Quantas mudanças genéticas criam novas espécies?

How many genetic changes create new species?

Patrik Nosil 1,2, Jeffrey L. Feder 3, Zachariah Gompert 2

See all authors and affiliations

Science 19 Feb 2021: Vol. 371, Issue 6531, pp. 777-779

DOI: 10.1126/science.abf6671

A genetic region that controls coloration generates morphs of Midas cichlid fish, but speciation involves traits controlled by a number of different genes.

PHOTO: AD KONINGS

The formation of new species generates biodiversity and is often driven by evolution through natural selection. However, the number of genetic changes involved in speciation is largely unknown. Many theoretical models predict that if speciation occurs without geographic isolation, it will be driven by a small number of genes. The logic is that only the few genes that experience the strongest natural selection can overcome the homogenizing effect of genetic mixing (i.e., gene flow) to diverge between populations. However, empirical studies in plants and animals now suggest that speciation—even with gene flow—involves differentiation in surprisingly many genetic regions. This is thought possible because the effects of selection can become coupled across correlated genes such that the selection each gene experiences is much stronger than it would receive in isolation. Thus, the potential for genes to evolve collectively because of coupling may be a key to understanding speciation.

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Evidência de proteínas, cromossomos e marcadores químicos de DNA em cartilagem de dinossauro excepcionalmente preservada!

Evidence of proteins, chromosomes and chemical markers of DNA in exceptionally preserved dinosaur cartilage

Alida M Bailleul, Wenxia Zheng, John R Horner, Brian K Hall, Casey M Holliday, Mary H Schweitzer

National Science Review, Volume 7, Issue 4, April 2020, Pages 815–822, https://doi.org/10.1093/nsr/nwz206

Published: 12 January 2020

Ground section of Hypacrosaurus (MOR 548) supraoccipital shows exceptional histological preservation of calcified cartilage. 

Abstract

A histological ground-section from a duck-billed dinosaur nestling (Hypacrosaurus stebingeri) revealed microstructures morphologically consistent with nuclei and chromosomes in cells within calcified cartilage. We hypothesized that this exceptional cellular preservation extended to the molecular level and had molecular features in common with extant avian cartilage. Histochemical and immunological evidence supports in situ preservation of extracellular matrix components found in extant cartilage, including glycosaminoglycans and collagen type II. Furthermore, isolated Hypacrosaurus chondrocytes react positively with two DNA intercalating stains. Specific DNA staining is only observed inside the isolated cells, suggesting endogenous nuclear material survived fossilization. Our data support the hypothesis that calcified cartilage is preserved at the molecular level in this Mesozoic material, and suggest that remnants of once-living chondrocytes, including their DNA, may preserve for millions of years.

cartilage, dinosaur, nuclei, chromosomes, collagen II, DNA markers

Issue Section: MOLECULAR BIOLOGY & GENETICS

Free PDF Gratis: National Science Review

Genes e genomas e complexidade desnecessária em medicina de precisão

Genes and genomes and unnecessary complexity in precision medicine

Rama S. Singh & Bhagwati P. Gupta

npj Genomic Medicine volume 5, Article number: 21 (2020)

Source/Fonte: GEN

Abstract

The sequencing of the human genome heralded the new age of ‘genetic medicine’ and raised the hope of precision medicine facilitating prolonged and healthy lives. Recent studies have dampened this expectation, as the relationships among mutations (termed ‘risk factors’), biological processes, and diseases have emerged to be more complex than initially anticipated. In this review, we elaborate upon the nature of the relationship between genotype and phenotype, between chance-laden molecular complexity and the evolution of complex traits, and the relevance of this relationship to precision medicine. Molecular contingency, i.e., chance-driven molecular changes, in conjunction with the blind nature of evolutionary processes, creates genetic redundancy or multiple molecular pathways to the same phenotype; as time goes on, these pathways become more complex, interconnected, and hierarchically integrated. Based on the proposition that gene-gene interactions provide the major source of variation for evolutionary change, we present a theory of molecular complexity and posit that it consists of two parts, necessary and unnecessary complexity, both of which are inseparable and increase over time. We argue that, unlike necessary complexity, comprising all aspects of the organism’s genetic program, unnecessary complexity is evolutionary baggage: the result of molecular constraints, historical circumstances, and the blind nature of evolutionary forces. In the short term, unnecessary complexity can give rise to similar risk factors with different genetic backgrounds; in the long term, genes become functionally interconnected and integrated, directly or indirectly, affecting multiple traits simultaneously. We reason that in addition to personal genomics and precision medicine, unnecessary complexity has consequences in evolutionary biology.

FREE PDF GRATIS: npj genomic medicine

Cientistas surpresos: descobriram plantas sob o gelo a quase mil e quatrocentos metros de profundidade na Groenlândia

A multimillion-year-old record of Greenland vegetation and glacial history preserved in sediment beneath 1.4 km of ice at Camp Century

Andrew J. Christ, Paul R. Bierman, Joerg M. Schaefer, Dorthe Dahl-Jensen, Jørgen P. Steffensen, Lee B. Corbett, Dorothy M. Peteet, Elizabeth K. Thomas, Eric J. Steig, Tammy M. Rittenour, Jean-Louis Tison, Pierre-Henri Blard, Nicolas Perdrial, David P. Dethier, Andrea Lini, Alan J. Hidy, Marc W. Caffee, and John Southon

PNAS March 30, 2021 118 (13) e2021442118; https://doi.org/10.1073/pnas.2021442118 

Edited by Mark Thiemens, University of California San Diego, La Jolla, CA, and approved January 27, 2021 (received for review October 23, 2020)

Source/Fonte: NASA

Significance

Understanding Greenland Ice Sheet history is critical for predicting its response to future climate warming and contribution to sea-level rise. We analyzed sediment at the bottom of the Camp Century ice core, collected 120 km from the coast in northwestern Greenland. The sediment, frozen under nearly 1.4 km of ice, contains well-preserved fossil plants and biomolecules sourced from at least two ice-free warm periods in the past few million years. Enriched stable isotopes in pore ice indicate precipitation at lower elevations than present, implying ice-sheet absence. The similarity of cosmogenic isotope ratios in the upper-most sediment to those measured in bedrock near the center of Greenland suggests that the ice sheet melted and re-formed at least once during the past million years.

