scholarly journals The Archean origin of oxygenic photosynthesis and extant cyanobacterial lineages

2021 ◽  
Vol 288 (1959) ◽  
Author(s):  
G. P. Fournier ◽  
K. R. Moore ◽  
L. T. Rangel ◽  
J. G. Payette ◽  
L. Momper ◽  
...  
Keyword(s):  
Fossil Record ◽  
Surface Oxidation ◽  
Oxygenic Photosynthesis ◽  
Evolutionary Models ◽  
Crown Group ◽  
Relative Dating ◽  
Wide Range ◽  
Rapid Diversification ◽  
Oxygenic Phototrophs ◽  
Age Estimates

The record of the coevolution of oxygenic phototrophs and the environment is preserved in three forms: genomes of modern organisms, diverse geochemical signals of surface oxidation and diagnostic Proterozoic microfossils. When calibrated by fossils, genomic data form the basis of molecular clock analyses. However, different interpretations of the geochemical record, fossil calibrations and evolutionary models produce a wide range of age estimates that are often conflicting. Here, we show that multiple interpretations of the cyanobacterial fossil record are consistent with an Archean origin of crown-group Cyanobacteria. We further show that incorporating relative dating information from horizontal gene transfers greatly improves the precision of these age estimates, by both providing a novel empirical criterion for selecting evolutionary models, and increasing the stringency of sampling of posterior age estimates. Independent of any geochemical evidence or hypotheses, these results support oxygenic photosynthesis evolving at least several hundred million years before the Great Oxygenation Event (GOE), a rapid diversification of major cyanobacterial lineages around the time of the GOE, and a post-Cryogenian origin of extant marine picocyanobacterial diversity.

scholarly journals Ecological innovations in the Cambrian and the origins of the crown group phyla

2016 ◽  
Vol 371 (1685) ◽  
pp. 20150287 ◽  
Author(s):  
Graham E. Budd ◽  
Illiam S. C. Jackson
Keyword(s):  
Fossil Record ◽  
Early Period ◽  
Trace Fossils ◽  
The Body ◽  
Trace Fossil ◽  
Simulation Studies ◽  
Crown Group ◽  
Relative Lack ◽  
Rapid Diversification ◽  
Body Fossil

Simulation studies of the early origins of the modern phyla in the fossil record, and the rapid diversification that led to them, show that these are inevitable outcomes of rapid and long-lasting radiations. Recent advances in Cambrian stratigraphy have revealed a more precise picture of the early bilaterian radiation taking place during the earliest Terreneuvian Series, although several ambiguities remain. The early period is dominated by various tubes and a moderately diverse trace fossil record, with the classical ‘Tommotian’ small shelly biota beginning to appear some millions of years after the base of the Cambrian at ca 541 Ma. The body fossil record of the earliest period contains a few representatives of known groups, but most of the record is of uncertain affinity. Early trace fossils can be assigned to ecdysozoans, but deuterostome and even spiralian trace and body fossils are less clearly represented. One way of explaining the relative lack of clear spiralian fossils until about 536 Ma is to assign the various lowest Cambrian tubes to various stem-group lophotrochozoans, with the implication that the groundplan of the lophotrochozoans included a U-shaped gut and a sessile habit. The implication of this view would be that the vagrant lifestyle of annelids, nemerteans and molluscs would be independently derived from such a sessile ancestor, with potentially important implications for the homology of their sensory and nervous systems.

scholarly journals Unbiased clade age estimation using a Bayesian Brownian Bridge

2021 ◽  
Author(s):  
Daniele Silvestro ◽  
Christine D. Bacon ◽  
Wenna Ding ◽  
Qiuyue Zhang ◽  
Philip C. J. Donoghue ◽  
...  
Keyword(s):  
Age Estimation ◽  
Fossil Record ◽  
High Probability ◽  
Brownian Bridge ◽  
New Model ◽  
Fossil Evidence ◽  
Wide Range ◽  
Fossil Data ◽  
Simplistic Model ◽  
Age Estimates

AbstractIn a recent paper1 we presented a new model, the Bayesian Brownian Bridge (BBB), to infer clade age based on fossil evidence and modern diversity. We benchmarked the method with extensive simulations, including a wide range of diversification histories and sampling heterogeneities that go well beyond the necessarily simplistic model assumptions. Applying BBB to 198 angiosperm families, we found that their fossil record is compatible with clade origins earlier than most contemporary palaeobotanical interpretations. In particular, we estimated with high probability that crown-angiosperms originated before the Cretaceous (> 145 Ma). Budd and colleagues2 critique our study, arguing that the BBB model is biased towards older estimates when fossil data are scarce or absent, that our underlying fossil dataset is unsound, that our clade age estimates are therefore biased by early diverging lineages that are underrepresented in the fossil record, and that pooling of fossil data for analysis at higher taxonomic ranks overcomes these biases. Here, we explore their points and perform new simulations to show that their critique has no merit.

