Os fósseis decretam cada vez mais a falência heurística da teoria da evolução de Darwin: alta disparidade morfológica em clades primitivos

Clades reach highest morphological disparity early in their evolution

Martin Hughes, Sylvain Gerber, and Matthew Albion Wills1

Author Affiliations

Edited by Steven M. Stanley, University of Hawaii, Honolulu, HI, and approved May 15, 2013 (received for review February 9, 2013)

Abstract

There are few putative macroevolutionary trends or rules that withstand scrutiny. Here, we test and verify the purported tendency for animal clades to reach their maximum morphological variety relatively early in their evolutionary histories (early high disparity). We present a meta-analysis of 98 metazoan clades radiating throughout the Phanerozoic. The disparity profiles of groups through time are summarized in terms of their center of gravity (CG), with values above and below 0.50 indicating top- and bottom-heaviness, respectively. Clades that terminate at one of the “big five” mass extinction events tend to have truncated trajectories, with a significantly top-heavy CG distribution overall. The remaining 63 clades show the opposite tendency, with a significantly bottom-heavy mean CG (relatively early high disparity). Resampling tests are used to identify groups with a CG significantly above or below 0.50; clades not terminating at a mass extinction are three times more likely to be significantly bottom-heavy than top-heavy. Overall, there is no clear temporal trend in disparity profile shapes from the Cambrian to the Recent, and early high disparity is the predominant pattern throughout the Phanerozoic. Our results do not allow us to distinguish between ecological and developmental explanations for this phenomenon. To the extent that ecology has a role, however, the paucity of bottom-heavy clades radiating in the immediate wake of mass extinctions suggests that early high disparity more probably results from the evolution of key apomorphies at the base of clades rather than from physical drivers or catastrophic ecospace clearing.

macroevolution morphological disparity morphospace clade shape clade center of gravity

Footnotes

1 To whom correspondence should be addressed. E-mail: m.a.wills@bath.ac.uk.

Author contributions: M.A.W. designed research; M.H., S.G., and M.A.W. performed research; M.H. and S.G. contributed new analytic tools; M.H., S.G., and M.A.W. analyzed data; and M.H., S.G., and M.A.W. wrote the paper.

The authors declare no conflict of interest.

This article is a PNAS Direct Submission.

This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1302642110/-/DCSupplemental.

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Professores, pesquisadores e alunos de universidades públicas e privadas com acesso ao site CAPES/Periódicos podem ler gratuitamente este artigo do PNAS e de mais 22.444 publicações científicas.

Palestra sobre algumas dificuldades da teoria da evolução (Síntese Evolutiva Moderna) no contexto de justificação teórica proferida na UFMT 05/06/2013

Diferenças epigenéticas entre chimpanzés e humanos

Journal of Human Genetics (2013) 58, 446–454; doi:10.1038/jhg.2013.55; published online 6 June 2013

Regional DNA methylation differences between humans and chimpanzees are associated with genetic changes, transcriptional divergence and disease genes

Open

Kei Fukuda1, Kenji Ichiyanagi1, Yoichi Yamada2, Yasuhiro Go3, Toshifumi Udono4,5, Seitaro Wada6, Toshiyuki Maeda7, Hidenobu Soejima7, Naruya Saitou8, Takashi Ito9 and Hiroyuki Sasaki1

1Division of Epigenomics and Development, Medical Institute of Bioregulation, and Epigenome Network Research Center, Kyushu University, Fukuoka, Japan

2Faculty of Electrical and Computer Engineering, Institute of Science and Engineering, Kanazawa University, Kanazawa, Japan

3Molecular Biology Section, Department of Cellular and Molecular Biology, Primate Research Institute, Kyoto University, Inuyama, Aichi, Japan

4Sanwa Kagaku Kenkyusho Co., Ltd., Uto, Kumamoto, Japan

5Kumamoto Sanctuary, Wildlife Research Center, Kyoto University, Uto, Kumamoto, Japan

