Our main line of research is centered on the discovery of the extent of all kinds of genome variation within phenotypically different genomes. Specifically, we study genome variation (centered on CNVs), gene expression and epigenetic differences in the human species in the context of great ape evolution and other mammalian genomes such as canids. Our goal is to create an integrated view of genome evolution by studying changes in the composition, frequency, size and location at every major branch point of recent human evolution.

Genomic variation in ape genomes

Characterizing the variation of thousands of human genomes is standard today. However, primates (our closest relatives) are the ideal set of species for studying the evolution of these features from both mechanistic and adaptive points of view. In this line of research, we use genomic approaches in humans and primates to understand the impact of variants in the evolution of every species to provide a proper perspective to the differences among species.

Epigenetics and transcriptomics of non-human primates

DNA methylation is an epigenetic modification involved in regulatory processes such as cell differentiation during development, X-chromosome inactivation, genomic imprinting and susceptibility to complex disease. However, the dynamics of DNA methylation changes between humans and their closest relatives is still poorly understood. In this project, we evaluate methylation patterns in recent human evolution. We identified a significant positive relationship between the rate of coding variation and alterations of methylation at the promoter level.

Canid evolution

The domestic dog has been widely recognized as an important organism for studying the relationship between selection, genome variation and phenotypic diversity. Both dogs and wolves have been extensively surveyed using mtDNA, microsatellites and SNPs,  but structural variation, including variation in multicopy gene families, has not been fully characterized in canines.


Lab website: Comparative Genomics Lab

Tomàs Marquès Bonet

Marquès Bonet, Tomàs
ICREA Research Professor
Comparative Genomics Lab

Alejandro Valenzuela Seba

Valenzuela Seba, Alejandro
Predoctoral Researcher
Genómica comparativa

Sandra Ruibal Puertas

Ruibal Puertas, Sandra
Laboratory Technician
Comparative Genomics

Marc Palmada Flores

Palmada Flores, Marc
Predoctoral Researcher
Comparative genomics

Cira Martinez de Pablo

Martinez de Pablo, Cira
Postdoctoral Researcher
Comparative Genomics


Postdoctoral Researcher
Comparative Genomics Lab

Johanna Krueger

Krueger , Johanna
Predoctoral Researcher
Comparative Genomics

David Alejandro Juan Sopeña

Juan Sopeña, David Alejandro
Postdoctoral Researcher
Comparative Genomics Lab

Paula Esteller Cucala

Esteller Cucala, Paula
Predoctoral Researcher
Comparative Genomics

Marina Alvarez Estapé

Alvarez Estapé, Marina
Predoctoral Researcher
Comparative Genomics

Barnett R, Westbury MV, Sandoval-Velasco M, Vieira FG, Jeon S, Zazula G, Martin MD, Ho SYW, Mather N, Gopalakrishnan S, Ramos-Madrigal J, de Manuel M, Zepeda-Mendoza ML, Antunes A, Baez AC, De Cahsan B, Larson G, O'Brien SJ, Eizirik E, Johnson WE, Koepfli KP, Wilting A, Fickel J, Dalén L, Lorenzen ED, Marques-Bonet T, Hansen AJ, Zhang G, Bhak J, Yamaguchi N, Gilbert MTP. 2020. Genomic Adaptations and Evolutionary History of the Extinct Scimitar-Toothed Cat, Homotherium latidens. Current Biology, 30(24):5018-5025. DOI: 10.1016/j.cub.2020.09.051

White LC, Fontsere C, Lizano E, Hughes DA, Angedakin S, Arandjelovic M, Granjon AC, Hans JB, Lester JD, Rabanus-Wallace MT, Rowney C, Städele V, Marques-Bonet T, Langergraber KE, Vigilant L. 2019. A roadmap for high-throughput sequencing studies of wild animal populations using noninvasive samples and hybridization capture. Molecular Ecology Resources, 19(3):609-622. DOI:10.1111/1755-0998.12993

