldorf, Düsseldorf, Germany
| | - Sven B. Gould
- Institute of Molecular Evolution, University of Düsseldorf, Düsseldorf, Germany
| | - Re-Young Yu
- Institute of Molecular Evolution, University of Düsseldorf, Düsseldorf, Germany
| | - Mark van der Giezen
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - Aloysius G. M. Tielens
- Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Center, Rotterdam, Netherlands
| | - William F. Martin
- Institute of Molecular Evolution, University of Düsseldorf, Düsseldorf, Germany
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Abstract
Life is a chemical reaction. Three major transitions in early evolution are considered without recourse to a tree of life. The origin of prokaryotes required a steady supply of energy and electrons, probably in the form of molecular hydrogen stemming from serpentinization. Microbial genome evolution is not a treelike process because of lateral gene transfer and the endosymbiotic origins of organelles. The lack of true intermediates in the prokaryote-to-eukaryote transition has a bioenergetic cause. This article was reviewed by Dan Graur, W. Ford Doolittle, Eugene V. Koonin and Christophe Malaterre.
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Affiliation(s)
- William F Martin
- Institut of Botany III, University of Düsseldorf, 40225 Düsseldorf, Germany.
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Yuan X, Chen Z, Xiao S, Zhou C, Hua H. An early Ediacaran assemblage of macroscopic and morphologically differentiated eukaryotes. Nature 2011; 470:390-3. [PMID: 21331041 DOI: 10.1038/nature09810] [Citation(s) in RCA: 229] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2010] [Accepted: 01/07/2011] [Indexed: 11/09/2022]
Abstract
The deep-water Avalon biota (about 579 to 565 million years old) is often regarded as the earliest-known fossil assemblage with macroscopic and morphologically complex life forms. It has been proposed that the rise of the Avalon biota was triggered by the oxygenation of mid-Ediacaran deep oceans. Here we report a diverse assemblage of morphologically differentiated benthic macrofossils that were preserved largely in situ as carbonaceous compressions in black shales of the Ediacaran Lantian Formation (southern Anhui Province, South China). The Lantian biota, probably older than and taxonomically distinct from the Avalon biota, suggests that morphological diversification of macroscopic eukaryotes may have occurred in the early Ediacaran Period, perhaps shortly after the Marinoan glaciation, and that the redox history of Ediacaran oceans was more complex than previously thought.
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Affiliation(s)
- Xunlai Yuan
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing 210008, China.
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Mentel M, Martin W. Anaerobic animals from an ancient, anoxic ecological niche. BMC Biol 2010; 8:32. [PMID: 20370917 PMCID: PMC2859860 DOI: 10.1186/1741-7007-8-32] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2010] [Accepted: 04/06/2010] [Indexed: 11/10/2022] Open
Abstract
Tiny marine animals that complete their life cycle in the total absence of light and oxygen are reported by Roberto Danovaro and colleagues in this issue of BMC Biology. These fascinating animals are new members of the phylum Loricifera and possess mitochondria that in electron micrographs look very much like hydrogenosomes, the H2-producing mitochondria found among several unicellular eukaryotic lineages. The discovery of metazoan life in a permanently anoxic and sulphidic environment provides a glimpse of what a good part of Earth's past ecology might have been like in 'Canfield oceans', before the rise of deep marine oxygen levels and the appearance of the first large animals in the fossil record roughly 550-600 million years ago. The findings underscore the evolutionary significance of anaerobic deep sea environments and the anaerobic lifestyle among mitochondrion-bearing cells. They also testify that a fuller understanding of eukaryotic and metazoan evolution will come from the study of modern anoxic and hypoxic habitats.
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Affiliation(s)
- Marek Mentel
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University, Mlynská dolina CH-1, Bratislava, Slovakia
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Fernandez-Busquets X, Kornig A, Bucior I, Burger MM, Anselmetti D. Self-Recognition and Ca2+-Dependent Carbohydrate-Carbohydrate Cell Adhesion Provide Clues to the Cambrian Explosion. Mol Biol Evol 2009; 26:2551-61. [DOI: 10.1093/molbev/msp170] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Xiao S, Laflamme M. On the eve of animal radiation: phylogeny, ecology and evolution of the Ediacara biota. Trends Ecol Evol 2009; 24:31-40. [DOI: 10.1016/j.tree.2008.07.015] [Citation(s) in RCA: 339] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2008] [Revised: 07/30/2008] [Accepted: 07/30/2008] [Indexed: 11/25/2022]
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Gaucher C, Sial AN, Halverson GP, Frimmel HE. Chapter 1 The Neoproterozoic and Cambrian: A Time of Upheavals, Extremes and Innovations. NEOPROTEROZOIC-CAMBRIAN TECTONICS, GLOBAL CHANGE AND EVOLUTION: A FOCUS ON SOUTH WESTERN GONDWANA 2009. [DOI: 10.1016/s0166-2635(09)01601-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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Sidlauskas B. CONTINUOUS AND ARRESTED MORPHOLOGICAL DIVERSIFICATION IN SISTER CLADES OF CHARACIFORM FISHES: A PHYLOMORPHOSPACE APPROACH. Evolution 2008; 62:3135-56. [DOI: 10.1111/j.1558-5646.2008.00519.x] [Citation(s) in RCA: 309] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Mentel M, Martin W. Energy metabolism among eukaryotic anaerobes in light of Proterozoic ocean chemistry. Philos Trans R Soc Lond B Biol Sci 2008; 363:2717-29. [PMID: 18468979 PMCID: PMC2606767 DOI: 10.1098/rstb.2008.0031] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Recent years have witnessed major upheavals in views about early eukaryotic evolution. One very significant finding was that mitochondria, including hydrogenosomes and the newly discovered mitosomes, are just as ubiquitous and defining among eukaryotes as the nucleus itself. A second important advance concerns the readjustment, still in progress, about phylogenetic relationships among eukaryotic groups and the roughly six new eukaryotic supergroups that are currently at the focus of much attention. From the standpoint of energy metabolism (the biochemical means through which eukaryotes gain their ATP, thereby enabling any and all evolution of other traits), understanding of mitochondria among eukaryotic anaerobes has improved. The mainstream formulations of endosymbiotic theory did not predict the ubiquity of mitochondria among anaerobic eukaryotes, while an alternative hypothesis that specifically addressed the evolutionary origin of energy metabolism among eukaryotic anaerobes did. Those developments in biology have been paralleled by a similar upheaval in the Earth sciences regarding views about the prevalence of oxygen in the oceans during the Proterozoic (the time from ca 2.5 to 0.6 Ga ago). The new model of Proterozoic ocean chemistry indicates that the oceans were anoxic and sulphidic during most of the Proterozoic. Its proponents suggest the underlying geochemical mechanism to entail the weathering of continental sulphides by atmospheric oxygen to sulphate, which was carried into the oceans as sulphate, fueling marine sulphate reducers (anaerobic, hydrogen sulphide-producing prokaryotes) on a global scale. Taken together, these two mutually compatible developments in biology and geology underscore the evolutionary significance of oxygen-independent ATP-generating pathways in mitochondria, including those of various metazoan groups, as a watermark of the environments within which eukaryotes arose and diversified into their major lineages.
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Affiliation(s)
| | - William Martin
- Institute of Botany, University of DüsseldorfUniversitätsstrasse 1, 40225 Düsseldorf, Germany
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