Conflict and complementarity of paleontological and molecular chronologies?

Paleobiology ◽  
2018 ◽  
Vol 45 (1) ◽  
pp. 7-20 ◽  
Author(s):  
Ofir Katz
Keyword(s):  
Evolutionary History ◽  
Oxygenic Photosynthesis ◽  
Gene Divergence ◽  
Geologic Time ◽  
Great Oxidation Event ◽  
Silicon Accumulation

AbstractEvolutionary history studies depend on having reliable chronologies of macroevolutionary processes. Construction of such chronologies often yields discrepancies between paleontological and molecular dates, which are sometimes viewed as conflicting. Nevertheless, each macroevolutionary process is composed of two main phases: emergence of a trait or clade and success of that trait or clade, which differ in mechanisms, drivers, and types of evidence. Moreover, emergence may be observed as gene divergence (which may be trait-coding or trait-unrelated genes), trait emergence, and clade emergence; whereas success can be observed as increase in abundance, diffusion, and/or diversity or as overall persistence over geologic time. Therefore, to fully and correctly understand any macroevolutionary process, it is of paramount importance to understand what event each date refers to, and how dates of various events and their integration reveal the complexity of macroevolutionary processes. I demonstrate this through three examples: the chronological gap between oxygenic photosynthesis emergence and the Great Oxidation Event, the chronological gap between paleontological and molecular dates of angiosperm emergence, and the evolution of plant silicon accumulation.

The Great Oxidation Event can be detected and dated through the genetic record

2021 ◽  
Author(s):  
Cara Magnabosco
Keyword(s):  
Feature Selection ◽  
Metabolic Pathways ◽  
Metabolic Networks ◽  
Data Science ◽  
Specific Protein ◽  
Oxygenic Photosynthesis ◽  
Selection Algorithm ◽  
Feature Selection Algorithm ◽  
Great Oxidation Event ◽  
Rock Record

<p>Traditionally, the biogeochemical information preserved in the rock record has been used to study the environmental conditions of Earth’s past. There is however another important record of Earth’s history that is only just beginning to be explored: the genomes of contemporary organisms (i.e. the genetic record). The genetic record is an under-utilized tool for studying Earth History. Like the rock record, the genomes of microorganisms have been imprinted with information regarding our changing planet. In this presentation, we will describe a framework for accessing and interpreting the “genetic scars” imprinted on the genomes of microorganisms to identify the timing of the Great Oxidation Event (GOE) independent of the geochemical record. This approach combines ideas from systems biology and data science to infer the timing of major changes in the evolution of microbial lineages and metabolic pathways. Briefly, a horizontal gene transfer constrained molecular clock provides timeline for major speciation events within the bacterial tree of life which can be used to date the emergence of specific protein families related to oxygenic photosynthesis and oxygen consumption. A feature selection algorithm for metabolic networks allows us to generalise this technique beyond the GOE and will enable us to better interpret isotope anomalies in the geochemical record.</p>

scholarly journals How has our knowledge of dinosaur diversity through geologic time changed through research history?

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4417 ◽  
Author(s):  
Jonathan P. Tennant ◽  
Alfio Alessandro Chiarenza ◽  
Matthew Baron
Keyword(s):  
Evolutionary History ◽  
Abundance Distribution ◽  
Geologic Time ◽  
Publication History ◽  
Publication Record ◽  
Secular Variations ◽  
History Of ◽  
Global Estimates ◽  
Dinosaur Evolution ◽  
Diversity Estimates

