Publications

 

 

• Human-specific gene expansions contribute to brain evolution.
  Soto DC, Uribe-Salazar JM, Kaya, Valdarrago R, Sekar A, Haghani NK, Hino K, La G, Mariano NAF, Ingamells C, Baraban A, Jamal Z, Turner TN, Green ED , Simo S, Quon G, Andrés AM, Dennis MY.
  Cell 188, 1–21, September 18, 2025. https://doi.org/10.1016/j.cell.2025.06.037

 

• Media article. English: Chimpanzee genes have changed over time to suit local conditions – new study. French: Les gènes des chimpanzés ont évolué pour s’adapter aux conditions locales, selon une nouvelle étude.
  Ostridge H,  Andrés AM, Arandjelovic M.
  The Conversation, March 2025.
  

 

• Local Genetic Adaptation to Habitat in Wild Chimpanzees. Free-access reprint HERE.
  Summary translations to French, Kiswahili/Swahili, Italian and Spanish here.
  Ostridge H, Fontsere C, Lizano E, Soto DC, Schmidt JM, Saxena V, Alvarez-Estape M, Barratt CD, Gratton P, Bocksberger G, Lester JD, Dieguez P,  Agbor A, Angedakin S, Assumang AK, Bailey E, Barubiyo D, Bessone M, Brazzola G, Chancellor R, Cohen H, Coupland C, Danquah E, Deschner T, Dotras L, Dupain J, Ebot Egbe V, Granjon AC, Head J, Hedwig D,  Hermans V,  Hernandez-Aguilar RA, Jeffery KJ, Jones S, Junker J, Kadam P, Kaiser M, Kalan AK, Kambere M, Kienast I, Kujirakwinja D, Langergraber KE, Lapuente J,  Larson B, Laudisoit A, Lee KC, Llana M, Maretti G, Martín R, Meier A, Morgan D, Neil E, Nicholl S, Nixon S, Normand E, Orbell C, Ormsby LJ, Orume R, Pacheco L, Preece J, Regnaut S, Robbins MM, Rundus A, Sanz C, Sciaky L, Sommer V, Stewart FA, Tagg N, Tédonzong LR, van Schijndel J, Vendras E,  Wessling EG, Willie J, Wittig RM, Yuh YG, Yurkiw K, Vigilant L, Piel A, Boesch C, Kühl HS, Dennis MY, Marques-Bonet T, Arandjelovic A, Andrés AM.
  Science 2025, 10 Jan 2025; 387(6730). doi: 10.1126/science.adn7954

 

• Deep Genetic Substructure within Bonobos.
  Summary translations to French, Spanish, German, Korean and Spanish here.
  Han S*, de Filippo C*, Parra G, Meneu JR, Laurent R, Frandsen P, Hvilsom C, Gronau I, Marques-Bonet T, Kuhlwilm M, Andrés AM.
  Current Biology 2024, 34:1-8. doi: 10.1016/j.cub.2024.09.043

 

• Ancient Loss of Catalytic Selenocysteine Spurred Convergent Adaptation in a Mammalian Oxidoreductase.
  Rees J, Sarangi G, Cheng Q, Floor M, Andrés AM, Oliva Miguel B, Villà-Freixa J, Arnér ESJ, Castellano S.
  Genome Biol Evol. 2024 Mar 2;16(3):evae041. doi: 10.1093/gbe/evae041.

 

• Ghost admixture in eastern gorillas.
  Pawar H, Cuadros S, de Manuel M, van der Valk T, Lobon I, Alvarez-Estape M, Haber M, Dolgova O, Han S, Ayub Q, Bautista R, Kelley JL, Cornejo OE, Lao O, Andrés AM, Guschanski K, Ssebide B, Cranfield M, Tyler-Smith K, Xue Y, Prado-Martinez J, Marques-Bonet T, Kuhlwilm M.
  Nature Ecology and Evolution 2023. 7: 1503–1514. https://doi.org/10.1101/2022.12.19.521012

 

• Inferring balancing selection from genome-scale data.
  Bitarello B, Brandt DYC, Meyer D and Andrés AM.
  Genome Biol Evol. 2023. 15(3):evad032. doi: 10.1093/gbe/evad032.

 

• Genetic adaptations to SIV across chimpanzee populations.
  Pawar H, Ostridge HJ, Schmidt JM, Andrés AM.
  PLoS Genet. 2022. 18(8): e1010337. https://doi.org/10.1371/journal.pgen.1010337

 

• Population dynamics and genetic connectivity in recent chimpanzee history.
  Fontserre C, … many authors … , Andrés AM, Hughes D, Kühl H, Lizano E, Arandjelovic M, Marques-Bonet T.
  Cell Genomics 2022 June 8; 6:100133. https://doi.org/10.1016/j.xgen.2022.100133

 

• Inferring human evolutionary history. Free-access reprint HERE.
  Rees J and Andrés AM.
  Science 2022 Feb 25;375(6583):817-818. doi: 10.1126/science.abo0498.

