ALFRED: allele frequency database
      The ALlele FREquency Database   
ALFRED is a resource of gene frequency data on human populations
supported by the U. S. National Science Foundation.
00ALFRED detailed record information

Population Information

NameALFRED UIDPrimary LanguageLanguage Family
BiakaPO000005FYAKANIGER-CONGO

Synonyms:
Geographic Location1:  5N, 15E; 2N, 20E  

Sites typed for this population: View List
Population Samples: See Sample Information
External Resources:  African Art Museum: Yaka (Reference)erence Record     Medical Research Council of S. Africa (Reference) Record    Ethnologue: Language Map Record     Baika Pygmies and Bantu of Central Africa Article Record     Forest Monitor: C.A.R. Country Profile Record    Ethnologue: Language Description Record     National Geographic: Bayaka (Reference) Record     African Art Museum: Tribal Map Record    
References: See references
Population Description: The Biaka (Bayaka) are one of Africa's major "pygmy" groups, sometimes referred to as the "Western Pygmies". They live in the tropical rainforest that expands in a southeastern direction from the Lobaye River, in the southern region of the Central African Republic. Although no accurate census of this population has been done, they are estimated to number approximately 30,000 people. Most Biaka speak Aka, a Nilo-Saharan language, which is also spoken by neighboring farmers.

The Biaka live in nomadic bands and subsist through hunting and gathering. Nowadays this lifestyle is augmented through trade with farming villages. This exchange provides the Biaka with salt, agricultural products, tobacco, and metal in exchange for farm labor and meat.

It is estimated that the differences between Pygmies and their closest African neighbors are great enough to have required at least 10-20,000 years of isolation, considering that the gene flow between this two groups occurs at the rate of only 0.7% per generation (Cavalli-Sforza 1986). This population is discussed in L.L. Cavalli-Sforza, ed. (1986) African Pygmies, Academic Press, Inc., Orlando, in which he estimates that the Biaka may be strongly admixed with neighboring Bantu farmers. Wijsman (op.cit) estimates Bantu contribution to the Biaka gene pool to be about 65% (with many caveats).
References:
- Bird S. "Multidimensional exploration of online linguistic field data". Notes on Linguistics 2:123-44. (1999)

- Heymer A. "Bayaka-Pygmies (central Africa): giving, taking, sharing and rank order demonstration in relation with these behaviour patterns ". Homo 31:252-65. (1980)

- Heymer A. "Becoming sedentary, acculturation and infectious diseases: socio-ecological problems of the Bayaka Pygmies". Bull. Soc. Pathol. Exot. Filiales 78:226-38. (1985)

- Hochegger H, wa Sesemba NK. "Les Bayaka". Cahiers des Religions Africaines 9:137-43. (1975)



Sample Information:

Graph estimated heterozygosities for various sites

Sample Name: Pygmy

Sample UID: SA000388T

Sample Description:The Pygmy sample consists of 70 unrelated Pygmies from the Aka tribe, located in the Central African Republic.

Number of Chromosomes: 140

Relation to Other Samples:

References:
- Zekraoui L, Lagarde JP, Raisonnier A, Gerard N, Aouizerate A, Lucotte G. "High Frequency of the Apolipoprotein E*4 Allele in African Pygmies and Most of the African Populations in Sub-Saharan Africa". Hum. Biol. 69:575-81. (1997) Online citation.


Sample Information:

Graph estimated heterozygosities for various sites

Sample Name: Biaka Pygmies

Sample UID: SA000005F

Sample Description:This sample is comprised of Biaka, living in the village of Bagandu, in the southwest corner of the Central African Republic (3.42N; 18E altitude approximately 500m). This group is probably an admixture of 3/4 "non-pygmy" African ancestry and 1/4 Mbuti ancestry. The transformed cell lines were established by Judith R. Kidd. The sources of this sample are L. Cavalli-Sforza (Stanford University) and K.K. Kidd, J.R. Kidd (Yale University).

