Skip to main content
  • Facebook
  • Twitter
  • YouTube
  • LinkedIn
  • Google Plus
  • Other GSA Resources
    • Genetics Society of America
    • G3: Genes | Genomes | Genetics
    • Genes to Genomes: The GSA Blog
    • GSA Conferences
    • GeneticsCareers.org
  • Log in
Genetics

Main menu

  • HOME
  • ISSUES
    • Current Issue
    • Early Online
    • Archive
  • ABOUT
    • About the journal
    • Why publish with us?
    • Editorial board
    • Early Career Reviewers
    • Contact us
  • SERIES
    • Centennial
    • Genetics of Immunity
    • Genetics of Sex
    • Genomic Prediction
    • Multiparental Populations
    • FlyBook
    • WormBook
    • YeastBook
  • ARTICLE TYPES
    • About Article Types
    • Commentaries
    • Editorials
    • GSA Honors and Awards
    • Methods, Technology & Resources
    • Perspectives
    • Primers
    • Reviews
    • Toolbox Reviews
  • PUBLISH & REVIEW
    • Scope & publication policies
    • Submission & review process
    • Article types
    • Prepare your manuscript
    • Submit your manuscript
    • After acceptance
    • Guidelines for reviewers
  • SUBSCRIBE
    • Why subscribe?
    • For institutions
    • For individuals
    • Email alerts
    • RSS feeds
  • Other GSA Resources
    • Genetics Society of America
    • G3: Genes | Genomes | Genetics
    • Genes to Genomes: The GSA Blog
    • GSA Conferences
    • GeneticsCareers.org

User menu

Search

  • Advanced search
Genetics

Advanced Search

  • HOME
  • ISSUES
    • Current Issue
    • Early Online
    • Archive
  • ABOUT
    • About the journal
    • Why publish with us?
    • Editorial board
    • Early Career Reviewers
    • Contact us
  • SERIES
    • Centennial
    • Genetics of Immunity
    • Genetics of Sex
    • Genomic Prediction
    • Multiparental Populations
    • FlyBook
    • WormBook
    • YeastBook
  • ARTICLE TYPES
    • About Article Types
    • Commentaries
    • Editorials
    • GSA Honors and Awards
    • Methods, Technology & Resources
    • Perspectives
    • Primers
    • Reviews
    • Toolbox Reviews
  • PUBLISH & REVIEW
    • Scope & publication policies
    • Submission & review process
    • Article types
    • Prepare your manuscript
    • Submit your manuscript
    • After acceptance
    • Guidelines for reviewers
  • SUBSCRIBE
    • Why subscribe?
    • For institutions
    • For individuals
    • Email alerts
    • RSS feeds
Previous ArticleNext Article

Maximum Likelihood Estimation of Fitness Components in Experimental Evolution

Jingxian Liu, Jackson Champer, Anna Maria Langmüller, Chen Liu, Joan Chung, Riona Reeves, Anisha Luthra, Yoo Lim Lee, Andrew H. Vaughn, Andrew G. Clark and Philipp W. Messer
Genetics Early online January 24, 2019; https://doi.org/10.1534/genetics.118.301893
Jingxian Liu
Cornell University
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Jackson Champer
Cornell University
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Anna Maria Langmüller
Cornell University; Vienna Graduate School of Population Genetics
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Chen Liu
Cornell University
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Joan Chung
Cornell University
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Riona Reeves
Cornell University
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Anisha Luthra
Cornell University
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Yoo Lim Lee
Cornell University
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Andrew H. Vaughn
Cornell University
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Andrew G. Clark
Cornell University
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Philipp W. Messer
Cornell University
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • For correspondence: messer@cornell.edu
  • Article
  • Figures & Data
  • Supplemental
  • Info & Metrics
Loading

Abstract

Estimating fitness differences between allelic variants is a central goal of experimental evolution. Current methods for inferring such differences from allele frequency time series typically assume that the effects of selection can be described by a fixed selection coefficient. However, fitness is an aggregate of several components including mating success, fecundity, and viability. Distinguishing between these components could be critical in many scenarios. Here we develop a flexible maximum likelihood framework that can disentangle different components of fitness from genotype frequency data and estimate them individually in males and females. As a proof-of-principle, we apply our method to experimentally-evolved cage populations of Drosophila melanogaster, in which we tracked the relative frequencies of a loss-of-function and wild-type allele of yellow. This X-linked gene produces a recessive yellow phenotype when disrupted and is involved in male courtship ability. We find that the fitness costs of the yellow phenotype take the form of substantially reduced mating preference of wild-type females for yellow males, together with a modest reduction in the viability of yellow males and females. Our framework should be generally applicable to situations where it is important to quantify fitness components of specific genetic variants, including quantitative characterization of the population dynamics of CRISPR gene drives.

