A Royal Society vai vindicar este blogger: Mudança paradigmática em evolução

domingo, dezembro 27, 2015

Royal Society Meeting to Discuss Evolution Paradigm Shift, What That Means for Science and for All

Fri Dec 25 10:15:19 EST 2015 | The Huffington Post

Nullius in verba/Take no-one's word for it

But Nurse, who will continue in his role as chief of Francis Crick Institute, has not left the Royal Society without first ensuring that the world's oldest scientific society remains relevant: a major Royal Society meeting in London has been called for November 7-9, 2016 on evolution paradigm shift with the understated working title, "New Trends in Evolutionary Biology: Philosophical and Social Science Implications." The conference is being co-sponsored by the British Academy for the humanities ...

Read more here/Leia mais aqui: Huffington Post e



Embora este blog tenha sido lançado em 2006, este blogger anunciou em 1998 para editores e jornalistas científicos que uma iminente e eminente mudança paradigmática em biologia evolucionária iria ocorrer. Não fui levado a sério por gente séria da Academia, e fui motivo de chacota pela Galera de meninos e meninas de Darwin.

Fui, nem sei por que, rachando de rir desses iluminados da Nomenklatura científica, alguns ainda meus amigos, e da Galera dos meninos e meninas de Darwin que pensam e anunciam o fato, Fato, FATO da evolução como sendo um fato científico já devidamente estabelecido pela montanha de evidências. Nada mais falso!!! 

Não se esqueçam dessa data: 7-9 de novembro de 2016.

Não se esqueçam desse local: The Royal Society of London.

Não se esqueçam do tema: Mudança paradigmática em biologia evolucionária (vindicando, sem querer querendo, o que este blogger afirmou em 1998!).

Para uma visão maior sobre a fragorosa falência epistêmica da teoria da evolução de Darwin através da seleção natural e n mecanismos evolucionários, faça uma busca neste blog: 16 de Altenberg. Especialmente o artigo-paródia:

Clóvis Rossi ‘falou e disse’: a era das certezas sobre o fato, Fato, FATO da evolução acabou

Visualização da montagem da face do micro compartimento bacteriano usando microscopia de força atômica de alta velocidade: mero acaso, fortuita necessidade ou design inteligente?

sábado, dezembro 26, 2015

Visualization of Bacterial Microcompartment Facet Assembly Using High-Speed Atomic Force Microscopy

† MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824, United States
‡ Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
§Institute of Integrative Biology and ∥Department of Physics, University of Liverpool, Liverpool L69 7ZB, United Kingdom
⊥ Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California 94720, United States
# Berkeley Synthetic Biology Institute, Berkeley, California 94720, United States
∇ Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, United States

Nano Lett., Article ASAP

Publication Date (Web): November 30, 2015
Copyright © 2015 American Chemical Society

*(L.-N.L.) E-mail: Luning.Liu@liverpool.ac.uk., *(C.K.) E-mail: ckerfeld@lbl.gov.

ACS AuthorChoice - This is an open access article published under a Creative Commons Attribution (CC-BY)License, which permits unrestricted use, distribution and reproduction in any medium, provided the author and source are cited.


Bacterial microcompartments (BMCs) are proteinaceous organelles widespread among bacterial phyla. They compartmentalize enzymes within a selectively permeable shell and play important roles in CO2 fixation, pathogenesis, and microbial ecology. Here, we combine X-ray crystallography and high-speed atomic force microscopy to characterize, at molecular resolution, the structure and dynamics of BMC shell facet assembly. Our results show that preformed hexamers assemble into uniformly oriented shell layers, a single hexamer thick. We also observe the dynamic process of shell facet assembly. Shell hexamers can dissociate from and incorporate into assembled sheets, indicating a flexible intermolecular interaction. Furthermore, we demonstrate that the self-assembly and dynamics of shell proteins are governed by specific contacts at the interfaces of shell proteins. Our study provides novel insights into the formation, interactions, and dynamics of BMC shell facets, which are essential for the design and engineering of self-assembled biological nanoreactors and scaffolds based on BMC architectures.

Keywords: Bacterial microcompartment; high-speed atomic force microscopy; protein dynamics; protein interaction; self-assembly

                            Sup. Info. 1
                            Sup. Info. 2 Zip 21.16 MBs

Causalidade de cima para baixo: um tema integrador dentro e entre as ciências?

Top-down causation: an integrating theme within and across the sciences?

