Skip to main content
bioRxiv
  • Home
  • About
  • Submit
  • ALERTS / RSS
Advanced Search
New Results

Allele frequency dynamics in a pedigreed natural population

View ORCID ProfileNancy Chen, Ivan Juric, Elissa J. Cosgrove, Reed Bowman, John W. Fitzpatrick, Stephan J. Schoech, Andrew G. Clark, Graham Coop
doi: https://doi.org/10.1101/388710
Nancy Chen
aCenter for Population Biology & Department of Evolution & Ecology, University of California, Davis, Davis, CA 95616
bDepartment of Biology, University of Rochester, Rochester, NY 14627
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Nancy Chen
  • For correspondence: nancy.chen@rochester.edu
Ivan Juric
cCleveland Clinic, Cleveland, OH 44195
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Elissa J. Cosgrove
dDepartment of Molecular Biology & Genetics, Cornell University, Ithaca, NY 14850
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Reed Bowman
eArchbold Biological Station, Venus, FL 33960
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
John W. Fitzpatrick
fCornell Lab of Ornithology, Cornell University, Ithaca, NY 14850
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Stephan J. Schoech
gDepartment of Biological Sciences, University of Memphis, Memphis, TN 38152
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Andrew G. Clark
dDepartment of Molecular Biology & Genetics, Cornell University, Ithaca, NY 14850
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Graham Coop
aCenter for Population Biology & Department of Evolution & Ecology, University of California, Davis, Davis, CA 95616
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Preview PDF
Loading

ABSTRACT

A central goal of population genetics is to understand how genetic drift, natural selection, and gene flow shape allele frequencies through time. However, the actual processes underlying these changes - variation in individual survival, reproductive success, and movement - are often difficult to quantify. Fully understanding these processes requires the population pedigree, the set of relationships among all individuals in the population through time. Here, we use extensive pedigree and genomic information from a long-studied natural population of Florida Scrub-Jays (Aphelocoma coerulescens) to directly characterize the relative roles of different evolutionary processes in shaping patterns of genetic variation through time. We performed gene dropping simulations to estimate individual genetic contributions to the population and model drift on the known pedigree. We found that observed allele frequency changes are generally well predicted by accounting for the different genetic contributions of founders. Our results show that the genetic contribution of recent immigrants is substantial, with some large allele frequency shifts that otherwise may have been attributed to selection actually due to gene flow. We identified a few SNPs under directional short-term selection after appropriately accounting for gene flow. Using models that account for changes in population size, we partitioned the proportion of variance in allele frequency change through time. Observed allele frequency changes are primarily due to variation in survival and reproductive success, with gene flow making a smaller contribution. This study provides one of the most complete descriptions of short-term evolutionary change in allele frequencies in a natural population to date.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
Back to top
PreviousNext
Posted August 09, 2018.
Download PDF
Email

Thank you for your interest in spreading the word about bioRxiv.

NOTE: Your email address is requested solely to identify you as the sender of this article.

Enter multiple addresses on separate lines or separate them with commas.
Allele frequency dynamics in a pedigreed natural population
(Your Name) has forwarded a page to you from bioRxiv
(Your Name) thought you would like to see this page from the bioRxiv website.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
Allele frequency dynamics in a pedigreed natural population
Nancy Chen, Ivan Juric, Elissa J. Cosgrove, Reed Bowman, John W. Fitzpatrick, Stephan J. Schoech, Andrew G. Clark, Graham Coop
bioRxiv 388710; doi: https://doi.org/10.1101/388710
Reddit logo Twitter logo Facebook logo LinkedIn logo Mendeley logo
Citation Tools
Allele frequency dynamics in a pedigreed natural population
Nancy Chen, Ivan Juric, Elissa J. Cosgrove, Reed Bowman, John W. Fitzpatrick, Stephan J. Schoech, Andrew G. Clark, Graham Coop
bioRxiv 388710; doi: https://doi.org/10.1101/388710

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
  • Tweet Widget
  • Facebook Like
  • Google Plus One

Subject Area

  • Evolutionary Biology
Subject Areas
All Articles
  • Animal Behavior and Cognition (4395)
  • Biochemistry (9619)
  • Bioengineering (7111)
  • Bioinformatics (24915)
  • Biophysics (12642)
  • Cancer Biology (9980)
  • Cell Biology (14388)
  • Clinical Trials (138)
  • Developmental Biology (7971)
  • Ecology (12135)
  • Epidemiology (2067)
  • Evolutionary Biology (16010)
  • Genetics (10938)
  • Genomics (14764)
  • Immunology (9889)
  • Microbiology (23719)
  • Molecular Biology (9493)
  • Neuroscience (50965)
  • Paleontology (370)
  • Pathology (1544)
  • Pharmacology and Toxicology (2688)
  • Physiology (4031)
  • Plant Biology (8685)
  • Scientific Communication and Education (1512)
  • Synthetic Biology (2403)
  • Systems Biology (6446)
  • Zoology (1346)