Literature DB >> 20182607

Deep phylogeny--how a tree can help characterize early life on Earth.

Eric A Gaucher1, James T Kratzer, Ryan N Randall.   

Abstract

The Darwinian concept of biological evolution assumes that life on Earth shares a common ancestor. The diversification of this common ancestor through speciation events and vertical transmission of genetic material implies that the classification of life can be illustrated in a tree-like manner, commonly referred to as the Tree of Life. This article describes features of the Tree of Life, such as how the tree has been both pruned and become bushier throughout the past century as our knowledge of biology has expanded. We present current views that the classification of life may be best illustrated as a ring or even a coral with tree-like characteristics. This article also discusses how the organization of the Tree of Life offers clues about ancient life on Earth. In particular, we focus on the environmental conditions and temperature history of Precambrian life and show how chemical, biological, and geological data can converge to better understand this history."You know, a tree is a tree. How many more do you need to look at?"--Ronald Reagan (Governor of California), quoted in the Sacramento Bee, opposing expansion of Redwood National Park, March 3, 1966.

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Year:  2010        PMID: 20182607      PMCID: PMC2827910          DOI: 10.1101/cshperspect.a002238

Source DB:  PubMed          Journal:  Cold Spring Harb Perspect Biol        ISSN: 1943-0264            Impact factor:   10.005


  65 in total

1.  The crystal structure of eEF1A refines the functional predictions of an evolutionary analysis of rate changes among elongation factors.

Authors:  Eric A Gaucher; Ujjwal K Das; Michael M Miyamoto; Steven A Benner
Journal:  Mol Biol Evol       Date:  2002-04       Impact factor: 16.240

Review 2.  The first cell membranes.

Authors:  David Deamer; Jason P Dworkin; Scott A Sandford; Max P Bernstein; Louis J Allamandola
Journal:  Astrobiology       Date:  2002       Impact factor: 4.335

3.  The ring of life provides evidence for a genome fusion origin of eukaryotes.

Authors:  Maria C Rivera; James A Lake
Journal:  Nature       Date:  2004-09-09       Impact factor: 49.962

4.  A vesicle bioreactor as a step toward an artificial cell assembly.

Authors:  Vincent Noireaux; Albert Libchaber
Journal:  Proc Natl Acad Sci U S A       Date:  2004-12-10       Impact factor: 11.205

5.  Protein disulfide oxidoreductases and the evolution of thermophily: was the last common ancestor a heat-loving microbe?

Authors:  Arturo Becerra; Luis Delaye; Antonio Lazcano; Leslie E Orgel
Journal:  J Mol Evol       Date:  2007-08-29       Impact factor: 2.395

6.  Phylogenetic structure of the prokaryotic domain: the primary kingdoms.

Authors:  C R Woese; G E Fox
Journal:  Proc Natl Acad Sci U S A       Date:  1977-11       Impact factor: 11.205

7.  A new method of inference of ancestral nucleotide and amino acid sequences.

Authors:  Z Yang; S Kumar; M Nei
Journal:  Genetics       Date:  1995-12       Impact factor: 4.562

8.  Complete chemical synthesis, assembly, and cloning of a Mycoplasma genitalium genome.

Authors:  Daniel G Gibson; Gwynedd A Benders; Cynthia Andrews-Pfannkoch; Evgeniya A Denisova; Holly Baden-Tillson; Jayshree Zaveri; Timothy B Stockwell; Anushka Brownley; David W Thomas; Mikkel A Algire; Chuck Merryman; Lei Young; Vladimir N Noskov; John I Glass; J Craig Venter; Clyde A Hutchison; Hamilton O Smith
Journal:  Science       Date:  2008-01-24       Impact factor: 47.728

9.  Ancestral sequence reconstruction in primate mitochondrial DNA: compositional bias and effect on functional inference.

Authors:  Neeraja M Krishnan; Hervé Seligmann; Caro-Beth Stewart; A P Jason De Koning; David D Pollock
Journal:  Mol Biol Evol       Date:  2004-06-30       Impact factor: 16.240

Review 10.  Synthetic biology.

