Comparative Genomics Lab
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
Melin AD, Orkin JD, Janiak MC, Valenzuela A, Kuderna L, Marrone F, Ramangason H, Horvath JE, Roos C, Kitchener AC, Khor CC, Lim WK, Lee JGH, Tan P, Umapathy G, Raveendran M, Alan Harris R, Gut I, Gut M, Lizano E, Nadler T, Zinner D, Le MD, Manu S, Rabarivola CJ, Zaramody A, Andriaholinirina N, Johnson SE, Jarvis ED, Fedrigo O, Wu D, Zhang G, Farh KK, Rogers J, Marques-Bonet T, Navarro A, Juan D, Arora PS, Higham JP. 2021. Variation in predicted COVID‐19 risk among lemurs and lorises. American Journal of Primatology, 83(6):1-12. DOI: 10.1002/ajp.23255
Liu S, Westbury MV, Dussex N, Mitchell KJ, Sinding MS, Heintzman PD, Duchêne DA, Kapp JD, von Seth J, Heiniger H, Sánchez-Barreiro F, Margaryan A, André-Olsen R, De Cahsan B, Meng G, Yang C, Chen L, van der Valk T, Moodley Y, Rookmaaker K, Bruford MW, Ryder O, Steiner C, Bruins-van Sonsbeek LGR, Vartanyan S, Guo C, Cooper A, Kosintsev P, Kirillova I, Lister AM, Marques-Bonet T, Gopalakrishnan S, Dunn RR, Lorenzen ED, Shapiro B, Zhang G, Antoine PO, Dalén L, Gilbert MTP. 2021. Ancient and modern genomes unravel the evolutionary history of the rhinoceros family. Cell, 184(19):4874-4885. DOI:10.1016/j.cell.2021.07.032
Kuhlwilm M, Fontsere C, Han S, Alvarez-Estape M, Marques-Bonet T. 2021. HuConTest: Testing human contamination in great ape samples. Genome Biology and Evolution, 13(6). DOI:10.1093/gbe/evab117
García-Pérez R, Esteller-Cucala P, Mas G, Lobón I, Di Carlo V, Riera M, Kuhlwilm M, Navarro A, Blancher A, Di Croce L, Gómez-Skarmeta JL, Juan D, Marquès-Bonet T. 2021. Epigenomic profiling of primate lymphoblastoid cell lines reveals the evolutionary patterns of epigenetic activities in gene regulatory architectures. Nature Communications, 12(1):1-17. DOI:10.1038/s41467-021-23397-1
Fontsere C, Alvarez-Estape M, Lester J, Arandjelovic M, Kuhlwilm M, Dieguez P, Agbor A, Angedakin S, Ayuk Ayimisin E, Bessone M, Brazzola G, Deschner T, Eno-Nku M, Granjon AC, Head J, Kadam P, Kalan AK, Kambi M, Langergraber K, Lapuente J, Maretti G, Jayne Ormsby L, Piel A, Robbins MM, Stewart F, Vergnes V, Wittig RM, Kühl HS, Marques-Bonet T, Hughes DA, Lizano E. 2021. Maximizing the acquisition of unique reads in noninvasive capture sequencing experiments. Molecular Ecology Resources, 21(3):745–761. DOI: 10.1111/1755-0998.13300.
