Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data.

Excoffier, L; Smouse, P E; Quattro, J M

doi:10.1093/genetics/131.2.479

Cited by 13,929Genetic diversity and population structureForensic and Genetic ResearchGenetic Associations and Epidemiology

Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data.

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Excoffier, L, Smouse, P E, Quattro, J M·1992·Genetics

DOI 10.1093/genetics/131.2.479

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Abstract

We present here a framework for the study of molecular variation within a single species. Information on DNA haplotype divergence is incorporated into an analysis of variance format, derived from a matrix of squared-distances among all pairs of haplotypes. This analysis of molecular variance (AMOVA) produces estimates of variance components and F-statistic analogs, designated here as phi-statistics, reflecting the correlation of haplotypic diversity at different levels of hierarchical subdivision. The method is flexible enough to accommodate several alternative input matrices, corresponding to different types of molecular data, as well as different types of evolutionary assumptions, without modifying the basic structure of the analysis. The significance of the variance components and phi-statistics is tested using a permutational approach, eliminating the normality assumption that is conventional for analysis of variance but inappropriate for molecular data. Application of AMOVA to human mitochondrial DNA haplotype data shows that population subdivisions are better resolved when some measure of molecular differences among haplotypes is introduced into the analysis. At the intraspecific level, however, the additional information provided by knowing the exact phylogenetic relations among haplotypes or by a nonlinear translation of restriction-site change into nucleotide diversity does not significantly modify the inferred population genetic structure. Monte Carlo studies show that site sampling does not fundamentally affect the significance of the molecular variance components. The AMOVA treatment is easily extended in several different directions and it constitutes a coherent and flexible framework for the statistical analysis of molecular data.

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Low genetic differentiation was found between the 60 ancient mtDNA HVR1 sequences and 246 modern homologous sequences from the same geographic region (FST = 0.00551; P = 0.0663).
“we compared the 60 mtDNA HVR1 sequences obtained from our ancient sample to 246 homologous modern sequences (29–31) from the same geographic region and found low genetic differentiation (FST = 0.00551; P = 0.0663) (32).”
From Direct evidence for positive selection of skin, hair, and eye pigmentation in Europeans during the last 5,000 y (2014) · cites this paper as [32]

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Untitled work
Bromhead, D., Scholey, V., Nicol, S., Margulies, D., Wexler, J., & Stein, M. (2015) · Deep-Sea Research II · doi:10.1016/j.dsr2.2015.04.017 · Cited by 12 · see citing works

Authors: Excoffier, L., Smouse, P. E., & Quattro, J. M.
Affiliations: Rutgers, The State University of New Jersey (US)
ORCID: Excoffier, L
Smouse, P E
Quattro, J M
Venue: Genetics
Publisher: Oxford University Press (OUP)
Published: 1992-06-01
Volume: 131
Issue: 2
Pages: 479-491
ISSN: 0016-6731 (ISSN-L)
1943-2631
DOI: 10.1093/genetics/131.2.479
OpenAlex: W1919772617
Cited by: 13,929
References: 43
Citations by year: 2026: 231 · 2025: 239 · 2024: 285 · 2023: 313 · 2022: 365 · 2021: 439 · 2020: 436 · 2019: 467 · 2018: 496 · 2017: 567 · 2016: 539 · 2015: 621 · 2014: 677 · 2013: 703 · 2012: 737
FWCI: 10.73
Type: journal article
Language: en
Open access: bronze
doi.org
Licence: academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model (vor)
Locations: Genetics (publishedVersion)
Europe PMC (PubMed Central) (publishedVersion)
PubMed (publishedVersion)
Zenodo (CERN European Organization for Nuclear Research) (cc-by)
Funders: U.S. Department of Agriculture
New Jersey Agricultural Experiment Station
Institut National de la Santé et de la Recherche Médicale
Fonds De La Recherche Scientifique - FNRS
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
Keywords: AMOVA, haplotype divergence, human mitochondrial DNA, restriction fragment length polymorphism, population structure, intraspecific variation, nucleotide diversity, phylogenetic relationships
MeSH terms: Analysis of Variance, DNA, Mitochondrial, Ethnicity, Gene Frequency, Haplotypes, Humans, Models, Genetic, Genetic Variation, Restriction Mapping

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Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data.

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