Authors:  Steven A Benner; A Michael Sismour
Journal:  Nat Rev Genet       Date:  2005-07       Impact factor: 53.242

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  14 in total

Review 1.  The Hadean-Archaean environment.

Authors:  Norman H Sleep
Journal:  Cold Spring Harb Perspect Biol       Date:  2010-05-05       Impact factor: 10.005

2.  Metazoan evolution of the armadillo repeat superfamily.

Authors:  Ismail Sahin Gul; Paco Hulpiau; Yvan Saeys; Frans van Roy
Journal:  Cell Mol Life Sci       Date:  2016-08-06       Impact factor: 9.261

Review 3.  The Astrobiology Primer v2.0.

Authors:  Shawn D Domagal-Goldman; Katherine E Wright; Katarzyna Adamala; Leigh Arina de la Rubia; Jade Bond; Lewis R Dartnell; Aaron D Goldman; Kennda Lynch; Marie-Eve Naud; Ivan G Paulino-Lima; Kelsi Singer; Marina Walther-Antonio; Ximena C Abrevaya; Rika Anderson; Giada Arney; Dimitra Atri; Armando Azúa-Bustos; Jeff S Bowman; William J Brazelton; Gregory A Brennecka; Regina Carns; Aditya Chopra; Jesse Colangelo-Lillis; Christopher J Crockett; Julia DeMarines; Elizabeth A Frank; Carie Frantz; Eduardo de la Fuente; Douglas Galante; Jennifer Glass; Damhnait Gleeson; Christopher R Glein; Colin Goldblatt; Rachel Horak; Lev Horodyskyj; Betül Kaçar; Akos Kereszturi; Emily Knowles; Paul Mayeur; Shawn McGlynn; Yamila Miguel; Michelle Montgomery; Catherine Neish; Lena Noack; Sarah Rugheimer; Eva E Stüeken; Paulina Tamez-Hidalgo; Sara Imari Walker; Teresa Wong
Journal:  Astrobiology       Date:  2016-08       Impact factor: 4.335

4.  Extremophiles: a special or general case in the search for extra-terrestrial life?

Authors:  Ian von Hegner
Journal:  Extremophiles       Date:  2019-11-09       Impact factor: 2.395

5.  Experimental evidence for the thermophilicity of ancestral life.

Authors:  Satoshi Akanuma; Yoshiki Nakajima; Shin-ichi Yokobori; Mitsuo Kimura; Naoki Nemoto; Tomoko Mase; Ken-ichi Miyazono; Masaru Tanokura; Akihiko Yamagishi
Journal:  Proc Natl Acad Sci U S A       Date:  2013-06-17       Impact factor: 11.205

Review 6.  The Ras protein superfamily: evolutionary tree and role of conserved amino acids.

Authors:  Ana Maria Rojas; Gloria Fuentes; Antonio Rausell; Alfonso Valencia
Journal:  J Cell Biol       Date:  2012-01-23       Impact factor: 10.539

Review 7.  Characterization of Reconstructed Ancestral Proteins Suggests a Change in Temperature of the Ancient Biosphere.

Authors:  Satoshi Akanuma
Journal:  Life (Basel)       Date:  2017-08-06

8.  AYbRAH: a curated ortholog database for yeasts and fungi spanning 600 million years of evolution.

Authors:  Kevin Correia; Shi M Yu; Radhakrishnan Mahadevan
Journal:  Database (Oxford)       Date:  2019-01-01       Impact factor: 3.451

9.  Phylogenetic analysis of mutational robustness based on codon usage supports that the standard genetic code does not prefer extreme environments.

Authors:  Ádám Radványi; Ádám Kun
Journal:  Sci Rep       Date:  2021-05-26       Impact factor: 4.379

10.  Phylogenetic and biological significance of evolutionary elements from metazoan mitochondrial genomes.

Authors:  Jianbo Yuan; Qingming Zhu; Bin Liu
Journal:  PLoS One       Date:  2014-01-20       Impact factor: 3.240

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