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

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)

Source/Fonte

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.

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

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)

doi:10.1038/srep19828

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.

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Os dois lados do cérebro processam números!

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

Source/Fonte

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.

• high-resolution fMRI
 
• inferior temporal gyrus
 
• letter
 
• number
 
• signal-to-noise ratio
• vision

• Received June 2, 2015.
• Revision received October 20, 2015.
• Accepted November 15, 2015.

• Copyright © 2016 the authors 0270-6474/16/360088-10$15.00/0

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A ilusão da árvore baseada em genes!!!

Molecular Phylogenetics and Evolution

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

The gene tree delusion

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

doi:10.1016/j.ympev.2015.07.018

Source/Fonte

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

DOI: http://dx.doi.org/10.1016/j.tree.2015.12.005

Article Info Publication History Published Online: December 30, 2015

Source/Fonte

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

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.

Source/Fonte

Abstract

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

© The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com

Relógios quânticos primordiais padrões

Quantum Primordial Standard Clocks

Xingang Chen, Mohammad Hossein Namjoo, Yi Wang

(Submitted on 14 Sep 2015 (v1), last revised 22 Jan 2016 (this version, v2))

Source/Fonte

Abstract

In this paper, we point out and study a generic type of signals existing in the primordial universe models, which can be used to model-independently distinguish the inflation scenario from alternatives. These signals are generated by massive fields that function as standard clocks. The role of massive fields as standard clocks has been realized in previous works. Although the existence of such massive fields is generic, the previous realizations require sharp features to classically excite the oscillations of the massive clock fields. Here, we point out that the quantum fluctuations of massive fields can actually serve the same purpose as the standard clocks. We show that they are also able to directly record the defining property of the scenario type, namely, the scale factor of the primordial universe as a function of time a(t), but through shape-dependent oscillatory features in non-Gaussianities. Since quantum fluctuating massive fields exist in any realistic primordial universe models, these quantum primordial standard clock signals are present in any inflation models, and should exist quite generally in alternative-to-inflation scenarios as well. However, the amplitude of such signals is very model-dependent.

Comments: 41 pages, v2, minor revision: clarification remarks added, minor corrections, references added, to appear in the Journal of Cosmology and Astroparticle Physics

Subjects: Cosmology and Nongalactic Astrophysics (astro-ph.CO); High Energy Physics - Phenomenology (hep-ph); High Energy Physics - Theory (hep-th)

Cite as: arXiv:1509.03930 [astro-ph.CO]

(or arXiv:1509.03930v2 [astro-ph.CO] for this version)

Submission history

From: Xingang Chen [view email] 

[v1] Mon, 14 Sep 2015 02:31:18 GMT (365kb,D)

[v2] Fri, 22 Jan 2016 17:25:40 GMT (370kb,D)

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Mohammad Hossein Namjoo

Primordial Standard Clock: Inflation or not Inflation 

Transição evolutiva do promotor e da metilação no corpo de gene do DNA através da fronteira de invertebrados-vertebrados

Evolutionary Transition of Promoter and Gene Body DNA Methylation across Invertebrate–Vertebrate Boundary

Thomas E. Keller 1, Priscilla Han 1 and Soojin V. Yi *,1

- Author Affiliations

1School of Biology, Georgia Institute of Technology

↵*Corresponding author: E-mail: soojinyi@gatech.edu.

Abstract

Genomes of invertebrates and vertebrates exhibit highly divergent patterns of DNA methylation. Invertebrate genomes tend to be sparsely methylated, and DNA methylation is mostly targeted to a subset of transcription units (gene bodies). In a drastic contrast, vertebrate genomes are generally globally and heavily methylated, punctuated by the limited local hypo-methylation of putative regulatory regions such as promoters. These genomic differences also translate into functional differences in DNA methylation and gene regulation. Although promoter DNA methylation is an important regulatory component of vertebrate gene expression, its role in invertebrate gene regulation has been little explored. Instead, gene body DNA methylation is associated with expression of invertebrate genes. However, the evolutionary steps leading to the differentiation of invertebrate and vertebrate genomic DNA methylation remain unresolved. Here we analyzed experimentally determined DNA methylation maps of several species across the invertebrate–vertebrate boundary, to elucidate how vertebrate gene methylation has evolved. We show that, in contrast to the prevailing idea, a substantial number of promoters in an invertebrate basal chordate Ciona intestinalis are methylated. Moreover, gene expression data indicate significant, epigenomic context-dependent associations between promoter methylation and expression in C. intestinalis. However, there is no evidence that promoter methylation in invertebrate chordate has been evolutionarily maintained across the invertebrate–vertebrate boundary. Rather, body-methylated invertebrate genes preferentially obtain hypo-methylated promoters among vertebrates. Conversely, promoter methylation is preferentially found in lineage- and tissue-specific vertebrate genes. These results provide important insights into the evolutionary origin of epigenetic regulation of vertebrate gene expression.

