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Author Julien Soubrier

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Whole-Genome Sequencing of SARS-CoV-2 from Quarantine Hotel Outbreak.

Lex E X Leong, Julien Soubrier, Mark Turra, Emma Denehy, Luke Walters, Karin Kassahn, Geoff Higgins, Tom Dodd, Robert Hall, Katina D'Onise, Nicola Spurrier, Ivan Bastian, Chuan K Lim,

Hotel quarantine for international travelers has been used to prevent coronavirus disease spread into Australia. A quarantine hotel-associated community outbreak was detected in South Australia. Real-time genomic sequencing enabled rapid confirmation tracking the outbreak to a recently returned traveler and linked 2 cases of infection in travelers at the same ... Read more >>

Emerg Infect Dis (Emerging infectious diseases)
[2021, 27(8):2219-2221]

Cited: 0 times

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Untangling the Evolutionary History of European Bison (Bison bonasus)

Ayla van Loenen, Emilia Hofman-Kamińska, Kieren Mitchell, Bastien Llamas, Hervé Bocherens, Julien Soubrier, Holly Heiniger, Martina Pacher, Daniel Makowiecki, Giedrė Piličiauskienė, Dorothée Drucker, Rafał Kowalczyk, Alan Cooper,

<h4>ABSTRACT</h4> European bison ( Bison bonasus ) are the largest endemic vertebrates in Europe, and one of the few megafaunal species to have survived the mass megafaunal extinction during the Pleistocene/Holocene transition (12-9 thousand years ago). Untangling their evolutionary history would provide valuable information about the response of European megafauna ... Read more >>

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Population size history from short genomic scaffolds: how short is too short?

Graham Gower, Jono Tuke, AB Rohrlach, Julien Soubrier, Bastien Llamas, Nigel Bean, Alan Cooper,

The Pairwise Sequentially Markov Coalescent (PSMC), and its extension PSMC′, model past population sizes from a single diploid genome. Both models have been widely applied, even to organisms with scaffold-level genome reference assemblies of limited contiguity. However it is unclear how PSMC and PSMC′ perform on short scaffolds. We evaluated ... Read more >>

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Genome of the Tasmanian tiger provides insights into the evolution and demography of an extinct marsupial carnivore.

Charles Y Feigin, Axel H Newton, Liliya Doronina, Jürgen Schmitz, Christy A Hipsley, Kieren J Mitchell, Graham Gower, Bastien Llamas, Julien Soubrier, Thomas N Heider, Brandon R Menzies, Alan Cooper, Rachel J O'Neill, Andrew J Pask,

The Tasmanian tiger or thylacine (Thylacinus cynocephalus) was the largest carnivorous Australian marsupial to survive into the modern era. Despite last sharing a common ancestor with the eutherian canids ~160 million years ago, their phenotypic resemblance is considered the most striking example of convergent evolution in mammals. The last known thylacine ... Read more >>

Nat Ecol Evol (Nature ecology & evolution)
[2018, 2(1):182-192]

Cited: 25 times

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Experimental conditions improving in‐solution target enrichment for ancient DNA

Diana I Cruz‐Dávalos, Ahmed H. Alfarhan, Alan Cooper, Amelie Scheu, Andaine Seguin‐Orlando, Antoine Fages, Arne Ludwig, Bastien Llamas, Charleen Gaunitz, Cristina Gamba, Eske Willerslev, Julien Soubrier, Khaled A. S. Al‐Rasheid, Ludovic Orlando, Mélanie Pruvost, Norbert Beneke, Pablo Librado, Saleh A. Alquraishi,

High‐throughput sequencing has dramatically fostered ancient DNA research in recent years. Shotgun sequencing, however, does not necessarily appear as the best‐suited approach due to the extensive contamination of samples with exogenous environmental microbial DNA. DNA capture‐enrichment methods represent cost‐effective alternatives that increase the sequencing focus on the endogenous fraction, whether ... Read more >>

Mol Ecol Resour (Molecular ecology resources)
[2017, 17(3):508-522]

Cited: 10 times

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Aboriginal mitogenomes reveal 50,000 years of regionalism in Australia.

