Human population phylogenetic studies using mithochondrial DNA

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Human population phylogenetic studies using
mithochondrial DNA
Dr Rym KEFI
MIGOD- Institut Pasteur -Tunis
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Plan
I- Introduction
II- Example I Mitochondrial DNA diversity of the
prehistoric population from Taforalt (12,000
years- Morocco).
II- Example Phylogenetic and Neandertal enigma.
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Introduction
The main aim of Human population genetics is to
find answers concerning

• Differentiation in single population
  (Bertranpetit et al 1995 Ann Hum Genet)

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• the migration patterns in certain geographic
  areas.

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• human evolution, and the spread of modern humans
  (Richards et al 1996, Am J Hum Genet )

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Mitochondrial DNA
an important tool for Human population genetics
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Mitochondrial DNA Studies history
Brown and Wallace in 1970 Pioneers in mtDNA
investigation

• 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 ) ,

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• on sequence analysis of the mtDNA control
  region

• 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)

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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

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Different mtDNA lineages have been diverged from
an ancestral women originated in Africa.
Mitochondrial Eve
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RFLPs studies of mtDNA from a wide range of
Human populations have revealed a number of
stable polymorphic sites in the mtDNA coding
region .
Define related groups of mtDNA called haplogroups

• 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

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• Alignment of sequences with mtDNA reference
  (CRS) using Blast 2 sequences

RFLP analysis
Haplotype and Haplogroup
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Examples
Individual 1
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Mitochondrial haplogroups
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• 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.

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Macaulay et al, 1999 , Am J Hum Genet,
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Example I Mitochondrial DNA diversity of the
prehistoric population from Taforalt (12,000
years- Morocco).
Dr Rym KEFI and Dr Eliane BERAUD-COLOMB U600
INSERM-FRE2059 CNRS Laboratoire d'Immunologie,
Hôpital de Sainte-Marguerite- Marseille- France
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Knowledge of the settlement of Northern Africa
region
Study of archaeological specimens and their
environment
Study of molecular diversity of modern Human
populations
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Anthropologic data
Transition from Homo erectus towards Homo
sapiens archaic
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Ibero-Maurusian man
Ibero-Maurusian industry
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(No Transcript)
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Ibero-maurusian man
Origins ???
1-Europian origin? (Vallois 1969, Ferembach 1985)

2- Near East origin ? (Vandermeersch 1978)
3- Subsaharian origin? (Ferembach 1976)
4- North African origin ? (Camps 1989, Dutour
1995)
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Genetic data
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

• Ancestral indigenous component U6- (Paleolithic
  45.000 years)

• Eurasiatic component T, H, U, J(Neolithic?
  9000 years)

• Sub-Saharan component L (Historic?)

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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
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The cave of Taforalt in Morocco
The cave of Taforalt is Located at 55 km in the
North-West of Oujda
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• 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)

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Mitochondrial DNA diversity of Taforalt
population

• 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.

• Genetic structure of Taforalt
• Eurasiatic Component
• H, U, JT, V 90,5
• North African component
• U6 9,5

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• 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
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Ibero-maurusian Origin
1-European origin? (Vallois 1969, Ferembach 1985)

2- Near East origin ? (Vandermeersch 1978)
3- Sub-Saharan origin? (Ferembach 1976)
4- local origin ? (Camps 1989, Dutour 1995)
Kefi et al 2005 Anthropologie Xliii/1 55-64
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Example 2
Phylogenetic and Neandertal enigma
Neandertal lived in Europe and west Asia
between 150.000 and 30.000 years (GrimaudHervé
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
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Many interrogations about the role of Neandertal
in the Human evolution.
Homo Sapiens sapiens
Homo neandertalensis

• Neandertal is he our ancestor?

• Did he belongs to another species?

• Did he contribute in our genetic inheritance? or

• did he disappear without leaving any trace in
  our genome?

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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.
Ancient bone
DNA
377 bp Neandertal sequence was aligned with CRS
(Cambridge reference sequence). The alignment
shows 27 differences (24 transitions, 2
tranversions, 1 deletion)
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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.
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NJ tree constructed with 986 modern Human mt DNA
sequences, 16 chimpanzee sequences and
Neandertal sequence
indicates that Neandertal position is distinct
from the group including all the Modern Human
sequences.
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Homo sapiens sapiens
Homo neandertalensis
These results show that Neandertal is not the
ancestor of the modern Human.
Homo sapiens sapiens and Homo neandertalensis
constitute two distinct species.
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Thank you
Marseille