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23 results on '"Antão, Tiago"'

1. Electric field control of moir\'e skyrmion phases in twisted multiferroic NiI$_2$ bilayers

Author

Antão, Tiago V. C., Lado, Jose L., and Fumega, Adolfo O.

Subjects
Condensed Matter - Strongly Correlated Electrons, Condensed Matter - Mesoscale and Nanoscale Physics, Condensed Matter - Materials Science
Abstract

Twisted magnetic van der Waals materials provide a flexible platform to engineer new forms of unconventional magnetism. Here we demonstrate the emergence of electrically tunable topological moir\'e magnetism in twisted bilayers of the spin-spiral multiferroic NiI$_2$. We establish a rich phase diagram featuring uniform spiral phases, a variety of $k\pi$-skyrmion lattices, and nematic spin textures ordered at the moir\'e scale. The emergence of these phases is driven by the local stacking and the resulting modulated frustration in the spin spiral stemming from the moir\'e pattern. Notably, when the spin-spiral wavelength is commensurate with the moir\'e length scale by an integer $k$, multi-walled skyrmions become pinned to the moir\'e pattern. We show that the strong magnetoelectric coupling displayed by the moir\'e multiferroic allows the electric control of the $k\pi$-skyrmion lattices by an out-of-plane electric field, which couples to the moir\'e-induced electric polarization. While adiabatic changes in the electric field preserve the topology of the spin configurations, abrupt variations can trigger transitions between different skyrmion lattice ground states. Our results establish a highly tunable platform for skyrmionics based on twisted van der Waals multiferroics, potentially enabling a new generation of ultrathin topologically-protected spintronic devices., Comment: 8 pages, 4 figures

Published
2024
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2. Coexistence of 1D and 2D topology and genesis of Dirac cones in the chiral Aubry-Andr\'e model

Author

Antão, Tiago V C, Miranda, Daniel A, and Peres, Nuno M R

Subjects
Condensed Matter - Mesoscale and Nanoscale Physics
Abstract

We construct a one-dimensional (1D) topological SSH-like model with chiral symmetry and a superimposed hopping modulation, which we call the chiral Aubry-Andr\'e model. We show that its topological properties can be described in terms of a pair (C,W) of a two-dimensional (2D) Chern number C, stemming from a superspace description of the model, and a 1D winding number W, originating in its chiral symmetric nature. Thus, we showcase for the first time explicit coexistence of 1D and 2D topology in a model existing in 1D physical space. We detail the superspace description by showcasing how our model can be mapped to a Harper-Hofstadter model, familiar from the description of the integer quantum Hall effect, and analyze the vanishing field limit analytically. An extension of the method used for vanishing fields is provided in order to handle any finite fields, corresponding to hopping modulations both commensurate and incommensurate with the lattice. In addition, this formalism allows us to obtain certain features of the 2D superspace model, such as its number of massless Dirac nodes, purely in terms of topological quantities, computed without the need to go into momentum space.

Published
2024
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3. A Selective Sweep on a Deleterious Mutation in CPT1A in Arctic Populations

Author

Clemente, Florian J, Cardona, Alexia, Inchley, Charlotte E, Peter, Benjamin M, Jacobs, Guy, Pagani, Luca, Lawson, Daniel J, Antão, Tiago, Vicente, Mário, Mitt, Mario, DeGiorgio, Michael, Faltyskova, Zuzana, Xue, Yali, Ayub, Qasim, Szpak, Michal, Mägi, Reedik, Eriksson, Anders, Manica, Andrea, Raghavan, Maanasa, Rasmussen, Morten, Rasmussen, Simon, Willerslev, Eske, Vidal-Puig, Antonio, Tyler-Smith, Chris, Villems, Richard, Nielsen, Rasmus, Metspalu, Mait, Malyarchuk, Boris, Derenko, Miroslava, and Kivisild, Toomas

Subjects
Biological Sciences, Genetics, Human Genome, Medical and Health Sciences, Genetics & Heredity, Biological sciences, Biomedical and clinical sciences, Health sciences
Abstract

