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DeSalle R, Riley M. Should Networks Supplant Tree Building? Microorganisms 2020; 8:E1179. [PMID: 32756444 PMCID: PMC7466111 DOI: 10.3390/microorganisms8081179] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 07/21/2020] [Accepted: 07/29/2020] [Indexed: 12/15/2022] Open
Abstract
Recent studies suggested that network methods should supplant tree building as the basis of genealogical analysis. This proposition is based upon two arguments. First is the observation that bacterial and archaeal lineages experience processes oppositional to bifurcation and hence the representation of the evolutionary process in a tree like structure is illogical. Second is the argument tree building approaches are circular-you ask for a tree and you get one, which pins a verificationist label on tree building that, if correct, should be the end of phylogenetic analysis as we currently know it. In this review, we examine these questions and suggest that rumors of the death of the bacterial tree of life are exaggerated at best.
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Affiliation(s)
- Rob DeSalle
- Sackler Institute for Comparative Genomics, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, USA;
| | - Margaret Riley
- Department of Biology, University of Massachusetts Amherst, 116 North Pleasant Street, Amherst, MA 01003, USA
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2
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Hördt A, López MG, Meier-Kolthoff JP, Schleuning M, Weinhold LM, Tindall BJ, Gronow S, Kyrpides NC, Woyke T, Göker M. Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria. Front Microbiol 2020; 11:468. [PMID: 32373076 PMCID: PMC7179689 DOI: 10.3389/fmicb.2020.00468] [Citation(s) in RCA: 223] [Impact Index Per Article: 55.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 03/04/2020] [Indexed: 11/13/2022] Open
Abstract
The class Alphaproteobacteria is comprised of a diverse assemblage of Gram-negative bacteria that includes organisms of varying morphologies, physiologies and habitat preferences many of which are of clinical and ecological importance. Alphaproteobacteria classification has proved to be difficult, not least when taxonomic decisions rested heavily on a limited number of phenotypic features and interpretation of poorly resolved 16S rRNA gene trees. Despite progress in recent years regarding the classification of bacteria assigned to the class, there remains a need to further clarify taxonomic relationships. Here, draft genome sequences of a collection of genomes of more than 1000 Alphaproteobacteria and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa recognized as problematic long ago but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera and of a variety of genera to other families. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which are confirmed as valuable taxonomic markers. Similarly, analysis of the gene content was shown to provide valuable taxonomic insights in the class. Significant incongruities between 16S rRNA gene and whole genome trees were not found in the class. The incongruities that became obvious when comparing the results of the present study with existing classifications appeared to be caused mainly by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. Another probable cause of misclassifications in the past is the partially low overall fit of phenotypic characters to the sequence-based tree. Even though a significant degree of phylogenetic conservation was detected in all characters investigated, the overall fit to the tree varied considerably.
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Affiliation(s)
- Anton Hördt
- Department of Bioinformatics, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - Marina García López
- Department of Bioinformatics, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - Jan P. Meier-Kolthoff
- Department of Bioinformatics, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - Marcel Schleuning
- Department of Bioinformatics, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - Lisa-Maria Weinhold
- Department of Bioinformatics, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, Czechia
| | - Brian J. Tindall
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - Sabine Gronow
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - Nikos C. Kyrpides
- Department of Energy, Joint Genome Institute, Berkeley, CA, United States
| | - Tanja Woyke
- Department of Energy, Joint Genome Institute, Berkeley, CA, United States
| | - Markus Göker
- Department of Bioinformatics, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
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3
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García-López M, Meier-Kolthoff JP, Tindall BJ, Gronow S, Woyke T, Kyrpides NC, Hahnke RL, Göker M. Analysis of 1,000 Type-Strain Genomes Improves Taxonomic Classification of Bacteroidetes. Front Microbiol 2019; 10:2083. [PMID: 31608019 PMCID: PMC6767994 DOI: 10.3389/fmicb.2019.02083] [Citation(s) in RCA: 174] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 08/23/2019] [Indexed: 11/25/2022] Open
Abstract
Although considerable progress has been made in recent years regarding the classification of bacteria assigned to the phylum Bacteroidetes, there remains a need to further clarify taxonomic relationships within a diverse assemblage that includes organisms of clinical, piscicultural, and ecological importance. Bacteroidetes classification has proved to be difficult, not least when taxonomic decisions rested heavily on interpretation of poorly resolved 16S rRNA gene trees and a limited number of phenotypic features. Here, draft genome sequences of a greatly enlarged collection of genomes of more than 1,000 Bacteroidetes and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa proposed long ago such as Bacteroides, Cytophaga, and Flavobacterium but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which can be considered valuable taxonomic markers. We detected many incongruities when comparing the results of the present study with existing classifications, which appear to be caused by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. The few significant incongruities found between 16S rRNA gene and whole genome trees underline the pitfalls inherent in phylogenies based upon single gene sequences and the impediment in using ordinary bootstrapping in phylogenomic studies, particularly when combined with too narrow gene selections. While a significant degree of phylogenetic conservation was detected in all phenotypic characters investigated, the overall fit to the tree varied considerably, which is one of the probable causes of misclassifications in the past, much like the use of plesiomorphic character states as diagnostic features.
