216 research outputs found
Morphometric, Behavioral, and Genomic Evidence for a New Orangutan Species
No full texthttp://dx.doi.org/10.13039/501100006447 University of Zurich (UZH)http://dx.doi.org/10.13039/501100001711 Swiss National Science Foundationhttp://dx.doi.org/10.13039/100005966 Leakey Foundationhttp://dx.doi.org/10.13039/501100006448 A.H. Schultz Foundationhttp://dx.doi.org/10.13039/501100006447 UZH Research Priority Program “Evolution in Action”Arcus Foundationhttp://dx.doi.org/10.13039/501100000995 Australian National University (ANU) research fundhttp://dx.doi.org/10.13039/501100000995 ANU Vice Chancellor Travel Granthttp://dx.doi.org/10.13039/501100000996 Australia Awards Scholarship-DFAThttp://dx.doi.org/10.13039/100010663 ERChttp://dx.doi.org/10.13039/100004410 EMBOhttp://dx.doi.org/10.13039/501100003329 MINECOFundacio Zoo BarcelonaJulius–Klaus FoundationMINECO/FEDERGates Cambridge Trust http://dx.doi.org/10.13039/501100005370http://dx.doi.org/10.13039/501100006447 Department of Anthropology at the University of Zuric
Simulating the effect of public health interventions using dated virus sequences and geographical data
No full textRecommendationInternational audienceA recommendation of the preprint: Simon Dellicour, Guy Baele, Gytis Dudas, Nuno R. Faria, Oliver G. Pybus, Marc A. Suchard, Andrew Rambaut, Philippe Lemey. Phylodynamic assessment of intervention strategies for the West African Ebola virus outbreak. (2018), bioRxiv, 163691, ver. 3 peer-reviewed by Peer Community in Evolutionary Biology. 10.1101/16369
Phylogeography and population dynamics of dengue viruses in the Americas
No full textChanges in Dengue virus (DENV) disease patterns in the Americas over recent decades have been attributed, at least in part, to repeated introduction of DENV strains from other regions, resulting in a shift from hypoendemicity to hyperendemicity. Using newly sequenced DENV-1 and DENV-3 envelope (E) gene isolates from 11 Caribbean countries, along with sequences available on GenBank, we sought to document the population genetic and spatiotemporal transmission histories of the four main invading DENV genotypes within the Americas and investigate factors that influence the rate and intensity of DENV transmission. For all genotypes, there was an initial invasion phase characterized by rapid increases in genetic diversity, which coincided with the first confirmed cases of each genotype in the region. Rapid geographic dispersal occurred upon each genotype's introduction, after which individual lineages were locally maintained, and gene flow was primarily observed among neighboring and nearby countries. There were, however, centers of viral diversity (Barbados, Puerto Rico, Colombia, Suriname, Venezuela, and Brazil) that were repeatedly involved in gene flow with more distant locations. For DENV-1 and DENV-2, we found that a "distance-informed" model, which posits that the intensity of virus movement between locations is inversely proportional to the distance between them, provided a better fit than a model assuming equal rates of movement between all pairs of countries. However, for DENV-3 and DENV-4, the more stochastic "equal rates" model was preferre
Recombination gives a new insight in the effective population size and history of the Old World human populations
No full textChristina J. Adler, Alan Cooper, Clio S. I. Der Sarkissian and Wolfgang Haak are members of the Genographic ConsortiumThe information left by recombination in our genomes can be used to make inferences on our recent evolutionary history. Specifically, the number of past recombination events in a population sample is a function of its effective population size (Ne). We have applied a method, Identifying Recombination in Sequences (IRiS), to detect specific past recombination events in 30 Old World populations to infer their Ne. We have found that sub-Saharan African populations have an Ne that is approximately four times greater than those of non-African populations and that outside of Africa, South Asian populations had the largest Ne. We also observe that the patterns of recombinational diversity of these populations correlate with distance out of Africa if that distance is measured along a path crossing South Arabia. No such correlation is found through a Sinai route, suggesting that anatomically modern humans first left Africa through the Bab-el-Mandeb strait rather than through present Egypt.Marta Melé, Asif Javed, Marc Pybus, Pierre Zalloua, Marc Haber, David Comas, Mihai G. Netea, Oleg Balanovsky, Elena Balanovska, Li Jin, Yajun Yang, R. M. Pitchappan, G. Arunkumar, Laxmi Parida, Francesc Calafell, Jaume Bertranpetit, and the Genographic Consortiu
