Diapositiva 1

1
THE ANCIENT PEOPLING OF CENTRAL AFRICA A
GENETIC PERSPECTIVE
PhD candidate Chiara Batini
Scuola di dottorato in Biologia Animale, XX
ciclo Dipartimento di Biologia Animale e
dellUomo Sapienza Università di Roma
Supervisors Giovanni Destro-Bisol (Sapienza
Università di Roma), David Comas (UPF, Barcelona)
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Central Africa because

• paleoanthropological record is absent for the
  first phases of modern Homo sapiens evolution
  (the most ancient fossil being dated at 20 kya in
  Democratic Republic of Congo)
• archaeological record has been intensively
  studied in recent years, but it is still
  fragmentary post-depositional disturbance
  processes make the general picture unstable but
  there are indications of an early occupance of
  the area
• paleoclimatological record offers a still
  unstable picture in which cycles of expansion and
  fragmentation of tropical forests are documented
  and dated, at least for the last 40 kya
• linguistic record is well studied and the
  expansion of Bantu-speaking populations seems to
  have erased any trace of the languages spoken
  before 5 kya
• Pygmy populations still inhabit the area
  although theories on their origin and evolution
  are controversial, these are supposed to be in
  genetic continuity with the first inhabitants of
  the area
• genetic knowledge on sub-Saharan Africa is
  increasing considerably, because of the key role
  of this part of the continent in the evolution of
  our species

molecular anthropology could provide an
alternative approach to the study of the ancient
peopling of the area
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Aims

• describing variation in
• three Western Pygmy (Babinga, Baka and Bakola)
• one Eastern Pygmy (Mbuti)
• four Bantu-speaking populations (Bateke, divided
  in North and South, Beti and Ngoumba)
• searching for the presence of signatures of
  demographic processes pre-dating the Bantu
  expansion
• testing different evolutionary scenarios for the
  peopling of Central Africa and the relations
  between Western and Eastern Pygmies, based on
  archaeological, climatological and linguistic
  record

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Populations analysed and the database
POPULATIONS DESCRIBED IN THE PRESENT
THESIS (Babinga, Baka, Bakola, Mbuti, BatekeN,
BatekeS, Beti, Ngoumba)
FOOD PRODUCERS (FPs)
30 populations Ntot more than 1000
individuals
HUNTER-GATHERERS (HGs), OR PREVIOUSLY HGs
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Methods and Approaches
detailed study on Pygmy pops

• mtDNA
• HVR-1
• HVR-1 HVR-2
• complete sequences

• population approach

• phylogeographic approach

• Y-chr
• 6 STRs
• 10 STRs
• SNPs

qualitative test of hypotheses
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detailed study on Pygmy pops

• mtDNA
• HVR-1
• HVR-1 HVR-2
• complete sequences

• population approach

• phylogeographic approach

• Y-chr
• 6 STRs
• 10 STRs
• SNPs

qualitative test of hypotheses
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Population approach genetic characterization of
uniparental markers in Central African
populations Intra-population variation
Description of new populations
HGs Babinga Baka Bakola Mbuti FPs Bateke
N Bateke S Beti Ngoumba
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Population approach genetic characterization of
uniparental markers in Central African
populations Intra-population variation
Description of new populations
HGs
FPs
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Population approach genetic characterization of
uniparental markers in Central African
populations Intra-population variation
Comparison with the database

• Mann-Whitney U test (HGs vs FPs)
• all four comparisons give p lt 0.001 for mtDNA
• only p shows a significant difference between
  the two groups

in bold, populations studied in the present thesis
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Population approach genetic characterization of
uniparental markers in Central African
populations Inter-population variation Genetic
distances (MDS)
Y-chr (Fst distances) stress 0.063
mtDNA (pairwise distances) stress 0.034
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Population approach genetic characterization of
uniparental markers in Central African
populations Inter-population variation AMOVA
a.g variance among groups a.p.w.g. variance
among populations within groups w.p. variance
within populations
in bold not significant values
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Population approach genetic characterization of
uniparental markers in Central African
populations Inter-population variation
Discussion

• significant lower values for mtDNA
  intra-population diversity in HGs than in FPs
  (signals of population expansions)
• Y-chr parameters overlap between the two groups,
  with the only exception of p (opposite pattern
  between mtDNA and Y-chr)
• inter-population variation shows structuring for
  mtDNA and homogeneity for Y-chr

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detailed study on Pygmy pops

• mtDNA
• HVR-1
• HVR-1 HVR-2
• complete sequences

• population approach

• phylogeographic approach

two haplogroups selected L1c for mtDNA B for
Y-chr

• Y-chr
• 6 STRs
• 10 STRs
• SNPs

qualitative test of hypotheses
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Phylogeographic approach signatures of ancient
and recent demographic events in Central
Africa L1c - Background
geographic distribution
phylogenetic position
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Phylogeographic approach signatures of ancient
and recent demographic events in Central
Africa L1c Database and Frequencies

















total sample 455 individuals (N 232), HVR1
and HVR2 sequences
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Phylogeographic approach signatures of ancient
and recent demographic events in Central
Africa L1c - Results
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Phylogeographic approach signatures of ancient
and recent demographic events in Central
Africa L1c - Results
L1c1a, L1c4 and L1c5 in agreement with
constant-size population histories L1c1b,
L1c1c and L1c2 in agreement with expanding
population histories
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Phylogeographic approach signatures of ancient
and recent demographic events in Central
Africa L1c - Discussion

