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Extinction Genomics SIGNED

Exploring and exploiting the potential of extinct genome sequencing

Total Cost €

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EC-Contrib. €

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Partnership

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Project "Extinction Genomics" data sheet

The following table provides information about the project.

Coordinator
KOBENHAVNS UNIVERSITET 

Organization address
address: NORREGADE 10
city: KOBENHAVN
postcode: 1165
website: www.ku.dk

contact info
title: n.a.
name: n.a.
surname: n.a.
function: n.a.
email: n.a.
telephone: n.a.
fax: n.a.

 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.

# participants  country  role  EC contrib. [€] 
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
List of publications.
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 Díez-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, Jazmín Ramos-Madrigal, Jonas Niemann, Jose A. Samaniego Castruita, Filipe G. Vieira, Christian Carøe, Marc de Manuel Montero, Lukas Kuderna, Aitor Serres, Víctor 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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