Arctic populations live in an environment characterized by extreme cold and the absence of plant foods for much of the year and are likely to have undergone genetic adaptations to these environmental conditions in the time they have been living there. Genome-wide selection scans based on genotype data from native Siberians have previously highlighted a 3 Mb chromosome 11 region containing 79 protein-coding genes as the strongest candidates for positive selection in Northeast Siberians. However, it was not possible to determine which of the genes might be driving the selection signal. Here, using whole-genome high-coverage sequence data, we identified the most likely causative variant as a nonsynonymous G>A transition (rs80356779; c.1436C>T [p.Pro479Leu] on the reverse strand) in CPT1A, a key regulator of mitochondrial long-chain fatty-acid oxidation. Remarkably, the derived allele is associated with hypoketotic hypoglycemia and high infant mortality yet occurs at high frequency in Canadian and Greenland Inuits and was also found at 68% frequency in our Northeast Siberian sample. We provide evidence of one of the strongest selective sweeps reported in humans; this sweep has driven this variant to high frequency in circum-Arctic populations within the last 6-23 ka despite associated deleterious consequences, possibly as a result of the selective advantage it originally provided to either a high-fat diet or a cold environment.

Published
2014

4. Evolutionary applications of population genetics with a focus on malaria : a computational approach

Author

Antão, Tiago Rodrigues

Subjects
614.532
Abstract

Malaria is a major public health concern for the one-third of the human population esti- mated to be exposed to the threat of the most virulent species, Plasmodium falciparum. Modern molecular and computational tools from population genetics may help to better understand and fight the burden of drug resistant malaria. Malaria biology is substantially different from the underlying paradigm of standard population genetics models, most notably because malaria has both a asexual haploid phase and a sexual diploid phase where selfing (i.e. mating between genetically identical parasites) is possible. It is therefore fundamental to understand if commonly used population genetics methods are robust to the deviations from standard expectations imposed by the malaria life-cycle. We build novel models of malaria population genetics and provide guidelines to interpret empirical studies of the spread of drug resistance. Using realistic models of epistasis between genes involved in drug resistance we suggest that all signals of linkage disequilibrium (LD) are possible and that researchers should be confident in reporting a lack of statistical association between genes involved in resistance to antimalarials. We also suggest that researchers should be cautious in interpreting changes in the prevalence of drug resistance after control interventions as reductions in transmission can cause a change in prevalence without concomitant change in frequency of resistance. We provide guidelines to better design and interpret studies related to estimating effective population size (Ne). We use computational simulations to study scenarios that can approximate control and elimination interventions (i.e. where a significant part of the population is killed). For Ne estimation our results suggest that researchers must increase the number of individuals and loci genotyped in order to have sufficiently precise Ne estimates. LD-based Ne estimators are more appropriate for early detection of control and elimination interventions than temporal-based Ne estimators. Long- term estimators based on heterozygosity should not be used to make inferences about contemporary demographic processes. We also applied our analysis to disease vectors and we concluded that LD-based estimation is able to detect demographic seasonality patterns (i.e. changes in population size due to variations imposed by wet and dry seasons) whereas temporal estimators will provide averages over longer periods of time. We also studied selection detection using FsT-outlier approaches. Our results suggest that temporal FST might not be appropriate for early detection of genes involved in drug resistance (e.g. in the case of artesunate derivatives). We also provide software and guidelines to better design and interpret studies (also across other taxa) of selection based on FsT-outlier approaches. Most notably our results suggest that sampling only one or two SNPs per locus (as it is done in many empirical studies) might not be sufficient to detect areas of the genome under selection, and that at least 4 SNPs per loci should be genotyped.

Published
2011
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7. Genetic diversity of the African malaria vector Anopheles gambiae

Author

Miles, Alistair, Harding, Nicholas J., Bottà, Giordano, Clarkson, Chris S., Antão, Tiago, Kozak, Krzysztof, Schrider, Daniel R., Kern, Andrew D., Redmond, Seth, Sharakhov, Igor, Pearson, Richard D., Bergey, Christina, Fontaine, Michael C., Donnelly, Martin J., Lawniczak, Mara K. N., Kwiatkowski, Dominic P., Ayala, Diego, Besansky, Nora J., Burt, Austin, Caputo, Beniamino, della Torre, Alessandra, Godfray, H. Charles J., Hahn, Matthew W., Midega, Janet, Neafsey, Daniel E., O’Loughlin, Samantha, Pinto, João, Riehle, Michelle M., Vernick, Kenneth D., Weetman, David, Wilding, Craig S., White, Bradley J., Troco, Arlete D., Diabaté, Abdoulaye, Costantini, Carlo, Rohatgi, Kyanne R., Elissa, Nohal, Coulibaly, Boubacar, Dinis, João, Mbogo, Charles, Bejon, Philip, Mawejje, Henry D., Stalker, Jim, Rockett, Kirk, Drury, Eleanor, Mead, Daniel, Jeffreys, Anna, Hubbart, Christina, Rowlands, Kate, Isaacs, Alison T., Jyothi, Dushyanth, Malangone, Cinzia, Vauterin, Paul, Jeffery, Ben, Wright, Ian, Hart, Lee, Kluczyński, Krzysztof, Cornelius, Victoria, MacInnis, Bronwyn, Henrichs, Christa, and Giacomantonio, Rachel