Abstract

Understanding the history of the Greenland Ice Sheet (GrIS) is critical for determining its sensitivity to warming and contribution to sea level; however, that history is poorly known before the last interglacial. Most knowledge comes from interpretation of marine sediment, an indirect record of past ice-sheet extent and behavior. Subglacial sediment and rock, retrieved at the base of ice cores, provide terrestrial evidence for GrIS behavior during the Pleistocene. Here, we use multiple methods to determine GrIS history from subglacial sediment at the base of the Camp Century ice core collected in 1966. This material contains a stratigraphic record of glaciation and vegetation in northwestern Greenland spanning the Pleistocene. Enriched stable isotopes of pore-ice suggest precipitation at lower elevations implying ice-sheet absence. Plant macrofossils and biomarkers in the sediment indicate that paleo-ecosystems from previous interglacial periods are preserved beneath the GrIS. Cosmogenic 26Al/10Be and luminescence data bracket the burial of the lower-most sediment between <3.2 ± 0.4 Ma and >0.7 to 1.4 Ma. In the upper-most sediment, cosmogenic 26Al/10Be data require exposure within the last 1.0 ± 0.1 My. The unique subglacial sedimentary record from Camp Century documents at least two episodes of ice-free, vegetated conditions, each followed by glaciation. The lower sediment derives from an Early Pleistocene GrIS advance. 26Al/10Be ratios in the upper-most sediment match those in subglacial bedrock from central Greenland, suggesting similar ice-cover histories across the GrIS. We conclude that the GrIS persisted through much of the Pleistocene but melted and reformed at least once since 1.1 Ma.

Pleistocene ice core Arctic climate ice sheet

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Mais uma hipótese sobre a origem da vida: Um raio antigo pode ter gerado vida na Terra!

Lightning strikes as a major facilitator of prebiotic phosphorus reduction on early Earth

Benjamin L. Hess, Sandra Piazolo & Jason Harvey

Nature Communications volume 12, Article number: 1535 (2021)

Source/Fonte

Abstract

When hydrated, phosphides such as the mineral schreibersite, (Fe,Ni)3P, allow for the synthesis of important phosphorus-bearing organic compounds. Such phosphides are common accessory minerals in meteorites; consequently, meteorites are proposed to be a main source of prebiotic reactive phosphorus on early Earth. Here, we propose an alternative source for widespread phosphorus reduction, arguing that lightning strikes on early Earth potentially formed 10–1000 kg of phosphide and 100–10,000 kg of phosphite and hypophosphite annually. Therefore, lightning could have been a significant source of prebiotic, reactive phosphorus which would have been concentrated on landmasses in tropical regions. Lightning strikes could likewise provide a continual source of prebiotic reactive phosphorus independent of meteorite flux on other Earth-like planets, potentially facilitating the emergence of terrestrial life indefinitely.

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Testes moleculares apoiam a viabilidade de elementos terrestres raros como agentes preservadores de biomoléculas fósseis

Molecular tests support the viability of rare earth elements as proxies for fossil biomolecule preservation

Paul V. Ullmann, Kristyn K. Voegele, David E. Grandstaff, Richard D. Ash, Wenxia Zheng, Elena R. Schroeter, Mary H. Schweitzer & Kenneth J. Lacovara

Scientific Reports volume 10, Article number: 15566 (2020)

Reproduced, with permission from Geochimica et Cosmochimica Acta, from Ullmann et al.

Abstract

The rare earth element (REE) composition of a fossil bone reflects its chemical alteration during diagenesis. Consequently, fossils presenting low REE concentrations and/or REE profiles indicative of simple diffusion, signifying minimal alteration, have been proposed as ideal candidates for paleomolecular investigation. We directly tested this prediction by conducting multiple biomolecular assays on a well-preserved fibula of the dinosaur Edmontosaurus from the Cretaceous Hell Creek Formation previously found to exhibit low REE concentrations and steeply-declining REE profiles. Gel electrophoresis identified the presence of organic material in this specimen, and subsequent immunofluorescence and enzyme-linked immunosorbant assays identified preservation of epitopes of the structural protein collagen I. Our results thereby support the utility of REE profiles as proxies for soft tissue and biomolecular preservation in fossil bones. Based on considerations of trace element taphonomy, we also draw predictions as to the biomolecular recovery potential of additional REE profile types exhibited by fossil bones.

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Um modelo do Cosmos no antigo mecanismo grego de Anticítera

A Model of the Cosmos in the ancient Greek Antikythera Mechanism

Tony Freeth, David Higgon, Aris Dacanalis, Lindsay MacDonald, Myrto Georgakopoulou & Adam Wojcik

Scientific Reports volume 11, Article number: 5821 (2021)

Source/Fonte: The New York Times

Abstract

The Antikythera Mechanism, an ancient Greek astronomical calculator, has challenged researchers since its discovery in 1901. Now split into 82 fragments, only a third of the original survives, including 30 corroded bronze gearwheels. Microfocus X-ray Computed Tomography (X-ray CT) in 2005 decoded the structure of the rear of the machine but the front remained largely unresolved. X-ray CT also revealed inscriptions describing the motions of the Sun, Moon and all five planets known in antiquity and how they were displayed at the front as an ancient Greek Cosmos. Inscriptions specifying complex planetary periods forced new thinking on the mechanization of this Cosmos, but no previous reconstruction has come close to matching the data. Our discoveries lead to a new model, satisfying and explaining the evidence. Solving this complex 3D puzzle reveals a creation of genius—combining cycles from Babylonian astronomy, mathematics from Plato’s Academy and ancient Greek astronomical theories.