Fontsere C, Frandsen P, Hernandez-Rodriguez J, Niemann J, Scharff-Olsen CH, Vallet D, Le Gouar P, Ménard N, Navarro A, Siegismund HR, Hvilsom C, Gilbert MTP, Kuhlwilm M, Hughes D, Marques-Bonet T. 2021. The genetic impact of an Ebola outbreak on a wild gorilla population. BMC Genomics, 22(1):735. DOI:10.1186/s12864-021-08025-y
de-Dios T, Carrión P, Olalde I, Nadal LL, Lizano E, Pàmies D, Marques-Bonet T, Balloux F, van Dorp L, Lalueza-Fox C. 2021. Salmonella enterica from a soldier from the 1652-siege of Barcelona (Spain) supports historical transatlantic epidemic contacts. iScience, 24(9):103021. DOI:10.1016/j.isci.2021.103021
Boubli JP, Janiak MC, Porter LM, Torre S, Cortés-Ortiz L, Da Silva MNF, Rylands AB, Nash S, Bertuol F, Byrne H, Silva FE, Rohe F, Vries D, Beck RMD, Ruiz-Gartzia I, Kuderna LFK, Marques-Bonet T, Hrbek T, Farias IP, Van Heteren AH, Roos C. 2021. Ancient DNA of the pygmy marmoset type specimen Cebuella pygmaea (Spix, 1823) resolves a taxonomic conundrum. Zoological Research, 42(6):761-771. DOI:10.24272/j.issn.2095-8137.2021.143
Welker F, Ramos-Madrigal J, Gutenbrunner P, Mackie M, Tiwary S, Rakownikow Jersie-Christensen R, Chiva C, Dickinson MR, Kuhlwilm M, de Manuel M, Gelabert P, Martinón-Torres M, Margvelashvili A, Arsuaga JL, Carbonell E, Marques-Bonet T, Penkman K, Sabidó E, Cox J, Olsen JV, Lordkipanidze D, Racimo F, Lalueza-Fox C, Bermúdez de Castro JM, Willerslev E, Cappellini E. 2020. The dental proteome of Homo antecessor. Nature, 580(7802):235-238. DOI:10.1038/s41586-020-2153-8
van Dorp L, Gelabert P, Rieux A, de Manuel M, de-Dios T, Gopalakrishnan S, Carøe C, Sandoval-Velasco M, Fregel R, Olalde I, Escosa R, Aranda C, Huijben S, Mueller I, Marquès-Bonet T, Balloux F, Gilbert MTP, Lalueza-Fox C. 2020. Plasmodium vivax Malaria Viewed through the Lens of an Eradicated European Strain. Molecular Biology and Evolution, 37(3):773–785. DOI: 10.1093/molbev/msz264
Sinding MS, Gopalakrishnan S, Ramos-Madrigal J, de Manuel M, Pitulko VV, Kuderna L, Feuerborn TR, Frantz LAF, Vieira FG, Niemann J, Samaniego Castruita JA, Carøe C, Andersen-Ranberg EU, Jordan PD, Pavlova EY, Nikolskiy PA, Kasparov AK, Ivanova VV, Willerslev E, Skoglund P, Fredholm M, Wennerberg SE, Heide-Jørgensen MP, Dietz R, Sonne C, Meldgaard M, Dalén L, Larson G, Petersen B, Sicheritz-Pontén T, Bachmann L, Wiig Ø, Marques-Bonet T, Hansen AJ, Gilbert MTP. 2020. Arctic-adapted dogs emerged at the Pleistocene–Holocene transition. Science, 368(6498):1495-1499. DOI:10.1126/science.aaz8599
Kuderna LFK, Solís-Moruno M, Batlle-Masó L, Julià E, Lizano E, Anglada R, Ramírez E, Bote A, Tormo M, Marquès-Bonet T, Fornas Ò, Casals F. 2020. Flow Sorting Enrichment and Nanopore Sequencing of Chromosome 1 From a Chinese Individual. Frontiers in Genetics, 10(1315). DOI: 10.3389/fgene.2019.01315
Kuderna LF, Esteller-Cucala P, Marques-Bonet T. 2020. Branching out: what omics can tell us about primate evolution. Current Opinion in Genetics & Development, 62:65–71. DOI: 10.1016/j.gde.2020.06.006
Khan N, de Manuel M, Peyregne S, Do R, Prufer K, Marques-Bonet T, Varki N, Gagneux P, Varki A. 2020. Multiple Genomic Events Altering Hominin SIGLEC Biology and Innate Immunity Predated the Common Ancestor of Humans and Archaic Hominins. Genome Biology and Evolution, 12(7):1040–1050. DOI: 10.1093/gbe/evaa125
Heredia-Genestar JM, Marquès-Bonet T, Juan D, Navarro A. 2020. Extreme differences between human germline and tumor mutation densities are driven by ancestral human-specific deviations. Nature Communications, 11(1):2512. DOI: 10.1038/s41467-020-16296-4.
Gokhman D, Nissim-Rafinia M, Agranat-Tamir L, Housman G, García-Pérez R, Lizano E, Cheronet O, Mallick S, Nieves-Colón MA, Li H, Alpaslan-Roodenberg S, Novak M, Gu H, Osinski JM, Ferrando-Bernal M, Gelabert P, Lipende I, Mjungu D, Kondova I, Bontrop R, Kullmer O, Weber G, Shahar T, Dvir-Ginzberg M, Faerman M, Quillen EE, Meissner A, Lahav Y, Kandel L, Liebergall M, Prada ME, Vidal JM, Gronostajski RM, Stone AC, Yakir B, Lalueza-Fox C, Pinhasi R, Reich D, Marques-Bonet T, Meshorer E, Carmel L. 2020. Differential DNA methylation of vocal and facial anatomy genes in modern humans. Nature Communications, 11(1):1189. DOI: 10.1038/s41467-020-15020-6.
