O vento não será a tua herança

segunda-feira, fevereiro 08, 2016


DISINHERIT THE WIND from Matt Chait on Vimeo.

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Matt Chait, dramaturgo e artista residente em Los Angeles vira de cabeça o filme O vento será a tua herança - mais uma peça de propaganda do que história qua história sobre o Processo do Macaco de Scopes, e acrescentou mais um personagem à estória: Robert Hawkins (soa como Richard Dawkins...).


Nova pesquisa contesta o papel de Júpiter como escudo planetário protetor da Terra

quinta-feira, fevereiro 04, 2016

Jupiter: Cosmic Jekyll and Hyde

To cite this article:

Grazier Kevin R.. Astrobiology. January 2016, 16(1): 23-38. doi:10.1089/ast.2015.1321.

Published in Volume: 16 Issue 1: January 20, 2016

Online Ahead of Print: December 23, 2015

Author information

Kevin R. Grazier
Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California.

Address correspondence to:

Kevin R. Grazier
Jet Propulsion Laboratory
California Institute of Technology
Pasadena, CA

E-mail: kevin_grazier@yahoo.com

Submitted 17 March 2015 Accepted 18 July 2015 


Source/Fonte: NASA

Abstract

It has been widely reported that Jupiter has a profound role in shielding the terrestrial planets from comet impacts in the Solar System, and that a jovian planet is a requirement for the evolution of life on Earth. To evaluate whether jovians, in fact, shield habitable planets from impacts (a phenomenon often referred to as the “Jupiter as shield” concept), this study simulated the evolution of 10,000 particles in each of the jovian inter-planet gaps for the cases of full-mass and embryo planets for up to 100 My. The results of these simulations predict a number of phenomena that not only discount the “Jupiter as shield” concept, they also predict that in a Solar System like ours, large gas giants like Saturn and Jupiter had a different, and potentially even more important, role in the evolution of life on our planet by delivering the volatile-laden material required for the formation of life.

The simulations illustrate that, although all particles occupied “non-life threatening” orbits at their onset of the simulations, a significant fraction of the 30,000 particles evolved into Earth-crossing orbits. A comparison of multiple runs with different planetary configurations revealed that Jupiter was responsible for the vast majority of the encounters that “kicked” outer planet material into the terrestrial planet region, and that Saturn assisted in the process far more than has previously been acknowledged. Jupiter also tends to “fix” the aphelion of planetesimals at its orbit irrespective of their initial starting zones, which has the effect of slowing their passages through the inner Solar System, and thus potentially improving the odds of accretion of cometary material by terrestrial planets. As expected, the simulations indicate that the full-mass planets perturb many objects into the deep outer Solar System, or eject them entirely; however, planetary embryos also did this with surprising efficiency. Finally, the simulations predict that Jupiter's capacity to shield or intercept Earth-bound comets originating in the outer Solar System is poor, and that the importance of jovian planets on the formation of life is not that they act as shields, but rather that they deliver life-enabling volatiles to the terrestrial planets. 

Key Words: Asteroid—Comets—Interstellar meteorites—Extrasolar terrestrial planets—Simulation. 

Astrobiology 16, 23–38.

FREE PDF GRATIS: Astrobiology

IsisCB Explore: um serviço Open Access de localização de artigos, dissertações, teses e pesquisas em História da Ciência


Please consider using the *IsisCB Explore History of Science Index* (isiscb.org/explore) for your research, and encourage your library or department to add it to their list of resources. Accessible to anyone on the web, *IsisCB Explore* is a completely open access service made possible by the History of Science Society with support from the University of Oklahoma.

*IsisCB Explore* opens up bibliographical research in the history of science, technology, and medicine. It is designed for students, scholars, librarians, and the general public. Users will find the data architecture intuitive and powerful, and librarians can trust that it will guide researchers to the best literature in the discipline.

