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MtDNA diversity in Central Africa: from hunter-gathering to agriculturalism

MtDNA diversity in Central Africa: from hunter-gathering to agriculturalism. CNRS-Institut Pasteur, Paris Lluis Quintana-Murci Blandine Massonnet Francesca Luca Hélène Quach. DDL, Lyon Lolke van der Veen Jean-Marie Hombert Lucas Sica Giselle X Patrick Mouguiama. MNHN, Paris

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MtDNA diversity in Central Africa: from hunter-gathering to agriculturalism

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  1. MtDNA diversity in Central Africa: from hunter-gathering to agriculturalism CNRS-Institut Pasteur, Paris Lluis Quintana-Murci Blandine Massonnet Francesca Luca Hélène Quach DDL, Lyon Lolke van der Veen Jean-Marie Hombert Lucas Sica Giselle X Patrick Mouguiama MNHN, Paris Evelyne Heyer Alain Froment Serge Bahuchet

  2. Questions • Is the linguistic grouping of populations supported by real genetic relationships? • Get genetic insights into the Bantu-speaking populations from Gabon • The putative Semitic origin of Fang populations • Clarify the origins of some mtDNA lineages • Shed light on the ways of migration of Bantu speaking populations from their homeland towards the east, southeast and southwest

  3. Questions…during the course of this project • Extending our area of study towards the north: Cameroon • Include Pygmy populations in our study • Understand to which extent the transition from hunter-gathering to agricultural lifestyle has influenced the genetic diversity of these populations • Evaluate the genetic exchange between agriculturalists and hunter-gatherers • Get insights into the gene pool of Pygmy populations: unique origin? Different origins? Common initial gene pool with agriculturalists?

  4. Central/West African collection: • 1258 samples from Gabon and Cameroon • 257 Pygmy samples • 1001 Bantu-speaking agriculturalists • Average sample size 55 (30-90) • - 20 Bantu-speaking agriculturalists pops: • GABON: Benga, Duma, Eviya, Fang, Galoa, Eshira, Kele, Kota, Makina, Ndumu, Nzebi, Obamba, Orungu, Punu, Shake, Teke, Tsogo • CAMEROON: Ewondo, Fang, Ngumba - 5 Pygmy populations: 2 Baka populations from Central/East Cameroon 1 Baka population from Gabon 1 Bakola population from Cameroon 1 Tikar/Medzan population from Cameroon

  5. D-LOOP OH 12S rRNA Cyt b mtDNA 16S rRNA ND5 ND6 ND1 - Maternally inherited Mitochondrial DNA 16.5 kb - No recombination ND2 ND4 OL ND4L - High mutation rate ND3 COX I A6 COX II A8 COX III

  6. Coding-region SNPs markers: • Advantages: • Define main lineage clusters in the mtDNA phylogeny • Reliable comparison of frequency clusters among populations • Mostly stable mutations • Disadvantages : • Bias in the definition of haplogroups? Partial information? • HVS-I sequence diversity: • Advantages: • No bias since all information is taken into consideration • High mutation rate -> useful in microevolutionary studies • Provide with useful information about demographic past • Disadvantages: • High mutation rate -> homoplasy -> under-estimation of population genetic distances Combined approach using both sets of markers

  7. Salas et al. 2002

  8. Schematic representation of African mtDNA phylogeny • Some lineages are defined on the basis of only HVS-I sequence data • Some HVS-I motifs are composed of highly-evolving mutations • Misleading phylogenetic classification of some lineages due to recurrent mutations Salas et al. AJHG (2002)

  9. COMPLETE MTDNA SEQUENCE LITERATURE -> L1 Root L2/L3

  10. L2 L3

  11. Our analyses • Sequence of HVS-I region • 25 coding-region SNP analyses taking into consideration previous phylogenies AND complete mtDNA sequence data phylogenies

  12. PYGMIES BANTUS Population diversity and structure Analysis of MOlecular VAriance • Entire sample • Among populations 8% • Within populations 92% Pygmies versus Bantu Among groups 16.3% Among population within groups 1.3% Within populations 82.3%

  13. Genetic diversity and neutrality tests • The 5 groups of Pygmies show signals of constant-size populations • All Bantu agriculturalists show signals of population expansion, with the exception of the Benga, the Eviya and the Ewondo

  14. SIGNIFICANT FST EXACT TEST OF SAMPLE DIFFERENTIATION POPULATION RELATIONSHIPS

  15. Northern cluster Principal components analyses 1,5 NZE MAK BEN FAN-C 1,0 DUM NGU TEK OBA KOT ,5 KEL GIS PC2 23% EWD FAN-G NDU 0,0 PUN -,5 SHA TSO -1,0 GAL -1,5 EVI -2,0 -3 -2 -1 0 1 2 PC1 50%

  16. Pygmy populations: Diversity and population distances

  17. 5 4 Khoisan 3 WA 2 Pygmies SEA PC2 16% 1 West/East/SE SA Pi 0 NA -1 Central Africa EA -2 CA_S North Africa -3 CA -3 -2 -1 0 1 2 PC1 28%

  18. MtDNA haplogroup diversity and phylogeography in Central Africa • Haplogroups L1c, L2a and L3e are the most represented in Central African populations • L1c is the most widespread lineage in all groups of Pygmies here studied (90-100%) • L1c is also the main lineage characterising Bantu-speaking agriculturalists from Gabon and Cameroon (25-50%)

  19. Frequency distribution of L1c and sublineages in Central Africa

  20. L1c phylogeny based on complete mtDNA sequences of Pygmy and Bantus

  21. Conclusions I • The linguistic northern cluster (Mitsogo, Galoa, Eviya) is supported by mtDNA data • The linguistic southern cluster seems less supported by genetic analyses, suggesting a more heterogeneous group of populations • Need for fine linguistic-genetic correlations studies

  22. Conclusions II • Apart of populations from the northern cluster, the Shake appears to be the most differentiated populations • The Fang population does not present an detectable trace of their Semitic origin -> Y-chromosome? • Our data suggest a Central African origin for L1c -> highest frequencies and diversity in Central Africa as compared to receivals areas such as the southwest and southeast

  23. Conclusions III: Pygmies • All Pygmy populations exhibit reduced diversity at both the haplogroup and sequence levels • Bantus and Pygmies share a common gene pool exemplified by the sharing of L1c lineage • Admixture between Pygmies and Bantus seems to have occurred in a single direction, since no other lineages than L1c have penetrated the Pygmy gene pool • In Western Pygmies, this lineage has reached almost fixation probably due to small population sizes and strong genetic drift • Need for further molecular characterization of L1c lineages since current phylogeny leads to misleading classification of some lineages

  24. Perspectives • Extending our analyses to the autosomes • Sequence-based genome-wide analyses in order to better infer demographic past of both agriculturalist and hunter-gatherer populations in central Africa • Infer the origin of Pygmy populations and evaluate genetic exchange with agriculturalist neighbors • Differential adaptation processes depending on lifestyle -> cultural behavior and infectious diseases

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