Tools
Tools
Scholz, Guillaume E., Popescu, Andrei-Alin, Taylor, Martin I. 
ORCID: https://orcid.org/0000-0002-3858-0712, Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Huber, Katharina T.
(2019)
OSF-Builder: A new tool for constructing and representing evolutionary histories involving introgression.
Systematic Biology, 68 (5).
717–729.
ISSN 1063-5157
Preview |
PDF (Accepted_manuscript)
- Accepted Version
Download (463kB) | Preview |
Abstract
Introgression is an evolutionary process which provides an important source of innovation for evolution. Although various methods have been used to detect introgression, very few methods are currently available for constructing evolutionary histories involving introgression. In this paper we propose a new method for constructing such evolutionary histories whose starting point is a species forest (consisting of a collection of lineage trees, usually arising as a collection of clades or monophyletic groups in a species tree), and a gene tree for a specific allele of interest, or allele tree for short. Our method is based on representing introgression in terms of a certain 'overlay' of the allele tree over the lineage trees, called an overlaid species forest (OSF). OSFs are similar to phylogenetic networks although a key difference is that they typically have multiple roots because each monophyletic group in the species tree has a different point of origin. Employing a new model for introgression, we derive an efficient algorithm for building OSFs called OSF-Builder that is guaranteed to return an optimal OSF in the sense that the number of potential introgression events is minimized. As well as using simulations to assess the performance of OSF-Builder, we illustrate its use on a butterfly dataset in which introgression has been previously inferred. The OSF-Builder software is available for download from https://www.uea.ac.uk/computing/software/OSF-Builder
| Item Type: | Article |
|---|---|
| Uncontrolled Keywords: | introgression,allele,lineage,phylogenetic network,osf-builder,fitch-hartigan algorithm |
| Faculty \ School: | Faculty of Science > School of Computing Sciences Faculty of Science > School of Biological Sciences |
| UEA Research Groups: | Faculty of Science > Research Groups > Organisms and the Environment Faculty of Science > Research Groups > Computational Biology Faculty of Science > Research Groups > Norwich Epidemiology Centre Faculty of Medicine and Health Sciences > Research Groups > Norwich Epidemiology Centre Faculty of Science > Research Centres > Centre for Ecology, Evolution and Conservation |
| Related URLs: | |
| Depositing User: | LivePure Connector |
| Date Deposited: | 21 Jan 2019 10:30 |
| Last Modified: | 09 Oct 2024 13:34 |
| URI: | https://ueaeprints.uea.ac.uk/id/eprint/69624 |
| DOI: | 10.1093/sysbio/syz004 |
Downloads
Downloads per month over past year
Actions (login required)
 |
View Item |