Evolutionary Genomics Lab
Life as we see it in our planet today has been shaped by many different biological processes, particularly natural selection, during billions of years. These processes leave a signature in our genomes in the form of differences between species, or between individuals of the same species. Interrogating these patterns of genome diversity we can infer what are the forces that affect living organisms, how and when they act and how do they affect such various things as biodiversity, human emotions or the differential susceptibility of different persons to certain diseases. All this knowledge empowers us to control our future but, above all, it is very fun to obtain.
Currently, the main research goals of the group focus on to elucidating how evolution, and particularly natural selection, has shaped genome and phenotype diversity in our lineage. To this end, we combine experiments, models and data analysis. Some specific research lines are as follows:
Chromosomal evolution and speciation
We study how large chromosomal rearrangements affect many aspects of genome structure and evolution, including how they may drive the generation of new species.
Segmental duplications and copy-number variation in primates
The genomes of humans and other primates show an enrichment in Segmental Duplications (SDs) with high sequence identity, plus they present may Copy-Number Variants (CNVs), large genome fragments of which different individuals present different copies. SDs and CNVs are fundamental for the creation of novel genes and may have been key in the evolution of our lineage. We study not only the frequencies and genome locations of these variants, but also the molecular evolution of their sequence content.
Detecting the genomic signature of natural selection
We try to detect the signature of adaptive changes out of single-copy protein-coding regions. We focus in how natural selection may have shaped variability patterns in introns and regulatory regions of genes.
Human disease and its evolutionary implications
We study world-wide patterns of disease susceptibility distribution to ascertain how these may have been influenced by recent human evolution. In addition, we investigate the possible origins of Multiple Sclerosis and its possible relationship with very recent natural selection events in humans.
Genoeconomics
Complex human traits that are exclusive of our lineage are the basis of our societies and have huge socio-economic impact. We deploy the latest tools of genomics for the dissection of human economic traits.
Lab website: Evolutionary Genomics Lab
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
Rodríguez JA, Marigorta UM, Hughes DA, Spataro N, Bosch E, Navarro A. 2017. Antagonistic pleiotropy and mutation accumulation influence human senescence and disease. Nature Ecology and Evolution, 1(3):1-5. DOI:10.1038/s41559-016-0055
Ravinet M, Faria R, Butlin RK, Galindo J, Bierne N, Rafajlović M, Noor MAF, Mehlig B, Westram AM. 2017. Interpreting the genomic landscape of speciation: a road map for finding barriers to gene flow. Journal of Evolutionary Biology, 30(8):1450-1477. DOI:10.1111/jeb.13047
Muntané G.; Santpere G.; Verendeev A.; Seeley W.W.; Jacobs B.; Hopkins W.D.; Navarro A.; Sherwood C.C. 2017. Erratum to: Interhemispheric gene expression differences in the cerebral cortex of humans and macaque monkeys (Brain Structure and Function, (2017), 222, 7, (3241-3254), 10.1007/s00429-017-1401-7). Brain Structure and Function, 227(7):3367-3368