FREE PDF GRATIS: Nature Communications Sup. Info. 4

Tubos de fibra óptica na retina fazem muito mais do que simples transferência de imagem: mero acaso, fortuita necessidade ou design inteligente?

Müller cells separate between wavelengths to improve day vision with minimal effect upon night vision

Amichai M. Labin, Shadi K. Safuri, Erez N. Ribak & Ido Perlman

Nature Communications volume 5, Article number: 4319 (2014)

Source/Fonte: vision-research.eu

Abstract

Vision starts with the absorption of light by the retinal photoreceptors—cones and rods. However, due to the ‘inverted’ structure of the retina, the incident light must propagate through reflecting and scattering cellular layers before reaching the photoreceptors. It has been recently suggested that Müller cells function as optical fibres in the retina, transferring light illuminating the retinal surface onto the cone photoreceptors. Here we show that Müller cells are wavelength-dependent wave-guides, concentrating the green-red part of the visible spectrum onto cones and allowing the blue-purple part to leak onto nearby rods. This phenomenon is observed in the isolated retina and explained by a computational model, for the guinea pig and the human parafoveal retina. Therefore, light propagation by Müller cells through the retina can be considered as an integral part of the first step in the visual process, increasing photon absorption by cones while minimally affecting rod-mediated vision.

FREE PDF GRATIS: Nature Communications Sup. Info.

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Having the photoreceptors at the back of the retina is not a design constraint, it is a design feature. The idea that the vertebrate eye, like a traditional front-illuminated camera, might have been improved somehow if it had only been able to orient its wiring behind the photoreceptor layer, like a cephalopod, is folly. 

Ter os fotorreceptores na parte posterior da retina não é uma limitação de design, é uma característica de design. A ideia de que o olho dos vertebrados, como uma câmera tradicional com iluminação frontal, poderia ter sido melhorada de alguma forma se tivesse sido capaz de orientar sua fiação atrás da camada fotorreceptora, como um cefalópode, é bobagem.

PhysOrg

A paleontologia molecular como uma área emocionante, desafiadora e controversa.

Molecular paleontology as an exciting, challenging and controversial field

Yanhong Pan

National Science Review, Volume 7, Issue 4, April 2020, Page 823, 

https://doi.org/10.1093/nsr/nwaa001  

Published: 07 January 2020

Source/Fonte

Abstract

Molecular paleontology is the study of ancient complex biomolecules associated within deep-time fossils, which may provide important information for understanding the organisms’ evolution and fossilization process at the molecular level, as well as facilitating the recognition of preserved biomarkers in order to identify life on other planets [1,2]. In the paper by Bailleul et al. [3], the authors report the discovery of well-preserved subcellular structures morphologically consistent with nuclei and chromosomes in histological ground sections from skull bones of an Upper Cretaceous baby dinosaur. However, as the authors have stated that morphology alone is insufficient to diagnose any cellular or subcellular structures, they conducted further histochemical (Alcian blue stain for extracellular matrix of cartilage; PI and DAPI stains for chemical markers consistent with DNA) and immunological (antibodies against avian collagen II) tests. All tests were positive, providing strong evidence suggesting in situ preservation of extracellular matrix components, and even endogenous nuclear materials. This case study reveals interesting evidence of exceptional preservation in fossils at both molecular and morphological levels, and opens the door for extensive further research, making the argument that DNA sequencing is worth exploring. The present study is significant for at least two reasons. First, it demonstrates that fossils displaying well-preserved cellular and subcellular structures may also preserve molecular information. Second, this study clearly shows that the search for ancient biomolecules should not be constrained by the so-called temporal limit, e.g. the assumption that proteins cannot survive in the fossil record beyond ∼1 Ma and ∼100 000 years for DNA. The preservation mechanism of soft tissues in fossils is far more complex than we have observed in modern environments through taphonomy experiments.

The last decade has borne witness to numerous discoveries that have provided mounting evidence of molecular preservation in deep-time fossils, e.g. proteins, certain carbohydrates such as chitin and cellulose, sterol lipids and pigments [4–8]. As this is a relatively new field, searching for ancient molecules in fossils is full of challenges, e.g. inevitable contaminations, immature techniques and unknown modifications of molecules over geological time. Thus, new discoveries in molecular paleontology are often accompanied by controversy. However, controversy is a crucial part of scientific progress and incorrect ideas do less harm to science than false evidence. To promote the discipline of molecular paleontology, we need to overcome bias and prejudice from colleagues in and outside the field, particularly with regard to the presumed ‘preservational limit’. Another common critic plaguing discoveries of ancient biomolecules concerns the repeatability of the results; however, it is an obvious bias to declare that the result cannot be replicated if different techniques or methods are used.

Finally, it is recognized that ‘exceptional claims require exceptional evidence’ and multiple independent lines of evidence should be provided in support of any new discovery of ancient biomolecules in deep-time fossils as done by Bailleul et al. [3]. With the recent and rapid technological developments, we are optimistic that the field of molecular paleontology will grow rapidly and provide additional evidence of unexpected fossil biomolecules from geological ages previously held to be too old for such biomolecules to survive.

