Rym kefi (1)
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Transcript of Rym kefi (1)
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 Polymorphism16126C, 16294T, 16296T, 16304C
+ RFLP (+13366 BamH1)
Haplotype Haplogroup: T 2
Individual 2:
HVS1 Polymorphism + RFLP 162 G - 7025 Alu I
H
Individual 1:
Mitochondrial haplogroups
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.
Macaulay et al, 1999; , Am J Hum Genet,
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 largeForte arcade sourcilièreOrbites rectangulairesPommettes saillantesMâchoire massivesquelette 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/ChloroformeExtraction
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 populationDébut et fin
de la séquenceTaf I 16054-16454 CRSTaf II 16054-16454 CRSTaf V 5 16054-16317 CRSTaf V 7 16081-16404 CRSTaf V 20 16054-16317 CRS H ou U ?Taf XVa 16054-16317 CRSTaf XV0 16054-16317 CRSTaf XVII 16054-16317 CRSTaf XIXa 16054-16317 CRSTaf XXI-6 16054-16317 CRSTaf XXV 16190-16317 CRSTaf 55-IB 16105-16317 16239 TTaf VI-10 16054-16317 16124T/C-16239T H ?Taf V 26 16054-16317 16204C-16226TTaf XVIa2-19 16054-16317 16189C-16261TTaf 55-I 16054-16454 16126C-16355TTaf V 18 16054-16317 16126C-16304C JTTaf XXV 3 16054-16317 16126 C Taf XXIV 16054-16317 16126C-16172C-
16174TU6
Taf VI9E 16054-16317 16172C-16174T U6Taf V 27 16054-16317 16298T/CTaf XIX 16054-16317 16179T-16298T/CTaf VIII 16054-16317 16223T L3, M, ou N ?
Spécimens Polymorphismes Haplogroupes
V
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 enigmaExample 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?
HomoSapienssapiens
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 boneDNA
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 sapiensHomo neandertalensis
Marseille