 

• The Genomics of Human Local Adaptation.
  Rees JS, Castellano S, Andrés AM.
  Trends Genet. 2020 Jun;36(6):415-428. doi: 10.1016/j.tig.2020.03.006.

 

• Identification of Structural Variation in Chimpanzees Using Optical Mapping and Nanopore Sequencing.
  Soto DC, Shew C, Mastoras M, Schmidt JM, Sahasrabudhe R, Kaya G, Andrés AM, Dennis MY.
  Genes (Basel). 2020 Mar 4;11(3):276. doi: 10.3390/genes11030276.

 

• The impact of genetic adaptation on chimpanzee subspecies differentiation.
  Schmidt JM, de Manuel M, Marques-Bonet T, Castellano S, Andrés AM.
  PLoS Genet. 2019 Nov 25;15(11):e1008485. doi: 10.1371/journal.pgen.1008485.

 

• Evolutionary and functional impact of common polymorphic inversions in the human genome.
  Giner-Delgado C, Villatoro S, Lerga-Jaso J, Gayà-Vidal M, Oliva M, Castellano D, Pantano L, Bitarello BD, Izquierdo D, Noguera I, Olalde I, Delprat A, Blancher A, Lalueza-Fox C, Esko T, O’Reilly PF, Andrés AM, Ferretti L, Puig M, Cáceres M.
  Nat Commun. 2019 Sep 17;10(1):4222. doi: 10.1038/s41467-019-12173-x.

 

• Genetic Variation in Pan Species Is Shaped by Demographic History and Harbors Lineage-Specific Functions. 
  Han S, Andrés AM, Marques-Bonet T, Kuhlwilm M.
  Genome Biol Evol. 2019 Apr 1;11(4):1178-1191. doi: 10.1093/gbe/evz047.

 

• Immune Gene Diversity in Archaic and Present-day Humans.
  Reher D, Key FM, Andrés AM, Kelso J.
  Genome Biol Evol. 2019 Jan 1;11(1):232-241. doi: 10.1093/gbe/evy271.

 

• Human local adaptation of the TRPM8 cold receptor along a latitudinal cline.
  Key FM, Abdul-Aziz MA, Mundry R, Peter BM, Sekar A, D’Amato M, Dennis MY, Schmidt JM, Andrés AM.
  PLoS Genet. 2018 May 3;14(5):e1007298. doi: 10.1371/journal.pgen.1007298.

 

• Signatures of Long-Term Balancing Selection in Human Genomes.
  Bitarello BD, de Filippo C, Teixeira JC, Schmidt JM, Kleinert P, Meyer D, Andrés AM.
  Genome Biol Evol. 2018 Mar 1;10(3):939-955. doi: 10.1093/gbe/evy054.

 

• A high-coverage Neandertal genome from Vindija Cave in Croatia.
  Prüfer K, de Filippo C, Grote S, Mafessoni F, 28 authors, Andrés AM, Kelso J, Meyer M, Pääbo S.
  Science, 358:655-658 (2017).

 

• Natural selection in the great apes.
  Cagan A*, Theunert C*, Laayouni H*, Santpere G*, Pybus M, Casals F, Prüfer K, Navarro A, Marques-Bonet T, Bertranpetit J^#, Andrés AM^#.
  Molecular Biology and Evolution, 33:268-283 (2016).

 

• Chimpanzee genomic diversity reveals ancient admixture with bonobos.
  de Manuel M*, Kuhlwilm M*, Frandsen P*, 25 authors, Andrés AM, Siegismund HR, Scally A, Excoffier L, Tyler-Smith C, Castellano S, Xue Y, Hvilsom C^#, Marques-Bonet T^#.
  Science, 354:477-481 (2016).

 

• Human adaptation and population differentiation in the light of ancient genomes.
  Key FM, Fu Q, Romaine F, Lachmann M, Andrés AM.
  Nature Communications 7:10775-86 (2016).

 

• Recent selective pressure changes in human genes previously affected by balancing selection.
  de Filippo C, Key FM, Ghirotto S, Benazzo A, Meneu JR, Weihmann A, NISC Comparative Sequence Program, Parra G, Green ED, Andrés AM.
  Molecular Biology and Evolution, 33: 1435-1447 (2016).