George F. R. Ellis, Denis Noble, Timothy O'Connor

Published 21 December 2011.DOI: 10.1098/rsfs.2011.0110


This issue of the journal is focused on ‘top-down (downward) causation'. The words in this title, however, already raise or beg many questions. Causation can be of many kinds. They form our ways of ordering our scientific understanding of the world, all the way from the reductive concept of cause as elementary objects exerting forces on each other, through to the more holistic concept of attractors towards which whole systems move, and to adaptive selection taking place in the context of an ecosystem. As for ‘top’ and ‘down’, in the present scientific context, these are clearly metaphorical, as some of the articles in this issue of the journal make clear. Do we therefore know what we are talking about? The meeting at the Royal Society on which this set of papers is based included philosophers as well as scientists, and some of those (Jeremy Butterfield, Barry Loewer, Alan Love, Samir Okasha and Eric Scerri) have contributed articles to this issue. We would like also to thank those (Claus Kiefer, Peter Menzies, Jerome Feldman and David Papineau) who contributed only to the discussion meeting. Their contributions were also valuable, both at the meeting and by influencing the articles that have been written by others. We include a glossary with this introduction, composed by one of us (O'Connor). The clarification of the use of words and their semantic frames is an important role of philosophy, and this was evident in the discussions at the meeting and is now evident in many of the articles published here. Moreover, philosophical analysis is not limited to the papers by the professional philosophers. The idea of top-down causation is intimately related to concepts of emergence; indeed, it is a key factor in strong theories of emergence.

FREE PDF GRATIS: Interface Focus

Tal pai, tal filho: epigenética em porquinhos da Índia selvagens

quinta-feira, dezembro 24, 2015

Paternal intergenerational epigenetic response to heat exposure in male Wild guinea pigs


Alexandra Weyrich, Dorina Lenz, Marie Jeschek, Tzu Hung Chung, Kathrin Rübensam, Frank Göritz, Katarina Jewgenow, Jörns Fickel

First published: 19 December 2015Full publication history


Epigenetic modifications, of which DNA methylation is the best studied one, can convey environmental information through generations via parental germ lines. Past studies have focused on the maternal transmission of epigenetic information to the offspring of isogenic mice and rats in response to external changes, whereas heterogeneous wild mammals as well as paternal epigenetic effects have been widely neglected. In most wild mammal species, males are the dispersing sex and have to cope with differing habitats and thermal changes. As temperature is a major environmental factor we investigated if genetically heterogeneous Wild guinea pig (Cavia aperea) males can adapt epigenetically to an increase in temperature and if that response will be transmitted to the next generation(s). Five adult male guinea pigs (F0) were exposed to an increased ambient temperature for 2 months, i.e. the duration of spermatogenesis. We studied the liver (as the main thermoregulatory organ) of F0 fathers and F1 sons, and testes of F1 sons for paternal transmission of epigenetic modifications across generation(s). Reduced representation bisulphite sequencing revealed shared differentially methylated regions in annotated areas between F0 livers before and after heat treatment, and their sons’ livers and testes, which indicated a general response with ecological relevance. Thus, paternal exposure to a temporally limited increased ambient temperature led to an ‘immediate’ and ‘heritable’ epigenetic response that may even be transmitted to the F2 generation. In the context of globally rising temperatures epigenetic mechanisms may become increasingly relevant for the survival of species.

FREE PDF GRATIS: Molecular Ecology



Lamarck, ei Lamarck! acho que você está sendo vindicado no contexto de justificação teórica, e a evolução já não é mais exclusivamente de Darwin... 

Fui, nem sei por que, rindo da cara de alguns cientistas da Nomenklatura científica que se recusam reconhecer a fragorosa falência epistêmica de Darwin, e da Galera dos meninos e meninas de Darwin que, a cada pesquisa, ficam cada vez mais órfãos - são as evidências que mandam em ciência, e não as teorias!!!