Key words DNA methylation chordate evolution promoter DNA methylation gene expression epigenetic regulation.

© The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com

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Dinâmica reguladora de lacuna de genes evolui ao longo de uma rede genotípica

Gap gene regulatory dynamics evolve along a genotype network

Anton Crombach1,2,*,†, Karl R. Wotton1,2,*, Eva Jiménez-Guri1,2 and Johannes Jaeger1,2,†

- Author Affiliations

1. EMBL/CRG Research Unit in Systems Biology, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003 Barcelona, Spain

2. Universitat Pompeu Fabra (UPF), 08002 Barcelona, Spain

↵† Corresponding authors: Anton Crombach: anton.crombach@crg.eu, Johannes Jaeger: yogi.jaeger@crg.eu, EMBL/CRG Research Unit in Systems Biology, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003 Barcelona, Spain. Tel.: +34 93 316 00 85, Fax: +34 93 396 99 83

Received September 8, 2015. Revision received December 4, 2015. Accepted January 11, 2016.

Abstract

Developmental gene networks implement the dynamic regulatory mechanisms that pattern and shape the organism. Over evolutionary time, the wiring of these networks changes, yet the patterning outcome is often preserved, a phenomenon known as “system drift”. System drift is illustrated by the gap gene network—involved in segmental patterning—in dipteran insects. In the classic model organism Drosophila melanogaster and the non-model scuttle fly Megaselia abdita, early activation and placement of gap gene expression domains show significant quantitative differences, yet the final patterning output of the system is essentially identical in both species. In this detailed modeling analysis of system drift, we use gene circuits which are fit to quantitative gap gene expression data in M. abdita and compare them to an equivalent set of models from D. melanogaster. The results of this comparative analysis show precisely how compensatory regulatory mechanisms achieve equivalent final patterns in both species. We discuss the larger implications of the work in terms of “genotype networks” and the ways in which the structure of regulatory networks can influence patterns of evolutionary change (evolvability).

© The Author(s) 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com

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A especiação e extinção conduzem ao surgimento do tamanho da faixa direcional de evolução em filogenias e o registro fóssil

Speciation and Extinction Drive the Appearance of Directional Range Size Evolution in Phylogenies and the Fossil Record

Alex L. Pigot 1,2,3*, Ian P. F. Owens 2,4, C. David L. Orme 2,3

1 Edward Grey Institute, Department of Zoology, University of Oxford, Oxford, United Kingdom, 2 Division of Biology, Department of Life Sciences, Imperial College

London, Ascot, United Kingdom, 3 Grantham Institute for Climate Change, Imperial College London, London, United Kingdom, 4 Natural History Museum, London, United Kingdom

Abstract

While the geographic range of a species is a fundamental unit of macroecology and a leading predictor of extinction risk, the evolutionary dynamics of species’ ranges remain poorly understood. Based on statistical associations between range size and species age, many studies have claimed support for general models of range evolution in which the area occupied by a species varies predictably over the course of its life. Such claims have been made using both paleontological data and molecular estimates of the age of extant species. However, using a stochastic model, we show that the appearance of trends in range size with species’ age can arise even when range sizes have evolved at random through time. This occurs because the samples of species used in existing studies are likely to be biased with respect to range size: for example, only those species that happened to have large or expanding ranges are likely to survive to the present, while extinct species will tend to be those whose ranges, by chance, declined through time. We compared the relationship between the age and range size of species arising under our stochastic model to those observed across 1,269 species of extant birds and mammals and 140 species of extinct Cenozoic marine mollusks. We find that the stochastic model is able to generate the full spectrum of empirical age–area relationships, implying that such trends cannot be simply interpreted as evidence for models of directional range size evolution. Our results therefore challenge the theory that species undergo predictable phases of geographic expansion and contraction through time.

Citation: Pigot AL, Owens IPF, Orme CDL (2012) Speciation and Extinction Drive the Appearance of Directional Range Size Evolution in Phylogenies and the Fossil

Record. PLoS Biol 10(2): e1001260. doi:10.1371/journal.pbio.1001260

Academic Editor: Craig Moritz, University of California Berkeley, United States of America

Received August 23, 2011; Accepted January 5, 2012; Published February 21, 2012

Copyright: 2012 Pigot 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.

