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

Bayesian Analysis of Evolutionary Divergence with Genomic Data Under Diverse Demographic Models

Yujin Chung, Jody Hey
doi: https://doi.org/10.1101/080606
Yujin Chung
1Center for Computational Genetics and Genomics, 1900 North 12th Street Philadelphia, PA 19122, USA
2Biology Department, Temple University, 1900 North 12th Street Philadelphia, PA 19122, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • For correspondence: yujin.chung@temple.edu
Jody Hey
1Center for Computational Genetics and Genomics, 1900 North 12th Street Philadelphia, PA 19122, USA
2Biology Department, Temple University, 1900 North 12th Street Philadelphia, PA 19122, USA
  • 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

We present a new Bayesian method for estimating demographic and phylogenetic history using population genomic data. Several key innovations are introduced that allow the study of diverse models within an Isolation with Migration framework. For the Markov chain Monte Carlo (MCMC) phase of the analysis, we use a reduced state space, consisting of simple coalescent trees without migration paths, and a simple importance sampling distribution without demography. Migration paths are analytically integrated using a Markov chain as a representation of genealogy. The new method is scalable to a large number of loci with excellent MCMC mixing properties. Once obtained, a single sample of trees is used to calculate the joint posterior density for model parameters under multiple diverse demographic models, without having to repeat MCMC runs. As implemented in the computer program MIST, we demonstrate the accuracy, scalability and other advantages of the new method using simulated data and DNA sequences of two common chimpanzee subspecies: Pan troglodytes troglodytes (P. t.) and P. t. verus.

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-NC-ND 4.0 International license.
Back to top
PreviousNext
Posted October 12, 2016.
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.
Bayesian Analysis of Evolutionary Divergence with Genomic Data Under Diverse Demographic Models
(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
Bayesian Analysis of Evolutionary Divergence with Genomic Data Under Diverse Demographic Models
Yujin Chung, Jody Hey
bioRxiv 080606; doi: https://doi.org/10.1101/080606
Digg logo Reddit logo Twitter logo Facebook logo Google logo LinkedIn logo Mendeley logo
Citation Tools
Bayesian Analysis of Evolutionary Divergence with Genomic Data Under Diverse Demographic Models
Yujin Chung, Jody Hey
bioRxiv 080606; doi: https://doi.org/10.1101/080606

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 (4087)
  • Biochemistry (8762)
  • Bioengineering (6479)
  • Bioinformatics (23341)
  • Biophysics (11750)
  • Cancer Biology (9149)
  • Cell Biology (13247)
  • Clinical Trials (138)
  • Developmental Biology (7416)
  • Ecology (11369)
  • Epidemiology (2066)
  • Evolutionary Biology (15087)
  • Genetics (10399)
  • Genomics (14009)
  • Immunology (9121)
  • Microbiology (22040)
  • Molecular Biology (8779)
  • Neuroscience (47367)
  • Paleontology (350)
  • Pathology (1420)
  • Pharmacology and Toxicology (2482)
  • Physiology (3704)
  • Plant Biology (8050)
  • Scientific Communication and Education (1431)
  • Synthetic Biology (2208)
  • Systems Biology (6016)
  • Zoology (1249)