Derived immune and ancestral pigmentation alleles in a 7,000-year-old Mesolithic European.
Ancient genomic sequences have started to reveal the origin and the demographic impact of farmers from the Neolithic period spreading into Europe. The adoption of farming, stock breeding and sedentary societies during the Neolithic may have resulted in adaptive changes in genes associated with immunity and diet. However, the limited data available from earlier hunter-gatherers preclude an understanding of the selective processes associated with this crucial transition to agriculture in recent human evolution. Here we sequence an approximately 7,000-year-old Mesolithic skeleton discovered at the La Braña-Arintero site in León, Spain, to retrieve a complete pre-agricultural European human genome. Analysis of this genome in the context of other ancient samples suggests the existence of a common ancient genomic signature across western and central Eurasia from the Upper Paleolithic to the Mesolithic. The La Braña individual carries ancestral alleles in several skin pigmentation genes, suggesting that the light skin of modern Europeans was not yet ubiquitous in Mesolithic times. Moreover, we provide evidence that a significant number of derived, putatively adaptive variants associated with pathogen resistance in modern Europeans were already present in this hunter-gatherer.
1] Institut de Biologia Evolutiva, CSIC-UPF, Barcelona 08003, Spain [2].
Iñigo
I
Olalde
1] Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen K, Denmark [2].
Morten E
ME
Allentoft
Institut de Biologia Evolutiva, CSIC-UPF, Barcelona 08003, Spain.
Federico
F
Sánchez-Quinto
Institut de Biologia Evolutiva, CSIC-UPF, Barcelona 08003, Spain.
Gabriel
G
Santpere
Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California 90095, USA.
Charleston W K
CW
Chiang
1] Department of Integrative Biology, University of California, Berkeley, California 94720, USA [2] Department of Biology, Pennsylvania State University, 502 Wartik Laboratory, University Park, Pennsylvania 16802, USA.
Michael
M
DeGiorgio
Institut de Biologia Evolutiva, CSIC-UPF, Barcelona 08003, Spain.
Javier
J
Prado-Martinez
Institut de Biologia Evolutiva, CSIC-UPF, Barcelona 08003, Spain.
Juan Antonio
JA
Rodríguez
Center for Biological Sequence Analysis, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark.
Simon
S
Rasmussen
Institut de Biologia Evolutiva, CSIC-UPF, Barcelona 08003, Spain.
Javier
J
Quilez
Institut de Biologia Evolutiva, CSIC-UPF, Barcelona 08003, Spain.
Oscar
O
Ramírez
Institut de Biologia Evolutiva, CSIC-UPF, Barcelona 08003, Spain.
Urko M
UM
Marigorta
Institut de Biologia Evolutiva, CSIC-UPF, Barcelona 08003, Spain.
Marcos
M
Fernández-Callejo
I.E.S.O. 'Los Salados', Junta de Castilla y León, E-49600 Benavente, Spain.
María Encina
ME
Prada
Junta de Castilla y León, Servicio de Cultura de León, E-24071 León, Spain.
Julio Manuel Vidal
JM
Encinas
Center for Theoretical Evolutionary Genomics, University of California, Berkeley, California 94720, USA.
Rasmus
R
Nielsen
Department of Medicine and Nijmegen Institute for Infection, Inflammation and Immunity, Radboud University Nijmegen Medical Centre, 6500 Nijmegen, The Netherlands.
Mihai G
MG
Netea
Department of Human Genetics, University of Chicago, Illinois 60637, USA.
John
J
Novembre
Institute for Molecular Bioscience, Melanogenix Group, The University of Queensland, Brisbane, Queensland 4072, Australia.
Richard A
RA
Sturm
1] Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA [2] Broad Institute of the Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA.
Pardis
P
Sabeti
1] Institut de Biologia Evolutiva, CSIC-UPF, Barcelona 08003, Spain [2] Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Catalonia, Spain.
Tomàs
T
Marquès-Bonet
1] Institut de Biologia Evolutiva, CSIC-UPF, Barcelona 08003, Spain [2] Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Catalonia, Spain [3] Centre de Regulació Genòmica (CRG), Barcelona 08003, Catalonia, Spain [4] National Institute for Bioinformatics (INB), Barcelona 08003, Catalonia, Spain.
Arcadi
A
Navarro
Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen K, Denmark.
Eske
E
Willerslev
Institut de Biologia Evolutiva, CSIC-UPF, Barcelona 08003, Spain.
Carles
C
Lalueza-Fox
D000383:Agriculture / Q000266:history; D000483:Alleles; D005075:Biological Evolution; D059552:Caves; D005127:Eye Color / Q000235:genetics; D005580:Fossils; D015894:Genome, Human / Q000235:genetics; D023281:Genomics; D049690:History, Ancient; D006801:Humans; D007109:Immunity / Q000235:genetics*; D007787:Lactose Intolerance / Q000235:genetics; D008297:Male; D010858:Pigmentation / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D025341:Principal Component Analysis; D012863:Skeleton; D012880:Skin Pigmentation / Q000235:genetics; D013030:Spain / Q000208:ethnology; D044465:White People / Q000235:genetics*