VERDU Paul

Résumé

2022 : Habilitation à Diriger des Recherches en Anthropologie et Génétique des Populations  
Délivrée par le Muséum National d’Histoire Naturelle 
Titre. :  Histoires de Métissages - Histories of Admixture : https://hal.science/tel-03817698

2015-présent : Co-coordinateur du plateau "Paléogénomique et génétique moléculaire" P2GM du MNHN au Musée de l’Homme 

2011-2015 : Conceptualisation, mise en oeuvre et maitrise d'oeuvre du chantier de construction du futur plateau Paléogénomique et génétique moléculaire P2GM du MNHN au Musée de l'Homme 
Travaux réalisés par les sociétés Léon Grosse, SDEL, UTB, Vulcain, Possémé, HeraSafe, Erlab et leurs sous-traitants, supervision OPPIC et MNHN 

2012-présent : Chargé de Recherche au CNRS affecté à l’UMR7206 
Section CoNRS de rattachement principale: Section 29 
Biodiversité, évolution et adaptations biologiques : des macromolécules aux communautés 
Section CoNRS de rattachement secondaire: Section 51 
Modélisation, et analyse des données et des systèmes biologiques : approches informatiques, mathématiques et physiques  

2011-2012 : Post Doctorat à Stanford University (Department of Biology, supervisor : Noah A. Rosenberg) 

2009-2011 : Post Doctorat à University of Michigan (Medical School, supervisor : Noah A. Rosenberg) 

2005-2009 : Thèse de doctorat en Anthropologie Biologique et Génétique des Populations Humaines 
Délivrée en janvier 2009 par l’Université Pierre et Marie Curie et le Muséum National d’Histoire Naturelle 
Dir. : Evelyne Heyer. Titre : Anthropologie Génétique des Populations Humaines d’Afrique Centrale : Histoire du Peuplement Pygmée 

2004-2005 : Master 2 de Génétique Humaine de l’Université Pierre et Marie Curie 

2001-2005 : Diplôme d’Ingénieur Agronome de l’AgroParisTech (anciennement INA P-G) 

1998-2001 : Classe Préparatoire Biologie, Chimie, Physique et Sciences de la Terre (Lycée Saint Louis, Paris)

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Research focus

Demographic, genetic, and cultural histories of modern human populations 
Sociocultural behaviours and human genetic diversity 
Cultural and anthropological categories and categorisation processes
Demographic inference with Approximate Bayesian Computation 
Mathematical modelling of complex admixture processes 
Computational sociolinguistics, language contacts and changes, population linguistics 
Human biological adaptation 

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Main Projects and Collaborations

Genetic and Linguistic admixture histories in Cabo Verde 
Funding 2015-2021 : ANR-15-CE32-0009-01

• Statistical description of genetic and linguistic diversity patterns within Cabo Verde
• Reconstructing genetic admixture histories with Approximate Bayesian Computations
• Reconstructing the history of linguistic diversity within the Kriolu language, as inter-individual manners of speaking Kriolu
• Joint reconstruction of genetic and linguistic histories with Approximate Bayesian Computations
  • Extrenal collaborators : Marlyse Baptista (University of Michigan) ; Jorge Rocha (CIBIO-Porto University) ;  Noah A. Rosenberg (Stanford University) ; Zachary S. Szpiech (Penn State University) ; Valentin Thouzeau (PSL University)
  • Intrenal collaborators UMR7206 : Romain Laurent ; Marta Ciccarella (PhD student, UMR7206)

 

METHIS : Influence of admixture histories on the genetic evolution of hybrid populations 
Funding 2015-2021 : ANR-15-CE32-0009-01

• Mathematical modelling of complex admixture histories
• Approximate Bayesian Computation methods for reconstructing complex admixture histories using genetic data
• Reconstructing the linguistic and genetic history of admixture in Cape Verdean Kriolu speaking populations
• Assortative mating, admixture-related natural selection and hybrid fitness in a re-introduced hybrid population of santworth (Arenaria grandiflora) : implications for bio-diversity conservation strategies
  • Extrenal collaborators : Marlyse Baptista (University of Michigan) ;  Erkan Buzbas (University of Idaho) ;  Nathalie Machon (MNHN Paris) ;  Jorge Rocha (CIBIO-Porto University) ;  Noah A. Rosenberg (Stanford University)
  • Intrenal collaborators UMR7206 : Frédéric Austerlitz  ;  Romain Laurent  ;  Bruno Toupance 

