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

ESTHER LIZANO GONZALEZ

LIZANO GONZALEZ, ESTHER
Postdoctoral Researcher
Comparative Genomics Lab

Johanna Krueger

Krueger, Johanna
Predoctoral Researcher
Comparative Genomics

Yee SW, Ferrández-Peral L, Alentorn-Moron P, Fontsere C, Ceylan M, Koleske ML, Handin N, Artegoitia VM, Lara G, Chien HC, Zhou X, Dainat J, Zalevsky A, Sali A, Brand CM, Wolfreys FD, Yang J, Gestwicki JE, Capra JA, Artursson P, Newman JW, Marquès-Bonet T, Giacomini KM. 2024. Illuminating the function of the orphan transporter, SLC22A10, in humans and other primates. Nature Communications, 15(1):4380. DOI:10.1038/s41467-024-48569-7

Talavera A, Palmada-Flores M, Burriel-Carranza B, Valbuena-Ureña E, Mochales-Riaño G, Adams DC, Tejero-Cicuéndez H, Soler-Membrives A, Amat F, Guinart D, Carbonell F, Obon E, Marquès-Bonet T, Carranza S. 2024. Genomic insights into the Montseny brook newt (Calotriton arnoldi), a Critically Endangered glacial relict. iScience, 27(1):108665. DOI:10.1016/j.isci.2023.108665

Larivière D, Abueg L, Brajuka N, Gallardo-Alba C, Grüning B, Ko BJ, Ostrovsky A, Palmada-Flores M, Pickett BD, Rabbani K, Antunes A, Balacco JR, Chaisson MJP, Cheng H, Collins J, Couture M, Denisova A, Fedrigo O, Gallo GR, Giani AM, Gooder GM, Horan K, Jain N, Johnson C, Kim H, Lee C, Marques-Bonet T, O'Toole B, Rhie A, Secomandi S, Sozzoni M, Tilley T, Uliano-Silva M, van den Beek M, Williams RW, Waterhouse RM, Phillippy AM, Jarvis ED, Schatz MC, Nekrutenko A, Formenti G. 2024. Scalable, accessible and reproducible reference genome assembly and evaluation in Galaxy. Nature Biotechnology, 5:10-13. DOI:10.1038/s41587-023-02100-3

Zhang BL, Chen W, Wang Z, Pang W, Luo MT, Wang S, Shao Y, He WQ, Deng Y, Zhou L, Chen J, Yang MM, Wu Y, Wang L, Fernández-Bellon H, Molloy S, Meunier H, Wanert F, Kuderna L, Marques-Bonet T, Roos C, Qi XG, Li M, Liu Z, Schierup MH, Cooper DN, Liu J, Zheng YT, Zhang G, Wu DD. 2023. Comparative genomics reveals the hybrid origin of a macaque group. Science Advances, 9(22):1-14. DOI:10.1126/sciadv.add3580

Zhang BL, Chen W, Wang Z, Pang W, Luo MT, Wang S, Shao Y, He WQ, Deng Y, Zhou L, Chen J, Yang MM, Wu Y, Wang L, Fernández-Bellon H, Molloy S, Meunier H, Wanert F, Kuderna L, Marques-Bonet T, Roos C, Qi XG, Li M, Liu Z, Schierup MH, Cooper DN, Liu J, Zheng YT, Zhang G, Wu DD. 2023. Eighty million years of rapid evolution of the primate Y chromosome. Nature Ecology & Evolution. DOI:10.1038/s41559-022-01974-x

