Bacterial Origin and Reductive Evolution of the CPR Group
Abstract
The candidate phyla radiation (CPR) is a proposed subdivision within the bacterial domain comprising several candidate phyla. CPR organisms are united by small genome and physical sizes, lack several metabolic enzymes, and populate deep branches within the bacterial subtree of life. Here, these features raise intriguing questions regarding their origin and mode of evolution. In this study, we performed a comparative and phylogenomic analysis to investigate CPR origin and evolution. Unlike previous gene/protein sequence-based reports of CPR evolution, we used protein domain superfamilies classified by protein structure databases to resolve the evolutionary relationships of CPR with non-CPR bacteria, Archaea, Eukarya, and viruses. Across all supergroups, CPR shared maximum superfamilies with non-CPR bacteria and were placed as deep branching bacteria in most phylogenomic trees. CPR contributed 1.22% of new superfamilies to bacteria including the ribosomal protein L19e and encoded four core superfamilies that are likely involved in cell-to-cell interaction and establishing episymbiotic lifestyles. Although CPR and non-CPR bacterial proteomes gained common superfamilies over the course of evolution, CPR and Archaea had more common losses. These losses mostly involved metabolic superfamilies. In fact, phylogenies built from only metabolic protein superfamilies separated CPR and non-CPR bacteria. These findings indicate that CPR are bacterialmore »
- Authors:
-
[5]
- COMSATS Univ., Islamabad (Pakistan)
- Georgia Inst. of Technology, Atlanta, GA (United States)
- Korea Polar Research Inst., Incheon (Korea)
- Univ. of Illinois at Urbana-Champaign, IL (United States)
- COMSATS Univ., Islamabad (Pakistan); Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
- Publication Date:
- Research Org.:
- Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
- Sponsoring Org.:
- USDOE Laboratory Directed Research and Development (LDRD) Program; National Science Foundation (NSF)
- OSTI Identifier:
- 1633566
- Report Number(s):
- LA-UR-19-24949
Journal ID: ISSN 1759-6653
- Grant/Contract Number:
- 89233218CNA000001
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Genome Biology and Evolution
- Additional Journal Information:
- Journal Volume: 12; Journal Issue: 3; Journal ID: ISSN 1759-6653
- Publisher:
- Society for Molecular Biology and Evolution
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; Biological science; candidate phyla radiation; tree of life; phylogenetics; reductive evolution; protein structure
Citation Formats
Bokhari, Rijja Hussain, Amirjan, Nooreen, Jeong, Hyeonsoo, Kim, Kyung Mo, Caetano-Anollés, Gustavo, and Nasir, Arshan. Bacterial Origin and Reductive Evolution of the CPR Group. United States: N. p., 2020.
Web. doi:10.1093/gbe/evaa024.
Bokhari, Rijja Hussain, Amirjan, Nooreen, Jeong, Hyeonsoo, Kim, Kyung Mo, Caetano-Anollés, Gustavo, & Nasir, Arshan. Bacterial Origin and Reductive Evolution of the CPR Group. United States. https://doi.org/10.1093/gbe/evaa024
Bokhari, Rijja Hussain, Amirjan, Nooreen, Jeong, Hyeonsoo, Kim, Kyung Mo, Caetano-Anollés, Gustavo, and Nasir, Arshan. Fri .
"Bacterial Origin and Reductive Evolution of the CPR Group". United States. https://doi.org/10.1093/gbe/evaa024. https://www.osti.gov/servlets/purl/1633566.
