Genetic Diversity and Selection (Aida Andrés)
(Former group hosted by the Department of Evolutionary Genetics)
The group was a member of the Genetics Department from 2010 to 2017 and is moving to University College London.
Our main interest is to understand the influence that natural selection has played in the evolution of humans and other primates. We are intrigued by how adaptation has shaped the evolution of relevant phenotypes. How has natural selection influenced the acquisition of species-specific traits? What selective forces are responsible for phenotypic diversity within populations? How does past selection affect our present-day phenotypes?
At present, we are actively working on these main research areas:
Balancing selection
Balancing selection maintains advantageous diversity in populations by a variety of mechanisms. In humans it is responsible, for example, for the extreme levels of genetic diversity of the MHC locus, and for the fascinating equilibrium that maintains sickle-cell anemia alleles in malaria-suffering populations due to heterozygotes advantage. In other species, balancing selection maintains diversity that is crucial for sex determination, self-incompatibility, defense against pathogens, or escape from predators. Our goal is to understand the influence of balancing selection in the genome (its prevalence, conservation among populations and species, its most common targets) and to unravel the biological factors behind its signatures (its specific targets, the functional consequences of selected variants, their contribution to phenotypic diversity in populations). For this, we combine genomic approaches with detailed population genetics, computational, and experimental studies, that allow us to go from the genome to the phenotype.
Representative publications
- de Filippo C, Key FM, Ghirotto S, Benazzo A, Meneu JR, Weihmann A; NISC Comparative Sequence Program, Parra G, Green ED, Andrés AM.
Recent selection changes in human genes under long-term balancing selection.
Molecular Biology and Evolution 33: 1435-1447 (2016) [Full text][PDF] - Teixeira JC*, de Filippo C*, Weihmann A, Meneu JR, Racimo F, Dannemann M, Nickel B, Fischer A, Halbwax M, Andre C, Atencia R, Meyer M, Parra G, Paabo S, Andrés AM.
Long-term balancing selection in LAD1 maintains a missense trans-species polymorphism in humans, chimpanzees and bonobos.
Molecular Biology and Evolution 32: 1186-1196 (2015) [Full text][PDF] - 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.
Balancing Selection Maintains a Form of ERAP2 that Undergoes Nonsense-Mediated Decay and Affects Antigen Presentation.
PLoS Genetics 6:e1001157 (2010). [PubMed] [Full text] [PDF] [Supplementary Material] - [see also Cagan et al., MBE 2016 in Comparative Population Genomics section below]
Ancient DNA
Recent technological advances have enabled the production of high-quality genome sequences of several archaic Homo individuals. This provides an unprecedented opportunity to study extinct populations and the ancestors of present-day modern humans. We use these genomes to study ancestral and modern human populations, with particular emphasis on the effects of natural selection in their evolution.
Representative publications
- Kuhlwilm M, Gronau I, Hubisz MJ, de Filippo C, Prado-Martinez J, Kircher M, Fu Q, Burbano HA, Lalueza-Fox C, de la Rasilla M, Rosas A, Rudan P, Brajkovic D, Kucan Ž, Gušic I, Marques-Bonet T, Andrés AM, Viola B, Pääbo S, Meyer M, Siepel A, Castellano S.
Ancient gene flow from early modern humans into Eastern Neanderthals.
Nature 530: 29–433 (2016) [Full text][PDF] - Dannemann D, Andrés AM, Kelso J.
Introgression of Neandertal- and Denisovan-like Haplotypes Contributes to Adaptive Variation in Human Toll-like Receptors
The American Journal of Human Genetics 98:22–33 (2016) - Castellano S, Parra G, Sánchez-Quinto FA, Racimo F, Kuhlwilm M, Kircher M, Sawyer S, Fu Q, Heinze A, Nickel B, Dabney J, Siebauer M, White L, Burbano HA, Renaud G, Stenzel U, Lalueza-Fox C, de la Rasilla M, Rosas A, Rudan P, Brajković D, Kucan Ž, Gušic I, Shunkov MV, Derevianko AP, Viola B, Meyer M, Kelso J, Andrés AM, Pääbo S.
