Cientistas "criam" animais com genes antigos para testar as causas da evolução

Experimental test and refutation of a classic case of molecular adaptation in Drosophila melanogaster

Mohammad A. Siddiq, David W. Loehlin, Kristi L. Montooth & Joseph W. Thornton

Nature Ecology & Evolution 1, Article number: 0025 (2017)

doi:10.1038/s41559-016-0025

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Evolutionary genetics Molecular evolution

Received: 13 September 2016 Accepted: 01 November 2016 Published online: 

13 January 2017

Sequence evolution on the phylogeny of D. melanogaster and closely related species.

Abstract

Identifying the genetic basis for adaptive differences between species requires explicit tests of historical hypotheses concerning the effects of past changes in gene sequence on molecular function, organismal phenotype and fitness. We address this challenge by combining ancestral protein reconstruction with biochemical experiments and physiological analysis of transgenic animals that carry ancestral genes. We tested a widely held hypothesis of molecular adaptation—that changes in the alcohol dehydrogenase protein (ADH) along the lineage leading to Drosophila melanogaster increased the catalytic activity of the enzyme and thereby contributed to the ethanol tolerance and adaptation of the species to its ethanol-rich ecological niche. Our experiments strongly refute the predictions of the adaptive ADH hypothesis and caution against accepting intuitively appealing accounts of historical molecular adaptation that are based on correlative evidence. The experimental strategy we employed can be used to decisively test other adaptive hypotheses and the claims they entail about past biological causality.

A central goal of molecular evolutionary biology is to identify the genes and biological mechanisms that mediated historical adaptation. Rigorously testing hypotheses in this area has been a major challenge. Many studies infer past selection from statistical signatures in genes that are involved in biological processes that might have suited species to their environments 1,​2,​3,​4 . But sequence signatures of selection can be forged by chance or demographic processes and it is difficult to predict from sequence alone how genetic changes affect phenotypes and fitness 5,​6,​7,​8 . Compelling evidence for molecular adaptation therefore requires formulating and testing explicit hypotheses about the causal links between specific evolutionary changes in gene sequence and the resulting changes in molecular function, organismal phenotype and fitness 6,​7,​8,​9,​10 . Advances in genetic mapping, experimental studies of molecular function and transgenic engineering have allowed hypotheses of molecular adaptation between recently diverged populations to be tested with increasing rigour 11,​12,​13,​14,​15,​16 . But hypotheses about adaptive divergence between species or at higher taxonomic levels are explicitly historical, so testing them requires the effect of genetic changes that occurred on phenotype and fitness in specific evolutionary lineages from the distant past to be measured. Here we address this challenge by combining ancestral protein reconstruction 17 with biochemical experiments and physiological analysis of transgenic animals that carry ancestral genes.

We applied this approach to a longstanding hypothesis of molecular adaptation—that changes in the alcohol dehydrogenase (ADH) protein of the fruit fly Drosophila melanogaster increased the catalytic activity of the enzyme and thereby contributed to the adaptation of the species to its ethanol-rich ecological niche 18,​19,​20 . This hypothesis was articulated decades ago 18,21 and became widely accepted 19,20,22,23 on the basis of several observations that were consistent with it, but did not directly address the putative causal links among historical changes in protein sequence, function and fitness. First, D. melanogaster evolved to colonize ethanol-rich habitats in rotting fruit after it split from its sister species, D. simulans, some two to four million years ago 24,25 . Second, fractionated cell extracts from D. melanogaster catalyse alcohol turnover more rapidly than those from D. simulans 18,26,27 . Third, the first-ever application of the McDonald–Kreitman (MK) test detected an excess of non-synonymous substitutions in an alignment of the ADH coding sequences of D. melanogaster and closely related species 28 , which was interpreted as evidence for adaptive evolution driving the divergence of the ADH protein between D. melanogaster and D. simulans 21,22,29,30 . These observations were integrated into a narrative in which adaptation to ethanol-rich habitats was driven by selection on the ADH protein sequence for increased catalytic activity. Other factors—particularly increases in the expression level 26,31,​32,​33 of ADH, changes at other genetic loci 34,​35,​36 and within-species polymorphisms 37,​38,​39 —also probably contributed to ethanol adaptation in D. melanogaster, but they are independent of and cannot explain the selection signature on the protein-coding sequence of the ADH enzyme found in the MK test.

We focused on the hypothesis of adaptive ADH protein evolution because it is widely accepted on the basis of correlated forms of variation in extant species and because it is particularly amenable to testing using the experimental approaches of ancestral reconstruction, biochemical characterization and engineering of transgenic organisms. The ADH adaptive hypothesis entails specific, testable predictions about how genetic changes that occurred in the ADH protein sequence during the historical divergence of D. melanogaster affect the phenotype at several levels, including molecular function (catalytic turnover of ethanol by pure ADH protein), physiology (ethanol catabolism in the tissues of D. melanogaster) and fitness components (survival in the presence of ethanol) (Fig. 1a). We tested these predictions by reconstructing the ADH protein from the last common ancestor of D. melanogaster and D. simulans (AncMS) and experimentally characterizing how changes in ADH sequence along the D. melanogaster lineage affected ADH function, physiology and fitness.

Additional information

How to cite this article: Siddiq, M. A., Loehlin, D. W., Montooth, K. L. & Thornton, J. W. Experimental test and refutation of a classic case of molecular adaptation in Drosophila melanogaster. Nat. Ecol. Evol. 1, 0025 (2017).

