cichlid: Cichlid dataset
In BMhyb: Comparative Methods for Phylogenetic Networks
Description
A dataset containing a phylogenetic network and trait data for cichlid species
Format
A list with two items:
- phy.graph
the phylogenetic network in ape::evonet format
- trait
a vector of trait data
- final.se
a vector of standard error
Details
The tree is made by doing a tree search with mitochondrial data from
Kobmuller, S., N. Duftner, K. M. Sefc, M. Aibara,M. Stipacek, M. Blanc, B. Egger, and C. Sturmbauer. 2007.Reticulate phylogeny of gastropod-shell-breeding cichlids from Lake Tanganyika: the result of repeated introgressive hybridization. BMC Evolutionary Biology 7:7.
https://bmcevolbiol.biomedcentral.com/articles/10.1186/1471-2148-7-7
We then added hybridization events based on their cartoon Fig. 4: https://media.springernature.com/full/springer-static/image/art
Hybridization events with solid lines (coeval events) were modeled as going from the later of the source or descendant nodes.
Hybridization events with dotted lines, indicating ghost lineages, went from the MRCA of the source clade to the MRCA of the recipient taxon.
Trait data comes from fishbase.
BMhyb documentation built on Aug. 3, 2019, 1:02 a.m.
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Description
A dataset containing a phylogenetic network and trait data for cichlid species
Format
A list with two items:
- phy.graph
the phylogenetic network in ape::evonet format
- trait
a vector of trait data
- final.se
a vector of standard error
Details
The tree is made by doing a tree search with mitochondrial data from Kobmuller, S., N. Duftner, K. M. Sefc, M. Aibara,M. Stipacek, M. Blanc, B. Egger, and C. Sturmbauer. 2007.Reticulate phylogeny of gastropod-shell-breeding cichlids from Lake Tanganyika: the result of repeated introgressive hybridization. BMC Evolutionary Biology 7:7.
https://bmcevolbiol.biomedcentral.com/articles/10.1186/1471-2148-7-7
We then added hybridization events based on their cartoon Fig. 4: https://media.springernature.com/full/springer-static/image/art
Hybridization events with solid lines (coeval events) were modeled as going from the later of the source or descendant nodes.
Hybridization events with dotted lines, indicating ghost lineages, went from the MRCA of the source clade to the MRCA of the recipient taxon.
Trait data comes from fishbase.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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