Extinction Genomics SIGNED
Exploring and exploiting the potential of extinct genome sequencing
Total Cost €
0EC-Contrib. €
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Explore the words cloud of the Extinction Genomics project. It provides you a very rough idea of what is the project "Extinction Genomics" about.
Project "Extinction Genomics" data sheet
The following table provides information about the project.
| Coordinator |
KOBENHAVNS UNIVERSITET
Organization address contact info |
| Coordinator Country | Denmark [DK] |
| Project website | http://geogenetics.ku.dk/research_groups/gilbert_groups/erc-extinction-genomics/ |
| Total cost | 2˙000˙000 € |
| EC max contribution | 2˙000˙000 € (100%) |
| Programme |
1. H2020-EU.1.1. (EXCELLENT SCIENCE - European Research Council (ERC)) |
| Code Call | ERC-2015-CoG |
| Funding Scheme | ERC-COG |
| Starting year | 2016 |
| Duration (year-month-day) | from 2016-04-01 to 2021-03-31 |
Partnership
Take a look of project's partnership.
| # | ||||
|---|---|---|---|---|
| 1 | KOBENHAVNS UNIVERSITET | DK (KOBENHAVN) | coordinator | 2˙000˙000.00 |
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Project objective
Palaeogenomics is the nascent discipline concerned with sequencing and analysis of genome-scale information from historic, ancient, and even extinct samples. While once inconceivable due to the challenges of DNA damage, contamination, and the technical limitations of PCR-based Sanger sequencing, following the dawn of the second-generation sequencing revolution, it has rapidly become a reality. Indeed, so much so, that popular perception has moved away from if extinct species’ genomes can be sequenced, to when it will happen - and even, when will the first extinct animals be regenerated. Unfortunately this view is naïve, and does not account for the financial and technical challenges that face such attempts. I propose an exploration of exactly what the limits on genome reconstruction from extinct or otherwise historic/ancient material are. This will be achieved through new laboratory and bioinformatic developments aimed at decreasing the cost, while concomitantly increasing the quality of genome reconstruction from poor quality materials. In doing so I aim to build a scientifically-grounded framework against which the possibilities and limitations of extinct genome reconstruction can be assessed. Subsequently genomic information will be generated from a range of extinct and near-extinct avian and mammalian species, in order to showcase the potential of reconstructed genomes across research questions spanning at least three different streams of research: De-extinction, Evolutionary Genomics, and Conservation Genomics. Ultimately, achievement of these goals requires formation of a dedicated, closely knit team, focusing on both the methodological challenges as well as their bigger picture application to high-risk high-gain ventures. With ERC funding this can become a reality, and enable palaeogenomics to be pushed to the limits possible under modern technology.
Publications
| year | authors and title | journal | last update |
|---|---|---|---|
| 2016 |
Mikkel-Holger S. Sinding, M. Thomas P. Gilbert The Draft Genome of Extinct European Aurochs and its Implications for De-Extinction published pages: 1-9, ISSN: 2055-298X, DOI: 10.5334/oq.25 |
Open Quaternary 2 | 2019-06-18 |
| 2017 |
Alicia Grealy, Matthew Phillips, Gifford Miller, M. Thomas P. Gilbert, Jean-Marie Rouillard, David Lambert, Michael Bunce, James Haile Eggshell palaeogenomics: Palaeognath evolutionary history revealed through ancient nuclear and mitochondrial DNA from Madagascan elephant bird ( Aepyornis sp.) eggshell published pages: 151-163, ISSN: 1055-7903, DOI: 10.1016/j.ympev.2017.01.005 |
Molecular Phylogenetics and Evolution 109 | 2019-06-18 |
| 2016 |
Douglas J. Richmond, Mikkel-Holger S. Sinding, M. Thomas P. Gilbert The potential and pitfalls of de-extinction published pages: 22-36, ISSN: 0300-3256, DOI: 10.1111/zsc.12212 |
Zoologica Scripta 45 | 2019-06-18 |
| 2017 |
Christian Carøe, Shyam Gopalakrishnan, Lasse Vinner, Sarah S. T. Mak, Mikkel Holger S. Sinding, José A. Samaniego, Nathan Wales, Thomas Sicheritz-Pontén, M. Thomas P. Gilbert Single-tube library preparation for degraded DNA published pages: , ISSN: 2041-210X, DOI: 10.1111/2041-210X.12871 |
Methods in Ecology and Evolution | 2019-06-18 |
| 2017 |
Shyam Gopalakrishnan, Jose A. Samaniego Castruita, Mikkel-Holger S. Sinding, Lukas F. K. Kuderna, Jannikke R?ikk?nen, Bent Petersen, Thomas Sicheritz-Ponten, Greger Larson, Ludovic Orlando, Tomas Marques-Bonet, Anders J. Hansen, Love Dal?n, M. Thomas P. Gilbert The wolf reference genome sequence (Canis lupus lupus) and its implications for Canis spp. population genomics published pages: , ISSN: 1471-2164, DOI: 10.1186/s12864-017-3883-3 |
BMC Genomics 18/1 | 2019-06-18 |
| 2017 |
Yan-Hu Liu, Lu Wang, Tao Xu, Xiaomin Guo, Yang Li, Ting-Ting Yin, He-Chuan Yang, Hu Yang, Adeniyi C. Adeola, Oscar J. Sanke, Newton O. Otecko, Meng Wang, Yaping Ma, Olaogun S. Charles, Mikkel-Holger S. Sinding, Shyam Gopalakrishnan, José Alfredo Samaniego, Anders J. Hansen, Carlos Fernandes, Philippe Gaubert, Jane Budd, Philip M. Dawuda, Eli Knispel Rueness, Lubin Jiang, Weiwei Zhai, M.T.P Gilbert, Min-Sheng Peng, Xiaopeng Qi, Guo-Dong Wang, Ya-Ping Zhang Whole-genome sequencing of African dogs provides insights into adaptations against tropical parasites published pages: , ISSN: 0737-4038, DOI: 10.1093/molbev/msx258 |
Molecular Biology and Evolution | 2019-06-18 |
| 2016 |
Pere Gelabert, Marcela Sandoval-Velasco, Iñigo Olalde, Rosa Fregel, Adrien Rieux, Raül Escosa, Carles Aranda, Krijn Paaijmans, Ivo Mueller, M. Thomas P. Gilbert, Carles Lalueza-Fox Mitochondrial DNA from the eradicated European Plasmodium vivax and P. falciparum from 70-year-old slides from the Ebro Delta in Spain published pages: 11495-11500, ISSN: 0027-8424, DOI: 10.1073/pnas.1611017113 |
Proceedings of the National Academy of Sciences 113/41 | 2019-06-18 |
| 2017 |
Sarah Siu Tze Mak, Shyam Gopalakrishnan, Christian Car?e, Chunyu Geng, Shanlin Liu, Mikkel-Holger S. Sinding, Lukas F.K. Kuderna, Wenwei Zhang, Shujin Fu, Filipe G. Vieira, Mietje Germonpr?, Herv? Bocherens, Sergey Fedorov, Bent Petersen, Thomas Sicheritz-Pont?n, Tomas Marques-Bonet, Guojie Zhang, Hui Jiang, M. Thomas P. Gilbert Comparative performance of the BGISEQ-500 versus Illumina HiSeq2500 sequencing platforms for palaeogenomic sequencing published pages: , ISSN: 2047-217X, DOI: 10.1093/gigascience/gix049 |
GigaScience | 2019-06-18 |
| 2019 |
Michael Knapp, Jessica E. Thomas, James Haile, Stefan Prost, Simon Y.W. Ho, Nicolas Dussex, Sophia Cameron-Christie, Olga Kardailsky, Ross Barnett, Michael Bunce, M. Thomas P. Gilbert, R. Paul Scofield Mitogenomic evidence of close relationships between New Zealand’s extinct giant raptors and small-sized Australian sister-taxa published pages: 122-128, ISSN: 1055-7903, DOI: 10.1016/j.ympev.2019.01.026 |
Molecular Phylogenetics and Evolution 134 | 2019-06-06 |
| 2019 |
Shaohong Feng, Qi Fang, Ross Barnett, Cai Li, Sojung Han, Martin Kuhlwilm, Long Zhou, Hailin Pan, Yuan Deng, Guangji Chen, Anita Gamauf, Friederike Woog, Robert Prys-Jones, Tomas Marques-Bonet, M. Thomas P. Gilbert, Guojie Zhang The Genomic Footprints of the Fall and Recovery of the Crested Ibis published pages: 340-349.e7, ISSN: 0960-9822, DOI: 10.1016/j.cub.2018.12.008 |
Current Biology 29/2 | 2019-06-06 |
| 2018 |