Wilder AP, Supple MA, Subramanian A, Mudide A, Swofford R, Serres-Armero A, Steiner C, Koepfli KP, Genereux DP, Karlsson EK, Lindblad-Toh K, Marques-Bonet T, Munoz Fuentes V, Foley K, Meyer WK; Zoonomia Consortium‡; Ryder OA, Shapiro B, Andrews G, Armstrong JC, Bianchi M, Birren BW, Bredemeyer KR, Breit AM, Christmas MJ, Clawson H, Damas J, Di Palma F, Diekhans M, Dong MX, Eizirik E, Fan K, Fanter C, Foley NM, Forsberg-Nilsson K, Garcia CJ, Gatesy J, Gazal S, Genereux DP, Goodman L, Grimshaw J, Halsey MK, Harris AJ, Hickey G, Hiller M, Hindle AG, Hubley RM, Hughes GM, Johnson J, Juan D, Kaplow IM, Karlsson EK, Keough KC, Kirilenko B, Koepfli KP, Korstian JM, Kowalczyk A, Kozyrev SV, Lawler AJ, Lawless C, Lehmann T, Levesque DL, Lewin HA, Li X, Lind A, Lindblad-Toh K, Mackay-Smith A, Marinescu VD, Marques-Bonet T, Mason VC, Meadows JRS, Meyer WK, Moore JE, Moreira LR, Moreno-Santillan DD, Morrill KM, Muntané G, Murphy WJ, Navarro A, Nweeia M, Ortmann S, Osmanski A, Paten B, Paulat NS, Pfenning AR, Phan BN, Pollard KS, Pratt HE, Ray DA, Reilly SK, Rosen JR, Ruf I, Ryan L, Ryder OA, Sabeti PC, Schäffer DE, Serres A, Shapiro B, Smit AFA, Springer M, Srinivasan C, Steiner C, Storer JM, Sullivan KAM, Sullivan PF, Sundström E, Supple MA, Swofford R, Talbot JE, Teeling E, Turner-Maier J, Valenzuela A, Wagner F, Wallerman O, Wang C, Wang J, Weng Z, Wilder AP, Wirthlin ME, Xue JR, Zhang X. 2023. The contribution of historical processes to contemporary extinction risk in placental mammals. Science, 380(6643). DOI:10.1126/science.abn5856

Sørensen EF, Harris RA, Zhang L, Raveendran M, Kuderna LFK, Walker JA, Storer JM, Kuhlwilm M, Fontsere C, Seshadri L, Bergey CM, Burrell AS, Bergman J, Phillips-Conroy JE, Shiferaw F, Chiou KL, Chuma IS, Keyyu JD, Fischer J, Gingras MC, Salvi S, Doddapaneni H, Schierup MH, Batzer MA, Jolly CJ, Knauf S, Zinner D, Farh KK, Marques-Bonet T, Munch K, Roos C, Rogers J. 2023. Genome-wide coancestry reveals details of ancient and recent male-driven reticulation in baboons. Science, 380(6648). DOI:10.1126/science.abn8153

Shao Y, Zhou L, Li F, Zhao L, Zhang BL, Shao F, Chen JW, Chen CY, Bi X, Zhuang XL, Zhu HL, Hu J, Sun Z, Li X, Wang D, Rivas-González I, Wang S, Wang YM, Chen W, Li G, Lu HM, Liu Y, Kuderna LFK, Farh KK, Fan PF, Yu L, Li M, Liu ZJ, Tiley GP, Yoder AD, Roos C, Hayakawa T, Marques-Bonet T, Rogers J, Stenson PD, Cooper DN, Schierup MH, Yao YG, Zhang YP, Wang W, Qi XG, Zhang G, Wu DD. 2023. Phylogenomic analyses provide insights into primate evolution. Science, 380(6648):913-924. DOI:10.1126/science.abn6919

Sánchez-Barreiro F, De Cahsan B, Westbury MV, Sun X, Margaryan A, Fontsere C, Bruford MW, Russo IM, Kalthoff DC, Sicheritz-Pontén T, Petersen B, Dalén L, Zhang G, Marquès-Bonet T, Gilbert MTP, Moodley Y. 2023. Historic sampling of a vanishing beast: population structure and diversity in the black rhinoceros. Molecular Biology and Evolution. DOI:10.1093/molbev/msad180

Pawar H, Rymbekova A, Cuadros-Espinoza S, Huang X, de Manuel M, van der Valk T, Lobon I, Alvarez-Estape M, Haber M, Dolgova O, Han S, Esteller-Cucala P, Juan D, Ayub Q, Bautista R, Kelley JL, Cornejo OE, Lao O, Andrés AM, Guschanski K, Ssebide B, Cranfield M, Tyler-Smith C, Xue Y, Prado-Martinez J, Marques-Bonet T, Kuhlwilm M. 2023. Ghost admixture in eastern gorillas. Nature Ecology & Evolution, 7(9): 1503-1514. DOI:10.1038/s41559-023-02145-2

Murat F, Mbengue N, Winge SB, Trefzer T, Leushkin E, Sepp M, Cardoso-Moreira M, Schmidt J, Schneider C, Mößinger K, Brüning T, Lamanna F, Belles MR, Conrad C, Kondova I, Bontrop R, Behr R, Khaitovich P, Pääbo S, Marques-Bonet T, Grützner F, Almstrup K, Schierup MH, Kaessmann H. 2023. The molecular evolution of spermatogenesis across mammals. Nature, 613(7943):308-316. DOI:10.1038/s41586-022-05547-7

