Universitat Pompeu Fabra
csicUniversitat Pompeu Fabra

Paleogenomics Lab

Lalueza_Foto grup2013

 

Group members

Lalueza2011

  • Carles Lalueza-Fox, Group Leader |  Research Scientist, CSIC 
  • Oscar Ramírez | Postdoctoral Researcher-JAEDOC-CSIC
  • Federico Sánchez, PhD Student  |  FPI Scholarship, MICINN 
  • Íñigo Olalde| PhD scholarship Gobierno Vasco 

RESEARCH OUTLINE

Our research group focuses on paleogenomics, the study of structure, function and organization of ancestral genomes. We are interested in different evolutionary problems that can be answered with ancient DNA data, involving human evolution, population dynamics and diversity, phylogenetics, phylogeography and adaptive processes. We work with different species and populations, including mammoths, cave bears, Myotragus balearicus, wolves and lynxs, but also with an extinct hominin species, the Neandertals. In our group we are basically interested in the genomic diversity among Neandertals, in the individualisation of a Neandertal family group from El Sidrón site (Asturias, Spain) and in investigating the functional implications of genetic variants exclusively found in Neandertals 

Research sublines

1. Adaptive traits and evolutionary history of Neandertals

We are currently retrieving genomic regions that are incompletely covered by the current genome draft. We are also conducting in vitro and in vivo functional studies related to genes that are known to be different between Neandertals and modern humans for trying to interpret the phenotypical consequences of these genomic differences.

2. Neandertal genomic diversity

We are analyzing different individuals from El Sidrón site in Asturias, Spain. This is a family group of at least 12 Neandertal individuals that became accidentally accumulated in a single, synchronic event within a subterranean karstic system. El Sidrón offers the unique opportunity of launching a genomic project for understanding the diversity and the kinship relationships within a Neandertal family group.

4. Phylogenetics, phylogeography and adaptation in extinct and living species

We are studying different extinct species, to answer specific questions about their phylogeny, adaptation and evolution. We are particularly interested in studying some insular endemics and the genomic basis of some common adaptive patterns observed among them such as body size reduction. We are also interested in the analysis of domestication processes at the genomic level, and we are currently comparing structural variations (CNVs) between dogs and wolves.

5. Extinct modern human populations

We are genetically analysing ancient samples from prehistoric European populations to reconstruct past human migrations. We are trying to developed new methodological tools for capturing targeted genomic regions and complete mitochondrial genomes combined with massively parallel sequencing technologies. We are specially interested in the Mesolithic-Neolithic shift.

PUBLICATIONS

 2014

  • Castellano S, Parra G, Sánchez-Quinto F, 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, Brajkovic D, Kucan Z, Gušic I, Shunkov MV, Derevianko AP, Viola B, Meyer M, Kelso J, Andrés AM, Pääbo S. (2014). Patterns of coding variation in the complete exomes of three Neandertals. Proceedings of the National Academy of Sciences USA (in press).
  • Olalde I, Sánchez-Quinto F, Datta D, Marigorta UM, Chiang CWK, 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 (in press).
  • Olalde I, Allentoft ME, Sánchez-Quinto F, Santpere G, Chiang CWK, DeGiorgio M, Prado-Martínez J, Rodríguez JA, Rasmussen S, Quilez J, Ramírez O, Marigorta UM, Fernández M, Prada ME, Vidal 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: 225-228.
  • Engelken J, Carnero-Montoro E, Pybus M, Andrews GK, Lalueza-Fox C, Comas D, Sekler I, de la Rasilla M, Rosas A, Stoneking M, Valverde MA, Vicente R, Bosch E. (2014) Extreme Population Differences in the Human Zinc Transporter ZIP4 (SLC39A4) are Explained by Positive Selection in Sub-Saharan Africa. Plos Genetics 10(2): e1004128.