Assessments of dinosaur macroevolution at any given time can be biased by the historical publication record. Recent studies have analysed patterns in dinosaur diversity that are based on secular variations in the numbers of published taxa. Many of these have employed a range of approaches that account for changes in the shape of the taxonomic abundance curve, which are largely dependent on databases compiled from the primary published literature. However, how these ‘corrected’ diversity patterns are influenced by the history of publication remains largely unknown. Here, we investigate the influence of publication history between 1991 and 2015 on our understanding of dinosaur evolution using raw diversity estimates and shareholder quorum subsampling for the three major subgroups: Ornithischia, Sauropodomorpha, and Theropoda. We find that, while sampling generally improves through time, there remain periods and regions in dinosaur evolutionary history where diversity estimates are highly volatile (e.g. the latest Jurassic of Europe, the mid-Cretaceous of North America, and the Late Cretaceous of South America). Our results show that historical changes in database compilation can often substantially influence our interpretations of dinosaur diversity. ‘Global’ estimates of diversity based on the fossil record are often also based on incomplete, and distinct regional signals, each subject to their own sampling history. Changes in the record of taxon abundance distribution, either through discovery of new taxa or addition of existing taxa to improve sampling evenness, are important in improving the reliability of our interpretations of dinosaur diversity. Furthermore, the number of occurrences and newly identified dinosaurs is still rapidly increasing through time, suggesting that it is entirely possible for much of what we know about dinosaurs at the present to change within the next 20 years.

scholarly journals Phylogeny and Evolutionary History of Respiratory Complex I Proteins in Melainabacteria

Genes ◽  
2021 ◽  
Vol 12 (6) ◽  
pp. 929
Author(s):  
Christen Grettenberger ◽  
Dawn Y. Sumner ◽  
Jonathan A. Eisen ◽  
Anne D. Jungblut ◽  
Tyler J. Mackey
Keyword(s):  
Complex I ◽  
Evolutionary History ◽  
Oxygenic Photosynthesis ◽  
Aerobic Respiration ◽  
Respiratory Complex ◽  
Earth’S Atmosphere ◽  
History Of ◽  
Respiratory Chains ◽  
Respiratory Complex I ◽  
Earth's Atmosphere

The evolution of oxygenic photosynthesis was one of the most transformative evolutionary events in Earth’s history, leading eventually to the oxygenation of Earth’s atmosphere and, consequently, the evolution of aerobic respiration. Previous work has shown that the terminal electron acceptors (complex IV) of aerobic respiration likely evolved after the evolution of oxygenic photosynthesis. However, complex I of the respiratory complex chain can be involved in anaerobic processes and, therefore, may have pre-dated the evolution of oxygenic photosynthesis. If so, aerobic respiration may have built upon respiratory chains that pre-date the rise of oxygen in Earth’s atmosphere. The Melainabacteria provide a unique opportunity to examine this hypothesis because they contain genes for aerobic respiration but likely diverged from the Cyanobacteria before the evolution of oxygenic photosynthesis. Here, we examine the phylogenies of translated complex I sequences from 44 recently published Melainabacteria metagenome assembled genomes and genomes from other Melainabacteria, Cyanobacteria, and other bacterial groups to examine the evolutionary history of complex I. We find that complex I appears to have been present in the common ancestor of Melainabacteria and Cyanobacteria, supporting the idea that aerobic respiration built upon respiratory chains that pre-date the evolution of oxygenic photosynthesis and the rise of oxygen.

scholarly journals Novel Gloeobacterales spp. from Diverse Environments across the Globe

mSphere ◽  
2021 ◽  
Author(s):  
Christen L. Grettenberger
Keyword(s):  
Circadian Rhythms ◽  
Evolutionary History ◽  
Oxygenic Photosynthesis ◽  
History Of

Early branching photosynthetic Cyanobacteria such as the Gloeobacterales may provide clues into the evolutionary history of oxygenic photosynthesis, but there are few genomes or cultured taxa from this order. Five new metagenome-assembled genomes suggest that members of the Gloeobacterales all contain reduced photosystems and lack genes associated with thylakoids and circadian rhythms.

scholarly journals Microbial helpers allow cyanobacteria to thrive in ferruginous waters

2020 ◽  
Author(s):  
Nadia Szeinbaum ◽  
Yael J Toporek ◽  
Christopher T Reinhard ◽  
Jennifer Blanchard Glass
Keyword(s):  
Hydroxyl Radical ◽  
Defense Mechanisms ◽  
Heterotrophic Bacteria ◽  
Cellular Damage ◽  
Oxygenic Photosynthesis ◽  
Great Oxidation Event ◽  
Radical Production ◽  
Rapid Accumulation ◽  
Protection Mechanisms ◽  
Negative Impacts