6Kyoto City Zoo, Okazaki Hoshojicho, Sakyo-ku, Kyoto, Japan

7Division of Molecular Genetics and Epigenetics, Department of Biomolecular Sciences, Faculty of Medicine, Saga University, Saga, Japan

8Division of Population Genetics, National Institute of Genetics, Mishima, Japan

9Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, Tokyo, Japan

Correspondence: Dr K Ichiyanagi or Professor H Sasaki, Division of Epigenomics and Development, Medical Institute of Bioregulation, and Epigenome Network Research Center, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan. E-mail: ichiyanagi@bioreg.kyushu-u.ac.jp or hsasaki@bioreg.kyushu-u.ac.jp

Received 13 March 2013; Revised 26 April 2013; Accepted 1 May 2013

Advance online publication 6 June 2013

Abstract

Changes in gene expression have been proposed to have an important role in the evolutionary changes in phenotypes. Interspecific changes in gene expression can result not only from genetic changes in regulatory regions but also from epigenetic changes in such regions. Here we report the identification of genomic regions showing differences in DNA methylation between humans and chimpanzees (termed S-DMRs for species-specific differentially methylated regions) on chromosomes 21 and 22. These regional methylation differences are frequently associated with genes, including those relevant to a disease, such as Alzheimer’s disease, diabetes mellitus or cancer. Methylation differences are often correlated with changes in promoter activity or alternative splicing. Comparative studies including other great ape species provide evidence for the contribution of genetic changes to some of these S-DMRs. Genetic changes responsible for the S-DMRs include gain or loss of CTCF-binding site and changes in CpG density in microsatellite repeats. Our results suggest that DNA methylation changes, often caused by small sequence changes, contribute to transcriptional and phenotypic diversification in hominid evolution.

Keywords: APP; CTCF; Epigenome; MN1; speciation

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Ildeu Moreira apresentou estudo sobre a obra de Alfred Rusell Wallace em conferência da 65a. Reunião Anual da SBPC

JC e-mail 4776, de 25 de Julho de 2013.

12. Estudo sobre obra do naturalista Alfred Wallace é apresentado em conferência na 65ª SBPC

Ildeu Moreira se apresentou em conferência na 65ª Reunião Anual da Sociedade Brasileira para o Progresso da Ciência

Um estudo apresentado na 65ª Reunião Anual da Sociedade Brasileira para o Progresso da Ciência (SBPC) mostrou que a descoberta da origem das espécies e a teoria da evolução não são obras unicamente de Darwin, como muitos pensam, mas há outro nome não tão famoso, mas com legado tão rico quanto o do naturalista britânico. Trata-se de Alfred Russel Wallace.

[Muitos pensam assim porque a Nomenklatura científica adotou uma camisa de força no ensino unilateral da evolução como sendo Darwin o homem que teve a maior ideia que toda a humanidade já teve. Nada mais falso. Nem Darwin nem Wallace são precursores do pensamento evolutivo sobre a origem e evolução das espécies : alguns filósofos gregos pagãos já pensavam assim]

A pesquisa foi realizada pelo doutor em Física e professor do Programa de Pós-Graduação em História da Ciência e das Técnicas em Epistemologia, pela Universidade Federal do Rio de Janeiro (UFRJ), Ildeu Moreira.

Os resultados foram apresentados durante a conferência 'Alfred Wallace: o parceiro de Darwin', no Auditório do Centro de Educação da Universidade Federal de Pernambuco (UFPE), que reuniu amantes da história para uma exposição de ideias abordando a vida desse biólogo que para muitos é desconhecido.

História

Nascido em uma família pobre, de nove irmãos, em 8 de janeiro de 1823, Alfred Wallace foi aprendiz de carpinteiro e aos 14 anos visitou uma casa da ciência inglesa. A partir daí, passou a se dedicar aos estudos científicos e, em paralelo, também dedicou sua vida aos avanços políticos da Inglaterra, por ser crítico do imperialismo inglês.