Acknowledgements

We thank L. Picton, K. O’Brien, K. Gordon and members of the C. Meiklejohn and K. Montooth laboratories for technical assistance. We thank D. Matute for providing polymorphism data for D. yakuba. We thank M. Kreitman, members of the J. Thornton laboratory and D. Anderson for comments and suggestions that enriched the project. The project was supported by a National Science Foundation (NSF) grant (DEB-1501877; J.W.T./M.A.S.), an NSF graduate research fellowship (M.A.S.), National Institutes of Health (NIH) grant (R01-GM104397; J.W.T.), NSF CAREER Award (1505247; K.L.M.) and an NIH training grant (T32-GM007197; M.A.S.). D.W.L. was supported by a Howard Hughes Medical Institute postdoctoral fellowship from the Life Sciences Research Foundation and an investigatorship to S. B. Carroll from the Howard Hughes Medical Institute.

Author information

Affiliations

Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, USA

Mohammad A. Siddiq & Joseph W. Thornton

Laboratory of Cell & Molecular Biology, University of Wisconsin-Madison, Madison, Wisconsin, USA

David W. Loehlin

Howard Hughes Medical Institute, University of Wisconsin-Madison, Madison, Wisconsin, USA

David W. Loehlin

School of Biological Sciences, University of Nebraska, Lincoln, Nebraska, USA

Kristi L. Montooth

Department of Human Genetics, University of Chicago, Chicago, Illinois, USA

Joseph W. Thornton

Contributions

M.A.S. and J.W.T. conceived the project. All authors participated in the experimental design. M.A.S. performed the phylogenetic and population genetic analyses. D.W.L. constructed the transgenic animals. M.A.S., D.W.L. and K.L.M. performed the functional experiments. All authors participated in data analysis and interpretation. M.A.S. and J.W.T. wrote the paper with contributions from D.W.L. and K.L.M.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Joseph W. Thornton.

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A nova teoria evolucionária: a evolução da teoria da evolução de Darwin

Origem da vida - como começou a vida na Terra há 4.5 bilhões de anos

O carbono, não é mais tetravalente? Um átomo de carbono faz seis ligações.

Crystal Structure Determination of the Pentagonal-Pyramidal Hexamethylbenzene Dication C6(CH3)62+

Authors

M. Sc. Moritz Malischewski, Prof. Dr. K. Seppelt

First published: 25 November 2016Full publication history

DOI: 10.1002/anie.201608795

Molecular structure of C6(CH3)62+ in C6(CH3)62+ (SbF6−)2⋅HSO3F, ellipsoids are shown at 50 % probability, C grey, H white; counteranions and co-crystallized HSO3F omitted for clarity.

Abstract

In contrast to the well-known 2-norbornyl cation, the structure of which was a matter of long debate until its pentacoordinated nature was recently proven by an X-ray structure, the pentagonal-pyramidal dication of hexamethylbenzene has received considerably less attention. This species was first prepared by Hogeveen in 1973 at low temperatures in magic acid (HSO3F/SbF5), for which he proposed a non-classical structure (containing a hexacoordinated carbon) based on NMR spectroscopy and reactivity studies, but no X-ray crystal structure has been reported. C6(CH3)62+ can be obtained through the dissolution of hexamethyl Dewar benzene epoxide in HSO3F/SbF5 and crystallized as the SbF6− salt upon addition of excess anhydrous hydrogen fluoride. The crystal structure of C6(CH3)62+ (SbF6−)2⋅HSO3F confirms the pentagonal pyramidal structure of the dication. The apical carbon is bound to one methyl group (distance 1.479(3) Å) and to the five basal carbon atoms (distances 1.694(2)–1.715(3) Å).

Dedicated to Professor Karl Otto Christe on the occasion of his 80th anniversary

Acknowledgements

This work was supported by the Free University Berlin, Verband der Chemischen Industrie (VCI) and Deutsche Forschungsgemeinschaft (GRK 1582 (Fluorine as a Key Element)). Computing time was made available by High-Performance Computing at ZEDAT/FU Berlin.

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+++++

NOTA DE AGRADECIMENTO DESTE BLOGGER:

Agradeço ao meu filho Ariel Eugênio Salgueiro de Almeida por chamar minha atenção para o significado científico desta pesquisa. 

A Archaea Asgard lança luz sobre a origem da complexidade celular eucariótica

Asgard archaea illuminate the origin of eukaryotic cellular complexity

Katarzyna Zaremba-Niedzwiedzka, Eva F. Caceres, Jimmy H. Saw, Disa Bäckström, Lina Juzokaite, Emmelien Vancaester, Kiley W. Seitz, Karthik Anantharaman, Piotr Starnawski, Kasper U. Kjeldsen, Matthew B. Stott, Takuro Nunoura, Jillian F. Banfield, Andreas Schramm, Brett J. Baker, Anja Spang & Thijs J. G. Ettema

AffiliationsContributionsCorresponding author

Nature (2017) doi:10.1038/nature21031

Received 30 June 2016 Accepted 02 December 2016 Published online 11 January 2017

Asgard archaea form a well-supported group with the eukaryotes in the tree of life.