Mochales-Riaño G, Fontsere C, de Manuel M, Talavera A, Burriel-Carranza B, Tejero-Cicuéndez H, AlGethami RHM, Shobrak M, Marques-Bonet T, Carranza S. 2023. Genomics reveals introgression and purging of deleterious mutations in the Arabian leopard (Panthera pardus nimr). iScience, 26(9):107481. DOI:10.1016/j.isci.2023.107481

Kuderna LFK, Ulirsch JC, Rashid S, Ameen M, Sundaram L, Hickey G, Cox AJ, Gao H, Kumar A, Aguet F, Christmas MJ, Clawson H, Haeussler M, Janiak MC, Kuhlwilm M, Orkin JD, Bataillon T, Manu S, Valenzuela A, Bergman J, Rouselle M, Silva FE, Agueda L, Blanc J, Gut M, de Vries D, Goodhead I, Harris RA, Raveendran M, Jensen A, Chuma IS, Horvath JE, Hvilsom C, Juan D, Frandsen P, Schraiber JG, de Melo FR, Bertuol F, Byrne H, Sampaio I, Farias I, Valsecchi J, Messias M, da Silva MNF, Trivedi M, Rossi R, Hrbek T, Andriaholinirina N, Rabarivola CJ, Zaramody A, Jolly CJ, Phillips-Conroy J, Wilkerson G, Abee C, Simmons JH, Fernandez-Duque E, Kanthaswamy S, Shiferaw F, Wu D, Zhou L, Shao Y, Zhang G, Keyyu JD, Knauf S, Le MD, Lizano E, Merker S, Navarro A, Nadler T, Khor CC, Lee J, Tan P, Lim WK, Kitchener AC, Zinner D, Gut I, Melin AD, Guschanski K, Schierup MH, Beck RMD, Karakikes I, Wang KC, Umapathy G, Roos C, Boubli JP, Siepel A, Kundaje A, Paten B, Lindblad-Toh K, Rogers J, Marques Bonet T, Farh KK. 2023. Identification of constrained sequence elements across 239 primate genomes. Nature. DOI:10.1038/s41586-023-06798-8

Kuderna LFK, Gao H, Janiak MC, Kuhlwilm M, Orkin JD, Bataillon T, Manu S, Valenzuela A, Bergman J, Rousselle M, Silva FE, Agueda L, Blanc J, Gut M, de Vries D, Goodhead I, Harris RA, Raveendran M, Jensen A, Chuma IS, Horvath JE, Hvilsom C, Juan D, Frandsen P, Schraiber JG, de Melo FR, Bertuol F, Byrne H, Sampaio I, Farias I, Valsecchi J, Messias M, da Silva MNF, Trivedi M, Rossi R, Hrbek T, Andriaholinirina N, Rabarivola CJ, Zaramody A, Jolly CJ, Phillips-Conroy J, Wilkerson G, Abee C, Simmons JH, Fernandez-Duque E, Kanthaswamy S, Shiferaw F, Wu D, Zhou L, Shao Y, Zhang G, Keyyu JD, Knauf S, Le MD, Lizano E, Merker S, Navarro A, Nadler T, Khor CC, Lee J, Tan P, Lim WK, Kitchener AC, Zinner D, Gut I, Melin AD, Guschanski K, Schierup MH, Beck RMD, Umapathy G, Roos C, Boubli JP, Rogers J, Farh KK, Marques Bonet T. 2023. A global catalog of whole-genome diversity from 233 primate species. Science. 2023;380(6648):906-913. DOI:10.1126/science.abn7829

Kubat J, Paterson R, Patramanis I, Barker G, Demeter F, Filoux A, Kullmer O, Mackie M, Marques-Bonet T, Huong NTM, Tuan NA, Pheng S, Rippengal J, Schrenk F, Souksavatdy V, Tshen LT, Wattanapituksakul A, Wang W, Zanolli C, Cappellini E, Bacon AM. 2023. Geometric morphometrics and paleoproteomics enlighten the paleodiversity of Pongo. PLOS ONE, 18(12):e0291308. DOI:10.1371/journal.pone.0291308

