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

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

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

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.

Integrity signals

Registry

Crossref · 10.1093/oxfordjournals.molbev.a040269

Cites

14 of 14 references verified0 citation errors · 0 not checkable

Statistics

Recomputing p-values needs the paper’s full text.

Claims the paper makes

We couldn’t retrieve this paper’s full text, so its claims and self-check weren’t run. The registry and citation checks still apply.

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

Cites

Flagged first, then by citations

Cited by

Sorted by citations

Authors
Excoffier, L., & Slatkin, M.
Affiliations
University of Geneva (CH)
Venue
Molecular Biology and Evolution
Published
1995-09
Volume
12
Issue
5
Pages
921-7
ISSN
  • 0737-4038 (ISSN-L)
  • 1537-1719
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
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

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review