Credit: Eva Fernandez-Caceres

The origin and cellular complexity of eukaryotes represent a major enigma in biology. Current data support scenarios in which an archaeal host cell and an alphaproteobacterial (mitochondrial) endosymbiont merged together, resulting in the first eukaryotic cell. The host cell is related to Lokiarchaeota, an archaeal phylum with many eukaryotic features. The emergence of the structural complexity that characterizes eukaryotic cells remains unclear. Here we describe the ‘Asgard’ superphylum, a group of uncultivated archaea that, as well as Lokiarchaeota, includes Thor-, Odin- and Heimdallarchaeota. Asgard archaea affiliate with eukaryotes in phylogenomic analyses, and their genomes are enriched for proteins formerly considered specific to eukaryotes. Notably, thorarchaeal genomes encode several homologues of eukaryotic membrane-trafficking machinery components, including Sec23/24 and TRAPP domains. Furthermore, we identify thorarchaeal proteins with similar features to eukaryotic coat proteins involved in vesicle biogenesis. Our results expand the known repertoire of ‘eukaryote-specific’ proteins in Archaea, indicating that the archaeal host cell already contained many key components that govern eukaryotic cellular complexity.

Acknowledgements

We thank L. Guy, S. L. Jørgensen, T. Williams, N. Lartillot, B. Quang Minh and J. Dacks for useful advice and discussions. We are grateful to D. R. Colman and C. Takacs-Vesbach for collecting the YNP sediment samples under permit #YELL-2010-SCI-5344, to the Japan Agency for Marine-Earth Science & Technology (JAMSTEC) for taking sediment samples from the Taketomi shallow submarine hydrothermal system, and to the Ngāti Tahu Ngāti Whaoa Runanga Trust for their enthusiasm for our research, and assistance in access and sampling of the Ngatamariki geothermal features. We acknowledge the Yellowstone Center for Resources for their assistance and for facilitating this research. We thank A. Simpson for suggesting the name ‘Heimdallarchaeota’. Sequencing of the White Oak River and Colorado River sediment metagenomes was conducted at the Joint Genome Institute, a US Department of Energy Office of Science User Facility, via the Community Science Program. The remaining metagenomes were sequenced at the National Genomics Infrastructure sequencing platforms at the Science for Life Laboratory at Uppsala University, a national infrastructure supported by the Swedish Research Council (VR-RFI) and the Knut and Alice Wallenberg Foundation. We thank the Uppsala Multidisciplinary Center for Advanced Computational Science (UPPMAX) at Uppsala University and the Swedish National Infrastructure for Computing (SNIC) at the PDC Center for High-Performance Computing for providing computational resources. This work was supported by grants of the European Research Council (ERC Starting grant 310039-PUZZLE_CELL), the Swedish Foundation for Strategic Research (SSF-FFL5) and the Swedish Research Council (VR grant 2015-04959) to T.J.G.E., by Marie Curie IIF (331291 to J.H.S.) and IEF (625521 to A.S.) grants by the European Union to the Ettema laboratory, by grants to Bo Barker Jørgensen (Aarhus University, Denmark) from the European Research Council (ERC Advanced Grant 294200-MICROENERGY) and the Danish National Research Foundation (DNRF104) to support the Center for Geomicrobiology at Aarhus University, and by the US Department of Energy (Sustainable Systems Scientific Focus Area grant DE-AC02-05CH11231 to J.F.B.).

Author information

Present address: Department of Plant Systems Biology, VIB and Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052 Ghent, Belgium.

Emmelien Vancaester

These authors contributed equally to this work.

Katarzyna Zaremba-Niedzwiedzka, Eva F. Caceres & Jimmy H. Saw

Affiliations

Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, SE-75123 Uppsala, Sweden

Katarzyna Zaremba-Niedzwiedzka, Eva F. Caceres, Jimmy H. Saw, Disa Bäckström, Lina Juzokaite, Emmelien Vancaester, Anja Spang & Thijs J. G. Ettema

Department of Marine Science, University of Texas-Austin, Marine Science Institute, Port Aransas, Texas 78373, USA

Kiley W. Seitz & Brett J. Baker

Department of Earth and Planetary Sciences, and Department of Environmental Science, Policy, and Management, University of California, Berkeley, California, USA

Karthik Anantharaman & Jillian F. Banfield

Section for Microbiology and Center for Geomicrobiology, Department of Bioscience, Aarhus University, DK-8000 Aarhus, Denmark

Piotr Starnawski, Kasper U. Kjeldsen & Andreas Schramm

GNS Science, Extremophile Research Group, Private Bag 2000, Taupō 3352, New Zealand

Matthew B. Stott

Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology, Yokosuka 237-0061, Japan

Takuro Nunoura

Contributions

T.J.G.E. conceived the study. A.Sc., P.S., K.U.K., M.B.S. and T.N. took/provided environmental samples. L.J. purified environmental DNA and prepared sequencing libraries. K.Z.-N., E.F.C, J.H.S., K.A., J.F.B, K.W.S., B.J.B. and E.V. performed metagenomic sequence assemblies and metagenomic binning analyses. K.Z.-N., E.F.C., J.H.S., A.Sp. and T.J.G.E. analysed genomic data and performed phylogenetic analyses. A.Sp., D.B., E.F.C. and T.J.G.E analysed genomic signatures. K.Z.-N., E.F.C., J.H.S., A.Sp. and T.J.G.E. wrote, and all authors edited and approved, the manuscript.

Competing financial interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to: Thijs J. G. Ettema

Reviewer Information Nature thanks J. Gilbert, E. Koonin, A. Roger and the other anonymous reviewer(s) for their contribution to the peer review of this work.

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Extended data figures and tables: 1, 2, 3, 4, 5, 6, 7, 8

Extended Data Tables: 1, 2.