Biologia dos dinossauros saurópodes: a evolução do gigantismo

Biology of the sauropod dinosaurs: the evolution of gigantism

P. Martin Sander 1,*, Andreas Christian 2, Marcus Clauss 3, Regina Fechner 4, Carole T. Gee 1, Eva-Maria Griebeler 5, Hanns-Christian Gunga 6, Jürgen Hummel 7, Heinrich Mallison 8, Steven F. Perry 9, Holger Preuschoft 10, Oliver W. M. Rauhut 4, Kristian Remes 1,4, Thomas Tütken 11, Oliver Wings 8 and Ulrich Witzel 12

Article first published online: 29 APR 2010

© 2010 The Authors. Biological Reviews © 2010 Cambridge Philosophical Society

Biological Reviews

Volume 86, Issue 1, pages 117–155, February 2011

Keywords: Dinosauria; Sauropoda; gigantism; Mesozoic; long neck; phylogenetic heritage; evolutionary innovation


The herbivorous sauropod dinosaurs of the Jurassic and Cretaceous periods were the largest terrestrial animals ever, surpassing the largest herbivorous mammals by an order of magnitude in body mass. Several evolutionary lineages among Sauropoda produced giants with body masses in excess of 50 metric tonnes by conservative estimates. With body mass increase driven by the selective advantages of large body size, animal lineages will increase in body size until they reach the limit determined by the interplay of bauplan, biology, and resource availability. There is no evidence, however, that resource availability and global physicochemical parameters were different enough in the Mesozoic to have led to sauropod gigantism.

We review the biology of sauropod dinosaurs in detail and posit that sauropod gigantism was made possible by a specific combination of plesiomorphic characters (phylogenetic heritage) and evolutionary innovations at different levels which triggered a remarkable evolutionary cascade. Of these key innovations, the most important probably was the very long neck, the most conspicuous feature of the sauropod bauplan. Compared to other herbivores, the long neck allowed more efficient food uptake than in other large herbivores by covering a much larger feeding envelope and making food accessible that was out of the reach of other herbivores. Sauropods thus must have been able to take up more energy from their environment than other herbivores.

The long neck, in turn, could only evolve because of the small head and the extensive pneumatization of the sauropod axial skeleton, lightening the neck. The small head was possible because food was ingested without mastication. Both mastication and a gastric mill would have limited food uptake rate. Scaling relationships between gastrointestinal tract size and basal metabolic rate (BMR) suggest that sauropods compensated for the lack of particle reduction with long retention times, even at high uptake rates.

The extensive pneumatization of the axial skeleton resulted from the evolution of an avian-style respiratory system, presumably at the base of Saurischia. An avian-style respiratory system would also have lowered the cost of breathing, reduced specific gravity, and may have been important in removing excess body heat. Another crucial innovation inherited from basal dinosaurs was a high BMR. This is required for fueling the high growth rate necessary for a multi-tonne animal to survive to reproductive maturity.

The retention of the plesiomorphic oviparous mode of reproduction appears to have been critical as well, allowing much faster population recovery than in megaherbivore mammals. Sauropods produced numerous but small offspring each season while land mammals show a negative correlation of reproductive output to body size. This permitted lower population densities in sauropods than in megaherbivore mammals but larger individuals.

Our work on sauropod dinosaurs thus informs us about evolutionary limits to body size in other groups of herbivorous terrestrial tetrapods. Ectothermic reptiles are strongly limited by their low BMR, remaining small. Mammals are limited by their extensive mastication and their vivipary, while ornithsichian dinosaurs were only limited by their extensive mastication, having greater average body sizes than mammals.

FREE PDF GRATIS: Biological Reviews

O que comparar e como: Transcriptômica comparativa para Evo-Devo

quarta-feira, dezembro 23, 2015

What to compare and how: Comparative transcriptomics for Evo-Devo

Julien Roux 1,2,3, Marta Rosikiewicz 1,2 and Marc Robinson-Rechavi 1,2,*

Article first published online: 10 APR 2015

© 2015 Wiley Periodicals, Inc.

Journal of Experimental Zoology Part B: Molecular and Developmental Evolution

Special Issue: Genomics and Evo-Devo

Volume 324, Issue 4, pages 372–382, June 15, 2015


Evolutionary developmental biology has grown historically from the capacity to relate patterns of evolution in anatomy to patterns of evolution of expression of specific genes, whether between very distantly related species, or very closely related species or populations. Scaling up such studies by taking advantage of modern transcriptomics brings promising improvements, allowing us to estimate the overall impact and molecular mechanisms of convergence, constraint or innovation in anatomy and development. But it also presents major challenges, including the computational definitions of anatomical homology and of organ function, the criteria for the comparison of developmental stages, the annotation of transcriptomics data to proper anatomical and developmental terms, and the statistical methods to compare transcriptomic data between species to highlight significant conservation or changes. In this article, we review these challenges, and the ongoing efforts to address them, which are emerging from bioinformatics work on ontologies, evolutionary statistics, and data curation, with a focus on their implementation in the context of the development of our database Bgee (http://bgee.org). J. Exp. Zool. (Mol. Dev. Evol.) 324B: 372–382, 2015. © 2015 Wiley Periodicals, Inc.

