Population dynamics and genetic connectivity in recent chimpanzee history

Fontsere, Claudia; Kuhlwilm, Martin; Morcillo-Suarez, Carlos; Alvarez-Estape, Marina; Lester, Jack D.; Gratton, Paolo; Schmidt, Joshua M.; Dieguez, Paula; Aebischer, Thierry; Álvarez-Varona, Paula; Agbor, Anthony; Angedakin, Samuel; Assumang, Alfred K.; Ayimisin, A. Emmanuel; Bailey, Emma; Barubiyo, Donatienne; Bessone, Mattia; Carretero-Alonso, Andrea; Chancellor, Rebecca; Cohen, Heather; Danquah, Emmanuel; Deschner, Tobias; Dunn, Andrew; Dupain, Jef; Egbe, Villard E.; Feliu, Olga; Goedmakers, Annemarie; Granjon, Anne-Céline; Head, Josephine S.; Hedwig, Daniela; Hermans, Veerle; Hernandez-Aguilar, R. Adriana; Imong, Inaoyom; Jones, Sorrel; Junker, Jessica; Kadam, Parag; Kaiser, Mike; Kambere, Mbangi; Vyalengerera, Magloire Kambale; Kalan, Ammie K.; Kienast, Ivonne; Kujirakwinja, Deo; Langergraber, Kevin; Lapuente, Juan; Larson, Bradley; Laudisoit, Anne; Lee, Kevin; Llana, Manuel; Llorente, Miquel; Marrocoli, Sergio; Morgan, David; Mulindahabi, Felix; Murai, Mizuki; Neil, Emily; Nicholl, Sonia; Nixon, Stuart; Normand, Emma; Orbell, Chris; Ormsby, Lucy Jayne; Pacheco, Liliana; Piel, Alex; Riera, Laura; Robbins, Martha M.; Rundus, Aaron; Sanz, Crickette; Sciaky, Lilah; Sommer, Volker; Stewart, Fiona A.; Tagg, Nikki; Tédonzong, Luc Roscelin; Ton, Els; van Schijndel, Joost; Vergnes, Virginie; Wessling, Erin G.; Willie, Jacob; Wittig, Roman M.; Yuh, Yisa G.; Yurkiw, Kyle; Zuberbuehler, Klaus; Hecht, Jochen; Vigilant, Linda; Boesch, Christophe; Andrés, Aida M.; Hughes, David A.; Kühl, Hjalmar S.; Lizano, Esther; Arandjelovic, Mimi; Marques-Bonet, Tomas

doi:10.1016/j.xgen.2022.100133

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Population dynamics and genetic connectivity in recent chimpanzee history

MPS-Authors

/persons/resource/persons181358

Lester, Jack D.
Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Max Planck Society;
The Leipzig School of Human Origins (IMPRS), Max Planck Institute for Evolutionary Anthropology, Max Planck Society;
Molecular Genetics Laboratory, Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Max Planck Society;

/persons/resource/persons191492

Gratton, Paolo
Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Max Planck Society;
Great Ape Evolutionary Ecology and Conservation, Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Max Planck Society;

/persons/resource/persons192158

Dieguez, Paula
Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Max Planck Society;

/persons/resource/persons199923

Agbor, Anthony
Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Max Planck Society;
Great Ape Evolutionary Ecology and Conservation, Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Max Planck Society;

/persons/resource/persons207390

Angedakin, Samuel
Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Max Planck Society;

/persons/resource/persons220640

Ayimisin, A. Emmanuel
Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Max Planck Society;

/persons/resource/persons230961

Bailey, Emma
Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Max Planck Society;
Great Ape Evolutionary Ecology and Conservation, Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Max Planck Society;

/persons/resource/persons230963

Barubiyo, Donatienne
Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Max Planck Society;

/persons/resource/persons220642

Bessone, Mattia
Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Max Planck Society;

/persons/resource/persons206536

Cohen, Heather
Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Max Planck Society;

/persons/resource/persons72641

Deschner, Tobias
Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Max Planck Society;
Chimpanzees, Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Max Planck Society;
Endocrinology Laboratory, Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Max Planck Society;

/persons/resource/persons230968

Egbe, Villard E.
Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Max Planck Society;

/persons/resource/persons192513

Granjon, Anne-Céline
Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Max Planck Society;
The Leipzig School of Human Origins (IMPRS), Max Planck Institute for Evolutionary Anthropology, Max Planck Society;
Gorillas, Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Max Planck Society;

/persons/resource/persons72737

Head, Josephine S.
Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Max Planck Society;
Gorillas, Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Max Planck Society;