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Informação - a simplicidade escondida da biologia: mero acaso, fortuita necessidade ou design inteligente?

The hidden simplicity of biology

Paul Davies, Sara Walker

Biodesign Institute CLAS-NS: Physics CLAS-NS: Beyond Center CLAS: Administration CLAS-NS: Earth and Space Exploration, School of (SESE)

Research output: Contribution to journal › Review article › peer-review

Source/Fonte

Abstract

Life is so remarkable, and so unlike any other physical system, that it is tempting to attribute special factors to it. Physics is founded on the assumption that universal laws and principles underlie all natural phenomena, but is it far from clear that there are 'laws of life' with serious descriptive or predictive power analogous to the laws of physics. Nor is there (yet) a 'theoretical biology' in the same sense as theoretical physics. Part of the obstacle in developing a universal theory of biological organization concerns the daunting complexity of living organisms. However, many attempts have been made to glimpse simplicity lurking within this complexity, and to capture this simplicity mathematically. In this paper we review a promising new line of inquiry to bring coherence and order to the realm of biology by focusing on 'information' as a unifying concept.

Original languageEnglish (US)

Article number102601

JournalReports on Progress in Physics

Volume79

Issue number10

StatePublished - Sep 9 2016

Access to Document

DOI: 10.1088/0034-4885/79/10/102601

Keywords

biological laws complexity emergence

Origem da vida: o problema do ovo e da galinha - mero acaso, fortuita necessidade ou design inteligente?

tRNA sequences can assemble into a replicator

Alexandra Kühnlein, Simon A Lanzmich, Dieter Braun Is a corresponding author

Systems Biophysics, Physics Department, Center for NanoScience, Ludwig-Maximilians-Universität München, Germany

Research Article Mar 2, 2021

Heat-driven replication by hybridization using hairpin structures inspired from transfer RNA.

Abstract

Can replication and translation emerge in a single mechanism via self-assembly? The key molecule, transfer RNA (tRNA), is one of the most ancient molecules and contains the genetic code. Our experiments show how a pool of oligonucleotides, adapted with minor mutations from tRNA, spontaneously formed molecular assemblies and replicated information autonomously using only reversible hybridization under thermal oscillations. The pool of cross-complementary hairpins self-selected by agglomeration and sedimentation. The metastable DNA hairpins bound to a template and then interconnected by hybridization. Thermal oscillations separated replicates from their templates and drove an exponential, cross-catalytic replication. The molecular assembly could encode and replicate binary sequences with a replication fidelity corresponding to 85–90 % per nucleotide. The replication by a self-assembly of tRNA-like sequences suggests that early forms of tRNA could have been involved in molecular replication. This would link the evolution of translation to a mechanism of molecular replication.

eLife digest

The genetic code stored within DNA contains the instructions for manufacturing all the proteins organisms need to develop, grow and survive. This requires molecular machines that ‘transcribe’ regions of the genetic code into RNA molecules which are then ‘translated’ into the string of amino acids that form the final protein. However, these molecular machines and other proteins are also needed to replicate and synthesize the sequences stored in DNA. This presents evolutionary biologists with a ‘chicken-and-egg’ situation: which came first, the DNA sequences needed to manufacture proteins or the proteins needed to transcribe and translate DNA?

Understanding the order in which DNA replication and protein translation evolved is challenging as these processes are tightly intertwined in modern-day species. One theory, known as the ‘RNA world hypothesis’, suggests that all life on Earth began with a single RNA molecule that was able to make copies of itself, as DNA does today. To investigate this hypothesis, Kühnlein, Lanzmich and Braun studied a molecule called transfer RNA (or tRNA for short) which is responsible for translating RNA into proteins. tRNA is assumed to be one of the earliest evolved molecules in biology. Yet, why it was present in early life forms before it was needed for translation still remained somewhat of a mystery.

To gain a better understanding of tRNA’s role early in evolution, Kühnlein, Lanzmich and Braun made small changes to its genetic code and then carried out tests on these tRNA-like sequences. The experiments showed these ‘early’ forms of tRNA can actually self-assemble into a molecule which is capable of replicating the information stored in its sequence. It suggests early forms of tRNA could have been involved in replication before modern tRNA developed its role in protein translation.

With these experiments, Kühnlein, Lanzmich and Braun have identified a possible evolutionary link between DNA replication and protein translation, suggesting the two processes emerged through one shared pathway: tRNA. This deepens our understanding about the origins of early life, while taking biochemists one step closer to their distant goal of recreating self-replicating molecular machines in the laboratory.

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Implicações para a evolução do DNA e darwinismo molecular

Energy mapping of the genetic code and genomic domains: implications for code evolution and molecular Darwinism

Published online by Cambridge University Press: 04 November 2020

Horst H. Klump, Jens Völker and Kenneth J. Breslauer

Abstract

When the iconic DNA genetic code is expressed in terms of energy differentials, one observes that information embedded in chemical sequences, including some biological outcomes, correlate with distinctive free energy profiles. Specifically, we find correlations between codon usage and codon free energy, suggestive of a thermodynamic selection for codon usage. We also find correlations between what are considered ancient amino acids and high codon free energy values. Such correlations may be reflective of the sequence-based genetic code fundamentally mapping as an energy code. In such a perspective, one can envision the genetic code as composed of interlocking thermodynamic cycles that allow codons to ‘evolve’ from each other through a series of sequential transitions and transversions, which are influenced by an energy landscape modulated by both thermodynamic and kinetic factors. As such, early evolution of the genetic code may have been driven, in part, by differential energetics, as opposed exclusively by the functionality of any gene product. In such a scenario, evolutionary pressures can, in part, derive from the optimization of biophysical properties (e.g. relative stabilities and relative rates), in addition to the classic perspective of being driven by a phenotypical adaptive advantage (natural selection). Such differential energy mapping of the genetic code, as well as larger genomic domains, may reflect an energetically resolved and evolved genomic landscape, consistent with a type of differential, energy-driven ‘molecular Darwinism’. It should not be surprising that evolution of the code was influenced by differential energetics, as thermodynamics is the most general and universal branch of science that operates over all time and length scales.

