A nuclear perspective on human evolution

Kidd, K.K.; Kidd, Judith R.

doi:10.1017/cbo9780511525643.018

Cited by 19 publications

(13 citation statements)

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“…The thousands of new genetic markers identified directly in DNA, of which SNPs are the largest class, are far less well-studied for gene frequency variation than the classical markers. However, the available data confirm the earlier studies that significant allele frequency variation among populations is the expectation (e.g., Kidd and Kidd, 1996;Calafell et al, 1998;Osier et al, 1999;Jorde et al, 2000); it will be a very rare SNP, STRP, or other DNA polymorphism that has nearly the same allele frequencies around the world.…”

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confidence: 79%

ALFRED: An allele frequency database for anthropology

Osier

Cheung

Kidd

et al. 2002

American J Phys Anthropol

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The deluge of data from the human genome project (HGP) presents new opportunities for molecular anthropologists to study human variation through the promise of vast numbers of new polymorphisms (e.g., single nucleotide polymorphisms or SNPs). Collecting the resulting data into a single, easily accessible resource will be important to facilitate this research. We created a prototype Web-accessible database named ALFRED (ALelle FREquency Database, http://alfred.med.yale.edu/alfred/) to store and make publicly available allele frequency data on diverse polymorphic sites for many populations. In constructing this database, we considered many different concerns relating to the types of information needed for anthropology, population genetics, molecular genetics, and statistics, as well as issues of data integrity and ease of access to data. We also developed links to other Web-based databases as well as procedures for others to make links to the data in ALFRED. Here we present an overview of the issues considered and provisional solutions, as well as an example of data already available. It is our hope that this database will be useful for research and teaching in a wide range of fields, and that colleagues from various fields will contribute to making ALFRED an important resource for many studies as yet unforeseen.

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supporting

confidence: 79%

ALFRED: An allele frequency database for anthropology

Osier

Cheung

Kidd

et al. 2002

American J Phys Anthropol

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“…In light of the reality of selection in the radiation of human mtDNA lineages (Ruiz-Pesini et al 2004), one could conclude that haplotypes distributed through and around some key nuclear genes, such as p53, will very useful for further population investigations because ''... they can be extremely valuable for elucidating not only the existing distribution of variation but also the more important causes of that distribution'' (Kidd and Kidd 1996).…”

Section: Discussionmentioning

confidence: 99%

p53 polymorphisms in Russia and Belarus: correlation of the 2-1-1 haplotype frequency with longitude

et al. 2005

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Four different polymorphisms in the human p53 gene (a 16-bp duplication in intron 3, and three RFLPs: for Bsh1236I at codon 72, for MspI in intron 6 and for BamHI in the 3' flanking region) and extended haplotypes were studied in nine geographically diverse populations from Russia and Belarus. The Yakuts differed from all other populations, as they had a significantly higher frequency of the BamHI A1 allele. Most populations did not differ significantly from each other in the frequency of the Bsh1236I polymorphism. The 16-bp duplication A1 allele and MspI A2 allele frequencies were significantly higher in the Yakut and Khant populations. Linkage disequilibrium values (D') between BamHI and other polymorphic sites were not significant in many cases; for this reason we have used the 16 bp-Bsh1236I-MspI haplotype frequencies only. Of eight possible haplotypes, five were observed in the populations investigated. Haplotype 1-2-2 was the most frequent in all populations. The next most common haplotype, 1-1-2, was present at very similar frequencies among the Byelorussians and Russians from Smolensk, but was more frequent in other populations. The frequency of haplotype 2-1-1 showed a nearly continuous decrease from West to East (from 17.857% among the Byelorussians to 0.685% in the Yakuts from the Verkhoyansk) and correlated with longitude (Spearman's r = -0.8667, P = 0.0025), which may be due to natural selection and adaptation. The relationships among populations were evaluated by means of Nei's D(A) distances for the 16 bp-Bsh1236I-MspI haplotype frequencies. Based on the multidimensional scaling analysis a correlation between p53 haplotype frequencies and ethnicity is supposed.

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“…Genetic trees show Africans at one end and, at successive splits, Europeans, East Asians, and Native Americans. A higher heterogeneity in Africans and/or a genetic tree in which Africans branch first have been repeatedly shown by different types of nuclear genetic markers: STRPs, 3,10,11,17,23 single nucleotide polymorphisms, 47 minisatellites, 54 haplotyes, 16,17,55 and Alu sequences. 56 This could be explained by a recent African origin of anatomically modern humans, which is consistent with the date estimates obtained by us and by Goldstein et al, 23 which place an upper limit for the generation of STRP variation at same 220 000 years ago.…”

Section: Genetic Driftmentioning

confidence: 95%

Short tandem repeat polymorphism evolution in humans

et al. 1998

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Forty-five dinucleotide short tandem repeat polymorphisms were typed in ten large samples of a globally distributed set of populations. Although these markers had been selected for high heterozygosity in European populations, we found them to be sufficiently informative for linkage analysis in nonEuropeans. Heterozygosity, mean number of alleles, and mean number of private alleles followed a common trend: they were highest in the African samples, were somewhat lower in Europeans and East Asians, and were lowest in Amerindians. Genetic distances also reflected this pattern, and distances modelled after the stepwise mutation model yielded trees that were less in agreement with other genetic and archaeological evidence than distances based on differentiation by drift (F ST ). Genetic variation in nonAfricans seems to be a subset of that in Africans, supporting the replacement hypothesis for the origin of modern humans.

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A nuclear perspective on human evolution

Cited by 19 publications

References 0 publications

ALFRED: An allele frequency database for anthropology

ALFRED: An allele frequency database for anthropology

p53 polymorphisms in Russia and Belarus: correlation of the 2-1-1 haplotype frequency with longitude

Short tandem repeat polymorphism evolution in humans

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