Darwin nasceu na aristocracia e estudou em Cambridge, já Alfred não chegou nem a ter formação de nível médio, porém, era um biólogo autodidata e hoje é considerado o pai da biogeografia. Ambos vieram ao Brasil para pesquisas e construíram suas teorias independentemente.

[Vide As contribuições de Alfred Rusell Wallace para a biogeografia, de Viviane Arruda do Carmo, Lilian Al-Chueyr Pereira Martins e Nélio Vincenzo Bizzo] 

Wallace viveu por quatro anos na Amazônia fazendo excursões naturalistas para conhecer e buscar resultados definitivos. Ele queria entender o fenômeno da origem das espécies. O plano era fazer uma coleção de objetos duplicados, um ia para o seu laboratório na Grã-Bretanha e outro pertencia a sua coleção particular.

Em sua excursão, chegou a ficar 14 meses em Belém e mais oito meses somente explorando o Rio Negro, para depois ir a outras localidades, mas todos os rascunhos, mapas, catalogações e desenhos foram perdidos, pois o navio no qual Alfred voltava para Inglaterra afundou uma semana depois da partida, por isso alguns dos seus livros foram escritos somente com as lembranças do que havia vivido, ao contrário das anotações de Darwin, em Galápagos, que o ajudaram a construir um livro mais denso.

Alfred explorou a fronteira geográfica e a distribuição de animais, entre as plantas, a palmeira era sua preferida. Foi ele quem descobriu a primeira palmeira piaçava. No Amazonas, chegou a recolher 14 mil espécies entre plantas e insetos. Ele também foi um dos precursores no estudo de insetos como alimentos.

Após chegar à Inglaterra fez mais uma viagem como naturalista, desta vez para a Indonésia, onde ficou por nove anos. Lá, descobriu aproximadamente 123 mil espécies de animais diferentes, um deles o macaco orangotango.

Muito ousado, colocou suas ideias no papel e escreveu uma carta acumulando fatos estudados e mandou para Darwin mostrando suas conclusões.

Até então, não havia nada publicado oficialmente, foi quando Darwin pegou parte da carta recebida, os textos manuscritos de 1842 o qual já estava esboçando e, junto com alguns amigos, fez uma apresentação conjunta na Sociedade Lineana de uma síntese da origem das espécies, que foi lançada em 1859.

[Darwin era extremamente cuidadoso com a sua correspondência. Estranho que a correspondência mantida com Wallace neste período sumiu. Muito mais estranho a ação de Charles Lyell e Joseph Hooker na apresentação conjunta dos trabalhos dos dois naturalistas. Tudo isso para manter a originalidade da ideia a favor de Darwin. Essa lacuna na correspondência pesa sobre Darwin como plagiador das ideias de Wallace: The Darwin Conspiracy, de Roy Davies.

Ao saber [Ildeu passou a ideia de que Wallace sabia da iniciativa de Lyell e Hooker, mas ele estava na Malásia e só ficou sabendo disso quase um ano depois!!!], Alfred ficou satisfeito por ter assinado a publicação com Darwin e, posteriormente, escreveu um livro no qual publicou a teoria novamente, mas dessa vez a batizando com o nome de 'darwinismo'. Os dois permaneceram amigos a vida toda e divergiram apenas intelectualmente já que Alfred acreditava que a teoria da seleção natural não era suficiente para explicar a cultura humana.

[Cultura humana ou evolução da mente humana???]

Sua autobiografia, escrita em 1905, não possui publicação em português, mas o livro 'A viagem ao Rio Negro' pode ser encontrado disponível na internet.

Questionado sobre o que o motivou a pesquisar sobre a vida de Alfred Wallace, o professor Ildeu Moreira disse acreditar que a ideia veio de sua curiosidade pessoal sobre a história do biólogo. "Sempre gostei de livros de história e, após ler o livro dele sobre a viagem ao Rio Negro, há uns 30 anos, eu fiquei fascinado pela descrição dele. Outro motivo é por ele ser um personagem muito importante e interessante da história da ciência. Isso mostra que as classes sociais perpassam a ciência - o idealismo do Wallace do ponto de vista político, o sonho da ciência, da igualdade, da cooperação - nós não podemos perder" disse.