Number of Chromosomes: 140

Relation to Other Samples:

References:
- Bowcock AM, Bucci C, Hebert JM, Kidd JR, Kidd KK, JS Friedlaender, Cavalli-Sforza LL "Study of 47 DNA markers in five populations from four continents.". Gene Geography 1:47. (1987) Online citation.

- Bowcock AM, Hebert JM, Mountain JM, Kidd JR, Rogers J, Kidd KK, Cavalli-Sforza LL. "Study of an additional 58 DNA markers in five populations from four continents". Gene Geography 5:151-73. (1991) Online citation.

- Bowcock AM, Kidd JR, Mountain JL, Hebert JM, Carotenuto L, Kidd KK, Cavalli-Sforza LL. "Drift, admixture, and selection in human evolution: A study with DNA polymorphisms". Proceedings of the National Academy of Science USA 88:839-43. (1991) Online citation.

- Castiglione CM, Deinard AS, Speed WC, Sirugo G, Rosenbaum HC, Zhang Y, Grandy DK, Grigorenko EL, Bonne-Tamir B, Pakstis AJ, Kidd JR, Kidd KK. "Evolution of haplotypes at the DRD2 locus". Am. J. Hum. Genet. 57:1445-56. (1995) Online citation.

- Chang FM, Kidd JR, Livak KJ, Pakstis AJ, Kidd KK. "The world-wide distribution of allele frequencies at the human dopamine D4 receptor locus". Hum. Genet. 98:91-101. (1996) Online citation.

- Kang AM, Palmatier MA, Kidd KK. "Global variation of a 40-bp VNTR in the 3'-untranslated region of the dopamine transporter gene (SLC6A3)". Biological Psychiatry 46:151-60. (1999) Online citation.

- Kidd JR, Pakstis AJ, Kidd KK. "Global levels of DNA variation". Proceedings of the 4th International Symposium on Human Identification 1993 (Promega) 21-30. (1993)

- Kidd JR. "Population genetics and population history of Amerindians as reflected by nuclear DNA variation". Ph.D. dissertation, Yale University (1993)

- Kidd KK et al. http://info.med.yale.edu/genetics/kkidd/pops.html

- Kidd KK, Morar B, Castiglione CM, Zhao H, Pakstis AJ, Speed WC, Bonne-Tamir B, Lu RB, Goldman D, Lee C, Nam YS, Grandy DK, Jenkins T, Kidd JR. "A global survey of haplotype frequencies and linkage disequilibrium at the DRD2 locus". Hum. Genet. 103:211-27. (1998) Online citation.

- Mateu E, Calafell F, Bonne-Tamir B, Kidd JR, Casals T, Kidd KK, Bertranpetit J. "Allele Frequencies in a Worldwide Survey of a CA Repeat in the First Intron of the CFTR Gene". Human Heredity 49:15-20. (1999) Online citation.

- Palmatier MA, Kang AM, Kidd KK. "Global variation in the frequencies of functionally different catechol-O-methyltransferase alleles". Biol. Psychiatry. 46:557-67. (1999) Online citation.

- Tishkoff SA, Dietzsch E, Speed W, Pakstis AJ, Cheung K, Kidd JR, Bonne-Tamir B, Santachiara-Benerecetti AS, Moral P, Watson E, Krings M, Paabo S, Risch N, Jenkins T, Kidd KK. "Global patterns of linkage disequilibrium at the CD4 locus and modern human origins". Science 271:1380-7. (1996) Online citation.

- Tishkoff SA, Goldman A, Calafell F, Speed WC, Deinard AS, Bonne-Tamir B, Kidd JR, Pakstis AJ, Jenkins T, Kidd KK. "A global haplotype analysis of the myotonic dystrophy locus: implications for the evolution of modern humans and for the origin of myotonic dystrophy mutations". Am. J. Hum. Genet. 62:1389-402. (1998) Online citation.

- Tishkoff SA, Goldman A, Calafell F, Speed WC, Deinard AS, Bonne-Tamir B, Kidd JR, Pakstis AJ, Jenkins T, Kidd KK. "A global haplotype analysis of the myotonic dystrophy locus: implications for the evolution of modern humans and for the origin of myotonic dystrophy mutations". Am. J. Hum. Genet. 62:1389-402. (1998) Online citation.