Based on the 100-year-old *Isis Current Bibliography of the History of Science*—the largest and most comprehensive in its field—it is supported by the discipline's flagship society, the History of Science Society. It will be expanded and updated annually.

Key features include:

- Nearly 200,000 interlinked bibliographic citations to books, chapters, articles, dissertations, and reviews from the *Isis Bibliography of the History of Science* 1974 to present. Annually updated.

- An authority index of over 150,000 curated entries. Includes historical concepts, persons, and institutions. Also indexes scholars, publishers, journals, and degree granting institutions.

- A navigation interface built specifically for history of science research. Enables focused searches on ancient, medieval, modern and non-Western topics.

- A state-of-the-art network architecture with complex interlinking of citation and authority records.

- Integrated social media tools, including public user comments as well as Twitter and Facebook sharing.

- User accounts with the ability to save searches.

- Zotero integration. Allows users to save individual citations as well as collected results.

- Automated access, with a REST API.

- A search widget for your website.

- *Coming soon:* A link resolver, giving library patrons immediate access to your library’s holdings.

There are some instructional videos on the IsisCB Explore YouTube Channel 


The introductory video 
<https://www.youtube.com/watch?v=ntqtn0tyy-E> gives you a quick overview. You can find more information about the history of the Isis

Bibliography on the main site: isiscb.org.

Contact Stephen Weldon (spweldon@ou.edu) with questions.

Stephen P. Weldon

Assistant Professor of History of Science
Editor, Isis Bibliography of the History of Science
Department of History of Science
University of Oklahoma
601 Elm, Room 618
Norman, OK 73019-3106


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NOTA DESTE BLOGGER:

Até que enfim, além do Google Scholar, surgiu um website de buscas sobre História da Ciência Open Access. Milhares de historiadores de ciência agora vão poder continuar suas pesquisas com mais facilidade e sem precisar se deslocar frequentemente para as bibliotecas universitárias.

Parabéns!!!

Pesquisadores desclassificam os dinossauros como sendo os tataravós das aves

terça-feira, fevereiro 02, 2016

Journal of Ornithology

October 2014, Volume 155, Issue 4, pp 841-851

First online: 09 July 2014

Jurassic archosaur is a non-dinosaurian bird

Stephen A. Czerkas, Alan Feduccia

Abstract

Re-examination utilizing Keyence 3D digital microscopy and low angled illumination of the fossil Scansoriopteryx, a problematic sparrow-size pre-Archaeopteryx specimen from the Jurassic Daohugou Biotas, provides new evidence which challenges the widely accepted hypothesis that birds are derived from dinosaurs in which avian flight originated from cursorial forms. Contrary to previous interpretations in which Scansoriopteryx was considered to be a coelurosaurian theropod dinosaur, the absence of fundamental dinosaurian characteristics demonstrates that it was not derived from a dinosaurian ancestry and should not be considered as a theropod dinosaur. Furthermore, the combination in which highly plesiomorphic non-dinosaurian traits are retained along with highly derived features, yet only the beginnings of salient birdlike characteristics, indicates that the basal origins of Aves stemmed from outside the Dinosauria and further back to basal archosaurs. Impressions of primitive elongate feathers on the forelimbs and hindlimbs suggest that Scansoriopteryx represents a basal form of “tetrapteryx” in which incipient aerodynamics involving parachuting or gliding was possible. Along with unique adaptations for an arboreal lifestyle, Scansoriopteryx fulfills predictions from the early twentieth century that the ancestors of birds did not evolve from dinosaurs, and instead were derived from earlier arboreal archosaurs which originated flight according to the traditional trees-down scenario.

Keywords

Scansoriopteryx Epidendrosaurus Theropod Archosaur Daohugou Biota Jurassic

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Subscription or payment needed/Requer assinatura ou pagamento: Journal of Ornithology.