(Laize Minelli, Agência CT&I Amazonas)

http://www.fapeam.am.gov.br/noticia.php?not=9087

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Leitura recomendada por este blogger: Alfred Rusell Wallace: a rediscovered life, de Michael Flannery.

Andreas Wagner 'falou e disse': a evolução é um fato, mas nós cientistas não sabemos como isso ocorre!!!

"...nós sabemos muito sobre como as inovações evolucionárias se espalham pelas populações, mas nós sabemos muito pouco sobre como elas se originam."

"...we know a lot about how evolutionary innovations spread through populations, but we know very little about how they originate."

Source/Fonte: The Scientist

Novo artigo da Nature desafia os limites convencionais entre os reinos de vida

Novo artigo da Nature desafia os limites convencionais entre os reinos de vida

15 Julho 2013 Postado por News sob Intelligent Design, News, speciation

University of California - Berkeley

De um artigo publicado online ontem na Nature,

“A pesquisa revela que algumas fronteiras convencionais entre os reinos de vida não são tão rígidas como tinham sido pensadas. Por exemplo, os pesquisadores sugerem que uma linhagem bacteriana sintetiza bases de purina — blocos construtores de DNA e RNA — usando enzimas previamente consideradas como existindo somente em arqueas. Entretanto, três das células de arqueas sequenciadas na pesquisa abrigam fatores sigma, que iniciam a transcrição de RNA e tinham sido encontradas anteriormente somente em bactérias.” 

“The work reveals that some conventional boundaries between the kingdoms of life are not as rigid as has been thought. For instance, the researchers suggest that one bacterial lineage synthesizes purine bases — building blocks of DNA and RNA — using enzymes previously thought to exist only in archaea. Meanwhile, three of the archaeal cells sequenced in the study harbour sigma factors, which initiate RNA transcription and have previously been found only in bacteria.”

E outra nova solução foi descoberta:

“Os pesquisadores também encontraram uma bacteria que tem ‘recodificado’ as séries de bases UGA de três letras — conhecida como códon de parada opala. Em quase todo outro organismo, esta sequência de nucleotídeo sinaliza para a célula parar de traduzir RNA em proteína. Mas neste organismo, ela diz para célula fazer aminoácido glicina. A equipe propôs colocá-la em novo filo bacteriano chamado de Gracilibacteria.”

“The researchers also found a bacterium that has ‘recoded’ the three-letter series of bases UGA — known as the opal stop codon. In almost every other organism, this nucleotide sequence signals the cell to stop translating RNA into protein. But in this organism, it tells the cell to make the amino acid glycine. The team propose to place it into a new bacterial phylum, called Gracilibacteria.”

SOURCE/FONTE

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Insights into the phylogeny and coding potential of microbial dark matter

Christian Rinke, Patrick Schwientek, Alexander Sczyrba, Natalia N. Ivanova, Iain J. Anderson, Jan-Fang Cheng, Aaron Darling, Stephanie Malfatti, Brandon K. Swan, Esther A. Gies, Jeremy A. Dodsworth, Brian P. Hedlund, George Tsiamis, Stefan M. Sievert, Wen-Tso Liu, Jonathan A. Eisen, Steven J. Hallam, Nikos C. Kyrpides, RamunasStepanauskas, Edward M. Rubin, Philip Hugenholtz & Tanja Woyke