- Tishkoff SA, Ruano G, Kidd JR, Kidd KK. "Distribution and frequency of a polymorphic Alu insertion at the plasminogen activator locus in humans". Hum. Genet. 97:759-64. (1996) Online citation.


Sample Information:

Graph estimated heterozygosities for various sites

Sample Name: Pygmy-CAR

Sample UID: SA000518O

Sample Description:This sample is comprised of Biaka, living in the village of Bagandu, in the southwest corner of the Central African Republic (3.42N; 18E altitude approximately 500m). This group is probably an admixture of 3/4 "non-pygmy" African ancestry and 1/4 Mbuti ancestry. The transformed cell lines were established by Judith R. Kidd. The sources of this sample are L. Cavalli-Sforza (Stanford University) and K.K. Kidd, J.R. Kidd (Yale University).

Number of Chromosomes: 34

Relation to Other Samples: Subset of SA000005F

References:
- Bowcock AM, Bucci C, Hebert JM, Kidd JR, Kidd KK, JS Friedlaender, Cavalli-Sforza LL "Study of 47 DNA markers in five populations from four continents.". Gene Geography 1:47. (1987) Online citation.


Sample Information:

Graph estimated heterozygosities for various sites

Sample Name: Biaka Pygmies

Sample UID: SA000481N

Sample Description:This sample is comprised of Biaka, living in the village of Bagandu, in the southwest corner of the Central African Republic (3.42N; 18E altitude approximately 500m). This group is probably an admixture of 3/4 "non-pygmy" African ancestry and 1/4 Mbuti ancestry. The transformed cell lines were established by Judith R. Kidd. The sources of this sample are L. Cavalli-Sforza (Stanford University) and K.K. Kidd, J.R. Kidd (Yale University).

Number of Chromosomes: 10

Relation to Other Samples: subset of sample SA000005F

References:
- Jorde LB, Bamshad MJ, Watkins WS, Zenger R, Fraley AE, Krakowiak PA, Carpenter KD, Soodyall H, Jenkins T, Rogers AR. "Origins and affinities of modern humans: a comparison of mitochondrial and nuclear genetic data.". Am. J. Hum. Genet. 57:523-538. (1995) Online citation.


Sample Information:

Graph estimated heterozygosities for various sites

Sample Name: Biaka

Sample UID: SA001803M

Sample Description:This sample is comprised of Biaka, living in the village of Bagandu, in the southwest corner of the Central African Republic (3.42N; 18E altitude approximately 500m). This group is probably an admixture of 3/4 "non-pygmy" African ancestry and 1/4 Mbuti ancestry. The transformed cell lines were established by Judith R. Kidd. The sources of this sample are L. Cavalli-Sforza (Stanford University) and K.K. Kidd, J.R. Kidd (Yale University).

This sample is a subset of SA000005F

Number of Chromosomes: 48

Relation to Other Samples: Subset of SA000005F

References:
- Verdu P, Barreiro LB, Patin E, Gessain A, Cassar O, Kidd JR, Kidd KK, Behar DM, Froment A, Heyer E, Sica L, Casanova J-L, Abel L, Quintana-Murci L. "Evolutionary Insights into the High Worldwide Prevalence of MBL2 Deficiency Alleles". Hum Mol Genet. 15:2650-2658. (2006) Online citation.


Sample Information:

Graph estimated heterozygosities for various sites

Sample Name: Biaka Pygmies, HGDP-CEPH

Sample UID: SA001465Q

Sample Description:This sample is part of the Human Genome Diversity Cell Line Panel collected by the Human Genome Diversity Project (HGDP) and the Foundation Jean Dausset (CEPH).

This sample is comprised of Biaka, living in the village of Bagandu, in the southwest corner of the Central African Republic (3.42N; 18E altitude approximately 500m). This group is probably an admixture of 3/4 "non-pygmy" African ancestry and 1/4 Mbuti ancestry. The transformed cell lines were established by Judith R. Kidd. The sources of this sample are L. Cavalli-Sforza (Stanford University) and K.K. Kidd, J.R. Kidd (Yale University).

