Presentation on theme: "Human population phylogenetic studies using mithochondrial DNA Dr Rym KEFI MIGOD- Institut Pasteur -Tunis."— Presentation transcript:
Human population phylogenetic studies using mithochondrial DNA Dr Rym KEFI MIGOD- Institut Pasteur -Tunis
Plan: I- Introduction II- Example : Phylogenetic and Neandertal enigma. II- Example I: Mitochondrial DNA diversity of the prehistoric population from Taforalt (12,000 years- Morocco).
The main aim of Human population genetics is to find answers concerning: Introduction Differentiation in single population (Bertranpetit et al 1995; Ann Hum Genet)
the migration patterns in certain geographic areas.
human evolution, and the spread of modern humans (Richards et al 1996, Am J Hum Genet )
mitochondria Eukariotic cellule 16569 bp circular DNA D-Loop: HVS I and HVS II segments Mitochondrial DNA maternal inheritance high mutation rate compared to nuclear DNA absence of recombination an important tool for Human population genetics
The studies of mtDNA polymorphism in human populations were based: initially on restriction enzyme (RFLP) analysis : Low resolution restriction and high resolution restriction mapping (Horai et al 1984, Johnson et al 1983, Horai et al 1984, Cann et al 1987, Torroni et al 1993 ), Brown and Wallace in 1970: Pioneers in mtDNA investigation Mitochondrial DNA Studies history:
on combined method using sequence analysis and restriction mapping (Bertranpetit et al 1995, Vigilant et al 1991, Richards et al 1996, Richards et al 1998, Macaulay 1999, Torroni et al 2001, Maca-Meyer et al 2001, Salas et al 2002) on sequence analysis of the mtDNA control region
Mitochondrial Eve Cann et al; Nature 1987 147 individuals from five geographic populations: Europe, Africa, Asia, Australia, New Guinea have been analysed by high- resolution restriction mapping Sub-Saharan African individuals present the most variable mtDNA sequences
Different mtDNA lineages have been diverged from an ancestral women originated in Africa. Mitochondrial Eve
RFLPs studies of mtDNA from a wide range of Human populations have revealed a number of stable polymorphic sites in the mtDNA coding region. Mutations observed in both mtDNA coding region and control region in modern human populations have occurred on these pre-existing haplogroups Define the individual mtDNA type or haplotypes Define related groups of mtDNA called haplogroups
Alignment of sequences with mtDNA reference (CRS) using “Blast 2 sequences” 16126C 16294T 16296T 16304C Haplotype and Haplogroup + RFLP analysis
Examples : HVS1 Polymorphism 16126C, 16294T, 16296T, 16304C + RFLP (+13366 BamH1) Haplotype Haplogroup: T 2 Individual 2: HVS1 Polymorphism + RFLP 162 G - 7025 Alu I H Individual 1:
The phylogenetic relationships between haplotypes were inferred in the first studies by Maximum parsimony tree Then by Neighbor- joining trees Later by Median joining network. Trees were based on distance data calculated from Nucleotide sequence or RFLPs data or Nucleotide sequence combined with RFLPs data.
Dr Rym KEFI and Dr Eliane BERAUD-COLOMB U600 INSERM-FRE2059 CNRS Laboratoire d'Immunologie, Hôpital de Sainte-Marguerite- Marseille- France Example I: Mitochondrial DNA diversity of the prehistoric population from Taforalt (12,000 years- Morocco).
Knowledge of the settlement of Northern Africa region Study of molecular diversity of modern Human populations Study of archaeological specimens and their environment
Anthropologic data Transition from Homo erectus towards Homo sapiens archaic From 40.000 years to 20.000 years: Homo sapiens sapiens (Dar Es Soltan, Temara, Maroc) Sidi Abderrahman: 200.000 years Aîn hanech, Salé: 160.000 years Djebel Irhoud: 100.000 years (Morocco) Homo erectus old of 700.000 years BP (site of Ternifine in Algeria). Aterian industry
Epipaleolitic period : 20.000 years to 10.000 years BP Ibero-Maurusian man Ibero-Maurusian industry
Face basse et large Forte arcade sourcilière Orbites rectangulaires Pommettes saillantes Mâchoire massive squelette robuste avulsion des incisives (Ferembach 1962-Camps 1989) Homme de Mechta El -Arbi Taforalt Afalou Columnata
Ibero-maurusian man 1-Europian origin? (Vallois 1969, Ferembach 1985) 2- Near East origin ? (Vandermeersch 1978) 4- North African origin ? (Camps 1989, Dutour 1995) 3- Subsaharian origin? (Ferembach 1976) Origins ???
