Ancient biomolecules and the reconstruction of

human population history

Dr. Roberta Lelli

Centre of Molecular Anthropology for the study of ancient DNADepartment of BiologyUniversity of Rome “Tor Vergata”

BIOSYSTEMS, ENERGY, AND CULTURAL HERITAGE:MATERIALS ENHANCEMENT FORTECHNOLOGICAL APPLICATION

1. ANCIENT DNA1.1. What is it?

Any DNA recovered from…

1. ANCIENT DNA1.2. History of ancient DNA studies

1. ANCIENT DNA1.3. Polymerase chain reaction - PCR

Amplification of few and damaged DNA molecules

1. ANCIENT DNA1.4. Problems of ancient DNA studies

- Contamination with modern DNA

- Molecular damage

Oxidation

Microorganisms Crosslinks

Hydrolysis

1. ANCIENT DNA1.5. The nine “gold criteria” - Cooper and Poinar, 2000“Ancient DNA: do it right or not at all.” Science 289, 1139

1. ANCIENT DNA1.6. Anthropological applications

1. Phylogenetic analysis

OL

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

malesfemales

1. ANCIENT DNA1.6. Anthropological applications

2. Human evolutionOrigin of modern humans:- single - African- recent

“Mitochondrial Eve”

1. ANCIENT DNA1.6. Anthropological applications

2. Human evolutionNeandertal:our direct ancestor or a separate species?

Neanderthal range(350,000-30,000 ya)

Specimens AgeGeographi

clocation

Reference

Feldhofer 1 40,000 BP Germany Krings et al.,1997

Vindija 75 42,000 BP Croatia Krings et al. 2000

Mezmaiskaya 29,000 BP Caucasus Ovchinnikov et al. 2000

Feldhofer 2 40,000 BP Germany Schmitz et al. 2002

La Chapelle-aux-Saints 40,000-50,000 BP France Serre et al. 2004

Engis 2 40,000-50,000 BP Belgium Serre et al. 2004

Vindija 80 38,000 BP Croatia Serre et al. 2004

Vindija 77 40,000 BP Croatia Serre et al. 2004

Les Rochers de Villeneuve

40,700 BP France Beauval et al. 2005

El Sidron 441, 1252 43,000 BP Spain Lalueza-Fox et al. 2005, 2006

Monti Lessini 50,000 BP Italy Caramelli et al. 2006

Scladina 100,000 BP Belgium Orlando et al. 2006

Thelwe Neandertal specimens analysed for mtDNA

1. ANCIENT DNA1.6. Anthropological applications

Homo neanderthalensis Homo sapiens

Two different species!

Neandertal

AfricansNot-Africans

Africans

Modernhumans

1. ANCIENT DNA1.6. Anthropological applications

Krause et al., 2007

Lalueza-Fox et al., 2007

1. ANCIENT DNA1.6. Anthropological applications

Green et al., 2006

Green et al., 2008

Noonan et al., 2006

Green et al., 2010

Next Generation Sequencing technologies (NGS)

1. ANCIENT DNA1.6. Anthropological applications

3. Human migration Neolithic transition in Europe

10000 BP

9000 BP

8000 BP

7500 BP

6000 BP

6000 BP

8000 BP

7500 BP

7500 BP

7500 BP

1. ANCIENT DNA1.6. Anthropological applications

4. Kinship analysis Genetic investigation of multiple burials

Inference on social organization and funeral practices of the population examined

5. Molecular sex determination

Amelogenin gene: present on both X- and Y-chromosome

♂ ♀

112 bp

106 bp

Length polymorphism: 106 bp (X-chromosome) 112 bp (Y-chromosome)

1. ANCIENT DNA1.6. 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 DNA1.6. 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• 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 DNA1.6. 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 ISOTOPES2.1. 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 synthesized from dietary proteins turnover rate: ca. 10-15 years

dietary record of ca. 10 years prior to death

b) Distinct 13C/12C and 15N/14N of food resources

2. STABLE ISOTOPES2.1. Carbon and nitrogen stable isotope analysis

Isotope values are expressed in delta notation (): fractional difference in parts per thousand (‰) from a common standard:

13C (13C/12C)the most of biological material contain less 13C than the mineral used as the standard (PDB)

<0

15N (15N/14N)

the most of biological materials contain more 15N than the standard (air)

>0

(in ‰) = (Rx / Rs - 1) x1000

R: heavy isotope / light isotope

x: sample

s: standard

2. STABLE ISOTOPES2.1. Carbon and nitrogen stable isotope analysis

MARINEECOSYSTEM

TERRESTRIALECOSYSTEM

Carnivores

Herbivores

Omnivores

Shellfish

Fishes

Ichthyophagi

Marine mammalsMARINE DIET

TERRESTRIALC3 DIET

(wheat, legumes)

TERRESTRIALC4 DIET

(maize, millet)

2. STABLE ISOTOPES2.1. 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

Technicians: Dr. Irene Contini Dr. Flavio De Angelis

Postdoctoral researchers: Dr. Roberta Lelli Dr. Gabriele Scorrano

PhD students: Alessandro Cianfanelli Tullia Di Corcia Micaela Gnes Giusy Primativo

THANK YOUFOR THE

ATTENTION!