Origins, migrations and differential adaptation of Central African Pygmy and non-Pygmy populations

• Central African peopling history : Origins and past demography of Pygmy and neighboring non-Pygmy populations
• Sociocultural interactions and admixture patterns among Central African Pygmy and neighbouring non-Pygmy populations
• Genetic determination and differential evolution of Central African Pygmy and non-Pygmy adult height
  • Collaborators : Frédéric Austerlitz, Evelyne Heyer, Myriam Georges, Sylvie Le Bomin, Marie-France Mifune, Serge Bahuchet (CNRS-MNHN UMR7206) ; Alain Froment (IRD) ; Barry S. Hewlett (Washington State University) ; Arnaud Estoup (CBGP/INRA, Montpellier) ; Etienne Patin, Lluis Quintana-Murci (Institut Pasteur) ; Mattias Jakobsson, Carina Schelbusch (Uppsala University) : Alain Froment (IRD) ; Noémie S.A. Becker (LMU) ; Noah A. Rosenberg (Stanford University) ; Barry S. Hewlett (Washington State University)

Anthropology, Genetics, and Linguistics Field Works

• Mar. 2006 (50 days): Field work conducted by Paul Verdu and Sylvie Le Bomin and supervised by Sylvie Le Bomin
  • Ethno-anthropological field work with Bongo populations in south-eastern Gabon (Haut-Ogooué). 46 sampled DNA and ethnographic, ethnomusicological, and morphological data collection. (8000 euros)

• Mar. 2007 (50 d): Field work conducted by Paul Verdu in collaboration with Sylvie Le Bomin, Serge Bahuchet, Florence Bikoma, and Jean-Marie Betsch
  • Ethno-anthropological field work with Bongo populations in central Gabon (Ogooué-Lolo and Ngunié). 63 sampled DNA and ethnographic, ethnomusicological, and morphological data collection. (11000 euros)

• Sept. 2007 (40 d): Mission Coordinator - field work conducted with Marie-France Mifune
  • Ethno-anthropological field work with Nsua, Konjo, and Bamba populations in Ouganda (Bundibugyo district, North Ituri border with North-Kivu). 48 sampled DNA and ethnographic, ethnomusicological data collection. (9000 euros)

• July 2010 (20 d): Field work conducted by Paul Verdu and Marlyse Baptista and supervised by Marlyse Baptista
  • Linguistic and Ethno-anthropological field work in Cape Verde (Santiago island). 20 sampled DNA and familial and linguistic ethnographic data collection. (9000 euros)

• Feb. 2011 (20 d): Mission Coordinator
  • Ethno-anthropological field work with Bezan populations in Cameroun (Région Centre, Tikar Country). 56 sampled DNA and ethnographic data on mobility behaviours. Project ANR C3A. (6000 euros)

• Dec. 2011 (20 d): Field work conducted by Paul Verdu and Marlyse Baptista and supervised by Marlyse Baptista
  • Linguistic and Ethno-anthropological field work in Cape Verde (Santiago island). 30 sampled DNA and familial and linguistic ethnographic data collection. (9000 euros)

• Nov. 2013 (15 d): Mission coordinator
  • Return from the Project ANR C3A to Bezan populations in Cameroun (Région Centre, Tikar Country). (4000 euros)

• May 2014 (20 d): Mission coordinator - field work conducted with Marlyse Baptista, Sergio A. Costa, Ethan Jewett (student), and Mirian Barbosa (student)
  • Linguistic and Ethno-anthropological field work in Cape Verde (Santiago and Saõ Vicente islands). 36 sampled DNA and familial and linguistic ethnographic data collection. (10000 euros)

• May 2016 (40 d): Mission co-coordinator with Trevor J. Pemberton (University of Manitoba, Canada) - field work conducted with Alain Froment, Fernando Ramirez-Rossi, and Alexandra Blant (student)
  • Ethnographic, Anthropometric and Genetic field work in the Bezan and Tikar populations in Cameroun (Région Centre, Tikar Country), and in Baka and Nzimé populations in Cameroun (Région Est). 400 sampled DNA and ethnographic, biometric, and physiological data collection. (18000 euros)