Comunicação direta entre a vigilância celular e a maquinaria sintetizadora de proteínas elimina erros genéticos: mero acaso, fortuita necessidade ou design inteligente???

ATP hydrolysis by UPF1 is required for efficient translation termination at premature stop codons

Lucas D. Serdar, DaJuan L. Whiteside & Kristian E. Baker

Nature Communications 7, Article number: 14021 (2016)

doi:10.1038/ncomms14021

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RibosomeRNA quality control

Received: 07 June 2016 Accepted: 22 November 2016 Published online: 23 December 2016

Abstract

Nonsense-mediated mRNA decay (NMD) represents a eukaryotic quality control pathway that recognizes and rapidly degrades transcripts harbouring nonsense mutations to limit accumulation of non-functional and potentially toxic truncated polypeptides. A critical component of the NMD machinery is UPF1, an RNA helicase whose ATPase activity is essential for NMD, but for which the precise function and site of action remain unclear. We provide evidence that ATP hydrolysis by UPF1 is required for efficient translation termination and ribosome release at a premature termination codon. UPF1 ATPase mutants accumulate 3′ RNA decay fragments harbouring a ribosome stalled during premature termination that impedes complete degradation of the mRNA. The ability of UPF1 to impinge on premature termination, moreover, requires ATP-binding, RNA-binding and NMD cofactors UPF2 and UPF3. Our results reveal that ATP hydrolysis by UPF1 modulates a functional interaction between the NMD machinery and terminating ribosomes necessary for targeting substrates to accelerated degradation.

Author information

Affiliations

Center for RNA Molecular Biology, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, USA

Lucas D. Serdar, DaJuan L. Whiteside & Kristian E. Baker

Contributions

L.D.S. and K.E.B. conceived and designed the study; L.D.S. and D.L.W. performed the experiments; and L.D.S., D.L.W. and K.E.B. wrote the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Kristian E. Baker.

FREE PDF GRATIS: Nature Communications Supplementary information

Neandertais eram tão humanos quanto nós - por que os cientistas erraram feio com eles???

Neanderthals Were People, Too

New research shows they shared many behaviors that we long believed to be uniquely human. Why did science get them so wrong?

BY JON MOOALLEMJAN. 11, 2017

Neanderthal sculptures, named Nana and Flint, at the Gibraltar Museum. 

Credit Jaap Scheeren for The New York Times

Joachim Neander was a 17th-century Calvinist theologian who often hiked through a valley outside Düsseldorf, Germany, writing hymns. Neander understood everything around him as a manifestation of the Lord’s will and work. There was no room in his worldview for randomness, only purpose and praise. “See how God this rolling globe/swathes with beauty as a robe,” one of his verses goes. “Forests, fields, and living things/each its Master’s glory sings.” He wrote dozens of hymns like this — awe-struck and simple-minded. Then he caught tuberculosis and died at 30.

Almost two centuries later, in the summer of 1856, workers quarrying limestone in that valley dug up an unusual skull. It was elongated and almost chinless, and the fossilized bones found alongside it were extra thick and fit together oddly. This was three years before Darwin published “The Origin of Species.” The science of human origins was not a science; the assumption was that our ancestors had always looked like us, all the way back to Adam. (Even distinguishing fossils from ordinary rock was beyond the grasp of many scientists. One popular method involved licking them; if the material had animal matter in it, it stuck to your tongue.) And so, as anomalous as these German bones seemed, most scholars had no trouble finding satisfying explanations. A leading theory held that this was the skeleton of a lost, bowlegged Cossack with rickets. The peculiar bony ridge over the man’s eyes was a result of the poor Cossack’s perpetually furrowing his brow in pain — because of the rickets.

One British geologist, William King, suspected something more radical. Instead of being the remains of an atypical human, they might have belonged to a typical member of an alternate humanity. In 1864, he published a paper introducing it as such — an extinct human species, the first ever discovered. King named this species after the valley where it was found, which itself had been named for the ecstatic poet who once wandered it. He called it Homo neanderthalensis: Neanderthal Man.

Who was Neanderthal Man? King felt obligated to describe him. But with no established techniques for interpreting archaeological material like the skull, he fell back on racism and phrenology. He focused on the peculiarities of the Neanderthal’s skull, including the “enormously projecting brow.” No living humans had skeletal features remotely like these, but King was under the impression that the skulls of contemporary African and Australian aboriginals resembled the Neanderthals’ more than “ordinary” white-people skulls. So extrapolating from his low opinion of what he called these “savage” races, he explained that the Neanderthal’s skull alone was proof of its moral “darkness” and stupidity. “The thoughts and desires which once dwelt within it never soared beyond those of a brute,” he wrote. Other scientists piled on. So did the popular press. We knew almost nothing about Neanderthals, but already we assumed they were ogres and losers.

The genesis of this idea, the historian Paige Madison notes, largely comes down to flukes of “timing and luck.” While King was working, another British scientist, George Busk, had the same suspicions about the Neander skull. He had received a comparable one, too, from the tiny British territory of Gibraltar. The Gibraltar skull was dug up long before the Neander Valley specimen surfaced, but local hobbyists simply labeled it “human skull” and forgot about it for the next 16 years. Its brow ridge wasn’t as prominent as the Neander skull’s, and its features were less imposing; it was a woman’s skull, it turns out. Busk dashed off a quick report but stopped short of naming the new creature. He hoped to study additional fossils and learn more. Privately, he considered calling it Homo calpicus, or Gibraltar Man.