 

• Ancient gene flow from early modern humans into Eastern Neanderthals.
  Kuhlwilm M*, Gronau I*, Hubisz JM, de Filippo C, Prado J, Kircher M, Fu Q, Lalueza-Fox C, de la Rasilla M, Rosas A, Rudan P, Brajkovic D, Kucan Z, Gusic I, Marques-Bonet T, Andrés AM, Viola B, Meyer M, Pääbo S, Siepel A and Castellano S.
  Nature 530: 429–433 (2016).

 

• Adaptive variation in human toll-like receptors is contributed by Neanderthal- and Denisova-like introgressed haplotypes.
  Danemann M, Andrés AM, Kelso J.
  The American Journal of Human Genetics 98: 22–33 (2016).

 

• Demographic History of the Genus Pan Inferred from Whole Mitochondrial Genome Reconstructions.
  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, Andrés AM, Barbujani G, Hvilsom C, Marques-Bonet T.
  Genome Biology and Evolution 8:2020-2030 (2016).

 

• Long-term balancing selection in LAD1 maintains a missense trans-species polymorphism in humans, chimpanzees and bonobos.
  Teixeira J*, Filippo C*, Weihmann A, Meneu JR, Racimo F, Dannemann M, Nickel B, Fischer A, Halbwax M, Andre C, Atencia R, Meyer M, Parra G, Pääbo S and Andrés AM.
  Molecular Biology and Evolution, 32: 1186-1196 (2015).

 

• Genetic adaptation to levels of dietary selenium in recent human history.
  White L, Romagné F, Erlebach E, Weihmann A, Parra G, Andrés AM, Castellano S.
  Molecular Biology and Evolution 32: 1507-1518 (2015).

 

• Selection on a variant associated with improved viral clearance induced local, adaptive pseudogenization of interferon lambda 4 (IFNL4).
  Key FM, Peter B, Dennis M, Huerta-Sánchez E, Tang W, Prokunina-Olsson L, Nielsen R, Andrés AM.
  PLoS Genetics 10:e1004681 (2014).

 

• Patterns of coding variation in the complete exomes of three Neandertals.
  Castellano S, Parra G, Sánchez-Quinto FA, Racimo F, 22 authors, Meyer M, Kelso J, Andrés AM, Pääbo S.
  Proc Natl Acad Sci USA, 111:6666-71 (2014).

 

• Advantageous diversity maintained by balancing selection in humans.
  Key FM, Teixeira JC, de Filippo C, Andrés AM.
  Curr Opin Genet Dev. 29:45-51 (2014).

 

• Sequence diversity of Pan troglodytes subspecies and the impact of WFDC6 selective constraints in reproductive immunity.
  Ferreira Z, Hurle B, Andrés AM, Kretzschmar W, Mullikin J, Cherukuri P, Cruz P, Gonder MK, Stone A, Tishkoff S, Swanson W, NISC Comparative Sequencing Program, Green E, Clark AG, Seixas S.
  Genome Biology and Evolution, 5:2512-2523 (2013).

 

• Great ape genetic diversity and population history.
  Prado-Martinez J, Sudmant PH, Kidd JM, 66 authors, Andrés AM, Wall JD, Bustamante CD, Hammer MF, Eichler EE, Marques-Bonet T.
  Nature, 499:471-5. (2013).

 

• Reproduction and Immunity-Driven Natural Selection in the Human WFDC Locus.
  Ferreira Z, Seixas S, Andrés AM, Kretzschmar WW, Mullikin JC, Cherukuri PF, Cruz P, Swanson WJ, NISC Comparative Sequencing Program, Clark AG, Green ED and Hurle B.
  Molecular Biology and Evolution 30: 938-950 (2013).

 

• A High-Coverage Genome Sequence from an Archaic Denisovan Individual.
  Meyer M, Kircher M, Gansauge MT, Li H, 24 authors, Andrés AM, Eichler EE, Slatkin M, Reich D, Kelso J, Pääbo S.
  Science 338:222-6 (2012). – Selected, Faculty of 1000 –

 

• The bonobo genome compared with the chimpanzee and human genomes.
  Prüfer K, Munch K, Hellmann I, Akagi K, 33 authors, Schierup MH, Andrés AM, Kelso J, Pääbo S.
  Nature, 486:527-31 (2012).

 

• Balancing selection maintains a form of ERAP2 that undergoes nonsense-mediated decay and affects antigen presentation.
  Andrés AM*, Dennis MY*, Kretzschmar WW, Cannons JL, Lee-Lin SQ, Hurle B; NISC Comparative Sequencing Program, Schwartzberg PL, Williamson SH, Bustamante CD, Nielsen R, Clark AG, Green ED.
  PLoS Genetics, 6:e1001157 (2010).

