Padrões evolutivos de montagem de genomas procarióticos

Evolutionary assembly patterns of prokaryotic genomes

Maximilian Press, Christine Queitsch, Elhanan Borenstein

doi: http://dx.doi.org/10.1101/027649

Source/Fonte

Abstract

Evolutionary innovation must occur in the context of some genomic background, which limits available evolutionary paths. For example, protein evolution by sequence substitution is constrained by epistasis between residues. In prokaryotes, evolutionary innovation frequently happens by macrogenomic events such as horizontal gene transfer (HGT). Previous work has suggested that HGT can be influenced by ancestral genomic content, yet the extent of such gene-level constraints has not yet been systematically characterized. Here, we evaluated the evolutionary impact of such constraints in prokaryotes, using probabilistic ancestral reconstructions from 634 extant prokaryotic genomes and a novel framework for detecting evolutionary constraints on HGT events. We identified 8,228 directional dependencies between genes, and demonstrated that many such dependencies reflect known functional relationships, including, for example, evolutionary dependencies of the photosynthetic enzyme RuBisCO. Modeling all dependencies as a network, we adapted an approach from graph theory to establish chronological precedence in the acquisition of different genomic functions. Specifically, we demonstrated that specific functions tend to be gained sequentially, suggesting that evolution in prokaryotes is governed by functional assembly patterns. Finally, we showed that these dependencies are universal rather than clade-specific and are often sufficient for predicting whether or not a given ancestral genome will acquire specific genes. Combined, our results indicate that evolutionary innovation via HGT is profoundly constrained by epistasis and historical contingency, similar to the evolution of proteins and phenotypic characters, and suggest that the emergence of specific metabolic and pathological phenotypes in prokaryotes can be predictable from current genomes.

Copyright 

The copyright holder for this preprint is the author/funder. It is made available under a CC-BY-NC 4.0 International license.

FREE PDF GRATIS: bioRxiv

Evidência química, experimental e morfológica de melanina diageneticamente alterada em fósseis excepcionalmente preservados

Chemical, experimental, and morphological evidence for diagenetically altered melanin in exceptionally preserved fossils

Caitlin Colleary a,b, Andrei Dolocan c, James Gardner d, Suresh Singh a, Michael Wuttke  e, Renate Rabenstein f, Jörg Habersetzer f, Stephan Schaal f, Mulugeta Feseha g, Matthew Clemens h, Bonnie F. Jacobs h, Ellen D. Currano i, Louis L. Jacobs h, Rene Lyng Sylvestersen j, Sarah E. Gabbott k, and Jakob Vinther a,d,l,1

aSchool of Earth Sciences, University of Bristol, Bristol BS8 1RJ, United Kingdom;

bDepartment of Geosciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24060;

cTexas Materials Institute, University of Texas at Austin, Austin, TX 78712;

dJackson School of Geosciences, University of Texas at Austin, Austin, TX 78712;

eDepartment for the Conservation of the Cultural Heritage of Rhineland-Palatinate, 55116 Mainz, Germany;

fDepartment of Palaeoanthropology and Messel Research, Senckenberg Research Institute, 60325 Frankfurt am Main, Germany;

gPaleoanthropology and Paleoenvironment Program, School of Earth Sciences, College of Natural Sciences, Addis Ababa University, Addis Ababa, Ethiopia;

hRoy M. Huffington Department of Earth Sciences, Southern Methodist University, Dallas, TX 75275;

iDepartments of Botany and Geology & Geophysics, University of Wyoming, Laramie, WY 82071;

jDivision of Natural History, Muse®um, 7800 Skive, Denmark;

kDepartment of Geology, University of Leicester, Leicester LE1 7RH, United Kingdom;

lSchool of Biological Sciences, University of Bristol, Bristol BS8 1TQ, United Kingdom

Edited by Donald E. Canfield, Institute of Biology and Nordic Center for Earth Evolution, University of Southern Denmark, Odense M., Denmark, and approved August 26, 2015 (received for review May 19, 2015)

Significance

Melanin is a widespread pigment that provides black to reddish brown hues to organisms. Recent evidence has shown that melanin is retained in exceptionally preserved fossils, including feathered dinosaurs, allowing the reconstruction of ancient color patterns. However, little is known about the chemical preservation of melanin or its distribution in the fossil record. Here, we show that melanin is preserved in a number of soft-bodied fossils, but its burial under high pressure and temperature for millions of years alters its original chemistry. The widespread occurrence of melanin substantiates the applicability of reconstructing aspects of original color patterns and allows us to dismiss the alternative suggestion that these structures are microbial in origin.