Patterns of coding variation in the complete exomes of three Neandertals.
PNAS 111:6666-71 (2014). [Full text][PDF] - [See also Key et al., Nat Comm 2016 in Local adaptation above]
Local adaptation
Through series of migration events, humans have colonizing virtually every habitable corner of the globe. Settling in such different environments was possible thanks to both cultural and biological adaptations. Although genetic differences among human groups are few and largely neutral, a few genetic differences are responsible for important phenotypic traits, including medically-related phenotypes. We are interested in measuring to what extent local selective pressures have influenced the genetic make up of humans, and which mechanisms mediated adaptation to each environment. We are particularly interested in complex genetic processes underlying local adaptation, such as changes in the strength or type of natural selection, and polygenic adaptation.
Representative publications
- Key FM, Fu Q, Romagné F, Lachmann M, Andrés AM.
Human adaptation and population differentiation in the light of ancient genomes.
Nature Communications 7:10775 (2016) [Full text][PDF] - Key FM, Peter B, Dennis MY, Huerta-Sánchez E, Tang W, Prokunina-Olsson L, Nielsen R, Andrés AM.
Selection on a Variant Associated with Improved Viral Clearance Drives Local, Adaptive Pseudogenization of Interferon Lambda 4 (IFNL4).
PLoS Genetics 10:e1004681 (2014). [Full text][PDF] - White L, Romagné F, Müller E, Erlebach E, Weihmann A, Parra G, Andrés AM, Castellano S.
Genetic adaptation to levels of dietary selenium in recent human history.
Molecular Biology and Evolution 32: 1507-1518 (2015) [Full text][PDF] - [See also de Filippo et al., MBE 2016 in Balancing selection above]
- [See also Dannemann et al., AJHG 2016 in Ancient DNA below]
Comparative population genomics
Considerable knowledge has accumulated on the influence of natural selection in specific human populations. Still, little is known about the conservation of such selective pressures, both among human populations and across different species. Loci under similar selective pressures are likely affected by common environmental factors and are behind shared phenotypes; loci under species- or population-specific selection are likely affected by local selective forces and are responsible for differential traits. Through a number of genomic approaches we aim at helping establish the level of conservation of different types of natural selection, and at identifying loci that are responsible for species- and population-specific traits.
Representative publications
- Cagan A*, Theunert C*, Laayouni H*, Santpere G*, Pybus M, Casals F, Prüfer K, Navarro A, Marques-Bonet T, Bertranpetit J#, Andrés AM#.
Natural selection in the great apes.
Molecular Biology and Evolution, 33:3268-3283 (2016) [Full text][PDF] - Manuel M*, Kuhlwilm M*, Frandsen P*, Sousa V, Desai T, Prado-Martinez J, Hernandez-Rodriguez J, Dupanloup I, Lao O, Hallast P, Schmidt JM, Heredia-Genestar JM, Benazzo A, Barbujani G, Peter B, Kuderna LFK, 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
Chimpanzee genomic diversity reveals ancient admixture with bonobos.
Science 354:477-481 )2016). [Full text][PDF] - 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, ..., Andrés AM, Wall JD, Bustamante CD, Hammer MF, Eichler EE, Marques-Bonet T.
Great ape genetic diversity and population history.