/persons/resource/persons207405

Jones, Sorrel
Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Max Planck Society;
Great Ape Evolutionary Ecology and Conservation, Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Max Planck Society;

/persons/resource/persons230974

Kambere, Mbangi
Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Max Planck Society;

/persons/resource/persons257925

Vyalengerera, Magloire Kambale
Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Max Planck Society;

/persons/resource/persons230978

Kienast, Ivonne
Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Max Planck Society;

/persons/resource/persons207408

Lapuente, Juan
Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Max Planck Society;
Great Ape Evolutionary Ecology and Conservation, Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Max Planck Society;

/persons/resource/persons230980

Larson, Bradley
Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Max Planck Society;

/persons/resource/persons200019

Lee, Kevin
Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Max Planck Society;
Great Ape Evolutionary Ecology and Conservation, Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Max Planck Society;

/persons/resource/persons192161

Marrocoli, Sergio
Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Max Planck Society;
Great Ape Evolutionary Ecology and Conservation, Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Max Planck Society;

/persons/resource/persons123126

Murai, Mizuki
Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Max Planck Society;

/persons/resource/persons206490

Neil, Emily
Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Max Planck Society;

/persons/resource/persons220648

Nicholl, Sonia
Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Max Planck Society;
Great Ape Evolutionary Ecology and Conservation, Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Max Planck Society;

/persons/resource/persons220650

Ormsby, Lucy Jayne
Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Max Planck Society;
Great Ape Evolutionary Ecology and Conservation, Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Max Planck Society;

/persons/resource/persons72936

Robbins, Martha M.
Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Max Planck Society;
Gorillas, Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Max Planck Society;

/persons/resource/persons247737

Sciaky, Lilah
Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Max Planck Society;

/persons/resource/persons207389

van Schijndel, Joost
Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Max Planck Society;

/persons/resource/persons73044

Wittig, Roman M.
Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Max Planck Society;
Chimpanzees, Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Max Planck Society;
Department of Human Behavior Ecology and Culture, Max Planck Institute for Evolutionary Anthropology, Max Planck Society;

/persons/resource/persons207402

Yuh, Yisa G.
Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Max Planck Society;
Great Ape Evolutionary Ecology and Conservation, Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Max Planck Society;

/persons/resource/persons230986

Yurkiw, Kyle
Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Max Planck Society;

/persons/resource/persons73023

Vigilant, Linda
Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Max Planck Society;
Molecular Genetics Laboratory, Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Max Planck Society;

/persons/resource/persons72593

Boesch, Christophe
Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Max Planck Society;
Great Ape Evolutionary Ecology and Conservation, Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Max Planck Society;
Chimpanzees, Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Max Planck Society;

/persons/resource/persons72806

Kühl, Hjalmar S.
Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Max Planck Society;
Great Ape Evolutionary Ecology and Conservation, Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Max Planck Society;
Chimpanzees, Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Max Planck Society;

/persons/resource/persons72566

Arandjelovic, Mimi
Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Max Planck Society;
Great Ape Evolutionary Ecology and Conservation, Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Max Planck Society;
Chimpanzees, Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Max Planck Society;

External Resource

https://github.com/kuhlwilm/rareCAGA
(Code)

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Fulltext (public)

Fontsere_Population_CellGen_2022.pdf
(Publisher version), 23MB

Supplementary Material (public)

Fontsere_Population_CellGen_Suppl_2022.zip
(Supplementary material), 63MB

Citation

Fontsere, C., Kuhlwilm, M., Morcillo-Suarez, C., Alvarez-Estape, M., Lester, J. D., Gratton, P., et al. (2022). Population dynamics and genetic connectivity in recent chimpanzee history. Cell Genomics, 2(6): 100133. doi:10.1016/j.xgen.2022.100133.

Cite as: https://hdl.handle.net/21.11116/0000-000A-955D-6

Abstract

Knowledge on the population history of endangered species is critical for conservation, but whole-genome data on chimpanzees (Pan troglodytes) is geographically sparse. Here, we produced the first non-invasive geolocalized catalog of genomic diversity by capturing chromosome 21 from 828 non-invasive samples collected at 48 sampling sites across Africa. The four recognized subspecies show clear genetic differentiation correlating with known barriers, while previously undescribed genetic exchange suggests that these have been permeable on a local scale. We obtained a detailed reconstruction of population stratification and fine-scale patterns of isolation, migration, and connectivity, including a comprehensive picture of admixture with bonobos (Pan paniscus). Unlike humans, chimpanzees did not experience extended episodes of long-distance migrations, which might have limited cultural transmission. Finally, based on local rare variation, we implement a fine-grained geolocalization approach demonstrating improved precision in determining the origin of confiscated chimpanzees.