Uma visão CRISPR de desenvolvimento

A CRISPR view of development

Melissa M. Harrison 1, Brian V. Jenkins 2, Kate M. O’Connor-Giles 3,4 and Jill Wildonger 2

- Author Affiliations

1Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53706, USA;

2Biochemistry Department, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA;

3Laboratory of Genetics,

4Laboratory of Cell and Molecular Biology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA

Corresponding author: wildonger@wisc.edu


Abstract

The CRISPR (clustered regularly interspaced short palindromic repeat)–Cas9 (CRISPR-associated nuclease 9) system is poised to transform developmental biology by providing a simple, efficient method to precisely manipulate the genome of virtually any developing organism. This RNA-guided nuclease (RGN)-based approach already has been effectively used to induce targeted mutations in multiple genes simultaneously, create conditional alleles, and generate endogenously tagged proteins. Illustrating the adaptability of RGNs, the genomes of >20 different plant and animal species as well as multiple cell lines and primary cells have been successfully modified. Here we review the current and potential uses of RGNs to investigate genome function during development.

Keywords

CRISPR Cas9 development genome editing genome engineering RNA-guided nuclease

Footnotes

Article is online at 


Freely available online through the Genes & Development Open Access option.

© 2014 Harrison et al.; Published by Cold Spring Harbor Laboratory Press

This article, published in Genes & Development, is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.

FREE PDF GRATIS: Genes and Development

Colocando limites em ruído bioquímico

segunda-feira, fevereiro 01, 2016

Constraints on Fluctuations in Sparsely Characterized Biological Systems

Andreas Hilfinger,1 Thomas M. Norman, 1 Glenn Vinnicombe, 2 and Johan Paulsson 1,*

Department of Systems Biology, Harvard University, 200 Longwood Avenue, Boston, Massachusetts 02115, USA 

Department of Engineering, University of Cambridge, Cambridge CB2 1PZ, United Kingdom

(Received 27 August 2015; published 1 February 2016)


Abstract

Biochemical processes are inherently stochastic, creating molecular fluctuations in otherwise identical cells. Such “noise” is widespread but has proven difficult to analyze because most systems are sparsely characterized at the single cell level and because nonlinear stochastic models are analytically intractable. Here, we exactly relate average abundances, lifetimes, step sizes, and covariances for any pair of components in complex stochastic reaction systems even when the dynamics of other components are left unspecified. Using basic mathematical inequalities, we then establish bounds for whole classes of systems. These bounds highlight fundamental trade-offs that show how efficient assembly processes must invariably exhibit large fluctuations in subunit levels and how eliminating fluctuations in one cellular component requires creating heterogeneity in another.

FREE PDF GRATIS: Physical Review Letters

Decifrando a linguagem do cérebro: Brain Activity Map Project

The Brain Activity Map Project and the Challenge of Functional Connectomics

A. Paul Alivisatos, Miyoung Chun, George M. Church, Ralph J. Greenspan, Michael L. Roukes, Rafael Yuste correspondence email

Open Archive




Summary

The function of neural circuits is an emergent property that arises from the coordinated activity of large numbers of neurons. To capture this, we propose launching a large-scale, international public effort, the Brain Activity Map Project, aimed at reconstructing the full record of neural activity across complete neural circuits. This technological challenge could prove to be an invaluable step toward understanding fundamental and pathological brain processes.

© 2012 Elsevier Inc. Published by Elsevier Inc.

FREE PDF GRATIS: Neuron

Mattick balançando os fundamentos da genética molecular

Rocking the foundations of molecular genetics

John S. Mattick

Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia



In PNAS, Nelson et al. present intriguing evidence that challenges the fundamental tenets of genetics (1). It has long been assumed that the inherited contribution to phenotype is embedded in DNA sequence variations in, and interactions between, the genes endogenous to the organism, i.e., alleles derived from parents with some degree of de novo variation. This assumption underlies most genetic analysis, including the fleet of genome-wide association studies launched in recent years to identify genomic loci that influence complex human traits and diseases. Not surprisingly, in contrast to mutations in protein-coding sequences, which underlie high penetrance monogenic disorders, the vast majority of the identified loci map to non–proteincoding intergenic and intronic regions, which comprise the vast majority of the genome. These regions contain the regulatory information that controls gene expression and underlies most phenotypic variation (2).

