Ancient biomolecules and the reconstruction of human population history Dr. Roberta Lelli Centre of Molecular Anthropology for the study of ancient DNA Department of Biology University of Rome Tor Vergata BIOSYSTEMS, ENERGY, AND CULTURAL HERITAGE: MATERIALS ENHANCEMENT FOR TECHNOLOGICAL APPLICATION

1. ANCIENT DNA 1.1. What is it? Any DNA recovered from…

1. ANCIENT DNA 1.2. History of ancient DNA studies

1. ANCIENT DNA 1.3. Polymerase chain reaction - PCR Amplification of few and damaged DNA molecules

1. ANCIENT DNA 1.4. Problems of ancient DNA studies - Contamination with modern DNA - Molecular damage Oxidation Microorganisms Crosslinks Hydrolysis

1. ANCIENT DNA 1.5. The nine gold criteria - Cooper and Poinar, 2000 Ancient DNA: do it right or not at all. Science 289, 1139

1. ANCIENT DNA 1.6. Anthropological applications 1. Phylogenetic analysis OLOL D-loop ATPase mtDNA molecule: 16,569 base pair in lenght ABUNDANCE IN HUMAN CELL : 100 to 10,000 copies per cell HIGH EVOLUTIONARY RATE : ca. 10 times faster than the nuclear genome MATERNAL INHERITANCE: no contribution of fathers to the mtDNA of their children males females

1. ANCIENT DNA 1.6. Anthropological applications 2. Human evolution Origin of modern humans: - single - African - recent Mitochondrial Eve

1. ANCIENT DNA 1.6. Anthropological applications 2. Human evolution Neandertal: our direct ancestor or a separate species? Neanderthal range (350,000-30,000 ya)

Thelwe Neandertal specimens analysed for mtDNA 1. ANCIENT DNA 1.6. Anthropological applications

Homo neanderthalensisHomo sapiens Two different species! Neandertal Africans Not-Africans Africans Modern humans

1. ANCIENT DNA 1.6. Anthropological applications Krause et al., 2007 Lalueza-Fox et al., 2007

1. ANCIENT DNA 1.6. Anthropological applications Green et al., 2006 Green et al., 2008 Noonan et al., 2006 Green et al., 2010 N ext G eneration S equencing technologies ( NGS )

1. ANCIENT DNA 1.6. Anthropological applications 3. Human migration Neolithic transition in Europe BP 9000 BP 8000 BP 7500 BP 6000 BP 8000 BP 7500 BP

1. ANCIENT DNA 1.6. Anthropological applications 4. Kinship analysis Genetic investigation of multiple burials Genetic investigation of multiple burials Inference on social organization and funeral practices of the population examined Inference on social organization and funeral practices of the population examined 5. Molecular sex determination Amelogenin gene : present on both X- and Y-chromosome Amelogenin gene : present on both X- and Y-chromosome 112 bp 106 bp Length polymorphism : Length polymorphism : 106 bp (X-chromosome) 106 bp (X-chromosome) 112 bp (Y-chromosome) 112 bp (Y-chromosome)

1. ANCIENT DNA 1.6. Anthropological applications Balzi Rossi site (Liguria, Italy – 20,000-25,000 BP) - excavation of a triple burial 1 male adult 2 female adolescents sharing the same mitochondrial profile more likely hypothesis: a father buried simultaneously with his daughters

1. ANCIENT DNA 1.6. Anthropological applications 6. Paleopathology - Identification of bacterial, protozoan and viral infections (i.e. Mycobacterium tubercolosis, Yersinia pestis, Plasmodium falciparum ) to: reconstruct the history of infectious disease in past civilization reconstruct the history of infectious disease in past civilization study the evolution of a pathogen study the evolution of a pathogen - Analysis of calcified dental plaque to evaluate changes in oral microbiota due to dietary shifts of the Neolithic

1. ANCIENT DNA 1.6. Anthropological applications 6. Paleopathology Cosa site (Tuscany, Italy – I century AD) - excavation of a female skeleton affected by celiac desease : the first case in Italy! - Molecular analysis of three HLA markers associated to celiac disease: DQ8 - DQ2.2 - DQ2.5 (Monsuur et al., 2008) - Diagnosis confirmed also on molecular level - Probable consumption of cereal

2. STABLE ISOTOPES 2.1. Carbon and nitrogen stable isotope analysis Valuable tool for the reconstruction of past population diets (or palaeodiets )

a) Conducted on bone collagen : ~90% of organic matter in bone ~90% of organic matter in bone synthesized from dietary proteins synthesized from dietary proteins turnover rate: ca years turnover rate: ca years dietary record of ca. 10 years prior to death b) Distinct 13 C/ 12 C and 15 N/ 14 N of food resources 2. STABLE ISOTOPES 2.1. Carbon and nitrogen stable isotope analysis

Isotope values are expressed in delta notation ( ): fractional difference in parts per thousand ( ) from a common standard: 13 C ( 13 C/ 12 C) 13 C ( 13 C/ 12 C) the most of biological material contain less 13 C than the mineral used as the standard (PDB) <0 15 N ( 15 N/ 14 N) 15 N ( 15 N/ 14 N) the most of biological materials contain more 15 N than the standard (air) >0 (in ) = (Rx / Rs - 1) x1000 (in ) = (Rx / Rs - 1) x1000 R : heavy isotope / light isotope x : sample s : standard 2. STABLE ISOTOPES 2.1. Carbon and nitrogen stable isotope analysis

MARINE ECOSYSTEM TERRESTRIAL ECOSYSTEM Carnivores Herbivores Omnivores Shellfish Fishes Ichthyophagi Marine mammals MARINE DIET TERRESTRIAL C3 DIET (wheat, legumes) TERRESTRIAL C4 DIET (maize, millet) 2. STABLE ISOTOPES 2.1. Carbon and nitrogen stable isotope analysis

CONCLUDING REMARK The integrated biomolecular approach is the most suitable tool to provide an accurate and complete view of human population history

Centre of Molecular Anthropology for the study of ancient DNA - Department of Biology - University of Rome Tor Vergata Director: Prof. Olga Rickards Researchers: Dr. Cristina Martìnez-Labarga Dr. Giuseppina Scano Dr. Giuseppina Scano Technicians: Dr. Irene Contini Dr. Flavio De Angelis Dr. Flavio De Angelis Postdoctoral researchers: Dr. Roberta Lelli Dr. Gabriele Scorrano Dr. Gabriele Scorrano PhD students: Alessandro Cianfanelli Tullia Di Corcia Tullia Di Corcia Micaela Gnes Micaela Gnes Giusy Primativo Giusy Primativo THANK YOU FOR THE ATTENTION!