Great ape genome variation now and then: current diversity and genomic relics of extinct primates

Project Information

ApeGenomeDiversity

Grant agreement ID: 864203

DOI

10.3030/864203

EC signature date 14 April 2020

Start date 1 June 2020

End date 30 November 2025

Funded under

• EXCELLENT SCIENCE - European Research Council (ERC)

Total cost

€ 1 896 875,00

EU contribution

€ 1 896 875,00

Coordinated by

UNIVERSIDAD POMPEU FABRA
Spain

CORDIS provides links to public deliverables and publications of HORIZON projects.

Links to deliverables and publications from FP7 projects, as well as links to some specific result types such as dataset and software, are dynamically retrieved from OpenAIRE .

Publications

Peer reviewed articles (28)

Past Connectivity but Recent Inbreeding in Cross River Gorillas Determined Using Whole Genomes from Single Hairs

Author(s): Marina Alvarez-Estape, Harvinder Pawar, Claudia Fontsere, Amber E. Trujillo, Jessica L. Gunson, Richard A. Bergl, Magdalena Bermejo, Joshua M. Linder, Kelley McFarland, John F. Oates, Jacqueline L. Sunderland-Groves, Joseph Orkin, James P. Higham, Karine A. Viaud-Martinez, Esther Lizano, Tomas Marques-Bonet
Published in: Genes, Issue 14, 2025, Page(s) 743, ISSN 2073-4425
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/genes14030743

Current advances in primate genomics: novel approaches for understanding evolution and disease

Author(s): David Juan, Gabriel Santpere, Joanna L. Kelley, Omar E. Cornejo, Tomas Marques-Bonet
Published in: Nature Reviews Genetics, Issue 24, 2023, Page(s) 314-331, ISSN 1471-0056
Publisher: Nature Publishing Group
DOI: 10.1038/s41576-022-00554-w

Genomic adaptation to small population size and saltwater consumption in the critically endangered Cat Ba langur

Author(s): Liye Zhang, Neahga Leonard, Rick Passaro, Mai Sy Luan, Pham Van Tuyen, Le Thi Ngoc Han, Nguyen Huy Cam, Larry Vogelnest, Michael Lynch, Amanda E. Fine, Nguyen Thi Thanh Nga, Nguyen Van Long, Benjamin M. Rawson, Alison Behie, Truong Van Nguyen, Minh D. Le, Tilo Nadler, Lutz Walter, Tomas Marques-Bonet, Michael Hofreiter, Ming Li, Zhijin Liu, Christian Roos
Published in: Nature Communications, Issue 15, 2024, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-024-52811-7

The genetic impact of an Ebola outbreak on a wild gorilla population

Author(s): Claudia Fontsere; Peter Frandsen; Jessica Hernandez-Rodriguez; Jonas Niemann; Camilla Hjorth Scharff-Olsen; Dominique Vallet; Pascaline Le Gouar; Nelly Ménard; Arcadi Navarro; Hans R. Siegismund; Christina Hvilsom; M. Thomas P. Gilbert; Martin Kuhlwilm; David Hughes; Tomas Marques-Bonet
Published in: BMC Genomics, Issue 9, 2021, ISSN 1471-2164
Publisher: BioMed Central
DOI: 10.1186/s12864-021-08025-y

Illuminating the function of the orphan transporter, SLC22A10, in humans and other primates

Author(s): Sook Wah Yee, Luis Ferrández-Peral, Pol Alentorn-Moron, Claudia Fontsere, Merve Ceylan, Megan L. Koleske, Niklas Handin, Virginia M. Artegoitia, Giovanni Lara, Huan-Chieh Chien, Xujia Zhou, Jacques Dainat, Arthur Zalevsky, Andrej Sali, Colin M. Brand, Finn D. Wolfreys, Jia Yang, Jason E. Gestwicki, John A. Capra, Per Artursson, John W. Newman, Tomàs Marquès-Bonet, Kathleen M. Giacomini
Published in: Nature Communications, Issue 15, 2024, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-024-48569-7