So, what if Busk — “a conscientious naturalist too cautious to make premature claims,” as Madison describes him — had beaten King to publication? Consider how different our first impressions of a Gibraltar Woman might have been from those of Neanderthal Man: what feelings of sympathy, or even kinship, this other skull might have stirred.

There is a worldview, the opposite of Joachim Neander’s, that sees our planet as a product of only tumult and indifference. In such a world, it’s possible for an entire species to be ground into extinction by forces beyond its control and then, 40,000 years later, be dug up and made to endure an additional century and a half of bad luck and abuse.

That’s what happened to the Neanderthals. And it’s what we did to them. But recently, after we’d snickered over their skulls for so long, it stopped being clear who the boneheads were.

I’ll start with a confession, an embarrassing but relevant one, because I would come to see our history with Neanderthals as continually distorted by an unfortunate human tendency to believe in ideas that are, in reality, incorrect — and then to leverage that conviction into a feeling of superiority over other people. And in retrospect, I realize I demonstrated that same tendency myself at the beginning of this project. Because I don’t want to come off as self-righteous, or as pointing fingers, here goes:

Before traveling to Gibraltar last summer, I had no idea what Gibraltar was. Or rather, I was sure I knew what Gibraltar was, but I was wrong. I thought it was just that famous Rock — an unpopulated hunk of free-floating geology, which, if I’m being honest, I recognized mostly from the Prudential logo: that limestone protuberance at the mouth of the Mediterranean, that elephantine white molar jutting into the sky. True, I was traveling to Gibraltar on short notice; when I cold-called the director of the Gibraltar Museum, Clive Finlayson, he told me the museum happened to be starting its annual excavation of a Neanderthal cave there the following week and invited me to join. Still, even a couple of days before I left, when a friend told me she faintly remembered spending an afternoon in Gibraltar once as a teenager, I gently mansplained to her that I was pretty sure she was mistaken: Gibraltar, I told her, wasn’t somewhere you could just go. In my mind, I had privileged access. I pictured myself and Finlayson taking a special little boat.

In fact, Gibraltar is a peninsula connected to Spain. It’s a lively British overseas territory, with 30,000 citizens living in a city on its western side — a city with bakeries and clothing stores and tourists buying all the usual kitsch. Some unusual kitsch, too — like a laminated child’s place mat I spotted that, in a typical tourist destination, might say something unexceptional like SOMEONE WHO LOVES ME WENT TO GIBRALTAR, but here read WE SHALL NEVER SURRENDER! BRITISH FOREVER!

The history of Gibraltar, given its strategic location, is a grinding saga of military sieges and ruthlessly contested changes in ownership. The residue of that strife, today, is a pronounced British patriotism and a never-ending exchange of slights with Spain, which still disputes Britain’s claim to the territory. After Queen Elizabeth II’s Diamond Jubilee, in 2012, when Gibraltar projected towering images of Her Majesty on a Spain-facing side of the Rock — “a clear act of provocation,” one reporter called it — Spain began inspecting vehicle after vehicle at the border, backing up the line for hours, stranding the bulk of Gibraltar’s work force, who commute in every day. The afternoon I showed up, activists from a far-right Spanish political party had crossed into Gibraltar and hung an enormous Spanish flag high up on the Rock. This wasn’t just mischief. It was regarded as an act of symbolic terrorism. When one of the men appeared in court two days later, I read, a woman screamed at him, “Gibraltar will never be Spanish!” She sounded like that defiant place mat come to life.

I happened to arrive in Gibraltar the week of the Brexit vote. Up in England, people were thundering about the working class versus elites, sovereignty and immigration, warning that British identity was being fouled by the European project. But in Gibraltar — a far-flung, fully detached nib of Britain, flanked by water on two sides and Spain on the third — the question was less philosophical: If the United Kingdom left the European Union, Spain might seize the opportunity to isolate Gibraltar, leaving the territory to shrivel up, like a flap of dead skin. The Gibraltarian government had already called on the House of Commons for help. There was concern that Spain would jam up the border again and that it might happen right away.

Around town, “Remain” signs hung everywhere. The atmosphere was edgy, as though everyone was holding hands, waiting to see whether a meteor would hit. It was like the hairline cracks between so many self-designated Us-es and Thems seemed to be widening, and some corrosive, molten goop was seeping out: mutual dependence curdled with contempt. Clearly it was happening back home in America too.

All in all, it was a good week to spend in a cave.

The openings to Gibraltar caves, including Gorham’s and Vanguard. 

Credit Jaap Scheeren for The New York Times

Gorham’s Cave is on Gibraltar’s rough-hewed eastern coast: a tremendous opening at the bottom of the sheer face of the Rock, shadowy and hallowed-seeming, like a cathedral. Its mouth is 200 feet across at the base and 120 feet tall. It tapers asymmetrically like a crumpled wizard’s hat.

Neanderthals inhabited Gorham’s Cave on and off for 100,000 years, as well as a second cave next to it, called Vanguard Cave. The artifacts they left behind were buried as wind pushed sand into the cave. This created a high sloping dune, composed of hundreds of distinct layers of sand, each of which was once the surface of the dune, the floor of the cave. The dune is enormous. It reaches about two-thirds of the way up Gorham’s walls, spilling out of the cave’s mouth and onto the rocky beach, like a colossal cat’s tongue lapping at the Mediterranean. Every summer, since 1989, a team of archaeologists has returned to meticulously clear that sand away and recover the material inside. “I realized a long time ago, I won’t live to see the end of this project,” Finlayson, who leads the excavation, told me. “But I think we’re in a great moment. We’re beginning to understand these people after a century of putting them down as apelike brutes.”

