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

Informacje na temat projektu

ApeGenomeDiversity

Identyfikator umowy o grant: 864203

DOI

10.3030/864203

Data podpisania przez KE 14 Kwietnia 2020

Data rozpoczęcia 1 Czerwca 2020

Data zakończenia 30 Listopada 2025

Finansowanie w ramach

• EXCELLENT SCIENCE - European Research Council (ERC)

Koszt całkowity

€ 1 896 875,00

Wkład UE

€ 1 896 875,00

Koordynowany przez

UNIVERSIDAD POMPEU FABRA
Spain

CORDIS oferuje możliwość skorzystania z odnośników do publicznie dostępnych publikacji i rezultatów projektów realizowanych w ramach programów ramowych HORYZONT.

Odnośniki do rezultatów i publikacji związanych z poszczególnymi projektami 7PR, a także odnośniki do niektórych konkretnych kategorii wyników, takich jak zbiory danych i oprogramowanie, są dynamicznie pobierane z systemu OpenAIRE .

Publikacje

Peer reviewed articles (28)

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

Autorzy: 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
Opublikowane w: Genes, Numer 14, 2025, Strona(/y) 743, ISSN 2073-4425
Wydawca: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/genes14030743

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

Autorzy: David Juan, Gabriel Santpere, Joanna L. Kelley, Omar E. Cornejo, Tomas Marques-Bonet
Opublikowane w: Nature Reviews Genetics, Numer 24, 2023, Strona(/y) 314-331, ISSN 1471-0056
Wydawca: 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

Autorzy: 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
Opublikowane w: Nature Communications, Numer 15, 2024, ISSN 2041-1723
Wydawca: Nature Publishing Group
DOI: 10.1038/s41467-024-52811-7

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

Autorzy: 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
Opublikowane w: BMC Genomics, Numer 9, 2021, ISSN 1471-2164
Wydawca: BioMed Central
DOI: 10.1186/s12864-021-08025-y

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

Autorzy: 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
Opublikowane w: Nature Communications, Numer 15, 2024, ISSN 2041-1723
Wydawca: Nature Publishing Group
DOI: 10.1038/s41467-024-48569-7

The landscape of tolerated genetic variation in humans and primates

Autorzy: 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
Opublikowane w: Science, Numer 380, 2024, ISSN 0036-8075
Wydawca: American Association for the Advancement of Science
DOI: 10.1126/science.abn8197

Rare penetrant mutations confer severe risk of common diseases

Autorzy: 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
Opublikowane w: Science, Numer 380, 2024, ISSN 0036-8075
Wydawca: American Association for the Advancement of Science
DOI: 10.1126/science.abo1131

The Diversity of Primates: From Biomedicine to Conservation Genomics.

Autorzy: Joseph D Orkin; Lukas F. K. Kuderna; Tomas Marques-Bonet
Opublikowane w: Annual Review of Animal Biosciences, Numer 9, 2021, ISSN 2165-8110
Wydawca: NA
DOI: 10.1146/annurev-animal-061220-023138

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

Autorzy: 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.
Opublikowane w: Science, Numer 380, 2024, ISSN 0036-8075
Wydawca: 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

Autorzy: Aitor Serres-Armero; Brian W. Davis; Inna S. Povolotskaya; Carlos Morcillo-Suarez; Jocelyn Plassais; David Juan; Elaine A. Ostrander; Tomas Marques-Bonet
Opublikowane w: Genome Res, Numer 4, 2021, ISSN 1549-5469
Wydawca: 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

Autorzy: 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
Opublikowane w: instname:Universitat Autònoma de Barcelona, Numer 3, 2021, ISSN 1091-6490
Wydawca: NA
DOI: 10.1073/pnas.2010632118

Comparative genomics reveals the hybrid origin of a macaque group

Autorzy: 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,
Opublikowane w: Science Advances, Numer 9, 2024, ISSN 2375-2548
Wydawca: Science direct
DOI: 10.1126/sciadv.add3580