Welker F, Ramos-Madrigal J, Kuhlwilm M, Liao W, Gutenbrunner P, de Manuel M, Samodova D, Mackie M, Allentoft ME, Bacon AM, Collins MJ, Cox J, Lalueza-Fox C, Olsen JV, Demeter F, Wang W, Marques-Bonet T, Cappellini E. 2019. Enamel proteome shows that Gigantopithecus was an early diverging pongine. Nature, 576(7786):262-265. DOI:10.1038/s41586-019-1728-8

van der Valk T, Díez-del-Molino D, Marques-Bonet T, Guschanski K, Dalén L. 2019. Historical Genomes Reveal the Genomic Consequences of Recent Population Decline in Eastern Gorillas. Current Biology, 29(1):165-170. DOI:10.1016/j.cub.2018.11.055

Tollis M, Robbins J, Webb AE, Kuderna LFK, Caulin AF, Garcia JD, Bèrubè M, Pourmand N, Marques-Bonet T, O'Connell MJ, Palsbøll PJ, Maley CC. 2019. Return to the Sea, Get Huge, Beat Cancer: An Analysis of Cetacean Genomes Including an Assembly for the Humpback Whale (Megaptera novaeangliae). Molecular Biology and Evolution, 36(8):1746-1763. DOI:10.1093/molbev/msz099

Schmidt JM, de Manuel M, Marques-Bonet T, Castellano S, Andrés AM. 2019. The impact of genetic adaptation on chimpanzee subspecies differentiation. PLOS Genetics, 15(11). DOI:10.1371/journal.pgen.1008485

Rogers J, Raveendran M, Harris RA, Mailund T, Leppälä K, Athanasiadis G, Schierup MH, Cheng J, Munch K, Walker JA, Konkel MK, Jordan V, Steely CJ, Beckstrom TO, Bergey C, Burrell A, Schrempf D, Noll A, Kothe M, Kopp GH, Liu Y, Murali S, Billis K, Martin FJ, Muffato M, Cox L, Else J, Disotell T, Muzny DM, Phillips-Conroy J, Aken B, Eichler EE, Marques-Bonet T, Kosiol C, Batzer MA, Hahn MW, Tung J, Zinner D, Roos C, Jolly CJ, Gibbs RA, Worley KC; Baboon Genome Analysis Consortium. 2019. The comparative genomics and complex population history of Papio baboons. Science Advances, 5(1):1-15. DOI:10.1126/sciadv.aau6947

McCartney AM, Hyland EM, Cormican P, Moran RJ, Webb AE, Lee KD, Hernandez-Rodriguez J, Prado-Martinez J, Creevey CJ, Aspden JL, McInerney JO, Marques-Bonet T, O'Connell MJ. 2019. Gene Fusions Derived by Transcriptional Readthrough are Driven by Segmental Duplication in Human. Genome Biology and Evolution, 11(9):2676-2690. DOI:10.1093/gbe/evz163

Lorente-Galdos B, Lao O, Serra-Vidal G, Santpere G, Kuderna LFK, Arauna LR, Fadhlaoui-Zid K, Pimenoff VN, Soodyall H, Zalloua P, Marques-Bonet T, Comas D. 2019. Whole-genome sequence analysis of a Pan African set of samples reveals archaic gene flow from an extinct basal population of modern humans into sub-Saharan populations. Genome Biology, 20(1):1-15. DOI:10.1186/s13059-019-1684-5

Kuhlwilm M, Boeckx C. 2019. A catalog of single nucleotide changes distinguishing modern humans from archaic hominins. Scientific Reports, 9(1):1-14. DOI:10.1038/s41598-019-44877-x

Kuhlwilm M, Han S, Sousa VC, Excoffier L, Marques-Bonet T. 2019. Ancient admixture from an extinct ape lineage into bonobos. Nature Ecology and Evolution, 3(6):957-965. DOI:10.1038/s41559-019-0881-7

Kuderna LFK, Lizano E, Julià E, Gomez-Garrido J, Serres-Armero A, Kuhlwilm M, Alandes RA, Alvarez-Estape M, Juan D, Simon H, Alioto T, Gut M, Gut I, Schierup MH, Fornas O, Marques-Bonet T. 2019. Selective single molecule sequencing and assembly of a human Y chromosome of African origin. Nature Communications, 10(1). DOI:10.1038/s41467-018-07885-5