Published
2017
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14. Adaptive introgression between Anopheles sibling species eliminates a major genomic island but not reproductive isolation

Author

Clarkson, Chris S., Weetman, David, Essandoh, John, Yawson, Alexander E., Maslen, Gareth, Manske, Magnus, Field, Stuart G., Webster, Mark, Antão, Tiago, MacInnis, Bronwyn, Kwiatkowski, Dominic, and Donnelly, Martin J.

Subjects
Evolution, Molecular, Insecticide Resistance, Reproductive Isolation, Genomic Islands, Anopheles, Mutation, Animals, Voltage-Gated Sodium Channels, Article
Abstract

Adaptive introgression can provide novel genetic variation to fuel rapid evolutionary responses, though it may be counterbalanced by potential for detrimental disruption of the recipient genomic background. We examine the extent and impact of recent introgression of a strongly selected insecticide-resistance mutation (Vgsc-1014F) located within one of two exceptionally large genomic islands of divergence separating the Anopheles gambiae species pair. Here we show that transfer of the Vgsc mutation results in homogenization of the entire genomic island region (~1.5% of the genome) between species. Despite this massive disruption, introgression is clearly adaptive with a dramatic rise in frequency of Vgsc-1014F and no discernable impact on subsequent reproductive isolation between species. Our results show (1) how resilience of genomes to massive introgression can permit rapid adaptive response to anthropogenic selection and (2) that even extreme prominence of genomic islands of divergence can be an unreliable indicator of importance in speciation., Highly divergent genomic islands segregate between a species pair of the mosquito, Anopheles gambiae. Here Clarkson et al. show that loss of one of the largest islands, driven by adaptive introgression of an insecticide-resistance mutation, had no impact on reproductive isolation.

Published
2014

15. Selective sweep on human amylase genes postdates the split with Neanderthals

Author

Inchley, Charlotte E., primary, Larbey, Cynthia D. A., additional, Shwan, Nzar A. A., additional, Pagani, Luca, additional, Saag, Lauri, additional, Antão, Tiago, additional, Jacobs, Guy, additional, Hudjashov, Georgi, additional, Metspalu, Ene, additional, Mitt, Mario, additional, Eichstaedt, Christina A., additional, Malyarchuk, Boris, additional, Derenko, Miroslava, additional, Wee, Joseph, additional, Abdullah, Syafiq, additional, Ricaut, François-Xavier, additional, Mormina, Maru, additional, Mägi, Reedik, additional, Villems, Richard, additional, Metspalu, Mait, additional, Jones, Martin K., additional, Armour, John A. L., additional, and Kivisild, Toomas, additional

Published
2016
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17. O espaço de habitar vernacular no barrocal algarvio

Author

Antão, Tiago Filipe Lampreia and Soares, João Candeias

Subjects
Barrocal algarvio, Algarve, Paisagem, Arquitectura popular, Vernacular Architecture, Algarve's barrocal, Landscape, Arquitectura vernacular
Published
2010