Nature 499:471-5 (2013). [PubMed] [Full text][PDF] - [See also Teixeira et al., MBE 2015 in Balancing selection above]
Former staff
- Aida Andrés (Group leader)
- Muslih Abdul-Aziz
- Àngel Belmonte Aguirre
- Bárbara Bitarello
- Katalina Bobowik
- Cesare de Filippo
- Felix-M. Key
- Philip Kleinert
- Romain Laurent
- Juan Ramón Meneu
- Homa Papoli
- Genís Parra
- David Reher
- Joshua Schmidt
- João Teixeira
Publications
2024
Han, S., de Filippo, C., Parra, G., Meneu Hernández, J. R., Laurent, R., Frandsen, P., Hvilsom, C., Gronau, I., Marques-Bonet, T., Kuhlwilm, M., & Andrés, A. M. (2024). Deep genetic substructure within bonobos (advance online). Current Biology. |
Open Access2023
Zavala, E. I., Jacobs, Z., Vernot, B., Shunkov, M. V., Kozlikin, M. B., Derevianko, A. P., Essel, E., de Filippo, C., Nagel, S., Richter, J., Romagné, F., Schmidt, A., Li, B., O'Gorman, K., Slon, V., Kelso, J., Pääbo, S., Roberts, R. G., & Meyer, M. (2023). The occupational history of Denisova Cave. American Journal of Biological Anthropology, 180(S75), 199-200. |
2019
Schmidt, J., de Manuel, M., Marques-Bonet, T., Castellano, S., & Andrés, A. M. (2019). The impact of genetic adaptation on chimpanzee subspecies differentiation. PLOS Genetics, 15(11), 1-32. |
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Giner-Delgado, C., Villatoro, S., Lerga-Jaso, J., Gayà-Vidal, M., Oliva, M., Castellano, D., Pantano, L., Bitarello, B. D., Izquierdo, D., Noguera, I., Olalde, I., Delprat, A., Blancher, A., Lalueza-Fox, C., Esko, T., O’Reilly, P. F., Andrés, A. M., Ferretti, L., Puig, M., & Cáceres, M. (2019). Evolutionary and functional impact of common polymorphic inversions in the human genome. Nature Communications, 10(4222). |
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Bokelmann, L., Hajdinjak, M., Peyrégne, S., Brace, S., Essel, E., de Filippo, C., Glocke, I., Grote, S., Mafessoni, F., Nagel, S., Kelso, J., Prüfer, K., Vernot, B., Barnes, I., Pääbo, S., Meyer, M., & Stringer, C. (2019). A genetic analysis of the Gibraltar Neanderthals. Proceedings of the National Academy of Sciences, 116(31), 15610-15615. |
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Peyrégne, S., Slon, V., Mafessoni, F., de Filippo, C., Hajdinjak, M., Nagel, S., Nickel, B., Essel, E., Le Cabec, A., Wehrberger, K., Conard, N. J., Kind, C. J., Posth, C., Krause, J., Abrams, G., Bonjean, D., Di Modica, K., Toussaint, M., Kelso, J., Meyer, M., Pääbo, S., & Prüfer, K. (2019). Nuclear DNA from two early Neandertals reveals 80,000 years of genetic continuity in Europe. Science Advances, 5(6): eaaw5873. |
2018
Key, F. M., Abdul-Aziz, M. A., Mundry, R., Peter, B. M., Sekar, A., D'Amato, M., Dennis, M. Y., Schmidt, J. M., & Andrés, A. M. (2018). Human local adaptation of the TRPM8 cold receptor along a latitudinal cline. PLoS Genetics, 14(5): e1007298. |
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Bitarello, B. D., de Filippo, C., Teixeira, J. C., Schmidt, J. M., Kleinert, P., Meyer, D., & Andrés, A. M. (2018). Signatures of long-term balancing selection in human genomes. Genome Biology and Evolution, 10(3), 939-955. |
2017
Prüfer, K., Filippo, C. d., Grote, S., Mafessoni, F., Korlevic, P., Hajdinjak, M., Vernot, B., Skov, L., Hsieh, P., Peyrégne, S., Reher, D., Hopfe, C., Nagel, S., Maricic, T., Fu, Q., Theunert, C., Rogers, R., Skoglund, P., Chintalapati, M., Dannemann, M., Nelson, B. J., Key, F. M., Rudan, P., Kucan, Ž., Gušic, I., Golovanova, L. V., Doronichev, V. B., Patterson, N., Reich, D., Eichler, E. E., Slatkin, M., Schierup, M. H., Andrés, A. M., Kelso, J., Meyer, M., & Pääbo, S. (2017). A high-coverage Neandertal genome from Vindija Cave in Croatia. Science, 358(6363), 655-658. |
