Population dynamics and genetic connectivity in recent chimpanzee history

• DOI: 10.1016/j.xgen.2022.100133
• Publication Date: 2022-06-01T14:42:10Z
• Authors: Claudia Fontsere; Martin Kuhlwilm; Carlos Morcillo-S...; Marina Alvarez-Es...; Jack D. Lester; Paolo Gratton; Joshua M. Schmidt; Paula Dieguez; Thierry Aebischer; Paula Álvarez-Varona; Anthony Agbor; Samuel Angedakin; Alfred K. Assumang; Emmanuel A. Ayimisin; Emma Bailey; Donatienne Barubiyo; Mattia Bessone; Andrea Carretero-...; Rebecca Chancellor; Heather Cohen; Emmanuel Danquah; Tobias Deschner; Andrew Dunn; Jef Dupain; Villard E. Egbe; Olga Feliu; Annemarie Goedmakers; Anne-Céline Granjon; Josephine Head; Daniela Hedwig; Veerle Hermans; R. Adriana Hernan...; Inaoyom Imong; Sorrel Jones; Jessica Junker; Parag Kadam; Mike Kaiser; Mbangi Kambere; Magloire V. Kambale; Ammie K. Kalan; Ivonne Kienast; Deo Kujirakwinja; Kevin Langergraber; Juan Lapuente; Bradley Larson; Anne Laudisoit; Kevin Lee; Manuel Llana; Miquel Llorente; Sergio Marrocoli; David Morgan; Felix Mulindahabi; Mizuki Murai; Emily Neil; Sonia Nicholl; Stuart Nixon; Emma Normand; Chris Orbell; Lucy J. Ormsby; Liliana Pacheco; Alex Piel; Laura Riera; Martha M. Robbins; Aaron Rundus; Crickette Sanz; Lilah Sciaky; Volker Sommer; Fiona A. Stewart; Nikki Tagg; Luc Roscelin Tédo...; Els Ton; Joost van Schijndel; Virginie Vergnes; Erin G. Wessling; Jacob Willie; Roman M. Wittig; Yisa G. Yuh; Kyle Yurkiw; Klaus Zuberbuehler; Jochen Hecht; Linda Vigilant; Christophe Boesch; Aida M. Andrés; David A. Hughes; Hjalmar S. Kühl; Esther Lizano; Mimi Arandjelovic; Tomas Marques-Bonet
• Keywords: 0301 basic medicine; 106014 Genomics; Chimpanzee; Population genetics; Chimpanzeenon-invasive samples; QH426-470; Settore BIO/05 - ZOOLOGIA; Fecal samples; population dynamics; Settore BIOS-14/A - Genetica; Internal medicine; GE; Genètica de poblacions; Settore BIO/18; Genomics; 106054 Zoologie; hybridization capture; Conservation genomics; 106012 Evolutionsforschung; 106012 Evolutionary research; 570; Population dynamics; Settore BIOS-03/A - Zoologia; 610; non-invasive samples; QH426 Genetics; Chimpanzee demography; 106054 Zoology; chimpanzee demography; Article; QH301; 03 medical and health sciences; chimpanzee; fecal samples; Geolocalization; 106014 Genomik; Genetics; Chimpanzees; QH426; MCC; QL; geolocalization; population genetics; DAS; QL Zoology; 15. Life on land; RC31-1245; Genòmica; Hybridization capture; Non-invasive samples; conservation genomics; Ximpanzés

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.