Gelabert P, Sandoval-Velasco M, Serres A, de Manuel M, Renom P, Margaryan A, Stiller J, de-Dios T, Fang Q, Feng S, Mañosa S, Pacheco G, Ferrando-Bernal M, Shi G, Hao F, Chen X, Petersen B, Olsen RA, Navarro A, Deng Y, Dalén L, Marquès-Bonet T, Zhang G, Antunes A, Gilbert MTP, Lalueza-Fox C. 2020. Evolutionary History, Genomic Adaptation to Toxic Diet, and Extinction of the Carolina Parakeet. Current Biology, 30(1):108-114. DOI: 10.1016/j.cub.2019.10.066
Frandsen P, Fontsere C, Nielsen SV, Hanghøj K, Castejon-Fernandez N, Lizano E, Hughes D, Hernandez-Rodriguez J, Korneliussen TS, Carlsen F, Siegismund HR, Mailund T, Marques-Bonet T, Hvilsom C. 2020. Targeted conservation genetics of the endangered chimpanzee. Heredity, 125(1-2):15-27. DOI:10.1038/s41437-020-0313-0
de Manuel M, Barnett R, Sandoval-Velasco M, Yamaguchi N, Garrett Vieira F, Zepeda Mendoza ML, Liu S, Martin MD, Sinding MS, Mak SST, Carøe C, Liu S, Guo C, Zheng J, Zazula G, Baryshnikov G, Eizirik E, Koepfli KP, Johnson WE, Antunes A, Sicheritz-Ponten T, Gopalakrishnan S, Larson G, Yang H, O'Brien SJ, Hansen AJ, Zhang G, Marques-Bonet T, Gilbert MTP. 2020. The evolutionary history of extinct and living lions. Proceedings of the National Academy of Sciences of the United States of America, 117(20): 10927–10934. DOI: 10.1073/pnas.1919423117
Dehasque M, Ávila‐Arcos MC, Díez‐del‐Molino D, Fumagalli M, Guschanski K, Lorenzen ED, Malaspinas A, Marques‐Bonet T, Martin MD, Murray GGR, Papadopulos AST, Therkildsen NO, Wegmann D, Dalén L, Foote AD. 2020. Inference of natural selection from ancient DNA. Evolution Letters, 4(2):94–108. DOI: 10.1002/evl3.165
Chicote JU, López-Sánchez M, Marquès-Bonet T, Callizo J, Pérez-Jurado LA, García-España A. 2020. Circular DNA intermediates in the generation of large human segmental duplications. BMC Genomics, 21(1):1–11. DOI: 10.1186/s12864-020-06998-w
Brasó-Vives M, Povolotskaya IS, Hartasánchez DA, Farré X, Fernandez-Callejo M, Raveendran M, Alan Harris R, Rosene DL, Lorente-Galdos B, Navarro A, Marques-Bonet T, Rogers J, Juan D. 2020. Copy number variants and fixed duplications among 198 rhesus macaques (Macaca mulatta). PLoS Genetics, 16(5). DOI: 10.1371/journal.pgen.1008742
Blake LE, Roux J, Hernando-Herraez I, Banovich NE, Perez RG, Hsiao CJ, Eres I, Cuevas C, Marques-Bonet T, Gilad Y. 2020. A comparison of gene expression and DNA methylation patterns across tissues and species. Genome Research, 30(2):250–262. DOI: 10.1101/gr.254904.119
Batlle-Masó L, Mensa-Vilaró A, Solís-Moruno M, Marquès-Bonet T, Arostegui JI, Casals F. 2020. Genetic diagnosis of autoinflammatory disease patients using clinical exome sequencing. European Journal of Medical Genetics, 63(5):103920. DOI: 10.1016/j.ejmg.2020.103920
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
Fontsere C, de Manuel M, Marques-Bonet T, Kuhlwilm M. 2019. Admixture in Mammals and How to Understand Its Functional Implications: On the Abundance of Gene Flow in Mammalian Species, Its Impact on the Genome, and Roads into a Functional Understanding. BioEssays, 41(12):1-14. DOI:10.1002/bies.201900123.
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