• June 2016 (20 d): Mission coordinator - field work conducted with Marlyse Baptista, Sergio A. Costa, Valentin Thouzeau (student), and Ethan Jewett (student)
  • Linguistic and Ethno-anthropological field work in Cape Verde (Santo Antaõ and Saõ Vicente islands). 50 sampled DNA and familial and linguistic ethnographic data collection. (11000 euros)

• May 2017 (20 d): Mission coordinator - field work conducted with Marlyse Baptista, Sergio A. Costa, and Cesar Fortes-Lima (student)
  • Linguistic and Ethno-anthropological field work in Cape Verde (Fogo and Brava islands). 57 sampled DNA and familial and linguistic ethnographic data collection. (10000 euros)

• May 2018 (25 d): Mission coordinator - field work conducted with Marlyse Baptista, and Sergio A. Costa
  • Linguistic and Ethno-anthropological field work in Cape Verde (Sao Nicolau, Boa Vista and Santiago islands). 68 sampled DNA and familial and linguistic ethnographic data collection. (10000 euros)

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Students

• Present

2021-present:

Juliette Sauvage (PhD student, co-supervision: Céline Bon (UMR7206) and Marie-Claude Marsolier-Kergoat (CEA-UMR7206)): "Reconstructing the peopling history of the Bassin Parisien between the Mesolithic and the Middle Ages with paleogenomics"

2020-present:

Marta Ciccarella (PhD student, co-supervision: Jorge Rocha (CIBIO-Porto University), International FCT funding): "Inferring sex-biased admixture processes in human populations with Approximate Bayesian Computations: the case of Atlantic Slave Trade admixture in Cape Verde and São Tomé e Principé"

• Former

- Post-doctorate

Cesar Fortes-Lima - 2016-2018

Kazunari Matsudaira (collaboration with Pr. Hiroki Oota, University of Tokyo) - 2018

- PhD

Gwenna Breton, Uppsala University (co-supervision Mattias Jakobsson, Carina Schlebusch, Per Sjödin, Uppsala University): "Human demographi history: Insights on the human past based on genomes from Southern through Central Africa" - 2015-2020

Valentin Thouzeau, MNHN (co-supervision Frédéric Austerlitz, CNRS): "Reconstruire l’évolution biologique et culturelle des populations humaines par l’analyse simultanée des diversités linguistiques et génétiques" - 2014-2017

- Master 1 & 2 - Licence

Maël Pretet (Université de Paris) - 2021

François Mallordy (Ecole Normale Supérieure Ulm) - 2019

Ferdinand Petit (Université de Paris) - 2019

Marta Ciccarella (University of Bologna) - 2018

Antoine Cools (Ecole Nationale Supérieure des Mines de Nantes) - 2018

Claire Stragier (Université Paris 7) - 2015

Mirian Barbosa (UniCV, Cabo Verde) - 2014

Margueritte Lapierre (Fonctionnement du Vivant, INA P-G) - 2014

Amy Goldberg (University of Michigan) - 2011

Noémie Becker (INA P-G) - 2007-2008

Viola Grugni (Master 2 Erasmus, Université Paris 7) - 2008

Héloïse Bastide (Université Paris 7) - 2006

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Bibliographie

------------- 2022

42. Verdu P (2022)
Histories of Admixture
Habilitation à Diriger les Recherches MNHN - https://hal.science/tel-03817698

41. Laurent R, Szpiech ZA, da Costa SS, Thouzeau V, Fortes-Lima CA, Dessarps-Freichey F, Lemée L, Utgé J, Rosenberg NA, Baptista M, and Verdu P (2022)
Complex sociocultural dynamics during the Trans-Atlantic Slave Trade influenced the genetic and linguistic admixture histories of Cabo Verde.
eLife under Review. Preprint: bioRxiv, https://doi.org/10.1101/2022.04.11.487833

40. Thouzeau V, Affholder A, Mennecier P, Verdu P, and Austerlitz F (2022)
Inferring linguistic transmission between generations at the scale of individuals
Journal of Language Computation in Press. Preprint: bioRxiv, https://doi.org/10.1101/441246

 