Muntané G, Santpere G, Verendeev A, Seeley WW, Jacobs B, Hopkins WD, Navarro A, Sherwood CC. 2017. Interhemispheric gene expression differences in the cerebral cortex of humans and macaque monkeys. Brain Structure and Function, 222(7):1-14. DOI:10.1007/s00429-017-1401-7
Martínez H, Barrachina S, Castillo M, Quintana-Ortí ES, Rambla De Argila J, Farré X, Navarro A. 2017. Accelerating FaST-LMM for Epistasis Tests. Nonlinear Digital Filters. Springer US, vol 10393:548-557. DOI:10.1007/978-3-319-65482-9_40
Marques JP, Sotelo G, Larsson T, Johannesson K, Panova M, Faria R. 2017. Comparative mitogenomic analysis of three species of periwinkles: Littorina fabalis, L. obtusata and L. saxatilis. Marine Genomics, 32:41-47. DOI:10.1016/j.margen.2016.10.006
Mandage R, Telford M, Rodríguez JA, Farré X, Layouni H, Marigorta UM, Cundiff C, Heredia-Genestar JM, Navarro A, Santpere G. 2017. Genetic factors affecting EBV copy number in lymphoblastoid cell lines derived from the 1000 Genome Project samples. PLoS ONE, 12(6):1-19. DOI:10.1371/journal.pone.0179446
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
Kolora SR, Faria R, Weigert A, Schaffer S, Grimm A, Henle K, Sahyoun AH, Stadler PF, Nowick K, Bleidorn C, Schlegel M. The complete mitochondrial genome of Lacerta bilineata and comparison with its closely related congener L. Viridis. Mitochondrial DNA Part A, 28(1):116-118. DOI:10.3109/19401736.2015.1111349
Gouy A, Daub JT, Excoffier L. 2017. Detecting gene subnetworks under selection in biological pathways. Nucleic Acids Research, 45(16):e149-e149. DOI:10.1093/nar/gkx626
Gaubert P, Patel RP, Veron G, Goodman SM, Willsch M, Vasconcelos R, Lourenço A, Sigaud M, Justy F, Joshi BD, Fickel J, Wilting A. 2017. Phylogeography of the small indian civet and origin of introductions to western indian ocean islands. Journal of Heredity, 108(3):270-279. DOI:10.1093/jhered/esw085
Fernández C, Bellosillo B, Ferraro M, Seoane A, Sánchez-González B, Pairet S, Pons A, Barranco L, Vela MC, Gimeno E, Colomo L, Besses C, Navarro A, Salar A. 2017. MicroRNAs 142-3p, miR-155 and miR-203 are deregulated in gastric MALT lymphomas compared to chronic gastritis. Cancer Genomics and Proteomics, 14(1):75-82. DOI:10.21873/cgp.20020
Alanis-Lobato G, Andrade-Navarro MA, Schaefer MH. 2017. HIPPIE v2.0: Enhancing meaningfulness and reliability of protein-protein interaction networks. Nucleic Acids Research, 45(D1):D408-D414. DOI:10.1093/nar/gkw985
Stange J, Dickhaus T, Navarro A, Schunk D. 2016. Multiplicity- and dependency-adjusted p-values for control of the family-wise error rate. Statistics and Probability Letters, 111:32-40. DOI:10.1016/j.spl.2016.01.005
Santpere G, Lopez-Valenzuela M, Petit-Marty N, Navarro A, Espinosa-Parrilla Y. 2016. Differences in molecular evolutionary rates among microRNAs in the human and chimpanzee genomes. BMC Genomics, 17(1):1-12. DOI:10.1186/s12864-016-2863-3
Pinho C, Faria R. 2016. Magadi tilapia ecological specialization: Filling the early gap in the speciation continuum. Molecular Ecology, 25(7):1420-1422. DOI:10.1111/mec.13598
Mieth B, Kloft M, Rodríguez JA, Sonnenburg S, Vobruba R, Morcillo-Suárez C, Farré X, Marigorta UM, Fehr E, Dickhaus T, Blanchard G, Schunk D, Navarro A, Müller KR. 2016. Combining multiple hypothesis testing with machine learning increases the statistical power of genome-wide association studies. Scientific Reports, 6(November):1-14. DOI:10.1038/srep36671