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Affiliation(s)
- Marina García-López
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Jan P. Meier-Kolthoff
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Brian J. Tindall
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Sabine Gronow
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Tanja Woyke
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, United States
| | - Nikos C. Kyrpides
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, United States
| | - Richard L. Hahnke
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Markus Göker
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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4
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Nouioui I, Carro L, García-López M, Meier-Kolthoff JP, Woyke T, Kyrpides NC, Pukall R, Klenk HP, Goodfellow M, Göker M. Genome-Based Taxonomic Classification of the Phylum Actinobacteria. Front Microbiol 2018; 9:2007. [PMID: 30186281 PMCID: PMC6113628 DOI: 10.3389/fmicb.2018.02007] [Citation(s) in RCA: 394] [Impact Index Per Article: 65.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 08/09/2018] [Indexed: 11/29/2022] Open
Abstract
The application of phylogenetic taxonomic procedures led to improvements in the classification of bacteria assigned to the phylum Actinobacteria but even so there remains a need to further clarify relationships within a taxon that encompasses organisms of agricultural, biotechnological, clinical, and ecological importance. Classification of the morphologically diverse bacteria belonging to this large phylum based on a limited number of features has proved to be difficult, not least when taxonomic decisions rested heavily on interpretation of poorly resolved 16S rRNA gene trees. Here, draft genome sequences of a large collection of actinobacterial type strains were used to infer phylogenetic trees from genome-scale data using principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families, and genera, as well as many species and a few subspecies were shown to be in need of revision leading to proposals for the recognition of 2 orders, 10 families, and 17 genera, as well as the transfer of over 100 species to other genera. In addition, emended descriptions are given for many species mainly involving the addition of data on genome size and DNA G+C content, the former can be considered to be a valuable taxonomic marker in actinobacterial systematics. Many of the incongruities detected when the results of the present study were compared with existing classifications had been recognized from 16S rRNA gene trees though whole-genome phylogenies proved to be much better resolved. The few significant incongruities found between 16S/23S rRNA and whole genome trees underline the pitfalls inherent in phylogenies based upon single gene sequences. Similarly good congruence was found between the discontinuous distribution of phenotypic properties and taxa delineated in the phylogenetic trees though diverse non-monophyletic taxa appeared to be based on the use of plesiomorphic character states as diagnostic features.