Neanderthals are people, too — a separate, shorn-off branch of our family tree. We last shared an ancestor at some point between 500,000 and 750,000 years ago. Then our evolutionary trajectory split. We evolved in Africa, while the Neanderthals would live in Europe and Asia for 300,000 years. Or as little as 60,000 years. It depends whom you ask. It always does: The study of human origins, I found, is riddled with vehement disagreements and scientists who readily dismantle the premises of even the most straightforward-seeming questions. (In this case, the uncertainty rests, in part, on when, in this long evolutionary process, Neanderthals officially became “Neanderthals.”) What is clearer is that roughly 40,000 years ago, just as our own lineage expanded from Africa and took over Eurasia, the Neanderthals disappeared. Scientists have always assumed that the timing wasn’t coincidental. Maybe we used our superior intellects to outcompete the Neanderthals for resources; maybe we clubbed them all to death. Whatever the mechanism of this so-called replacement, it seemed to imply that our kind was somehow better than their kind. We’re still here, after all, and their path ended as soon as we crossed paths.

But Neanderthals weren’t the slow-witted louts we’ve imagined them to be — not just a bunch of Neanderthals. As a review of findings published last year put it, they were actually “very similar” to their contemporary Homo sapiens in Africa, in terms of “standard markers of modern cognitive and behavioral capacities.” We’ve always classified Neanderthals, technically, as human — part of the genus Homo. But it turns out they also did the stuff that, you know, makes us human.

Neanderthals buried their dead. They made jewelry and specialized tools. They made ocher and other pigments, perhaps to paint their faces or bodies — evidence of a “symbolically mediated worldview,” as archaeologists call it. Their tracheal anatomy suggests that they were capable of language and probably had high-pitched, raspy voices, like Julia Child. They manufactured glue from birch bark, which required heating the bark to at least 644 degrees Fahrenheit — a feat scientists find difficult to duplicate without a ceramic container. In Gibraltar, there’s evidence that Neanderthals extracted the feathers of certain birds — only dark feathers — possibly for aesthetic or ceremonial purposes. And while Neanderthals were once presumed to be crude scavengers, we now know they exploited the different terrains on which they lived. They took down dangerous game, including an extinct species of rhinoceros. Some ate seals and other marine mammals. Some ate shellfish. Some ate chamomile. (They had regional cuisines.) They used toothpicks.

Wearing feathers, eating seals — maybe none of this sounds particularly impressive. But it’s what our human ancestors were capable of back then too, and scientists have always considered such behavioral flexibility and complexity as signs of our specialness. When it came to Neanderthals, though, many researchers literally couldn’t see the evidence sitting in front of them. A lot of the new thinking about Neanderthals comes from revisiting material in museum collections, excavated decades ago, and re-examining it with new technology or simply with open minds. The real surprise of these discoveries may not be the competence of Neanderthals but how obnoxiously low our expectations for them have been — the bias with which too many scientists approached that other Us. One archaeologist called these researchers “modern human supremacists.”

...

READ MORE HERE/LEIA MAIS AQUI: The New York Times

Um modelo funcional das relações profundas de diversas linhagens humanas modernas fora de África

A working model of the deep relationships of diverse modern human genetic lineages outside of Africa

Mark Lipson 1,* and David Reich 1,2,3,**

- Author Affiliations

1Department of Genetics, Harvard Medical School, Boston, MA 02115, USA

2Medical and Population Genetics Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA

3Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA

↵* Correspondence: mlipson@genetics.med.harvard.edu

↵** Correspondence: reich@genetics.med.harvard.edu

Source/Fonte: MemeBurn

Abstract

A major topic of interest in human prehistory is how the large-scale genetic structure of modern populations outside of Africa was established. Demographic models have been developed that capture the relationships among small numbers of populations or within particular geographical regions, but constructing a phylogenetic tree with gene flow events for a wide diversity of non-Africans remains a difficult problem. Here, we report a model that provides a good statistical fit to allele-frequency correlation patterns among East Asians, Australasians, Native Americans, and ancient western and northern Eurasians, together with archaic human groups. The model features a primary eastern/western bifurcation dating to at least 45,000 years ago, with Australasians nested inside the eastern clade, and a parsimonious set of admixture events. While our results still represent a simplified picture, they provide a useful summary of deep Eurasian population history that can serve as a null model for future studies and a baseline for further discoveries.

© The Author(s) 2017. 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

FREE PDF GRATIS: Molecular Biology Evolution

Darwin, cientistas descobrem um motor molecular com "engrenagem" de comutação direcional

The mitotic kinesin-14 KlpA contains a context-dependent directionality switch

Andrew R. Popchock, Kuo-Fu Tseng, Pan Wang, P. Andrew Karplus, Xin Xiang & Weihong Qiu

Nature Communications 8, Article number: 13999 (2017)

doi: 10.1038/ncomms13999

Download Citation

KinesinSingle-molecule biophysics

Received: 16 June 2016 Accepted: 17 November 2016 Published online: 04 January 2017

Source/Fonte: Dynamic Science

Abstract

Kinesin-14s are commonly known as nonprocessive minus end-directed microtubule motors that function mainly for mitotic spindle assembly. Here we show using total internal reflection fluorescence microscopy that KlpA—a kinesin-14 from Aspergillus nidulans—is a context-dependent bidirectional motor. KlpA exhibits plus end-directed processive motility on single microtubules, but reverts to canonical minus end-directed motility when anchored on the surface in microtubule-gliding experiments or interacting with a pair of microtubules in microtubule-sliding experiments. Plus end-directed processive motility of KlpA on single microtubules depends on its N-terminal nonmotor microtubule-binding tail, as KlpA without the tail is nonprocessive and minus end-directed. We suggest that the tail is a de facto directionality switch for KlpA motility: when the tail binds to the same microtubule as the motor domain, KlpA is a plus end-directed processive motor; in contrast, when the tail detaches from the microtubule to which the motor domain binds, KlpA becomes minus end-directed.

