Now showing items 81-100 of 106

    • Plasmodium vivax Malaria Viewed through the Lens of an Eradicated European Strain 

      van Dorp, Lucy; Gelabert, Pere; Rieux, Adrien; De Manuel, Marc; De-Dios, Toni; Gopalakrishnan, Shyam; Carøe, Christian; Sandoval-Velasco, Marcela; Fregel, Rosa; Olalde, Iñigo; Escosa, Raül; Aranda, Carles; Huijben, Silvie; Mueller, Ivo; Marques-Bonet, Tomas; Balloux, Francois; Gilbert, Marcus Thomas Pius; Lalueza-Fox, Carles (Peer reviewed; Journal article, 2020)
      The protozoan Plasmodium vivax is responsible for 42% of all cases of malaria outside Africa. The parasite is currently largely restricted to tropical and subtropical latitudes in Asia, Oceania, and the Americas. Though, ...
    • Population genomics of grey wolves and wolf-like canids in North America 

      Sinding, Mikkel Holger Strander; Gopalakrishnan, Shyam; Vieira, Filipe G.; Samaniego, Jose A; Raundrup, Katrine; Heide Jørgensen, Mads Peter; Meldgaard, Morten; Petersen, Bent; Sicheritz-Ponten, Thomas; Mikkelsen, Johan Brus; Marquard-Petersen, Ulf; Dietz, Rune; Sonne, Christian; Dalén, Love; Bachmann, Lutz; Wiig, Øystein; Hansen, Anders J.; Gilbert, Marcus Thomas Pius (Journal article; Peer reviewed, 2018)
      North America is currently home to a number of grey wolf (Canis lupus) and wolf-like canid populations, including the coyote (Canis latrans) and the taxonomically controversial red, Eastern timber and Great Lakes wolves. ...
    • Population genomics of the Viking world 

      Margaryan, Ashot; Lawson, Daniel J.; Sikora, Martin; Racimo, Fernando; Rasmussen, Simon; Moltke, Ida; Cassidy, Lara M.; Jørsboe, Emil; Ingason, Andres; Pedersen, Mikkel Winther; Korneliussen, Thorfinn; Wilhelmson, Helene; Bus, Magdalena M.; de Barros Damgaard, Peter; Martiniano, Rui; Renaud, Gabriel; Bhérer, Claude; Moreno-Mayar, J. Víctor; Fotakis, Anna K.; Allen, Marie; Allmäe, Raili; Molak, Martyna; Cappellini, Enrico; Scorrano, Gabriele; McColl, Hugh; Buzhilova, Alexandra; Fox, Allison; Albrechtsen, Anders; Schütz, Berit; Skar, Birgitte; Arcini, Caroline; Falys, Ceri; Jonson, Charlotte Hedenstierna; Błaszczyk, Dariusz; Pezhemsky, Denis; Turner-Walker, Gordon; Gestsdóttir, Hildur; Lundstrøm, Inge; Gustin, Ingrid; Mainland, Ingrid; Potekhina, Inna; Muntoni, Italo M.; Cheng, Jade Y.; Stenderup, Jesper; Ma, Jilong; Gibson, Julie; Peets, Jüri; Gustafsson, Jörgen; Iversen, Katrine Højholt; Simpson, Linzi; Strand, Lisa Mariann; Loe, Louise; Sikora, Maeve; Florek, Marek; Vretemark, Maria; Redknap, Mark; Bajka, Monika; Pushkina, Tamara; Søvsø, Morten; Grigoreva, Natalia; Christensen, Tom; Kastholm, Ole; Uldum, Otto; Favia, Pasquale; Holck, Per; Sten, Sabine; Arge, Símun V; Ellingvåg, Sturla; Moiseyev, Vayacheslav; Bogdanowicz, Wiesław; Magnusson, Yvonne; Orlando, Ludovic; Pentz, Peter; Jessen, Mads Dengsø; Pedersen, Anne; Collard, Mark; Bradley, Daniel G.; Jørkov, Marie Louise; Arneborg, Jette; Lynnerup, Niels; Price, Neil; Gilbert, Marcus Thomas Pius; Allentoft, Morten E.; Bill, Jan; Sindbæk, Søren M; Hedeager, Lotte; Kristiansen, Kristian; Nielsen, Rasmus; Werge, Thomas; Willerslev, Eske (Peer reviewed; Journal article, 2020)
      The maritime expansion of Scandinavian populations during the Viking Age (about ad 750–1050) was a far-flung transformation in world history1,2. Here we sequenced the genomes of 442 humans from archaeological sites across ...
    • The potential of aquatic bloodfeeding and nonbloodfeeding leeches as a tool for iDNA characterisation 