Lobon I, Tucci S, de Manuel M, Ghirotto S, Benazzo A, Prado-Martinez J, Lorente-Galdos B, Nam K, Dabad M, Hernandez-Rodriguez J, Comas D, Navarro A, Schierup MH, Andres AM, Barbujani G, Hvilsom C, Marques-Bonet T. 2016. Demographic history of the genus Pan inferred from whole mitochondrial genome reconstructions. Genome Biology and Evolution, 8(6):2020-2030. DOI:10.1093/gbe/evw124
Hartasánchez DA, Brasó-Vives M, Fuentes-Díaz J, Vallès-Codina O, Navarro A. 2016. SeDuS: Segmental duplication simulator. Bioinformatics, 32(1):148-150. DOI:10.1093/bioinformatics/btv481
Gallego A, Melé M, Balcells I, García-Ramallo E, Torruella-Loran I, Fernández-Bellon H, Abelló T, Kondova I, Bontrop R, Hvilsom C, Navarro A, Marquès-Bonet T, Espinosa-Parrilla Y. 2016. Functional Implications of Human-Specific Changes in Great Ape microRNAs. PLoS ONE, 11(4):1-20. DOI:10.1371/journal.pone.0154194
Dopazo J, Amadoz A, Bleda M, Garcia-Alonso L, Alemán A, García-García F, Rodriguez JA, Daub JT, Muntané G, Rueda A, Vela-Boza A, López-Domingo FJ, Florido JP, Arce P, Ruiz-Ferrer M, Méndez-Vidal C, Arnold TE, Spleiss O, Alvarez-Tejado M, Navarro A, Bhattacharya SS, Borrego S, Santoyo-López J, Antiñolo G. 2016. 267 Spanish Exomes Reveal Population-Specific Differences in Disease-Related Genetic Variation. Molecular Biology and Evolution, 33(5):1205-1218. DOI:10.1093/molbev/msw005
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 LF, 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. 2016. Chimpanzee genomic diversity reveals ancient admixture with bonobos. Science, 354(6311):477-481. DOI:10.1126/science.aag2602
Corrales E, Navarro A, Cuenca P, Campos D. 2016. Candidate gene study reveals DRD1 and DRD2 as putative interacting risk factors for youth depression. Psychiatry Research, 244:71-77. DOI:10.1016/j.psychres.2016.07.032
Chavan R, Shinde P, Girkar K, Madage R, Chowdhary A. 2016. Assessment of Anti-Influenza activity and hemagglutination inhibition of Plumbago indica and Allium sativum extracts. Pharmacognosy Research, 8(2):105. DOI:10.4103/0974-8490.172562
Carvalho J, Sotelo G, Galindo J, Faria R. 2016. Genetic characterization of flat periwinkles (Littorinidae) from the Iberian Peninsula reveals interspecific hybridization and different degrees of differentiation. Biological Journal of the Linnean Society, 118(3):503-519. DOI:10.1111/bij.12762
Cagan A, Theunert C, Laayouni H, Santpere G, Pybus M, Casals F, Prüfer K, Navarro A, Marques-Bonet T, Bertranpetit J, Andrés AM. 2016. Natural selection in the great apes. Molecular Biology and Evolution, 33(12):3268-3283. DOI:10.1093/molbev/msw215
Buzdugan L, Kalisch M, Navarro A, Schunk D, Fehr E, Bühlmann P. 2016. Assessing statistical significance in multivariable genome wide association analysis. Bioinformatics, 32(13):1990-2000. DOI:10.1093/bioinformatics/btw128
Santpere G, Carnero-Montoro E, Petit N, Serra F, Hvilsom C, Rambla J, Heredia-Genestar JM, Halligan DL, Dopazo H, Navarro A, Bosch E. 2015. Analysis of five gene sets in chimpanzees suggests decoupling between the action of selection on protein-coding and on noncoding elements. Genome Biology and Evolution, 7(6):1490-1505. DOI:10.1093/gbe/evv082
Montes A, Roca G, Sabate S, Lao JI, Navarro A, Cantillo J, Canet J; GENDOLCAT Study Group. 2015. Genetic and Clinical Factors Associated with Chronic Postsurgical Pain after Hernia Repair, Hysterectomy, and Thoracotomy: A Two-year Multicenter Cohort Study. Anesthesiology, 122(5):1123-1141. DOI:10.1097/ALN.0000000000000611