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Affiliation(s)
- Imen Nouioui
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Lorena Carro
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Marina García-López
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Jan P. Meier-Kolthoff
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Tanja Woyke
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, United States
| | - Nikos C. Kyrpides
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, United States
| | - Rüdiger Pukall
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Hans-Peter Klenk
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Michael Goodfellow
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Markus Göker
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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5
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Montero-Calasanz MDC, Meier-Kolthoff JP, Zhang DF, Yaramis A, Rohde M, Woyke T, Kyrpides NC, Schumann P, Li WJ, Göker M. Genome-Scale Data Call for a Taxonomic Rearrangement of Geodermatophilaceae. Front Microbiol 2017; 8:2501. [PMID: 29312207 PMCID: PMC5742155 DOI: 10.3389/fmicb.2017.02501] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 12/01/2017] [Indexed: 11/13/2022] Open
Abstract
Geodermatophilaceae (order Geodermatophilales, class Actinobacteria) form a comparatively isolated family within the phylum Actinobacteria and harbor many strains adapted to extreme ecological niches and tolerant against reactive oxygen species. Clarifying the evolutionary history of Geodermatophilaceae was so far mainly hampered by the insufficient resolution of the main phylogenetic marker in use, the 16S rRNA gene. In conjunction with the taxonomic characterisation of a motile and aerobic strain, designated YIM M13156T and phylogenetically located within the family, we here carried out a phylogenetic analysis of the genome sequences now available for the type strains of Geodermatophilaceae and re-analyzed the previously assembled phenotypic data. The results indicated that the largest genus, Geodermatophilus, is not monophyletic, hence the arrangement of the genera of Geodermatophilaceae must be reconsidered. Taxonomic markers such as polar lipids and fatty-acids profile, cellular features and temperature ranges are indeed heterogeneous within Geodermatophilus. In contrast to previous studies, we also address which of these features can be interpreted as apomorphies of which taxon, according to the principles of phylogenetic systematics. We thus propose a novel genus, Klenkia, with the type species Klenkia marina sp. nov. and harboring four species formerly assigned to Geodermatophilus, G. brasiliensis, G. soli, G. taihuensis, and G. terrae. Emended descriptions of all species of Geodermatophilaceae are provided for which type-strain genome sequences are publicly available. Our study again demonstrates that the principles of phylogenetic systematics can and should guide the interpretation of both genomic and phenotypic data.
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Affiliation(s)
- Maria del Carmen Montero-Calasanz
- School of Biology, Newcastle University, Newcastle upon Tyne, United Kingdom
- Leibniz Institute, German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Jan P. Meier-Kolthoff
- Leibniz Institute, German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Dao-Feng Zhang
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Adnan Yaramis
- School of Biology, Newcastle University, Newcastle upon Tyne, United Kingdom
- Department of Biotechnology, Middle East Technical University, Ankara, Turkey
| | - Manfred Rohde
- Central Facility for Microscopy, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Tanja Woyke
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, United States
| | - Nikos C. Kyrpides
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, United States
| | - Peter Schumann
- Leibniz Institute, German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Markus Göker
- Leibniz Institute, German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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6
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Hahnke RL, Meier-Kolthoff JP, García-López M, Mukherjee S, Huntemann M, Ivanova NN, Woyke T, Kyrpides NC, Klenk HP, Göker M. Genome-Based Taxonomic Classification of Bacteroidetes. Front Microbiol 2016; 7:2003. [PMID: 28066339 PMCID: PMC5167729 DOI: 10.3389/fmicb.2016.02003] [Citation(s) in RCA: 145] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 11/30/2016] [Indexed: 01/15/2023] Open
Abstract
The bacterial phylum Bacteroidetes, characterized by a distinct gliding motility, occurs in a broad variety of ecosystems, habitats, life styles, and physiologies. Accordingly, taxonomic classification of the phylum, based on a limited number of features, proved difficult and controversial in the past, for example, when decisions were based on unresolved phylogenetic trees of the 16S rRNA gene sequence. Here we use a large collection of type-strain genomes from Bacteroidetes and closely related phyla for assessing their taxonomy based on the principles of phylogenetic classification and trees inferred from genome-scale data. No significant conflict between 16S rRNA gene and whole-genome phylogenetic analysis is found, whereas many but not all of the involved taxa are supported as monophyletic groups, particularly in the genome-scale trees. Phenotypic and phylogenomic features support the separation of Balneolaceae as new phylum Balneolaeota from Rhodothermaeota and of Saprospiraceae as new class Saprospiria from Chitinophagia. Epilithonimonas is nested within the older genus Chryseobacterium and without significant phenotypic differences; thus merging the two genera is proposed. Similarly, Vitellibacter is proposed to be included in Aequorivita. Flexibacter is confirmed as being heterogeneous and dissected, yielding six distinct genera. Hallella seregens is a later heterotypic synonym of Prevotella dentalis. Compared to values directly calculated from genome sequences, the G+C content mentioned in many species descriptions is too imprecise; moreover, corrected G+C content values have a significantly better fit to the phylogeny. Corresponding emendations of species descriptions are provided where necessary. Whereas most observed conflict with the current classification of Bacteroidetes is already visible in 16S rRNA gene trees, as expected whole-genome phylogenies are much better resolved.