Abstract

In living organisms, color patterns, behavior, and ecology are closely linked. Thus, detection of fossil pigments may permit inferences about important aspects of ancient animal ecology and evolution. Melanin-bearing melanosomes were suggested to preserve as organic residues in exceptionally preserved fossils, retaining distinct morphology that is associated with aspects of original color patterns. Nevertheless, these oblong and spherical structures have also been identified as fossilized bacteria. To date, chemical studies have not directly considered the effects of diagenesis on melanin preservation, and how this may influence its identification. Here we use time-of-flight secondary ion mass spectrometry to identify and chemically characterize melanin in a diverse sample of previously unstudied extant and fossil taxa, including fossils with notably different diagenetic histories and geologic ages. We document signatures consistent with melanin preservation in fossils ranging from feathers, to mammals, to amphibians. Using principal component analyses, we characterize putative mixtures of eumelanin and phaeomelanin in both fossil and extant samples. Surprisingly, both extant and fossil amphibians generally exhibit melanosomes with a mixed eumelanin/phaeomelanin composition rather than pure eumelanin, as assumed previously. We argue that experimental maturation of modern melanin samples replicates diagenetic chemical alteration of melanin observed in fossils. This refutes the hypothesis that such fossil microbodies could be bacteria, and demonstrates that melanin is widely responsible for the organic soft tissue outlines in vertebrates found at exceptional fossil localities, thus allowing for the reconstruction of certain aspects of original pigment patterns.

paleocolor melanosome mass spectrometry diagenesis pigmentation

Footnotes

1To whom correspondence should be addressed. Email: jakob.vinther{at}bristol.ac.uk.

Author contributions: J.V. designed research; C.C., A.D., and J.V. performed research; A.D., J.G., M.W., R.R., J.H., S. Schaal, M.F., M.C., B.F.J., E.D.C., L.L.J., R.L.S., and S.E.G. contributed new reagents/analytic tools; C.C., A.D., S. Singh, and J.V. analyzed data; and C.C., A.D., and J.V. 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.1509831112/-/DCSupplemental.

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Professores, pesquisadores e alunos de universidades públicas e privadas com acesso ao Portal de Periódicos CAPES/MEC podem ler gratuitamente este artigo do PNAS e mais 30.000 publicações científicas.

Evolução de Sísifo nos tentilhões de Darwin

Sisyphean evolution in Darwin's finches

Bailey D. McKay1,* andRobert M. Zink2,3

Article first published online: 8 JUL 2014

DOI: 10.1111/brv.12127

Biological Reviews Volume 90, Issue 3, pages 689–698, August 2015

Keywords: adaptation; Darwin's finches; Darwin's ground finches; Geospiza; Sisyphean evolution; speciation

ABSTRACT

The trajectory of speciation involves geographic isolation of ancestral populations followed by divergence by natural selection, genetic drift or sexual selection. Once started, the process may experience fits and starts, as sometimes diverging populations intermittently reconnect. In theory populations might cycle between stages of differentiation and never attain species status, a process we refer to as Sisyphean evolution. We argue that the six putative ground finch species (genus Geospiza) of the Galápagos Islands represent a dramatic example of Sisyphean evolution that has been confused with the standard model of speciation. The dynamic environment of the Galápagos, closely spaced islands, and frequent dispersal and introgression have prevented the completion of the speciation process. We suggest that morphological clusters represent locally adapted ecomorphs, which might mimic, and have been confused with, species, but these ecomorphs do not form separate gene pools and are ephemeral in space and time. Thus the pattern of morphological, behavioural and genetic variation supports recognition of a single species of Geospiza, which we suggest should be recognized as Darwin's ground finch (Geospiza magnirostris). We argue that instead of providing an icon of insular speciation and adaptive radiation, which is featured in nearly every textbook on evolutionary biology, Darwin's ground finch represents a potentially more interesting phenomenon, one of transient morphs trapped in an unpredictable cycle of Sisyphean evolution. Instead of revealing details of the origin of species, the mechanisms underlying the transient occurrence of ecomorphs provide one of the best illustrations of the antagonistic effects of natural selection and introgression.

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Mais um ícone do fato, Fato, FATO da evolução indo para a lata do lixo da História da Ciência? Alô MEC, hora de revisar a abordagem da evolução nos livros didáticos do ensino médio.

A engenharia do DNA para o armazenamento de informação digital a longo prazo: mero acaso, fortuita necessidade ou design inteligente?

The engineering of DNA for the long-term storage of digital information

Abstract

The long term preservation of the vast amounts of information our modern world creates is an emerging problem. As (bio)chemical engineers we see DNA as a possibility of preserving large amounts of information: about 750 megabytes of genetic information are stored in every cell of our body and theoretically one gram of DNA could store > 300'000 terabytes of information.[1] Furthermore, it is known from archeology studies that if well preserved, DNA can endure for several hundred thousand years.[2]

Within this presentation we will show how we can use modern chemical and information engineering tools for the safeguarding of actual digital information in the form of DNA. For this we have combined the information theory concept of forward error correction with the chemical tool of DNA encapsulation.[3,4] In a first experimental validation of the idea 83kB of digital information were encoded by a Reed-Solomon error correction code and translated to DNA sequences (4991 sequences each 117bp long). The DNA sequences were synthesized by a microarray technology and encapsulated into a silica matrix. This encapsulation resulted in very low DNA degradation rates, which were measured by accelerated aging experiments in various atmospheres. Following a simulated 2'000 year room temperature storage of the DNA the digital information could be recovered without error by the aid of the error correction capabilities introduced during the coding. Aside of giving an insight into the state of the art of information preservation in DNA we will also discuss future challenges and needs of digital data preservation in the form of chemical information.