Han S, Andre AM, Marques-Bonet T, Kuhlwilm M. 2019. Genetic variation in pan species is shaped by demographic history and harbors lineage-specific functions. Genome Biology and Evolution, 11(4):1178-1191. DOI:10.1093/gbe/evz047

Gokhman D, Mishol N, de Manuel M, de Juan D, Shuqrun J, Meshorer E, Marques-Bonet T, Rak Y, Carmel L. 2019. Reconstructing Denisovan Anatomy Using DNA Methylation Maps. Cell, 179(1):180-192. DOI:10.1016/j.cell.2019.08.035

Feng S, Fang Q, Barnett R, Li C, Han S, Kuhlwilm M, Zhou L, Pan H, Deng Y, Chen G, Gamauf A, Woog F, Prys-Jones R, Marques-Bonet T, Gilbert MTP, Zhang G. 2019. The Genomic Footprints of the Fall and Recovery of the Crested Ibis. Current Biology, 29(2):340-349.e7. DOI:10.1016/j.cub.2018.12.008

Besenbacher S, Hvilsom C, Marques-Bonet T, Mailund T, Schierup MH. 2019. Direct estimation of mutations in great apes reconciles phylogenetic dating. Nature Ecology and Evolution, 3(2):286-292. DOI:10.1038/s41559-018-0778-x.

Zhu Y, Sousa AMM, Gao T, Skarica M, Li M, Santpere G, Esteller-Cucala P, Juan D, Ferrández-Peral L, Gulden FO, Yang M, Miller DJ, Marques-Bonet T, Imamura Kawasawa Y, Zhao H, Sestan N.  Spatiotemporal transcriptomic divergence across human and macaque brain development. Science, 362(6420):eaat8077. DOI:10.1126/science.aat8077

Warren WC, García-Pérez R, Xu S, Lampert KP, Chalopin D, Stöck M, Loewe L, Lu Y, Kuderna L, Minx P, Montague MJ, Tomlinson C, Hillier LW, Murphy DN, Wang J, Wang Z, Garcia CM, Thomas GCW, Volff JN, Farias F, Aken B, Walter RB, Pruitt KD, Marques-Bonet T, Hahn MW, Kneitz S, Lynch M, Schartl M. 2018. Clonal polymorphism and high heterozygosity in the celibate genome of the Amazon molly. Nature Ecology & Evolution, 2(4):669-679. DOI:10.1038/s41559-018-0473-y

Steely CJ, Baker JN, Walker JA, Loupe CD, Batzer MA. 2018. Analysis of lineage-specific Alu subfamilies in the genome of the olive baboon, Papio anubis. Mobile DNA, 9(1):10. DOI:10.1186/s13100-018-0115-6

Nye J, Laayouni H, Kuhlwilm M, Mondal M, Marques-Bonet T, Bertranpetit J. 2018. Selection in the introgressed regions of the chimpanzee genome. Genome Biology and Evolution, 10(4):1132-1138. DOI:10.1093/gbe/evy077

Mattle-Greminger MP, Bilgin Sonay T, Nater A, Pybus M, Desai T, de Valles G, Casals F, Scally A, Bertranpetit J, Marques-Bonet T, van Schaik CP, Anisimova M, Krützen M. 2018. Genomes reveal marked differences in the adaptive evolution between orangutan species. Genome Biology, 19(1):193. DOI:10.1186/s13059-018-1562-6

Marques-Bonet T, Hvilsom C. 2018. Genomic variation of the great apes and the application to conservation. International Zoo Yearbook, 52(1):25-33. DOI:10.1111/izy.12185

Kuhlwilm M. 2018. The evolution of FOXP2 in the light of admixture. Current Opinion in Behavioral Sciences, 21:120-126. DOI:10.1016/j.cobeha.2018.04.006