@article{osti_1633566,
title = {Bacterial Origin and Reductive Evolution of the CPR Group},
author = {Bokhari, Rijja Hussain and Amirjan, Nooreen and Jeong, Hyeonsoo and Kim, Kyung Mo and Caetano-Anollés, Gustavo and Nasir, Arshan},
abstractNote = {The candidate phyla radiation (CPR) is a proposed subdivision within the bacterial domain comprising several candidate phyla. CPR organisms are united by small genome and physical sizes, lack several metabolic enzymes, and populate deep branches within the bacterial subtree of life. Here, these features raise intriguing questions regarding their origin and mode of evolution. In this study, we performed a comparative and phylogenomic analysis to investigate CPR origin and evolution. Unlike previous gene/protein sequence-based reports of CPR evolution, we used protein domain superfamilies classified by protein structure databases to resolve the evolutionary relationships of CPR with non-CPR bacteria, Archaea, Eukarya, and viruses. Across all supergroups, CPR shared maximum superfamilies with non-CPR bacteria and were placed as deep branching bacteria in most phylogenomic trees. CPR contributed 1.22% of new superfamilies to bacteria including the ribosomal protein L19e and encoded four core superfamilies that are likely involved in cell-to-cell interaction and establishing episymbiotic lifestyles. Although CPR and non-CPR bacterial proteomes gained common superfamilies over the course of evolution, CPR and Archaea had more common losses. These losses mostly involved metabolic superfamilies. In fact, phylogenies built from only metabolic protein superfamilies separated CPR and non-CPR bacteria. These findings indicate that CPR are bacterial organisms that have probably evolved in an Archaea-like manner via the early loss of metabolic functions. We also discovered that phylogenies built from metabolic and informational superfamilies gave contrasting views of the groupings among Archaea, Bacteria, and Eukarya, which add to the current debate on the evolutionary relationships among superkingdoms.},
doi = {10.1093/gbe/evaa024},
journal = {Genome Biology and Evolution},
number = 3,
volume = 12,
place = {United States},
year = {Fri Feb 07 00:00:00 EST 2020},
month = {Fri Feb 07 00:00:00 EST 2020}
}
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Works referenced in this record:
Asgard archaea do not close the debate about the universal tree of life topology
journal, March 2018
- Da Cunha, Violette; Gaia, Morgan; Nasir, Arshan
- PLOS Genetics, Vol. 14, Issue 3
Comparative analysis of ribosomal proteins in complete genomes: an example of reductive evolution at the domain scale
journal, December 2002
- Lecompte, O.
- Nucleic Acids Research, Vol. 30, Issue 24
Wagner Networks and Ancestors
journal, December 1972
- Lundberg, John G.
- Systematic Zoology, Vol. 21, Issue 4
Rooting Phylogenies and the Tree of Life While Minimizing Ad Hoc and Auxiliary Assumptions
journal, January 2018
- Caetano-Anollés, Gustavo; Nasir, Arshan; Kim, Kyung Mo
- Evolutionary Bioinformatics, Vol. 14
Phylogenomics provides robust support for a two-domains tree of life
journal, December 2019
- Williams, Tom A.; Cox, Cymon J.; Foster, Peter G.
- Nature Ecology & Evolution, Vol. 4, Issue 1
Asgard archaea illuminate the origin of eukaryotic cellular complexity
journal, January 2017
- Zaremba-Niedzwiedzka, Katarzyna; Caceres, Eva F.; Saw, Jimmy H.
- Nature, Vol. 541, Issue 7637
Dendroscope: An interactive viewer for large phylogenetic trees
journal, November 2007
- Huson, Daniel H.; Richter, Daniel C.; Rausch, Christian
- BMC Bioinformatics, Vol. 8, Issue 1
Testing Empirical Support for Evolutionary Models that Root the Tree of Life
journal, March 2019
- Caetano-Anollés, Derek; Nasir, Arshan; Kim, Kyung Mo
- Journal of Molecular Evolution, Vol. 87, Issue 2-3
Ancestrality and Mosaicism of Giant Viruses Supporting the Definition of the Fourth TRUC of Microbes
journal, November 2018
- Colson, Philippe; Levasseur, Anthony; La Scola, Bernard
- Frontiers in Microbiology, Vol. 9
Extreme genome reduction in symbiotic bacteria
journal, November 2011
- McCutcheon, John P.; Moran, Nancy A.
- Nature Reviews Microbiology, Vol. 10, Issue 1
Reductive evolution of architectural repertoires in proteomes and the birth of the tripartite world
journal, November 2007
- Wang, M.; Yafremava, L. S.; Caetano-Anolles, D.
- Genome Research, Vol. 17, Issue 11
HGTree: database of horizontally transferred genes determined by tree reconciliation
journal, November 2015
- Jeong, Hyeonsoo; Sung, Samsun; Kwon, Taehyung
- Nucleic Acids Research, Vol. 44, Issue D1
Global Phylogeny Determined by the Combination of Protein Domains in Proteomes
journal, September 2006
- Wang, Minglei; Caetano-Anollés, Gustavo
- Molecular Biology and Evolution, Vol. 23, Issue 12
BadiRate: estimating family turnover rates by likelihood-based methods
journal, November 2011
- Librado, P.; Vieira, F. G.; Rozas, J.