From epic journeys of freedom: runaway slaves of the American revolution and their global quest for liberty
No full textPEI: Y; PD: bibl fSource type: Electronic(1
Direct evidence of extensive diversity of HIV-1 in Kinshasa by 1960
No full textHuman immunodeficiency virus type 1 (HIV-1) sequences that pre-date the recognition of AIDS are critical to defining the time of origin and the timescale of virus evolution. A viral sequence from 1959 (ZR59) is the oldest known HIV-1 infection. Other historically documented sequences, important calibration points to convert evolutionary distance into time, are lacking, however; ZR59 is the only one sampled before 1976. Here we report the amplification and characterization of viral sequences from a Bouin's-fixed paraffin-embedded lymph node biopsy specimen obtained in 1960 from an adult female in Léopoldville, Belgian Congo (now Kinshasa, Democratic Republic of the Congo (DRC)), and we use them to conduct the first comparative evolutionary genetic study of early pre-AIDS epidemic HIV-1 group M viruses. Phylogenetic analyses position this viral sequence (DRC60) closest to the ancestral node of subtype A (excluding A2). Relaxed molecular clock analyses incorporating DRC60 and ZR59 date the most recent common ancestor of the M group to near the beginning of the twentieth century. The sizeable genetic distance between DRC60 and ZR59 directly demonstrates that diversification of HIV-1 in west-central Africa occurred long before the recognized AIDS pandemic. The recovery of viral gene sequences from decades-old paraffin-embedded tissues opens the door to a detailed palaeovirological investigation of the evolutionary history of HIV-1 that is not accessible by other method
Detection and classification of positive selection in human populations
No full textDetecting positive selection in genomic regions is a recurrent topic in human population genetics studies. Over the years, many positive selection tests have been implemented to highlight specific genomic patterns left by a selective event when compared to neutral expectations. However, there is little consistency among the regions detected in several genome-wide scans using different tests and/or populations: population-specific demographic dynamics, local genomic features or different types of selection acting along the genome at different times and selective coefficients might explain such discrepancies. The present doctoral thesis is focused in the study of this problem and the development of a innovative solution: a machine-learning classification framework that exploits the combined ability of some selection tests to uncover the different features expected under the hard sweep model, such as sweep completeness and age of onset. The method was calibrated and applied to three reference populations from The 1000 Genome Project to generate a genome-wide classification map of hard selective sweeps. This study improves the way a selective sweep is detected by overcoming the classical selection vs. no-selection classification strategy, and offers an explanation to the lack of consistency observed among selection tests when applied to real data.La detecció de selecció positiva en regions genòmiques ha estat un tema recurrent en molts estudis de genètica de poblacions humanes. En conseqüència, durant els últims anys s'han publicat molts mètodes estadístics per detectar els senyals genòmics creats per un procés de selecció molecular. No obstant això, en general hi ha poca consistència entre les regions detectades pels diferents mètodes: dinàmiques demogràfiques especifiques de població, propietats locals de les regions analitzades o diferents tipus de selecció actuant a diferents marcs temporals