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Affiliation(s)
- Richard L. Hahnke
- Department of Microorganisms, Leibniz Institute DSMZ–German Collection of Microorganisms and Cell CulturesBraunschweig, Germany
| | - Jan P. Meier-Kolthoff
- Department of Microorganisms, Leibniz Institute DSMZ–German Collection of Microorganisms and Cell CulturesBraunschweig, Germany
| | - Marina García-López
- Department of Microorganisms, Leibniz Institute DSMZ–German Collection of Microorganisms and Cell CulturesBraunschweig, Germany
| | - Supratim Mukherjee
- Department of Energy Joint Genome Institute (DOE JGI)Walnut Creek, CA, USA
| | - Marcel Huntemann
- Department of Energy Joint Genome Institute (DOE JGI)Walnut Creek, CA, USA
| | - Natalia N. Ivanova
- Department of Energy Joint Genome Institute (DOE JGI)Walnut Creek, CA, USA
| | - Tanja Woyke
- Department of Energy Joint Genome Institute (DOE JGI)Walnut Creek, CA, USA
| | - Nikos C. Kyrpides
- Department of Energy Joint Genome Institute (DOE JGI)Walnut Creek, CA, USA
- Department of Biological Sciences, Faculty of Science, King Abdulaziz UniversityJeddah, Saudi Arabia
| | | | - Markus Göker
- Department of Microorganisms, Leibniz Institute DSMZ–German Collection of Microorganisms and Cell CulturesBraunschweig, Germany
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Salomon M, Dassy B. Partitional Classification: A Complement to Phylogeny. Evol Bioinform Online 2016; 12:149-56. [PMID: 27346943 PMCID: PMC4912232 DOI: 10.4137/ebo.s38288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Revised: 03/21/2016] [Accepted: 03/27/2016] [Indexed: 11/30/2022] Open
Abstract
The tree of life is currently an active object of research, though next to vertical gene transmission non vertical gene transfers proved to play a significant role in the evolutionary process. To overcome this difficulty, trees of life are now constructed from genes hypothesized vital, on the assumption that these are all transmitted vertically. This view has been challenged. As a frame for this discussion, we developed a partitional taxonomical system clustering taxa at a high taxonomical rank. Our analysis (1) selects RNase P RNA sequences of bacterial, archaeal, and eucaryal genera from genetic databases, (2) submits the sequences, aligned, to k-medoid analysis to obtain clusters, (3) establishes the correspondence between clusters and taxa, (4) constructs from the taxa a new type of taxon, the genetic community (GC), and (5) classifies the GCs: Archaea-Eukaryotes contrastingly different from the six others, all bacterial. The GCs would be the broadest frame to carry out the phylogenies.
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Affiliation(s)
- Marc Salomon
- Sorbonne Universités, UPMC Université Paris 06, Faculté de Biologie, Paris, France
| | - Bruno Dassy
- Sorbonne Universités, UPMC Université Paris 06, Faculté de Biologie, Paris, France
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8
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Schierwater B, Holland PWH, Miller DJ, Stadler PF, Wiegmann BM, Wörheide G, Wray GA, DeSalle R. Never Ending Analysis of a Century Old Evolutionary Debate: “Unringing” the Urmetazoon Bell. Front Ecol Evol 2016. [DOI: 10.3389/fevo.2016.00005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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9
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Caetano-Anollés G. Creationism and intelligent design are incompatible with scientific progress: A response to Shanta and Vêdanta. Commun Integr Biol 2016; 9:e1123356. [PMID: 27066185 PMCID: PMC4802803 DOI: 10.1080/19420889.2015.1123356] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 11/17/2015] [Indexed: 10/26/2022] Open
Abstract
In a recent opinion paper, B.K. Shanta claims science leaves no room for the subjective aspect of consciousness, and in doing so, attacks both origin of life and evolutionary research. He claims Vêdanta, one of the 6 orthodox schools of Hindu philosophy, offers an explanation: "the origin of everything material and nonmaterial is sentient and absolute." Here I discuss how the pseudoscience of these creationist views, which are aligned with Intelligent Design, are incompatible with scientific progress and should not be published in scientific journals.