- Bioinformatics, Vol. 28, Issue 2
A phylogenomic data-driven exploration of viral origins and evolution
journal, September 2015
- Nasir, Arshan; Caetano-Anollés, Gustavo
- Science Advances, Vol. 1, Issue 8
The distinction of CPR bacteria from other bacteria based on protein family content
journal, September 2019
- Méheust, Raphaël; Burstein, David; Castelle, Cindy J.
- Nature Communications, Vol. 10, Issue 1
Reductive evolution of proteomes and protein structures
journal, July 2011
- Wang, M.; Kurland, C. G.; Caetano-Anolles, G.
- Proceedings of the National Academy of Sciences, Vol. 108, Issue 29
Evolutionary genomics of nucleo-cytoplasmic large DNA viruses
journal, April 2006
- Iyer, Lakshminarayan M.; Balaji, S.; Koonin, Eugene V.
- Virus Research, Vol. 117, Issue 1
Tailed giant Tupanvirus possesses the most complete translational apparatus of the known virosphere
journal, February 2018
- Abrahão, Jônatas; Silva, Lorena; Silva, Ludmila Santos
- Nature Communications, Vol. 9, Issue 1
Testing the Hypothesis of Common Ancestry
journal, October 2002
- Sober, E.
- Journal of Theoretical Biology, Vol. 218, Issue 4
The Relationship Between Domain Duplication and Recombination
journal, February 2005
- Vogel, Christine; Teichmann, Sarah A.; Pereira-Leal, Jose
- Journal of Molecular Biology, Vol. 346, Issue 1
Two fundamental questions about protein evolution
journal, December 2015
- Penny, David; Zhong, Bojian
- Biochimie, Vol. 119
Supra-domains: Evolutionary Units Larger than Single Protein Domains
journal, February 2004
- Vogel, Christine; Berzuini, Carlo; Bashton, Matthew
- Journal of Molecular Biology, Vol. 336, Issue 3
Global Patterns of Protein Domain Gain and Loss in Superkingdoms
journal, January 2014
- Nasir, Arshan; Kim, Kyung Mo; Caetano-Anollés, Gustavo
- PLoS Computational Biology, Vol. 10, Issue 1
Identification of Capsid/Coat Related Protein Folds and Their Utility for Virus Classification
journal, March 2017
- Nasir, Arshan; Caetano-Anollés, Gustavo
- Frontiers in Microbiology, Vol. 8
Giant viruses, giant chimeras: The multiple evolutionary histories of Mimivirus genes
journal, January 2008
- Moreira, David; Brochier-Armanet, Céline
- BMC Evolutionary Biology, Vol. 8, Issue 1
Structure Unifies the Viral Universe
journal, July 2012
- Abrescia, Nicola G. A.; Bamford, Dennis H.; Grimes, Jonathan M.
- Annual Review of Biochemistry, Vol. 81, Issue 1
Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya.
journal, June 1990
- Woese, C. R.; Kandler, O.; Wheelis, M. L.
- Proceedings of the National Academy of Sciences, Vol. 87, Issue 12
A General Framework of Persistence Strategies for Biological Systems Helps Explain Domains of Life
journal, January 2013
- Yafremava, Liudmila S.; Wielgos, Monica; Thomas, Suravi
- Frontiers in Genetics, Vol. 4
A Phylogenomic Census of Molecular Functions Identifies Modern Thermophilic Archaea as the Most Ancient Form of Cellular Life
journal, January 2014
- Nasir, Arshan; Kim, Kyung Mo; Caetano-Anollés, Gustavo
- Archaea, Vol. 2014
Archaea-First and the Co-Evolutionary Diversification of Domains of Life
journal, June 2018
- Staley, James T.; Caetano-Anollés, Gustavo
- BioEssays, Vol. 40, Issue 8
Did Viruses Evolve As a Distinct Supergroup from Common Ancestors of Cells?
journal, August 2016
- Harish, Ajith; Abroi, Aare; Gough, Julian
- Genome Biology and Evolution, Vol. 8, Issue 8
Horizontal gene transfer in human-associated microorganisms inferred by phylogenetic reconstruction and reconciliation
journal, April 2019
- Jeong, Hyeonsoo; Arif, Bushra; Caetano-Anollés, Gustavo
- Scientific Reports, Vol. 9, Issue 1
A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life
journal, August 2018
- Parks, Donovan H.; Chuvochina, Maria; Waite, David W.