Descoberta epigenética sugere que as modificações do DNA são mais diversificadas do que se pensava antes


Identification of methylated deoxyadenosines in vertebrates reveals diversity in DNA modifications

Magdalena J Koziol, Charles R Bradshaw, George E Allen, Ana S H Costa, Christian Frezza & John B Gurdon

Nature Structural & Molecular Biology (2015) 

Received 22 July 2015 Accepted 18 November 2015 Published online 21 December 2015


Methylation of cytosine deoxynucleotides generates 5-methylcytosine (m5dC), a well-established epigenetic mark. However, in higher eukaryotes much less is known about modifications affecting other deoxynucleotides. Here, we report the detection of N6-methyldeoxyadenosine (m6dA) in vertebrate DNA, specifically in Xenopus laevis but also in other species including mouse and human. Our methylome analysis reveals that m6dA is widely distributed across the eukaryotic genome and is present in different cell types but is commonly depleted from gene exons. Thus, direct DNA modifications might be more widespread than previously thought.

Subject terms: DNA DNA methylation

Estrutura e função dos complexos de proteína da membrana mitocondrial

Structure and function of mitochondrial membrane protein complexes

Werner Kühlbrandt Email author

BMC Biology201513:89

© Kühlbrandt. 2015

Published: 29 October 2015

Fig. 2 - Membrane protein complexes of the respiratory chain.


Biological energy conversion in mitochondria is carried out by the membrane protein complexes of the respiratory chain and the mitochondrial ATP synthase in the inner membrane cristae. Recent advances in electron cryomicroscopy have made possible new insights into the structural and functional arrangement of these complexes in the membrane, and how they change with age. This review places these advances in the context of what is already known, and discusses the fundamental questions that remain open but can now be approached.

Mitochondria are the powerhouses of the cell. In all eukaryotes that do not depend on photosynthesis, the mitochondria are the main source of adenosine triphosphate (ATP), the energy-rich compound that drives fundamental cell functions. These functions include force generation (for example, in muscle contraction and cell division), the biosynthesis, folding and degradation of proteins, and the generation and maintenance of membrane potentials. ATP is produced on a massive scale in the human body, amounting to 50 kg per day in a healthy adult, but considerably more in a long-distance runner. ATP is generated by the mitochondrial ATP synthase from ADP and phosphate ions. These are the products of ATP hydrolysis at the sites where energy is needed in the cell. Apart from cellular respiration and ATP synthesis, mitochondria have numerous other essential functions, including the production of NADH and GTP in the citric acid cycle, the biosynthesis of amino acids, heme groups and iron-sulfur clusters or the synthesis of phospholipids for membrane biogenesis. They also act in calcium signaling [1], stress responses [2] and generally as cellular signaling hubs [3]. Not surprisingly, mitochondria play a fundamental role in human health. Mitochondrial dysfunction is the cause of severe, often maternally inherited diseases. Moreover, mitochondria are deeply implicated in apoptosis and ageing [4].

In many respects, mitochondria resemble α-proteobacteria, from which they are thought to have originated by endocytosis some 1.6 billion years ago. The most striking evidence of this evolutionary relationship is the close homology of bacterial and mitochondrial respiratory chain complexes. Mitochondria have their own genetic system, which uses a distinct DNA code that differs both from that of their bacterial ancestors and their eukaryotic hosts [5]. They have their own protein translation machinery, complete with ribosomes, tRNAs and associated protein factors that more or less resemble those of their bacterial ancestors. Very recently, the first high-resolution structure of a mitochondrial ribosome, determined by single-particle electron cryomicroscopy (cryo-EM), has revealed a fascinating patchwork of similarities to and differences from bacterial ribosomes [6]. Nevertheless, mitochondria make surprisingly little use of their specialized protein production machinery. In the course of evolution they have transferred up to 99 % of their genes to the nucleus. Today, the vast majority of mitochondrial proteins are produced in the cytoplasm and imported into the organelle by an elaborate set of protein translocases [7]. In humans, only 13 mitochondrial proteins are organelle-encoded, all of them central, hydrophobic subunits of respiratory chain complexes or of the ATP synthase.