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Affiliation(s)
- Gustavo Caetano-Anollés
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois , Urbana, IL, USA
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10
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Caetano-Anollés D, Caetano-Anollés G. Ribosomal accretion, apriorism and the phylogenetic method: a response to Petrov and Williams. Front Genet 2015; 6:194. [PMID: 26082795 PMCID: PMC4451634 DOI: 10.3389/fgene.2015.00194] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Accepted: 05/14/2015] [Indexed: 12/21/2022] Open
Abstract
Historical (ideographic) and non-historical (nomothetic) studies of ribosomal accretion appear to arrive at diametrically opposite conclusions. Phylogenetic analysis of thousands of RNA molecules and protein structures in hundreds of genomes supports the structural origin of the ribosome in RNA decoding and ribosomal mechanics. Predictions from extant features in a handful of rRNA structural models of the large ribosomal subunit support its origin in protein biosynthesis. In recent correspondence, one of us reported that correcting dismissals of conflicting data and avoiding unwarranted assumptions of the nomothetic method reconciled conclusions. In response, Petrov and Williams dismissed our arguments claiming we did not understand their algorithmic model of ribosomal apical growth. Instead, they controverted the historical approach. Here we show that their objections to the phylogenetic method are unjustified, that their algorithm subjectively guarantees back-in-time molecular deconstructions toward the protein biosynthetic core, and that processes of ribosomal growth are much more complex. We prompt abandoning apriorism, decreasing ad hoc hypotheses and integrating historical and non-historical scientific methods.
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Affiliation(s)
- Derek Caetano-Anollés
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL, USA
| | - Gustavo Caetano-Anollés
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL, USA
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois, Urbana, IL, USA
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11
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Breider S, Scheuner C, Schumann P, Fiebig A, Petersen J, Pradella S, Klenk HP, Brinkhoff T, Göker M. Genome-scale data suggest reclassifications in the Leisingera-Phaeobacter cluster including proposals for Sedimentitalea gen. nov. and Pseudophaeobacter gen. nov. Front Microbiol 2014; 5:416. [PMID: 25157246 PMCID: PMC4127530 DOI: 10.3389/fmicb.2014.00416] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Accepted: 07/22/2014] [Indexed: 11/13/2022] Open
Abstract
Earlier phylogenetic analyses of the marine Rhodobacteraceae (class Alphaproteobacteria) genera Leisingera and Phaeobacter indicated that neither genus might be monophyletic. We here used phylogenetic reconstruction from genome-scale data, MALDI-TOF mass-spectrometry analysis and a re-assessment of the phenotypic data from the literature to settle this matter, aiming at a reclassification of the two genera. Neither Phaeobacter nor Leisingera formed a clade in any of the phylogenetic analyses conducted. Rather, smaller monophyletic assemblages emerged, which were phenotypically more homogeneous, too. We thus propose the reclassification of Leisingera nanhaiensis as the type species of a new genus as Sedimentitalea nanhaiensis gen. nov., comb. nov., the reclassification of Phaeobacter arcticus and Phaeobacter leonis as Pseudophaeobacter arcticus gen. nov., comb. nov. and Pseudophaeobacter leonis comb. nov., and the reclassification of Phaeobacter aquaemixtae, Phaeobacter caeruleus, and Phaeobacter daeponensis as Leisingera aquaemixtae comb. nov., Leisingera caerulea comb. nov., and Leisingera daeponensis comb. nov. The genera Phaeobacter and Leisingera are accordingly emended.