      Lynggaard, Christina; Oceguera-Figueroa, Alejandro; Kvist, Sebastian; Gilbert, Marcus Thomas Pius; Bohmann, Kristine (Peer reviewed; Journal article, 2021)
      Leeches play important roles in food webs due to their abundance, diversity and feeding habits. Studies using invertebrate-derived DNA (iDNA) extracted from leech gut contents to target vertebrate DNA have focused on the ...
    • Pre-extinction demographic stability and genomic signatures of adaptation in the woolly rhinoceros 

      Lord, Edana; Dussex, Nicolas; Kierczak, Marcin; Díez-del-Molino, David; Ryder, Oliver A.; Stanton, David W. G.; Gilbert, Marcus Thomas Pius; Sánchez-Barreiro, Fatima; Zhang, Guojie; Sinding, Mikkel-Holger S.; Lorenzen, Eline D.; Willerslev, Eske; Protopov, Albert; Shidlovskiy, Fedor K.; Fedorov, Sergey; Bocherens, Hervé; Nathan, Senthilvel K.S.S.; Goossens, Benoit; Johannes, van der Plicht; Chan, Yvonne L.; Prost, Stefan; Potapova, Olga R; Kirillova, Irina V.; Lister, Adrian M.; Heintzman, Peter D.; Kapp, Joshua D.; Shapiro, Beth; Vartanyan, Sergey; Götherström, Anders; Dalén, Love (Peer reviewed; Journal article, 2020)
      Ancient DNA has significantly improved our understanding of the evolution and population history of extinct megafauna. However, few studies have used complete ancient genomes to examine species responses to climate change ...
    • Probing the genomic limits of de-extinction in the Christmas Island rat 

      Lin, Jianqing; Duchêne, David; Carøe, Christian; Smith, Oliver; Ciucani, Marta Maria; Niemann, Jonas; Richmond, Douglas; Greenwood, Alex D.; MacPhee, Ross; Zhang, Guojie; Gopalakrishnan, Shyam; Gilbert, Marcus Thomas Pius (Peer reviewed; Journal article, 2022)
      Three principal methods are under discussion as possible pathways to “true” de-extinction; i.e., back-breeding, cloning, and genetic engineering.1,2 Of these, while the latter approach is most likely to apply to the largest ...
    • Protective role of the vulture facial skin and gut microbiomes aid adaptation to scavenging 

      Zepeda Mendoza, M. Lisandra; Roggenbuck, Michael; Manzano Vargas, Karla; Hestbjerg Hansen, Lars; Brunak, Søren; Gilbert, Marcus Thomas Pius; Sicheritz-Ponten, Thomas (Journal article; Peer reviewed, 2018)
      Background Vultures have adapted the remarkable ability to feed on carcasses that may contain microorganisms that would be pathogenic to most other animals. The holobiont concept suggests that the genetic basis of such ...
    • Rapid discovery of novel prophages using biological feature engineering and machine learning 

      Sirén, Kimmo; Millard, Andrew; Petersen, Bent; Gilbert, Marcus Thomas Pius; Clokie, Martha R.J.; Sicheritz-Pontén, Thomas (Peer reviewed; Journal article, 2021)
      Prophages are phages that are integrated into bacterial genomes and which are key to understanding many aspects of bacterial biology. Their extreme diversity means they are challenging to detect using sequence similarity, ...
    • Reconsidering domestication from a process archaeology perspective 