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Reher, D., Klink, B., Deutsch, A., & Voss-Böhme, A. (2017). Cell adhesion heterogeneity reinforces tumour cell dissemination: Novel insights from a mathematical model. Biology Direct, 12: 18. |
2016
de Manuel, M., Kuhlwilm, M., Frandsen, P., Sousa, V. C., Desai, T., Prado-Martinez, J., Hernandez-Rodriguez, J., Dupanloup, I., Lao, O., Hallast, P., Schmidt, J. M., Heredia-Genestar, J. M., Benazzo, A., Barbujani, G., Peter, B. M., Kuderna, L. F. K., Casals, F., Angedakin, S., Arandjelovic, M., Boesch, C., Kühl, H. S., Vigilant, L., Langergraber, K., Novembre, J., Gut, M., Gut, I., Navarro, A., Carlsen, F., Andrés, A. M., Siegismund, H. R., 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. |
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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, M. H., Andrés, A. M., 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(10), 2020-2030. |
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de Filippo, C., Key, F. M., Ghirotto, S., Benazzo, A., Meneu, J. R., Weihmann, A., NISC Comparative Sequence Program, Parra, G., Green, E. D., & Andrés, A. M. (2016). Recent selection changes in human genes under long-term balancing selection. Molecular Biology and Evolution, 33(6), 1435-1447. |
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Meyer, M., Arsuaga, J.-L., de Filippo, C., Nagel, S., Aximu-Petri, A., Nickel, B., Martínez, I., Gracia, A., Bermúdez de Castro, J. M., Carbonell, E., Viola, B., Kelso, J., Prüfer, K., & Pääbo, S. (2016). Nuclear DNA sequences from the Middle Pleistocene Sima de los Huesos hominins. Nature, 531(7595), 504-507. |
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Key, F. M., Fu, Q., Romagné, F., Lachmann, M., & Andrés, A. M. (2016). Human adaptation and population differentiation in the light of ancient genomes. Nature Communications, 7: 10775. |
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Andrés, A. M., Dannemann, M., Teixeira, J. C., & Kelso, J. (2016). Balancing selection and adaptive introgression as sources of advantageous genetic diversity in populations. American Journal of Physical Anthropology, 159(S62), 80-81. |
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Kuhlwilm, M., Gronau, I., Hubisz, M. J., de Filippo, C., Prado-Martinez, J., Kircher, M., Fu, Q., Burbano, H. A., Lalueza-Fox, C., de la Rasilla, M., Rosas, A., Rudan, P., Brajkovic, D., Kucan, Ž., Gušic, I., Marques-Bonet, T., Andrés, A. M., Viola, B., Pääbo, S., Meyer, M., Siepel, A., & Castellano, S. (2016). Ancient gene flow from early modern humans into Eastern Neanderthals. Nature, 530(7591), 429-433. |
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Dannemann, M., Andrés, A. M., & Kelso, J. (2016). Introgression of Neandertal- and Denisovan-like haplotypes contributes to adaptive variation in human toll-like receptors. The American Journal of Human Genetics, 98(1), 22-33. |
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Cagan, A., Theunert, C., Laayouni, H., Santpere, G., Pybus, M., Casals, F., Prüfer, K., Navarro, A., Marques-Bonet, T., Bertranpetit, J., & Andrés, A. M. (2016). Natural selection in the great apes. Molecular Biology and Evolution, 33(12), 3268-3283. |
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Key, F. M. (2016). Human adaptation in the light of ancient and modern genomes. PhD Thesis, Univ., Leipzig. |
2015