Mitochondria are highly dynamic [8]. In the cell, they form a tubular network that constantly changes by division and fusion (Additional file 1). Both processes are accomplished by multi-component molecular machineries that include a number of dynamin-related GTPases [9, 10]. When mitochondria are isolated from cells, the network breaks up into fragments that spontaneously reseal. Isolated mitochondria are fully competent for respiration and ATP synthesis [11]. They maintain their membrane composition, organization and membrane potential, as well as the ability to fuse [12] and to import proteins [7]. We owe much of what we know about mitochondria and how they work at the molecular level to in vitro studies with isolated mitochondria, or even mitochondrial membrane fractions, which still carry out oxidative phosphorylation and ATP synthesis [13].

Mitochondria can be seen in the light microscope, but their detailed internal structure is only revealed by electron microscopy. In the 1990s, the structure of mitochondria was investigated by electron tomography of thin plastic sections [14]. While this yielded striking three-dimensional (3D) images of their internal membrane system, molecular detail was lost due to chemical fixation, dehydration and heavy-metal staining. Cryo-EM of unfixed, unstained organelles is now revealing the architecture of mitochondrial membranes and their macromolecular components at increasing levels of detail. Single-particle cryo-EM of isolated, detergent-solubilized membrane protein complexes reaches near-atomic resolution [15, 16]. Electron cryo-tomography (cryo-ET) of intact isolated mitochondria or mitochondrial membranes is resolving their macromolecular components in situ [17], and averaging of tomographic volumes can attain sub-nanometer resolution [18].


                            Aditional File 1 Vídeo

                            Aditional File 2 Vídeo

Replicando pesquisa em ecologia e evolução: da viabilidade, incentivos e o enigma do custo-benefício

Replicating research in ecology and evolution: feasibility, incentives, and the cost-benefit conundrum

Shinichi Nakagawa Email author and Timothy H. Parker

BMC Biology201513:88

© Nakagawa and Parker. 2015

Published: 28 October 2015


We believe that replicating studies in ecology and evolution is extremely valuable, but replication within species and systems is troublingly rare, and even ‘quasi-replications’ in different systems are often insufficient. We make a case for supporting multiple types of replications and point out that the current incentive structure needs to change if ecologists and evolutionary biologist are to value scientific replication sufficiently.




Mais ciência através do contexto de justificação teórica é a luta deste blogger desde 1998!!!

Cientistas modelam pequeníssima 'nanomáquina' celular de diacilglicerol quinase: 100% design inteligente!

Ternary structure reveals mechanism of a membrane diacylglycerol kinase

Dianfan Li, Phillip J. Stansfeld, Mark S. P. Sansom, Aaron Keogh, Lutz Vogeley, Nicole Howe, Joseph A. Lyons, David Aragao, Petra Fromme, Raimund Fromme, Shibom Basu, Ingo Grotjohann, Christopher Kupitz, Kimberley Rendek, Uwe Weierstall, Nadia A. Zatsepin, Vadim Cherezov, Wei Liu, Sateesh Bandaru, Niall J. English et al.

Affiliations Contributions Corresponding author

Nature Communications 6, Article number: 10140 doi:10.1038/ncomms10140

Received 25 April 2015 Accepted 09 November 2015 Published 17 December 2015

Figure 1: Overall structure of the DgkA-ACP-lipid ternary complex.


Diacylglycerol kinase catalyses the ATP-dependent conversion of diacylglycerol to phosphatidic acid in the plasma membrane of Escherichia coli. The small size of this integral membrane trimer, which has 121 residues per subunit, means that available protein must be used economically to craft three catalytic and substrate-binding sites centred about the membrane/cytosol interface. How nature has accomplished this extraordinary feat is revealed here in a crystal structure of the kinase captured as a ternary complex with bound lipid substrate and an ATP analogue. Residues, identified as essential for activity by mutagenesis, decorate the active site and are rationalized by the ternary structure. The γ-phosphate of the ATP analogue is positioned for direct transfer to the primary hydroxyl of the lipid whose acyl chain is in the membrane. A catalytic mechanism for this unique enzyme is proposed. The active site architecture shows clear evidence of having arisen by convergent evolution.

Subject terms: Biological sciences Biochemistry Biophysics

FREE PDF GRATIS: Nature Communications

                            Sup. Info.