[1] Church et al. Science 2012, 337, 6102. 

[2] Meyer et al. Nature 2014, 505, 403. 

[3] Paunescu et al. Nat. Protoc. 2013, 8, 2440. 

[4] Grass et al. Angew. Chem. Int. Ed. 2015, 54, 2552.

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This research was presented at the 250th National Meeting & Exposition of the American Chemical Society (ACS) on Aug. 17, 2015.

Esta pesquisa foi apresentada na 250o. Encontro e Exposição Naacional da Sociedade Americana da Química (ACS) no dia 17 de agosto de 2015.

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PERGUNTA DESTE BLOGGER:

Mero acaso? Fortuita necessidade? Ou 100% Design Inteligente???

Ah, a TDI ao considerar a informação complexa especificada (William Dembski) encontrada no DNA como sendo um dos sinais de inteligência empiricamente detectados na natureza, também é uma teoria de informação...

David Baltimore, biólogo molecular americano (prêmio Nobel em 1975, juntamente com Renato Dulbecco e Howard Martin Temin, pelas descobertas da interação entre os vírus de tumores e o material genético da célula) afirmou: 

“A biologia moderna é uma ciência de informação”.

David Baltimore Pic/Foto

Capacidades auditivas do hominin inicial

Early hominin auditory capacities

Rolf Quam 1,2,3,*, Ignacio Martínez 2,4, Manuel Rosa 5, Alejandro Bonmatí 2,6, Carlos Lorenzo 7,8,2, Darryl J. de Ruiter 9, Jacopo Moggi-Cecchi 10, Mercedes Conde Valverde 4, Pilar Jarabo 5, Colin G. Menter 11, J. Francis Thackeray 12 and Juan Luis Arsuaga 2,6

- Author Affiliations

1Department of Anthropology, Binghamton University [State University of New York (SUNY)], Binghamton, NY 13902–6000, USA.

2Centro de Investigación (UCM-ISCIII) sobre Evolución y Comportamiento Humanos, Avda. Monforte de Lemos, 5, 28029 Madrid, Spain.

3Division of Anthropology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, USA.

4Departamento de Ciencias de la Vida, Universidad de Alcalá, Edificio de Ciencias, Campus Universitario, 28805 Alcalá de Henares, Spain.

5Departamento de Teoría de la Señal y Comunicaciones, Universidad de Alcalá, Escuela Politécnica Superior, Campus Universitario, 28805 Alcalá de Henares, Spain.

6Departamento de Paleontología, Universidad Complutense de Madrid, Facultad de Ciencias Geológicas, Ciudad Universitaria s/n, 28040 Madrid, Spain.

7Área de Prehistoria, Universitat Rovira i Virgili, Avinguda Catalunya 35, 43002 Tarragona, Spain.

8Institut Català de Paleoecologia Humana i Evolució Social (IPHES), Campus Sescelades URV (Edifici W3), 43007 Tarragona, Spain.

9Department of Anthropology, Texas A&M University, College Station, TX 77843, USA.

10Laboratori di Antropologia, Dipartimento di Biologia, Universita’ di Firenze, via del Proconsolo, 12 50122 Firenze, Italy.

11Centre for Anthropological Research, Humanities Research Village, University of Johannesburg, PO Box 524, Auckland Park 2006, South Africa.

12Evolutionary Studies Institute, University of the Witwatersrand, PO WITS, Johannesburg 2050, South Africa.

↵*Corresponding author. E-mail: rquam@binghamton.edu

Science Advances 25 Sep 2015:

Vol. 1, no. 8, e1500355

DOI: 10.1126/sciadv.1500355

Credit/Crédito: Rolf Quam

Abstract

Studies of sensory capacities in past life forms have offered new insights into their adaptations and lifeways. Audition is particularly amenable to study in fossils because it is strongly related to physical properties that can be approached through their skeletal structures. We have studied the anatomy of the outer and middle ear in the early hominin taxa Australopithecus africanus and Paranthropus robustus and estimated their auditory capacities. Compared with chimpanzees, the early hominin taxa are derived toward modern humans in their slightly shorter and wider external auditory canal, smaller tympanic membrane, and lower malleus/incus lever ratio, but they remain primitive in the small size of their stapes footplate. Compared with chimpanzees, both early hominin taxa show a heightened sensitivity to frequencies between 1.5 and 3.5 kHz and an occupied band of maximum sensitivity that is shifted toward slightly higher frequencies. The results have implications for sensory ecology and communication, and suggest that the early hominin auditory pattern may have facilitated an increased emphasis on short-range vocal communication in open habitats.