 

• Targets of balancing selection in the human genome.
  Andrés AM, Hubisz MJ, Indap A, Degenhartl J, Boyco AR, Gutenkunst RN, White T, Green ED, Bustamante CD, Clark AG, and Nielsen R.
  Molecular Biology and Evolution, 26:2755-64 (2009). – Selected, Faculty of 1000 –

 

• Low exchangeability of selenocysteine, the 21^st amino acid, in vertebrate proteins.
  Castellano S*, Andrés AM*, Bosch E, Bayes M, Guigó R, and Clark AG.
  Molecular Biology and Evolution, 26:2031-40 (2009).

 

• Darwinian and demographic forces affecting human protein coding genes.
  Nielsen R, Hubisz MJ, Hellmann I, Torgerson D, Andrés AM, Albrechtsen A, Gutenkunst R, Adams MD, Cargill M, Boyko A, Indap A, Bustamante CD, and Clark AG.
  Genome Research, 19:838-49 (2009). – Selected, Faculty of 1000 –

 

• Heterogenetous rate of protein evolution in serotonin genes.
  Andrés AM, de Hemptinne C, and Bertranpetit J.
  Molecular Biology and Evolution, 24:2707-15 (2007).

 

• Understanding the accuracy of statistical haplotype inference with sequence data of known phase.
  Andrés AM, Clark AG, Shimmin L, Boerwinkle E, Sing CF, and Hixson JE.
  Genetic Epidemiology, 31:659-71 (2007).

 

• The prion protein gene in humans revisited: lessons from a worldwide resequencing study.
  Soldevila M, Andrés AM, Helgason A, Ramírez-Soriano A, Marqués-Bonet T, Sigurdadottir S, Calafell F, Navarro A, Stefánsson K, and Bertranpetit J.
  Genome Research 16:231-9 (2006).

 

• Positive selection in MAOA gene is human exclusive: determination of the putative amino acid change selected in the human lineage.
  Andrés AM, Soldevila M, Navarro A, Kidd KK, Oliva B, and Bertranpetit J.
  Human Genetics 115:377-86 (2004).

 

• Comparative genetics of functional trinucleotide tandem repeats in humans and apes.
  Andrés AM, Soldevila M, Lao O, Volpini V, Saitou N, Jacobs HT, Hayasaka I, Calafell F, and Bertranpetit J.
  Journal of Molecular Evolution 59:329-39 (2004).

 

• Variation in the prion gene in chimpanzees and its implication for prion diseases.
  Soldevila M, Andrés AM, Blancher A, Calafell F, Ordoñnez M, Pumarola M, Oliva B, Aramburu J, and Bertranpetit J.
  Neuroscience Letters 355:157-16 (2004).

 

• A prevalent POLG CAG microsatellite length allele in humans and African great apes.
  Rovio AT, Abel J, Ahola AL, Andrés AM, 29 aditional authors, Jacobs HT.
  Mammalian Genome 15:492-502 (2004).

 

• Comparative analysis of Alu insertion sequences in the APP 5’flanking region in humans and other primates.
  Clarimón J, Andrés AM, Bertranpetit J, and Comas D.
  Journal of Molecular Evolution 58:722-731 (2004).

 

• Prion Susceptibility and Protective Alleles Exhibit Marked Geographic Differences.
  Soldevila M, Calafell F, Andrés AM, Yague J, Helgason A, Stefánsson K, and Bertranpetit J.
  Human Mutation 22:104-5 (2003).

 

• Spatial patterns of cystic fibrosis mutation spectra in European populations.
  Lao O, Andrés AM, Mateu E, Bertranpetit J and Calafell F.
  European Journal of Human Genetics 11:385-94 (2003).

 

• Dynamics of CAG repeat loci revealed by the analysis of their variability.
  Andrés AM, Lao O, Soldevila M, Calafell F, and Bertranpetit J.
  Human Mutation 21:61-70 (2003).

 

• Understanding the dynamics of Spinocerebellar Ataxia 8 (SCA8) locus through a comparative genetic approach in humans and apes.
  Andrés AM, Soldevila M, Saitou N, Volpini V, Calafell F, and Bertranpetit J.
  Neuroscience Letters 336:143-46 (2003).

 

• PKLR – GBA region shows almost complete linkage disequilibrium over 70 kb in a set of worldside populations.
  Mateu E, Pérez-Lezaun A, Martínez-Arias R, Andrés A, Valles M, Bertranpetit J, and Calafell F.
  Human Genetics 110:532-544 (2002).

 

• Sequence variability of a human pseudogene.
  Martínez-Arias R, Calafell R, Mateu E, Comas D, Andrés A, and Bertranpetit J.
  Genome Research 11:1071-1085 (2002).