Teixeira, J. C., de Filippo, C., Weihmann, A., Meneu, J. R., Racimo, F., Dannemann, M., Nickel, B., Fischer, A., Halbwax, M., Andre, C., Atencia, R., Meyer, M., Parra, G., Pääbo, S., & Andrés, A. M. (2015). Long-term balancing selection in LAD1 maintains a missense trans-species polymorphism in humans, chimpanzees and bonobos. Molecular Biology and Evolution, 32(5), 1186-1196. |
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White, L., Romagné, F., Müller, E., Erlebach, E., Weihmann, A., Parra, G., Andrés, A. M., & Castellano, S. (2015). Genetic adaptation to levels of dietary selenium in recent human history. Molecular Biology and Evolution, 32(6), 1507-1518. |
2014
Andrés, A. M., & Nowick, K. ( |
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Andrés, A. M., & Nowick, K. (2014). Editorial overview: Genetics of human evolution: The genetics of human origins. Current Opinion in Genetics & Development, 29, v-vii. |
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Key, F. M., Teixeira, J. C., de Filippo, C., & Andrés, A. M. (2014). Advantageous diversity maintained by balancing selection in humans. Current Opinion in Genetics & Development, 29, 45-51. |
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Key, F. M., Peter, B., Dennis, M. Y., Huerta-Sanchez, E., Tang, W., Prokunina-Olsson, L., Nielsen, R., & Andrés, A. M. (2014). Selection on a variant associated with improved viral clearance drives local, adaptive pseudogenization of Interferon Lambda 4 (IFNL 4). PLoS Genetics, 10(10): e1004681. |
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Prüfer, K., Racimo, F., Patterson, N., Jay, F., Sankararaman, S., Sawyer, S., Heinze, A., Renaud, G., Sudmant, P. H., de Filippo, C., Li, H., Mallick, S., Dannemann, M., Fu, Q., Kircher, M., Kuhlwilm, M., Lachmann, M., Meyer, M., Ongyerth, M., Siebauer, M. F., Theunert, C., Tandon, A., Moorjani, P., Pickrell, J., Mullikin, J. C., Vohr, S. H., Green, R. E., Hellmann, I., Johnson, P. L. F., Blanche, H., Cann, H., Kitzman, J. O., Shendure, J., Eichler, E. E., Lein, E. S., Bakken, T. E., Golovanova, L. V., Doronichev, V. B., Shunkov, M. V., Derevianko, A. P., Viola, B., Slatkin, M., Reich, D., Kelso, J., & Pääbo, S. (2014). The complete genome sequence of a Neanderthal from the Altai Mountains. Nature, 505(7481), 43-49. |
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Castellano, S., Parra, G., Sánchez-Quinto, F. A., Racimo, F., Kuhlwilm, M., Kircher, M., Sawyer, S., Fu, Q., Heinze, A., Nickel, B., Dabney, J., Siebauer, M. F., White, L., Burbano, H. A., Renaud, G., Stenzel, U., Lalueza-Fox, C., de la Rasilla, M., Rosas, A., Rudan, P., Brajkovic, D., Kucan, Ž., Gušic, I., Shunkov, M. V., Derevianko, A. P., Viola, B., Meyer, M., Kelso, J., Andrés, A. M., & Pääbo, S. (2014). Patterns of coding variation in the complete exomes of three Neandertals. Proceedings of the National Academy of Sciences of the United States of America, 111(18), 6666-6671. |
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Hajdinjak, M., Korlević, P., Gansauge, M.-T., Dabney, J., Slon, V., Glocke, I., Sawyer, S., Nickel, B., Nagel, S., Gerber, T., Hopfe, C., Stenzel, U., Renaud, G., Andrés, A. M., Castellano, S., Kelso, J., Prüfer, K., Meyer, M., & Pääbo, S. (2014). Neandertal genetic diversity. Poster presented at XVII World UISPP Congress, Burgos, Spain. |
2013
