ALFRED: allele frequency database

The ALlele FREquency Database
ALFRED is a resource of gene frequency data on human populations
supported by the Yale Center for Medical Informatics.

00ALFRED detailed record information

Population Information

Name	ALFRED UID	Primary Language	Language Family
Pima, Mexico	PO000034H	PIMA BAJO, SONORA	UTO-AZTECAN

Synonyms:
Geographic Location¹: 30.5N, 109.5W; 28N, 108W

Sites typed for this population: View List
Population Samples: See Sample Information
External Resources: Fighting the Thrifty Gene Record Tepiman family Record Ethnologue: Language Map Record obesity and diabetes Record Ethnologue: Language Description Record
References: See references
Population Description: The Pima Bajo, also known as the "Mountain Pima" or O'ob, live in Mexico's Sierra Madre Mountains along the Sonora-Chihuahua border (roughly 200 miles south of Arizona). An estimated 2000 people speak their Uto-Aztecan language, which is similar but not identical to the Pima language spoken in Arizona. They still live in the Sierra Madre heartland. They have their own beliefs about their highland cousins that are distinct from their relatives in Arizona. The Mountain Pima live in small villages, making a living through subsistence farming for corn and beans, supplemented by local work and seasonal labor. The districts Yecora, Maycoba, and Yepachic are historic areas of the Pima Bajo have been lived on by the Pima for hundreds of years. Ethnographers believe that it is possible that the Pimas split shortly after the first contact with Europeans, perhaps as early as 1540.
References:
- Estrada Z "Pima Bajo dialectal variation ". Anthropological Linguistics 36:223-39. (1994)

- Laferriere JE "A dynamic nonlinear optimization study of Mountain Pima subsistence technology". Human ecology. 23:1-28. (1995)

- Laferriere JE. "Cultural and environmental response to drought among the Mountain Pima". Ecology of Food and Nutrition 28:1-9. (1992)

Sample Information:

Graph estimated heterozygosities for various sites

Sample Name: Mexican Pima, Related

Sample UID: SA000034H

Sample Description:Mexican Pima. This sample includes related individuals and is a superset of SA000026I.

Number of Chromosomes: 198

Relation to Other Samples: superset SA000026I

References:
- 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.

- Schulz LO, Bennett PH, Ravussin E, Kidd JR, Kidd KK, Esparza J, Valencia ME. "Effects of traditional and western environments on prevalence of type 2 diabetes in Pima Indians in Mexico and the U.S". Diabetes Care. 29:1866-71. (2006) 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.

Sample Information:

Graph estimated heterozygosities for various sites

Sample Name: Mexican Pima, Unrelated

Sample UID: SA000026I

Sample Description:Collected with informed consent from Pima individuals living near the eastern border of the state of Sonora, Mexico in the region around the village of Maycoba. Individuals of Pima heritage were identified by census of the region. Subjects were considered full Pima if both their parents were full Pima. This sample was Collected by L.O. Shulz.

Number of Chromosomes: 106

Relation to Other Samples: Unrelated individuals from the family material in SA000034H

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

- Knowler WC, Bennet PH, Hamman RF, Miller M. "Diabetes incidence and prevalence in Pima Indians: a 19-fold greater incidence than in Rochester, Minnesota". Am. J. Epidemiology 108:497. (1978) 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.

Sample Information:

Graph estimated heterozygosities for various sites

Sample Name: Pima, HGDP-CEPH

Sample UID: SA001511I

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).

Collected from Pima living near the eastern border of the state of Sonora, Mexico. Collected by L.O. Shulz.

Note: In many publications subset H952 of the HGDP panel (with first and second degree relatives excluded from the original set) was typed and for this population that decreases the sample size from 25 to 14 individuals.

Number of Chromosomes: 50

Relation to Other Samples: Subset of SA000026I

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.

- 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: Pima Mexico

Sample UID: SA003955W

Sample Description:This sample is the subset of the Kidd Lab Mexican Pima population sample.

Number of Chromosomes: 50

Relation to Other Samples: Subset of Sample SA000026I

References:
- Publication pending

Sample Information:

Graph estimated heterozygosities for various sites

Sample Name: Pima Mexico

Sample UID: SA004724R

Sample Description:This sample consists of Pima individuals from Mexico. 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: 196

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.

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Originally prototyped by Michael Osier with the aid of Kei Cheung
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