Keywords Codon energy distribution spectrum, codon free energies, codon usage frequency, energy code, interlocking thermodynamic cycles, molecular evolution

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Mais uma hipótese da origem da vida: a evolução darwinista começou antes da própria vida!

Structured sequences emerge from random pool when replicated by templated ligation

Patrick W. Kudella, Alexei V. Tkachenko, Annalena Salditt, Sergei Maslov, and Dieter Braun

PNAS February 23, 2021 118 (8) e2018830118; https://doi.org/10.1073/pnas.2018830118 

Edited by Eugene V. Koonin, National Institutes of Health, Bethesda, MD, and approved January 20, 2021 (received for review September 7, 2020)

Significance

The structure of life emerged from randomness. This is attributed to selection by molecular Darwinian evolution. This study found that random templated ligation led to the simultaneous elongation and sequence selection of oligomers. Product strands showed highly structured sequence motifs which inhibited self-folding and built self-templating reaction networks. By the reduction of the sequence space, the kinetics of duplex formation increased and led to a faster replication through the ligation process. These findings imply that elementary binding properties of nucleotides can lead to an early selection of sequences even before the onset of Darwinian evolution. This suggests that such a simplification of sequence space could result in faster downstream selection for sequence-based function for the origin of life.

Abstract

The central question in the origin of life is to understand how structure can emerge from randomness. The Eigen theory of replication states, for sequences that are copied one base at a time, that the replication fidelity has to surpass an error threshold to avoid that replicated specific sequences become random because of the incorporated replication errors [M. Eigen, Naturwissenschaften 58 (10), 465–523 (1971)]. Here, we showed that linking short oligomers from a random sequence pool in a templated ligation reaction reduced the sequence space of product strands. We started from 12-mer oligonucleotides with two bases in all possible combinations and triggered enzymatic ligation under temperature cycles. Surprisingly, we found the robust creation of long, highly structured sequences with low entropy. At the ligation site, complementary and alternating sequence patterns developed. However, between the ligation sites, we found either an A-rich or a T-rich sequence within a single oligonucleotide. Our modeling suggests that avoidance of hairpins was the likely cause for these two complementary sequence pools. What emerged was a network of complementary sequences that acted both as templates and substrates of the reaction. This self-selecting ligation reaction could be restarted by only a few majority sequences. The findings showed that replication by random templated ligation from a random sequence input will lead to a highly structured, long, and nonrandom sequence pool. This is a favorable starting point for a subsequent Darwinian evolution searching for higher catalytic functions in an RNA world scenario.

Keywords origin of life DNA replication Darwinian evolution templated ligation sequence entropy

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Imagens de alta resolução do DNA surpreendentemente desconcertantes: mero acaso, fortuita necessidade ou design inteligente?

Base-pair resolution analysis of the effect of supercoiling on DNA flexibility and major groove recognition by triplex-forming oligonucleotides

Alice L. B. Pyne, Agnes Noy, Kavit H. S. Main, Victor Velasco-Berrelleza, Michael M. Piperakis, Lesley A. Mitchenall, Fiorella M. Cugliandolo, Joseph G. Beton, Clare E. M. Stevenson, Bart W. Hoogenboom, Andrew D. Bates, Anthony Maxwell & Sarah A. Harris 

Nature Communications volume 12, Article number: 1053 (2021)

Abstract

In the cell, DNA is arranged into highly-organised and topologically-constrained (supercoiled) structures. It remains unclear how this supercoiling affects the detailed double-helical structure of DNA, largely because of limitations in spatial resolution of the available biophysical tools. Here, we overcome these limitations, by a combination of atomic force microscopy (AFM) and atomistic molecular dynamics (MD) simulations, to resolve structures of negatively-supercoiled DNA minicircles at base-pair resolution. We observe that negative superhelical stress induces local variation in the canonical B-form DNA structure by introducing kinks and defects that affect global minicircle structure and flexibility. We probe how these local and global conformational changes affect DNA interactions through the binding of triplex-forming oligonucleotides to DNA minicircles. We show that the energetics of triplex formation is governed by a delicate balance between electrostatics and bonding interactions. Our results provide mechanistic insight into how DNA supercoiling can affect molecular recognition, that may have broader implications for DNA interactions with other molecular species.

FREE PDF GRATIS: Nature Communications Sup. Info. Peer Reviewer File

Michael Behe vindicado, mas não citado em artigo da Nature Heredity apoiando sua hipótese de Involução

The population genomics of adaptive loss of function

J. Grey Monroe, John K. McKay, Detlef Weigel & Pádraic J. Flood 

Heredity (2021)

Abstract

Discoveries of adaptive gene knockouts and widespread losses of complete genes have in recent years led to a major rethink of the early view that loss-of-function alleles are almost always deleterious. Today, surveys of population genomic diversity are revealing extensive loss-of-function and gene content variation, yet the adaptive significance of much of this variation remains unknown. Here we examine the evolutionary dynamics of adaptive loss of function through the lens of population genomics and consider the challenges and opportunities of studying adaptive loss-of-function alleles using population genetics models. We discuss how the theoretically expected existence of allelic heterogeneity, defined as multiple functionally analogous mutations at the same locus, has proven consistent with empirical evidence and why this impedes both the detection of selection and causal relationships with phenotypes. We then review technical progress towards new functionally explicit population genomic tools and genotype-phenotype methods to overcome these limitations. More broadly, we discuss how the challenges of studying adaptive loss of function highlight the value of classifying genomic variation in a way consistent with the functional concept of an allele from classical population genetics.