However, the perplexing and much debated surprise has been that most genomewide association studies have superficially failed to locate more than a small percentage of the inherited component of complex traits. This may be a result of a number of possibilities that are not mutually exclusive (3, 4), including systematic underestimation of the fraction of the heritability and epistatic interactions measured by common SNPs used to monitor haplotype blocks, a larger than expected contribution of rare recent variants that lie under the SNP typing radar, and intergenerational epigenetic inheritance (5), which is not polled by DNA sequence. However, the latter has not thus far been paid much attention or given much credence as a major factor.
...

FREE PDF GRATIS: PNAS

Assimetria quântica entre tempo e espaço: por que o tempo segue em frente?

Quantum asymmetry between time and space

Joan A. Vaccaro

Published 20 January 2016.DOI: 10.1098/rspa.2015.0670


Sketches illustrate the translation of wave functions along (a) the x-axis and (b) the time axis. In (a), the wave functions represent the position eigenket |xx and an arbitrary state |χ〉 and the translation is by a distance δx. In (b), the wave function represents the state |f〉 and the translation is by an interval t.

Abstract

An asymmetry exists between time and space in the sense that physical systems inevitably evolve over time, whereas there is no corresponding ubiquitous translation over space. The asymmetry, which is presumed to be elemental, is represented by equations of motion and conservation laws that operate differently over time and space. If, however, the asymmetry was found to be due to deeper causes, this conventional view of time evolution would need reworking. Here we show, using a sum-over-paths formalism, that a violation of time reversal (T) symmetry might be such a cause. If T symmetry is obeyed, then the formalism treats time and space symmetrically such that states of matter are localized both in space and in time. In this case, equations of motion and conservation laws are undefined or inapplicable. However, if T symmetry is violated, then the same sum over paths formalism yields states that are localized in space and distributed without bound over time, creating an asymmetry between time and space. Moreover, the states satisfy an equation of motion (the Schrödinger equation) and conservation laws apply. This suggests that the time–space asymmetry is not elemental as currently presumed, and that T violation may have a deep connection with time evolution.

FREE PDF GRATIS: Proc. R. Soc. A

Tentando resolver as discrepâncias entre o relógio molecular e a evolução humanos/hominídeos

domingo, janeiro 31, 2016

Life history effects on the molecular clock of autosomes and sex chromosomes

Guy Amster a,1 and Guy Sella a,1

Author Affiliations

aDepartment of Biological Sciences, Columbia University, New York, NY 10027

Edited by Michael Lynch, Indiana University, Bloomington, IN, and approved December 7, 2015 (received for review August 9, 2015)


Significance

Recent estimates of mutation rates obtained by sequencing human pedigrees have challenged conceptions about split times between humans and our closest living relatives. In particular, estimates of human split times from chimpanzees and gorillas based on the new mutation rate estimates are more than twofold shorter than previously believed, seemingly at odds with the fossil record. Here we show that accounting for the effects of sex-specific life histories on mutation rates along the hominid phylogeny largely bridges this apparent gap and leads to more accurate split time estimates. Doing so can also explain other intriguing phylogenetic patterns in hominid and mammalian evolution.