      Bogaard, Amy; Allaby, Robin G.; Arbuckle, Benjamin; Bendrey, Robin; Crowley, Sarah; Cucchi, Thomas; Denham, Tim; Frantz, Laurent; Fuller, Dorian; Gilbert, Marcus Thomas Pius; Karlsson, Elinor K.; Manin, Aurélie; Marshall, Fiona; Mueller, Natalie; Peters, Joris; Stépanoff, Charles; Weide, Alexander; Larson, Greger (Journal article; Peer reviewed, 2021)
    • Redefining the Evolutionary History of the Rock Dove, Columba livia, Using Whole Genome Sequences 

      Hernández-Alonso, Germán; Ramos-Madrigal, Jazmín; van Grouw, Hein; Ciucani, MartaMaria; Cavill, Emily Louisa; Sinding, Mikkel-Holger S.; Gopalakrishnan, Shyam; Pacheco, George; Gilbert, Marcus Thomas Pius (Peer reviewed; Journal article, 2023)
      The domestic pigeon's exceptional phenotypic diversity was key in developing Darwin's Theory of Evolution and establishing the concept of artificial selection. However, unlike its domestic counterpart, its wild progenitor, ...
    • Relative performance of two DNA extraction and library preparation methods on archaeological human teeth samples 

      Sandoval-Velasco, Marcela; Lundstrøm, Inge K. C.; Wales, Nathan; Ávila-Arcos, María C; Schroeder, Hannes; Gilbert, Marcus Thomas Pius (Journal article; Peer reviewed, 2017)
      DNA extraction and library preparation are crucial steps in any ancient DNA study. Although palaeogenomic researchers are facing a growing choice of DNA extraction and sequencing library preparation methods, how their ...
    • Releasing the microbes from old bones: the effect of different DNA extraction protocols on microbial community profiling 

      Eriksen, Anne Marie Høier; Gilbert, Marcus Thomas Pius (Peer reviewed; Journal article, 2020)
      DNA-based characterisation of microbial communities can enable those interested in bone diagenesis to address questions relating to the complexity and diversity of said microbial communities. We explored whether biases ...
    • Runs of homozygosity in killer whale genomes provide a global record of demographic histories 

      Foote, Andrew; Hooper, Rebecca; Alexander, Alana; Baird, Robin; Baker, Scott; Ballance, Lisa; Barlow, Jay; Brownlow, Andrew; Collins, Tim; Constantine, Rochelle; Rosa, Luciano Dalla; Davison, Nicholas J.; Durban, John; Esteban, Ruth; Excoffier, Laurent; Forney, Karin A.; Gerrodette, Tim; Gilbert, Marcus Thomas Pius; Guinet, Christophe; Hanson, M. Bradley; Li, Songhai; Martin, Sarah; Martin, Michael David; Robertson, Kelly M.; Samarra, Filipa I.P.; de Stephanis, Renaud; Tavares, Sara B.; Tixier, Paul; Totterdell, John A.; Wade, Paul; Wolf, Jochen B.W.; Fan, Guangyi; Zhang, Yaolei; Morin, Phillip A. (Peer reviewed; Journal article, 2021)
      Runs of homozygosity (ROH) occur when offspring inherit haplotypes that are identical by descent from each parent. Length distributions of ROH are informative about population history; specifically, the probability of ...
    • A simplified protocol for DNA extraction from FTA cards for faecal microbiome studies 

      Bolt Botnen, Amanda; Bjørnsen, Mads Bjørn; Alberdi, Antton; Gilbert, Marcus Thomas Pius; Aizpurua, Ostaizka (Peer reviewed; Journal article, 2023)
      As metagenomic studies continue to increase in size and complexity, they are often required to incorporate data from geographically isolated locations or longitudinal time samples. This represents a technical challenge, ...
    • Skmer: assembly-free and alignment-free sample identification using genome skims 

      Sarmashghi, Shahab; Bohmann, Kristine; Gilbert, Marcus Thomas Pius; Bafna, Vineet; Mirarab, Siavash (Journal article; Peer reviewed, 2019)
      The ability to inexpensively describe taxonomic diversity is critical in this era of rapid climate and biodiversity changes. The recent genome-skimming approach extends current barcoding practices beyond short markers by ...
    • Specialized sledge dogs accompanied Inuit dispersal across the North American Arctic 