2013

  • Lalueza-Fox, C. (2013). Agreements and Misunderstandings among Three Scientific Fields:Paleogenomics, Archaeology, and Human Paleontology. Current Anthropology 54 (S8): S214-S220. 
  • 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 14:363.
  • Ramírez O, Gómez-Díaz E, Olalde I, Illera JC, Rando JC, González-Solís J, Lalueza-Fox C. (2013). Population connectivity buffers genetic diversity loss in a seabird. Frontiers in Zoology 10(1):28.
  • Dean MC, Rosas A, Estalrrich A, García-Tabernero A, Huguet R, Lalueza-Fox C, Bastir M, de la Rasilla M. (2013). Longstanding dental pathology in Neandertals from El Sidrón (Asturias, Spain) with a probable familial basis. Journal of Human Evolution 64(6):678-686.
  • Charlier P, Lalueza-Fox C, Hervé C. (2013). Medical recollections. The head of Henri IV: identification and ethical issues. Revue du Praticien 63(2): 289-293.
  • Charlier P, Olalde I, Solé N, Ramírez O, Babelon J-P, Galland B, Calafell F, Lalueza-Fox C. (2013). Genetic comparison of the head of Henri IV and the presumptive blood from Louis XVI (both Kings of France). Forensic Science International 226(1-3):38-40.
  • Maricic T, Günther V, Georgiev O, Gehre S, Ćurlin M, Schreiweis C, Naumann R, Burbano HA, Meyer M, Lalueza-Fox C, de la Rasilla M, Rosas A, Gajović S, Kelso J, Enard W, Schaffner W, Pääbo S. (2012). A recent evolutionary change affects a regulatory element in the human FOXP2 gene. Molecular Biology and Evolution 30(4):844-852.
  • Wood RE, Higham TFG, de Torres T, Tisnérat-Laborde N, Valladas H, Ortiz JE, Lalueza-Fox C, Sánchez-Moral S, Cañaveras JC, Rosas A, Santamaría D, de la Rasilla M. (2013). A new date for the Neanderthals of El Sidrón Cave (Asturias,
    Northern Spain). Archaeometry 55 (1):148-158

2012

  • González-Ruiz M, Santos C, Jordana X, Simón M, Lalueza-Fox C, Gigli E, Aluja MP, Malgosa A.(2012). Tracing the origin of the East-west population admixture in the Altai region (Central Asia). PLoS ONE 7(11):e48904.
  • Mannino MA, Catalano G, Talamo S, Mannino G, Di Salvo R, Schimmenti V, Lalueza-Fox C, Messina A, Petruso D, Caramelli D, Richards MP, Sineo L. (2012). Origin and diet of the prehistoric hunter-gatherers on the mediterranean island of Favignana (Ègadi Islands, Sicily). PLoS ONE 7(11):e49802.
  • Sánchez-Quinto F, Rodriguez-Botigué L, Civit S, Arenas C, Ávila-Arcos MC, Bustamante CD, Comas D, Lalueza-Fox C. (2012). North African populations carry the signature of admixture with Neandertals. PLos ONE 7(10):e47765.
  • Sánchez-Quinto F, Schroeder H, Ramirez O, Ávila-Arcos MC, Pybus M, Olalde I, Velazquez AMV, Prada Marcos ME, Vidal Encinas JM, Bertranpetit J, Orlando L,  Gilbert, MTP, Lalueza-Fox C. (2012). Genomic affinities of two 7,000-year-old Iberian hunter-gatherers. Current Biology 22: 1494-1499.
  • Frayer D, Fiore I, Lalueza-Fox C, Radovčić J, Bondioli L. (2012). Replay to Benítez-Burraco and Longa: When is enough, enough? Journal of Anthropological Science 90: 1-6.
  • Burbano H, Green RE, Maricic T, Lalueza-Fox C, de la Rasilla M, Rosas A, Kelso J, Pollard, KS, Lachmann M, Paabo S. (2012). Analysis of Human Accelerated DNA Regions Using Archaic Hominin Genomes. PLoS ONE 7(3): e32877.
  • Lopez-Valenzuela M, Ramírez O, Rosas A, García-Vargas S, de la Rasilla M, Lalueza-Fox C, Espinosa-Parrilla Y. (2012). An ancestral allele of miR-1304 present in Neanderthals regulates genes involved in enamel formation and could explain dental differences with modern humans. Molecular Biology and Evolution 29(7):1797-1806.
  • Hardy K, Buckley S, Collins MJ, Estalrrich A, Brothwell D, Copeland L, García-Tabernero A, García-Vargas S, de la Rasilla M, Lalueza-Fox C, Huguet R, Bastir M, Santamaría D, Madella M, Fernández Cortés A, Rosas A. (2012). Neanderthal medics? Evidence for food, cooking and medicinal plants entrapped in Neanderthal dental calculus. Naturwissenschaften 99(8):617-626.
  • Rosas A, Estalrrich A, García-Tabernero A, Bastir M, García-Vargas S, Sánchez-Meseguer A, Huguet R, Lalueza-Fox C, Peña-Melián A, Kranioti EF, Santamaría D, de la Rasilla M, Fortea F. (2012). Les Néandertaliens d'El Sidrón (Asturies, Espagne). Actualisation d'un nouvel échantillon. L'Anthropologie 116 (1): 57-76.
  • Lalueza-Fox C, Gigli E, Sánchez-Quinto F, de la Rasilla M, Fortea J, Rosas A. (2012) Issues from Neandertal genomics: Diversity, adaptation and hybridisation revised from the El Sidrón case study. Quaternary International 247: 10-14.
  • Lalueza-Fox C, Rosas A, de la Rasilla M. (2012). Palaeogenetic research at El Sidrón Neandertal site. Annals of Anatomy 194(1):133-137.