Ray Tobler, Adam Rohrlach, Julien Soubrier, Pere Bover, Bastien Llamas, Jonathan Tuke, Nigel Bean, Ali Abdullah-Highfold, Shane Agius, Amy O'Donoghue, Isabel O'Loughlin, Peter Sutton, Fran Zilio, Keryn Walshe, Alan N Williams, Chris S M Turney, Matthew Williams, Stephen M Richards, Robert J Mitchell, Emma Kowal, John R Stephen, Lesley Williams, Wolfgang Haak, Alan Cooper,

Aboriginal Australians represent one of the longest continuous cultural complexes known. Archaeological evidence indicates that Australia and New Guinea were initially settled approximately 50 thousand years ago (ka); however, little is known about the processes underlying the enormous linguistic and phenotypic diversity within Australia. Here we report 111 mitochondrial genomes ... Read more >>

Nature (Nature)
[2017, 544(7649):180-184]

Cited: 29 times

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Neanderthal behaviour, diet, and disease inferred from ancient DNA in dental calculus.

Laura S Weyrich, Sebastian Duchene, Julien Soubrier, Luis Arriola, Bastien Llamas, James Breen, Alan G Morris, Kurt W Alt, David Caramelli, Veit Dresely, Milly Farrell, Andrew G Farrer, Michael Francken, Neville Gully, Wolfgang Haak, Karen Hardy, Katerina Harvati, Petra Held, Edward C Holmes, John Kaidonis, Carles Lalueza-Fox, Marco de la Rasilla, Antonio Rosas, Patrick Semal, Arkadiusz Soltysiak, Grant Townsend, Donatella Usai, Joachim Wahl, Daniel H Huson, Keith Dobney, Alan Cooper,

Recent genomic data have revealed multiple interactions between Neanderthals and modern humans, but there is currently little genetic evidence regarding Neanderthal behaviour, diet, or disease. Here we describe the shotgun-sequencing of ancient DNA from five specimens of Neanderthal calcified dental plaque (calculus) and the characterization of regional differences in Neanderthal ... Read more >>

Nature (Nature)
[2017, 544(7650):357-361]

Cited: 90 times

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Early cave art and ancient DNA record the origin of European bison.

Julien Soubrier, Graham Gower, Kefei Chen, Stephen M Richards, Bastien Llamas, Kieren J Mitchell, Simon Y W Ho, Pavel Kosintsev, Michael S Y Lee, Gennady Baryshnikov, Ruth Bollongino, Pere Bover, Joachim Burger, David Chivall, Evelyne Crégut-Bonnoure, Jared E Decker, Vladimir B Doronichev, Katerina Douka, Damien A Fordham, Federica Fontana, Carole Fritz, Jan Glimmerveen, Liubov V Golovanova, Colin Groves, Antonio Guerreschi, Wolfgang Haak, Tom Higham, Emilia Hofman-Kamińska, Alexander Immel, Marie-Anne Julien, Johannes Krause, Oleksandra Krotova, Frauke Langbein, Greger Larson, Adam Rohrlach, Amelie Scheu, Robert D Schnabel, Jeremy F Taylor, Małgorzata Tokarska, Gilles Tosello, Johannes van der Plicht, Ayla van Loenen, Jean-Denis Vigne, Oliver Wooley, Ludovic Orlando, Rafał Kowalczyk, Beth Shapiro, Alan Cooper,

The two living species of bison (European and American) are among the few terrestrial megafauna to have survived the late Pleistocene extinctions. Despite the extensive bovid fossil record in Eurasia, the evolutionary history of the European bison (or wisent, Bison bonasus) before the Holocene (<11.7 thousand years ago (kya)) remains ... Read more >>

Nat Commun (Nature communications)
[2016, 7:13158]

Cited: 16 times

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Experimental conditions improving in-solution target enrichment for ancient DNA.

Diana I Cruz-Dávalos, Bastien Llamas, Charleen Gaunitz, Antoine Fages, Cristina Gamba, Julien Soubrier, Pablo Librado, Andaine Seguin-Orlando, Mélanie Pruvost, Ahmed H Alfarhan, Saleh A Alquraishi, Khaled A S Al-Rasheid, Amelie Scheu, Norbert Beneke, Arne Ludwig, Alan Cooper, Eske Willerslev, Ludovic Orlando,

High-throughput sequencing has dramatically fostered ancient DNA research in recent years. Shotgun sequencing, however, does not necessarily appear as the best-suited approach due to the extensive contamination of samples with exogenous environmental microbial DNA. DNA capture-enrichment methods represent cost-effective alternatives that increase the sequencing focus on the endogenous fraction, whether ... Read more >>

Mol Ecol Resour (Molecular ecology resources)
[2017, 17(3):508-522]

Cited: 16 times

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Ancient mitochondrial DNA provides high-resolution time scale of the peopling of the Americas.