Lappalainen I, Almeida-King J, Kumanduri V, Senf A, Spalding JD, Ur-Rehman S, Saunders G, Kandasamy J, Caccamo M, Leinonen R, Vaughan B, Laurent T, Rowland F, Marin-Garcia P, Barker J, Jokinen P, Torres AC, de Argila JR, Llobet OM, Medina I, Puy MS, Alberich M, de la Torre S, Navarro A, Paschall J, Flicek P. 2015. The European Genome-phenome Archive of human data consented for biomedical research. Nature Genetics, 47(7):692-695. DOI:10.1038/ng.3312
Hughes DA, Kircher M, He Z, Guo S, Fairbrother GL, Moreno CS, Khaitovich P, Stoneking M. 2015. Evaluating intra- and inter-individual variation in the human placental transcriptome. Genome Biology, 16(1):1-18. DOI:10.1186/s13059-015-0627-z
Bustamante MF, Morcillo-Suárez C, Malhotra S, Rio J, Leyva L, Fernández O, Zettl UK, Killestein J, Brassat D, García-Merino JA, Sánchez AJ, Urcelay E, Alvarez-Lafuente R, Villar LM, Alvarez-Cermeño JC, Farré X, Lechner-Scott J, Vandenbroeck K, Rodríguez-Antigüedad A, Drulovic JS, Martinelli Boneschi F, Chan A, Oksenberg J, Navarro A, Montalban X, Comabella M. 2015. Pharmacogenomic study in patients with multiple sclerosis Responders and nonresponders to IFN-β. Neurology: Neuroimmunology and NeuroInflammation, 2(5):e154. DOI:10.1212/NXI.0000000000000154
Sotelo G, Andree KB, López MA, Alexandrino P, Gisbert E. 2014. The puzzling demographic history and genetic differentiation of the twaite shad (Alosa fallax) in the Ebro River. Conservation Genetics, 15(5):1037-1052. DOI:10.1007/s10592-014-0597-9
Santpere G, Darre F, Blanco S, Alcami A, Villoslada P, Mar Albà M, Navarro A. 2014. Genome-wide analysis of wild-type epstein-barr virus genomes derived from healthy individuals of the 1000 genomes project. Genome Biology and Evolution, 6(4):846-860. DOI:10.1093/gbe/evu054
Rodríguez JA, Marigorta UM, Navarro A. 2014. Integrating genomics into evolutionary medicine. Current Opinion in Genetics and Development, 29:97-102. DOI:10.1016/j.gde.2014.08.009
Pineda S, Milne RL, Calle ML, Rothman N, López de Maturana E, Herranz J, Kogevinas M, Chanock SJ, Tardón A, Márquez M, Guey LT, García-Closas M, Lloreta J, Baum E, González-Neira A, Carrato A, Navarro A, Silverman DT, Real FX, Malats N. 2014. Genetic variation in the TP53 pathway and bladder cancer risk. A comprehensive analysis. PLoS ONE, 9(5):1-8. DOI:10.1371/journal.pone.0089952
Olalde I, Sánchez-Quinto F, Datta D, Marigorta UM, Chiang CW, Rodríguez JA, Fernández-Callejo M, González I, Montfort M, Matas-Lalueza L, Civit S, Luiselli D, Charlier P, Pettener D, Ramírez O, Navarro A, Himmelbauer H, Marquès-Bonet T, Lalueza-Fox C. 2014. Genomic analysis of the blood attributed to Louis XVI (1754-1793), king of France. Scientific Reports, 4:1-7. DOI:10.1038/srep04666
Olalde I, Allentoft ME, Sánchez-Quinto F, Santpere G, Chiang CW, DeGiorgio M, Prado-Martinez J, Rodríguez JA, Rasmussen S, Quilez J, Ramírez O, Marigorta UM, Fernández-Callejo M, Prada ME, Encinas JM, Nielsen R, Netea MG, Novembre J, Sturm RA, Sabeti P, Marquès-Bonet T, Navarro A, Willerslev E, Lalueza-Fox C. 2014. Derived immune and ancestral pigmentation alleles in a 7,000-year-old Mesolithic European. Nature, 507(7491):225-228. DOI:10.1038/nature12960
Navarro A, Faria R. 2014. Pool and conquer: New tricks for (c)old problems. Molecular Ecology, 23(7):1653-1655. DOI:10.1111/mec.12685
Hartasánchez DA, Vallès-Codina O, Brasó-Vives M, Navarro A. 2014. Interplay of interlocus gene conversion and crossover in segmental duplications under a neutral scenario. G3: Genes, Genomes, Genetics, 4(8):1479-1489. DOI:10.1534/g3.114.012435
