Comparative analysis of the Y chromosome in humans and great apes
Evolutionary Cell and Developmental Biology (Zoology)
Final Report Abstract
The main objective of this proposal was the comparative analysis of several Y chromosomes from humans and all great ape species, in order to determine evolutionary patterns. This approach relied on the availability of high-quality individual chromosome assemblies, which were to be generated using novel sequencing technologies, combined with sorting of chromosomes using flow cytometry. We were able to assemble a Y chromosome from one human individual from Africa, but we could not generate the diversity data needed for the envisioned analyses due to unforeseen technical problems. Additionally, we found that the sequencing strategy employed still have high error rates when compared to short-read sequencing strategies. Since we were not able to generate data from several individuals from different great ape species, I could not perform the envisioned population genetic analyses. Instead, I focused on population genetics of the whole genomes of great apes, with a special emphasis on admixture. We found evidence for gene flow from bonobos into several chimpanzee subspecies by analysing 75 genomes across their geographic range. This study reveals that our closest living relatives experienced a history of admixture similar to that within the Homo clade. Thus, gene flow might have been widespread during the evolution of the great apes and hominins. This finding gained widespread attention, and in further work I contributed to a follow-up study showing evidence for signatures of selection on introgressed bonobo-like fragments in chimpanzees. When comparing the landscape of introgression between these populations and hominins, I found that a possible incompatibility for admixture around the FOXP2 locus is restricted to modern humans, suggesting that this region is exposed to different evolutionary pressures in humans and their living relatives. Another follow-up study on archaic admixture in bonobos is currently in revision. Overall, the study of population genetics in great apes turned out to be a fruitful research path given the availability of data and resources. The picture of gene flow in humans and other species is of great interest for understanding evolutionary history, and my work has contributed important aspects to this topic.
Publications
- Chimpanzee genomic diversity reveals ancient admixture with bonobos. Science (80). 2016;354(6311)
De Manuel M, Kuhlwilm M, Frandsen P, Sousa, VC, Desai T, Prado-Martinez J, Hernandez- Rodriguez J, Dupanloup I, Lao O, Hallast P, Schmidt JM, Heredia-Genestar JM, Benazzo A, Barbujani G, Peter BM, Kuderna LFK, Casals F, Angedakin S, Arandjelovic M, Boesch C, Kühl H, Vigilant L, Langergraber K, Novembre J, Gut M, Gut I, Navarro A, Carlsen F, Andrés AM, Siegismund HR, Scally A, Excoffier L, Tyler-Smith C, Castellano S, Xue Y, Hvilsom C, Marques- Bonet T
(See online at https://doi.org/10.1126/science.aag2602) - Selection in the Introgressed Regions of the Chimpanzee Genome. Genome Biol Evol. 2018 Apr 1;10(4):1132-1138
Nye J, Laayouni H, Kuhlwilm M, Mondal M, Marques-Bonet T, Bertranpetit J
(See online at https://doi.org/10.1093/gbe/evy077) - The evolution of FOXP2 in the light of admixture. Curr Opin Behav Sci. 2018; 21, 120-126
Kuhlwilm M.
(See online at https://doi.org/10.1016/j.cobeha.2018.04.006) - Selective single molecule sequencing and assembly of a human Y chromosome of African origin. Nat Commun. 2019;10(1):4.
Kuderna LFK, Lizano E, Julià E, Gomez-Garrido J, Serres-Armero A, Kuhlwilm M, Alandes RA, Alvarez-Estape M, Juan D, Heath S, Alioto T, Gut M, Gut I, Schierup MH, Fornas O, Marques- Bonet T
(See online at https://doi.org/10.1038/s41467-018-07885-5)