Juan D, Santpere G, Kelley JL, Cornejo OE, Marques-Bonet T. 2023. Current advances in primate genomics: novel approaches for understanding evolution and disease. Nature Reviews Genetics, 24(5):314-331. DOI:10.1038/s41576-022-00554-w

Jensen A, Swift F, de Vries D, Beck R, Kuderna LFK, Knauf S, Chuma IS, Keyyu JD, Kitchener AC, Farh K, Rogers J, Marques-Bonet T, Detwiler KM, Roos C, Guschanski K. 2023. Complex evolutionary history with extensive ancestral gene flow in an African primate radiation. Molecular Biology and Evolution, (March):1-18. DOI:10.1093/molbev/msad247

Gao H, Hamp T, Ede J, Schraiber JG, McRae J, Singer-Berk M, Yang Y, Dietrich ASD, Fiziev PP, Kuderna LFK, Sundaram L, Wu Y, Adhikari A, Field Y, Chen C, Batzoglou S, Aguet F, Lemire G, Reimers R, Balick D, Janiak MC, Kuhlwilm M, Orkin JD, Manu S, Valenzuela A, Bergman J, Rousselle M, Silva FE, Agueda L, Blanc J, Gut M, de Vries D, Goodhead I, Harris RA, Raveendran M, Jensen A, Chuma IS, Horvath JE, Hvilsom C, Juan D, Frandsen P, de Melo FR, Bertuol F, Byrne H, Sampaio I, Farias I, do Amaral JV, Messias M, da Silva MNF, Trivedi M, Rossi R, Hrbek T, Andriaholinirina N, Rabarivola CJ, Zaramody A, Jolly CJ, Phillips-Conroy J, Wilkerson G, Abee C, Simmons JH, Fernandez-Duque E, Kanthaswamy S, Shiferaw F, Wu D, Zhou L, Shao Y, Zhang G, Keyyu JD, Knauf S, Le MD, Lizano E, Merker S, Navarro A, Bataillon T, Nadler T, Khor CC, Lee J, Tan P, Lim WK, Kitchener AC, Zinner D, Gut I, Melin A, Guschanski K, Schierup MH, Beck RMD, Umapathy G, Roos C, Boubli JP, Lek M, Sunyaev S, O'Donnell-Luria A, Rehm HL, Xu J, Rogers J, Marques-Bonet T, Farh KK. 2023. The landscape of tolerated genetic variation in humans and primates. Science. 2023;380(6648). DOI:10.1126/science.abn8197

Fiziev PP, McRae J, Ulirsch JC, Dron JS, Hamp T, Yang Y, Wainschtein P, Ni Z, Schraiber JG, Gao H, Cable D, Field Y, Aguet F, Fasnacht M, Metwally A, Rogers J, Marques-Bonet T, Rehm HL, O'Donnell-Luria A, Khera AV, Farh KK. 2023. Rare penetrant mutations confer severe risk of common diseases. Science, 380(6648). DOI:10.1126/science.abo1131

Esteller-Cucala P, Palmada-Flores M, Kuderna LFK, Fontsere C, Serres-Armero A, Dabad M, Torralvo M, Faella A, Ferrández-Peral L, Llovera L, Fornas O, Julià E, Ramírez E, González I, Hecht J, Lizano E, Juan D, Marquès-Bonet T. 2023. Y chromosome sequence and epigenomic reconstruction across human populations. Communications Biology, 6(1):623. DOI:10.1038/s42003-023-05004-9

de Dios T, Fontsere C, Renom P, Stiller J, Llovera L, Uliano-Silva M, Sánchez-Gracia A, Wright C, Lizano E, Caballero B, Navarro A, Civit S, Robbins RK., Blaxter M, Marquès-Bonet T, Vila R, Lalueza-Fox C. 2023. Whole-genomes from the extinct Xerces Blue butterfly can help identify declining insect species. eLife. DOI: https://DOI.org/10.7554/eLife.87928.1