Affiliations Contributions Corresponding authors

Nature (2013) doi:10.1038/nature12352

Abstract

Genome sequencing enhances our understanding of the biological world by providing blueprints for the evolutionary and functional diversity that shapes the biosphere. However, microbial genomes that are currently available are of limited phylogenetic breadth, owing to our historical inability to cultivate most microorganisms in the laboratory. We apply single-cell genomics to target and sequence 201 uncultivated archaeal and bacterial cells from nine diverse habitats belonging to 29 major mostly uncharted branches of the tree of life, so-called ‘microbial dark matter’. With this additional genomic information, we are able to resolve many intra- and inter-phylum-level relationships and to propose two new superphyla. We uncover unexpected metabolic features that extend our understanding of biology and challenge established boundaries between the three domains of life. These include a novel amino acid use for the opal stop codon, an archaeal-type purine synthesis in Bacteria and complete sigma factors in Archaea similar to those in Bacteria. The single-cell genomes also served to phylogenetically anchor up to 20% of metagenomic reads in some habitats, facilitating organism-level interpretation of ecosystem function. This study greatly expands the genomic representation of the tree of lie and provides a systematic step towards a better understanding of biological evolution on our planet.

Received 14 January 2013 Accepted 04 June 2013 Published online 14 July 2013

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NOTA DESTE BLOGGER:

A Árvore da Vida é uma miragem imposta sobre a ciência para fortalecer posicionamentos filosóficos naturalistas/materialistas. A cada dia que passa a hipótese de ancestralidade comum universal recebe uma pá de cal pelas evidências encontradas no contexto de justificação teórica.

Pela leitura do artigo, depreende-se:

1. A ancestralidade comum com diversificação ao longo do tempo é uma ilusão de ótica epistêmica.

2. O tal de DNA “lixo” é outra ilusão de ótica epistêmica.

3. Os processos gradualistas darwinistas se revelam totalmente incapazes de terem produzido toda essa complexidade e diversidade de formas biológicas.

4. Tem cheiro de Design Inteligente na parada.

Pano rápido - DARWIN KAPUT!!!

Queria ver a cara de alguns cientistas da Nomenklatura científica e da Galera dos meninos e meninas de Darwin - cada vez mais sem pai nem mãe no contexto de justificação teórica!!!

Dan Graur 'falou e disse': se o ENCODE estiver certo, então a EVOLUÇÃO está errada!

Source/Fonte

NOTA DESTE BLOGGER:

O Projeto ENCODE enterrou de vez a hipótese de que o DNA "lixo" era lixo, ao demonstrar que 80% do genoma é funcional. O que isso significa para a especulação transformista de Darwin? Dan Graur disse tudo no slide 5 de sua palestra na Society for Molecular Biology and Evolution em Chicago:

"Se o ENCODE estiver certo, então a EVOLUÇÃO está errada!"

Entende agora o desespero da Nomenklatura científica e da Galera dos meninos e meninas de Darwin com as consequências de o DNA "lixo" ser funcional e não meramento lixo da história evolucionária???

Design Inteligente em ação diante de nossos olhos, oops em nossos olhos...

Switchable telescopic contact lens

Eric. J. Tremblay, Igor Stamenov, R. Dirk Beer, Ashkan Arianpour, and Joseph E. Ford

Optics Express, Vol. 21, Issue 13, pp. 15980-15986 (2013)

Abstract

We present design and first demonstration of optics for a telescopic contact lens with independent optical paths for switching between normal and magnified vision. The magnified optical path incorporates a telescopic arrangement of positive and negative annular concentric reflectors to achieve 2.8x magnification on the eye, while light passing through a central clear aperture provides unmagnified vision. We present an experimental demonstration of the contact lens mounted on a life-sized optomechanical model eye and, using a pair of modified commercial 3D television glasses, demonstrate electrically operated polarization switching between normal and magnified vision.

© 2013 OSA

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NOTA DO BLOGGER

Darwin sentia calafrios só de pensar como teria sido a história evolutiva da visão. Simples assim, Darwin - DESIGN INTELIGENTE!!!

Colocando os cientistas no seu devido lugar em política!!!

Point of view: Making science count in government

Ian Boyd

Department of Environment, Food and Rural Affairs, United Kingdom

DOI: http://dx.doi.org/10.7554/eLife.01061

Published July 2, 2013

Cite as eLife 2013;2:e01061

Abstract

Science is an essential component of policy-making in most areas of government, but the scientific community does not always understand its role in this process.