------------- 2021

39. Choin J, Mendoza-Revilla J, Arauna LR, Cuadros-Espinoza S, Cassar O, Larena M, Min-Shan Ko A, Harmant C, Laurent R, Verdu P, Laval G, Boland A, Olaso R, Deleuze JF, Valentin F, Ko YC, Jakobsson M, Gessain A, Excoffier L, Stoneking M, Patin E, Quintana-Murci Ll (2021)
Genomic insights into population history and biological adaptation in Oceania
Nature 592 (7855), 583-589. https://doi.org/10.1038/s41586-021-03236-5

38. Fortes-Lima CA*, Laurent R*, Thouzeau V, Toupance, B and Verdu P (2021) * equal contributors
Complex genetic admixture histories reconstructed with Approximate Bayesian Computation 
Molecular Ecology Resources Online ahead of print  https://doi.org/10.1111/1755-0998.13325

> Editor's choice for Mol Ecol Res special issue "Machine Learning in Molecular Ecology"

 

------------- 2020

37. Fortes-Lima CA, Verdu P (2020)
Anthropological Genetics perspectives on the Transatlantic Slave Trade 
Human Molecular Genetics Online ahead of print  https://doi.org/10.1093/hmg/ddaa271

> Editor's invited Review article

 

------------- 2019

36. Verdu P (2019) 
Do You Consent to Participate in the Research Study? 
in The Secret Lives of Anthropologists: Lessons from the field. Ed. Bonnie L. Hewlett, Pub. Routledge Taylor and Francis, Chap. 14, pp. 279-298

35. Lopez M, Choin J, Sikora M, Siddle K, Harmant C, Costa HA, Silvert M, Mouguiama-Daouda P, Hombert JM, Froment A, Le Bomin S, Perry GH, Barreiro LB, Bustamante CD, Verdu P, Patin E and Quintana-Murci Ll (2019) 
Genomic Evidence for Local Adaptation of Hunter-Gatherers to the African Rainforest 
Current Biology Vol 29, pp.1-10

34. Verdu P (2019) 
Pourquoi la génétique des populations ne dit-elle rien sur l'autochtonie des populations Pygmées d'Afrique Centrale ? 
in Quel devenir pour les pygmées à l'orée du XXIe siècle ? Ed. Kulesza P and Robillard M, Editions L'Harmattan

 

------------- 2018

33. Estoup A, Verdu P, Marin J-M, Robert C, Dehne-Garcia A, Cornuet J-M, and Pudlo P (2018) 
Application of ABC to infer the genetic history of Pygmy hunter-gatherer populations from Western Central Africa 
in Handbook of Approximate Bayesian Computation Chapman and Hall/CRC, p. 541-567

32. Pemberton TJ*, Verdu P*, Becker NS, Willer CJ, Hewlett BS, Le Bomin S, Froment A, Rosenberg NA, and Heyer E (2018) * equal contributors 
A genome scan for genes underlying adult body size differences between Central African hunter-gatherers and farmers 
Human Genetics 137 (6-7), 487-509

31. Fortes-Lima C, Bybjerg-Grauholm J, Marin-Padrón LC, Gomez-Cabezas EJ, Bækvad-Hansen M, Søholm Hansen M, Le P, Hougaard DM, Verdu P, Mors O, Parra EJ, and Marcheco-Teruel B (2018) 
Exploring Cuba’s population structure and demographic history using genome-wide data 
Scientific Reports 8 (1), 11422

30. Lopez M*, Kousathanas A*, Quach H, Harmant C, Mouguiama-Daouda P, Hombert J-M, Froment A, Perry G.H., Barreiro L.B., Verdu P, Patin E and Quintana-Murci LL (2018)* equal contributors 
The demographic history and mutational load of African hunter-gatherers and farmers 
Nature Ecology & Evolution 2 (4), 721

29. Buzbas EO, Verdu P (2018) 
Inference on admixture fractions in a mechanistic model of recurrent admixture 
Theoretical Population Biology 122, 149-157

> Editor's choice for TPB special issue Paul Joyce 

28. Estoup A, Raynal L, Verdu P and Marin JM (2018) 
Model choice using Approximate Bayesian Computation and Random Forests: analyses based on model grouping to make inferences about the genetic history of Pygmy human populations 
Journal de la Société Française de Statistique 159 (3), 167-190

 