Christmas MJ, Kaplow IM, Genereux DP, Dong MX, Hughes GM, Li X, Sullivan PF, Hindle AG, Andrews G, Armstrong JC, Bianchi M, Breit AM, Diekhans M, Fanter C, Foley NM, Goodman DB, Goodman L, Keough KC, Kirilenko B, Kowalczyk A, Lawless C, Lind AL, Meadows JRS, Moreira LR, Redlich RW, Ryan L, Swofford R, Valenzuela A, Wagner F, Wallerman O, Brown AR, Damas J, Fan K, Gatesy J, Grimshaw J, Johnson J, Kozyrev SV, Lawler AJ, Marinescu VD, Morrill KM, Osmanski A, Paulat NS, Phan BN, Reilly SK, Schäffer DE, Steiner C, Supple MA, Wilder AP, Wirthlin ME, Xue JR; Zoonomia Consortium§; Birren BW, Gazal S, Hubley RM, Koepfli KP, Marques-Bonet T, Meyer WK, Nweeia M, Sabeti PC, Shapiro B, Smit AFA, Springer MS, Teeling EC, Weng Z, Hiller M, Levesque DL, Lewin HA, Murphy WJ, Navarro A, Paten B, Pollard KS, Ray DA, Ruf I, Ryder OA, Pfenning AR, Lindblad-Toh K, Karlsson EK, Andrews G, Armstrong JC, Bianchi M, Birren BW, Bredemeyer KR, Breit AM, Christmas MJ, Clawson H, Damas J, Di Palma F, Diekhans M, Dong MX, Eizirik E, Fan K, Fanter C, Foley NM, Forsberg-Nilsson K, Garcia CJ, Gatesy J, Gazal S, Genereux DP, Goodman L, Grimshaw J, Halsey MK, Harris AJ, Hickey G, Hiller M, Hindle AG, Hubley RM, Hughes GM, Johnson J, Juan D, Kaplow IM, Karlsson EK, Keough KC, Kirilenko B, Koepfli KP, Korstian JM, Kowalczyk A, Kozyrev SV, Lawler AJ, Lawless C, Lehmann T, Levesque DL, Lewin HA, Li X, Lind A, Lindblad-Toh K, Mackay-Smith A, Marinescu VD, Marques-Bonet T, Mason VC, Meadows JRS, Meyer WK, Moore JE, Moreira LR, Moreno-Santillan DD, Morrill KM, Muntané G, Murphy WJ, Navarro A, Nweeia M, Ortmann S, Osmanski A, Paten B, Paulat NS, Pfenning AR, Phan BN, Pollard KS, Pratt HE, Ray DA, Reilly SK, Rosen JR, Ruf I, Ryan L, Ryder OA, Sabeti PC, Schäffer DE, Serres A, Shapiro B, Smit AFA, Springer M, Srinivasan C, Steiner C, Storer JM, Sullivan KAM, Sullivan PF, Sundström E, Supple MA, Swofford R, Talbot JE, Teeling E, Turner-Maier J, Valenzuela A, Wagner F, Wallerman O, Wang C, Wang J, Weng Z, Wilder AP, Wirthlin ME, Xue JR, Zhang X. 2023. Evolutionary constraint and innovation across hundreds of placental mammals. Science, 380(6643). DOI:10.1126/science.abn3943

Bentley BP, Carrasco-Valenzuela T, Ramos EKS, Pawar H, Souza Arantes L, Alexander A, Banerjee SM, Masterson P, Kuhlwilm M, Pippel M, Mountcastle J, Haase B, Uliano-Silva M, Formenti G, Howe K, Chow W, Tracey A, Sims Y, Pelan S, Wood J, Yetsko K, Perrault JR, Stewart K, Benson SR, Levy Y, Todd EV, Shaffer HB, Scott P, Henen BT, Murphy RW, Mohr DW, Scott AF, Duffy DJ, Gemmell NJ, Suh A, Winkler S, Thibaud-Nissen F, Nery MF, Marques-Bonet T, Antunes A, Tikochinski Y, Dutton PH, Fedrigo O, Myers EW, Jarvis ED, Mazzoni CJ, Komoroske LM. 2023. Divergent sensory and immune gene evolution in sea turtles with contrasting demographic and life histories. Proceedings of the National Academy of Sciences, 120(7):2017. DOI:10.1073/pnas.2201076120

Alvarez-Estape M, Pawar H, Fontsere C, Trujillo AE, Gunson JL, Bergl RA, Bermejo M, Linder JM, McFarland K, Oates JF, Sunderland-Groves JL, Orkin J, Higham JP, Viaud-Martinez KA, Lizano E, Marques-Bonet T. 2023. Past Connectivity but Recent Inbreeding in Cross River Gorillas Determined Using Whole Genomes from Single Hairs. Genes, 14(3):743. DOI:10.3390/genes14030743