Funding: This work was funded by a Grantham Studentship to ALP from the Grantham Institute for Climate Change, Imperial College London, and an RCUK Fellowship to CDLO. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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

* E-mail: alex.pigot@zoo.ox.ac.uk

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Superposição quântica, entrelaçamento e estado de teletransporte de um microorganismo em um oscilador eletromecânico

Article Physics & Astronomy

Science Bulletin

pp 1-9

First online: 11 January 2016

Quantum superposition, entanglement, and state teleportation of a microorganism on an electromechanical oscillator

Tongcang Li , Zhang-Qi Yin

Source/Fonte

Abstract

Schrödinger’s thought experiment to prepare a cat in a superposition of both alive and dead states reveals profound consequences of quantum mechanics and has attracted enormous interests. Here we propose a straightforward method to create quantum superposition states of a living microorganism by putting a small cryopreserved bacterium on top of an electromechanical oscillator. Our proposal is based on recent developments that the center-of-mass oscillation of a 15-μm-diameter aluminum membrane has been cooled to its quantum ground state (Teufel et al. in Nature 475:359, 2011), and entangled with a microwave field (Palomaki et al. in Science 342:710, 2013). A microorganism with a mass much smaller than the mass of the electromechanical membrane will not significantly affect the quality factor of the membrane and can be cooled to the quantum ground state together with the membrane. Quantum superposition and teleportation of its center-of-mass motion state can be realized with the help of superconducting microwave circuits. More importantly, the internal states of a microorganism, such as the electron spin of a glycine radical, can be entangled with its center-of-mass motion and teleported to a remote microorganism. Our proposal can be realized with state-of-the-art technologies. The proposed setup is a quantum-limited magnetic resonance force microscope. Since internal states of an organism contain information, our proposal also provides a scheme for teleporting information or memories between two remote organisms.

Keywords

Quantum superposition Quantum entanglement Quantum teleportation Schrödinger's cat Electromechanical Oscillator Cryopreserved microorganism

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Molecular and Genome Evolution, de Dan Graur (defensor ferrenho do DNA lixo)

Molecular and Genome Evolution

Dan Graur, University of Houston

Edition: First Copyright Year: 2016

Subject: Biology, Evolutionary Biology, Genetics and Genomics

Suggested Price: US$ 124.95

Description

This book describes the driving forces behind the evolutionary process at the molecular and genome levels, the effects of the various molecular mechanisms on the structure of genes, proteins, and genomes, the methodology and the analytical tools involved in dealing with molecular data from an evolutionary perspective, and the logic of evolutionary hypothesis testing. Evolutionary phenomena at the molecular level are detailed in a way that can be understood without much prerequisite knowledge of molecular biology, evolution, or mathematics. Numerous examples that support and clarify the theoretical arguments and methodological discussions are included.

About the Author(s)

Dan Graur is John and Rebecca Moores Professor in the Department of Biology and Biochemistry at the University of Houston and Professor Emeritus of Zoology at Tel Aviv University, Israel. Having earned a B.Sc. (Biology) and an M.Sc. (Zoology) at Tel Aviv University, he completed a Ph.D. (Genetics) at University of Texas Health Science Center at Houston. Coauthor of two editions of Fundamentals of Molecular Evolution (Sinauer Associates, 1991 and 2000), Dr. Graur has published close to 200 articles, book chapters, encyclopedia entries, commentaries, technical notes, and book reviews. He has served as Associate Editor of Molecular Biology and Evolution (1995–2011) and Genome Biology and Evolution (since 2009). Dr. Graur received an Alexander von Humboldt Research Award in 2011 and, in 2015, was elected a Fellow of the American Association for the Advancement of Science. In addition to his research in molecular and genome evolution, Dr. Graur is interested in the societal implications of genetics and molecular biology.

Sample Content

Table of Contents

DNA "refugo": a fração não funcional do genoma humano

Rubbish DNA: The Functionless Fraction of the Human Genome

Dan Graur

University of Houston

Source/Fonte

Abstract

Because genomes are products of natural processes rather than “intelligent design,” all genomes contain functional and nonfunctional parts. The fraction of the genome that has no biological function is called “rubbish DNA.” Rubbish DNA consists of “junk DNA,” i.e., the fraction of the genome on which selection does not operate, and “garbage DNA,” i.e., sequences that lower the fitness of the organism, but exist in the genome because purifying selection is neither omnipotent nor instantaneous. In this chapter, I (1) review the concepts of genomic function and functionlessness from an evolutionary perspective, (2) present a precise nomenclature of genomic function, (3) discuss the evidence for the existence of vast quantities of junk DNA within the human genome, (4) discuss the mutational mechanisms responsible for generating junk DNA, (5) spell out the necessary evolutionary conditions for maintaining junk DNA, (6) outline various methodologies for estimating the functional fraction within the genome, and (7) present a recent estimate for the functional fraction of our genome.

FREE PDF GRATIS: ArXiv

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NOTA DESTE BLOGGER:

O Prof. Dr. Dan Graur é um dos maiores defensores do DNA lixo e um ferrenho oponente do Design Inteligente e dos resultados do ENCODE nos Estados Unidos.

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