- Nature Biotechnology, Vol. 36, Issue 10
DendroPy: a Python library for phylogenetic computing
journal, April 2010
- Sukumaran, J.; Holder, M. T.
- Bioinformatics, Vol. 26, Issue 12
Viral evolution: Primordial cellular origins and late adaptation to parasitism
journal, September 2012
- Nasir, Arshan; Kim, Kyung Mo; Caetano-Anollés, Gustavo
- Mobile Genetic Elements, Vol. 2, Issue 5
Biosynthetic capacity, metabolic variety and unusual biology in the CPR and DPANN radiations
journal, September 2018
- Castelle, Cindy J.; Brown, Christopher T.; Anantharaman, Karthik
- Nature Reviews Microbiology, Vol. 16, Issue 10
Asgard archaea are the closest prokaryotic relatives of eukaryotes
journal, March 2018
- Spang, Anja; Eme, Laura; Saw, Jimmy H.
- PLOS Genetics, Vol. 14, Issue 3
Increased Taxon Sampling Greatly Reduces Phylogenetic Error
journal, July 2002
- Zwickl, Derrick J.; Hillis, David M.
- Systematic Biology, Vol. 51, Issue 4
Comparative Analysis of Proteomes and Functionomes Provides Insights into Origins of Cellular Diversification
journal, January 2013
- Nasir, Arshan; Caetano-Anollés, Gustavo
- Archaea, Vol. 2013
SCOPe: Structural Classification of Proteins—extended, integrating SCOP and ASTRAL data and classification of new structures
journal, December 2013
- Fox, Naomi K.; Brenner, Steven E.; Chandonia, John-Marc
- Nucleic Acids Research, Vol. 42, Issue D1
Horizontal gene transfer: building the web of life
journal, July 2015
- Soucy, Shannon M.; Huang, Jinling; Gogarten, Johann Peter
- Nature Reviews Genetics, Vol. 16, Issue 8
Microbial diversity: The tree of life comes of age
journal, April 2016
- Spang, Anja; Ettema, Thijs J. G.
- Nature Microbiology, Vol. 1, Issue 5
The Common Ancestor of Archaea and Eukarya Was Not an Archaeon
journal, January 2013
- Forterre, Patrick
- Archaea, Vol. 2013
Manipulation of cellular syntheses and the nature of viruses: The virocell concept
journal, April 2011
- Forterre, Patrick
- Comptes Rendus Chimie, Vol. 14, Issue 4
Annotation of Protein Domains Reveals Remarkable Conservation in the Functional Make up of Proteomes Across Superkingdoms
journal, November 2011
- Nasir, Arshan; Naeem, Aisha; Khan, Muhammad Jawad
- Genes, Vol. 2, Issue 4
Eocytes: a new ribosome structure indicates a kingdom with a close relationship to eukaryotes.
journal, June 1984
- Lake, J. A.; Henderson, E.; Oakes, M.
- Proceedings of the National Academy of Sciences, Vol. 81, Issue 12
Predicted microbial secretomes and their target substrates in marine sediment
journal, October 2017
- Orsi, William D.; Richards, Thomas A.; Francis, Warren R.
- Nature Microbiology, Vol. 3, Issue 1
Empirical genome evolution models root the tree of life
journal, July 2017
- Harish, Ajith; Kurland, Charles G.
- Biochimie, Vol. 138
Diversity and evolution of the emerging Pandoraviridae family
journal, June 2018
- Legendre, Matthieu; Fabre, Elisabeth; Poirot, Olivier
- Nature Communications, Vol. 9, Issue 1
Common Origin of Four Diverse Families of Large Eukaryotic DNA Viruses
journal, December 2001
- Iyer, L. M.; Aravind, L.; Koonin, E. V.
- Journal of Virology, Vol. 75, Issue 23
An archaeal origin of eukaryotes supports only two primary domains of life
journal, December 2013
- Williams, Tom A.; Foster, Peter G.; Cox, Cymon J.