Abstract

One of the foundational results in molecular evolution is that the rate at which neutral substitutions accumulate on a lineage equals the rate at which mutations arise. Traits that affect rates of mutation therefore also affect the phylogenetic “molecular clock.” We consider the effects of sex-specific generation times and mutation rates in species with two sexes. In particular, we focus on the effects that the age of onset of male puberty and rates of spermatogenesis have likely had in hominids (great apes), considering a model that approximates features of the mutational process in mammals, birds, and some other vertebrates. As we show, this model can account for a number of seemingly disparate observations: notably, the puzzlingly low X-to-autosome ratios of substitution rates in humans and chimpanzees and differences in rates of autosomal substitutions among hominine lineages (i.e., humans, chimpanzees, and gorillas). The model further suggests how to translate pedigree-based estimates of human mutation rates into split times among extant hominoids (apes), given sex-specific life histories. In so doing, it largely bridges the gap reported between estimates of split times based on fossil and molecular evidence, in particular suggesting that the human–chimpanzee split may have occurred as recently as 6.6 Mya. The model also implies that the “generation time effect” should be stronger in short-lived species, explaining why the generation time has a major influence on yearly substitution rates in mammals but only a subtle one in human pedigrees.

molecular clock mutational slowdown generation time effect human–chimpanzee split male mutation bias

Footnotes

1To whom correspondence may be addressed. Email: ga2373@columbia.edu or gs2747@columbia.edu.

Author contributions: G.A. and G.S. designed research; G.A. and G.S. performed research; and G.A. and G.S. 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.1515798113/-/DCSupplemental.

Freely available online through the PNAS open access option.

FREE PDF GRATIS: PNAS

Tamanho das pernas associado à capacidade de corrida em dinossauros carnívoros bípedes

sábado, janeiro 30, 2016

An approach to scoring cursorial limb proportions in carnivorous dinosaurs and an attempt to account for allometry

W. Scott Persons IV & Philip J. Currie

Scientific Reports 6, Article number: 19828 (2016)


Biomechanics | Palaeontology

Received: 18 June 2015 Accepted: 15 December 2015 
Published online: 27 January 2016




Abstract

From an initial dataset of 53 theropod species, the general relationship between theropod lower-leg length and body mass is identified. After factoring out this allometric relationship, theropod hindlimb proportions are assessed irrespective of body mass. Cursorial-limb-proportion (CLP) scores derived for each of the considered theropod taxa offer a measure of the extent to which a particular species deviates in favour of higher or lower running speeds. Within the same theropod species, these CLP scores are found to be consistent across multiple adult specimens and across disparate ontogenetic stages. Early theropods are found to have low CLP scores, while the coelurosaurian tyrannosauroids and compsognathids are found to have high CLP scores. Among deinonychosaurs, troodontids have consistently high CLP scores, while many dromaeosaur taxa, including Velociraptor and Deinonychus, have low CLP scores. This indicates that dromaeosaurs were not, overall, a particularly cursorily adapted group. Comparisons between the CLP scores of Tyrannosaurus and specimens referred to the controversial genus Nanotyrannus indicate a strong discrepancy in cursorial adaptations, which supports the legitimacy of Nanotyrannus and the previous suggestions of ecological partitioning between Nanotyrannus and the contemporaneous Tyrannosaurus.

FREE PDF GRATIS: Scientific Reports

Os dois lados do cérebro processam números!

sexta-feira, janeiro 29, 2016

Neuroimaging Evidence of a Bilateral Representation for Visually Presented Numbers

Mareike Grotheer 1,2, Karl-Heinz Herrmann 3, and Gyula Kovács 1,2

-Show Affiliations

1Institute of Psychology, Friedrich Schiller University Jena, 07737 Jena, Germany,

2Deutsche Forschungsgemeinschaft Research Unit Person Perception, Friedrich Schiller University Jena, 07743 Jena, Germany, and

3Medical Physics Group, Institute for Diagnostic and Interventional Radiology, Jena University Hospital, 07743 Jena, Germany

Author contributions: M.G., K.-H.H., and G.K. designed research; M.G. and K.-H.H. performed research; M.G. analyzed data; M.G., K.-H.H., and G.K. wrote the paper.

