• Ancient DNA reveals the timing and persistence of organellar genetic bottlenecks over 3,000 years of sunflower domestication and improvement 

      Wales, Nathan; Akman, Melis; Watson, Ray H B; Sánchez Barreiro, Fatima; Smith, Bruce D; Gremillion, Kristen J; Gilbert, Marcus Thomas Pius; Blackman, Benjamin K (Journal article; Peer reviewed, 2019)
      Here, we report a comprehensive paleogenomic study of archaeological and ethnographic sunflower remains that provides significant new insights into the process of domestication of this important crop. DNA from both ancient ...
    • Ancient genomes from Iceland reveal the making of a human population 

      Ebenesersdóttir, Sigríður Sunna; Sandoval-Velasco, Marcela; Gunnarsdóttir, Ellen D.; Jagadeesan, Anuradha; Guðmundsdóttir, Valdís B.; Thordardóttir, Elísabet L.; Einarsdóttir, Margrét S.; Moore, Kristjan H. S.; Sigurðsson, Ásgeir; Magnúsdóttir, Droplaug N.; Jónsson, Hákon; Snorradóttir, Steinunn; Hovig, Eivind; Møller, Pål; Kockum, Ingrid; Olsson, Tomas; Alfredsson, Lars; Hansen, Thomas F.; Werge, Thomas; Cavalleri, Gianpiero L.; Gilbert, Edmund; Lalueza-Fox, Carles; Walser III, Joe W.; Kristjánsdóttir, Steinunn; Gopalakrishnan, Shyam; Arnadottir, Lilja; Magnússon, Ólafur Þ.; Gilbert, Marcus Thomas Pius; Stefánsson, Kári; Helgason, Agnar (Journal article; Peer reviewed, 2018)
      Opportunities to directly study the founding of a human population and its subsequent evolutionary history are rare. Using genome sequence data from 27 ancient Icelanders, we demonstrate that they are a combination of ...
    • An expanded mammal mitogenome dataset from Southeast Asia 

      Salleh, Faezah Mohd; Ramos-Madrigal, Jazmín; Peñaloza, Fernando; Liu, Shanlin; Sinding, Mikkel Holger Strander; Patel, Riddhi P.; Martins, Renata; Lenz, Dorina; Fickel, Jörns; Roos, Christian; Shamsir, Mohd Shahir; Azman, Mohammad Shahfiz; Lim, Burton K.; Rossiter, Stephen J.; Wilting, Andreas; Gilbert, Marcus Thomas Pius (Journal article; Peer reviewed, 2017)
      Southeast (SE) Asia is 1 of the most biodiverse regions in the world, and it holds approximately 20% of all mammal species. Despite this, the majority of SE Asia's genetic diversity is still poorly characterized. The growing ...
    • An ‛Aukward’ tale: a genetic approach to discover the whereabouts of the last Great Auks 

      Thomas, Jessica E; Carvalho, Gary R.; Haile, James; Martin, Michael David; Castruita, Jose A. Samaniego; Niemann, Jonas; Sinding, Mikkel Holger Strander; Sandoval-Velasco, Marcela; Rawlence, Nicolas J.; Fuller, Errol; Fjeldså, Jon; Hofreiter, Michael; Stewart, John R; Gilbert, Marcus Thomas Pius; Knapp, Michael (Journal article; Peer reviewed, 2017)
      One hundred and seventy-three years ago, the last two Great Auks, Pinguinus impennis, ever reliably seen were killed. Their internal organs can be found in the collections of the Natural History Museum of Denmark, but the ...
    • Comparative performance of the BGISEQ-500 vs Illumina HiSeq2500 sequencing platforms for palaeogenomic sequencing 

      Mak, Sarah S.T.; Gopalakrishnan, Shyam; Carøe, Christian; Geng, Chunyu; Liu, Shanlin; Sinding, Mikkel Holger Strander; Kuderna, Lukas FK; Zhang, Wenwei; Fu, Shujin; Vieira, Filipe G.; Germonpre, Mietje; Bocherens, Hervé; Fedorov, Sergey; Petersen, Bent; Sicheritz-Pontén, Thomas; Marques-Bonet, Tomas; Zhang, Guojie; Jiang, Hui; Gilbert, Marcus Thomas Pius (Journal article; Peer reviewed, 2017)
      Ancient DNA research has been revolutionized following development of next-generation sequencing platforms. Although a number of such platforms have been applied to ancient DNA samples, the Illumina series are the dominant ...
    • Functional roles of Aves class-specific cis-regulatory elements on macroevolution of bird-specific features 

      Seki, Ryohei; Li, Caí; Fang, Qi; Hayashi, Shinichi; Egawa, Shiro; Hu, Jiang; Xu, Luohao; Pan, Hailin; Kondo, Mao; Sato, Tomohiko; Matsubara, Haruka; Kamiyama, Namiko; Kitajima, Keiichi; Saito, Daisuke; Liu, Yang; Gilbert, Marcus Thomas Pius; Zhou, Qi; Xu, Xing; Shiroishi, Toshihiko; Irie, Naoki; Tamura, Koji; Zhang, Guojie (Journal article; Peer reviewed, 2017)
      Unlike microevolutionary processes, little is known about the genetic basis of macroevolutionary processes. One of these magnificent examples is the transition from non-avian dinosaurs to birds that has created numerous ...
    • Identification of transcription factor genes involved in anthocyanin biosynthesis in carrot (Daucus carota L.) using RNA-Seq 

