Population genomics of the critically endangered kākāpō
Nicolas Dussex,Tom van der Valk,Hernán E. Morales,Christopher W. Wheat,David Díez-del-Molino,Johanna von Seth,Johanna von Seth,Yasmin Foster,Verena E. Kutschera,Katerina Guschanski,Katerina Guschanski,Arang Rhie,Adam M. Phillippy,Jonas Korlach,Kerstin Howe,William Chow,Sarah Pelan,Joanna D. Mendes Damas,Harris A. Lewin,Alex Hastie,Giulio Formenti,Giulio Formenti,Olivier Fedrigo,Joseph Guhlin,Thomas W. R. Harrop,Marissa F. Le Lec,Peter K. Dearden,Leanne Haggerty,Fergal J. Martin,Vamsi K. Kodali,Françoise Thibaud-Nissen,David Iorns,Michael Knapp,Neil J. Gemmell,Fiona Robertson,Ron Moorhouse,Andrew Digby,Daryl Eason,Deidre Vercoe,Jason T. Howard,Jason T. Howard,Erich D. Jarvis,Erich D. Jarvis,Bruce C. Robertson,Love Dalén,Love Dalén +45 more
- Vol. 1, Iss: 1, pp 100002
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TLDR
The first genome-wide analyses of the species are reported, including a high-quality genome assembly for kākāpō, one of the first chromosome-level reference genomes sequenced by the Vertebrate Genomes Project (VGP).Abstract:
Summary The kākāpō is a flightless parrot endemic to New Zealand. Once common in the archipelago, only 201 individuals remain today, most of them descending from an isolated island population. We report the first genome-wide analyses of the species, including a high-quality genome assembly for kākāpō, one of the first chromosome-level reference genomes sequenced by the Vertebrate Genomes Project (VGP). We also sequenced and analyzed 35 modern genomes from the sole surviving island population and 14 genomes from the extinct mainland population. While theory suggests that such a small population is likely to have accumulated deleterious mutations through genetic drift, our analyses on the impact of the long-term small population size in kākāpō indicate that present-day island kākāpō have a reduced number of harmful mutations compared to mainland individuals. We hypothesize that this reduced mutational load is due to the island population having been subjected to a combination of genetic drift and purging of deleterious mutations, through increased inbreeding and purifying selection, since its isolation from the mainland ∼10,000 years ago. Our results provide evidence that small populations can survive even when isolated for hundreds of generations. This work provides key insights into kākāpō breeding and recovery and more generally into the application of genetic tools in conservation efforts for endangered species.read more
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The era of reference genomes in conservation genomics.
Giulio Formenti,Kathrin Theissinger,Carlos Fernandes,Iliana Bista,Aureliano Bombarely,Christoph Bleidorn,Claudio Ciofi,Angelica Crottini,José Alberto Godoy Godoy,Jacob Höglund,Joanna Malukiewicz,Alice Mouton,Rebekah A. Oomen,Sadye Paez,Per J. Palsbøll,Christophe Pampoulie,Hannes Svardal,Constantina Theofanopoulou,Jan de Vries,Ann-Marie Waldvogel,Guojie Zhang,Camila J. Mazzoni,Miklós Bálint,Fedor Čiampor,J. Hoglund,María José Ruiz-López,Goujie Zhang,Erich D. Jarvis,Sargis A. Aghayan,Tyler Alioto,Isabel Almudi,Nadir Alvarez,Paulo C. Alves,Isabel R. Amorim,Agostinho Antunes,Paula Arribas,Petr Baldrian,Paul R. Berg,Giorgio Bertorelle,Astrid Böhne,Andrea Bonisoli-Alquati,Ljudevit Luka Boštjančić,Bastien Boussau,Catherine Breton,Elena Buzan,Paula F. Campos,Carlos Carreras,Luis Filipe Castro,Luis J. Chueca,Elena Conti,Robert