scholarly journals Flying rocks and flying clocks: disparity in fossil and molecular dates for birds

2014 ◽  
Vol 281 (1788) ◽  
pp. 20140677 ◽  
Author(s):  
Daniel T. Ksepka ◽  
Jessica L. Ware ◽  
Kristin S. Lamm
Keyword(s):  
Analytical Methods ◽  
Fossil Record ◽  
Tree Of Life ◽  
Temporal Information ◽  
Molecular Dating ◽  
Critical Nodes ◽  
Molecular Divergence ◽  
Divergence Dates ◽  
Divergence Estimates ◽  
Age Estimates

Major disparities are recognized between molecular divergence dates and fossil ages for critical nodes in the Tree of Life, but broad patterns and underlying drivers remain elusive. We harvested 458 molecular age estimates for the stem and crown divergences of 67 avian clades to explore empirical patterns between these alternate sources of temporal information. These divergence estimates were, on average, over twice the age of the oldest fossil in these clades. Mitochondrial studies yielded older ages than nuclear studies for the vast majority of clades. Unexpectedly, disparity between molecular estimates and the fossil record was higher for divergences within major clades (crown divergences) than divergences between major clades (stem divergences). Comparisons of dates from studies classed by analytical methods revealed few significant differences. Because true divergence ages can never be known with certainty, our study does not answer the question of whether fossil gaps or molecular dating error account for a greater proportion of observed disparity. However, empirical patterns observed here suggest systemic overestimates for shallow nodes in existing molecular divergence dates for birds. We discuss underlying biases that may drive these patterns.

scholarly journals Insights into the evolution of oxygenic photosynthesis from a phylogenetically novel, low-light cyanobacterium

2018 ◽  
Author(s):  
Christen L. Grettenberger ◽  
Dawn Y. Sumner ◽  
Kate Wall ◽  
C. Titus Brown ◽  
Jonathan Eisen ◽  
...  
Keyword(s):  
Atmospheric Oxygen ◽  
Evolutionary Model ◽  
Reaction Centers ◽  
Oxygenic Photosynthesis ◽  
Oxygen Production ◽  
Crown Group ◽  
Low Light ◽  
Extrinsic Proteins ◽  
Structural Parts ◽  
Life On Earth

AbstractAtmospheric oxygen level rose dramatically around 2.4 billion years ago due to oxygenic photosynthesis by the Cyanobacteria. The oxidation of surface environments permanently changed the future of life on Earth, yet the evolutionary processes leading to oxygen production are poorly constrained. Partial records of these evolutionary steps are preserved in the genomes of organisms phylogenetically placed between non-photosynthetic Melainabacteria, crown-group Cyanobacteria, and Gloeobacter, representing the earliest-branching Cyanobacteria capable of oxygenic photosynthesis. Here, we describe nearly complete, metagenome assembled genomes of an uncultured organism phylogenetically placed between the Melainabacteria and crown-group Cyanobacteria, for which we propose the name Candidatus Aurora vandensis {au.rora Latin noun dawn and vand.ensis, originating from Vanda}.The metagenome assembled genome of A. vandensis contains homologs of most genes necessary for oxygenic photosynthesis including key reaction center proteins. Many extrinsic proteins associated with the photosystems in other species are, however, missing or poorly conserved. The assembled genome also lacks homologs of genes associated with the pigments phycocyanoerethrin, phycoeretherin and several structural parts of the phycobilisome. Based on the content of the genome, we propose an evolutionary model for increasing efficiency of oxygenic photosynthesis through the evolution of extrinsic proteins to stabilize photosystem II and I reaction centers and improve photon capture. This model suggests that the evolution of oxygenic photosynthesis may have significantly preceded oxidation of Earth’s atmosphere due to low net oxygen production by early Cyanobacteria.

scholarly journals Early fossil record of Euarthropoda and the Cambrian Explosion