Acknowledgements

We thank Drs C. Mathews (Oregon State University), X. Su (UCSF) and B. Liu (UC Davis) for critical reading of the manuscript, and Mr Chun Liu (Pearl River Fisheries Research Institute, China) for initial plasmid construction. This work was supported in part by the National Science Foundation (MCB-1616462 to W.Q.).

Author information

Author notes

Andrew R. Popchock & Kuo-Fu Tseng

These authors contributed equally to this work

Affiliations

Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331, USA

Andrew R. Popchock, P. Andrew Karplus & Weihong Qiu

Department of Physics, Oregon State University, Corvallis, Oregon 97331, USA

Kuo-Fu Tseng, Pan Wang & Weihong Qiu

School of Physics and Electronics, Henan University, Kaifeng, Henan 475004, China

Pan Wang

Department of Biochemistry and Molecular Biology, The Uniformed Services University of the Health Sciences, Bethesda, Maryland 20814, USA

Xin Xiang

Contributions

W.Q. conceived, designed and supervised the study; A.R.P. and K.-F.T. performed the experiments; K.-F.T. and P.W. contributed all KlpA constructs. All authors participated in discussing and interpreting the results. P.A.K., X.X. and W.Q. wrote the manuscript with input from all other authors.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Weihong Qiu.

FREE PDF GRATIS: Nature Communications Sup. Info. Videos 1, 2, 3, 4, 5, 6, 7, 8, 9, 10.

Esplendor e miséria da adaptação, ou a importância do nulo neutro para a compreensão da evolução

Splendor and misery of adaptation, or the importance of neutral null for understanding evolution

Eugene V. Koonin Email author

BMC Biology201614:114

DOI: 10.1186/s12915-016-0338-2 © The Author(s). 2016

Published: 23 December 2016

Source/Fonte: Holt Biology

Abstract

The study of any biological features, including genomic sequences, typically revolves around the question: what is this for? However, population genetic theory, combined with the data of comparative genomics, clearly indicates that such a “pan-adaptationist” approach is a fallacy. The proper question is: how has this sequence evolved? And the proper null hypothesis posits that it is a result of neutral evolution: that is, it survives by sheer chance provided that it is not deleterious enough to be efficiently purged by purifying selection. To claim adaptation, the neutral null has to be falsified. The adaptationist fallacy can be costly, inducing biologists to relentlessly seek function where there is none.

FREE PDF GRATIS: BMC Biology

Darwin, o olho continua sendo absurdamente resultado da evolução: imagem de neurônios individuais na camada de células ganglionares da retina do olho vivo

Imaging individual neurons in the retinal ganglion cell layer of the living eye

Ethan A. Rossi a,1,2, Charles E. Granger a,b,3, Robin Sharma a,3, Qiang Yang a, Kenichi Saito c, Christina Schwarz a, Sarah Walters a,b, Koji Nozato c, Jie Zhang a, Tomoaki Kawakami c, William Fischer d, Lisa R. Latchney d, Jennifer J. Hunter a,d, Mina M. Chung a,d, and David R. Williams a,b

Author Affiliations

aCenter for Visual Science, University of Rochester, Rochester, NY 14642;

bThe Institute of Optics, University of Rochester, Rochester, NY 14620;

cCanon USA, Inc., Melville, NY 11747;

dFlaum Eye Institute, University of Rochester Medical Center, Rochester, NY 14642

Edited by Stephen Burns, Indiana University System, Bloomington, IN, and accepted by Editorial Board Member Jeremy Nathans December 6, 2016 (received for review August 19, 2016)

Significance

Retinal ganglion cells are the primary output neurons of the retina that process visual information and transmit it to the brain. We developed a method to reveal these cells in the living eye that does not require the fluorescent labels or high light levels that characterize more invasive methods. The death of these cells causes vision loss in glaucoma, the second leading cause of blindness worldwide. The ability to image these cells in the living eye could accelerate our understanding of their role in normal vision and provide a diagnostic tool for evaluating new therapies for retinal disease.

Abstract

Although imaging of the living retina with adaptive optics scanning light ophthalmoscopy (AOSLO) provides microscopic access to individual cells, such as photoreceptors, retinal pigment epithelial cells, and blood cells in the retinal vasculature, other important cell classes, such as retinal ganglion cells, have proven much more challenging to image. The near transparency of inner retinal cells is advantageous for vision, as light must pass through them to reach the photoreceptors, but it has prevented them from being directly imaged in vivo. Here we show that the individual somas of neurons within the retinal ganglion cell (RGC) layer can be imaged with a modification of confocal AOSLO, in both monkeys and humans. Human images of RGC layer neurons did not match the quality of monkey images for several reasons, including safety concerns that limited the light levels permissible for human imaging. We also show that the same technique applied to the photoreceptor layer can resolve ambiguity about cone survival in age-related macular degeneration. The capability to noninvasively image RGC layer neurons in the living eye may one day allow for a better understanding of diseases, such as glaucoma, and accelerate the development of therapeutic strategies that aim to protect these cells. This method may also prove useful for imaging other structures, such as neurons in the brain.

imaging adaptive optics retinal ganglion cells photoreceptors retina

Footnotes

1Present address: Department of Ophthalmology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213.