Cook-Deegan,Daniel Croll,Mónica V. Cunha,Frédéric Delsuc,Alice B. Dennis,Dimitar Dimitrov,Rui Faria,Adrien Favre,Olivier Fedrigo,Rosa Fernández,Gentile Francesco Ficetola,Jean-François Flot,Toni Gabaldón,Dolores R. Galea Agius,Guido Roberto Gallo,Alice Maria Giani,M. Thomas P. Gilbert,Tine Grebenc,Katerina Guschanski,Romain Guyot,Bernhard Hausdorf,Oliver Hawlitschek,Peter D. Heintzman,Berthold Heinze,Michael Hiller,Martin Husemann,Alessio Iannucci,Iker Irisarri,Kjetill S. Jakobsen,Sissel Jentoft,Peter Klinga,Agnieszka Kloch,Claudius F. Kratochwil,Henrik Kusche,Kara K S Layton,Jennifer A. Leonard,Emmanuelle Lerat,Gianni Liti,Tereza Manousaki,Tomas Marques-Bonet,Pável Matos-Maraví,Michael Matschiner,Florian Maumus,Ann M Mc Cartney,Shai Meiri,José Melo-Ferreira,Ximo Mengual,Michael T. Monaghan,Matteo Montagna,Robert W. Mysłajek,Marco T. Neiber,Violaine Nicolas,Marta Novo,Petar Ozretić,Ferran Palero,Lucian Pârvulescu,Marta Pascual,Octávio S. Paulo,Martina Pavlek,Cinta Pegueroles,Loïc Pellissier,Graziano Pesole,Craig R. Primmer,Ana Riesgo,Lukas Rüber,Diego Rubolini,Daniel Salvi,Ole Seehausen,Matthias Seidel,Simona Secomandi,Bruno Studer,Spyros Theodoridis,Marco Thines,Lara Urban,Anti Vasemägi,Adriana Vella,Noel Vella,Sonja C. Vernes,Cristiano Vernesi,David R. Vieites,Robert M. Waterhouse,Christopher W. Wheat,Gert Wörheide,Yannick Wurm,Gabrielle Zammit +134 more
TL;DR: In this article , a large-scale generation of reference genomes representing global biodiversity is discussed. But the authors focus on the large-size generation of the reference genomes and do not discuss how to generate reference genomes for the conservation genomics.
Journal ArticleDOI
Genetic load: genomic estimates and applications in non-model animals
Giorgio Bertorelle,Francesca Raffini,Mirte Bosse,Chiara Bortoluzzi,Alessio Iannucci,Emiliano Trucchi,Hernán E. Morales,Cock van Oosterhout +7 more
TL;DR: In this paper , the authors present approaches to quantify the genetic load in whole-genome sequence data based on evolutionary conservation and annotations, and show that splitting the load into its two components -the realized load and the masked load -can improve our understanding of the population genetics of deleterious mutations.
Journal ArticleDOI
Reference genomes for conservation
TL;DR: High-quality reference genomes for non-model species can benefit conservation and help improve the quality of reference genomes used in science and conservation.
Journal ArticleDOI
Ancient and historical DNA in conservation policy.
Evelyn L. Jensen,David Díez-del-Molino,M. Thomas P. Gilbert,Laura D. Bertola,Filipa Borges,Vlatka Cubric-Curik,Miguel de Navascués,Peter Frandsen,Myriam Heuertz,Christina Hvilsom,Belén Jiménez-Mena,Antti Miettinen,Markus Moest,Patrícia Pečnerová,Ian Barnes,Cristiano Vernesi +15 more
TL;DR: In this article , the authors discuss how genetic information from ancient and historical specimens can play a central role in preserving biodiversity and highlight specific conservation policies that could incorporate such data to help countries meet their CBD obligations.
Posted ContentDOI
Using computational simulations to quantify genetic load and predict extinction risk
TL;DR: Comparing modern simulation tools to those that have long been employed in population viability analysis, weighing the pros and cons of a ‘genomics-informed’ simulation approach, and discussing key areas for future research are compared.
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