Keywords Australopithecus Paranthropus audition communication sensory ecologyearevolution

Copyright © 2015, The Authors

This is an open-access article distributed under the terms of the Creative Commons Attribution-NonCommercial license, which permits use, distribution, and reproduction in any medium, so long as the resultant use is not for commercial advantage and provided the original work is properly cited.

Uma exploração controlada por dados filogenômicos das origens virais e da evolução

A phylogenomic data-driven exploration of viral origins and evolution

Arshan Nasir* and Gustavo Caetano-Anollés†

- Author Affiliations

Evolutionary Bioinformatics Laboratory, Department of Crop Sciences and Illinois Informatics Institute, University of Illinois, Urbana, IL 61801, USA.

↵†Corresponding author. E-mail: gca@illinois.edu

↵* Present address: Department of Biosciences, COMSATS Institute of Information Technology, Islamabad 45550, Pakistan.

Science Advances 25 Sep 2015:

Vol. 1, no. 8, e1500527

DOI: 10.1126/sciadv.1500527

Source/Fonte: Julie McMahon

Abstract

The origin of viruses remains mysterious because of their diverse and patchy molecular and functional makeup. Although numerous hypotheses have attempted to explain viral origins, none is backed by substantive data. We take full advantage of the wealth of available protein structural and functional data to explore the evolution of the proteomic makeup of thousands of cells and viruses. Despite the extremely reduced nature of viral proteomes, we established an ancient origin of the “viral supergroup” and the existence of widespread episodes of horizontal transfer of genetic information. Viruses harboring different replicon types and infecting distantly related hosts shared many metabolic and informational protein structural domains of ancient origin that were also widespread in cellular proteomes. Phylogenomic analysis uncovered a universal tree of life and revealed that modern viruses reduced from multiple ancient cells that harbored segmented RNA genomes and coexisted with the ancestors of modern cells. The model for the origin and evolution of viruses and cells is backed by strong genomic and structural evidence and can be reconciled with existing models of viral evolution if one considers viruses to have originated from ancient cells and not from modern counterparts.

Key words fold horizontal gene transfer phylogenetic analysis origin of life protein domain structure taxonomy tree of life virus

Copyright © 2015, The Authors

FREE PDF GRATIS: Science Advances

A unificação da matemática via teoria de topos

Nós vivemos em um mundo com relações matemáticas exatas na sua estrutura, e a Matemática tem sido definida como o estudo formal da lógica da quantidade, estrutura e relações associadas. 

Tendo isso em mente, considere cum grano salis a proposição deste artigo:

The unification of Mathematics via Topos Theory

Olivia Caramello∗

June 20, 2010

Abstract

We present a set of principles and methodologies which may serve as foundations of a unifying theory of Mathematics. These principles are based on a new view of Grothendieck toposes as unifying spaces being able to act as ‘bridges’ for transferring information, ideas and results between distinct mathematical theories.

FREE PDF GRATIS: ArXiv

Descoberta macabra: crânio de decapitado há cerca de 9.000 anos, Lagoa Santa, Brasil

The Oldest Case of Decapitation in the New World (Lapa do Santo, East-Central Brazil)

André Strauss , Rodrigo Elias Oliveira, Danilo V. Bernardo, Domingo C. Salazar-García, Sahra Talamo, Klervia Jaouen, Mark Hubbe, Sue Black, Caroline Wilkinson, Michael Phillip Richards, Astolfo G. M. Araujo, Renato Kipnis, Walter Alves Neves

Published: September 23, 2015

DOI: 10.1371/journal.pone.0137456

Source/Fonte: Danilo Bernardo, PLoS One

Abstract

We present here evidence for an early Holocene case of decapitation in the New World (Burial 26), found in the rock shelter of Lapa do Santo in 2007. Lapa do Santo is an archaeological site located in the Lagoa Santa karst in east-central Brazil with evidence of human occupation dating as far back as 11.7–12.7 cal kyBP (95.4% interval). An ultra-filtered AMS age determination on a fragment of the sphenoid provided an age range of 9.1–9.4 cal kyBP (95.4% interval) for Burial 26. The interment was composed of an articulated cranium, mandible and first six cervical vertebrae. Cut marks with a v-shaped profile were observed in the mandible and sixth cervical vertebra. The right hand was amputated and laid over the left side of the face with distal phalanges pointing to the chin and the left hand was amputated and laid over the right side of the face with distal phalanges pointing to the forehead. Strontium analysis comparing Burial 26’s isotopic signature to other specimens from Lapa do Santo suggests this was a local member of the group. Therefore, we suggest a ritualized decapitation instead of trophy-taking, testifying for the sophistication of mortuary rituals among hunter-gatherers in the Americas during the early Archaic period. In the apparent absence of wealth goods or elaborated architecture, Lapa do Santo’s inhabitants seemed to use the human body to express their cosmological principles regarding death.