Faria R, Renaut S, Galindo J, Pinho C, Melo-Ferreira J, Melo M, Jones F, Salzburger W, Schluter D, Butlin R. 2014. Advances in Ecological Speciation: An integrative approach. Molecular Ecology, 23(3):513-521. DOI:10.1111/mec.12616
Serrano-Munuera C, Corral-Juan M, Stevanin G, San Nicolás H, Roig C, Corral J, Campos B, de Jorge L, Morcillo-Suárez C, Navarro A, Forlani S, Durr A, Kulisevsky J, Brice A, Sánchez I, Volpini V, Matilla-Dueñas A. 2013. New subtype of spinocerebellar ataxia with altered vertical eye movements mapping to chromosome 1p32. JAMA Neurology, 70(6):764-771. DOI:10.1001/jamaneurol.2013.2311
Segarra G, Santpere G, Elena G, Trillas I. 2013. Enhanced Botrytis cinerea Resistance of Arabidopsis Plants Grown in Compost May Be Explained by Increased Expression of Defense-Related Genes, as Revealed by Microarray Analysis. PLoS ONE, 8(2). DOI:10.1371/journal.pone.0056075
Prado-Martinez J, Sudmant PH, Kidd JM, Li H, Kelley JL, Lorente-Galdos B, Veeramah KR, Woerner AE, O'Connor TD, Santpere G, Cagan A, Theunert C, Casals F, Laayouni H, Munch K, Hobolth A, Halager AE, Malig M, Hernandez-Rodriguez J, Hernando-Herraez I, Prüfer K, Pybus M, Johnstone L, Lachmann M, Alkan C, Twigg D, Petit N, Baker C, Hormozdiari F, Fernandez-Callejo M, Dabad M, Wilson ML, Stevison L, Camprubí C, Carvalho T, Ruiz-Herrera A, Vives L, Mele M, Abello T, Kondova I, Bontrop RE, Pusey A, Lankester F, Kiyang JA, Bergl RA, Lonsdorf E, Myers S, Ventura M, Gagneux P, Comas D, Siegismund H, Blanc J, Agueda-Calpena L, Gut M, Fulton L, Tishkoff SA, Mullikin JC, Wilson RK, Gut IG, Gonder MK, Ryder OA, Hahn BH, Navarro A, Akey JM, Bertranpetit J, Reich D, Mailund T, Schierup MH, Hvilsom C, Andrés AM, Wall JD, Bustamante CD, Hammer MF, Eichler EE, Marques-Bonet T. 2013. Great ape genetic diversity and population history. Nature, 499(7459):471-475. DOI:10.1038/nature12228
Prado-Martinez J, Hernando-Herraez I, Lorente-Galdos B, Dabad M, Ramirez O, Baeza-Delgado C, Morcillo-Suarez C, Alkan C, Hormozdiari F, Raineri E, Estellé J, Fernandez-Callejo M, Valles M, Ritscher L, Schöneberg T, de la Calle-Mustienes E, Casillas S, Rubio-Acero R, Melé M, Engelken J, Caceres M, Gomez-Skarmeta JL, Gut M, Bertranpetit J, Gut IG, Abello T, Eichler EE, Mingarro I, Lalueza-Fox C, Navarro A, Marques-Bonet T. 2013. The genome sequencing of an albino Western lowland gorilla reveals inbreeding in the wild. BMC Genomics, 14(1). DOI:10.1186/1471-2164-14-363
Marigorta UM, Navarro A. 2013. High Trans-ethnic Replicability of GWAS Results Implies Common Causal Variants. PLoS Genetics, 9(6). DOI:10.1371/journal.pgen.1003566
Malhotra S, Morcillo-Suárez C, Nurtdinov R, Rio J, Sarro E, Moreno M, Castilló J, Navarro A, Montalban X, Comabella M. 2013. Roles of the ubiquitin peptidase USP18 in multiple sclerosis and the response to interferon-β treatment. European Journal of Neurology, 20(10):1390-1397. DOI:10.1111/ene.12193
Lorente-Galdos B, Bleyhl J, Santpere G, Vives L, Ramírez O, Hernandez J, Anglada R, Cooper GM, Navarro A, Eichler EE, Marques-Bonet T. 2013. Accelerated exon evolution within primate segmental duplications. Genome Biology, 14(1):R9. DOI: 10.1186/gb-2013-14-1-r9
Hernando-Herraez I, Prado-Martinez J, Garg P, Fernandez-Callejo M, Heyn H, Hvilsom C, Navarro A, Esteller M, Sharp AJ, Marques-Bonet T. 2013. Dynamics of DNA Methylation in Recent Human and Great Ape Evolution. PLoS Genetics, 9(9). DOI:10.1371/journal.pgen.1003763