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Affiliation(s)
- Sven Breider
- Department of Biology of Geological Processes - Aquatic Microbial Ecology, Institute for Chemistry and Biology of the Marine Environment (ICBM), University of OldenburgOldenburg, Germany
| | - Carmen Scheuner
- Department of Microorganisms, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell CulturesBraunschweig, Germany
| | - Peter Schumann
- Department of Microorganisms, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell CulturesBraunschweig, Germany
| | - Anne Fiebig
- Department of Microorganisms, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell CulturesBraunschweig, Germany
| | - Jörn Petersen
- Department of Microorganisms, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell CulturesBraunschweig, Germany
| | - Silke Pradella
- Department of Microorganisms, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell CulturesBraunschweig, Germany
| | - Hans-Peter Klenk
- Department of Microorganisms, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell CulturesBraunschweig, Germany
| | - Thorsten Brinkhoff
- Department of Biology of Geological Processes - Aquatic Microbial Ecology, Institute for Chemistry and Biology of the Marine Environment (ICBM), University of OldenburgOldenburg, Germany
| | - Markus Göker
- Department of Microorganisms, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell CulturesBraunschweig, Germany
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12
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Kim KM, Nasir A, Caetano-Anollés G. The importance of using realistic evolutionary models for retrodicting proteomes. Biochimie 2014; 99:129-37. [DOI: 10.1016/j.biochi.2013.11.019] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Accepted: 11/22/2013] [Indexed: 01/16/2023]
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13
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Caetano-Anollés G, Wang M, Caetano-Anollés D. Structural phylogenomics retrodicts the origin of the genetic code and uncovers the evolutionary impact of protein flexibility. PLoS One 2013; 8:e72225. [PMID: 23991065 PMCID: PMC3749098 DOI: 10.1371/journal.pone.0072225] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Accepted: 07/07/2013] [Indexed: 11/18/2022] Open
Abstract
The genetic code shapes the genetic repository. Its origin has puzzled molecular scientists for over half a century and remains a long-standing mystery. Here we show that the origin of the genetic code is tightly coupled to the history of aminoacyl-tRNA synthetase enzymes and their interactions with tRNA. A timeline of evolutionary appearance of protein domain families derived from a structural census in hundreds of genomes reveals the early emergence of the 'operational' RNA code and the late implementation of the standard genetic code. The emergence of codon specificities and amino acid charging involved tight coevolution of aminoacyl-tRNA synthetases and tRNA structures as well as episodes of structural recruitment. Remarkably, amino acid and dipeptide compositions of single-domain proteins appearing before the standard code suggest archaic synthetases with structures homologous to catalytic domains of tyrosyl-tRNA and seryl-tRNA synthetases were capable of peptide bond formation and aminoacylation. Results reveal that genetics arose through coevolutionary interactions between polypeptides and nucleic acid cofactors as an exacting mechanism that favored flexibility and folding of the emergent proteins. These enhancements of phenotypic robustness were likely internalized into the emerging genetic system with the early rise of modern protein structure.
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Affiliation(s)
- Gustavo Caetano-Anollés
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois, Urbana, Illinois, United States of America
- * E-mail:
| | - Minglei Wang
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois, Urbana, Illinois, United States of America
| | - Derek Caetano-Anollés
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois, Urbana, Illinois, United States of America
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Affiliation(s)
- James S Farris
- Göteborgs Botaniska Trädgård, Carl Skottsbergs Gata 22A, SE-413 19, Göteborg, Sweden.,Molekylärsystematiska laboratoriet, Naturhistoriska riksmuseet, Box 50007, SE-104 05, Stockholm, Sweden.,Division of Invertebrate Zoology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, USA
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15
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Pavlinov IY. The contemporary concepts of homology in biology: A theoretical review. ACTA ACUST UNITED AC 2012. [DOI: 10.1134/s2079086412010057] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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16
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Kämpfer P, Glaeser SP. Prokaryotic taxonomy in the sequencing era - the polyphasic approach revisited. Environ Microbiol 2011; 14:291-317. [DOI: 10.1111/j.1462-2920.2011.02615.x] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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17