Citation: Strauss A, Oliveira RE, Bernardo DV, Salazar-García DC, Talamo S, Jaouen K, et al. (2015) The Oldest Case of Decapitation in the New World (Lapa do Santo, East-Central Brazil). PLoS ONE 10(9): e0137456. doi:10.1371/journal.pone.0137456

Editor: John P. Hart, New York State Museum, UNITED STATES

Received: April 21, 2015; Accepted: August 17, 2015; Published: September 23, 2015

Copyright: © 2015 Strauss et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Data Availability: All relevant data are within the paper and its Supporting Information files.

Funding: The excavation of Lapa do Santo was significantly funded by the São Paulo Research Foundation (FAPESP) through two research grants obtained by WN (99/0670-7 and 04/01321-6). FAPESP also provided a post-doctoral fellowship to RK (01/06881-1), PhD scholarship (08/58729-8 to DVB), and a MSc scholarship (08/51747-0 to AS). The Brazilian National Council for Scientific and Technological Development (CNPq) WAN with a productivity grant (300818/2007-6). The Max Planck Society provided a PhD scholarship for AS. DCSG acknowledges the Generalitat Valenciana (VALi+d APOSTD/2014/123) and the European Union (FP7/2007-2013 - MSCA-COFUND, n°245743) through a Braudel-IFER-FMSH in collaboration with the LAMPEA lab at the Université d'Aix-Marseille. RK is currently employed in a commercial company that provided support only in the form of salaries, but did not have any additional role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. The specific roles of these authors are articulated in the ‘author contributions’ section”.

Competing interests: The authors of this manuscript have the following competing interests: Author Renato Kipnis is employed by Scientia Consultoria Científica Ltda. There are no patents, products in development or marketed products to declare. This does not alter their adherence to all the PLOS ONE policies on sharing data and materials.

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Contribuições axiológicas à educação científica: valores cognitivos e a seleção natural de Darwin

Ciência & Educação (Bauru)

Print version ISSN 1516-7313

Ciênc. educ. (Bauru) vol.19 no.1 Bauru 2013

Contribuições axiológicas à educação científica: valores cognitivos e a seleção natural de Darwin

Axiological contributions to science education: cognitive values and Darwin's natural selection

Irinéa de Lourdes Batista I; Lucken Bueno Lucas II

I Programa de Pós-Graduação em Ensino de Ciências e Educação Matemática (PECEM), Universidade Estadual de Londrina (UEL). Rodovia Celso Garcia Cid (PR 445, Km 380), Campus Universitário, Caixa postal 6001. Londrina, PR, Brasil. 86.051-990. irinea@uel.br 

II Doutorando, PECEM, UEL. Londrina, PR, Brasil

RESUMO

Nos últimos anos, muitos autores têm discorrido sobre o papel dos valores nas atividades científicas. Ao se buscar por novas maneiras de se compreenderem os motivos, processos e resultados dessas atividades, considerável relevância é atribuída ao fato de que as práticas científicas devem ser compreendidas segundo seu contexto histórico-social. Pautando-se na pertinência de pesquisas comprometidas com o estudo das influências axiológicas na dinâmica da Ciência, apresenta-se, neste artigo, uma discussão acerca do papel que os valores cognitivos podem desempenhar na compreensão de uma teoria biológica – seleção natural – mediante uma síntese histórico-epistemológica e demais aportes histórico-filosóficos, com o objetivo de investigar o desenvolvimento de uma nova estratégia de abordagem para o ensino dos conteúdos evolutivos no ensino de Biologia.

Palavras-chave: Valor cognitivo. Teoria da Seleção Natural. História da ciência. Filosofia da ciência. Ensino-aprendizagem. Ensino de Biologia.

ABSTRACT

In recent years, many authors have discussed the role of values in scientific activities. When searching for new ways to understand the reasons, processes and results of these activities, considerable relevance is given to the fact that scientific practices should be understood according to their social historical context. Based on the relevance of research committed to the study of the axiological influences on the dynamics of science, the present article discusses the role that the cognitive values may have upon the understanding of a biological theory – natural selection – through an epistemological historical synthesis and other philosophic historical contributions, aiming to investigate the development of a new strategic approach to teaching the evolutionary content in Biology teaching.

Keywords: Cognitive values. Theory of Natural Selection. History of science. Philosophy of science. Teaching-learning. Biology teaching.

FREE PDF GRATIS: SCIELO

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Procurem este blogger no texto e bibliografia deste artigo.

Algumas ponderações sobre a pesquisa da síntese da filogenia e taxonomia em uma árvore da vida abrangente

Ponderações sobre a pesquisa publicada no PNAS:

Synthesis of phylogeny and taxonomy into a comprehensive tree of life

E ao destaque dado no HypeScience: Revelada "árvore da vida" com 2.3 milhões de espécies.