2018 ◽  
Vol 115 (21) ◽  
pp. 5323-5331 ◽  
Author(s):  
Allison C. Daley ◽  
Jonathan B. Antcliffe ◽  
Harriet B. Drage ◽  
Stephen Pates
Keyword(s):  
Fossil Record ◽  
Trace Fossils ◽  
Cambrian Explosion ◽  
Burgess Shale ◽  
Crown Group ◽  
Total Group ◽  
Stem Lineage ◽  
Coherent Picture ◽  
Insight Into ◽  
Phosphate Deposits

Euarthropoda is one of the best-preserved fossil animal groups and has been the most diverse animal phylum for over 500 million years. Fossil Konservat-Lagerstätten, such as Burgess Shale-type deposits (BSTs), show the evolution of the euarthropod stem lineage during the Cambrian from 518 million years ago (Ma). The stem lineage includes nonbiomineralized groups, such as Radiodonta (e.g., Anomalocaris) that provide insight into the step-by-step construction of euarthropod morphology, including the exoskeleton, biramous limbs, segmentation, and cephalic structures. Trilobites are crown group euarthropods that appear in the fossil record at 521 Ma, before the stem lineage fossils, implying a ghost lineage that needs to be constrained. These constraints come from the trace fossil record, which show the first evidence for total group Euarthropoda (e.g., Cruziana, Rusophycus) at around 537 Ma. A deep Precambrian root to the euarthropod evolutionary lineage is disproven by a comparison of Ediacaran and Cambrian lagerstätten. BSTs from the latest Ediacaran Period (e.g., Miaohe biota, 550 Ma) are abundantly fossiliferous with algae but completely lack animals, which are also missing from other Ediacaran windows, such as phosphate deposits (e.g., Doushantuo, 560 Ma). This constrains the appearance of the euarthropod stem lineage to no older than 550 Ma. While each of the major types of fossil evidence (BSTs, trace fossils, and biomineralized preservation) have their limitations and are incomplete in different ways, when taken together they allow a coherent picture to emerge of the origin and subsequent radiation of total group Euarthropoda during the Cambrian.

scholarly journals Fossil-calibrated molecular phylogeny of atlantid heteropods (Gastropoda, Pterotracheoidea)

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Deborah Wall-Palmer ◽  
Arie W. Janssen ◽  
Erica Goetze ◽  
Le Qin Choo ◽  
Lisette Mekkes ◽  
...  
Keyword(s):  
Fossil Record ◽  
Large Scale ◽  
Global Scale ◽  
The Other ◽  
The Past ◽  
The Family ◽  
Rapid Diversification ◽  
Maximum Likelihood Phylogeny ◽  
Extinction Events ◽  
Ribosomal Rrna

Abstract Background The aragonite shelled, planktonic gastropod family Atlantidae (shelled heteropods) is likely to be one of the first groups to be impacted by imminent ocean changes, including ocean warming and ocean acidification. With a fossil record spanning at least 100 Ma, atlantids have experienced and survived global-scale ocean changes and extinction events in the past. However, the diversification patterns and tempo of evolution in this family are largely unknown. Results Based on a concatenated maximum likelihood phylogeny of three genes (cytochrome c oxidase subunit 1 mitochondrial DNA, 28S and 18S ribosomal rRNA) we show that the three extant genera of the family Atlantidae, Atlanta, Protatlanta and Oxygyrus, form monophyletic groups. The genus Atlanta is split into two groups, one exhibiting smaller, well ornamented shells, and the other having larger, less ornamented shells. The fossil record, in combination with a fossil-calibrated phylogeny, suggests that large scale atlantid extinction was accompanied by considerable and rapid diversification over the last 25 Ma, potentially driven by vicariance events. Conclusions Now confronted with a rapidly changing modern ocean, the ability of atlantids to survive past global change crises gives some optimism that they may be able to persist through the Anthropocene.

Implications for the study of fossil Asteroidea (Echinodermata) of new genera and species from the Eocene of Florida

2009 ◽  
Vol 83 (4) ◽  
pp. 562-574 ◽  
Author(s):  
Daniel B. Blake ◽  
Roger W. Portell
Keyword(s):  
Family History ◽  
New Taxa ◽  
Middle Jurassic ◽  
Fossil Record ◽  
New Genera ◽  
Crown Group ◽  
Marine Communities ◽  
The Family ◽  
Ocala Limestone