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The Quarterly Review of Biology

Experimental evolution, loss-of-function mutations, and “the first rule of adaptive evolution”

Michael J.   Behe, and Daniel E.   Dykhuizen

Abstract

Adaptive evolution can cause a species to gain, lose, or modify a function; therefore, it is of basic interest to determine whether any of these modes dominates the evolutionary process under particular circumstances. Because mutation occurs at the molecular level, it is necessary to examine the molecular changes produced by the underlying mutation in order to assess whether a given adaptation is best considered as a gain, loss, or modification of function. Although that was once impossible, the advance of molecular biology in the past half century has made it feasible. In this paper, I review molecular changes underlying some adaptations, with a particular emphasis on evolutionary experiments with microbes conducted over the past four decades. I show that by far the most common adaptive changes seen in those examples are due to the loss or modification of a pre-existing molecular function, and I discuss the possible reasons for the prominence of such mutations.

Forças motrizes nas origens da vida: mero acaso, fortuita necessidade ou design inteligente?

Driving forces in the origins of life

K. A. Dill and L. Agozzino

Published:03 February 2021 https://doi.org/10.1098/rsob.200324

Source/Fonte

Abstract

What were the physico-chemical forces that drove the origins of life? We discuss four major prebiotic ‘discoveries’: persistent sampling of chemical reaction space; sequence-encodable foldable catalysts; assembly of functional pathways; and encapsulation and heritability. We describe how a ‘proteins-first’ world gives plausible mechanisms. We note the importance of hydrophobic and polar compositions of matter in these advances.

FREE PDF GRATIS: Open Biology

A evolução de nosso planeta dinâmico: um bilhão de anos em 40 segundos!

Earth-Science Reviews

Volume 214, March 2021, 103477

Extending full-plate tectonic models into deep time: Linking the Neoproterozoic and the Phanerozoic

Andrew S. Merdith a Simon E. Williams b Alan S. Collins c Michael G. Tetley a Jacob A. Mulder d Morgan L. Blades c Alexander Young e Sheree E. Armistead f John Cannon g Sabin Zahirovic g R. Dietmar Müller

https://www.youtube.com/watch?v=5_jhIv5mRP8&feature=emb_logo

Abstract

Recent progress in plate tectonic reconstructions has seen models move beyond the classical idea of continental drift by attempting to reconstruct the full evolving configuration of tectonic plates and plate boundaries. A particular problem for the Neoproterozoic and Cambrian is that many existing interpretations of geological and palaeomagnetic data have remained disconnected from younger, better-constrained periods in Earth history. An important test of deep time reconstructions is therefore to demonstrate the continuous kinematic viability of tectonic motions across multiple supercontinent cycles. We present, for the first time, a continuous full-plate model spanning 1 Ga to the present-day, that includes a revised and improved model for the Neoproterozoic–Cambrian (1000–520 Ma) that connects with models of the Phanerozoic, thereby opening up pre-Gondwana times for quantitative analysis and further regional refinements. In this contribution, we first summarise methodological approaches to full-plate modelling and review the existing full-plate models in order to select appropriate models that produce a single continuous model. Our model is presented in a palaeomagnetic reference frame, with a newly-derived apparent polar wander path for Gondwana from 540 to 320 Ma, and a global apparent polar wander path from 320 to 0 Ma. We stress, though while we have used palaeomagnetic data when available, the model is also geologically constrained, based on preserved data from past-plate boundaries. This study is intended as a first step in the direction of a detailed and self-consistent tectonic reconstruction for the last billion years of Earth history, and our model files are released to facilitate community development.

Keywords Palaeogeography Rodinia Gondwana Plate tectonics Neoproterozoic

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Origens da ancestralidade humana moderna: nem o registro genético ou fóssil até agora revelou um tempo e lugar definidos para a origem de nossa espécie.

Origins of modern human ancestry

Anders Bergström, Chris Stringer, Mateja Hajdinjak, Eleanor M. L. Scerri & Pontus Skoglund

Nature volume 590, pages 229–237(2021)

Modern human origins and diversification in Africa in the past 300 thousand years.

Abstract

New finds in the palaeoanthropological and genomic records have changed our view of the origins of modern human ancestry. Here we review our current understanding of how the ancestry of modern humans around the globe can be traced into the deep past, and which ancestors it passes through during our journey back in time. We identify three key phases that are surrounded by major questions, and which will be at the frontiers of future research. The most recent phase comprises the worldwide expansion of modern humans between 40 and 60 thousand years ago (ka) and their last known contacts with archaic groups such as Neanderthals and Denisovans. The second phase is associated with a broadly construed African origin of modern human diversity between 60 and 300 ka. The oldest phase comprises the complex separation of modern human ancestors from archaic human groups from 0.3 to 1 million years ago. We argue that no specific point in time can currently be identified at which modern human ancestry was confined to a limited birthplace, and that patterns of the first appearance of anatomical or behavioural traits that are used to define Homo sapiens are consistent with a range of evolutionary histories.

Subscription or Payment needed/Requer assinatura ou pagamento: Nature

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Co-author Pontus Skoglund from The Francis Crick Institute said: "Contrary to what many believe, neither the genetic or fossil record have so far revealed a defined time and place for the origin of our species. Such a point in time, when the majority of our ancestry was found in a small geographic region and the traits we associate with our species appeared, may not have existed. For now, it would be useful to move away from the idea of a single time and place of origin."