Esta pesquisa precisa ser lida cum grano salis – com ceticismo saudável, pois revela muitos pontos em que erros científicos crassos podem ocorrer:

1. Ignorância declarada:

“Despite decades of effort and thousands of phylogenetic studies on diverse clades, we lack a comprehensive tree of life, or even a summary of our current knowledge.”

“Apesar de décadas de esforços e milhares de estudos filogenéticos sobre diversos clades, nós não temos uma árvore da vida abrangente, ou até um sumário do nosso conhecimento atual.”

2. Preenchimento questionável de lacunas:

“When source phylogenies are absent or sparsely sampled, taxonomic hierarchies provide structure and completeness.”

“Taxonomies contribute to the structure only where we do not have phylogenetic trees.” 

“Quando as filogenias de origem estiverem ausentes ou esparsamente analisado, as hierarquias taxonômicas fornecem estrutura e completude.”

“As taxonomias contribuem para a estrutura somente quando nós não temos árvores filogenéticas.”

 

E se as duas proposições forem dependentes da aceitação a priori da pressuposição de ancestralidade comum universal?

3. Primeiro passo, direção incerta?

“Although a massive undertaking in its own right, this draft tree of life represents only a first step.”

“Embora seja um grande empreendimento em si mesmo, este esboço de árvore da vida representa apenas um primeiro passo.”

4. Destruição de dados:

“585,081 of the names are classified as nonphylogenetic units (e.g.,incertae sedis [of uncertain placement]) and were therefore not included in the synthesis pipeline.”

“585.081 dos nomes são classificados como unidades não filogenéticas (e.g., incertae sedis [de localização incerta]) e por isso não incluídos no processo de síntese.”

Algumas vezes o verdadeiro tesouro está no lixo. Lembram do DNA lixo??? Um verdadeiro tesouro genético que a cada dia o ENCODE vai revelando.

5. Inclusão seletiva:

“The complete database contains 6,810 trees from 3,062 studies. At the time of publication, 484 studies in our database are incorporated into the draft tree of life.”

“O banco de dados completo contém 6.810 árvores de 3.062 estudos. Por ocasião da publicação, 484 estudos em nosso banco de dados foram incorporados no esboço da árvore da vida.”

E o que isso significa? Que 20% dos estudos, e 10% das árvores – implica que muitos desses estudos apresentaram duas ou mais filogenias conflitantes dos mesmos dados. Além disso, eles não puderam usar filogenias análogas que foram apresentadas, por exemplo, como diagramas impressos nos artigos.

6. Pré-conceito:

“Our goal is to generate a best estimate of phylogenetic knowledge; based on our tests, we give several reasons not to use all available trees for synthesis. First, including trees that are incorrect does not improve the synthetic estimate.”

“Nosso objetivo é gerar uma melhor estimativa do conhecimento filogenético; baseado em nossos testes, nós demos diversas razões em não usar todas as árvores disponíveis para a síntese. Primeiro, incluir árvores que estão incorretas não melhora a estimativa sintética.”

E quem decide o que é a melhor árvore? E quem decide quais árvores publicadas são incorretas?

7. Consenso não é ciência:

“In each major clade, expert curators selected and ranked input trees for inclusion based on date of publication, underlying data, and methods of inference (see Materials and Methods for details). These rankings generally reflect community consensus about phylogenetic hypotheses.”

“Em cada clade principal, curadores especialistas selecionaram e classificaram árvores  de entrada para inclusão baseado na data de publicação, dados subjacentes, e métodos de inferência (vide Materials and Methods para detalhes). Essas classificações geralmente refletem o consenso da comunidade sobre hipóteses filogenéticas.”

Perguntas: Desde quando que data de publicação é critério de exatidão? Quem é que decide se os dados são bons? Quem é que decide quais métodos são os melhores? A classificação é garantida para reforçar o consenso atual, que pressupõe a ancestralidade comum universal. Céticos e dissidentes são eliminados logo no começo pelos “especialistas” – quem os classificou assim?

8. Viciando o jogo:

“Not all trees are sufficiently well-curated; at this point, we have focused curation efforts on trees that will most improve the synthetic tree.”  

“Nem todas as árvores foram suficientemente bem consideradas pelos especialistas; a esta altura, nós focalizamos os esforços dos conhecimentos especializados em árvores que irão melhorar mais a árvore sintética.”

Perceberam? Os dados não estão falando objetivamente; os pesquisadores garantiram o que se propuseram descobrir.

9. Os outros que sejam rigorosos:

“The full set of trees in the database is important for other questions such as estimating conflict or studying the history of inference in a clade, highlighting the importance of continued deposition and curation of trees into public data repositories.”