------------- 2017

27. Thouzeau V, Mennecier P, Verdu P*, Austerlitz F* (2017) * equal supervisors 
Genetic and linguistic histories in Central Asia inferred using Approximate Bayesian computations 
Proceedings of the Royal Society B 284 (1861), 20170706

26. Verdu P*, Jewett EM*, Pemberton TJ, Rosenberg NA** and Baptista M** (2017) * equal contributors,** equal supervisors 
Parallel Trajectories of Genetic and Linguistic Admixture in a Genetically Admixed Creole Population 
Current Biology Vol 27, Issue 16, pp. 2529–2535

25. Patin E*, Lopez M, Grollemund R, Verdu P, Harmant C, Quach H, Laval G, Perry GH, Barreiro LB, Froment A, Heyer E, Massougbodji A, Fortes-Lima C, Migot-Nabias F, Bellis G, Dugoujon J-M, Pereira JB, Fernandes V, Pereira L, Van der Veen L, Mouguiama-Daouda P, Bustamante CD, Hombert JM, Quintana-Murci Ll* (2017) * equal contributors 
Dispersals and genetic adaptation of Bantu-speaking populations in Africa and North America 
Science 356, 543–546

24. George H Perry and Verdu P (2017) 
Genomic perspectives on the history and evolutionary ecology of tropical rainforest occupation by humans 
Quaternary International 448, 150-157

> Editor's invited Review article

 

------------- 2016

23. Verdu P (Accepted 2015) 
Sociocultural behaviors and human genetic diversity 
in International Encyclopedia of Anthropology Wiley Publishing Group (Cambridge, UK)

> Editor's invited Review article

22. Verdu P (2016) 
African Pygmies 
Current Biology Jan 11 ;26(1):R12-4. doi:0.1016/j.cub.2015.10.023

> Editor's invited Review article

 

------------- 2015

21. Ségurel L and Verdu P (2015) 
Peut−on voir nos différences génétiques ? 
in Une Belle Histoire de l’Homme Ed. Evelyne Heyer ; Flammarion−MNHN, p. 24−26

20. Verdu P and Bahuchet S (2015) 
Comments on "Middle to Late Holocene Paleoclimatic Change and the Early Bantu Expansion in the Rain Forests of Western Central Africa" by K Bostoen, et al. 
Current Anthropology 56 (3), 354−384

19. Verdu P and Austerlitz F (2015) 
Post marital residence behaviours shape genetic variation in hunter−gatherer and agricultural populations from Central Africa 
Hunter Gatherer Research 1 (1), 107−124

 

------------- 2014

18. Goldberg A, Verdu P, and Rosenberg NA (2014) 
Autosomal admixture levels are informative about sex bias in admixed populations 
Genetics 198 (3), 1209−1229

17. Verdu P, Pemberton TJ, Laurent R, Kemp BM, Gonzalez-Oliver A, Gorodezky C, Hughes CE, Shattuck MR, Petzelt B, Mitchell J, Harry H, William T, Worl R, Cybulski JS, Rosenberg NA, and Malhi RS. (2014) 
Patterns of admixture and population structure in native populations of northwest North America 
Plos Genetics 10(8):e1004530. doi : 0.1371/journal.pgen.1004530. eCollection 2014.

16. Patin E, Siddle KJ, Laval G, Quach H, Harmant C, Becker N, Froment A, Régnault B, Lemée L, Gravel S, Hombert JM, Van der Veen L, Dominy NJ, Perry GH, Barreiro LB, Verdu P, Heyer E, and Quintana-Murci L (2014) 
The impact of agricultural emergence on the genetic history of African rainforest hunter-gatherers and agriculturalists 
Nature Communications 5:3163. doi : 10.1038/ncomms4163

15. Aimé C, Verdu P, Ségurel L, Martinez-Cruz B, Hegay T, Heyer E, and Austerlitz F (2014) 
Microsatellite data show recent demographic expansions in sedentary but not in nomadic human populations in Africa and Eurasia 
European Journal of Human Genetics doi : 10.1038/ejhg.2014.2

14. Verdu P (2014) 
Population Genetics of Central African Pygmies and non-Pygmies 
in Hunter-Gatherers of the Congo Basin : Culture, History and Biology of African Pygmies Ed. Barry S. Hewlett, Transaction Publishers, New Brunswick (New Jersey)

 