Ancestral indigenous component: U6- (Paleolithic: 45.000 years) Eurasiatic component: T, H, U, J…(Neolithic?: 9000 years) Sub-Saharan component : L (Historic?) Former studies using Mitochondrial DNA (Côrte-Real et al. 1996; Rando et al. 1998; Comas et al. 2000; Brakez et al. 2001; Esteban et al. 2004 … ) showed that the genetic structure of North Africa is composed of 3 components: Genetic data
to contribute to the knowledge of North Africa settlement We proposed to analyse the mitochondrial DNA diversity of the prehistoric population from Taforalt (13,000 years BP- Morocco). Aim:
The population of Taforalt (13,000 years BP- Morocco). The cave of Taforalt in Morocco 28 burials 200 skeletons The cave of Taforalt is Located at 55 km in the North- West of Oujda
Ancient DNA was extracted from 31 bone remains from Taforalt Phenol/Chloroforme Extraction Dissolution of bone powders ADN Hypervariable segment 1 (HVS1) of control region (D-Loop) was amplified by PCR and sequenced (R. Kefi et al; C.R.Palévol 2003)
Mitochondrial DNA diversity of Taforalt population Genetic structure of Taforalt: Eurasiatic Component : H, U, JT, V: 90,5% North African component: U6: 9,5% 42,8% (9/21) H ou U 14,2% (3/21) JT 2 individuals (9,5%) U6 In modern Human population, JT is presents only in: 1,6% Berbers from the North of Morocco 1,8% of Sicilians, 1,6% of Italians. 19% (4/21) H 2 individuals (9,5%) V
The genetic inheritance of Taforalt population (12,000 years) is composed of: Eurasiatic component (J/T, H, U et V) North African component (U6). Similarities between Taforalt and Moroccan populations (Berbers from the North of Morocco) Underline a genetic continuity
Ibero-maurusian Origin 4- local origin ? (Camps 1989, Dutour 1995) 3- Sub-Saharan origin? (Ferembach 1976) 1-European origin? (Vallois 1969, Ferembach 1985) 2- Near East origin ? (Vandermeersch 1978) Kefi et al 2005 Anthropologie ; Xliii/1: 55-64
Phylogenetic and Neandertal enigma Example 2: Neandertal lived in Europe and west Asia between 150.000 and 30.000 years (Grimaud–Hervé et al 2001, Klein et al 2003) Neandertal has specific morphological characters (lengthened Cranium, presence of Taurus on orbits, big cranial capacity...) which distinguish him from the anatomically modern man Neandertal coexisted with anatomically modern man, before disappearing 30.000 years ago
Many interrogations about the role of Neandertal in the Human evolution. Neandertal is he our ancestor? Did he contribute in our genetic inheritance? or did he disappear without leaving any trace in our genome? Homo Sapiens sapiens Homo neandertalensis Did he belongs to another species?
Krings and collaborators (Krings et al. 1997, Cell) studied for the first time ancient DNA extracted from Neandertal humerus. Neandertal was discovered in West Germany. 377 bp Neandertal sequence was aligned with CRS (Cambridge reference sequence). The alignment shows 27 differences (24 transitions, 2 tranversions, 1 deletion) Ancient bone DNA
Neandertal sequence was compared to 994 mt DNA sequences from the five continents. The difference between the Modern Man and Neandertal is higher than the intra specific diversity in Modern Human specie.
indicates that Neandertal position is distinct from the group including all the Modern Human sequences. NJ tree constructed with 986 modern Human mt DNA sequences, 16 chimpanzee sequences and Neandertal sequence
These results show that Neandertal is not the ancestor of the modern Human. Homo sapiens sapiens and Homo neandertalensis constitute two distinct species. Homo sapiens sapiens Homo neandertalensis