Wu DD, Qi XG, Yu L, Li M, Liu ZJ, Yoder AD, Roos C, Hayakawa T, Rogers J, Marques-Bonet T, Su B, Yao YG, Zhang YP, Zhang G. 2022. Initiation of the Primate Genome Project. Zoological Research, 43(2):147-149. DOI:10.24272/j.issn.2095-8137.2022.001

Ruiz‐Gartzia I, Lizano E, Marques‐Bonet T, Kelley JL. 2022. Recovering the genomes hidden in museum wet collections. Molecular Ecology Resources, 22(6): 2127-2129. DOI:10.1111/1755-0998.13631

Palmada-Flores M, Orkin JD, Haase B, Mountcastle J, Bertelsen MF, Fedrigo O, Kuderna LFK, Jarvis ED, Marques-Bonet T. 2022. A high-quality, long-read genome assembly of the endangered ring-tailed lemur (Lemur catta). GigaScience, 11:1-7. DOI:10.1093/gigascience/giac026

Paez S, Kraus RHS, Shapiro B, Gilbert MTP, Jarvis ED; Vertebrate Genomes Project Conservation Group, Al-Ajli FO, Ceballos G, Crawford AJ, Fedrigo O, Johnson RN, Johnson WE, Marques-Bonet T, Morin PA, Mueller RC, Ryder OA, Teeling EC, Venkatesh B. 2022. Reference genomes for conservation. Science, 377(6604):364-366. DOI:10.1126/science.abm8127

Lobon I, Solís-Moruno M, Juan D, Muhaisen A, Abascal F, Esteller-Cucala P, García-Pérez R, Martí MJ, Tolosa E, Ávila J, Rahbari R, Marques-Bonet T, Casals F, Soriano E. 2022. Somatic Mutations Detected in Parkinson Disease Could Affect Genes With a Role in Synaptic and Neuronal Processes. Frontiers in Aging, 3(April):1-14. DOI:10.3389/fragi.2022.851039

Janiak MC, Silva FE, Beck RMD, de Vries D, Kuderna LFK, Torosin NS, Melin AD, Marquès-Bonet T, Goodhead IB, Messias M, da Silva MNF, Sampaio I, Farias IP, Rossi R, de Melo FR, Valsecchi J, Hrbek T, Boubli JP. 2022. 205 newly assembled mitogenomes provide mixed evidence for rivers as drivers of speciation for Amazonian primates. Molecular Ecology, 31(14):3888-3902. DOI:10.1111/mec.16554

Gopalakrishnan S, Ebenesersdóttir SS, Lundstrøm IKC, Turner-Walker G, Moore KHS, Luisi P, Margaryan A, Martin MD, Ellegaard MR, Magnússon ÓÞ, Sigurðsson Á, Snorradóttir S, Magnúsdóttir DN, Laffoon JE, van Dorp L, Liu X, Moltke I, Ávila-Arcos MC, Schraiber JG, Rasmussen S, Juan D, Gelabert P, de-Dios T, Fotakis AK, Iraeta-Orbegozo M, Vågene ÅJ, Denham SD, Christophersen A, Stenøien HK, Vieira FG, Liu S, Günther T, Kivisild T, Moseng OG, Skar B, Cheung C, Sandoval-Velasco M, Wales N, Schroeder H, Campos PF, Guðmundsdóttir VB, Sicheritz-Ponten T, Petersen B, Halgunset J, Gilbert E, Cavalleri GL, Hovig E, Kockum I, Olsson T, Alfredsson L, Hansen TF, Werge T, Willerslev E, Balloux F, Marques-Bonet T, Lalueza-Fox C, Nielsen R, Stefánsson K, Helgason A, Gilbert MTP. 2022. The population genomic legacy of the second plague pandemic. Current Biology, 32(21):4743-4751. DOI:10.1016/j.cub.2022.09.023