The Great Oxidation Event (GOE) was a rapid accumulation of oxygen in the atmosphere as a result of the photosynthetic activity of cyanobacteria. This accumulation reflected the pervasiveness of O2 on the planet's surface, indicating that cyanobacteria had become ecologically successful in Archean oceans. Micromolar concentrations of Fe2+ in Archean oceans would have reacted with hydrogen peroxide, a byproduct of oxygenic photosynthesis, to produce hydroxyl radicals, which cause cellular damage. Yet cyanobacteria colonized Archean oceans extensively enough to oxygenate the atmosphere, which likely required protection mechanisms against the negative impacts of hydroxyl radical production in Fe2+-rich seas. We identify several factors that could have acted to protect early cyanobacteria from the impacts of hydroxyl radical production and hypothesize that microbial cooperation may have played an important role in protecting cyanobacteria from Fe2+ toxicity before the GOE. We found that several strains of facultative anaerobic heterotrophic bacteria (Shewanella) with defense mechanisms against oxidative stress increase the fitness of cyanobacteria (Synechococcus) in ferruginous waters. Shewanella species with manganese transporters provided the most protection. Our results suggest that a tightly regulated response to prevent Fe2+ toxicity could have been important for the colonization of ancient ferruginous oceans, particularly in the presence of high manganese concentrations, and may expand the upper bound for tolerable Fe2+ concentrations for cyanobacteria.

scholarly journals Heimdallarchaeota harness light energy through photosynthesis

2020 ◽  
Author(s):  
Rui Liu ◽  
Ruining Cai ◽  
Jing Zhang ◽  
Chaomin Sun
Keyword(s):  
Molecular Evolution ◽  
Origin Of Life ◽  
Metabolic Pathways ◽  
Evolutionary History ◽  
Waste Product ◽  
Photosynthetic Apparatus ◽  
Strong Support ◽  
Oxygenic Photosynthesis ◽  
Photosynthetic Organisms ◽  
The Origin Of Life

AbstractPhotosynthesis is an ancient process that originated after the origin of life, and has only been found in the Bacterial and Eukaryotic kingdoms, but has never been reported in any member of the domain Archaea. Heimdallarchaeota, a member of Asgard archaea, are supposed as the most probable candidates (to date) for the archaeal protoeukaryote ancestor and might exist in light-exposed habitats during their evolutionary history. Here we describe the discovery that Heimdallarchaeota genomes are enriched for proteins formerly considered specific to photosynthetic apparatus and are suggestive performing oxygenic photosynthesis. Our results provide strong support for hypotheses in which Heimdallarchaeota harvest light by bacteriochlorophyll and/or carotenoid, then transport electron from photosystems to Calvin-Benson-Bassham cycle along with CO2 fixation and ATP biosynthesis, and release oxygen as a waste product. Given the possessing of phototrophic lifestyle together with other anaerobic and aerobic metabolic pathways, Heimdallarchaeota are firmly believed to be photomixotrophic and have a facultative aerobic metabolism. Our results expand our knowledge that archaea have played an important role in the molecular evolution of eukaryotic photosynthesis and raise the significant possibility that Heimdallarchaeota might be ancestor of eukaryotic photosynthetic organisms.

scholarly journals Post-Triassic Spermatophyta Timetree Adding the Quaternary Radiated Asarum Wild Gingers

2020 ◽  
Author(s):  
Soichi Osozawa ◽  
Cunio Nackejima ◽  
John Wakabayashi
Keyword(s):  
Adaptive Radiation ◽  
Substitution Rate ◽  
Evolutionary History ◽  
Base Substitution ◽  
C4 Grasses ◽  
Glacial Period ◽  
Fossil Calibration ◽  
Geologic Time ◽  
Exponential Increase ◽  
Base Substitution Rate

