Phylogeny Estimation and Hypothesis Testing Using Maximum Likelihood
Abstract
One of the strengths of the maximum likelihood method of phylogenetic estimation is the ease with which hypotheses can be formulated and tested. Maximum likelihood analysis of DNA and amino acid sequence data has been made practical with recent advances in models of DNA substitution, computer programs, and computational speed. Here, we describe the maximum likelihood method and the recent improvements in models of substitution. We also describe how likelihood ratio tests of a variety of biological hypotheses can be formulated and tested using computer simulation to generate the null distribution of the likelihood ratio test statistic.
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Statistical tests for rate changes along a phylogeny have been a part of phylogenetic methodology for several decades and are closely tied to tests for a molecular clock.
“Statistical tests for rate changes along a phylogeny have been a part of phylogenetic methodology for several decades, and are closely tied to tests for a molecular clock”
From Bayesian Detection of Convergent Rate Changes of Conserved Noncoding Elements on Phylogenetic Trees (2019) · cites this paper as Huelsenbeck and Crandall 1997
Cites
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Bayesian Detection of Convergent Rate Changes of Conserved Noncoding Elements on Phylogenetic Trees
Hu, Z., Sackton, T. B., Edwards, S. V., & Liu, J. S. (2019) · Molecular Biology and Evolution · doi:10.1093/molbev/msz049 · Cited by 69 · see citing works
- Authors
- Huelsenbeck, J. P., & Crandall, K. A.
- Affiliations
- Smithsonian Institution (US)
- Brigham Young University (US)
- Venue
- Annual Review of Ecology and Systematics
- Publisher
- Annual Reviews
- Published
- 1997-11
- Volume
- 28
- Issue
- 1
- Pages
- 437-466
- ISSN
- 0066-4162 (ISSN-L)
- OpenAlex
- W2116709453
- Cited by
- 1,018
- References
- 6
- Citations by year
- 2026: 4 · 2025: 13 · 2024: 14 · 2023: 13 · 2022: 11 · 2021: 21 · 2020: 17 · 2019: 19 · 2018: 14 · 2017: 20 · 2016: 13 · 2015: 21 · 2014: 31 · 2013: 27 · 2012: 27
- FWCI
- 8.77
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Annual Review of Ecology and Systematics (publishedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Physical Sciences › Earth and Planetary Sciences › Paleontology › Evolution and Paleontology Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Keywords
- likelihood ratio test, amino acid substitution models, computer simulation, DNA sequence data
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