Fontsere C, Kuhlwilm M, Morcillo-Suarez C, Alvarez-Estape M, Lester JD, Gratton P, Schmidt JM, Dieguez P, Aebischer T, Álvarez-Varona P, Agbor A, Angedakin S, Assumang AK, Ayimisin EA, Bailey E, Barubiyo D, Bessone M, Carretero-Alonso A, Chancellor R, Cohen H, Danquah E, Deschner T, Dunn A, Dupain J, Egbe VE, Feliu O, Goedmakers A, Granjon AC, Head J, Hedwig D, Hermans V, Hernandez-Aguilar RA, Imong I, Jones S, Junker J, Kadam P, Kaiser M, Kambere M, Kambale MV, Kalan AK, Kienast I, Kujirakwinja D, Langergraber K, Lapuente J, Larson B, Laudisoit A, Lee K, Llana M, Llorente M, Marrocoli S, Morgan D, Mulindahabi F, Murai M, Neil E, Nicholl S, Nixon S, Normand E, Orbell C, Ormsby LJ, Pacheco L, Piel A, Riera L, Robbins MM, Rundus A, Sanz C, Sciaky L, Sommer V, Stewart FA, Tagg N, Tédonzong LR, Ton E, van Schijndel J, Vergnes V, Wessling EG, Willie J, Wittig RM, Yuh YG, Yurkiw K, Zuberbuehler K, Hecht J, Vigilant L, Boesch C, Andrés AM, Hughes DA, Kühl HS, Lizano E, Arandjelovic M, Marques-Bonet T. 2022. Population dynamics and genetic connectivity in recent chimpanzee history. Cell Genomics, 2(6):100133. DOI:10.1016/j.xgen.2022.100133

Ferrandez-Peral L, Zhan X, Alvarez-Estape M, Chiva C, Esteller-Cucala P, Garcia-Perez R, Julia E, Lizano E, Fornas O, Sabido E, Li Q, Marques-Bonet T, Juan D, Zhang G. 2022. Transcriptome innovations in primates revealed by single-molecule long-read sequencing. Genome Research, 32(8):1448-1462. DOI:10.1101/gr.276395.121

Alvarez-Estape M, Fontsere C, Serres-Armero A, Kuderna LFK, Dobrynin P, Guidara H, Pukazhenthi BS, Koepfli KP, Marques-Bonet T, Moreno E, Lizano E. 2022. Insights from the rescue and breeding management of Cuvier’s gazelle (Gazella cuvieri) through whole‐genome sequencing. Evolutionary Applications, 15(3):351-364. DOI:10.1111/eva.13336

White AE, de-Dios T, Carrión P, Bonora GL, Llovera L, Cilli E, Lizano E, Khabdulina MK, Tleugabulov DT, Olalde I, Marquès-Bonet T, Balloux F, Pettener D, van Dorp L, Luiselli D, Lalueza-Fox C. 2021. Genomic Analysis of 18th-Century Kazakh Individuals and Their Oral Microbiome. Biology, 10(12):1324. DOI:10.3390/biology10121324

Westbury MV, Barnett R, Sandoval-Velasco M, Gowe G, Vieira FG, de Manuel M, Hansen AJ, Yamaguch N, Werdelin L, Marques-Bonet T, Gilbert MTP, Lorenzen ED. 2021. A genomic exploration of the early evolution of extant cats and their sabre-toothed relatives. Open Research Europe, 1:25. DOI:10.12688/openreseurope.13104.1

Wang Y, Bae T, Thorpe J, Sherman MA, Jones AG, Cho S, Daily K, Dou Y, Ganz J, Galor A, Lobon I, Pattni R, Rosenbluh C, Tomasi S, Tomasini L, Yang X, Zhou B, Akbarian S, Ball LL, Bizzotto S, Emery SB, Doan R, Fasching L, Jang Y, Juan D, Lizano E, Luquette LJ, Moldovan JB, Narurkar R, Oetjens MT, Rodin RE, Sekar S, Shin JH, Soriano E, Straub RE, Zhou W, Chess A, Gleeson JG, Marquès-Bonet T, Park PJ, Peters MA, Pevsner J, Walsh CA, Weinberger DR; Brain Somatic Mosaicism Network, Vaccarino FM, Moran JV, Urban AE, Kidd JM, Mills RE, Abyzov A. 2021. Comprehensive identification of somatic nucleotide variants in human brain tissue. Genome Biology, 22(1): 1–32. DOI: 10.1186/s13059-021-02285-3

Solís-Moruno M, Mensa-Vilaró A, Batlle-Masó L, Lobón I, Bonet N, Marquès-Bonet T, Aróstegui JI, Casals F. 2021. Assessment of the gene mosaicism burden in blood and its implications for immune disorders. Scientific Reports, 11(1):12940. DOI:10.1038/s41598-021-92381-y