                            Sup. Info. Movie 1 25 MBs

                            Sup. Info. Movie 2 19.8 MBs


Mero acaso? Fortuita necessidade? 100% design inteligente! O Abstract usou de linguagem teleológica, e sem saber (?), os cientistas realizaram a pesquisa nos moldes teóricos do design inteligente: a busca de sinais de inteligência/teleologia nas coisas bióticas.

O mal de Alzheimer provocado por fungos???

terça-feira, dezembro 22, 2015

Different Brain Regions are Infected with Fungi in Alzheimer’s Disease

Diana Pisa, Ruth Alonso, Alberto Rábano, Izaskun Rodal & Luis Carrasco

Scientific Reports 5, Article number: 15015 (2015)

Fungal immune evasion | Fungi

Received: 19 May 2015 Accepted: 15 September 2015 Published online: 15 October 2015


The possibility that Alzheimer’s disease (AD) has a microbial aetiology has been proposed by several researchers. Here, we provide evidence that tissue from the central nervous system (CNS) of AD patients contain fungal cells and hyphae. Fungal material can be detected both intra- and extracellularly using specific antibodies against several fungi. Different brain regions including external frontal cortex, cerebellar hemisphere, entorhinal cortex/hippocampus and choroid plexus contain fungal material, which is absent in brain tissue from control individuals. Analysis of brain sections from ten additional AD patients reveals that all are infected with fungi. Fungal infection is also observed in blood vessels, which may explain the vascular pathology frequently detected in AD patients. Sequencing of fungal DNA extracted from frozen CNS samples identifies several fungal species. Collectively, our findings provide compelling evidence for the existence of fungal infection in the CNS from AD patients, but not in control individuals.

FREE PDF GRATIS: Scientific Reports

Uma perspectiva embriológica no registro fóssil inicial de artrópodes

segunda-feira, dezembro 21, 2015

BMC Evolutionary Biology

December 2015, 15:285

First online: 18 December 2015

An embryological perspective on the early arthropod fossil record

Ariel D. Chipman



Our understanding of the early evolution of the arthropod body plan has recently improved significantly through advances in phylogeny and developmental biology and through new interpretations of the fossil record. However, there has been limited effort to synthesize data from these different sources. Bringing an embryological perspective into the fossil record is a useful way to integrate knowledge from different disciplines into a single coherent view of arthropod evolution.


I have used current knowledge on the development of extant arthropods, together with published descriptions of fossils, to reconstruct the germband stages of a series of key taxa leading from the arthropod lower stem group to crown group taxa. These reconstruction highlight the main evolutionary transitions that have occurred during early arthropod evolution, provide new insights into the types of mechanisms that could have been active and suggest new questions and research directions.


The reconstructions suggest several novel homology hypotheses – e.g. the lower stem group head shield and head capsules in the crown group are all hypothesized to derive from the embryonic head lobes. The homology of anterior segments in different groups is resolved consistently. The transition between “lower-stem” and “upper-stem” arthropods is highlighted as a major transition with a concentration of novelties and innovations, suggesting a gap in the fossil record. A close relationship between chelicerates and megacheirans is supported by the embryonic reconstructions, and I suggest that the depth of the mandibulate-chelicerate split should be reexamined.


Arthropods Paleontology Evo-devo Embryology Germband Cambrian Explosion

FREE PDF GRATIS: BMC Evolutionary Biology

Uma nova árvore temporal revela a impressão da história da Terra na evolução das aves modernas

A new time tree reveals Earth history’s imprint on the evolution of modern birds

Santiago Claramunt* and Joel Cracraft*

- Author Affiliations

Department of Ornithology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, USA.

↵*Corresponding author. E-mail: sclaramunt@amnh.org (S.C.); jlc@amnh.org (J.C.)

Science Advances 11 Dec 2015:

Vol. 1, no. 11, e1501005

DOI: 10.1126/sciadv.1501005


Determining the timing of diversification of modern birds has been difficult. We combined DNA sequences of clock-like genes for most avian families with 130 fossil birds to generate a new time tree for Neornithes and investigated their biogeographic and diversification dynamics. We found that the most recent common ancestor of modern birds inhabited South America around 95 million years ago, but it was not until the Cretaceous-Paleogene transition (66 million years ago) that Neornithes began to diversify rapidly around the world. Birds used two main dispersion routes: reaching the Old World through North America, and reaching Australia and Zealandia through Antarctica. Net diversification rates increased during periods of global cooling, suggesting that fragmentation of tropical biomes stimulated speciation. Thus, we found pervasive evidence that avian evolution has been influenced by plate tectonics and environmental change, two basic features of Earth’s dynamics.