i intensitats podrien explicar aquestes discrepàncies. Aquesta tesi doctoral està centrada en l'estudi d'aquest problema i en el desenvolupament d'una solució: un mètode de classificació de selecció positiva basat en algoritmes d'aprenentatge automàtic. El mètode combina diferents tests per detectar selecció positiva per obtenir informació sobre el tipus i mode de selecció que afecta una regió genòmica determinada. Aquest nou mètode presenta una alta sensitivitat cap a senyals de selecció positiva i és capaç de proveir informació sobre l'edat del esdeveniment selectiu, així com del seu estat final. Aquest treball millora la forma en què la selecció positiva és detectada avui en dia i proporciona una explicació a la falta de consistència observada entre els mètodes de detecció de selecció positiva quan s'apliquen en dades reals.Programa de doctorat en Biomedicin
Recombination networks as genetic markers in a human variation study of the Old World
No full textChristina J. Adler, Alan Cooper, Clio S. I. Der Sarkissian and Wolfgang Haak are members of The Genographic ConsortiumWe have analyzed human genetic diversity in 33 Old World populations including 23 populations obtained through Genographic Project studies. A set of 1,536 SNPs in five X chromosome regions were genotyped in 1,288 individuals (mostly males). We use a novel analysis employing subARG network construction with recombining chromosomal segments. Here, a subARG is constructed independently for each of five gene-free regions across the X chromosome, and the results are aggregated across them. For PCA, MDS and ancestry inference with STRUCTURE, the subARG is processed to obtain feature vectors of samples and pairwise distances between samples. The observed population structure, estimated from the five short X chromosomal segments, supports genome-wide frequency-based analyses: African populations show higher genetic diversity, and the general trend of shared variation is seen across the globe from Africa through Middle East, Europe, Central Asia, Southeast Asia, and East Asia in broad patterns. The recombinational analysis was also compared with established methods based on SNPs and haplotypes. For haplotypes, we also employed a fixed-length approach based on information-content optimization. Our recombinational analysis suggested a southern migration route out of Africa, and it also supports a single, rapid human expansion from Africa to East Asia through South Asia.Asif Javed, Marta Melé, Marc Pybus, Pierre Zalloua, Marc Haber, David Comas, Mihai G. Netea, Oleg Balanovsky, Elena Balanovska, Li Jin, Yajun Yang, GaneshPrasad ArunKumar, Ramasamy Pitchappan, Jaume Bertranpetit, Francesc Calafell, Laxmi Parida, The Genographic Consortiu
Figure S3 in Morphometric, Behavioral, and Genomic Evidence for a New Orangutan Species
No full textFigure S3. Signatures of recent inbreeding in different orangutan populations. Related to Figure 3C. Number of genomic fragments that are autozygous (y-axis) plotted against the total fraction of the genome covered by such fragments (x-axis). Each dot represents and individual, with sample origins represented by colors corresponding to those in Figure 2A.Published as part of Alexander Nater, Maja P. Mattle-Greminger, Anton Nurcahyo, Matthew G. Nowak, Marc de Manuel, Tariq Desai, Colin Groves, Marc Pybus, Tugce Bilgin Sonay, Christian Roos, Adriano R. Lameira, Serge A. Wich, James Askew, Marina Davila-Ross, Gabriella Fredriksson, Guillem de Valles, Ferran Casals, avier Prado-Martinez, Benoit Goossens, Ernst J. Verschoor, Kristin S. Warren, Ian Singleton, David A. Marques, Joko Pamungkas, Dyah Perwitasari-Farajallah, Puji Rianti, Augustine Tuuga, Ivo G. Gut, Marta Gut, Pablo Orozco-terWengel, Carel P. van Schaik, Jaume Bertranpetit, Maria Anisimova, Aylwyn Scally, Tomas Marques-Bonet, Erik Meijaard & Michael Krüzen, 2017, Current Biology 27 on pages 1-40, DOI: 10.1016/j.cub.2017.09.047, http://zenodo.org/record/104134
Portrait of Cassandra Pybus, non-fiction author [picture] /
No full textTitle from accession record.; One of a series of portraits taken at the Word Festival Canberra, 21-24 March 1997.; P1841/17
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