“A série completa de árvores no banco de dados é importante para outras questões tais como calcular o conflito ou estudar a história da inferência em um clade, destacando a importância da deposição continuada e do estudo especializado de árvores em repositórios de dados públicos.”

É bom manter todos os dados públicos, mas quem irá realmente conferi-los?

10. Inputs altamente pré-concebidos:

“Most tips in the synthetic tree (98%) come from taxonomy only, reflecting both the need to incorporate more species into phylogenies and the need to make published phylogenies available.”

“A maioria dos ramos na árvore sintética (98%) vem somente da taxonomia, refletindo tanto a necessidade de se incorporar mais espécies nas filogenias e a necessidade de tornar disponíveis as filogenias publicadas.”

Isso quer dizer que somente 2% usam os altamente anunciados métodos filogenéticos moleculares de se inferir ancestralidade.

11. Resultados altamente pré-concebidos:

“We obtained trees from digital repositories and also by contacting authors directly, but our overall success rate was only 16%.”

“Nós obtivemos árvores do repositários digitais e também contatando diretamente os autores, mas a nossa taxa de sucesso geral foi somente de 16%.”

Na seção Materials and Methods, os autores disseram:

“The data retrieved are by no means a complete representation of phylogenetic knowledge because we obtained digital phylogeny files for only 16% of recently published trees.”

“Os dados obtidos não são de modo algum uma representação completa do conhecimento filogenético, pois nós obtivemos arquivos digitais de filogenia de apenas 16% das árvores publicadas recentemente.”

12. Nem precisava mencionar, mas não houve nenhuma inclusão de ceticismo, nem mesmo ceticismo saudável, quanto à ancestralidade comum universal...

+++++

Sobre os ombros de um gigante.

Primeiro artigo dentro do escopo da Síntese Evolutiva Ampliada? Lançando os dados duas vezes: evoluindo antigas proteínas reconstruídas em organismos atuais

Rolling the Dice Twice: Evolving Reconstructed Ancient Proteins in Extant Organisms

Betul Kacar

Source/Fonte

Abstract

Scientists have access to artifacts of evolutionary history (namely, the fossil record and genomic sequences of living organisms) but they have limited means with which to infer the exact evolutionary events that occurred to produce today s living world. An intriguing question to arise from this historical limitation is whether the evolutionary paths of organisms are dominated by internal or external controlled processes (i.e., Life as a factory) or whether they are inherently random and subject to completely different outcomes if repeated under identical conditions (i.e., Life as a casino parlor). Two experimental approaches, ancestral sequence reconstruction and experimental evolution with microorganisms, can be used to recapitulate ancient adaptive pathways and provide valuable insights into the mutational steps that constitute an organism s genetic heritage. Ancestral sequence reconstruction follows a backwards-from-present-day strategy in which various ancestral forms of a modern gene or protein are reconstructed and then studied mechanistically. Experimental evolution, by contrast, follows a forward-from-present day strategy in which microbial populations are evolved in the laboratory under defined conditions in which their evolutionary paths may be closely monitored. Here I describe a novel hybrid of these two methods, in which synthetic components constructed from inferred ancestral gene or protein sequences are placed into the genomes of modern organisms that are then experimentally evolved. Through this system, we aim to establish the comparative study of ancient phenotypes as a novel, statistically rigorous methodology with which to explore the respective impacts of biophysics and chance in evolution within the scope of the Extended Synthesis.

Copyright 

The copyright holder for this preprint is the author/funder. It is made available under a CC-BY-NC-ND 4.0 International license.

FREE PDF GRATIS: bioRxiv

Momento de mudança na esqueletização de trilobita, anterior a 365 MA, congelado no tempo e espaço

A moment from before 365 Ma frozen in time and space

Błażej Błażejowski, Piotr Gieszcz, Carlton E. Brett & Marcin Binkowski

Scientific Reports 5, Article number: 14191 (2015)

doi:10.1038/srep14191

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Palaeontology | Physiology

Received:

12 May 2015

Accepted:

27 July 2015

Published online:

18 September 2015

Abstract

This study presents a detailed analysis of an exceptionally well-preserved articulated specimen of the trilobite Trimerocephalus from the Late Devonian of the Holy Cross Mountains in Poland. X-ray microtomography reveals the oldest direct evidence for a moulting episode known from the fossil record. The process of moulting as well as associated features observed in the investigated specimen are interpreted by comparison with extinct and extant Xiphosurida arthropods, which survived global P/T extinction and are among the closest extant relatives of trilobites. A very special moment frozen in time and space millions years ago provides rare insights into the behavior and physiology of these long-extinct arthropods.