Oyenaster oblidus, Ocalaster timucum, and Ocalaster seloyi are new genera and species of the family Goniasteridae (Asteroidea) described from the Eocene Ocala Limestone of Florida. Although the fossil record of asteroids is sketchy, goniasterids appear to have been important contributors to marine communities since at least the Middle Jurassic. Similarities between living goniasterids and their fossil precursors indicate that plesiomorphy and convergence have been important in family history, and as a result, taxonomic interpretation is challenging. Even partial fossil goniasterids are rare, forcing systematists to rely heavily on isolated marginal ossicles, although some authors have expressed the need for caution. Building around three new taxa, we suggest that broader approaches can aid systematic interpretation of all crown-group asteroids. We also suggest that the inevitably idiosyncratic interpretations of marginal-based systematics can be partially tested using blind evaluations.

scholarly journals Characterizing Blue Straggler Star Populations in Globular Clusters using HST Photometric Survey Data

2015 ◽  
Vol 11 (A29B) ◽  
pp. 149-150
Author(s):  
Mirko Simunovic ◽  
Thomas H. Puzia
Keyword(s):  
Detailed Analysis ◽  
Survey Data ◽  
Proper Motion ◽  
Globular Clusters ◽  
Stellar Mass ◽  
Evolutionary Models ◽  
Early Results ◽  
Blue Straggler ◽  
Age Estimates

AbstractWe present early results from a detailed analysis of the BSS population in Galactic GCs based on HST data. Using proper motion cleaning of the color-magnitude diagrams we construct a large catalog of BSSs and study some population properties. Stellar evolutionary models are used to find stellar mass and age estimates for the BSS populations in order to establish constraints related to the dynamical interactions in which they may have formed.

scholarly journals The fossil record of early eukaryotic diversification

2004 ◽  
Vol 10 ◽  
pp. 35-50 ◽  
Author(s):  
Susannah M. Porter
Keyword(s):  
Fossil Record ◽  
Main Phase ◽  
Cambrian Explosion ◽  
Evolution Of Sex ◽  
Crown Group ◽  
Long Period ◽  
Stem Group ◽  
Group Evolution ◽  
Domains Of Life ◽  
Ecology And Environment

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.

scholarly journals tRNA functional signatures classify plastids as late-branching cyanobacteria

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Travis J Lawrence ◽  
Katherine CH Amrine ◽  
Wesley D Swingley ◽  
David H Ardell
Keyword(s):  
Machine Learning ◽  
Trna Gene ◽  
Learning Algorithm ◽  
Oxygenic Photosynthesis ◽  
Evolutionary Models ◽  
Independent Evidence ◽  
Phylogenetic Studies ◽  
Plastid Genomes ◽  
Unbalanced Sampling

Abstract Background Eukaryotes acquired the trait of oxygenic photosynthesis through endosymbiosis of the cyanobacterial progenitor of plastid organelles. Despite recent advances in the phylogenomics of Cyanobacteria, the phylogenetic root of plastids remains controversial. Although a single origin of plastids by endosymbiosis is broadly supported, recent phylogenomic studies are contradictory on whether plastids branch early or late within Cyanobacteria. One underlying cause may be poor fit of evolutionary models to complex phylogenomic data. Results Using Posterior Predictive Analysis, we show that recently applied evolutionary models poorly fit three phylogenomic datasets curated from cyanobacteria and plastid genomes because of heterogeneities in both substitution processes across sites and of compositions across lineages. To circumvent these sources of bias, we developed CYANO-MLP, a machine learning algorithm that consistently and accurately phylogenetically classifies (“phyloclassifies”) cyanobacterial genomes to their clade of origin based on bioinformatically predicted function-informative features in tRNA gene complements. Classification of cyanobacterial genomes with CYANO-MLP is accurate and robust to deletion of clades, unbalanced sampling, and compositional heterogeneity in input tRNA data. CYANO-MLP consistently classifies plastid genomes into a late-branching cyanobacterial sub-clade containing single-cell, starch-producing, nitrogen-fixing ecotypes, consistent with metabolic and gene transfer data. Conclusions Phylogenomic data of cyanobacteria and plastids exhibit both site-process heterogeneities and compositional heterogeneities across lineages. These aspects of the data require careful modeling to avoid bias in phylogenomic estimation. Furthermore, we show that amino acid recoding strategies may be insufficient to mitigate bias from compositional heterogeneities. However, the combination of our novel tRNA-specific strategy with machine learning in CYANO-MLP appears robust to these sources of bias with high accuracy in phyloclassification of cyanobacterial genomes. CYANO-MLP consistently classifies plastids as late-branching Cyanobacteria, consistent with independent evidence from signature-based approaches and some previous phylogenetic studies.

Sign in / Sign up

Export Citation Format

Share Document