Prado-Martinez, J., Sudmant, P. H., Kidd, J. M., Li, H., Kelley, J. L., Lorente-Galdos, B., Veeramah, K. R., Woerner, A. E., O’Connor, T. D., Santpere, G., Cagan, A., Theunert, C., Casals, F., Laayouni, H., Munch, K., Hobolth, A., Halager, A. E., 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, M. L., Stevison, L., Camprubí, C., Carvalho, T., Ruiz-Herrera, A., Vives, L., Mele, M., Abello, T., Kondova, I., Bontrop, R. E., Pusey, A., Lankester, F., Kiyang, J. A., Bergl, R. A., Lonsdorf, E., Myers, S., Ventura, M., Gagneux, P., Comas, D., Siegismund, H., Blanc, J., Agueda-Calpena, L., Gut, M., Fulton, L., Tishkoff, S. A., Mullikin, J. C., Wilson, R. K., Gut, I. G., Gonder, M. K., Ryder, O. A., Hahn, B. H., Navarro, A., Akey, J. M., Bertranpetit, J., Reich, D., Mailund, T., Schierup, M. H., Hvilsom, C., Andrés, A. M., Wall, J. D., Bustamante, C. D., Hammer, M. F., Eichler, E. E., & Marques-Bonet, T. (2013). Great ape genetic diversity and population history. Nature, 499, 471-475. |
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Ferreira, Z., Seixas, S., Andrés, A. M., Kretzschmar, W. W., Mullikin, J. C., Cherukuri, P. F., Cruz, P., Swanson, W. J., Clark, A. G., Green, E. D., & Hurle, B. (2013). Reproduction and immunity-driven natural selection in the human WFDC locus. Molecular Biology and Evolution, 30(4), 938-950. |
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Ferreira, Z., Hurle, B., Andrés, A. M., Kretzschmar, W. W., Mullikin, J. C., Cherukuri, P. F., Cruz, P., Gonder, M. K., Stone, A. C., Tishkoff, S., Swanson, W. J., NISC Comparative Sequencing Program, Green, E. D., Clark, A. G., & Seixas, S. (2013). Sequence diversity of Pan troglodytes subspecies and the impact of WFDC6 selective constraints in reproductive immunity. Genome Biology and Evolution, 5(12), 2512-2523. |
2012
Meyer, M., Kircher, M., Gansauge, M.-T., Li, H., Racimo, F., Mallick, S., Schraiber, J. G., Jay, F., Prüfer, K., Filippo, C. d., Sudmant, P. H., Alkan, C., Fu, Q., Do, R., Rohland, N., Tandon, A., Siebauer, M., Green, R. E., Bryc, K., Briggs, A. W., Stenzel, U., Dabney, J., Shendure, J., Kitzman, J., Hammer, M. F., Shunkov, M. V., Derevianko, A. P., Patterson, N., Andrés, A. M., Eichler, E. E., Slatkin, M., Reich, D., Kelso, J., & Pääbo, S. (2012). A high-coverage genome sequence from an archaic Denisovan individual. Science, 338(6104), 222-226. |
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Prüfer, K., Munch, K., Hellmann, I., Akagi, K., Miller, J. R., Walenz, B., Koren, S., Sutton, G., Kodira, C., Winer, R., Knight, J. R., Mullikin, J. C., Meader, S. J., Ponting, C. P., Lunter, G., Higashino, S., Hobolth, A., Dutheil, J., Karakoç, E., Alkan, C., Sajjadian, S., Catacchio, C. R., Ventura, M., Marques-Bonet, T., Eichler, E. E., André, C., Atencia, R., Mugisha, L., Junhold, J., Patterson, N., Siebauer, M., Good, J. M., Fischer, A., Ptak, S. E., Lachmann, M., Symer, D. E., Mailund, T., Schierup, M. H., Andrés, A. M., Kelso, J., & Pääbo, S. (2012). The bonobo genome compared with the chimpanzee and human genomes. Nature, 486(7404), 527-531. |
2011
Andrés, A. M. (2011). Balancing selection in the human genome. In Encyclopedia of Life Sciences. Chichester [u.a.]: Wiley. |
2010
Andrés, A. M., Dennis, M. Y., Kretzschmar, W. W., Cannons, J. L., Lee-Lin, S.-Q., Hurle, B., NISC Comparative Sequencing Program, Schwartzberg, P. L., Williamson, S. H., Bustamante, C. D., Nielsen, R., Clark, A. G., & Green, E. D. (2010). Balancing selection maintains a form of ERAP2 that undergoes nonsense-mediated decay and affects antigen presentation. PLoS Genetics, 6(10): e1001157. |
Selected publications before 2010
Andrés AM, Hubisz MJ, Indap A, Torgerson DG, Degenhardt JD, Boyko AR, Gutenkunst RN, White TJ, Green ED, Bustamante CD, Clark AG, Nielsen R. (2009). Targets of balancing selection in the human genome. Molecular Biology and Evolution, 26:2755-64.