- Nature, Vol. 504, Issue 7479
Do Viruses Exchange Genes across Superkingdoms of Life?
journal, October 2017
- Malik, Shahana S.; Azem-e-Zahra, Syeda; Kim, Kyung Mo
- Frontiers in Microbiology, Vol. 8
The rapidly expanding universe of giant viruses: Mimivirus, Pandoravirus, Pithovirus and Mollivirus
journal, September 2015
- Abergel, Chantal; Legendre, Matthieu; Claverie, Jean-Michel
- FEMS Microbiology Reviews, Vol. 39, Issue 6
Giant viruses coexisted with the cellular ancestors and represent a distinct supergroup along with superkingdoms Archaea, Bacteria and Eukarya
journal, January 2012
- Nasir, Arshan; Kim, Kyung; Caetano-Anolles, Gustavo
- BMC Evolutionary Biology, Vol. 12, Issue 1
To be or not to be alive: How recent discoveries challenge the traditional definitions of viruses and life
journal, October 2016
- Forterre, Patrick
- Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences, Vol. 59
Protein Family Expansions and Biological Complexity
journal, January 2006
- Vogel, Christine; Chothia, Cyrus
- PLoS Computational Biology, Vol. 2, Issue 5
Giant viruses: The difficult breaking of multiple epistemological barriers
journal, October 2016
- Claverie, Jean-Michel; Abergel, Chantal
- Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences, Vol. 59
Genome reduction as the dominant mode of evolution: Prospects & Overviews
journal, June 2013
- Wolf, Yuri I.; Koonin, Eugene V.
- BioEssays, Vol. 35, Issue 9
Unusual biology across a group comprising more than 15% of domain Bacteria
journal, June 2015
- Brown, Christopher T.; Hug, Laura A.; Thomas, Brian C.
- Nature, Vol. 523, Issue 7559
A Universal Molecular Clock of Protein Folds and Its Power in Tracing the Early History of Aerobic Metabolism and Planet Oxygenation
journal, August 2010
- Wang, Minglei; Jiang, Ying-Ying; Kim, Kyung Mo
- Molecular Biology and Evolution, Vol. 28, Issue 1
Cultivation of a human-associated TM7 phylotype reveals a reduced genome and epibiotic parasitic lifestyle
journal, December 2014
- He, Xuesong; McLean, Jeffrey S.; Edlund, Anna
- Proceedings of the National Academy of Sciences, Vol. 112, Issue 1
Phylogenetic structure of the prokaryotic domain: The primary kingdoms
journal, November 1977
- Woese, C. R.; Fox, G. E.
- Proceedings of the National Academy of Sciences, Vol. 74, Issue 11
Structure is three to ten times more conserved than sequence-A study of structural response in protein cores
journal, November 2009
- Illergård, Kristoffer; Ardell, David H.; Elofsson, Arne
- Proteins: Structure, Function, and Bioinformatics, Vol. 77, Issue 3
Origin and Evolution of Protein Fold Designs Inferred from Phylogenomic Analysis of CATH Domain Structures in Proteomes
journal, March 2013
- Bukhari, Syed Abbas; Caetano-Anollés, Gustavo
- PLoS Computational Biology, Vol. 9, Issue 3
Pandoravirus Celtis Illustrates the Microevolution Processes at Work in the Giant Pandoraviridae Genomes
journal, March 2019
- Legendre, Matthieu; Alempic, Jean-Marie; Philippe, Nadège
- Frontiers in Microbiology, Vol. 10
Major New Microbial Groups Expand Diversity and Alter our Understanding of the Tree of Life
journal, March 2018
- Castelle, Cindy J.; Banfield, Jillian F.
- Cell, Vol. 172, Issue 6
Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure
journal, November 2001
- Gough, Julian; Karplus, Kevin; Hughey, Richard
- Journal of Molecular Biology, Vol. 313, Issue 4
A new view of the tree of life
journal, April 2016
- Hug, Laura A.; Baker, Brett J.; Anantharaman, Karthik
- Nature Microbiology, Vol. 1, Issue 5
Lokiarchaeota: eukaryote-like missing links from microbial dark matter?
journal, August 2015
- Nasir, Arshan; Kim, Kyung Mo; Caetano-Anollés, Gustavo
- Trends in Microbiology, Vol. 23, Issue 8
Lokiarchaea are close relatives of Euryarchaeota, not bridging the gap between prokaryotes and eukaryotes
journal, June 2017
- Da Cunha, Violette; Gaia, Morgan; Gadelle, Daniele
- PLOS Genetics, Vol. 13, Issue 6
Can Sequence Phylogenies Safely Infer the Origin of the Global Virome?