20. Genomic analyses inform on migration events during the peopling of Eurasia

Author

Pagani, Luca, Lawson, Daniel John, Jagoda, Evelyn, Mörseburg, Alexander, Eriksson, Anders, Mitt, Mario, Clemente, Florian, Hudjashov, Georgi, DeGiorgio, Michael, Saag, Lauri, Wall, Jeffrey D., Cardona, Alexia, Mägi, Reedik, Wilson Sayres, Melissa A., Kaewert, Sarah, Inchley, Charlotte, Scheib, Christiana L., Järve, Mari, Karmin, Monika, Jacobs, Guy S., Antao, Tiago, Iliescu, Florin Mircea, Kushniarevich, Alena, Ayub, Qasim, Tyler-Smith, Chris, Xue, Yali, Yunusbayev, Bayazit, Tambets, Kristiina, Mallick, Chandana Basu, Saag, Lehti, Pocheshkhova, Elvira, Andriadze, George, Muller, Craig, Westaway, Michael C., Lambert, David M., Zoraqi, Grigor, Turdikulova, Shahlo, Dalimova, Dilbar, Sabitov, Zhaxylyk, Sultana, Gazi Nurun Nahar, Lachance, Joseph, Tishkoff, Sarah, Momynaliev, Kuvat, Isakova, Jainagul, Damba, Larisa D., Gubina, Marina, Nymadawa, Pagbajabyn, Evseeva, Irina, Atramentova, Lubov, Utevska, Olga, Ricaut, François-Xavier, Brucato, Nicolas, Sudoyo, Herawati, Letellier, Thierry, Cox, Murray P., Barashkov, Nikolay A., Skaro, Vedrana, Mulahasanovic, Lejla, Primorac, Dragan, Sahakyan, Hovhannes, Mormina, Maru, Eichstaedt, Christina A., Lichman, Daria V., Abdullah, Syafiq, Chaubey, Gyaneshwer, Wee, Joseph T. S., Mihailov, Evelin, Karunas, Alexandra, Litvinov, Sergei, Khusainova, Rita, Ekomasova, Natalya, Akhmetova, Vita, Khidiyatova, Irina, Marjanović, Damir, Yepiskoposyan, Levon, Behar, Doron M., Balanovska, Elena, Metspalu, Andres, Derenko, Miroslava, Malyarchuk, Boris, Voevoda, Mikhail, Fedorova, Sardana A., Osipova, Ludmila P., Lahr, Marta Mirazón, Gerbault, Pascale, Leavesley, Matthew, Migliano, Andrea Bamberg, Petraglia, Michael, Balanovsky, Oleg, Khusnutdinova, Elza K., Metspalu, Ene, Thomas, Mark G., Manica, Andrea, Nielsen, Rasmus, Villems, Richard, Willerslev, Eske, Kivisild, Toomas, and Metspalu, Mait

Published
2016
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22. Evolution of the Pygmy Phenotype: Evidence of Positive Selection from Genome-wide Scans in African, Asian, and Melanesian Pygmies

Author

Migliano, Andrea Bamberg, Romero, Irene Gallego, Metspalu, Mait, Leavesley, Matthew, Pagani, Luca, Antao, Tiago, Huang, Da-Wei, Sherman, Brad T., Siddle, Katharine, Scholes, Clarissa, Hudjashov, Georgi, Kaitokai, Elton, Babalu, Avis, Belatti, Maggie, Cagan, Alex, Hopkinshaw, Bryony, Shaw, Colin, Nelis, Mari, Metspalu, Ene, Mägi, Reedik, Lempicki, Richard A., Villems, Richard, Lahr, Marta Mirazon, and Kivisild, Toomas

Published
2013

23. Selective sweep on human amylase genes postdates the split with Neanderthals

Author

Inchley, Charlotte E., Larbey, Cynthia D.A., Shwan, Nzar A.A., Pagani, Luca, Saag, Lauri, Antão, Tiago, Jacobs, Guy, Hudjashov, Georgi, Metspalu, Ene, Mitt, Mario, Eichstaedt, Christina A., Malyarchuk, Boris, Derenko, Miroslava, Wee, Joseph, Abdullah, Syafiq, Ricaut, François-Xavier, Mormina, Maru, Mägi, Reedik, Villems, Richard, Metspalu, Mait, Jones, Martin K., Armour, John A.L., Kivisild, Toomas, Inchley, Charlotte E., Larbey, Cynthia D.A., Shwan, Nzar A.A., Pagani, Luca, Saag, Lauri, Antão, Tiago, Jacobs, Guy, Hudjashov, Georgi, Metspalu, Ene, Mitt, Mario, Eichstaedt, Christina A., Malyarchuk, Boris, Derenko, Miroslava, Wee, Joseph, Abdullah, Syafiq, Ricaut, François-Xavier, Mormina, Maru, Mägi, Reedik, Villems, Richard, Metspalu, Mait, Jones, Martin K., Armour, John A.L., and Kivisild, Toomas

Abstract

Humans have more copies of amylase genes than other primates. It is still poorly understood, however, when the copy number expansion occurred and whether its spread was enhanced by selection. Here we assess amylase copy numbers in a global sample of 480 high coverage genomes and find that regions flanking the amylase locus show notable depression of genetic diversity both in African and non-African populations. Analysis of genetic variation in these regions supports the model of an early selective sweep in the human lineage after the split of humans from Neanderthals which led to the fixation of multiple copies of AMY1 in place of a single copy. We find evidence of multiple secondary losses of copy number with the highest frequency (52%) of a deletion of AMY2A and associated low copy number of AMY1 in Northeast Siberian populations whose diet has been low in starch content.

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