Phylogenomic analyses provide insights into primate evolution

Autorzy: 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
Opublikowane w: Science, Numer 380, 2024, Strona(/y) 913-924, ISSN 0036-8075
Wydawca: American Association for the Advancement of Science
DOI: 10.1126/science.abn6919

Deep genetic substructure within bonobos

Autorzy: 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
Opublikowane w: Current Biology, Numer 34, 2024, Strona(/y) 5341-5348.e3, ISSN 0960-9822
Wydawca: Cell Press
DOI: 10.1016/j.cub.2024.09.043

Ghost admixture in eastern gorillas

Autorzy: 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
Opublikowane w: Nature Ecology & Evolution, Numer 7, 2023, Strona(/y) 1503-1514, ISSN 2397-334X
Wydawca: Nature PUblisher group
DOI: 10.1038/s41559-023-02145-2

How genomics can help biodiversity conservation

Autorzy: 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
Opublikowane w: Trends in Genetics, Numer 39, 2023, Strona(/y) 545-559, ISSN 0168-9525
Wydawca: 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

Autorzy: 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
Opublikowane w: Communications Biology, Numer 7, 2024, ISSN 2399-3642
Wydawca: Nature publisher group
DOI: 10.1038/s42003-024-06901-3

Identification of constrained sequence elements across 239 primate genomes

Autorzy: 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,
Opublikowane w: Nature, Numer 625, 2024, Strona(/y) 735-742, ISSN 0028-0836
Wydawca: Nature Publishing Group
DOI: 10.1038/s41586-023-06798-8

Y chromosome sequence and epigenomic reconstruction across human populations

Autorzy: 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
Opublikowane w: Communications Biology, Numer 6, 2023, ISSN 2399-3642
Wydawca: Nature Research
DOI: 10.1038/s42003-023-05004-9

Evolutionary constraint and innovation across hundreds of placental mammals

Autorzy: 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
Opublikowane w: Science, Numer 380, 2024, ISSN 0036-8075
Wydawca: American Association for the Advancement of Science
DOI: 10.1126/science.abn3943

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

Autorzy: 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
Opublikowane w: Nature Ecology & Evolution, 2024, ISSN 2397-334X
Wydawca: Nature publisher group
DOI: 10.1038/s41559-024-02596-1

Eighty million years of rapid evolution of the primate Y chromosome

Autorzy: 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
Opublikowane w: Nature Ecology & Evolution, Numer 7, 2023, Strona(/y) 1114-1130, ISSN 2397-334X
Wydawca: Natre Publisher group
DOI: 10.1038/s41559-022-01974-x

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

Autorzy: 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
Opublikowane w: Science, Numer 380, 2024, Strona(/y) 906-913, ISSN 0036-8075
Wydawca: American Association for the Advancement of Science
DOI: 10.1126/science.abn7829

Branching out: what omics can tell us about primate evolution

Autorzy: Lukas F. K. Kuderna; Paula Esteller-Cucala; Tomas Marques-Bonet
Opublikowane w: Current Opinion Genet Dev, Numer 8, 2020, ISSN 0959-437X
Wydawca: Elsevier BV
DOI: 10.1016/j.gde.2020.06.006

Maximizing the acquisition of unique reads in noninvasive capture sequencing experiments

Autorzy: 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
Opublikowane w: instname:, Numer 1, 2020, ISSN 1755-0998
Wydawca: NA
DOI: 10.1111/1755-0998.13300

HuConTest: Testing Human Contamination in Great Ape Samples

Autorzy: Martin Kuhlwilm; Claudia Fontsere; Sojung Han; Marina Alvarez-Estape; Tomas Marques-Bonet
Opublikowane w: Genome Biol Evol ., Numer 8, 2021, ISSN 1759-6653
Wydawca: Oxford University Press
DOI: 10.1093/gbe/evab117

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

Autorzy: 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
Opublikowane w: Science, Numer 380, 2024, ISSN 0036-8075
Wydawca: 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

Autorzy: 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
Opublikowane w: Molecular Ecology, Numer 11, 2022, ISSN 0962-1083
Wydawca: Blackwell Publishing Inc.
DOI: 10.1111/mec.16554