Serres-Armero A, Davis BW, Povolotskaya IS, Morcillo-suarez C, Plassais J, Juan D, Ostrander EA, Marques-Bonet T. 2021. Copy number variation underlies complex phenotypes in domestic dog breeds and other canids. Genome Research, 31(5): 762–774. DOI: 10.1101/gr.266049.120.762

Sánchez-Barreiro F, Gopalakrishnan S, Ramos-Madrigal J, Westbury MV, de Manuel M, Margaryan A, Ciucani MM, Vieira FG, Patramanis Y, Kalthoff DC, Timmons Z, Sicheritz-Pontén T, Dalén L, Ryder OA, Zhang G, Marquès-Bonet T, Moodley Y, Gilbert MTP. 2021. Historical population declines prompted significant genomic erosion in the northern and southern white rhinoceros ( Ceratotherium simum ). Molecular Ecology, 10(23):6355-6369. DOI:10.1111/mec.16043

Rhie A, McCarthy SA, Fedrigo O, Damas J, Formenti G, Koren S, Uliano-Silva M, Chow W, Fungtammasan A, Kim J, Lee C, Ko BJ, Chaisson M, Gedman GL, Cantin LJ, Thibaud-Nissen F, Haggerty L, Bista I, Smith M, Haase B, Mountcastle J, Winkler S, Paez S, Howard J, Vernes SC, Lama TM, Grutzner F, Warren WC, Balakrishnan CN, Burt D, George JM, Biegler MT, Iorns D, Digby A, Eason D, Robertson B, Edwards T, Wilkinson M, Turner G, Meyer A, Kautt AF, Franchini P, Detrich HW 3rd, Svardal H, Wagner M, Naylor GJP, Pippel M, Malinsky M, Mooney M, Simbirsky M, Hannigan BT, Pesout T, Houck M, Misuraca A, Kingan SB, Hall R, Kronenberg Z, Sović I, Dunn C, Ning Z, Hastie A, Lee J, Selvaraj S, Green RE, Putnam NH, Gut I, Ghurye J, Garrison E, Sims Y, Collins J, Pelan S, Torrance J, Tracey A, Wood J, Dagnew RE, Guan D, London SE, Clayton DF, Mello CV, Friedrich SR, Lovell PV, Osipova E, Al-Ajli FO, Secomandi S, Kim H, Theofanopoulou C, Hiller M, Zhou Y, Harris RS, Makova KD, Medvedev P, Hoffman J, Masterson P, Clark K, Martin F, Howe K, Flicek P, Walenz BP, Kwak W, Clawson H, Diekhans M, Nassar L, Paten B, Kraus RHS, Crawford AJ, Gilbert MTP, Zhang G, Venkatesh B, Murphy RW, Koepfli KP, Shapiro B, Johnson WE, Di Palma F, Marques-Bonet T, Teeling EC, Warnow T, Graves JM, Ryder OA, Haussler D, O'Brien SJ, Korlach J, Lewin HA, Howe K, Myers EW, Durbin R, Phillippy AM, Jarvis ED. 2021.Towards complete and error-free genome assemblies of all vertebrate species. Nature, 592(7856):737-746. DOI: 10.1038/s41586-021-03451-0.

Renom P, de-Dios T, Civit S, Llovera L, Sánchez-Gracia A, Lizano E, Rando JC, Marquès-Bonet T, Kergoat GJ, Casanovas-Vilar I, Lalueza-Fox C. 2021. Genetic data from the extinct giant rat from Tenerife (Canary Islands) points to a recent divergence from mainland relatives. Biology Letters, 17(12):0-5. DOI:10.1098/rsbl.2021.0533

Orkin JD, Montague MJ, Tejada-Martinez D, de Manuel M, Del Campo J, Cheves Hernandez S, Di Fiore A, Fontsere C, Hodgson JA, Janiak MC, Kuderna LFK, Lizano E, Martin MP, Niimura Y, Perry GH, Valverde CS, Tang J, Warren WC, de Magalhães JP, Kawamura S, Marquès-Bonet T, Krawetz R, Melin AD. 2021. The genomics of ecological flexibility, large brains, and long lives in capuchin monkeys revealed with fecalFACS. Proceedings of the National Academy of Sciences of the United States of America, 118(7). DOI: 10.1073/pnas.2010632118. 

Orkin JD, Kuderna LFK, Marques-Bonet T. 2021. The Diversity of Primates: From Biomedicine to Conservation Genomics. Annual Review of Animal Biosciences, 9:103-124. DOI:10.1146/annurev-animal-061220-023138

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

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