The Journal of Neuroscience, 6 January 2016, 36(1): 88-97; doi: 10.1523/JNEUROSCI.2129-15.2016


Abstract

The clustered architecture of the brain for different visual stimulus categories is one of the most fascinating topics in the cognitive neurosciences. Interestingly, recent research suggests the existence of additional regions for newly acquired stimuli such as letters (letter form area; LFA; Thesen et al., 2012) and numbers (visual number form area; NFA;Shum et al., 2013). However, neuroimaging methods thus far have failed to visualize the NFA in healthy participants, likely due to fMRI signal dropout caused by the air/bone interface of the petrous bone (Shum et al., 2013). In the current study, we combined a 64-channel head coil with high spatial resolution, localized shimming, and liberal smoothing, thereby decreasing the signal dropout and increasing the temporal signal-to-noise ratio in the neighborhood of the NFA. We presented subjects with numbers, letters, false numbers, false letters, objects and their Fourier randomized versions. A group analysis showed significant activations in the inferior temporal gyrus at the previously proposed location of the NFA. Crucially, we found the NFA to be present in both hemispheres. Further, we could identify the NFA on the single-subject level in most of our participants. A detailed analysis of the response profile of the NFA in two separate experiments confirmed the whole-brain results since responses to numbers were significantly higher than to any other presented stimulus in both hemispheres. Our results show for the first time the existence and stimulus selectivity of the NFA in the healthy human brain.
SIGNIFICANCE STATEMENT This fMRI study shows for the first time a cluster of neurons selective for visually presented numbers in healthy human adults. This visual number form area (NFA) was found in both hemispheres. Crucially, numbers have gained importance for humans too recently for neuronal specialization to be established by evolution. Therefore, investigations of this region will greatly advance our understanding of learning and plasticity in the brain. In addition, these results will aid our knowledge regarding related neurological illnesses (e.g., dyscalculia). To overcome the fMRI signal dropout in the neighborhood of the NFA, we combined high spatial resolution with liberal smoothing. We believe that this approach will be useful to the broad neuroimaging community.
  • Received June 2, 2015.
  • Revision received October 20, 2015.
  • Accepted November 15, 2015.
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A ilusão da árvore baseada em genes!!!

quinta-feira, janeiro 28, 2016

Molecular Phylogenetics and Evolution

Volume 94, Part A, January 2016, Pages 1–33


Mark S. Springe, John Gatesy, 

Department of Biology, University of California, Riverside, CA 92521, USA

Received 19 March 2015, Revised 4 June 2015, Accepted 22 July 2015, Available online 31 July 2015



Highlights

• Empirical data suggest coalescence-genes are tiny owing to the recombination ratchet.

• Coalescence methods have not solved difficult problems in mammalian phylogeny.

• Recent simulation studies that favor coalescence over concatenation are flawed.