2To whom correspondence should be addressed. Email: rossiea@pitt.edu.

3C.E.G. and R.S. contributed equally to this work.

Author contributions: E.A.R. designed research; E.A.R., C.E.G., R.S., K.S., C.S., S.W., K.N., J.Z., T.K., W.F., L.R.L., and M.M.C. performed research; E.A.R. and Q.Y. contributed new reagents/analytic tools; E.A.R., C.E.G., R.S., K.S., and K.N. analyzed data; E.A.R., C.E.G., R.S., K.S., C.S., S.W., J.J.H., M.M.C., and D.R.W. wrote the paper; and D.R.W. supervised the project.

Conflict of interest statement: E.A.R. has filed patent applications on aspects of the technology described in this manuscript. D.R.W. and Q.Y. have patents on aspects of the technology described in this manuscript. Some of D.R.W.’s patents have been licensed by Canon, Inc.

This article is a PNAS Direct Submission. S.B. is a Guest Editor invited by the Editorial Board.

This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1613445114/-/DCSupplemental.

Freely available online through the PNAS open access option.

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Darwin, que tal uma nova teoria da evolução com menos seleção natural???

How About a New Theory of Evolution with Less Natural Selection?

November 28, 2016 by ROBBY BERMAN

Science! (BOBVDK)

In early November, a group of preeminent biologists, doctors, anthropologists, and computer scientists met in London to consider making a major change to the concept of evolutionary biology introduced by Charles Darwin in Origin of the Species in 1859. It’s not that they’re interested in throwing out the idea of natural selection. It’s just that they think recent research suggests it doesn’t account for evolution all by itself. This isn’t the first time such a revision has happened, actually. And it’s not clear that it will this time: Conference co-host Kevin Layland told Quanta magazine mid-conference, ““I think it’s going quite well,” Laland said. “It hasn’t gone to fisticuffs yet.”

The current understanding of evolution, known as “modern evolutionary synthesis,” is itself a combination of natural selection and the 1865 genetics work of Gregor Mendel, published six years after Origin of the Species.

Mendel's peas

Mendel’s peas

The modern synthesis emerged in the 1930s and 1940s, and it’s what’s taught in schools today. It states that evolution is the product of small genetic variations (Mendel’s contribution) that survive, or not (Darwin’s process of natural selection).

Some of the scientists at the Royal Society’s “New Trends in Evolutionary Biology” meeting say that this isn’t quite the case, and that there’s a third element that needs to be incorporated: Behavior and environment can also cause evolutionary changes. Carl Zimmer of Quanta, who attended the conference, says, "The researchers don’t argue that the modern synthesis is wrong — just that it doesn’t capture the full richness of evolution.”

To that end some attendees at the conference proposed a new understanding they call the “extended evolutionary synthesis.” What it adds to Darwin’s and Mendel’s work is an awareness of epigenetics.

The word “epigenetics” means “in addition to changes in genetic sequence.” According to science journalist Tabitha M. Powledge, “Broadly speaking, epigenetics is how nurture shapes nature.” The field looks at inheritable genetic changes that don’t involve the changing of a DNA sequence, but rather the activation or deactivation of genes via the epigenome, a layer of chemical tags covering and shaping the structure of a genome to turn individual genes on or off depending on the purpose of a cell, using a variety of chemical processes. The University of Utah has a great video explaining what an epigenome is.

Read more here/Leia mais aqui: Big Think

+++++

NOTA DESTE BLOGGER:

Desde 1998 este blogger fez vários contatos com editores e jornalistas científicos da Grande Mídia alertando que uma iminente e eminente mudança paradigmática ocorreria em biologia evolucionária, e que se fazia necessária uma nova teoria geral da evolução.

Alguns cientistas da Nomenklatura científica caíram de pau no então "simples professorzinho do Ensino Médio" que não sabe o que é ciência e nem fazer ciência. Pior então foram os ataques ferinos da Galera dos meninos e meninas de Darwin - "o anta do Enézio" y otros epítetos. O professor do Ensino Médio - tenho orgulho de tê-lo sido, é mestre em História da Ciência pela PUC de São Paulo, SP, com dissertação demonstrando que as críticas à teoria da evolução de Darwin através da seleção natural não se deram somente por razões religiosas, mas científicas, e por um que fazia parte do círculo íntimo de Charles Darwin, e que foi recomendado por ele e Thomas Huxley a ser um FRS: St. George Jackson Mivart.

Como é bom ser vindicado por evolucionistas honestos! Queria ver a cara desses cientistas da Nomenklatura científica e da Galera dos meninos e meninas de Darwin: menos seleção natural, caras pálidas!!!

Fui, pois a biologia evolucionária não somente está em crise, mas está sem uma teoria geral da evolução, embora a Síntese Evolutiva Ampliada/Estendida tenha sido lançada em agosto de 2015. Sob qual referencial teórico está sendo feita ciência normal em biologia evolucionária? Abracadabra? Entranhas de animais? Astrologia? Cartas de Tarô? Horóscopo???