      Ameen, Carly; Feuerborn, Tatiana R.; Brown, Sarah K.; Linderholm, Anna; Hulme-Beaman, Ardern; Lebrasseur, Ophelie; Sinding, Mikkel Holger Strander; Lounsberry, Zachary T.; Lin, Audrey T.; Appelt, Martin; Bachmann, Lutz; Betts, Matthew; Britton, Kate; Darwent, John; Dietz, Rune; Fredholm, Merethe; Gopalakrishnan, Shyam; Goruinova, Olga I.; Grønnow, Bjarne; Haile, James; Hallsson, Jón Hallsteinn; Harrison, Ramona; Heide-Jørgensen, Mads-Peter; Knecht, Rick; Losey, Robert J.; Masson-MacLean, Edouard; McGovern, Thomas H.; McMagnus-Fry, Ellen; Meldgaard, Morten; Midtdal, Åslaug; Moss, Madonna L.; Nikitin, Iurii G.; Nomokonova, Tatiana; Palsdottir, Albina Hulda; Perri, Angela; Popov, Aleksandr N.; Rankin, Lisa; Reuther, Joshua D.; Sablin, Mikhail V.; Schmidt, Anne Lisbeth; Shirar, Scott; Smiarowski, Konrad; Sonne, Christian; Stiner, Mary C.; Vasyukov, Mitya; West, Catherine F.; Ween, Gro Birgit; Wennerberg, Sanne Eline; Wiig, Øystein; Woollett, James; Dalén, Love; Hansen, Anders J.; Gilbert, Marcus Thomas Pius; Sacks, Benjamin N; Frantz, Laurent A.F.; Larson, Greger; Dobney, Keith; Darwent, Christyann M.; Evin, Allowen (Journal article; Peer reviewed, 2019)
      Domestic dogs have been central to life in the North American Arctic for millennia. The ancestors of the Inuit were the first to introduce the widespread usage of dog sledge transportation technology to the Americas, but ...
    • Taxonomic and functional characterization of the microbial community during spontaneous in vitro fermentation of riesling must 

      Sirén, Kimmo; Mak, Sarah Siu Tze; Melkonian, Chrats; Carøe, Christian; Swiegers, Jan Hendrik; Molenaar, Douwe; Fischer, Ulrich; Gilbert, Marcus Thomas Pius (Journal article; Peer reviewed, 2019)
      Although there is an extensive tradition of research into the microbes that underlie the winemaking process, much remains to be learnt. We combined the high-throughput sequencing (HTS) tools of metabarcoding and metagenomics, ...
    • The population genomic basis of geographic differentiation in North American common ragweed (Ambrosia artemisiifolia L.) 

      Martin, Michael D; Olsen, Morten T; Samaniego, Jose; Zimmer, Elizabeth A; Gilbert, Marcus Thomas Pius (Journal article; Peer reviewed, 2016)
      Common ragweed (Ambrosia artemisiifolia L.) is an invasive, wind‐pollinated plant nearly ubiquitous in disturbed sites in its eastern North American native range and present across growing portions of Europe, Africa, Asia, ...
    • The wolf reference genome sequence (Canis lupus lupus) and its implications for Canis spp. population genomics 

      Gopalakrishnan, Shyam; Samaniego Castruita, José Alfredo; Sinding, Mikkel Holger Strander; Kuderna, Lukas FK; Räikkönen, Jannikke; Petersen, Bent; Sicheritz-Ponten, Thomas; Larson, Greger; Orlando, Ludovic; Marques-Bonet, Tomas; Hansen, Anders J.; Dalén, Love; Gilbert, Marcus Thomas Pius (Journal article; Peer reviewed, 2017)
      Background: An increasing number of studies are addressing the evolutionary genomics of dog domestication, principally through resequencing dog, wolf and related canid genomes. There is, however, only one de novo assembled ...
    • To bee, or not to bee? One leg is the question 

      Cavill, Emily; Liu, Shanlin; Zhou, Xin; Gilbert, Marcus Thomas Pius (Journal article; Peer reviewed, 2021)
      Temporal genomic studies that utilise museum insects are invaluable for understanding changes in ecological processes in which insects are essential, such as wild and agricultural pollination, seed dispersal, nutrient ...