Abstract

Higher-level relationships among placental mammals are mostly resolved, but several polytomies remain contentious. Song et al. (2012) claimed to have resolved three of these using shortcut coalescence methods (MP-EST, STAR) and further concluded that these methods, which assume no within-locus recombination, are required to unravel deep-level phylogenetic problems that have stymied concatenation. Here, we reanalyze Song et al.’s (2012) data and leverage these re-analyses to explore key issues in systematics including the recombination ratchet, gene tree stoichiometry, the proportion of gene tree incongruence that results from deep coalescence versus other factors, and simulations that compare the performance of coalescence and concatenation methods in species tree estimation. Song et al. (2012) reported an average locus length of 3.1 kb for the 447 protein-coding genes in their phylogenomic dataset, but the true mean length of these loci (start codon to stop codon) is 139.6 kb. Empirical estimates of recombination breakpoints in primates, coupled with consideration of the recombination ratchet, suggest that individual coalescence genes (c-genes) approach ∼12 bp or less for Song et al.’s (2012) dataset, three to four orders of magnitude shorter than the c-genes reported by these authors. This result has general implications for the application of coalescence methods in species tree estimation. We contend that it is illogical to apply coalescence methods to complete protein-coding sequences. Such analyses amalgamate c-genes with different evolutionary histories (i.e., exons separated by >100,000 bp), distort true gene tree stoichiometry that is required for accurate species tree inference, and contradict the central rationale for applying coalescence methods to difficult phylogenetic problems. In addition, Song et al.’s (2012) dataset of 447 genes includes 21 loci with switched taxonomic names, eight duplicated loci, 26 loci with non-homologous sequences that are grossly misaligned, and numerous loci with >50% missing data for taxa that are misplaced in their gene trees. These problems were compounded by inadequate tree searches with nearest neighbor interchange branch swapping and inadvertent application of substitution models that did not account for among-site rate heterogeneity. Sixty-six gene trees imply unrealistic deep coalescences that exceed 100 million years (MY). Gene trees that were obtained with better justified models and search parameters show large increases in both likelihood scores and congruence. Coalescence analyses based on a curated set of 413 improved gene trees and a superior coalescence method (ASTRAL) support a Scandentia (treeshrews) + Glires (rabbits, rodents) clade, contradicting one of the three primary systematic conclusions of Song et al. (2012). Robust support for a Perissodactyla + Carnivora clade within Laurasiatheria is also lost, contradicting a second major conclusion of this study. Song et al.’s (2012) MP-EST species tree provided the basis for circular simulations that led these authors to conclude that the multispecies coalescent accounts for 77% of the gene tree conflicts in their dataset, but many internal branches of their MP-EST tree are stunted by an order of magnitude or more due to wholesale gene tree reconstruction errors. An independent assessment of branch lengths suggests the multispecies coalescent accounts for ⩽15% of the conflicts among Song et al.’s (2012) 447 gene trees. Unfortunately, Song et al.’s (2012) flawed phylogenomic dataset has been used as a model for additional simulation work that suggests the superiority of shortcut coalescence methods relative to concatenation. Investigator error was passed on to the subsequent simulation studies, which also incorporated further logical errors that should be avoided in future simulation studies. Illegitimate branch length switches in the simulation routines unfairly protected coalescence methods from their Achilles’ heel, high gene tree reconstruction error at short internodes. These simulations therefore provide no evidence that shortcut coalescence methods out-compete concatenation at deep timescales. In summary, the long c-genes that are required for accurate reconstruction of species trees using shortcut coalescence methods do not exist and are a delusion. Coalescence approaches based on SNPs that are widely spaced in the genome avoid problems with the recombination ratchet and merit further pursuit in both empirical systematic research and simulations.

Abbreviations

ASTRAL, Accurate Species TRee ALgorithm; bp, basepairs; c-gene, coalescence gene; CI, consistency index; CUs, coalescent units; GTR, general time reversible; ILS, incomplete lineage sorting; ML, maximum likelihood; MP-EST, maximum pseudo-likelihood for estimating species trees; MY, million years; MYA, million years ago; NNI, nearest neighbor interchange; RF distance, Robinson–Foulds distance; SNPs, single nucleotide polymorphisms; SPR, subtree pruning and regrafting; STAR, species tree estimation using average ranks of coalescences; TBR, tree bisection and reconnection; UCEs, ultra-conserved elements

Keywords: C-gene; Concatalescence; Deep coalescence; Gene tree; Species tree

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Homologia complexa e a evolução dos sistemas nervosos

Complex Homology and the Evolution of Nervous Systems

Benjamin J. Liebeskind correspondence email, David M. Hillis, Harold H. Zakon, Hans A. Hofmann


Article Info Publication History Published Online: December 30, 2015



Summary

We examine the complex evolution of animal nervous systems and discuss the ramifications of this complexity for inferring the nature of early animals. Although reconstructing the origins of nervous systems remains a central challenge in biology, and the phenotypic complexity of early animals remains controversial, a compelling picture is emerging. We now know that the nervous system and other key animal innovations contain a large degree of homoplasy, at least on the molecular level. Conflicting hypotheses about early nervous system evolution are due primarily to differences in the interpretation of this homoplasy. We highlight the need for explicit discussion of assumptions and discuss the limitations of current approaches for inferring ancient phenotypic states.