On the origin of our species - Science Daily

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O dobramento incomum do DNA aumenta as taxas de mutações: isso pode mudar a forma como pensamos sobre a evolução.

Non-B DNA: a major contributor to small- and large-scale variation in nucleotide substitution frequencies across the genome

Wilfried M. Guiblet, Marzia A Cremona, Robert S Harris, Di Chen, Kristin A Eckert, Francesca Chiaromonte, Yi-Fei Huang, Kateryna D Makova Author Notes

Nucleic Acids Research, gkaa1269, https://doi.org/10.1093/nar/gkaa1269

Published: 15 January 2021

Schematic of different types of non-B DNA structures. (A) G-quadruplex, (B) H-DNA, (C) Z-DNA, (D) cruciform, (E) slipped strands and (F) A-tract bending.

INTRODUCTION

Mutation rates vary across the genome (1,2), and this phenomenon contributes to differences in the levels of intra- and interspecific genetic variation (henceforth called ‘diversity’ and ‘divergence’, respectively). As a result, certain genomic regions may be at a higher (or at a lower) risk of acquiring mutations important for adaptation and/or genetic diseases (1–3). In a broad sense, deciphering the causes of regional variation in mutation rates is essential to understanding both evolution and diseases (1,2).

Numerous genomic features contribute to regional variation in mutation rates, but those identified to date cannot account for all such variation. Some features are directly related to DNA sequence and usually act at the scale of single nucleotides, e.g. guanines and cytosines are more mutable than adenines and thymines (4,5). Neighboring nucleotides also have an effect, e.g. methylated cytosines in CpG dinucleotides are 10 times more mutable than other sites because of their spontaneous deamination (6), and several other contexts leading to guanine holes and increased mutagenesis were previously identified (7). Other genomic features—such as recombination rate (8), replication timing (9), chromatin accessibility (10,11), histone modifications (12,13), and Lamina Associated Domains (14)—contribute to regional variation in mutation rates through the variable activity of different enzymatic processes along the genome. These frequently act at larger scales, from several hundreds of kilobases to several megabases (Mbs). The magnitude of regional variation in mutation rates decreases with the increase in the genomic scale considered; most such regional variation in fact occurs at the single-nucleotide scale (1). At the 1-Mb scale, which is considered the natural long-range variation scale for mammalian genomes (15), most regions have mutation rates deviating by ∼2-fold (1). Notably, at this scale, several analyses indicated that the genomic features listed above explain only ∼50% of the regional variation in mutation rates (12,16,17). The correlation in regional variation in mutation rates between human and great apes (18) suggests that the unexplained portion of this variation is not random, and that additional factors remain to be discovered. Non-B DNA may be one such factor.

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Cientistas falam sobre evidências de design inteligente na natureza

https://youtu.be/cEps6lzWUKk

Evolução dinâmica dos cromossomos Y do grande símio

Dynamic evolution of great ape Y chromosomes

Monika Cechova, Rahulsimham Vegesna, Marta Tomaszkiewicz, Robert S. Harris, Di Chen, Samarth Rangavittal, Paul Medvedev, and Kateryna D. Makova

PNAS October 20, 2020 117 (42) 26273-26280; first published October 5, 2020; https://doi.org/10.1073/pnas.2001749117

Edited by Amanda M. Larracuente, University of Rochester, Rochester, NY, and accepted by Editorial Board Member Daniel L. Hartl September 3, 2020 (received for review January 30, 2020)

Evolution of Y chromosome gene content in great apes. 

Significance

The male-specific Y chromosome harbors genes important for sperm production. Because Y is repetitive, its DNA sequence was deciphered for only a few species, and its evolution remains elusive. Here we compared the Y chromosomes of great apes (human, chimpanzee, bonobo, gorilla, and orangutan) and found that many of their repetitive sequences and multicopy genes were likely already present in their common ancestor. Y repeats had increased intrachromosomal contacts, which might facilitate preservation of genes and gene regulatory elements. Chimpanzee and bonobo, experiencing high sperm competition, underwent many DNA changes and gene losses on the Y. Our research is significant for understanding the role of the Y chromosome in reproduction of nonhuman great apes, all of which are endangered.

Abstract

The mammalian male-specific Y chromosome plays a critical role in sex determination and male fertility. However, because of its repetitive and haploid nature, it is frequently absent from genome assemblies and remains enigmatic. The Y chromosomes of great apes represent a particular puzzle: their gene content is more similar between human and gorilla than between human and chimpanzee, even though human and chimpanzee share a more recent common ancestor. To solve this puzzle, here we constructed a dataset including Ys from all extant great ape genera. We generated assemblies of bonobo and orangutan Ys from short and long sequencing reads and aligned them with the publicly available human, chimpanzee, and gorilla Y assemblies. Analyzing this dataset, we found that the genus Pan, which includes chimpanzee and bonobo, experienced accelerated substitution rates. Pan also exhibited elevated gene death rates. These observations are consistent with high levels of sperm competition in Pan. Furthermore, we inferred that the great ape common ancestor already possessed multicopy sequences homologous to most human and chimpanzee palindromes. Nonetheless, each species also acquired distinct ampliconic sequences. We also detected increased chromatin contacts between and within palindromes (from Hi-C data), likely facilitating gene conversion and structural rearrangements. Our results highlight the dynamic mode of Y chromosome evolution and open avenues for studies of male-specific dispersal in endangered great ape species.

sex chromosomespalindromesgene content evolution

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Capturando o momento do surgimento do núcleo de cristal da desordem.