• identification of Western Pygmy mtDNA lineages
  (L1c1a, L1c4 and L1c5)
• common ancient origin of the ancestors of extant
  Bantu-speaking and Western Pygmy populations (90
  kya)
• ancient separation between the ancestors of the
  two groups (60-30 kya)
• recent gene flow from Western Pygmy to
  Bantu-speaking populations

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Phylogeographic approach signatures of ancient
and recent demographic events in Central Africa B
- Background
3 SNPs 16 STRs (only 10 STRs used in network
reconstructions for comparison with literature
data)
phylogenetic position geographic distribution
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Phylogeographic approach signatures of ancient
and recent demographic events in Central Africa B
Database and Frequencies













total sample 234 individuals (N 74), 10 STRs
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Phylogeographic approach signatures of ancient
and recent demographic events in Central Africa B
Results and Discussion
B2a
B2b
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Phylogeographic approach signatures of ancient
and recent demographic events in Central Africa B
Results and Discussion
B2a in agreement with expanding population
histories B2b in agreement with constant-size
population histories
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Phylogeographic approach signatures of ancient
and recent demographic events in Central Africa B
Results and Discussion

• recent origin of B2a in ancestral Bantu-speaking
  populations
• ancient origin of B2b, signals of a deep
  structure among hunter-gahterer populations
• further analyses in order to unravel the
  structure of B2b and better define the relations
  among HG haplotypes

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detailed study on Pygmy pops

• mtDNA
• HVR-1
• HVR-1 HVR-2
• complete sequences

• population approach

• phylogeographic approach

• Y-chr
• 6 STRs
• 10 STRs
• SNPs

qualitative test of hypotheses
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Complete mitochondrial variation in Pygmy
populations Database and Results
Intra-population
10 populations 206 individuals
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Complete mitochondrial variation in Pygmy
populations Results Inter-population
populations
69.1 of inertia represented
haplogroups
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Complete mitochondrial variation in Pygmy
populations Results Phylogenetic reconstruction
L0a
L1c
L5
L2a
L3
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Complete mitochondrial variation in Pygmy
populations Discussion and future studies

• clear-cut separation between Western and Eastern
  Pygmies
• new L2a branch
• future studies reconstruction of a
  maximum-parsimony tree calculation of the TMRCA
  for Eastern Pygmy specific clades

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detailed study on Pygmy pops

• mtDNA
• HVR-1
• HVR-1 HVR-2
• complete sequences

• population approach

• phylogeographic approach

• Y-chr
• 6 STRs
• 10 STRs
• SNPs

qualitative test of hypotheses
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A qualitative test of hypotheses presentation of
the three scenarios
HYPOTHESIS 1 (RECENT DIVERGENCE) Ancient unique
origin of Pygmies and recent contact with Bantu
(Cavalli-Sforza, 1986)
HYPOTHESIS 1 (RECENT DIVERGENCE) Ancient unique
origin of Pygmies and recent contact with Bantu
(Cavalli-Sforza, 1986)
HYPOTHESIS 2 (ANCIENT SEPARATION) Ancient
independent origin of Pygmies and recent contact
with Bantu (Cornelissen, 2002 Hiernaux, 1977)
HYPOTHESIS 2 (ANCIENT SEPARATION) Ancient
independent origin of Pygmies and recent contact
with Bantu (Cornelissen, 2002 Hiernaux, 1977)
HYPOTHESIS 3 (BLENCH) Recent origin of Pygmies as
a sub-group of Bantu (Blench, 1999)
HYPOTHESIS 3 (BLENCH) Recent origin of Pygmies as
a sub-group of Bantu (Blench, 1999)
P
P, Pygmies B, Bantu
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A qualitative test of hypotheses presentation of
the expected results
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A qualitative test of hypotheses presentation of
the observed results
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A qualitative test of hypotheses presentation of
the observed results
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A qualitative test of hypotheses Discussion

• the second scenario (ancient separation) is
  favoured, although some parameters show
  exceptions
• these exceptions can be explained by the
  influence of sociocultural factors and different
  population histories
• complete mitochondrial genome variation agrees
  with the second hypothesis
• the hypothesis proposed by Blench (Pygmies as a
  sub-group of Bantu speakers) is not supported by
  any of the parameters analysed

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Conclusions some general remarks and future
directions

• the population analyses confirmed the importance
  of sociocultural factors in shaping genetic
  diversity in sub-Saharan populations
• the phylogeographic analysis (L1c and B)
  highlighted signatures of ancient and recent
  demographic processes, providing a time-scale
  relative to the genetic systems considered
• the study of complete mitochondrial genomes
  confirmed the clear-cut difference between
  Western and Eastern Pygmies future studies will
  be necessary to better define specific Eastern
  Pygmy clades in order to calculate their TMRCAs
• the qualitative test of hypotheses allowed to
  define a working scenario, in which Western and
  Eastern Pygmy populations would have originated
  in separate processes, and would have shared a
  common history with FP populations of the same
  area
• a genomic approach would be necessary to gain a
  complete genetic perspective on the ancient
  peopling of Central Africa

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Acknowledgements
All blood donors that made this study possible.
UPF, Barcelona Jaume Bertranpetit Francesc
Calafell Monica Valles Stephanie Plaza Roger
Anglada
Sapienza Università di Roma Gabriella
Spedini Cinzia Battaggia Francesco Vecchi
RMCA, Tervuren Els Cornelissen Koen Bostoen
University of Utah, Salt Lake City Lynn Jorde
University of Oxford Cristian Capelli
Molecular Medicine Laboratory, Haifa Doron Behar