      Kodama, Miyako; Brinch-Pedersen, Henrik; Sharma, Shrikant; Holme, Inger B.; Joernsgaard, Bjarne; Dzhanfezova, Tsaneta; Amby, Daniel Buchvaldt; Vieira, Filipe G.; Liu, Shanlin; Gilbert, Marcus Thomas Pius (Journal article; Peer reviewed, 2018)
      Background Anthocyanins are water-soluble colored flavonoids present in multiple organs of various plant species including flowers, fruits, leaves, stems and roots. DNA-binding R2R3-MYB transcription factors, basic ...
    • Improved Genome Assembly and Annotation for the Rock Pigeon (Columba livia) 

      Holt, Carson; Campbell, Michael; Keays, David Anthony; Edelman, Nathaniel; Kapusta, Aurélie; Maclary, Emily; Domyan, Eric T.; Suh, Alexander; Warren, Wesley C.; Yandell, Mark; Gilbert, Marcus Thomas Pius; Shapiro, Michael D. (Journal article; Peer reviewed, 2018)
      The domestic rock pigeon (Columba livia) is among the most widely distributed and phenotypically diverse avian species. C. livia is broadly studied in ecology, genetics, physiology, behavior, and evolutionary biology, and ...
    • Mind the gut: genomic insights to population divergence and gut microbial composition of two marine keystone species 

      Fietz, Katharina; Hintze, Christian O.R.; Skovrind, Mikkel; Nielsen, Tue Kjærgaard; Limborg, Morten; Krag, Marcus A.; Palsbøll, Per J.; Hansen, Lars Hestbjerg; Møller, Peter Rask; Gilbert, Marcus Thomas Pius (Journal article; Peer reviewed, 2018)
      Background Deciphering the mechanisms governing population genetic divergence and local adaptation across heterogeneous environments is a central theme in marine ecology and conservation. While population divergence and ...
    • Molecular clocks indicate turnover and diversification of modern coleoid cephalopods during the Mesozoic marine revolution 

      Tanner, Alastair R; Fuchs, Dirk; Winkelmann, Inger E; Gilbert, Marcus Thomas Pius; Pankey, M Sabrina; Ribeiro, Angela; Kocot, Kevin M.; Halanych, Kenneth M; Oakley, Todd H; Da Fonseca, Rute R.; Pisani, Davide; Vinther, Jakob (Journal article; Peer reviewed, 2017)
      Coleoid cephalopod molluscs comprise squid, cuttlefish and octopuses, and represent nearly the entire diversity of modern cephalopods. Sophisticated adaptations such as the use of colour for camouflage and communication, ...
    • Natural selection shaped the rise and fall of passenger pigeon genomic diversity 

      Murray, Gemma G.R.; Soares, André E.R.; Novak, Ben J.; Schaefer, Nathan K.; Cahill, James A.; Baker, Allan J.; Demboski, John R.; Doll, Andrew; Da Fonseca, Rute R.; Fulton, Tara L.; Gilbert, Marcus Thomas Pius; Heintzman, Peter D.; Letts, Brandon; McIntosh, George; O'Connell, Brendan L.; Peck, Mark; Pipes, Marie-Lorraine; Rice, Edward S.; Santos, Kathryn M.; Sohrweide, A. Gregory; Vohr, Samuel H.; Corbett-Detig, Russell B.; Green, Richard E.; Shapiro, Beth (Journal article; Peer reviewed, 2017)
      The extinct passenger pigeon was once the most abundant bird in North America, and possibly the world. Although theory predicts that large populations will be more genetically diverse, passenger pigeon genetic diversity ...
    • 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. ...
    • 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 ...
    • 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 ...
    • 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 ...
    • Whole-genome sequencing of African dogs provides insights into adaptations against tropical parasites 

      Liu, Yan-Hu; Wang, Lu; Xu, Tao; Guo, Xiaomin; Li, Yang; Yin, Ting-Ting; Yang, He-Chuan; Hu, Yang; Adeola, Adeniyi C.; Sanke, Oscar J.; Otecko, Newton O.; Wang, Meng; Ma, Yaping; Charles, Olaogun S.; Sinding, Mikkel Holger Strander; Gopalakrishnan, Shyam; Samaniego, José Alfredo; Hansen, Anders J.; Fernandes, Carlos; Gaubert, Philippe; Budd, Jane; Dawuda, Philip M.; Rueness, Eli Knispel; Jiang, Lubin; Zhai, Weiwei; Gilbert, Marcus Thomas Pius; Peng, Min-Sheng; Qi, Xiaopeng; Wang, Guo-Dong; Zhang, Ya-ping (Journal article; Peer reviewed, 2017)
      Natural selection in domestic dogs is of great interest in evolutionary biology since dogs have migrated to every inhabited continent of the world alongside humans, and adapted to diverse environments. Here, we explored ...