Bastien Llamas, Lars Fehren-Schmitz, Guido Valverde, Julien Soubrier, Swapan Mallick, Nadin Rohland, Susanne Nordenfelt, Cristina Valdiosera, Stephen M Richards, Adam Rohrlach, Maria Inés Barreto Romero, Isabel Flores Espinoza, Elsa Tomasto Cagigao, Lucía Watson Jiménez, Krzysztof Makowski, Ilán Santiago Leboreiro Reyna, Josefina Mansilla Lory, Julio Alejandro Ballivián Torrez, Mario A Rivera, Richard L Burger, Maria Constanza Ceruti, Johan Reinhard, R Spencer Wells, Gustavo Politis, Calogero M Santoro, Vivien G Standen, Colin Smith, David Reich, Simon Y W Ho, Alan Cooper, Wolfgang Haak,

The exact timing, route, and process of the initial peopling of the Americas remains uncertain despite much research. Archaeological evidence indicates the presence of humans as far as southern Chile by 14.6 thousand years ago (ka), shortly after the Pleistocene ice sheets blocking access from eastern Beringia began to retreat. ... Read more >>

Sci Adv (Science advances)
[2016, 2(4):e1501385]

Cited: 70 times

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Environmental metabarcodes for insects: in silico PCR reveals potential for taxonomic bias

Laurence J Clarke, Julien Soubrier, Laura S Weyrich, Alan Cooper,

Studies of insect assemblages are suited to the simultaneous DNA‐based identification of multiple taxa known as metabarcoding. To obtain accurate estimates of diversity, metabarcoding markers ideally possess appropriate taxonomic coverage to avoid PCR‐amplification bias, as well as sufficient sequence divergence to resolve species. We used in silico PCR to compare ... Read more >>

Mol Ecol Resour (Molecular ecology resources)
[2014, 14(6):1160-1170]

Cited: 64 times

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Environmental metabarcodes for insects: in silico PCR reveals potential for taxonomic bias.

Laurence J Clarke, Julien Soubrier, Laura S Weyrich, Alan Cooper,

Studies of insect assemblages are suited to the simultaneous DNA-based identification of multiple taxa known as metabarcoding. To obtain accurate estimates of diversity, metabarcoding markers ideally possess appropriate taxonomic coverage to avoid PCR-amplification bias, as well as sufficient sequence divergence to resolve species. We used in silico PCR to compare ... Read more >>

Mol Ecol Resour (Molecular ecology resources)
[2014, 14(6):1160-1170]

Cited: 26 times

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Ancient DNA reveals elephant birds and kiwi are sister taxa and clarifies ratite bird evolution.

Kieren J Mitchell, Bastien Llamas, Julien Soubrier, Nicolas J Rawlence, Trevor H Worthy, Jamie Wood, Michael S Y Lee, Alan Cooper,

The evolution of the ratite birds has been widely attributed to vicariant speciation, driven by the Cretaceous breakup of the supercontinent Gondwana. The early isolation of Africa and Madagascar implies that the ostrich and extinct Madagascan elephant birds (Aepyornithidae) should be the oldest ratite lineages. We sequenced the mitochondrial genomes ... Read more >>

Science (Science (New York, N.Y.))
[2014, 344(6186):898-900]

Cited: 78 times

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Rates of phenotypic and genomic evolution during the Cambrian explosion.

Michael S Y Lee, Julien Soubrier, Gregory D Edgecombe,

The near-simultaneous appearance of most modern animal body plans (phyla) ~530 million years ago during the Cambrian explosion is strong evidence for a brief interval of rapid phenotypic and genetic innovation, yet the exact speed and nature of this grand adaptive radiation remain debated. Crucially, rates of morphological evolution in ... Read more >>

Curr Biol (Current biology : CB)
[2013, 23(19):1889-1895]

Cited: 56 times

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Pleistocene Chinese cave hyenas and the recent Eurasian history of the spotted hyena, Crocuta crocuta.

Gui-Lian Sheng, Julien Soubrier, Jin-Yi Liu, Lars Werdelin, Bastien Llamas, Vicki A Thomson, Jonathan Tuke, Lian-Juan Wu, Xin-Dong Hou, Quan-Jia Chen, Xu-Long Lai, Alan Cooper,

The living hyena species (spotted, brown, striped and aardwolf) are remnants of a formerly diverse group of more than 80 fossil species, which peaked in diversity in the Late Miocene (about 7-8 Ma). The fossil history indicates an African origin, and morphological and ancient DNA data have confirmed that living ... Read more >>

Mol Ecol (Molecular ecology)
[2014, 23(3):522-533]

Cited: 8 times

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Modular tagging of amplicons using a single PCR for high-throughput sequencing.