journal, April 2019
- Holmes, Edward C.; Duchêne, Sebastián
- mBio, Vol. 10, Issue 2
Ten reasons to exclude viruses from the tree of life
journal, March 2009
- Moreira, David; López-García, Purificación
- Nature Reviews Microbiology, Vol. 7, Issue 4
Phylogenetic Tracings of Proteome Size Support the Gradual Accretion of Protein Structural Domains and the Early Origin of Viruses from Primordial Cells
journal, June 2017
- Nasir, Arshan; Kim, Kyung Mo; Caetano-Anollés, Gustavo
- Frontiers in Microbiology, Vol. 8
Stable isotope informed genome-resolved metagenomics reveals that Saccharibacteria utilize microbially-processed plant-derived carbon
journal, July 2018
- Starr, Evan P.; Shi, Shengjing; Blazewicz, Steven J.
- Microbiome, Vol. 6, Issue 1
The proteomic complexity and rise of the primordial ancestor of diversified life
journal, May 2011
- Kim, Kyung Mo; Caetano-Anollés, Gustavo
- BMC Evolutionary Biology, Vol. 11, Issue 1
The importance of using realistic evolutionary models for retrodicting proteomes
journal, April 2014
- Kim, Kyung Mo; Nasir, Arshan; Caetano-Anollés, Gustavo
- Biochimie, Vol. 99
Pandoraviruses: Amoeba Viruses with Genomes Up to 2.5 Mb Reaching That of Parasitic Eukaryotes
journal, July 2013
- Philippe, N.; Legendre, M.; Doutre, G.
- Science, Vol. 341, Issue 6143
Data growth and its impact on the SCOP database: new developments
journal, December 2007
- Andreeva, A.; Howorth, D.; Chandonia, J. -M.
- Nucleic Acids Research, Vol. 36, Issue Database
The evolutionary history of protein fold families and proteomes confirms that the archaeal ancestor is more ancient than the ancestors of other superkingdoms
journal, January 2012
- Kim, Kyung Mo; Caetano-Anollés, Gustavo
- BMC Evolutionary Biology, Vol. 12, Issue 1
Complex archaea that bridge the gap between prokaryotes and eukaryotes
journal, May 2015
- Spang, Anja; Saw, Jimmy H.; Jørgensen, Steffen L.
- Nature, Vol. 521, Issue 7551
SUPERFAMILY—sophisticated comparative genomics, data mining, visualization and phylogeny
journal, November 2008
- Wilson, Derek; Pethica, Ralph; Zhou, Yiduo
- Nucleic Acids Research, Vol. 37, Issue suppl_1
Insights into the phylogeny and coding potential of microbial dark matter
journal, July 2013
- Rinke, Christian; Schwientek, Patrick; Sczyrba, Alexander
- Nature, Vol. 499, Issue 7459
A Preliminary List of Horizontally Transferred Genes in Prokaryotes Determined by Tree Reconstruction and Reconciliation
journal, August 2017
- Jeong, Hyeonsoo; Nasir, Arshan
- Frontiers in Genetics, Vol. 8
SUPERFAMILY: HMMs representing all proteins of known structure. SCOP sequence searches, alignments and genome assignments
journal, January 2002
- Gough, J.
- Nucleic Acids Research, Vol. 30, Issue 1
The Dynamics and Evolutionary Potential of Domain Loss and Emergence
journal, October 2011
- Moore, A. D.; Bornberg-Bauer, E.
- Molecular Biology and Evolution, Vol. 29, Issue 2
Arguments Reinforcing the Three-Domain View of Diversified Cellular Life
journal, January 2016
- Nasir, Arshan; Kim, Kyung Mo; Da Cunha, Violette
- Archaea, Vol. 2016
The RCSB Protein Data Bank: views of structural biology for basic and applied research and education
journal, November 2014
- Rose, Peter W.; Prlić, Andreas; Bi, Chunxiao
- Nucleic Acids Research, Vol. 43, Issue D1
A Tree of Cellular Life Inferred from a Genomic Census of Molecular Functions
journal, August 2014
- Kim, Kyung Mo; Nasir, Arshan; Hwang, Kyuin
- Journal of Molecular Evolution, Vol. 79, Issue 5-6
Weighted parsimony outperforms other methods of phylogenetic inference under models appropriate for morphology
journal, June 2017
- Goloboff, Pablo A.; Torres, Ambrosio; Arias, J. Salvador
- Cladistics, Vol. 34, Issue 4