  • natural selection
  • fitness
  • maximum likelihood
  • experimental evolution
  • time-series data
  • Received December 20, 2018.
  • Accepted January 15, 2019.
  • Copyright © 2019, Genetics
Previous ArticleNext Article
Back to top

PUBLICATION INFORMATION

Volume 211 Issue 2, February 2019

Genetics: 211 (2)

ARTICLE CLASSIFICATION

Investigation
Email

Thank you for sharing this Genetics article.

NOTE: We request your email address only to inform the recipient that it was you who recommended this article, and that it is not junk mail. We do not retain these email addresses.

Enter multiple addresses on separate lines or separate them with commas.
Maximum Likelihood Estimation of Fitness Components in Experimental Evolution
(Your Name) has forwarded a page to you from Genetics
(Your Name) thought you would be interested in this article in Genetics.
Alerts
Enter your email below to set up alert notifications for new article, or to manage your existing alerts.
SIGN UP OR SIGN IN WITH YOUR EMAIL
View PDF
Share

Maximum Likelihood Estimation of Fitness Components in Experimental Evolution

Jingxian Liu, Jackson Champer, Anna Maria Langmüller, Chen Liu, Joan Chung, Riona Reeves, Anisha Luthra, Yoo Lim Lee, Andrew H. Vaughn, Andrew G. Clark and Philipp W. Messer
Genetics Early online January 24, 2019; https://doi.org/10.1534/genetics.118.301893
Jingxian Liu
Cornell University
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Jackson Champer
Cornell University
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Anna Maria Langmüller
Cornell University; Vienna Graduate School of Population Genetics
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Chen Liu
Cornell University
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Joan Chung
Cornell University
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Riona Reeves
Cornell University
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Anisha Luthra
Cornell University
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Yoo Lim Lee
Cornell University
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Andrew H. Vaughn
Cornell University
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Andrew G. Clark
Cornell University
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Philipp W. Messer
Cornell University
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • For correspondence: messer@cornell.edu
del.icio.us logo Digg logo Reddit logo Twitter logo CiteULike logo Facebook logo Google logo Mendeley logo
Citation

Maximum Likelihood Estimation of Fitness Components in Experimental Evolution

Jingxian Liu, Jackson Champer, Anna Maria Langmüller, Chen Liu, Joan Chung, Riona Reeves, Anisha Luthra, Yoo Lim Lee, Andrew H. Vaughn, Andrew G. Clark and Philipp W. Messer
Genetics Early online January 24, 2019; https://doi.org/10.1534/genetics.118.301893
Jingxian Liu
Cornell University
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Jackson Champer
Cornell University
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Anna Maria Langmüller
Cornell University; Vienna Graduate School of Population Genetics
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Chen Liu
Cornell University
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Joan Chung
Cornell University
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Riona Reeves
Cornell University
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Anisha Luthra
Cornell University
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Yoo Lim Lee
Cornell University
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Andrew H. Vaughn
Cornell University
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Andrew G. Clark
Cornell University
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Philipp W. Messer
Cornell University
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • For correspondence: messer@cornell.edu

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero

Related Articles

Cited By

More in this TOC Section

  • Long-Term Population Studies Uncover the Genome Structure and Genetic Basis of Xenobiotic and Host Plant Adaptation in the Herbivore Tetranychus urticae
  • Modulation of Gene Silencing by Cdc7p via H4 K16 Acetylation and Phosphorylation of Chromatin Assembly Factor CAF-1 in Saccharomyces cerevisiae
  • Integration of Self and Non-self Recognition Modulates Asexual Cell-to-Cell Communication in Neurospora crassa
Show more Investigation
  • Top
  • Article
  • Figures & Data
  • Supplemental
  • Info & Metrics

GSA

The Genetics Society of America (GSA), founded in 1931, is the professional membership organization for scientific researchers and educators in the field of genetics. Our members work to advance knowledge in the basic mechanisms of inheritance, from the molecular to the population level.

Online ISSN: 1943-2631

  • For Authors
  • For Reviewers
  • For Subscribers
  • Submit a Manuscript
  • Editorial Board
  • Press Releases

SPPA Logo

GET CONNECTED

RSS  Subscribe with RSS.

email  Subscribe via email. Sign up to receive alert notifications of new articles.

  • Facebook
  • Twitter
  • YouTube
  • LinkedIn
  • Google Plus

Copyright © 2019 by the Genetics Society of America

  • About GENETICS
  • Terms of use
  • Advertising
  • Permissions
  • Contact us
  • International access