PubMed Full text PDF Supplementary Material
Castellano S*, Andrés AM*, Bosch E, Bayes M, Guigó R, Clark AG. (2009). Low exchangeability of selenocysteine, the 21st amino acid, in vertebrate proteins. Molecular Biology and Evolution, 26:2031-40.
PubMed Full Text PDF Supplementary Material
* Denotes equal contribution.
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. (2009). Darwinian and demographic forces affecting human protein coding genes. Genome Research, 19:838-49.
PubMed Full Text PDF Supplementary Material
Andrés AM, Clark AG, Shimmin L, Boerwinkle E, Sing CF and Hixson JE. (2007). Understanding the accuracy of statistical haplotype inference with sequence data of known phase. Genetic Epidemiology, 31:659-71.
PubMed PDF
Andrés AM, de Hemptinne C and Bertranpetit J. (2007). Heterogenetous rate of protein evolution in serotonin genes. Molecular Biology and Evolution, 24:2707-15.
PubMed Full text PDF Supplementary Material
Soldevila M, Andrés AM, Helgason A, Ramírez-Soriano A, Marquès-Bonet T, Sigurdadóttir S, Calafell F, Navarro A, Stefánsson K and Bertranpetit J. (2006). The prion protein gene in humans revisited: lessons from a worldwide resequencing study. Genome Research, 16:231-9.
PubMed Full text PDF
Andrés AM, Soldevila M, Navarro A, Kidd KK, Oliva B and Bertranpetit J. (2004). Positive selection in MAOA gene is human exclusive: determination of the putative amino acid change selected in the human lineage. Human Genetics 115:377-86.
PubMed Full text PDF
Andrés AM, Soldevila M, Lao O, Volpini V, Saitou N, Jacobs HT, Hayasaka I, Calafell F and Bertranpetit J. (2004). Comparative genetics of functional trinucleotide tandem repeats in humans and apes. Journal of Molecular Evolution 59:329-39.
PubMed Full text PDF
Clarimón J, Andrés AM, Bertranpetit J and Comas D. (2004). Comparative analysis of Alu insertion sequences in the APP 5’flanking region in humans and other primates. Journal of Molecular Evolution 58:722-731 (2004).
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Soldevila M, Andrés AM, Blancher A, Calafell F, Ordoñez M, Pumarola M, Oliva B, Aramburu J and Bertranpetit J. (2004). Variation of the prion gene in chimpanzees and its implication for prion diseases. Neuroscience Letters 355:157-60.
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Andrés AM, Soldevila M, Saitou N, Volpini V, Calafell F and Bertranpetit J. (2003). Understanding the dynamics of Spinocerebellar Ataxia 8 (SCA8) locus through a comparative genetic approach in humans and apes. Neuroscience Letters 336:143-146.
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Andrés AM, Lao O, Soldevila M, Calafell F and Bertranpetit J. (2003). Dynamics of CAG repeat loci revealed by the analysis of their variability. Human Mutation 21:61-70.
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Martínez-Arias R, Calafell R, Mateu E, Comas D, Andrés A and Bertranpetit J. (2002). Sequence variability of a human pseudogene. Genome Research 11:1071-1085.
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