Abstract BackgroundAngiospermae radiation was known as the mid-Cretaceous event, but adaptive radiation of Asarum is also expected in the Quaternary. In order to know such the Angiospermae evolutionary history through the time, we constructed a whole Spermatophyta timetree employing BEAST v1. X associated with robust fossil calibration function.ResultsWe successfully and precisely dated the Spermatophyta phylogeny, and the Angiospermae topology was concordant to the APG system. Using another function of BEAST, we discovered the exponential increase in base substitution rate in recent geologic time, and another rise of rate at the mid-Cretaceous time. These increasing events correspond to the Quaternary and mid-Cretaceous Angiospermae radiations.ConclusionsA probable cause of the recently increasing rate and the consequent radiation was ultimately generation of C4 grasses, reduction of atomospheric CO2, and the start of the Quaternary glacial period. Mid-Cretaceous event was explained by co-radiation with insect beetles as the food plant.

Evolution of Oxygenic Photosynthesis

2017 ◽  
Author(s):  
Donald Eugene Canfield
Keyword(s):  
Photosystem Ii ◽  
Photosystem I ◽  
Evolutionary History ◽  
Oxygenic Photosynthesis ◽  
Oxygen Evolving Complex ◽  
History Of ◽  
Oxygen Evolving ◽  
Evolution Of Oxygen ◽  
Basic Constituent ◽  
Key Questions

This chapter discusses the evolution of oxygen-producing organisms by considering the evolution and assembly of its basic constituent parts. It focuses on the following key questions: (1) What is the evolutionary history of chlorophyll? (2) What are the evolutionary histories of photosystem I and photosystem II (PSII)? (3) What is the origin of the oxygen-evolving complex in PSII? And finally, (4) what is the evolutionary history of Rubisco? In addressing these, the chapter seeks to understand the complex path leading to the evolution of oxygenic photosynthesis on Earth. This event was one of the major transforming events in the history of life. With no oxygenic photosynthesis, there would be no oxygen in the atmosphere; there would also be no plants, no animals, and nobody to tell this story.

scholarly journals Benthic perspective on Earth’s oldest evidence for oxygenic photosynthesis

2015 ◽  
Vol 112 (4) ◽  
pp. 995-1000 ◽  
Author(s):  
Stefan V. Lalonde ◽  
Kurt O. Konhauser
Keyword(s):  
Atmospheric Chemistry ◽  
Microbial Mats ◽  
Atmospheric Oxygen ◽  
Estuarine Sediments ◽  
Oxygenic Photosynthesis ◽  
Isotopic Signatures ◽  
Great Oxidation Event ◽  
Mass Independent Fractionation ◽  
History Of ◽  
Redox Disequilibrium

The Great Oxidation Event (GOE) is currently viewed as a protracted process during which atmospheric oxygen increased above ∼10−5 times the present atmospheric level (PAL). This threshold represents an estimated upper limit for sulfur isotope mass-independent fractionation (S-MIF), an Archean signature of atmospheric anoxia that begins to disappear from the rock record at 2.45 Ga. However, an increasing number of papers have suggested that the timing for oxidative continental weathering, and by conventional thinking the onset of atmospheric oxygenation, was hundreds of million years earlier than previously thought despite the presence of S-MIF. We suggest that this apparent discrepancy can be resolved by the earliest oxidative-weathering reactions occurring in benthic and soil environments at profound redox disequilibrium with the atmosphere, such as biological soil crusts and freshwater microbial mats covering riverbed, lacustrine, and estuarine sediments. We calculate that oxygenic photosynthesis in these millimeter-thick ecosystems provides sufficient oxidizing equivalents to mobilize sulfate and redox-sensitive trace metals from land to the oceans while the atmosphere itself remained anoxic with its attendant S-MIF signature. As continental freeboard increased significantly between 3.0 and 2.5 Ga, the chemical and isotopic signatures of benthic oxidative weathering would have become more globally significant from a mass-balance perspective. These observations help reconcile evidence for pre-GOE oxidative weathering with the history of atmospheric chemistry, and support the plausible antiquity of a terrestrial biosphere populated by cyanobacteria well before the GOE.

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