Cited by 1,950Genetic diversity and population structureForensic and Genetic ResearchGenetic Associations and Epidemiology

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Maximum-likelihood estimation of molecular haplotype frequencies in a diploid population.

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Laurent Excoffier, Montgomery Slatkin·1995·Molecular Biology and Evolution

DOI 10.1093/oxfordjournals.molbev.a040269

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Abstract

Molecular techniques allow the survey of a large number of linked polymorphic loci in random samples from diploid populations. However, the gametic phase of haplotypes is usually unknown when diploid individuals are heterozygous at more than one locus. To overcome this difficulty, we implement an expectation-maximization (EM) algorithm leading to maximum-likelihood estimates of molecular haplotype frequencies under the assumption of Hardy-Weinberg proportions. The performance of the algorithm is evaluated for simulated data representing both DNA sequences and highly polymorphic loci with different levels of recombination. As expected, the EM algorithm is found to perform best for large samples, regardless of recombination rates among loci. To ensure finding the global maximum likelihood estimate, the EM algorithm should be started from several initial conditions. The present approach appears to be useful for the analysis of nuclear DNA sequences or highly variable loci. Although the algorithm, in principle, can accommodate an arbitrary number of loci, there are practical limitations because the computing time grows exponentially with the number of polymorphic loci. Although the algorithm, in principle, can accommodate an arbitrary number of loci, there are practical limitations because the computing time grows exponentially with the number of polymorphic loci.

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Authors: Excoffier, L., & Slatkin, M.
Affiliations: University of Geneva (CH)
ORCID: Laurent Excoffier
Montgomery Slatkin
Venue: Molecular Biology and Evolution
Publisher: Oxford University Press (OUP)
Published: 1995-09
Volume: 12
Issue: 5
Pages: 921-7
ISSN: 0737-4038 (ISSN-L)
1537-1719
DOI: 10.1093/oxfordjournals.molbev.a040269
OpenAlex: W1891283710
Cited by: 1,950
References: 14
Citations by year: 2026: 5 · 2025: 8 · 2024: 14 · 2023: 19 · 2022: 18 · 2021: 20 · 2020: 32 · 2019: 29 · 2018: 30 · 2017: 20 · 2016: 46 · 2015: 41 · 2014: 52 · 2013: 69 · 2012: 76
FWCI: 3.10
Type: journal article
Language: en
Open access: bronze
doi.org
Locations: Molecular Biology and Evolution (publishedVersion)
PubMed (publishedVersion)
Funders: National Science Foundation
Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (39847)
National Institutes of Health
National Institute of General Medical Sciences (GM-40282, R01GM040282)
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: haplotype frequencies, maximum likelihood estimation, expectation-maximization algorithm, Hardy-Weinberg equilibrium, recombination, heterozygosity, diploid populations, multilocus analysis, computational complexity
MeSH terms: Algorithms, Animals, Diploidy, Gene Frequency, Haplotypes, Humans, Genetic Linkage, Mathematics, Models, Genetic, Monte Carlo Method, Probability, Regression Analysis, Models, Statistical

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Maximum-likelihood estimation of molecular haplotype frequencies in a diploid population.

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