Analysis of DNA Diversity by Spatial Autocorrelation

Overview

Journal Genetics

Publisher Oxford University Press

Specialty Genetics

Date 1995 Jun 1

PMID 7498756

Citations 19

Authors

G Bertorelle

G Barbujani

Affiliations

Soon will be listed here.

Abstract

Two statistics are proposed for summarizing spatial patterns of DNA diversity. These autocorrelation indices for DNA analysis, or AIDAs, can be applied to RFLP and sequence data; the resulting set of autocorrelation coefficients, or correlogram, measures whether, and to what extent, individual DNA sequences or haplotypes resemble the haplotypes sampled at arbitrarily chosen spatial distances. Analyses of computer-generated sets of data, and of RFLP data from two natural populations, show that AIDAs allow one to objectively and simply identify basic patterns in the spatial distribution of haplotypes. These statistics, therefore, seem to be a useful tool both to explore the genetic structure of a population and to suggest hypotheses on the evolutionary processes that shaped the observed patterns.

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References

Mantel N . The detection of disease clustering and a generalized regression approach. Cancer Res. 1967; 27(2):209-20. View

Excoffier L, Smouse P . Using allele frequencies and geographic subdivision to reconstruct gene trees within a species: molecular variance parsimony. Genetics. 1994; 136(1):343-59. PMC: 1205785. DOI: 10.1093/genetics/136.1.343. View

Watterson G . On the number of segregating sites in genetical models without recombination. Theor Popul Biol. 1975; 7(2):256-76. DOI: 10.1016/0040-5809(75)90020-9. View

Slatkin M, Maruyama T . Genetic drift in a cline. Genetics. 1975; 81(1):209-22. PMC: 1213384. DOI: 10.1093/genetics/81.1.209. View

Kreitman M . Nucleotide polymorphism at the alcohol dehydrogenase locus of Drosophila melanogaster. Nature. 1983; 304(5925):412-7. DOI: 10.1038/304412a0. View

Slatkin M . Gene flow and the geographic structure of natural populations. Science. 1987; 236(4803):787-92. DOI: 10.1126/science.3576198. View

Templeton A, Boerwinkle E, Sing C . A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping. I. Basic theory and an analysis of alcohol dehydrogenase activity in Drosophila. Genetics. 1987; 117(2):343-51. PMC: 1203209. DOI: 10.1093/genetics/117.2.343. View

Barbujani G . Autocorrelation of gene frequencies under isolation by distance. Genetics. 1987; 117(4):777-82. PMC: 1203249. DOI: 10.1093/genetics/117.4.777. View

Cavalli-Sforza L, Piazza A, Menozzi P, Mountain J . Reconstruction of human evolution: bringing together genetic, archaeological, and linguistic data. Proc Natl Acad Sci U S A. 1988; 85(16):6002-6. PMC: 281893. DOI: 10.1073/pnas.85.16.6002. View

10.

Barrantes R, Smouse P, Mohrenweiser H, GERSHOWITZ H, Azofeifa J, Arias T . Microevolution in lower Central America: genetic characterization of the Chibcha-speaking groups of Costa Rica and Panama, and a consensus taxonomy based on genetic and linguistic affinity. Am J Hum Genet. 1990; 46(1):63-84. PMC: 1683538. View

11.

Slatkin M, Maddison W . Detecting isolation by distance using phylogenies of genes. Genetics. 1990; 126(1):249-60. PMC: 1204129. DOI: 10.1093/genetics/126.1.249. View

12.

Rapacz J, Chen L, Wu M, Butler R, Schumaker V . Identification of the ancestral haplotype for apolipoprotein B suggests an African origin of Homo sapiens sapiens and traces their subsequent migration to Europe and the Pacific. Proc Natl Acad Sci U S A. 1991; 88(4):1403-6. PMC: 51026. DOI: 10.1073/pnas.88.4.1403. View

13.

Costa R, Peixoto A, Barbujani G, Kyriacou C . A latitudinal cline in a Drosophila clock gene. Proc Biol Sci. 1992; 250(1327):43-9. DOI: 10.1098/rspb.1992.0128. View

14.

Valdes A, Slatkin M, Freimer N . Allele frequencies at microsatellite loci: the stepwise mutation model revisited. Genetics. 1993; 133(3):737-49. PMC: 1205356. DOI: 10.1093/genetics/133.3.737. View

15.

Nevo E, Honeycutt R, Yonekawa H, Nelson K, Hanzawa N . Mitochondrial DNA polymorphisms in subterranean mole-rats of the Spalax ehrenbergi superspecies in Israel, and its peripheral isolates. Mol Biol Evol. 1993; 10(3):590-604. DOI: 10.1093/oxfordjournals.molbev.a040026. View

16.

Kimura M . The number of heterozygous nucleotide sites maintained in a finite population due to steady flux of mutations. Genetics. 1969; 61(4):893-903. PMC: 1212250. DOI: 10.1093/genetics/61.4.893. View