Hernandez-Rodriguez J, Arandjelovic M, Lester J, de Filippo C, Weihmann A, Meyer M, Angedakin S, Casals F, Navarro A, Vigilant L, Kühl HS, Langergraber K, Boesch C, Hughes D, Marques-Bonet T. 2018. The impact of endogenous content, replicates and pooling on genome capture from faecal samples. Molecular Ecology Resources, 18(2):319-333. DOI:10.1111/1755-0998.12728

Gopalakrishnan S, Sinding MS, Ramos-Madrigal J, Niemann J, Samaniego Castruita JA, Vieira FG, Carøe C, Montero MM, Kuderna L, Serres A, González-Basallote VM, Liu YH, Wang GD, Marques-Bonet T, Mirarab S, Fernandes C, Gaubert P, Koepfli KP, Budd J, Rueness EK, Sillero C, Heide-Jørgensen MP, Petersen B, Sicheritz-Ponten T, Bachmann L, Wiig Ø, Hansen AJ, Gilbert MTP. 2018. Interspecific Gene Flow Shaped the Evolution of the Genus Canis. Current Biology, 28(21):3441-3449. DOI:10.1016/j.cub.2018.08.041

Gómez-Sánchez D, Olalde I, Sastre N, Enseñat C, Carrasco R, Marques-Bonet T, Lalueza-Fox C, Leonard JA, Vilà C, Ramírez O. 2018. On the path to extinction: Inbreeding and admixture in a declining grey wolf population. Molecular Ecology, 27(18):3599-3612. DOI:10.1111/mec.14824

de Valles-Ibáñez G, Esteve-Solé A, Piquer M, González-Navarro EA, Hernandez-Rodriguez J, Laayouni H, González-Roca E, Plaza-Martin AM, Deyà-Martínez Á, Martín-Nalda A, Martínez-Gallo M, García-Prat M, Del Pino-Molina L, Cuscó I, Codina-Solà M, Batlle-Masó L, Solís-Moruno M, Marquès-Bonet T, Bosch E, López-Granados E, Aróstegui JI, Soler-Palacín P, Colobran R, Yagüe J, Alsina L, Juan M, Casals F. 2018. Evaluating the genetics of common variable immunodeficiency: Monogenetic model and beyond. Frontiers in Immunology, 9:1-15. DOI:10.3389/fimmu.2018.00636

de Manuel M, Shiina T, Suzuki S, Dereuddre-Bosquet N, Garchon HJ, Tanaka M, Congy-Jolivet N, Aarnink A, Le Grand R, Marques-Bonet T, Blancher A. 2018. Whole genome sequencing in the search for genes associated with the control of SIV infection in the Mauritian macaque model. Scientific Reports, 8(1):7131. DOI:10.1038/s41598-018-25071-x

Zhang Z, Gu Q, de Manuel Montero M, Bravo IG, Marques-Bonet T, Häussinger D, Münk C. 2017. Stably expressed APOBEC3H forms a barrier for cross-species transmission of simian immunodeficiency virus of chimpanzee to humans. PLoS Pathogens, 13(12):1-25. DOI:10.1371/journal.ppat.1006746

Warren WC, Kuderna L, Alexander A, Catchen J, Pérez-Silva JG, López-Otín C, Quesada V, Minx P, Tomlinson C, Montague MJ, Farias FHG, Walter RB, Marques-Bonet T, Glenn T, Kieran TJ, Wise SS, Wise JP Jr, Waterhouse RM, Wise JP Sr. 2017. The Novel Evolution of the Sperm Whale Genome. Genome Biology and Evolution, 9(12):3260-3264. DOI:10.1093/gbe/evx187

Sullivan AP, de Manuel M, Marques-Bonet T, Perry GH. 2017. An evolutionary medicine perspective on Neandertal extinction. Journal of Human Evolution, 108:62-71. DOI:10.1016/j.jhevol.2017.03.004

Staes N, Sherwood CC, Wright K, de Manuel M, Guevara EE, Marques-Bonet T, Krützen M, Massiah M, Hopkins WD, Ely JJ, Bradley BJ. 2017. FOXP2 variation in great ape populations offers insight into the evolution of communication skills. Scientific Reports, 7(1):1-10. DOI:10.1038/s41598-017-16844-x