2011

  • Lalueza-Fox C, Gilbert MTP. (2011). Paleogenomics of Archaic Hominins. Current Biology 21(24): R1002-R1009.
  • García-Garcerà M, Gigli E, Sanchez-Quinto F, Ramirez O, Calafell F, Civit S, Lalueza-Fox C. (2011). Fragmentation of contaminant and endogenous DNA in ancient samples determined by shotgun sequencing; prospects for human palaeogenomics. PLoS One. 6(8):e24161
  • Rodríguez R, Ramírez O, Valdiosera CE, García N, Alda F, Madurell-Malapeira J, Marmi J, Doadrio I, Willerslev E, Götherström A, Arsuaga JL, Thomas MG, Lalueza-Fox C., Dalén L. (2011). 50,000 years of genetic uniformity in the critically endangered Iberian lynx. Molecular Ecology 20(18):3785-3795.
  • Lalueza-Fox C, Rosas A, Rasilla M, Gilbert MTP, Willerslev E. (2011). Reply to Vigilant and Langergraber: Patrilocality in Neandertals is still the most plausible explanation. Proceedings of the National Academy of Sciences 2011 May 3, 108(18): E88.
  • Lalueza-Fox C, Rosas A, Estalrrich A, Gigli E, Campos PF, García-Tabernero A, García-Vargas S, Sánchez-Quinto F, Ramírez O, Civit S, Bastir M, Huguet R, Santamaría D, P Gilbert MT, Willerslev E, de la Rasilla M. (2011). Genetic evidence for patrilocal mating behavior among Neandertal groups. Proceedings of the National Academy of Sciences USA 108(1): 250-253.
  • Lalueza-Fox C, Gigli E, Bini C, Calafell F, Luiselli D, Pelotti S, Pettener D. (2011). Genetic analysis of the presumptive blood from Louis XVI, king of France. Forensic Science International 5(5):459-63.
  • Ebenesersdóttir SS, Sigurðsson A, Sánchez-Quinto F, Lalueza-Fox C, Stefánsson K, Helgason A. (2011). A new subclade of mtDNA haplogroup C1 found in Icelanders: evidence of pre-Columbian contact? American Journal of Physical Anthropology 144(1): 92-99.