Maiken Hemme Bro-Jørgensen, Christian Carøe, Filipe G. Vieira, Sofia Nestor, Ann Hallström, Kristian M. Gregersen, Vivian Etting, M. Thomas P. Gilbert, Mikkel-Holger S. Sinding Ancient DNA analysis of Scandinavian medieval drinking horns and the horn of the last aurochs bull published pages: 47-54, ISSN: 0305-4403, DOI: 10.1016/j.jas.2018.09.001 |
Journal of Archaeological Science 99 | 2019-04-18 |
| 2018 |
David DÃez-del-Molino, Fatima Sánchez-Barreiro, Ian Barnes, M. Thomas P. Gilbert, Love Dalén Quantifying Temporal Genomic Erosion in Endangered Species published pages: 176-185, ISSN: 0169-5347, DOI: 10.1016/j.tree.2017.12.002 |
Trends in Ecology & Evolution 33/3 | 2019-04-18 |
| 2018 |
Shyam Gopalakrishnan, Mikkel-Holger S. Sinding, JazmÃn Ramos-Madrigal, Jonas Niemann, Jose A. Samaniego Castruita, Filipe G. Vieira, Christian Carøe, Marc de Manuel Montero, Lukas Kuderna, Aitor Serres, VÃctor Manuel González-Basallote, Yan-Hu Liu, Guo-Dong Wang, Tomas Marques-Bonet, Siavash Mirarab, Carlos Fernandes, Philippe Gaubert, Klaus-Peter Koepfli, Jane Budd, Eli Knispel Rueness, Mads Peter Heide-Jørgensen, Bent Petersen, Thomas Sicheritz-Ponten, Lutz Bachmann, Øystein Wiig, Anders J. Hansen, M. Thomas P. Gilbert Interspecific Gene Flow Shaped the Evolution of the Genus Canis published pages: 3441-3449.e5, ISSN: 0960-9822, DOI: 10.1016/j.cub.2018.08.041 |
Current Biology 28/21 | 2019-04-18 |
| 2018 |
M. Lisandra Zepeda Mendoza, Zijun Xiong, Marina Escalera-Zamudio, Anne Kathrine Runge, Julien Thézé, Daniel Streicker, Hannah K. Frank, Elizabeth Loza-Rubio, Shengmao Liu, Oliver A. Ryder, Jose Alfredo Samaniego Castruita, Aris Katzourakis, George Pacheco, Blanca Taboada, Ulrike Löber, Oliver G. Pybus, Yang Li, Edith Rojas-Anaya, Kristine Bohmann, Aldo Carmona Baez, Carlos F. Arias, Shiping Liu, Alex D. Greenwood, Mads F. Bertelsen, Nicole E. White, Michael Bunce, Guojie Zhang, Thomas Sicheritz-Pontén, M. P. Thomas Gilbert Hologenomic adaptations underlying the evolution of sanguivory in the common vampire bat published pages: 659-668, ISSN: 2397-334X, DOI: 10.1038/s41559-018-0476-8 |
Nature Ecology & Evolution 2/4 | 2019-04-18 |
| 2018 |
Ross Barnett, Mikkel-Holder S. Sinding, Filipe G. Vieira, Marie Lisandra Zepeda Mendoza, Matthieu Bonnet, Alessandro Araldi, Ivonne Kienast, Alice Zambarda, Nobuyuki Yamaguchi, Philipp Henschel, M. Thomas P. Gilbert No longer locally extinct? Tracing the origins of a lion (Panthera leo) living in Gabon published pages: 611-618, ISSN: 1566-0621, DOI: 10.1007/s10592-017-1039-2 |
Conservation Genetics 19/3 | 2019-04-18 |
| 2018 |
Mikkel-Holger S. Sinding, Shyam Gopalakrishan, Filipe G. Vieira, Jose A. Samaniego Castruita, Katrine Raundrup, Mads Peter Heide Jørgensen, Morten Meldgaard, Bent Petersen, Thomas Sicheritz-Ponten, Johan Brus Mikkelsen, Ulf Marquard-Petersen, Rune Dietz, Christian Sonne, Love Dalén, Lutz Bachmann, Øystein Wiig, Anders J. Hansen, M. Thomas P. Gilbert Population genomics of grey wolves and wolf-like canids in North America published pages: e1007745, ISSN: 1553-7404, DOI: 10.1371/journal.pgen.1007745 |
PLOS Genetics 14/11 | 2019-04-18 |
| 2018 |
Carson Holt, Michael Campbell, David A. Keays, Nathaniel Edelman, Aurélie Kapusta, Emily Maclary, Eric T. Domyan, Alexander Suh, Wesley C. Warren, Mark Yandell, M. Thomas P. Gilbert, Michael D. Shapiro Improved Genome Assembly and Annotation for the Rock Pigeon ( Columba livia ) published pages: 1391-1398, ISSN: 2160-1836, DOI: 10.1534/g3.117.300443 |
\"G3: Genes|Genomes|Genetics\" 8/5 | 2019-04-18 |
| 2018 |
Morten T. Limborg, Antton Alberdi, Miyako Kodama, Michael Roggenbuck, Karsten Kristiansen, M. Thomas P. Gilbert Applied Hologenomics: Feasibility and Potential in Aquaculture published pages: 252-264, ISSN: 0167-7799, DOI: 10.1016/j.tibtech.2017.12.006 |
Trends in Biotechnology 36/3 | 2019-04-18 |
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