Sousa AMM, Zhu Y, Raghanti MA, Kitchen RR, Onorati M, Tebbenkamp ATN, Stutz B, Meyer KA, Li M, Kawasawa YI, Liu F, Perez RG, Mele M, Carvalho T, Skarica M, Gulden FO, Pletikos M, Shibata A, Stephenson AR, Edler MK, Ely JJ, Elsworth JD, Horvath TL, Hof PR, Hyde TM, Kleinman JE, Weinberger DR, Reimers M, Lifton RP, Mane SM, Noonan JP, State MW, Lein ES, Knowles JA, Marques-Bonet T, Sherwood CC, Gerstein MB, Sestan N. 2017. Molecular and cellular reorganization of neural circuits in the human lineage. Science, 358(6366):1027-1032. DOI:10.1126/science.aan3456

Solis-Moruno M, de Manuel M, Hernandez-Rodriguez J, Fontsere C, Gomara-Castaño A, Valsera-Naranjo C, Crailsheim D, Navarro A, Llorente M, Riera L, Feliu-Olleta O, Marques-Bonet T. 2017. Potential damaging mutation in LRP5 from genome sequencing of the first reported chimpanzee with the Chiari malformation. Scientific Reports, 7(1):1-8. DOI:10.1038/s41598-017-15544-w

Serres-Armero A, Povolotskaya IS, Quilez J, Ramirez O, Santpere G, Kuderna LFK, Hernandez-Rodriguez J, Fernandez-Callejo M, Gomez-Sanchez D, Freedman AH, Fan Z, Novembre J, Navarro A, Boyko A, Wayne R, Vilà C, Lorente-Galdos B, Marques-Bonet T. 2017. Similar genomic proportions of copy number variation within gray wolves and modern dog breeds inferred from whole genome sequencing. BMC Genomics, 18(1):1-15. DOI:10.1186/s12864-017-4318-x

Nater A, Mattle-Greminger MP, Nurcahyo A, Nowak MG, de Manuel M, Desai T, Groves C, Pybus M, Sonay TB, Roos C, Lameira AR, Wich SA, Askew J, Davila-Ross M, Fredriksson G, de Valles G, Casals F, Prado-Martinez J, Goossens B, Verschoor EJ, Warren KS, Singleton I, Marques DA, Pamungkas J, Perwitasari-Farajallah D, Rianti P, Tuuga A, Gut IG, Gut M, Orozco-terWengel P, van Schaik CP, Bertranpetit J, Anisimova M, Scally A, Marques-Bonet T, Meijaard E, Krützen M. 2017. Morphometric, Behavioral, and Genomic Evidence for a New Orangutan Species. Current Biology, 27(22):3487-3498.e10. DOI:10.1016/j.cub.2017.09.047

Nam K, Munch K, Mailund T, Nater A, Greminger MP, Krützen M, Marquès-Bonet T, Schierup MH. 2017. Evidence that the rate of strong selective sweeps increases with population size in the great apes. Proceedings of the National Academy of Sciences of the United States of America, 114(7):1613-1618. DOI:10.1073/pnas.1605660114

Meyer KA, Marques-Bonet T, Sestan N. 2017. Differential Gene Expression in the Human Brain Is Associated with Conserved, but Not Accelerated, Noncoding Sequences. Molecular Biology and Evolution, 34(5):1217-1229. DOI:10.1093/molbev/msx076

Mak SST, Gopalakrishnan S, Carøe C, Geng C, Liu S, Sinding MS, Kuderna LFK, Zhang W, Fu S, Vieira FG, Germonpré M, Bocherens H, Fedorov S, Petersen B, Sicheritz-Pontén T, Marques-Bonet T, Zhang G, Jiang H, Gilbert MTP. 2017. Comparative performance of the BGISEQ-500 vs Illumina HiSeq2500 sequencing platforms for palaeogenomic sequencing. GigaScience, 6(8):1-13. DOI:10.1093/gigascience/gix049

Maibach V, Hans JB, Hvilsom C, Marques-Bonet T, Vigilant L. 2017. MHC class I diversity in chimpanzees and bonobos. Immunogenetics, 69(10):661-676. DOI:10.1007/s00251-017-0990-x