The landscape of tolerated genetic variation in humans and primates

Author(s): Hong Gao, Tobias Hamp, Jeffrey Ede, Joshua G. Schraiber, Jeremy McRae, Moriel Singer-Berk, Yanshen Yang, Anastasia S. D. Dietrich, Petko P. Fiziev, Lukas F. K. Kuderna, Laksshman Sundaram, Yibing Wu, Aashish Adhikari, Yair Field, Chen Chen, Serafim Batzoglou, Francois Aguet, Gabrielle Lemire, Rebecca Reimers, Daniel Balick, Mareike C. Janiak, Martin Kuhlwilm, Joseph D. Orkin, Shivakumara Manu, Ale
Published in: Science, Issue 380, 2024, ISSN 0036-8075
Publisher: American Association for the Advancement of Science
DOI: 10.1126/science.abn8197

Rare penetrant mutations confer severe risk of common diseases

Author(s): Petko P. Fiziev, Jeremy McRae, Jacob C. Ulirsch, Jacqueline S. Dron, Tobias Hamp, Yanshen Yang, Pierrick Wainschtein, Zijian Ni, Joshua G. Schraiber, Hong Gao, Dylan Cable, Yair Field, Francois Aguet, Marc Fasnacht, Ahmed Metwally, Jeffrey Rogers, Tomas Marques-Bonet, Heidi L. Rehm, Anne O'Donnell-Luria, Amit V. Khera, Kyle Kai-How Farh
Published in: Science, Issue 380, 2024, ISSN 0036-8075
Publisher: American Association for the Advancement of Science
DOI: 10.1126/science.abo1131

The Diversity of Primates: From Biomedicine to Conservation Genomics.

Author(s): Joseph D Orkin; Lukas F. K. Kuderna; Tomas Marques-Bonet
Published in: Annual Review of Animal Biosciences, Issue 9, 2021, ISSN 2165-8110
Publisher: NA
DOI: 10.1146/annurev-animal-061220-023138

The contribution of historical processes to contemporary extinction risk in placental mammals

Author(s): Aryn P. Wilder, Megan A. Supple, Ayshwarya Subramanian, Anish Mudide, Ross Swofford, Aitor Serres-Armero, Cynthia Steiner, Klaus-Peter Koepfli, Diane P. Genereux, Elinor K. Karlsson, Kerstin Lindblad-Toh, Tomas Marques-Bonet, Violeta Munoz Fuentes, Kathleen Foley, Wynn K. Meyer, null null, Oliver A. Ryder, Beth Shapiro, Gregory Andrews, Joel C. Armstrong, Matteo Bianchi, Bruce W. Birren, Kevin R.
Published in: Science, Issue 380, 2024, ISSN 0036-8075
Publisher: American Association for the Advancement of Science
DOI: 10.1126/science.abn5856

Copy number variation underlies complex phenotypes in domestic dog breeds and other canids

Author(s): Aitor Serres-Armero; Brian W. Davis; Inna S. Povolotskaya; Carlos Morcillo-Suarez; Jocelyn Plassais; David Juan; Elaine A. Ostrander; Tomas Marques-Bonet
Published in: Genome Res, Issue 4, 2021, ISSN 1549-5469
Publisher: Cold Spring Harbor, N.Y
DOI: 10.1101/gr.266049.120

The genomics of ecological flexibility, large brains, and long lives in capuchin monkeys revealed with fecalFACS

Author(s): Joseph D. Orkin; Joseph D. Orkin; Joseph D. Orkin; Michael J. Montague; Daniela Tejada-Martinez; Daniela Tejada-Martinez; Daniela Tejada-Martinez; Marc de Manuel; Javier del Campo; Saul Cheves Hernandez; Anthony Di Fiore; Anthony Di Fiore; Claudia Fontsere; Jason A. Hodgson; Jason A. Hodgson; Mareike C. Janiak; Mareike C. Janiak; Mareike C. Janiak; Lukas F. K. Kuderna; Esther Lizano; Esther Lizano
Published in: instname:Universitat Autònoma de Barcelona, Issue 3, 2021, ISSN 1091-6490
Publisher: NA
DOI: 10.1073/pnas.2010632118