Keywords avian evolution global biogeography divergence times diversification rates K-Pg mass extinction

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.

FREE PDF GRATIS: Science Advances

A transcrição embriônica é controlada pelo estado da cromatina definido maternalmente

domingo, dezembro 20, 2015

Embryonic transcription is controlled by maternally defined chromatin state

Saartje Hontelez, Ila van Kruijsbergen, Georgios Georgiou, Simon J. van Heeringen, Ozren Bogdanovic, Ryan Lister & Gert Jan C. Veenstra

Affiliations Contributions Corresponding author

Nature Communications 6, Article number: 10148 doi:10.1038/ncomms10148

Received 12 May 2015 Accepted 10 November 2015 Published 18 December 2015

Article tools


Histone-modifying enzymes are required for cell identity and lineage commitment, however little is known about the regulatory origins of the epigenome during embryonic development. Here we generate a comprehensive set of epigenome reference maps, which we use to determine the extent to which maternal factors shape chromatin state in Xenopus embryos. Using α-amanitin to inhibit zygotic transcription, we find that the majority of H3K4me3- and H3K27me3-enriched regions form a maternally defined epigenetic regulatory space with an underlying logic of hypomethylated islands. This maternal regulatory space extends to a substantial proportion of neurula stage-activated promoters. In contrast, p300 recruitment to distal regulatory regions requires embryonic transcription at most loci. The results show that H3K4me3 and H3K27me3 are part of a regulatory space that exerts an extended maternal control well into post-gastrulation development, and highlight the combinatorial action of maternal and zygotic factors through proximal and distal regulatory sequences.

Subject terms: Biological sciences Developmental biology Molecular biology

FREE PDF GRATIS: Nature Communications

Grátis livro sobre o Caso de Dover contra o Design Inteligente

sábado, dezembro 19, 2015

Livro Digital Grátis: Traipsing Into Evolution: Intelligent Design and the Kitzmiller vs. Dover Decision

A metilação do DNA: intuições na evolução humana

sexta-feira, dezembro 18, 2015

DNA Methylation: Insights into Human Evolution

Irene Hernando-Herraez , Raquel Garcia-Perez , Andrew J. Sharp , Tomas Marques-Bonet 

Published: December 10, 2015

Source/Fonte: New Scientist, Sep. 2015


A fundamental initiative for evolutionary biologists is to understand the molecular basis underlying phenotypic diversity. A long-standing hypothesis states that species-specific traits may be explained by differences in gene regulation rather than differences at the protein level. Over the past few years, evolutionary studies have shifted from mere sequence comparisons to integrative analyses in which gene regulation is key to understanding species evolution. DNA methylation is an important epigenetic modification involved in the regulation of numerous biological processes. Nevertheless, the evolution of the human methylome and the processes driving such changes are poorly understood. Here, we review the close interplay between Cytosine-phosphate-Guanine (CpG) methylation and the underlying genome sequence, as well as its evolutionary impact. We also summarize the latest advances in the field, revisiting the main literature on human and nonhuman primates. We hope to encourage the scientific community to address the many challenges posed by the field of comparative epigenomics.


Universo eterno? Nunca houve um Big Bang?

Physics Letters B

Volume 741, 4 February 2015, Pages 276–279

Cosmology from quantum potential

Ahmed Farag Ali a,b,∗, Saurya Das c

a Center for Fundamental Physics, Zewail City of Science and Technology, Giza, 12588, Egypt 

b Dept. of Physics, Faculty of Sciences, Benha University, Benha, 13518, Egypt 

c Department of Physics and Astronomy, University of Lethbridge, 4401 University Drive, Lethbridge, Alberta, T1K 3M4, Canada

Source/Fonte: Internet

It was shown recently that replacing classical geodesics with quantal (Bohmian) trajectories gives rise to a quantum corrected Raychaudhuri equation (QRE). In this article we derive the second order Friedmann equations from the QRE, and show that this also contains a couple of quantum correction terms, the first of which can be interpreted as cosmological constant (and gives a correct estimate of its observed value), while the second as a radiation term in the early universe, which gets rid of the big-bang singularity and predicts an infinite age of our universe.