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EXCERPT:

"This highlights a further issue of confusion often prevalent among scientists and that politicians often perpetuate when challenged--the belief that all decisions need to be evidence-based. My experience is that most policy decisions are informed to greater or lesser degrees by evidence but rarely is it practical or even desirable to base decisions entirely upon scientific evidence. THE WORLD DOES NOT STOP AT THE POINT WHERE SCIENTIFIC CERTAINTY ENDS, and those implementing policy usually have no choice but to continue making decisions and implementing actions when there is scientific uncertainty.

This perhaps represents the greatest disparity between the aspirations of scientists and the reality faced by policy-makers. Moreover, the clarion call from scientists 'we need to do more research' is guaranteed to boil the blood of some policy-makers, especially when past investment in science has, if anything, added to the level of apparent scientific uncertainty. THE INTEGRITY OF SCIENCE STARTS TO BE UNDERMINED WHEN SCIENTISTS THEMSELVES SUGGEST THAT THE GREY AREA OF UNCERTAINTY SHOULD BE OCCUPIED BY THEM ALONE rather than being shared with those implementing policy. This has happened in many of the most controversial areas in my portfolio including bovine TB, pesticides and marine management."  

Tentando salvar a lavoura de Darwin: Transferência lateral de genes, rearranjo e reconciliação

Lateral Gene Transfer, Rearrangement and Reconciliation

Murray Patterson, Gergely J Szöllősi, Vincent Daubin, Eric Tannier

(Submitted on 27 Jun 2013)

Background. 

Models of ancestral gene order reconstruction have progressively integrated different evolutionary patterns and processes such as unequal gene content, gene duplications, and implicitly sequence evolution via reconciled gene trees. In unicellular organisms, these models have so far ignored lateral gene transfer, even though it can have an important confounding effect on such models, as well as a rich source of information on the function of genes through the detection of transfers of entire clusters of genes. 

Result. 

We report an algorithm together with its implementation, DeCoLT, that reconstructs ancestral genome organization based on reconciled gene trees which summarize information on sequence evolution, gene origination, duplication, loss, and lateral transfer. DeCoLT finds in polynomial time the minimum number of rearrangements, computed as the number of gains and breakages of adjacencies between pairs of genes. We apply DeCoLT to 1099 gene families from 36 cyanobacteria genomes. 

Conclusion. 

DeCoLT is able to reconstruct adjacencies in 35 ancestral bacterial genomes with a thousand genes families in a few hours, and detects clusters of co-transferred genes. As there is no constraint on genome organization, adjacencies can be generalized to any relationship between genes to reconstruct ancestral interactions, functions or complexes with the same framework.

Comments: submitted for RECOMB CG 2013

Subjects: Populations and Evolution (q-bio.PE); Genomics (q-bio.GN)

Cite as: arXiv:1306.6656 [q-bio.PE]

(or arXiv:1306.6656v1 [q-bio.PE] for this version)

Submission history

From: Gergely J Szöllősi [view email] 

[v1] Thu, 27 Jun 2013 20:38:34 GMT (123kb,D)

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Um grande dilúvio em Marte. Na Terra... nem pensar, Juvenal!!!

Fill and spill of giant lakes in the eastern Valles Marineris region of Mars

Nicholas H. Warner1,*, Mariam Sowe2, Sanjeev Gupta1, Alexander Dumke2 and Kate Goddard1

- Author Affiliations

1Department of Earth Science and Engineering, Imperial College London, South Kensington Campus, London SW7 2AZ, UK

2Institute of Geological Sciences, Planetary Sciences and Remote Sensing, Freie Universitaet Berlin, Malteserstrasse 74-100, D-12249 Berlin, Germany

↵*Current address: Jet Propulsion Laboratory, 4800 Oak Grove Drive, Pasadena, California 91109, USA; E-mail: Nicholas.H.Warner@jpl.nasa.gov.

