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.

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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.

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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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Professores, pesquisadores e alunos de universidades públicas e privadas com acesso ao Portal de Periódicos CAPES-MEC podem ler gratuitamente este artigo da Nature e mais 33.000 periódicos científicos.

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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