Universitat Pompeu Fabra
csicUniversitat Pompeu Fabra

Paleogenomics Lab

Lalueza group

 

Group members

Carles Lalueza

  • Carles Lalueza-Fox, Group Leader |  Research Scientist, CSIC -
  • Oscar Ramírez | Postdoctoral Researcher-JAEDOC-CSIC
  • Federico Sánchez, PhD Student  |  FPI Scholarship, MICINN 
  • Íñigo Olalde| Master student - La Caixa

 

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

2012

  • Sánchez-Quinto, F., Schroeder, H., Ramirez, O., Ávila-Arcos, M.C. , Pybus, M., Olalde, I., Velazquez, A.M.V., Prada Marcos, M.E., Vidal Encinas, J.M., Bertranpetit, J., Orlando, L.,  Gilbert, M.T.P., Lalueza-Fox, C. (2012). Genomic affinities of two 7,000-year-old Iberian hunter-gatherers. Curr. Biol. (in press).
  • Frayer D, Fiore I, Lalueza-Fox C, Radovčić J, Bondioli L. (2012). Replay to Benítez-Burraco and Longa: When is enough, enough? J. Anthropol. Sci. 90: 1-6.
  • Burbano, H., Green, R.E., Maricic, T., Lalueza-Fox, C., de la Rasilla, M., Rosas, A., Kelso, J., Pollard, K.S., 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. Mol. Biol. Evol. (doi: 10.1093/molbev/mss023).
  • Rosas A, Estalrrich A, García-Tabernero A, Bastir M, García-Vargas S, Sánchez-Meseguer A, Huguet R, Lalueza-Fox C, Peña-Melián A, Kranioti E.F, 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