------------- 2013

13. Aimé C, Laval G, Patin E, Verdu P, Segurel L, Chaix R, Hegay T, Quintana-Murci L, Heyer E, and Austerlitz F (2013) 
Human genetic data reveal contrasting demographic patterns between sedentary and nomadic populations that predate the emergence of farming 
Molecular Biology and Evolution 30(12):2629-44

12. Verdu P, Becker NS, Froment A, Georges M, Grugni V, Quintana-Murci L, Hombert JM, Van der Veen L, Le Bomin S, Bahuchet S, Heyer E, and Austerlitz F (2013) 
Sociocultural behavior, sex-biased admixture, and effective population sizes in Central African Pygmies and non-Pygmies 
Molecular Biology and Evolution 30(4):918-937

11. Verdu P (2013) 
Perspectives de la génétique humaine sur l’origine et la diversité des populations pygmées d’Afrique centrale 
Journal des Africanistes Tome 82 - Fascicule 1-2 pp. 53-72

10. Becker NS, Verdu P, Georges M, Duquesnoy P, Froment A, Amselem S, Le Bouc Y, and Heyer E (2013) 
The role of GHR and IGF1 genes in the genetic determination of African pygmies’ short stature 
European Journal of Human Genetics 21(6):653-658

 

------------- 2012

9. Verdu P and Destro-Bisol G (2012) 
African Pygmies, what’s behind a name ? 
Human Biology 84(1):1-10

> Invited editorial

 

------------- 2011

8. Verdu P and Rosenberg NA (2011) 
A general mechanistic model for admixture histories of hybrid populations 
Genetics 189(4):1413-1426

> Editor's choice for the Decembre 2011 journal-issue highlights 

7. Becker NS*, Verdu P*, Froment A, Le Bomin S, Pagezy H, Bahuchet S, and Heyer E (2011) * equal contributors 
Indirect evidence for the genetic determination of short stature in African Pygmies 
American Journal of Physical Anthropology 145(3):390-401

 

------------- 2010

6. Verdu P, Leblois R, Froment A, Thery S, Bahuchet S, Rousset F, Heyer E, and Vitalis R (2010) 
Limited dispersal in mobile hunter-gatherer Baka Pygmies 
Biology Letters 6(6):858-861>/p>

5. Becker NS*, Verdu P*, Hewlett B*, and Pavard S* (2010) * equal contributors 
Can life history trade-offs explain the evolution of short stature in human pygmies ? A response to Migliano et al. (2007) 
Human Biology 82(1):17-27

 

------------- 2009

4. Verdu P, Austerlitz F, Estoup A, Vitalis R, Georges M, Thery S, Froment A, Le Bomin S, Gessain A, Hombert JM, Van der Veen L, Quintana-Murci L, Bahuchet S, and Heyer E (2009) 
Origins and genetic diversity of pygmy hunter-gatherers from Western Central Africa 
Current Biology 19(4):312-318

> Nature News 

> Science News 

 

------------- 2008

3. Quintana-Murci L, Quach H, Harmant C, Luca F, Massonnet B, Patin E, Sica L, Mouguiama-Daouda P, Comas D, Tzur S, Balanovsky O, Kidd KK, Kidd JR, van der Veen L, Hombert JM, Gessain A, Verdu P, Froment A, Bahuchet S, Heyer E, Dausset J, Salas A, and Behar DM (2008) 
Maternal traces of deep common ancestry and asymmetric gene flow between Pygmy hunter-gatherers and Bantu-speaking farmers 
Proceedings of the National Academy of Sciences 105(5):1596-1601

 

------------- 2006

2. Verdu P*, Barreiro LB*, Patin E, Gessain A, Cassar O, Kidd JR, Kidd KK, Behar DM, Froment A, Heyer E, Sica L, Casanova JL, Abel L, and Quintana-Murci L (2006) * equal contributors 
Evolutionary insights into the high worldwide prevalence of MBL2 deficiency alleles 
Human Molecular Genetics 15(17):2650-2658

> Editor's choice for cover image 

 

------------- 2005

1. Kim JJ, Verdu P, Pakstis AJ, Speed WC, Kidd JR, and Kidd KK (2005) 
Use of autosomal loci for clustering individuals and populations of East Asian origin 
Human Genetics 117(6):511-519