Comparative genomics reveals the hybrid origin of a macaque group

Author(s): Bao-Lin Zhang, Wu Chen, Zefu Wang, Wei Pang, Meng-Ting Luo, Sheng Wang, Yong Shao, Wen-Qiang He, Yuan Deng, Long Zhou, Jiawei Chen, Min-Min Yang, Yajiang Wu, Lu Wang, Hugo Fernández-Bellon, Sandra Molloy, Hélène Meunier, Fanélie Wanert, Lukas Kuderna, Tomas Marques-Bonet, Christian Roos, Xiao-Guang Qi, Ming Li, Zhijin Liu, Mikkel Heide Schierup, David N. Cooper, Jianquan Liu, Yong-Tang Zheng,
Published in: Science Advances, Issue 9, 2024, ISSN 2375-2548
Publisher: Science direct
DOI: 10.1126/sciadv.add3580

Phylogenomic analyses provide insights into primate evolution

Author(s): Yong Shao, Long Zhou, Fang Li, Lan Zhao, Bao-Lin Zhang, Feng Shao, Jia-Wei Chen, Chun-Yan Chen, Xupeng Bi, Xiao-Lin Zhuang, Hong-Liang Zhu, Jiang Hu, Zongyi Sun, Xin Li, Depeng Wang, Iker Rivas-González, Sheng Wang, Yun-Mei Wang, Wu Chen, Gang Li, Hui-Meng Lu, Yang Liu, Lukas F. K. Kuderna, Kyle Kai-How Farh, Peng-Fei Fan, Li Yu, Ming Li, Zhi-Jin Liu, George P. Tiley, Anne D. Yoder, Christian Roo
Published in: Science, Issue 380, 2024, Page(s) 913-924, ISSN 0036-8075
Publisher: American Association for the Advancement of Science
DOI: 10.1126/science.abn6919

Deep genetic substructure within bonobos

Author(s): Sojung Han, Cesare de Filippo, Genís Parra, Juan Ramon Meneu, Romain Laurent, Peter Frandsen, Christina Hvilsom, Ilan Gronau, Tomas Marques-Bonet, Martin Kuhlwilm, Aida M. Andrés
Published in: Current Biology, Issue 34, 2024, Page(s) 5341-5348.e3, ISSN 0960-9822
Publisher: Cell Press
DOI: 10.1016/j.cub.2024.09.043

Ghost admixture in eastern gorillas

Author(s): Harvinder Pawar, Aigerim Rymbekova, Sebastian Cuadros-Espinoza, Xin Huang, Marc de Manuel, Tom van der Valk, Irene Lobon, Marina Alvarez-Estape, Marc Haber, Olga Dolgova, Sojung Han, Paula Esteller-Cucala, David Juan, Qasim Ayub, Ruben Bautista, Joanna L. Kelley, Omar E. Cornejo, Oscar Lao, Aida M. Andrés, Katerina Guschanski, Benard Ssebide, Mike Cranfield, Chris Tyler-Smith, Yali Xue, Javier Pr
Published in: Nature Ecology & Evolution, Issue 7, 2023, Page(s) 1503-1514, ISSN 2397-334X
Publisher: Nature PUblisher group
DOI: 10.1038/s41559-023-02145-2

How genomics can help biodiversity conservation

Author(s): Kathrin Theissinger, Carlos Fernandes, Giulio Formenti, Iliana Bista, Paul R. Berg, Christoph Bleidorn, Aureliano Bombarely, Angelica Crottini, Guido R. Gallo, José A. Godoy, Sissel Jentoft, Joanna Malukiewicz, Alice Mouton, Rebekah A. Oomen, Sadye Paez, Per J. Palsbøll, Christophe Pampoulie, María J. Ruiz-López, Simona Secomandi, Hannes Svardal, Constantina Theofanopoulou, Jan de Vries, Ann-M
Published in: Trends in Genetics, Issue 39, 2023, Page(s) 545-559, ISSN 0168-9525
Publisher: Elsevier BV
DOI: 10.1016/j.tig.2023.01.005

Whole genomes of Amazonian uakari monkeys reveal complex connectivity and fast differentiation driven by high environmental dynamism

Author(s): Núria Hermosilla-Albala, Felipe Ennes Silva, Sebastián Cuadros-Espinoza, Claudia Fontsere, Alejandro Valenzuela-Seba, Harvinder Pawar, Marta Gut, Joanna L. Kelley, Sandra Ruibal-Puertas, Pol Alentorn-Moron, Armida Faella, Esther Lizano, Izeni Farias, Tomas Hrbek, Joao Valsecchi, Ivo G. Gut, Jeffrey Rogers, Kyle Kai-How Farh, Lukas F. K. Kuderna, Tomas Marques-Bonet, Jean P. Boubli
Published in: Communications Biology, Issue 7, 2024, ISSN 2399-3642
Publisher: Nature publisher group
DOI: 10.1038/s42003-024-06901-3