FREE PDF GRATIS: Scientific Reports

Síntese da filogenia e taxonomia para uma árvore da vida abrangente

Synthesis of phylogeny and taxonomy into a comprehensive tree of life

Cody E. Hinchliff a,1, Stephen A. Smith a,1,2, James F. Allman b, J. Gordon Burleigh c, Ruchi Chaudhary c, Lyndon M. Coghill d, Keith A. Crandall e, Jiabin Deng c, Bryan T. Drew f, Romina Gazis g, Karl Gude h, David S. Hibbett g, Laura A. Katz i, H. Dail Laughinghous e, IVi, Emily Jane McTavish j, Peter E. Midford d, Christopher L. Owen c, Richard H. Ree d, Jonathan A. Rees k, Douglas E. Soltis c,l, Tiffani Williams m, and Karen A. Cranston k,2

a Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109;

b Interrobang Corporation, Wake Forest, NC 27587;

c Department of Biology, University of Florida, Gainesville, FL 32611;

d Field Museum of Natural History, Chicago, IL 60605;

e Computational Biology Institute, George Washington University, Ashburn, VA 20147;

f Department of Biology, University of Nebraska-Kearney, Kearney, NE 68849;

g Department of Biology, Clark University, Worcester, MA 01610;

h School of Journalism, Michigan State University, East Lansing, MI 48824;

i Biological Science, Clark Science Center, Smith College, Northampton, MA 01063;

j Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045;

k National Evolutionary Synthesis Center, Duke University, Durham, NC 27705;

l Florida Museum of Natural History, University of Florida, Gainesville, FL 32611;

m Computer Science and Engineering, Texas A&M University, College Station, TX 77843

Edited by David M. Hillis, The University of Texas at Austin, Austin, TX, and approved July 28, 2015 (received for review December 3, 2014)

Source/Fonte: Open Tree of Life Org.

Significance

Scientists have used gene sequences and morphological data to construct tens of thousands of evolutionary trees that describe the evolutionary history of animals, plants, and microbes. This study is the first, to our knowledge, to apply an efficient and automated process for assembling published trees into a complete tree of life. This tree and the underlying data are available to browse and download from the Internet, facilitating subsequent analyses that require evolutionary trees. The tree can be easily updated with newly published data. Our analysis of coverage not only reveals gaps in sampling and naming biodiversity but also further demonstrates that most published phylogenies are not available in digital formats that can be summarized into a tree of life.

Abstract

Reconstructing the phylogenetic relationships that unite all lineages (the tree of life) is a grand challenge. The paucity of homologous character data across disparately related lineages currently renders direct phylogenetic inference untenable. To reconstruct a comprehensive tree of life, we therefore synthesized published phylogenies, together with taxonomic classifications for taxa never incorporated into a phylogeny. We present a draft tree containing 2.3 million tips—the Open Tree of Life. Realization of this tree required the assembly of two additional community resources: (i) a comprehensive global reference taxonomy and (ii) a database of published phylogenetic trees mapped to this taxonomy. Our open source framework facilitates community comment and contribution, enabling the tree to be continuously updated when new phylogenetic and taxonomic data become digitally available. Although data coverage and phylogenetic conflict across the Open Tree of Life illuminate gaps in both the underlying data available for phylogenetic reconstruction and the publication of trees as digital objects, the tree provides a compelling starting point for community contribution. This comprehensive tree will fuel fundamental research on the nature of biological diversity, ultimately providing up-to-date phylogenies for downstream applications in comparative biology, ecology, conservation biology, climate change, agriculture, and genomics.

phylogeny taxonomy tree of life biodiversity synthesis

Footnotes

1C.E.H. and S.A.S. contributed equally to this work.

2To whom correspondence may be addressed. Email: karen.cranston{at}gmail.com or eebsmith{at}umich.edu.

Author contributions: C.E.H., S.A.S., J.G.B., R.C., K. A. Crandall, K.G., D.S.H., L.A.K., R.H.R., D.E.S., T.W., and K. A. Cranston designed research; C.E.H., S.A.S., J.G.B., R.C., L.M.C., K. A. Crandall, J.D., B.T.D., R.G., D.S.H., H.D.L., E.J.M., P.E.M., C.L.O., R.H.R., J.A.R., D.E.S., and K. A. Cranston performed research; C.E.H., S.A.S., J.F.A., J.G.B., R.C., L.M.C., E.J.M., P.E.M., R.H.R., and J.A.R. contributed new reagents/analytic tools; C.E.H., S.A.S., J.G.B., R.C., L.M.C., B.T.D., R.G., D.S.H., H.D.L., C.L.O., J.A.R., and D.E.S. analyzed data; C.E.H., S.A.S., J.F.A., J.G.B., R.C., K. A. Crandall, L.A.K., H.D.L., E.J.M., J.A.R., D.E.S., and K. A. Cranston wrote the paper; J.F.A. conducted user interface development; and K.G. provided graphic design.

The authors declare no conflict of interest.

This article is a PNAS Direct Submission.

Data deposition: The Open Tree of Life taxonomy, the synthetic tree, and processed inputs are available from the Dryad database, dx.doi.org/10.5061/dryad.8j60q.

This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1423041112/-/DCSupplemental.

Freely available online through the PNAS open access option.

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