Number of Chromosomes: 72

Relation to Other Samples: Subset of SA000005F

References:
- Rosenberg NA, Pritchard JK, Weber JL, Cann HM, Kidd KK, Zhivotovsky LA, Feldman MW. "Genetic structure of human populations". Science 298:2381-2385. (2002) Online citation.


Sample Information:

Graph estimated heterozygosities for various sites

Sample Name: Biaka Pygmies, HGDP-CEPH

Sample UID: SA002256P

Sample Description:This sample is part of the Human Genome Diversity Cell Line Panel collected by the Human Genome Diversity Project (HGDP) and the Foundation Jean Dausset (CEPH).

This sample is comprised of Biaka, living in the village of Bagandu, in the southwest corner of the Central African Republic (3.42N; 18E altitude approximately 500m). This group is probably an admixture of 3/4 "non-pygmy" African ancestry and 1/4 Mbuti ancestry. The transformed cell lines were established by Judith R. Kidd. The sources of this sample are L. Cavalli-Sforza (Stanford University) and K.K. Kidd, J.R. Kidd (Yale University).

This sample is known as dataset "H1048" and is a subset of SA001465Q.

Note: In many publications subset H952 of the HGDP panel (with first and second degree relatives excluded ) was typed and for this population that decreases the sample size from 32 to 23 individuals. Studies that typed subset "H971" of the HGDP panel with only the first degree relatives excluded the sample size decreases from 32 to 27.

Number of Chromosomes: 64

Relation to Other Samples: Subset of SA001465Q

References:
- Rosenberg NA. "Standardized subsets of the HGDP-CEPH Human Genome Diversity Cell Line Panel, accounting for atypical and duplicated samples and pairs of close relatives.". Ann Hum Genet. 70:841-847. (2006) Online citation.


Sample Information:

Graph estimated heterozygosities for various sites

Sample Name: Biaka Pygmy

Sample UID: SA002346P

Sample Description:This sample consists of Biaka Pygmies.

Number of Chromosomes: 70

Relation to Other Samples:

References:
- Su B, Jin L, Hu F, Xiao J, Luo J, Lu D, Zhang W, Chu J, Du R, Geng Z, Qiu X, Xue J, Tan J, O'Brien SJ, Chakraborty R "Distribution of two HIV-1-resistant polymorphisms (SDF1-3'A and CCR2-64I) in East Asian and world populations and its implication in AIDS epidemiology". Am J Hum Genet. 65:1047-53. (1999) Online citation.

- Su B, Sun G, Lu D, Xiao J, Hu F, Chakraborty R, Deka R, Jin L "Distribution of three HIV-1 resistance-conferring polymorphisms (SDF1-3'A, CCR2-641, and CCR5-delta32) in global populations". Eur J Hum Genet. 8:975-9. (2000) Online citation.


Sample Information:

Graph estimated heterozygosities for various sites

Sample Name: Biaka Pygmy

Sample UID: SA004686Y

Sample Description:This sample consists of Biaka individuals from Central Africa. Written informed consent was obtained from all individuals. This sample is part of Caixia Li's group in Institute of Forensic Science, Beijing, China. It was provided by the Kenneth K. Kidd's laboratory to Caixia lab.

Number of Chromosomes: 140

Relation to Other Samples:

References:
- Jiang L, Wei YL, Zhao L, Li N, Liu T, Liu HB, Ren LJ, Li JL, Hao HF, Li Q, Li CX. "Global analysis of population stratification using a smart panel of 27 continental ancestry-informative SNPs". Forensic Sci Int Genet. 35:e10-e12. (2018) Online citation.


1Geographic Coordinates represent two opposite corners of a rectangle encompassing the area where the population lives.This data is preliminary and changing.

Top


© 2018 Kenneth K Kidd, Yale University. All rights reserved. The full Copyright Notification is also available.
Originally prototyped by Michael Osier with the aid of Kei Cheung
Upgrades and maintenance since 2002 by Haseena Rajeevan