Identification of constrained sequence elements across 239 primate genomes

Author(s): Lukas F. K. Kuderna, Jacob C. Ulirsch, Sabrina Rashid, Mohamed Ameen, Laksshman Sundaram, Glenn Hickey, Anthony J. Cox, Hong Gao, Arvind Kumar, Francois Aguet, Matthew J. Christmas, Hiram Clawson, Maximilian Haeussler, Mareike C. Janiak, Martin Kuhlwilm, Joseph D. Orkin, Thomas Bataillon, Shivakumara Manu, Alejandro Valenzuela, Juraj Bergman, Marjolaine Rouselle, Felipe Ennes Silva, Lidia Agueda,
Published in: Nature, Issue 625, 2024, Page(s) 735-742, ISSN 0028-0836
Publisher: Nature Publishing Group
DOI: 10.1038/s41586-023-06798-8

Y chromosome sequence and epigenomic reconstruction across human populations

Author(s): Paula Esteller-Cucala, Marc Palmada-Flores, Lukas F. K. Kuderna, Claudia Fontsere, Aitor Serres-Armero, Marc Dabad, María Torralvo, Armida Faella, Luis Ferrández-Peral, Laia Llovera, Oscar Fornas, Eva Julià, Erika Ramírez, Irene González, Jochen Hecht, Esther Lizano, David Juan, Tomàs Marquès-Bonet
Published in: Communications Biology, Issue 6, 2023, ISSN 2399-3642
Publisher: Nature Research
DOI: 10.1038/s42003-023-05004-9

Evolutionary constraint and innovation across hundreds of placental mammals

Author(s): Matthew J. Christmas, Irene M. Kaplow, Diane P. Genereux, Michael X. Dong, Graham M. Hughes, Xue Li, Patrick F. Sullivan, Allyson G. Hindle, Gregory Andrews, Joel C. Armstrong, Matteo Bianchi, Ana M. Breit, Mark Diekhans, Cornelia Fanter, Nicole M. Foley, Daniel B. Goodman, Linda Goodman, Kathleen C. Keough, Bogdan Kirilenko, Amanda Kowalczyk, Colleen Lawless, Abigail L. Lind, Jennifer R. S. Meado
Published in: Science, Issue 380, 2024, ISSN 0036-8075
Publisher: American Association for the Advancement of Science
DOI: 10.1126/science.abn3943

Ecological and anthropogenic effects on the genomic diversity of lemurs in Madagascar

Author(s): Joseph D. Orkin, Lukas F. K. Kuderna, Núria Hermosilla-Albala, Claudia Fontsere, Megan L. Aylward, Mareike C. Janiak, Nicole Andriaholinirina, Patricia Balaresque, Mary E. Blair, Jean-Luc Fausser, Ivo Glynne Gut, Marta Gut, Matthew W. Hahn, R. Alan Harris, Julie E. Horvath, Christine Keyser, Andrew C. Kitchener, Minh D. Le, Esther Lizano, Stefan Merker, Tilo Nadler, George H. Perry, Clément J. R
Published in: Nature Ecology & Evolution, 2024, ISSN 2397-334X
Publisher: Nature publisher group
DOI: 10.1038/s41559-024-02596-1

Eighty million years of rapid evolution of the primate Y chromosome

Author(s): Yang Zhou, Xiaoyu Zhan, Jiazheng Jin, Long Zhou, Juraj Bergman, Xuemei Li, Marjolaine Marie C. Rousselle, Meritxell Riera Belles, Lan Zhao, Miaoquan Fang, Jiawei Chen, Qi Fang, Lukas Kuderna, Tomas Marques-Bonet, Haruka Kitayama, Takashi Hayakawa, Yong-Gang Yao, Huanming Yang, David N. Cooper, Xiaoguang Qi, Dong-Dong Wu, Mikkel Heide Schierup, Guojie Zhang
Published in: Nature Ecology & Evolution, Issue 7, 2023, Page(s) 1114-1130, ISSN 2397-334X
Publisher: Natre Publisher group
DOI: 10.1038/s41559-022-01974-x