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Kurt Lienau E, DeSalle R, Allard M, Brown EW, Swofford D, Rosenfeld JA, Sarkar IN, Planet PJ. The mega-matrix tree of life: using genome-scale horizontal gene transfer and sequence evolution data as information about the vertical history of life. Cladistics 2011; 27:417-427. [PMID: 34875790 DOI: 10.1111/j.1096-0031.2010.00337.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Because horizontal gene transfer can confound the recovery of the largely prokaryotic tree of life (ToL), most genome-based techniques seek to eliminate horizontal signal from ToL analyses, commonly by sieving out incongruent genes and data. This approach greatly limits the number of gene families analysed to a subset thought to be representative of vertical evolutionary history. However, formalized tests have not been performed to determine whether combining the massive amounts of information available in fully sequenced genomes can recover a reasonable ToL. Consequently, we used empirically defined gene homology definitions from a previous study that delineate xenologous gene families (gene families derived from a common transfer event) to generate a massively concatenated, combined-data ToL matrix derived from 323 404 translated open reading frames arranged into 12 381 gene homologue groups coded as amino acid data and 63 336, 64 105, 65 153, 66 922 and 67 109 gene homologue groups coded as gene presence/absence data for 166 fully sequenced genomes. This whole-genome gene presence/absence and amino acid sequence ToL data matrix is composed of 4867 184 characters (a combined data-type mega-matrix). Phylogenetic analysis of this mega-matrix yielded a fully resolved ToL that classifies all three commonly accepted domains of life as monophyletic and groups most taxa in traditionally recognized locations with high support. Most importantly, these results corroborate the existence of a common evolutionary history for these taxa present in both data types that is evident only when these data are analysed in combination. © The Willi Hennig Society 2010.
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Affiliation(s)
- E Kurt Lienau
- Sackler Institute for Comparative Genomics, American Museum of Natural History, Central Park West at 79th St, New York, NY 10024, USA.,Department of Biology, Graduate School of Arts and Science, New York University, 100 Washington Square East, New York, NY 10003, USA.,Division of Microbiology, Center for Food Safety and Nutrition, Food and Drug Administration, 5100 Paint Branch Parkway, College Park, MD 20740, USA
| | - Rob DeSalle
- Sackler Institute for Comparative Genomics, American Museum of Natural History, Central Park West at 79th St, New York, NY 10024, USA
| | - Marc Allard
- Division of Microbiology, Center for Food Safety and Nutrition, Food and Drug Administration, 5100 Paint Branch Parkway, College Park, MD 20740, USA
| | - Eric W Brown
- Division of Microbiology, Center for Food Safety and Nutrition, Food and Drug Administration, 5100 Paint Branch Parkway, College Park, MD 20740, USA
| | - David Swofford
- Duke Institute for Genomes and Science Policy, 366 BioSci, Duke University, Durham, NC 27708, USA
| | - Jeffrey A Rosenfeld
- Department of Biology, Graduate School of Arts and Science, New York University, 100 Washington Square East, New York, NY 10003, USA
| | - Indra N Sarkar
- Marine Biological Laboratory, 7 MBL Street, Woods Hole, MA 02543, USA
| | - Paul J Planet
- Sackler Institute for Comparative Genomics, American Museum of Natural History, Central Park West at 79th St, New York, NY 10024, USA.,Department of Pediatrics, Children's Hospital of New York, Columbia University, College of Physicians and Surgeons, New York, NY 10032, USA
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Tao W, Zou M, Wang X, Gan X, Mayden RL, He S. Phylogenomic analysis resolves the formerly intractable adaptive diversification of the endemic clade of east Asian Cyprinidae (Cypriniformes). PLoS One 2010; 5:e13508. [PMID: 20976012 PMCID: PMC2958143 DOI: 10.1371/journal.pone.0013508] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2010] [Accepted: 09/21/2010] [Indexed: 11/19/2022] Open
Abstract
Despite their great diversity and biological importance, evolutionary relationships among the endemic clade of East Asian Cyprinidae remain ambiguous. Understanding the phylogenetic history of this group involves many challenges. For instance, ecomorphological convergence may confound morphology-based phylogenetic inferences, and previous molecular phylogenetic studies based on single genes have often yielded contradictory and poorly supported trees. We assembled a comprehensive data matrix of 100 nuclear gene segments (∼ 71132 base pairs) for representative species of the endemic East Asian cyprinid fauna and recovered a robust phylogeny from this genome-wide signal supported by multiple analytical methods, including maximum parsimony, maximum likelihood and Bayesian inference. Relaxed molecular clock analyses indicated species radiations of this clade concentrated at approximately 1.9–7.6 MYA. We provide evidence that the bursts of diversification in this fauna are directly linked to major paleoenvironmental events associated with monsoon evolution occurring from late Miocene to Pliocene. Ancestral state reconstruction reveals convergent morphological characters are hypothesized to be independent products of similar selective pressures in ecosystems. Our study is the first comprehensive phylogenetic study of the enigmatic East-Asian cyprinids. The explicit molecular phylogeny provides a valuable framework for future research in genome evolution, adaptation and speciation of cyprinids.