© 2015 The Authors. Published by Elsevier B.V. This is an open access article under the CC BY license

FREE PDF GRATIS: Physics Letters B

Fêmur de hominin tem semelhança com o do gênero Homo de 14.000 anos atrás

A Hominin Femur with Archaic Affinities from the Late Pleistocene of Southwest China

Darren Curnoe , Xueping Ji , Wu Liu, Zhende Bao, Paul S. C. Taçon, Liang Ren

Published: December 17, 2015

Femur MLDG 1678: (A) Anterior view. (B) CT-scan slices at subtrochanteric, approximate half-way and mid-shaft levels. (C) 


The number of Late Pleistocene hominin species and the timing of their extinction are issues receiving renewed attention following genomic evidence for interbreeding between the ancestors of some living humans and archaic taxa. Yet, major gaps in the fossil record and uncertainties surrounding the age of key fossils have meant that these questions remain poorly understood. Here we describe and compare a highly unusual femur from Late Pleistocene sediments at Maludong (Yunnan), Southwest China, recovered along with cranial remains that exhibit a mixture of anatomically modern human and archaic traits. Our studies show that the Maludong femur has affinities to archaic hominins, especially Lower Pleistocene femora. However, the scarcity of later Middle and Late Pleistocene archaic remains in East Asia makes an assessment of systematically relevant character states difficult, warranting caution in assigning the specimen to a species at this time. The Maludong fossil probably samples an archaic population that survived until around 14,000 years ago in the biogeographically complex region of Southwest China.

Citation: Curnoe D, Ji X, Liu W, Bao Z, Taçon PSC, Ren L (2015) A Hominin Femur with Archaic Affinities from the Late Pleistocene of Southwest China. PLoS ONE 10(12): e0143332. doi:10.1371/journal.pone.0143332

Editor: David Caramelli, University of Florence, ITALY

Received: June 3, 2015; Accepted: November 3, 2015; Published: December 17, 2015

Copyright: © 2015 Curnoe 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 available in the paper and its Supporting Information files.

Funding: The authors wish to thank the Australian Research Council (grants DP0877603 & FT120100168), the Yunnan Institute of Cultural Relics and Archaeology (Key Project Grant A-201301), and the University of New South Wales and Griffith University for funding this research.

Competing interests: The authors have declared that no competing interests exist.


A origem e diversificação dos eucariotos: problemas com a filogenética molecular e cálculo do relógio molecular

The origin and diversification of eukaryotes: problems with molecular phylogenetics and molecular clock estimation

Andrew J Roger, Laura A Hug

Published 29 June 2006.DOI: 10.1098/rstb.2006.1845


Determining the relationships among and divergence times for the major eukaryotic lineages remains one of the most important and controversial outstanding problems in evolutionary biology. The sequencing and phylogenetic analyses of ribosomal RNA (rRNA) genes led to the first nearly comprehensive phylogenies of eukaryotes in the late 1980s, and supported a view where cellular complexity was acquired during the divergence of extant unicellular eukaryote lineages. More recently, however, refinements in analytical methods coupled with the availability of many additional genes for phylogenetic analysis showed that much of the deep structure of early rRNA trees was artefactual. Recent phylogenetic analyses of a multiple genes and the discovery of important molecular and ultrastructural phylogenetic characters have resolved eukaryotic diversity into six major hypothetical groups. Yet relationships among these groups remain poorly understood because of saturation of sequence changes on the billion-year time-scale, possible rapid radiations of major lineages, phylogenetic artefacts and endosymbiotic or lateral gene transfer among eukaryotes.

Estimating the divergence dates between the major eukaryote lineages using molecular analyses is even more difficult than phylogenetic estimation. Error in such analyses comes from a myriad of sources including: (i) calibration fossil dates, (ii) the assumed phylogenetic tree, (iii) the nucleotide or amino acid substitution model, (iv) substitution number (branch length) estimates, (v) the model of how rates of evolution change over the tree, (vi) error inherent in the time estimates for a given model and (vii) how multiple gene data are treated. By reanalysing datasets from recently published molecular clock studies, we show that when errors from these various sources are properly accounted for, the confidence intervals on inferred dates can be very large. Furthermore, estimated dates of divergence vary hugely depending on the methods used and their assumptions. Accurate dating of divergence times among the major eukaryote lineages will require a robust tree of eukaryotes, a much richer Proterozoic fossil record of microbial eukaryotes assignable to extant groups for calibration, more sophisticated relaxed molecular clock methods and many more genes sampled from the full diversity of microbial eukaryotes.

I would not say that the future is necessarily less predictable than the past. I think the past was not predictable when it started. (Donald Rumsfeld)