Laurence J Clarke, Paul Czechowski, Julien Soubrier, Mark I Stevens, Alan Cooper,

High-throughput sequencing (HTS) of PCR amplicons is becoming the method of choice to sequence one or several targeted loci for phylogenetic and DNA barcoding studies. Although the development of HTS has allowed rapid generation of massive amounts of DNA sequence data, preparing amplicons for HTS remains a rate-limiting step. For ... Read more >>

Mol Ecol Resour (Molecular ecology resources)
[2014, 14(1):117-121]

Cited: 15 times

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The origins of the enigmatic Falkland Islands wolf.

Jeremy J Austin, Julien Soubrier, Francisco J Prevosti, Luciano Prates, Valentina Trejo, Francisco Mena, Alan Cooper,

The origins of the extinct Falkland Islands wolf (FIW), Dusicyon australis, have remained a mystery since it was first recorded by Europeans in the seventeenth century. It is the only terrestrial mammal on the Falkland Islands (also known as the Malvinas Islands), which lie ~460 km from Argentina, leading to ... Read more >>

Nat Commun (Nature communications)
[2013, 4:1552]

Cited: 7 times

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Neolithic mitochondrial haplogroup H genomes and the genetic origins of Europeans.

Paul Brotherton, Wolfgang Haak, Jennifer Templeton, Guido Brandt, Julien Soubrier, Christina Jane Adler, Stephen M Richards, Clio Der Sarkissian, Robert Ganslmeier, Susanne Friederich, Veit Dresely, Mannis van Oven, Rosalie Kenyon, Mark B Van der Hoek, Jonas Korlach, Khai Luong, Simon Y W Ho, Lluis Quintana-Murci, Doron M Behar, Harald Meller, Kurt W Alt, Alan Cooper, ,

Haplogroup H dominates present-day Western European mitochondrial DNA variability (>40%), yet was less common (~19%) among Early Neolithic farmers (~5450 BC) and virtually absent in Mesolithic hunter-gatherers. Here we investigate this major component of the maternal population history of modern Europeans and sequence 39 complete haplogroup H mitochondrial genomes from ... Read more >>

Nat Commun (Nature communications)
[2013, 4:1764]

Cited: 78 times

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The influence of rate heterogeneity among sites on the time dependence of molecular rates.

Julien Soubrier, Mike Steel, Michael S Y Lee, Clio Der Sarkissian, Stéphane Guindon, Simon Y W Ho, Alan Cooper,

Molecular evolutionary rate estimates have been shown to depend on the time period over which they are estimated. Factors such as demographic processes, calibration errors, purifying selection, and the heterogeneity of substitution rates among sites (RHAS) are known to affect the accuracy with which rates of evolution are estimated. We ... Read more >>

Mol Biol Evol (Molecular biology and evolution)
[2012, 29(11):3345-3358]

Cited: 60 times

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Time-dependent rates of molecular evolution.

Simon Y W Ho, Robert Lanfear, Lindell Bromham, Matthew J Phillips, Julien Soubrier, Allen G Rodrigo, Alan Cooper,

For over half a century, it has been known that the rate of morphological evolution appears to vary with the time frame of measurement. Rates of microevolutionary change, measured between successive generations, were found to be far higher than rates of macroevolutionary change inferred from the fossil record. More recently, ... Read more >>

Mol Ecol (Molecular ecology)
[2011, 20(15):3087-3101]

Cited: 237 times

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Multiple geographic origins of commensalism and complex dispersal history of Black Rats.

Ken P Aplin, Hitoshi Suzuki, Alejandro A Chinen, R Terry Chesser, José Ten Have, Stephen C Donnellan, Jeremy Austin, Angela Frost, Jean Paul Gonzalez, Vincent Herbreteau, Francois Catzeflis, Julien Soubrier, Yin-Ping Fang, Judith Robins, Elizabeth Matisoo-Smith, Amanda D S Bastos, Ibnu Maryanto, Martua H Sinaga, Christiane Denys, Ronald A Van Den Bussche, Chris Conroy, Kevin Rowe, Alan Cooper,

The Black Rat (Rattus rattus) spread out of Asia to become one of the world's worst agricultural and urban pests, and a reservoir or vector of numerous zoonotic diseases, including the devastating plague. Despite the global scale and inestimable cost of their impacts on both human livelihoods and natural ecosystems, ... Read more >>

PLoS One (PloS one)
[2011, 6(11):e26357]

Cited: 80 times

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