Librado P, Gamba C, Gaunitz C, Der Sarkissian C, Pruvost M, Albrechtsen A, Fages A, Khan N, Schubert M, Jagannathan V, Serres-Armero A, Kuderna LFK, Povolotskaya IS, Seguin-Orlando A, Lepetz S, Neuditschko M, Thèves C, Alquraishi S, Alfarhan AH, Al-Rasheid K, Rieder S, Samashev Z, Francfort HP, Benecke N, Hofreiter M, Ludwig A, Keyser C, Marques-Bonet T, Ludes B, Crubézy E, Leeb T, Willerslev E, Orlando L. 2017. Ancient genomic changes associated with domestication of the horse. Science, 356(6336):442-445. DOI:10.1126/science.aam5298.

Kuderna LFK, Tomlinson C, Hillier LW, Tran A, Fiddes IT, Armstrong J, Laayouni H, Gordon D, Huddleston J, Garcia Perez R, Povolotskaya I, Serres Armero A, Gómez Garrido J, Ho D, Ribeca P, Alioto T, Green RE, Paten B, Navarro A, Betranpetit J, Herrero J, Eichler EE, Sharp AJ, Feuk L, Warren WC, Marques-Bonet T. 2017. A 3-way hybrid approach to generate a new high-quality chimpanzee reference genome. GigaScience,6(11):1-6. DOI:10.1093/gigascience/gix098

Gopalakrishnan S, Samaniego Castruita JA, Sinding MS, Kuderna LFK, Räikkönen J, Petersen B, Sicheritz-Ponten T, Larson G, Orlando L, Marques-Bonet T, Hansen AJ, Dalén L, Gilbert MTP. 2017. The wolf reference genome sequence (Canis lupus lupus) and its implications for Canis spp. population genomics. BMC Genomics, 18(1):1-11. DOI:10.1186/s12864-017-3883-3

Carrillo-de-Santa-Pau E, Juan D, Pancaldi V, Were F, Martin-Subero I, Rico D, Valencia A; BLUEPRINT Consortium. 2017. Automatic identification of informative regions with epigenomic changes associated to hematopoiesis. Nucleic Acids Research, 45(16):9244-9259. DOI:10.1093/nar/gkx618

Valles-Ibáñez G de, Hernandez-Rodriguez J, Prado-Martinez J, Luisi P, Marquès-Bonet T, Casals F. 2016. Genetic Load of Loss-of-Function Polymorphic Variants in Great Apes. Genome Biology and Evolution, 8(3):871-877. DOI:10.1093/gbe/evw040

Stevison LS, Woerner AE, Kidd JM, Kelley JL, Veeramah KR, McManus KF; Great Ape Genome Project, Bustamante CD, Hammer MF, Wall JD. 2016. The time scale of recombination rate evolution in great apes. Molecular Biology and Evolution, 33(4):928-945. DOI:10.1093/molbev/msv331

Sanchez-Delgado M, Court F, Vidal E, Medrano J, Monteagudo-Sánchez A, Martin-Trujillo A, Tayama C, Iglesias-Platas I, Kondova I, Bontrop R, Poo-Llanillo ME, Marques-Bonet T, Nakabayashi K, Simón C, Monk D. 2016. Human Oocyte-Derived Methylation Differences Persist in the Placenta Revealing Widespread Transient Imprinting. PLoS Genetics, 12(11):1-23. DOI:10.1371/journal.pgen.1006427

Morgan PPG. 2016. Mitochondria Research Society/United Mitochondrial Disease Foundation Meeting Abstracts. Mitochondrion, 31:89-117. DOI:10.1016/j.mito.2016.08.010

Marsden CD, Ortega-Del Vecchyo D, O'Brien DP, Taylor JF, Ramirez O, Vilà C, Marques-Bonet T, Schnabel RD, Wayne RK, Lohmueller KE. 2016. Bottlenecks and selective sweeps during domestication have increased deleterious genetic variation in dogs. Proceedings of the National Academy of Sciences of the United States of America, 113(1):152-157. DOI:10.1073/pnas.1512501113

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