2010

  • Green, R.E., Krause, J., Briggs, A.W., Maricic, T., Stenzel, U., Kircher, M., Patterson, N., et al. 2010. A draft sequence of the Neandertal genome. Science 328: 710-722. 
  • de Torres, T., Ortiz, J.E., Grün, R., Eggins, S., Valladas, H., Mercier, N., Tisnérat-Laborde, N., Juliá, R., Soler, V., Martínez, E., Sánchez-Moral, S., Cañaveras, J.C., Lario, J., Badal, E., Lalueza-Fox, C., Rosas, A., Santamaría, D., de La Rasilla, M., and Fortea, J. 2010. Dating of the Hominid (Homo neanderthalensis) remains accumulation from El Sidrón cave (Piloña, Asturias, north Spain): an example of multi-methodological approach to the dating of Upper Pleistocene sites. Archaeometry 52 (4): 680-705.
  • Santamaría, D., Fortea, J., de la Rasilla, M., Martínez, L., Martínez, E., Cañaveras, J.C., Sánchez-Moral, S., Rosas, A., Estalrrich, A., García-Tabernero, A., and Lalueza-Fox, C. 2010. The technological and typological behaviour of a Neanderthal group from El Sidrón cave (Asturias, Spain). The Technological and typological behaviour of a Neanderthal group from El Sidrón cave (Asturias, Spain). Oxford Journal of Archaeology 29 (2): 119-148.
  • Frayer, D.W., Fiore, I., Lalueza-Fox, C., Radovcić, J., and Bondioli, L. 2010. Right handed Neandertals: Vindija and beyond. Journal of Anthropological Science 88: 113-127.
  • Ramirez, O., Illera, J.C., Rando, J.C., González-Solís, J., Alcover, J.A., and Lalueza-Fox, C. 2010. Ancient DNA of the Extinct Lava Shearwater (Puffinus olsoni) from the Canary Islands Reveals Incipient Differentiation within the P. puffinus Complex. PLoS ONE 5 (12): e16072.

 Book Chapters:

  • Lalueza-Fox, C. 2010. El Proyecto Genoma Neandertal: ¿hacia una definición genética de nuestra especie? In: "150 años después de Darwin: ¿evolución, futuro o crisis?". Edited by Instituto Tomás Pascual Sanz- CENIEH. ISBN: 978-84-7867-057-4.
  • Lalueza-Fox, C. 2010. Genómica Neandertal. In: "Encuentros con la Ciencia II. Del macrocosmos al microcosmos" (ed. Enrique Viguera, Ana Grande y José Lozano). Publicaciones de la Universidad de Málaga. ISBN: 978-84-9747-339-2.
  • Lalueza-Fox, C. 2010. El Proyecto Genoma Neandertal. In: "Fósiles y moléculas. Aproximaciones a la historia evolutiva de Homo sapiens" (ed. Antonio González-Martín). Memorias de la Real Sociedad Española de Historia Natural. Segunda época. ISBN: 978-84-936677-5-7.
  • Lalueza-Fox, C. 2010. ADN i arqueologia. In: "Restes de vida, restes de mort; la mort en la prehistòria". Publicacions del Museu de Prehistòria de València, Diputació de València. ISBN: 978-84-7795-557-3.

Former Publications (2000-2008)

DATA SETS

"La Braña Mesolithic genomic data"

FUNDED PROJECTS

Project Title: Diversidad genética y adaptación en Neandertales
Financed by:   CSIC ("Proyectos Intramurales
Especiales"). 
Years: 2008-2009
PI: Carles Lalueza-Fox  

Project Title: Neandertal genome diversity analyzed by ultrasequencing techniques (REF: BFU2009 06974
Financed by: Ministry of Science and Innovation, Spain.
Years: 2010-2012
PI: Carles Lalueza-Fox