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Affiliation(s)
- Wenjing Tao
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, People's Republic of China
- Graduate University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Ming Zou
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, People's Republic of China
- Graduate University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Xuzhen Wang
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, People's Republic of China
- Graduate University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Xiaoni Gan
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, People's Republic of China
- Graduate University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Richard L. Mayden
- Laboratory of Integrated Genomics, Biodiversity, and Conservation, Department of Biology, Saint Louis University, Saint Louis, Missouri, United States of America
| | - Shunping He
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, People's Republic of China
- * E-mail:
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En route to a genome-based classification of Archaea and Bacteria? Syst Appl Microbiol 2010; 33:175-82. [PMID: 20409658 DOI: 10.1016/j.syapm.2010.03.003] [Citation(s) in RCA: 250] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2009] [Revised: 03/10/2010] [Accepted: 03/17/2010] [Indexed: 11/23/2022]
Abstract
Given the considerable promise whole-genome sequencing offers for phylogeny and classification, it is surprising that microbial systematics and genomics have not yet been reconciled. This might be due to the intrinsic difficulties in inferring reasonable phylogenies from genomic sequences, particularly in the light of the significant amount of lateral gene transfer in prokaryotic genomes. However, recent studies indicate that the species tree and the hierarchical classification based on it are still meaningful concepts, and that state-of-the-art phylogenetic inference methods are able to provide reliable estimates of the species tree to the benefit of taxonomy. Conversely, we suspect that the current lack of completely sequenced genomes for many of the major lineages of prokaryotes and for most type strains is a major obstacle in progress towards a genome-based classification of microorganisms. We conclude that phylogeny-driven microbial genome sequencing projects such as the Genomic Encyclopaedia of Archaea and Bacteria (GEBA) project are likely to rectify this situation.
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Alves R, Vilaprinyo E, Sorribas A, Herrero E. Evolution based on domain combinations: the case of glutaredoxins. BMC Evol Biol 2009; 9:66. [PMID: 19321008 PMCID: PMC2679010 DOI: 10.1186/1471-2148-9-66] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2008] [Accepted: 03/25/2009] [Indexed: 11/12/2022] Open
Abstract
Background Protein domains represent the basic units in the evolution of proteins. Domain duplication and shuffling by recombination and fusion, followed by divergence are the most common mechanisms in this process. Such domain fusion and recombination events are predicted to occur only once for a given multidomain architecture. However, other scenarios may be relevant in the evolution of specific proteins, such as convergent evolution of multidomain architectures. With this in mind, we study glutaredoxin (GRX) domains, because these domains of approximately one hundred amino acids are widespread in archaea, bacteria and eukaryotes and participate in fusion proteins. GRXs are responsible for the reduction of protein disulfides or glutathione-protein mixed disulfides and are involved in cellular redox regulation, although their specific roles and targets are often unclear. Results In this work we analyze the distribution and evolution of GRX proteins in archaea, bacteria and eukaryotes. We study over one thousand GRX proteins, each containing at least one GRX domain, from hundreds of different organisms and trace the origin and evolution of the GRX domain within the tree of life. Conclusion Our results suggest that single domain GRX proteins of the CGFS and CPYC classes have, each, evolved through duplication and divergence from one initial gene that was present in the last common ancestor of all organisms. Remarkably, we identify a case of convergent evolution in domain architecture that involves the GRX domain. Two independent recombination events of a TRX domain to a GRX domain are likely to have occurred, which is an exception to the dominant mechanism of domain architecture evolution.
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Affiliation(s)
- Rui Alves
- Departament de Ciències Mèdiques Bàsiques, Universitat de Lleida, IRBLleida, Lleida, Spain.
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