Trends

New phylogenetic evidence suggests that nervous systems are not monophyletic. There is a debate about whether this indicates a single origin of nervous systems with several losses or multiple independent origins of neurons.

Comparative genomics studies have found that many of the gene families associated with extant nervous system function were present before the origin of animals. However, changes at the biophysical level and gene family expansions occurred independently in several animal lineages, suggesting widespread homoplasy in nervous systems.

Fossils of the first animals are microscopic, about the same size as the larvae of various extant marine species, which display complex behavior although only some have nervous systems. Together with colonial choanoflagellates, these larvae may provide the best model systems for understanding behavior and the origin of nervous systems in early animals.

A escala de tempo da taxa de recombinação da evolução em grandes primatas

terça-feira, janeiro 26, 2016

The Time Scale of Recombination Rate Evolution in Great Apes

Laurie S. Stevison *,1,2, August E. Woerner 3,4, Jeffrey M. Kidd 5,6, Joanna L. Kelley 7,8, Krishna R. Veeramah 3,9, Kimberly F. McManus 10,11, Great Ape Genome Project 12, Carlos D. Bustamante 8, Michael F. Hammer 3,13,14 and Jeffrey D. Wall *,1,15

+ Author Affiliations

1Institute for Human Genetics, University of California San Francisco

2Department of Biological Sciences, Auburn University

3Arizona Research Laboratories, Division of Biotechnology, University of Arizona

4Department of Genetics, University of Arizona

5Department of Human Genetics, University of Michigan

6Department of Computational Medicine & Bioinformatics, University of Michigan

7School of Biological Sciences, Washington State University

8Department of Genetics, Stanford University

9Department of Ecology and Evolution, Stony Brook University

10Department of Biology, Stanford University

11Department of Biomedical Informatics, Stanford University

12Great Ape Genome Project, contributors Listed in Supplement

13Department of Ecology and Evolutionary Biology, University of Arizona

14Department of Anthropology, University of Arizona

15Department of Epidemiology & Biostatistics, University of California San Francisco

↵*Corresponding author: E-mail: lss0021@auburn.edu; wallj@humgen.ucsf.edu.

Received May 24, 2015. Revision received November 19, 2015. Accepted November 23, 2015.



We present three linkage-disequilibrium (LD)-based recombination maps generated using whole-genome sequence data from 10 Nigerian chimpanzees, 13 bonobos, and 15 western gorillas, collected as part of the Great Ape Genome Project (Prado-Martinez J, et al. 2013. Great ape genetic diversity and population history. Nature 499:471–475). We also identified species-specific recombination hotspots in each group using a modified LDhot framework, which greatly improves statistical power to detect hotspots at varying strengths. We show that fewer hotspots are shared among chimpanzee subspecies than within human populations, further narrowing the time scale of complete hotspot turnover. Further, using species-specific PRDM9 sequences to predict potential binding sites (PBS), we show higher predicted PRDM9 binding in recombination hotspots as compared to matched cold spot regions in multiple great ape species, including at least one chimpanzee subspecies. We found that correlations between broad-scale recombination rates decline more rapidly than nucleotide divergence between species. We also compared the skew of recombination rates at centromeres and telomeres between species and show a skew from chromosome means extending as far as 10–15 Mb from chromosome ends. Further, we examined broad-scale recombination rate changes near a translocation in gorillas and found minimal differences as compared to other great ape species perhaps because the coordinates relative to the chromosome ends were unaffected. Finally, on the basis of multiple linear regression analysis, we found that various correlates of recombination rate persist throughout the African great apes including repeats, diversity, and divergence. Our study is the first to analyze within- and between-species genome-wide recombination rate variation in several close relatives.

Key words recombination PRDM9 hotspots primates

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