SiPhyNetwork: An R package for simulating phylogenetic networks
Abstract Gene flow is increasingly recognized as an important macroevolutionary process. The many mechanisms that contribute to gene flow (e.g. introgression, hybridization, lateral gene transfer) uniquely affect the diversification of dynamics of species, making it important to be able to account f...
| Main Authors: | , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Wiley
2023-07-01
|
| Series: | Methods in Ecology and Evolution |
| Subjects: | |
| Online Access: | https://doi.org/10.1111/2041-210X.14116 |
| _version_ | 1797766994322259968 |
|---|---|
| author | Joshua A. Justison Claudia Solis‐Lemus Tracy A. Heath |
| author_facet | Joshua A. Justison Claudia Solis‐Lemus Tracy A. Heath |
| author_sort | Joshua A. Justison |
| collection | DOAJ |
| description | Abstract Gene flow is increasingly recognized as an important macroevolutionary process. The many mechanisms that contribute to gene flow (e.g. introgression, hybridization, lateral gene transfer) uniquely affect the diversification of dynamics of species, making it important to be able to account for these idiosyncrasies when constructing phylogenetic models. Existing phylogenetic‐network simulators for macroevolution are limited in the ways they model gene flow. We present SiPhyNetwork, an R package for simulating phylogenetic networks under a birth–death‐hybridization process. Our package unifies the existing birth–death‐hybridization models while also extending the toolkit for modelling gene flow. This tool can create patterns of reticulation such as hybridization, lateral gene transfer, and introgression. Specifically, we model different reticulate events by allowing events to either add, remove or keep constant the number of lineages. Additionally, we allow reticulation events to be trait dependent, creating the ability to model the expanse of isolating mechanisms that prevent gene flow. This tool makes it possible for researchers to model many of the complex biological factors associated with gene flow in a phylogenetic context. |
| first_indexed | 2024-03-12T20:32:19Z |
| format | Article |
| id | doaj.art-7423a88c92af417d929e33f1393380c5 |
| institution | Directory Open Access Journal |
| issn | 2041-210X |
| language | English |
| last_indexed | 2024-03-12T20:32:19Z |
| publishDate | 2023-07-01 |
| publisher | Wiley |
| record_format | Article |
| series | Methods in Ecology and Evolution |
| spelling | doaj.art-7423a88c92af417d929e33f1393380c52023-08-01T18:55:57ZengWileyMethods in Ecology and Evolution2041-210X2023-07-011471687169810.1111/2041-210X.14116SiPhyNetwork: An R package for simulating phylogenetic networksJoshua A. Justison0Claudia Solis‐Lemus1Tracy A. Heath2Department of Ecology Evolution and Organismal Biology Iowa State University Ames Iowa USAWisconsin Institute for Discovery and Department of Plant Pathology University of Wisconsin‐Madison Madison Wisconsin USADepartment of Ecology Evolution and Organismal Biology Iowa State University Ames Iowa USAAbstract Gene flow is increasingly recognized as an important macroevolutionary process. The many mechanisms that contribute to gene flow (e.g. introgression, hybridization, lateral gene transfer) uniquely affect the diversification of dynamics of species, making it important to be able to account for these idiosyncrasies when constructing phylogenetic models. Existing phylogenetic‐network simulators for macroevolution are limited in the ways they model gene flow. We present SiPhyNetwork, an R package for simulating phylogenetic networks under a birth–death‐hybridization process. Our package unifies the existing birth–death‐hybridization models while also extending the toolkit for modelling gene flow. This tool can create patterns of reticulation such as hybridization, lateral gene transfer, and introgression. Specifically, we model different reticulate events by allowing events to either add, remove or keep constant the number of lineages. Additionally, we allow reticulation events to be trait dependent, creating the ability to model the expanse of isolating mechanisms that prevent gene flow. This tool makes it possible for researchers to model many of the complex biological factors associated with gene flow in a phylogenetic context.https://doi.org/10.1111/2041-210X.14116birth‐death‐hybridization processmacroevolutionphylogenetic networkssimulation |
| spellingShingle | Joshua A. Justison Claudia Solis‐Lemus Tracy A. Heath SiPhyNetwork: An R package for simulating phylogenetic networks Methods in Ecology and Evolution birth‐death‐hybridization process macroevolution phylogenetic networks simulation |
| title | SiPhyNetwork: An R package for simulating phylogenetic networks |
| title_full | SiPhyNetwork: An R package for simulating phylogenetic networks |
| title_fullStr | SiPhyNetwork: An R package for simulating phylogenetic networks |
| title_full_unstemmed | SiPhyNetwork: An R package for simulating phylogenetic networks |
| title_short | SiPhyNetwork: An R package for simulating phylogenetic networks |
| title_sort | siphynetwork an r package for simulating phylogenetic networks |
| topic | birth‐death‐hybridization process macroevolution phylogenetic networks simulation |
| url | https://doi.org/10.1111/2041-210X.14116 |
| work_keys_str_mv | AT joshuaajustison siphynetworkanrpackageforsimulatingphylogeneticnetworks AT claudiasolislemus siphynetworkanrpackageforsimulatingphylogeneticnetworks AT tracyaheath siphynetworkanrpackageforsimulatingphylogeneticnetworks |