Abstract

The existence of Hesperian age (3.7–3.4 Ga) surface water bodies on Mars is a contentious issue, often conflicting with favored climate models. Extensive lakes are proposed to have filled parts of Valles Marineris during this period, yet evidence for their presence and temporal continuity is poorly constrained. Here we report geomorphic and chronologic evidence for the initiation and demise of a voluminous lake system within the basins of eastern Valles Marineris. We find that independent, kilometer-deep lakes were present here well after the wetter, global climate optimum that characterized the previous Noachian epoch (4.1–3.7 Ga). Relative and impact crater chronologies of flood channels emerging from lake basins indicate relatively late lake spillover in the Early Amazonian (ca. 3.0 Ga). Drawdown of the lake and cessation of interbasin sedimentation may be recorded by a similar Early Amazonian (ca. 3.1 Ga) crater retention age on the surface of Capri Mensa, a 4-km-tall, sulfate-bearing interior layered deposit. The topography data demonstrate that incision of the bedrock barriers between the basins during spillover was driven by a dramatic local base-level difference between the lake surface and downstream basin floors. We postulate that the lake spillover process created an integrated drainage routing system between a voluminous equatorial water supply and the northern plains basin.

Received 25 October 2012.

Revision received 14 January 2013.

Accepted 17 January 2013.

© 2013 Geological Society of America

As bactérias detonaram a robustez heurística da teoria da evolução: mudança paradigmática JÁ!!!

Animals in a bacterial world, a new imperative for the life sciences

Margaret McFall-Ngaia,1, Michael G. Hadfieldb,1, Thomas C. G. Boschc, Hannah V. Careyd, Tomislav Domazet-Lošoe, Angela E. Douglasf, Nicole Dubilierg, Gerard Eberlh, Tadashi Fukamii, Scott F. Gilbertj, Ute Hentschelk, Nicole Kingl, Staffan Kjellebergm, Andrew H. Knolln, Natacha Kremera, Sarkis K. Mazmaniano, Jessica L. Metcalfp, Kenneth Nealsonq, Naomi E. Piercer, John F. Rawlss, Ann Reidt, Edward G. Rubya, Mary Rumphou, Jon G. Sandersr, Diethard Tautzv, and Jennifer J. Wernegreenw

Author Affiliations

Edited by David M. Karl, University of Hawaii, Honolulu, HI, and approved January 17, 2013 (received for review December 2, 2012)

Abstract

In the last two decades, the widespread application of genetic and genomic approaches has revealed a bacterial world astonishing in its ubiquity and diversity. This review examines how a growing knowledge of the vast range of animal–bacterial interactions, whether in shared ecosystems or intimate symbioses, is fundamentally altering our understanding of animal biology. Specifically, we highlight recent technological and intellectual advances that have changed our thinking about five questions: how have bacteria facilitated the origin and evolution of animals; how do animals and bacteria affect each other’s genomes; how does normal animal development depend on bacterial partners; how is homeostasis maintained between animals and their symbionts; and how can ecological approaches deepen our understanding of the multiple levels of animal–bacterial interaction. As answers to these fundamental questions emerge, all biologists will be challenged to broaden their appreciation of these interactions and to include investigations of the relationships between and among bacteria and their animal partners as we seek a better understanding of the natural world.

Key words

bacterial roles animal origins reciprocal effects animal–bacterial genomics bacteria-driven development microbiome and host physiology nested ecosystems

Footnotes

1To whom correspondence may be addressed. E-mail: mjmcfallngai@wisc.edu or hadfield@hawaii.edu.

Author contributions: M.M.-N., M.G.H., T.C.G.B., H.V.C., T.D.-L., A.E.D., N.D., G.E., T.F., S.F.G., U.H., N. King, S.K., A.H.K., N. Kremer, S.K.M., J.L.M., K.N., N.E.P., J.F.R., A.R., E.G.R., M.R., J.G.S., D.T., and J.J.W. wrote the paper.

The authors declare no conflict of interest.

This article is a PNAS Direct Submission.

This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1218525110/-/DCSupplemental.

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O mundo antigo dos vírus e a evolução das células

The ancient Virus World and evolution of cells

Eugene V Koonin1*, Tatiana G Senkevich2 and Valerian V Dolja3

* Corresponding author: Eugene V Koonin koonin@ncbi.nlm.nih.gov

Author Affiliations

1 National Center for Biotechnology Information, National Library of Medicine, USA

2 Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20894, USA

3 Department of Botany and Plant Pathology and Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR 97331, USA

For all author emails, please log on.

Biology Direct 2006, 1:29 doi:10.1186/1745-6150-1-29

Received: 11 September 2006

Accepted: 19 September 2006

Published: 19 September 2006

© 2006 Koonin et al; licensee BioMed Central Ltd. 

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

Background

Recent advances in genomics of viruses and cellular life forms have greatly stimulated interest in the origins and evolution of viruses and, for the first time, offer an opportunity for a data-driven exploration of the deepest roots of viruses. Here we briefly review the current views of virus evolution and propose a new, coherent scenario that appears to be best compatible with comparative-genomic data and is naturally linked to models of cellular evolution that, from independent considerations, seem to be the most parsimonious among the existing ones.

Results

Several genes coding for key proteins involved in viral replication and morphogenesis as well as the major capsid protein of icosahedral virions are shared by many groups of RNA and DNA viruses but are missing in cellular life forms. On the basis of this key observation and the data on extensive genetic exchange between diverse viruses, we propose the concept of the ancient virus world. The virus world is construed as a distinct contingent of viral genes that continuously retained its identity throughout the entire history of life. Under this concept, the principal lineages of viruses and related selfish agents emerged from the primordial pool of primitive genetic elements, the ancestors of both cellular and viral genes. Thus, notwithstanding the numerous gene exchanges and acquisitions attributed to later stages of evolution, most, if not all, modern viruses and other selfish agents are inferred to descend from elements that belonged to the primordial genetic pool. In this pool, RNA viruses would evolve first, followed by retroid elements, and DNA viruses. The Virus World concept is predicated on a model of early evolution whereby emergence of substantial genetic diversity antedates the advent of full-fledged cells, allowing for extensive gene mixing at this early stage of evolution. We outline a scenario of the origin of the main classes of viruses in conjunction with a specific model of precellular evolution under which the primordial gene pool dwelled in a network of inorganic compartments. Somewhat paradoxically, under this scenario, we surmise that selfish genetic elements ancestral to viruses evolved prior to typical cells, to become intracellular parasites once bacteria and archaea arrived at the scene. Selection against excessively aggressive parasites that would kill off the host ensembles of genetic elements would lead to early evolution of temperate virus-like agents and primitive defense mechanisms, possibly, based on the RNA interference principle. The emergence of the eukaryotic cell is construed as the second melting pot of virus evolution from which the major groups of eukaryotic viruses originated as a result of extensive recombination of genes from various bacteriophages, archaeal viruses, plasmids, and the evolving eukaryotic genomes. Again, this vision is predicated on a specific model of the emergence of eukaryotic cell under which archaeo-bacterial symbiosis was the starting point of eukaryogenesis, a scenario that appears to be best compatible with the data.

Conclusion

The existence of several genes that are central to virus replication and structure, are shared by a broad variety of viruses but are missing from cellular genomes (virus hallmark genes) suggests the model of an ancient virus world, a flow of virus-specific genes that went uninterrupted from the precellular stage of life's evolution to this day. This concept is tightly linked to two key conjectures on evolution of cells: existence of a complex, precellular, compartmentalized but extensively mixing and recombining pool of genes, and origin of the eukaryotic cell by archaeo-bacterial fusion. The virus world concept and these models of major transitions in the evolution of cells provide complementary pieces of an emerging coherent picture of life's history.

Reviewers

W. Ford Doolittle, J. Peter Gogarten, and Arcady Mushegian.

Open peer review

This article was reviewed by W. Ford Doolittle, J. Peter Gogarten, and Arcady Mushegian.

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