Capturing the Moment of Emergence of Crystal Nucleus from Disorder

Takayuki Nakamuro, Masaya Sakakibara, Hiroki Nada, Koji Harano, and Eiichi Nakamura*

Cite this: J. Am. Chem. Soc. 2021, XXXX, XXX, XXX-XXX

Publication Date:January 21, 2021

https://doi.org/10.1021/jacs.0c12100

© 2021 American Chemical Society

Abstract

Crystallization is the process of atoms or molecules forming an organized solid via nucleation and growth. Being intrinsically stochastic, the research at an atomistic level has been a huge experimental challenge. We report herein in situ detection of a crystal nucleus forming during nucleation/growth of a NaCl nanocrystal, as video recorded in the interior of a vibrating conical carbon nanotube at 20–40 ms frame–1 with localization precision of <0.1 nm. We saw NaCl units assembled to form a cluster fluctuating between featureless and semiordered states, which suddenly formed a crystal. Subsequent crystal growth at 298 K and shrinkage at 473 K took place also in a stochastic manner. Productive contributions of the graphitic surface and its mechanical vibration have been experimentally indicated.

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A filogenômica revela discordância da árvore genética primordial na árvore da vida dos anfíbios

Phylogenomics Reveals Ancient Gene Tree Discordance in the Amphibian Tree of Life 

Paul M Hime, Alan R Lemmon, Emily C Moriarty Lemmon, Elizabeth Prendini, Jeremy M Brown, Robert C Thomson, Justin D Kratovil, Brice P Noonan, R Alexander Pyron, Pedro L V Peloso, Michelle L Kortyna, J Scott Keogh, Stephen C Donnellan, Rachel Lockridge Mueller, Christopher J Raxworthy, Krushnamegh Kunte, Santiago R Ron, Sandeep Das, Nikhil Gaitonde, David M Green, Jim Labisko, Jing Che, David W Weisrock

Author Notes

Systematic Biology, Volume 70, Issue 1, January 2021, Pages 49–66, https://doi.org/10.1093/sysbio/syaa034

Published: 30 June 2020

Source/Fonte: Taran Grant, via AMNH

Abstract

Molecular phylogenies have yielded strong support for many parts of the amphibian Tree of Life, but poor support for the resolution of deeper nodes, including relationships among families and orders. To clarify these relationships, we provide a phylogenomic perspective on amphibian relationships by developing a taxon-specific Anchored Hybrid Enrichment protocol targeting hundreds of conserved exons which are effective across the class. After obtaining data from 220 loci for 286 species (representing 94% of the families and 44% of the genera), we estimate a phylogeny for extant amphibians and identify gene tree–species tree conflict across the deepest branches of the amphibian phylogeny. We perform locus-by-locus genealogical interrogation of alternative topological hypotheses for amphibian monophyly, focusing on interordinal relationships. We find that phylogenetic signal deep in the amphibian phylogeny varies greatly across loci in a manner that is consistent with incomplete lineage sorting in the ancestral lineage of extant amphibians. Our results overwhelmingly support amphibian monophyly and a sister relationship between frogs and salamanders, consistent with the Batrachia hypothesis. Species tree analyses converge on a small set of topological hypotheses for the relationships among extant amphibian families. These results clarify several contentious portions of the amphibian Tree of Life, which in conjunction with a set of vetted fossil calibrations, support a surprisingly younger timescale for crown and ordinal amphibian diversification than previously reported. More broadly, our study provides insight into the sources, magnitudes, and heterogeneity of support across loci in phylogenomic data sets.[AIC; Amphibia; Batrachia; Phylogeny; gene tree–species tree discordance; genomics; information theory.]

Associate Editor: Adam Leaché

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O osso não precisa permanecer um elefante na sala de datação por radiocarbono!

Bone need not remain an elephant in the room for radiocarbon dating

Salvador Herrando-Pérez

Published:13 January 2021https://doi.org/10.1098/rsos.201351

Elephant in the room - Tiedemann

Abstract

Radiocarbon (14C) analysis of skeletal remains by accelerator mass spectrometry is an essential tool in multiple branches of science. However, bone 14C dating results can be inconsistent and not comparable due to disparate laboratory pretreatment protocols that remove contamination. And, pretreatments are rarely discussed or reported by end-users, making it an ‘elephant in the room’ for Quaternary scientists. Through a questionnaire survey, I quantified consensus on the reliability of collagen pretreatments for 14C dating across 132 experts (25 countries). I discovered that while more than 95% of the audience was wary of contamination and would avoid gelatinization alone (minimum pretreatment used by most 14C facilities), 52% asked laboratories to choose the pretreatment method for them, and 58% could not rank the reliability of at least one pretreatment. Ultrafiltration was highly popular, and purification by XAD resins seemed restricted to American researchers. Isolating and dating the amino acid hydroxyproline was perceived as the most reliable pretreatment, but is expensive, time-consuming and not widely available. Solid evidence supports that only molecular-level dating accommodates all known bone contaminants and guarantees complete removal of humic and fulvic acids and conservation substances, with three key areas of progress: (i) innovation and more funded research is required to develop affordable analytical chemistry that can handle low-mass samples of collagen amino acids, (ii) a certification agency overseeing dating-quality control is needed to enhance methodological reproducibility and dating accuracy among laboratories, and (iii) more cross-disciplinary work with better 14C reporting etiquette will promote the integration of 14C dating across disciplines. Those developments could conclude long-standing debates based on low-accuracy data used to build chronologies for animal domestications, human/megafauna extirpations and migrations, archaeology, palaeoecology, palaeontology and palaeoclimate models.

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