A global catalog of whole-genome diversity from 233 primate species

Author(s): Lukas F. K. Kuderna, Hong Gao, Mareike C. Janiak, Martin Kuhlwilm, Joseph D. Orkin, Thomas Bataillon, Shivakumara Manu, Alejandro Valenzuela, Juraj Bergman, Marjolaine Rousselle, Felipe Ennes Silva, Lidia Agueda, Julie Blanc, Marta Gut, Dorien de Vries, Ian Goodhead, R. Alan Harris, Muthuswamy Raveendran, Axel Jensen, Idrissa S. Chuma, Julie E. Horvath, Christina Hvilsom, David Juan, Peter Frandse
Published in: Science, Issue 380, 2024, Page(s) 906-913, ISSN 0036-8075
Publisher: American Association for the Advancement of Science
DOI: 10.1126/science.abn7829

Branching out: what omics can tell us about primate evolution

Author(s): Lukas F. K. Kuderna; Paula Esteller-Cucala; Tomas Marques-Bonet
Published in: Current Opinion Genet Dev, Issue 8, 2020, ISSN 0959-437X
Publisher: Elsevier BV
DOI: 10.1016/j.gde.2020.06.006

Maximizing the acquisition of unique reads in noninvasive capture sequencing experiments

Author(s): Claudia Fontsere; Marina Alvarez-Estape; Jack D. Lester; Mimi Arandjelovic; Martin Kuhlwilm; Paula Dieguez; Anthony Agbor; Samuel Angedakin; Emmanuel Ayuk Ayimisin; Mattia Bessone; Gregory Brazzola; Tobias Deschner; Manasseh Eno-Nku; Anne-Céline Granjon; Josephine Head; Parag Kadam; Ammie K. Kalan; Mohamed Kambi; Kevin E. Langergraber; Juan Lapuente; Giovanna Maretti; Lucy Jayne Ormsby; Alex K. P
Published in: instname:, Issue 1, 2020, ISSN 1755-0998
Publisher: NA
DOI: 10.1111/1755-0998.13300

HuConTest: Testing Human Contamination in Great Ape Samples

Author(s): Martin Kuhlwilm; Claudia Fontsere; Sojung Han; Marina Alvarez-Estape; Tomas Marques-Bonet
Published in: Genome Biol Evol ., Issue 8, 2021, ISSN 1759-6653
Publisher: Oxford University Press
DOI: 10.1093/gbe/evab117

Genome-wide coancestry reveals details of ancient and recent male-driven reticulation in baboons

Author(s): Erik F. Sørensen, R. Alan Harris, Liye Zhang, Muthuswamy Raveendran, Lukas F. K. Kuderna, Jerilyn A. Walker, Jessica M. Storer, Martin Kuhlwilm, Claudia Fontsere, Lakshmi Seshadri, Christina M. Bergey, Andrew S. Burrell, Juraj Bergman, Jane E. Phillips-Conroy, Fekadu Shiferaw, Kenneth L. Chiou, Idrissa S. Chuma, Julius D. Keyyu, Julia Fischer, Marie-Claude Gingras, Sejal Salvi, Harshavardhan Dodd
Published in: Science, Issue 380, 2024, ISSN 0036-8075
Publisher: American Association for the Advancement of Science
DOI: 10.1126/science.abn8153

Two hundred and five newly assembled mitogenomes provide mixed evidence for rivers as drivers of speciation for Amazonian primates

Author(s): Mareike C. Janiak; Felipe E. Silva; Robin M. D. Beck; Dorien de Vries; Lukas F. K. Kuderna; Nicole S. Torosin; Amanda D. Melin; Tomàs Marquès‐Bonet; Ian B. Goodhead; Mariluce Messias; Maria N. F. da Silva; Iracilda Sampaio; Izeni P. Farias; Rogerio Rossi; Fabiano R. de Melo; João Valsecchi; Tomas Hrbek; Jean P. Boubli
Published in: Molecular Ecology, Issue 11, 2022, ISSN 0962-1083
Publisher: Blackwell Publishing Inc.
DOI: 10.1111/mec.16554