Data from: A genetic demographic analysis of Lake Malawi rock-dwelling cichlids using spatio-temporal sampling

Husemann M, Nguyen R, Ding B, Danley PD

Date Published: April 14, 2015

DOI: http://dx.doi.org/10.5061/dryad.53686

 

Files in this package

Content in the Dryad Digital Repository is offered "as is." By downloading files, you agree to the Dryad Terms of Service. To the extent possible under law, the authors have waived all copyright and related or neighboring rights to this data. CC0 (opens a new window) Open Data (opens a new window)

Title Maylandia_13usats_GENEPOP_Mol_Ecol
Downloaded 10 times
Description Genepop file containing data from 13 microsatellites for three temporal samples (1996, 2010, 2012) of three populations of Maylandia zebra (Mazinzi Reef, Harbor Island, Illala Gap) and Maylandia benetos (Mazinzi Reef)
Download Maylandia_13usats_GENEPOP_Mol_Ecol.txt (38.29 Kb)
Details View File Details
Title Maylandia_DLoop_alignment_Mol_Ecol
Downloaded 3 times
Description Alignment (Geneious) of 695 bp of the mitochondrial DLoop for 317 individuals sampled at three points in time (1996, 2010, 2012) from three populations of Maylandia zebra (Mazinzi Reef, Harbour Island, Illala Gap) and Maylandia benetos (Mazinzi Reef).
Download Maylandia_DLoop_alignment_Mol_Ecol.nex (231.7 Kb)
Details View File Details
Title Maylandia_DLoop_dated_tree_Mol_Ecol
Downloaded 5 times
Description Dated phylogenetic tree for 317 individuals of Maylandia zebra and Maylandia benetos generated with BEAST v.1.7.4. We used the HKY + I model and a substitution rate of 0.0324. The simplest coalescent model (constant size) was used. The best clock model was estimated by running all four available clock models and using Tracer to determine the best model for our data set. All analyses were run for 100 million generations sampling every 10,000 generations for a total of 10,000 samples. Convergence of the run was confirmed with Tracer by checking the highest effective sample size (ESS). The exponential relaxed clock had the best likelihood scores (-1371.613, second best: lognormal relaxed clock -1381.808) and was therefore chosen as best clock model. The tree was summarized with TreeAnnotator v.1.7.4.
Download Maylandia_DLoop_dated_tree_Mol_Ecol (327.7 Kb)
Details View File Details

When using this data, please cite the original publication:

Husemann M, Nguyen R, Ding B, Danley PD (2015) A genetic demographic analysis of Lake Malawi rock-dwelling cichlids using spatio-temporal sampling. Molecular Ecology 24(11): 2686-2701. http://dx.doi.org/10.1111/mec.13205

Additionally, please cite the Dryad data package:

Husemann M, Nguyen R, Ding B, Danley PD (2015) Data from: A genetic demographic analysis of Lake Malawi rock-dwelling cichlids using spatio-temporal sampling. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.53686
Cite | Share
Download the data package citation in the following formats:
   RIS (compatible with EndNote, Reference Manager, ProCite, RefWorks)
   BibTex (compatible with BibDesk, LaTeX)

Search for data

Be part of Dryad

We encourage organizations to: